Astronomy

The Universe as a Simple Mathematical System

Marek Demianski, Doroshkevich, S.Pilipenko and S.Gottlöber

Monthly Notices of the Royal Astronomical Society, 1 June, DOI: 10.1111/j.1365-2966.2011.18265.x, 14 pp. (2010)

We analyze the evolution of the basic properties of the simulated elements of the large-scale structure of the Universe (LSS) formed by dark matter (DM), and we confront it with the observed evolution of the Lyman α forest. In three high-resolution simulations, we have selected samples of compact DM clouds of moderate overdensity. Clouds are selected at redshifts 0 ≤z≤ 3 with the minimal spanning tree technique. The main properties of the clouds selected in this way are analyzed in three-dimensional space and with the core-sampling approach. This allows us to compare estimates of the DM LSS evolution obtained with two different techniques, and to clarify some important aspects of the LSS evolution. In both cases, we find that regular redshift variations of the mean characteristics of the DM LSS are accompanied only by small variations of their probability distribution functions (PDFs), which indicates the self-similar characteristic of the DM LSS evolution. A high degree of relaxation of DM particles, compressed within the LSS, is found along the shortest principal axis of the clouds. We see that the internal structure of the selected clouds depends upon the mass resolution and scale of the perturbations achieved in the simulations. It is found that the low-mass tail of the PDFs of the LSS characteristics depends upon the procedure of cloud selection.

The Gamma Ray Bursts Hubble Diagram in Quintessential Cosmological Models

Marek Demianski, E.Piedipalumbo, and C.Rubano

Monthly Notices of the Royal Astronomical Society, 411, 1213-1222, 15 November 2010

It has been recently empirically established that some of the directly observed parameters of gamma-ray bursts (GRBs) are correlated with their important intrinsic parameters, such as the luminosity or the total radiated energy. These correlations were derived, tested and used to standardize GRBs, i.e. to derive their luminosity or radiated energy from one or more observables, in order to construct an estimated fiducial Hubble diagram (HD), assuming that radiation propagates in the standard Λ cold dark matter cosmological model. We extend these analyses by considering more general models of dark energy and an updated data set of high-redshift GRBs. We show that the correlation parameters only weakly depend on the cosmological model. Moreover we apply a local regression technique to estimate, in a model-independent way, the distance modulus from the recently updated Type Ia supernova (SNIa) sample containing 307 SNIa, in order to calibrate the GRBs 2D correlations, by considering only GRBs with z≤ 1.4. The derived calibration parameters are used to construct a new GRBs HD, which we call the calibrated GRBs HD. We also compare the estimated and calibrated GRBs HDs. It turns out that for the common GRBs they are fully statistically consistent, thus indicating that both of them are not affected by any systematic bias induced by the different standardizing procedures. We finally apply our methods to calibrate 95 long GRBs with the well-known Amati relation and construct the estimated and calibrated GRBs HD that extends to redshifts z~8. Even in this case there is consistency between these data sets. This means that the high-redshift GRBs can be used to test different models of dark energy. We used the calibrated GRBs HD to constrain our quintessential cosmological model and derived the likelihood values of Ωm and w(0).

 

Abundances of Oxygen in Anticenter Planetary Nebulae and the Oxygen Abundance Gradient in the Galactic Disk

R.B.C.Henry, Karen B. Kwitter, Anne E.Jaskot ’08, B.Balick, M.Morrison and J.B.Milingo

Astrophysical Journal, 724, 748-761 (2010)

We have obtained spectrophotometric observations of 41 anticenter planetary nebulae (PNe) located in the disk of the Milky Way. Electron temperatures and densities, as well as chemical abundances for He, N, O, Ne, S, Cl, and Ar were determined. Incorporating these results into our existing database of PN abundances yielded a sample of 124 well-observed objects with homogeneously determined abundances extending from 0.9 to 21 kpc in galactocentric distance. We performed a detailed regression analysis which accounted for uncertainties in both oxygen abundances and radial distances in order to establish the metallicity gradient across the disk to be 12 + log(O/H) = (9.09±0.05)−(0.058±0.006)×Rg, with Rg in kpc. While we see some evidence that the gradient steepens at large galactocentric distances, more objects toward the anticenter need to be observed in order to confidently establish the true form of the metallicity gradient. We find no compelling evidence that the gradient differs between Peimbert Types I and II, nor is oxygen abundance related to the vertical distance from the galactic plane. Our gradient agrees well with analogous results for H II regions but is steeper than the one recently published by Stanghellini & Haywood over a similar range in galactocentric distance. A second analysis using PN distances from a different source implied a flatter gradient, and we suggest that we have reached a confusion limit which can only be resolved with greatly improved distance measurements and an understanding of the natural scatter in oxygen abundances.

The Galactic Disk Oxygen Gradient and the Limit of Confusion

R.B.C.Henry, Karen B. Kwitter, Anne E.Jaskot ’08, B.Balick, M.Morrison and J.B.Milingo

Bulletin of the American Astronomical Society, 256.07 (2011)

We have obtained spectrophotometric observations of 41 anticenter planetary nebulae (PNe) located in the disk of the Milky Way. Oxygen abundance results of these objects plus those in our pre-existing database yield a sample of 124 PNe with which to study the oxygen abundance gradient in the disk of the Galaxy between 0.9 and 21 kpc in galactocentric distance. Accounting for both abundance and distance uncertainties, we find an oxygen gradient of −0.058±0.006 dex/kpc. We see some evidence that the gradient may steepen at large galactocentric distances but no compelling evidence that the gradient differs between Peimbert Types I and II nor that the oxygen abundance is related to the vertical distance from the Galactic plane. A second analysis using PN distances from Stanghellini et al. (ApJ, 689, 194, 2008) implies a flatter gradient, and we suggest that we have reached a confusion limit which can only be resolved with greatly improved distance measurements and an understanding of the natural scatter in oxygen abundances. RBCH, KK, and BB gratefully acknowledge support from NSF Grants AST-0806577, AST-0806490, and AST-0880201, respectively.

Abundances in a Sample of Halo/Thick Disk Planetary Nebulae in M31

Karen B. Kwitter, Emma M. M. Lehman’10, B.Balick and R.B.C.Henry

Bulletin of the American Astronomical Society, 256.08 (2011)

We present preliminary abundances for 16 planetary nebulae in M31 identified by Merrett et al. (MNRAS, 369, 120, 2006). Our objects are the brightest 16 in a λ5007 flux-ranked subsample (m5007 between 20.45 and 20.88) whose distances from the major axis of M31, measured parallel to the minor axis, are between 15 and 50 arcminutes. This group presumably includes non-thin-disk objects, i.e., members of the thick disk and halo of M31, but may also sample possible tidal streams. Spectroscopic data were obtained with the DIS instrument on the 3.5-m ARC telescope at Apache Point Observatory (3700-9600 Å) and with GMOS on the Gemini North 8.1-m telescope (3700-6400 Å). Abundances were derived using our ELSA package (Johnson et al., IAU Symp. #234, 439, 2006). The resulting preliminary average abundances based on observations to date are as follows: He/H=0.107(±0.010), O/H=4.29(±1.24)x10-4, N/O=0.703(±0.618), and Ne/O=0.212(±0.019). There remain six PNe for which we have only Gemini spectra; in the fall of 2010 we plan to complete our observations and obtain companion red spectra at APO, allowing an improved analysis. For now, we note that the average He/H ratio is similar to the average of Milky Way halo PNe (Henry, Kwitter & Balick, A.J., 127, 2284, 2004), and below that for a similar-sized sample of mostly bulge PNe in M31 reported by Jacoby & Ciardullo (Ap.J., 515, 169, 1999). Our O/H ratio is well above the Milky Way halo PN value, and slightly above that of the Jacoby & Ciardullo sample.

KBK, RBCH and BB are grateful to their respective institutions and to the NSF for support under grants #AST-0806490, AST-0806577, and AST-0880201, respectively. KBK and EML thank NOAO for their generous travel support.

Spectra of 12 New Planetary Nebulae in the Milky Way Galaxy

J.McKeever, T.Gomez, B.Balick, J.Lutz, Karen B. Kwitter, and S.Snedden

Bulletin of the American Astronomical Society, 256.09 (2011)

There are many planetary nebulae known in our own galaxy but the vast majority are located close to the plane. However studies of M31 show thousands of PN in its thick disk and halo, so we surmise that there are more halo PN to be discovered for the MWG. Halo PN are important for studying the chemical evolution of the MWG, since they reflect the composition of the galaxy when the first generation of stars formed. We have been searching for PN within the galactic halo, and have found three new PN that may be classified as “halo” PN. We have also discovered nine other new PN within the thick disk and plane of the galaxy. Candidates for our spectral observations were chosen through a multi-step process. First, colors within SDSS and 2MASS were compared to find initial targets, which were then followed up with imaging in g’ and [OIII] filters to pick out [OIII] bright candidates. Apache Point Observatory DIS spectroscopy of our candidates has resulted in identification of twelve likely new PN, based on the observed emission lines, and ratios of these lines. We present spectra and images of some for these targets.

A Comparison of the Red and Green Coronal Line Intensities at the 29 March 2006 and the 1 August 2008 Total Solar Eclipses: Considerations of the Temperature of the Solar Corona

A.Voulgaris, T.Athanasiadis, J.H.Seiradakis, and Jay M. Pasachoff

Solar Physics 264, #1, 45-55. DOI 10.1007/s11207-010-9575-7. (2010)

During the total solar eclipse at Akademgorodok, Siberia, Russia, on 1 August 2008, we imaged the flash spectrum with a slitless spectrograph. We have spectroscopically determined the duration of totality, the epoch of the 2nd and 3rd contacts and the duration of the flash spectrum. Here we compare the 2008 flash spectra with those that we similarly obtained from the total solar eclipse of 29 March 2006, at Kastellorizo, Greece. Any changes of the intensity of the coronal emission lines, in particularly those of [Fe X] and [Fe XIV], could give us valuable information about the temperature of the corona. The results show that the ionization state of the corona, as manifested especially by the [Fe XIV] emission line, was much weaker during the 2008 eclipse, indicating that following the long, inactive period during the solar minimum, there was a drop in the overall temperature of the solar corona.

An Old World with a Fresh Surface

J.L.Elliot, M.J.Person, C.A.Zuluaga, A.S.Bosh, E.R.Adams, T.C.Brothers, A.A.S.Gulbis, S.E.Levine, M.Lockhart, A.M.Zangari, Bryce A. Babcock, Katherine DuPré’10, Jay M. Pasachoff, Stephen P. Souza, W.Rosing, N.Secrest, L.Bright, E.W.Dunham, S.S.Sheppard, M.Kakkala, T.Tilleman, B.Berger, J.W.Briggs, G.Jacobson, P.Valleli, B.Volz, S.Rapoport, R.Hart, M.Brucker, R.Michel, A.Mattingly, L.Zambrano-Marin, A.W.Meyer, J.Wolf, E.V.Ryan, W.H.Ryan, K.Morzinsky, B.Grigsby, J.Brimacombe, D.Ragozzine, H.G.Montano, and A.Gilmore

Nature, June 17 (2010)

The Kuiper belt is a collection of dwarf planets and other small bodies that lie beyond the orbit of Neptune. Believed to have formed contemporaneously with the planets (or soon thereafter), Kuiper belt objects (KBOs) offer clues, through their spatial distribution and physical properties, to conditions during the formation of the solar system. Unfortunately, due to their small size and great instance, few methods allow detailed investigations of these frigid bodies. Here we report the first multi-chord observations of a KBO stellar occultation, which occurred on 2009 October 9 (UT). We find that the KBO 55636 (2002 TX300), which is a member of the water-ice rich Hauymea KBO collisional family, has a mean radius of 143 ± 5 km (circular solution). Allowing for possible elliptical shapes we find a geometric albedo 0.88 (+0.06, –0.14) in the V photometric band, which firmly establishes that 55636 is smaller than previously thought and, like its parent body Haumea, is among the most highly reflective objects in the Solar System. Dynamical calculations by two groups indicate that the collision that created 55636 occurred at least 1 Gyr ago, which raises the question of how such a small, ancient body can have a highly reflective surface.

Resource Letter SP-1 on Solar Physics

Jay M. Pasachoff

American Journal of Physics, 78, September, 890-901 (2010)

This Resource Letter provides a guide to printed literature and online resources about scientific and cultural references to the sun and related topics such as solar spectroscopy.  Items in the Resource Letter below are labeled with the letter E to indicate elementary level or material of general interest to persons seeking to become informed in the field, the letter I to indicate intermediate level or somewhat specialized material, or the letter A to indicate advanced or specialized material.

At the turn of the 20th century, much of astronomy was positional. Studies of the Sun played a major role in bringing astronomy to the astrophysical position that it enjoys today. The 21st-century solar physics is a vibrant science, with solar telescopes on the ground, including soon the Advanced Technology Solar Telescope about to be erected on Maui, joining dozens of spacecraft studying the Sun. NASA’s Living with a Star program positions the Sun as a major influence on space weather and thus on the Earth. This Resource Letter does not include solar energy as an energy resource.

The Origin and Diffusion of the H and K Notation

Jay M. Pasachoff and TA.Suer

Journal of Astronomical History and Heritage, 13 (2), 121-127 (2010)

Though many or most astronomers and astronomy students may think that H and K, as in the Ca II “H and K lines,” were named by Fraunhofer, actually only the H line was in Fraunhofer’s original notation. He also used “I” to indicate the end of the spectrum in his widely reproduced 1814 drawing, of which an engraved version was published in 1817. We have searched references from 19th-century books and journals to find the first use of “K” to indicate the ionized-calcium spectral line at 393.3 nm and located the probable first use and eventually the reuse of the notation.

Simultaneous Observations of the Chromosphere with TRACE and SUMER

Jay M. Pasachoff, E.Tingle, I.E.Dammasch, and A.C.Sterling

Solar Physics 268, No. 1, 151-163; http://dx.doi.org/10.1007/s11207-010-9673-6 (2010)

Using the 1600 Å continuum and 1216 Å Lyman-alpha filters aboard the TRACE satellite, we observed the short yet complete lifetime of a transient, bright chromospheric loop. Simultaneous observations with the SUMER instrument aboard the SOHO spacecraft revealed interesting material velocities existing above the chromospheric loop imaged with TRACE, possibly corresponding to extended non-visible loops, or the base of an X-ray jet.

High-resolution Satellite Imaging of the 2004 Transit of Venus and Asymmetries in the Cytherean Atmosphere

Jay M. Pasachoff, G.Schneider, and T.Widemann

Astron. J., 141, #3, 112-120 (March). doi: 10.1088/0004-6256/141/4/112 (2011)

The paper presents the only space-borne observations of the 8 June 2004 transit of Venus, the first such transit visible from Earth since AD 1882. The high-resolution, high-cadence satellite images we arranged from NASA’s Transition Region and Coronal Explorer (TRACE), reveal the onset of visibility of Venus’s atmosphere and give further information about the black-drop effect, whose causes we previously demonstrated from TRACE observations of a transit of Mercury (Pasachoff et al. 2003, 2004). The atmosphere is gradually revealed before second contact and after third contact, resulting from the changing depth of atmospheric layers refracting the photospheric surface into the observer’s direction. We use Venus Express observations to relate the atmospheric arcs seen during the transit to the atmospheric structure of Venus. Finally, we relate the transit images to current and future exoplanet observations, providing a sort of ground-truth showing an analogue in our solar system to effects observable only with light curves in other solar systems with the Kepler and CoRoT missions and ground-based exoplanet-transit observations.

Size and Albedo of Kuiper Belt Object 55636 from a Stellar Occultation

J.L Elliot, M.J.Person, C.A.Zuluaga, A.S.Bosh, E.R.Adams, T.C.Brothers, A.A.S.Gulbis, S.E.Levine, M.Lockhart, A.M.Zangari, Bryce A. Babcock, Katherine DuPré’10, Jay M. Pasachoff, Steven P. Souza, W.Rosing, N.Secrest, L.Bright, E.W.Dunham, S.S.Sheppard, M.Kakkala, T.Tilleman, B.Berger, J.W.Briggs, G.Jacobson, P.Valleti, B.Volz, S.Rapoport, R.Hart, M.Brucker, R.Michel, A.Mattingley, L.Zambrano-Marin, A.W.Meyer, J.Wolf, E.V.Ryan, W.H.Ryan, K.Morzinski, B.Grigsby, J.Brimacombe, D.Ragozine, H.G.Montano, and A.Gilmore

Nature, 465,897-900, June 17 (2010)

The Kuiper belt is a collection of small bodies (Kuiper belt objects, KBOs) that lie beyond the orbit of Neptune and which are believed to have formed contemporaneously with the planets. Their small size and great distance make them difficult to study. KBO 55636 (2002 TX300) is a member of the water-ice-rich Haumea KBO collisional family. The Haumea family are among the most highly reflective objects in the Solar System. Dynamical calculations indicate that the collision that created KBO 55636 occurred at least 1 Gyr ago. Here we report observations of a multi-chord stellaroccultation by KBO 55636, which occurred on 9 October 2009 UT. We find that it has a mean radius of 143 6 5 km (assuming a circular solution). Allowing for possible elliptical shapes, we find a geometric albedo of 0:88 in the V photometric band, which establishes that KBO 55636 is smaller than previously thought and that, like its parent body, it is highly reflective. The dynamical age implies either that KBO 55636 has an active resurfacing mechanism, or that fresh water-ice in the outer Solar System can persist for gigayear timescales.

PICO: Portable Instrument for Capturing Occultations

M.Lockhart, M.J.Person, J.L.Elliot and Steven P.Souza

Publications of the Astronomical Society of the Pacific, 122, 1207-1213 (2010)

We describe a portable imaging photometer for the observation of stellar occultation events by Kuiper Belt objects (KBOs) and other small bodies. The system is referred to as the Portable Instrument for capturing Occultations (PICO). It is designed to be transportable to remote observing sites by a single observer. A GPS timing system is used to trigger exposures of a Finger Lakes Instrumentation ML261E-25 camera to facilitate the combination of observational results from multiple sites. The system weighs a total of 11 kg when packed into its single rigid 55:1 × 35:8 × 22:6 cm container, meeting current airline size and weight limits for carry-on baggage. Twelve such systems have been constructed. Nine systems were deployed for observation of a stellar occultation by Kuiper Belt object 55636 in 2009 October. During the same month, one system was used to record a stellar occultation by minor planet 762 Pulcova.

Biology

Journal of Comparative Neurology, 10, 1979-98. doi: 10.1002/cne.2261 (2011)

Studies on the Mauthner cell (M-cell) of goldfish, Carassius auratus, have facilitated our understanding of how sensory information is integrated in the hindbrain to initiate C-type fast startle responses (C-starts). The goldfish M-cell initial segment/axon hillock is surrounded by a composite axon cap consisting of a central core and a peripheral zone covered by a glial cell layer. The high resistivity of the axon cap results in “signature” field potentials recorded on activation of the M-cell, allowing unequivocal physiological identification of the M-cell and of its feedback and reciprocal inhibitory networks that are crucial in ensuring that only one M-cell is active and that it fires only once. Phylogenetic mapping of axon cap morphology to muscle activity patterns and behavior predicts that teleost fishes that have a composite axon cap, like that of the goldfish, will perform C-start behavior with primarily unilateral muscle activity.

We have chosen to study these predictions in the northern sea robin, Prionotus carolinus, a percomorph fish. Although sea robins have a very different phylogenetic position, body form, and habitat compared with the goldfish, they display the correlation of axon cap morphology to physiology and C-start behavior. Differences in response parameters suggest some evolutionary trade- offs in sea robin C-start behavior compared with that of the goldfish, but the correlations in morphology, physiology, and behavior are common features of both otophysan and nonotophysan teleosts. The M-cell will continue to provide an unprecedented opportunity to study the evolution of a neural circuit in the context of behavior.

Sphagnum moss disperses spores with vortex rings

D.L. Whitaker and Joan Edwards,

Science, 329, 406 (2010)

Sphagnum spores, which have low terminal velocities, are carried by turbulent wind currents to establish colonies many kilometers away. However, spores that are easily kept aloft are also rapidly decelerated in still air; thus, dispersal range depends strongly on release height. Vascular plants grow tall to lift spores into sufficient wind currents for dispersal, but nonvascular plants such as Sphagnum cannot grow sufficiently high. High-speed videos show that exploding capsules of Sphagnum generate vortex rings to efficiently carry spores high enough to be dispersed by turbulent air currents. Spores launched ballistically at similar speeds through still air would travel a few millimeters and not easily reach turbulent air. Vortex rings are used by animals; here, we report vortex rings generated by plants.

Mechanics without muscle: biomechanical inspiration from the plant world

P.T.Martone, M.Boller, I.Burgert, J.Dumais, Joan Edwards, K.Mach, N.Rowe, M.Rueggeberg, R.Seidel and T.Speck

Integrative and Comparative Biology, 50, 888-908 (2010)

Plant and animal biomechanists have much in common. Although their frame of reference differs, they think about the natural world in similar ways. While researchers studying animals might explore airflow around flapping wings, the actuation of muscles in arms and legs, or the material properties of spider silk, researchers studying plants might explore the flow of water around fluttering seaweeds, the grasping ability of climbing vines, or the material properties of wood. Here we summarize recent studies of plant biomechanics highlighting several current research themes in the field: expulsion of high-speed reproductive projectiles, generation of slow movements by shrinking and swelling cell walls, effects of ontogenetic shifts in mechanical properties of stems, flexible reconfiguration and material properties of seaweeds under crashing waves, and the development of botanically-inspired commercial products. Our hope is that this synopsis will resonate with both plant and animal biologists, encourage cross-pollination across disciplines, and promote fruitful interdisciplinary collaborations in the future.

An Agrobacterium VirB10 Mutation Conferring a Type IV Secretion System Gating Defect

Lois M.Banta, J.E.Kerr, E.Cascales, Megan E.Giuliano’05, Megan E.Bailey’08, C.McKay, V.Chandran, G.Waksman, P.J.Christie

Journal of Bacteriology 193(10):2566-74 (2011).

Agrobacterium VirB7, VirB9, and VirB10 form a “core complex” during biogenesis of the VirB/VirD4 type IV secretion system (T4SS). VirB10 spans the cell envelope and, in response to sensing of ATP energy consumption by the VirB/D4 ATPases, undergoes a conformational change required for DNA transfer across the outer membrane (OM). Here, we tested a model in which VirB10 regulates substrate passage by screening for mutations that allow for unregulated release of the VirE2 secretion substrate to the cell surface independently of target cell contact. One mutation, G272R, conferred VirE2 release and also rendered VirB10 conformationally insensitive to cellular ATP depletion. Strikingly, G272R did not affect substrate transfer to target cells (Tra-) but did block pilus production (Pil-). The G272R mutant strain displayed enhanced sensitivity to vancomycin and SDS but did not nonspecifically release periplasmic proteins or VirE2 truncated of its secretion signal. G272 is highly conserved among VirB10 homologs, including pKM101 TraF, and in the TraF X-ray structure the corresponding Gly residue is positioned near an α-helical domain termed the antenna projection (AP), which is implicated in formation of the OM pore. A partial AP deletion mutation (ΔAP) also confers a Tra- Pil- phenotype; however, this mutation did not allow VirE2 surface exposure but instead allowed the release of pilin monomers or short oligomers to the milieu. We propose that (i) G272R disrupts a gating mechanism in the core chamber that regulates substrate passage across the OM and (ii) the G272R and ΔAP mutations block pilus production at distinct steps of the pilus biogenesis pathway

Model selection analysis of temporal variation in benefit for an ant-tended treehopper.

Morales, Manuel A

Ecology 92:709–719. [doi:10.1890/10-1154.1]  (2011)

Recent studies of mutualism have emphasized both that the net benefit to participants depends on the ecological context and that the density-dependent pattern of benefit is key to understanding the population dynamics of mutualism. Indeed, changes in the ecological context are likely to drive changes in both the magnitude of benefit and the density-dependent pattern of benefit. Despite the close linkage between these two areas of research, however, few studies have addressed the factors underlying variation in the density-dependent pattern of benefit. Here I use model selection to evaluate how variation in the benefits of a mutualism drives temporal variation in the density-dependent pattern of net benefit for the ant-tended treehopper Publilia concava. In the interaction between ants and treehoppers in the genus Publilia, ants collect the sugary excretions of treehoppers as a food resource, and treehoppers benefit both directly (e.g., by feeding facilitation) and indirectly (e.g., by predator protection). Results presented here show that temporal changes in the relative magnitude of direct and indirect benefit components of ant tending, especially the effectiveness of predator protection by ants, qualitatively change the overall pattern of density-dependent benefit between years with maximum benefit shifting from treehoppers in small to large aggregations. These results emphasize the need for empirical studies that evaluate the long-term dynamics of mutualism and theoretical studies that consider the population dynamics consequences of variation in the density-dependent pattern of benefit.

Context-Dependent Function of “GATA Switch” Sites In Vivo

Jon W.Snow, J.J.Trowbridge, K.D.Johnson, T.Fujiwara, N.R.Emambokus, J.A.Grass, S.H.Orkin, and E.H.Bresnick

Blood (18):4769-72 (2010).

Master transcriptional regulators of development often function through dispersed cis elements at endogenous target genes. While cis-elements are routinely studied in transfection and transgenic reporter assays, it is challenging to ascertain how they function in vivo. To address this problem in the context of the locus encoding the critical hematopoietic transcription factor Gata2, we engineered mice lacking a cluster of GATA motifs 2.8 kb upstream of the Gata2 transcriptional start site. We demonstrate that the -2.8 kb site confers maximal Gata2 expression in hematopoietic stem cells and specific hematopoietic progenitors. By contrast to our previous demonstration that a palindromic GATA motif at the neighboring -1.8 kb site maintains Gata2 repression in terminally differentiating erythroid cells, the -2.8 kb site was not required to initiate or maintain repression. These analyses reveal qualitatively distinct functions of 2 GATA motif-containing regions in vivo.

Separable Core Pluripotency and Myc Network Modules in Embryonic Stem Cells and Cancer

J.Kim, A.J.Woo, J.Chu, Jon W.Snow, Y.Fujiwara, C.G.Kim, A.B.Cantor, and S.H.Orkin

Cell 143(2):313-24 (2010).

c-Myc (Myc) is an important transcriptional regulator in embryonic stem (ES) cells, somatic cell reprogramming, and cancer. Here, we identify a Myc-centered regulatory network in ES cells by combining protein-protein and protein-DNA interaction studies and show that Myc interacts with the NuA4 complex, a regulator of ES cell identity. In combination with regulatory network information, we define three ES cell modules (Core, Polycomb, and Myc) and show that the modules are functionally separable, illustrating that the overall ES cell transcription program is composed of distinct units. With these modules as an analytical tool, we have reassessed the hypothesis linking an ES cell signature with cancer or cancer stem cells. We find that the Myc module, independent of the Core module, is active in various cancers and predicts cancer outcome. The apparent similarity of cancer and ES cell signatures reflects, in large part, the pervasive nature of Myc regulatory networks.

A single cis element maintains repression of the key developmental regulator Gata2

Jon W.Snow, J.J.Trowbridge, T.Fujiwara, J.A.Grass, N.R.Emambokus, S.H.Orkin, and E.H.Bresnick

PLoS Genetics 6(9):e1001103 (2010).

In development, lineage-restricted transcription factors simultaneously promote differentiation while repressing alternative fates. Molecular dissection of this process has been challenging as transcription factor loci are regulated by many trans-acting factors functioning through dispersed cis elements. It is not understood whether these elements function collectively to confer transcriptional regulation, or individually to control specific aspects of activation or repression, such as initiation versus maintenance. Here, we have analyzed cis element regulation of the critical hematopoietic factor Gata2, which is expressed in early precursors and repressed as GATA-1 levels rise during terminal differentiation. We engineered mice lacking a single cis element -1.8 kb upstream of the Gata2 transcriptional start site. Although Gata2 is normally repressed in late-stage erythroblasts, the -1.8 kb mutation unexpectedly resulted in reactivated Gata2 transcription, blocked differentiation, and an aberrant lineage-specific gene expression pattern. Our findings demonstrate that the -1.8 kb site selectively maintains repression, confers a specific histone modification pattern and expels RNA Polymerase II from the locus. These studies reveal how an individual cis element establishes a normal developmental program via regulating specific steps in the mechanism by which a critical transcription factor is repressed.

Sumoylation regulates interaction of FOG1 with CTBP

Jon W.Snow, J.Kim, C.Currie, J.Xu, and S.H.Orkin

 Journal of Biological Chemistry 285(36):28064-75 (2010).

Erythropoietic and megakaryocytic programs are specified from multipotential progenitors by the transcription factor GATA1. FOG1, a GATA1-interaction partner, is critical for GATA1 function in several contexts by bringing multiple complexes into association with GATA1 to facilitate activation or repression of target genes. To further elucidate regulation of these associations by cellular and extracellular cues, we examined FOG1 for post-translational modifications. We found that FOG1 is SUMOylated and phosphorylated in erythroid cells in a differentiation-dependent manner. Removal of the SUMOylation sites in FOG1 does not impair nuclear localization, protein stability, or chromatin occupancy. However, SUMOylation of FOG1 modulates interactions with C-terminal binding protein family members, specifically promoting CTBP1 binding. Phosphorylation of FOG1 modulates SUMOylation and, therefore, indirectly regulates the CTBP interaction. Post-translational modification of FOG1 may contribute to control of co-occupancy by CTBP family members, the NuRD complex, and GATA1 at differentially regulated genes.

Characterisation and expression of microRNAs in developing wings of the neotropical butterfly Heliconius melpomene

A.K.Surridge, S.Lopez-Gomollon, S.Moxon, Luana S.Maroja, T.Rathjen, J.Nadeau n, T.Ddalmay and C.D.Jiggins

BMC Genomics 12: 62doi:10.1186/1471-2164-12-62 (2011)

Background

Heliconius butterflies are an excellent system for studies of adaptive convergent and divergent phenotypic traits. Wing colour patterns are used as signals to both predators and potential mates and are inherited in a Mendelian manner. The underlying genetic mechanisms of pattern formation have been studied for many years and shed light on broad issues, such as the repeatability of evolution. In Heliconius melpomene, the yellow hindwing bar is controlled by the HmYb locus. MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that have key roles in many biological processes, including development. miRNAs could act as regulators of genes involved in wing development, patterning and pigmentation. For this reason we characterised miRNAs in developing butterfly wings and examined differences in their expression between colour pattern races.

Results

We sequenced small RNA libraries from two colour pattern races and detected 142 Heliconius miRNAs with homology to others found in miRBase. Several highly abundant miRNAs were differentially represented in the libraries between colour pattern races. These candidates were tested further using Northern blots, showing that differences in expression were primarily due to developmental stage rather than colour pattern. Assembly of sequenced reads to the HmYb region identified hme-miR-193 and hme-miR-2788; located 2380 bp apart in an intergenic region. These two miRNAs are expressed in wings and show an upregulation between 24 and 72 hours post-pupation, indicating a potential role in butterfly wing development. A search for miRNAs in all available H. melpomene BAC sequences (~ 2.5 Mb) did not reveal any other miRNAs and no novel miRNAs were predicted.

Conclusions

Here we describe the first butterfly miRNAs and characterise their expression in developing wings. Some show differences in expression across developing pupal stages and may have important functions in butterfly wing development. Two miRNAs were located in the HmYb region and were expressed in developing pupal wings. Future work will examine the expression of these miRNAs in different colour pattern races and identify miRNA targets among wing patterning genes.

Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade

S.W.Baxter, N.Nadeau, Luana S.Maroja, P.Wilkinson, B.C.ounterman, A.Dawson, M.Beltran, S.Perez-Espona, N.Chamberlain, L.Ferguson, R.Clark, C.Davidson, R.Glithero, J.Mallet, W.O.McMillan, M.Kronforst, M.Joron, R.H.Ffrench-Constant and C.D.Jiggins

PLoS Genetics 6(2): e1000794. doi:10.1371/journal.pgen.1000794 (2010)

Wing patterning in Heliconius butterflies is a longstanding example of both Müllerian mimicry and phenotypic radiation under strong natural selection. The loci controlling such patterns are “hotspots” for adaptive evolution with great allelic diversity across different species in the genus. We characterise nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium, and candidate gene expression at two loci and across multiple hybrid zones in Heliconius melpomene and relatives. Alleles at HmB control the presence or absence of the red forewing band, while alleles at HmYb control the yellow hindwing bar. Across HmYb two regions, separated by ~100 kb, show significant genotype-by-phenotype associations that are replicated across independent hybrid zones. In contrast, at HmB a single peak of association indicates the likely position of functional sites at three genes, encoding a kinesin, a G-protein coupled receptor, and an mRNA splicing factor. At both HmYb and HmB there is evidence for enhanced linkage disequilibrium (LD) between associated sites separated by up to 14 kb, suggesting that multiple sites are under selection. However, there was no evidence for reduced variation or deviations from neutrality that might indicate a recent selective sweep, consistent with these alleles being relatively old. Of the three genes showing an association with the HmB locus, the kinesin shows differences in wing disc expression between races that are replicated in the co-mimic, Heliconius erato, providing striking evidence for parallel changes in gene expression between Müllerian co-mimics. Wing patterning loci in Heliconius melpomene therefore show a haplotype structure maintained by selection, but no evidence for a recent selective sweep. The complex genetic pattern contrasts with the simple genetic basis of many adaptive traits studied previously, but may provide a better model for most adaptation in natural populations that has arisen over millions rather than tens of years.

Chemistry

Single Molecules Reveal the Dynamics of Heterogeneities in a Polymer at the Glass Transition

Dieter Bingemann, Rachel M. Allen ’08, and Scott W. Olesen’10

Journal of Chemical Physics 134, 024513 (2011)

The notion of heterogeneous dynamics in glasses, that is, the spatial and temporal variations of structural relaxation rates, explains many of the puzzling features of glass dynamics. The nature and the dynamics of these heterogeneities, however, have been very controversial. Single rhodamine B molecules in poly(vinyl acetate) at the glass transition reorient through sudden jumps. With a statistical search for the most likely break points in the logarithm of the ratio of the two perpendicular fluorescence polarizations, we determine the times of these angular jumps. We interpret these jumps as an indication for individual glass rearrangements in the vicinity of the probe molecule. Time-series analysis of the resulting sequence of waiting times between jumps shows that dynamic heterogeneities in the matrix exist, but are short lived. From the correlation of the logarithm of the waiting time between subsequent jumps, we determine an upper limit for the lifetime of heterogeneities in the sample. The correlation time of ô het = 32 s is three times shorter than the orientational correlation time of the probe molecule, τ orient = 90 s, in the sample at this temperature, but 13 times longer than the structural relaxation time, ôá = 2.5 s, estimated for this sample from dielectric experiments. We present a model for glass dynamics in which each rearrangement in one region causes a random change in the barrier height for subsequent rearrangements in a neighboring region. This model, which equates the dynamics of the heterogeneities with the dynamics of the glass itself and thus implies a factor of one between heterogeneity lifetime and structural relaxation time, successfully reproduces the statistics of the experimentally observed waiting time sequences.

Effects of Polymer Molecular Weight on the Size, Activity, and Stability of PEG-functionalized Trypsin

K.Chiu’10, L.Agoubi’13, I.Lee ’09, M.T.Limpar ’09, J.W.Lowe Jr. ’09, and Sarah L.Goh

Biomacromolecules 11, 3688-3692 (2011)

Polymer conjugation increases an enzyme’s circulation time and stability for use as a therapeutic agent, but this attachment indubitably affects its properties. Covalent attachment of multiple polyethylene glycol chains with sizes of either 2, 5, 10, or 20 kDa increases the molecular weight and hydrodynamic radius of the model enzyme trypsin. The sizes of these polymer−enzyme conjugates are increased to be within the recommended limits for PDEPT applications. The Td increases from 49 to 60 °C to expand the enzyme’s workable range of conditions. This functionalization with PEG polymers of varying lengths maintains trypsin’s enzymatic activity. Conjugate activities are 79−120% that of native trypsin at room temperature and 221−432% that of trypsin at 37 °C.

Self-Assembly of Di- and Tri-Block PEG-Pentavaline Amphiphiles

E.Hwang’13, T.Wilson-Hill ’09, J.W.Ahn’12, A.Platt ’07, K.Rutledge ’05, and Sarah L.Goh

Journal of Polymer Science Part A: Polymer Chemistry 49, 871-878 (2011)

Nanoparticles formed from amphiphilic block copolymers can be used as drug delivery vehicles for hydrophilic therapeutics. Poly(ethylene glycol) (PEG)-peptide copolymers were investigated for their self-assembling properties and as consequent potential delivery systems. Mono- and dihydroxy PEGs were functionalized with a pentavaline sequence bearing Fmoc end groups. The molecular weight of the PEG component was varied to evaluate copolymer size and block number. These di- and tri-block copolymers readily self-assemble in aqueous solution with critical aggregation concentrations (CACs) of 0.46–16.29 ìM. At concentrations above the CAC, copolymer solutions form spherical assemblies. Dynamic light scattering studies indicate these aggregates have a broad size distribution, with average diameters between 33 and 127 nm. The copolymers are comprised â-conformations that are stable up to 80 °C, as observed by circular dichroism. This peptide secondary structure is retained in solutions up to 50% MeOH as well. The triblock copolymers proved to be the most stable, with copolymers synthesized from 10 kDa PEG having the most stable particles. Loading of carboxyfluorescein at 2–5 mol % shows that these copolymers have the potential to encapsulate hydrophilic drugs for delivery applications.

Particle in a One-Dimensional Finite and Semi-Infinite Well Revisited

Enrique Peacock-López

The Chemical Educator 16, 148-154 (2011)

For the quantum particle in a finite and semi-infinite well, we scale space and energy to consider a dimensionless Schrödinger equation that can be solved for the allowed energy levels. In contrast to traditional approaches that determine the energies from dimensional transcendental equations associated with the boundary conditions, we solve for the square root of the dimensionless energies, which are also solutions of dimensionless transcendental equations. Our ability to define classes of wells depends on the value of the square root of the dimensionless well depth. We are also able to determine the maximum number of energy levels quite easily, and, besides deriving the relevant transcendental equations, we obtain a simple expression for the corresponding wave functions, which can be plotted using the numerical values of the allowed energies.

The Relevance of Cross-Diffusion in the Formation of Turing Patterns

Enrique Peacock-López

Nonlinear Dynamics, Psychology, and Life Sciences 15, 1-10 (2011)

Over the years, the Rosenzweig-MacArthur (RM) model has been used to study simple prey-predator systems. It has been observed, however, that the RM model cannot sustain Turing patterns when using a diagonal diffusion tensor. As a result, researchers have introduced changes to the RM model that induce stable Turing patterns. In most cases, the changes have been made to the so-called response function, changing the interspecies interaction, or by adding an intraspecies interaction to the model. In this communication, we study the original RM model but we include cross-diffusion, which considers off diagonal elements in the diffusion tensor. Although cross-diffusion is well characterized in multicomponent solutions, including electrolytes, it has an apparent counterintuitive meaning in predator-prey systems. We observe, however, that in plant and fish systems, the lack of predator mobility is compensated by their ability to camouflage and attract their prey, which yields a negative cross-diffusion coefficient. We show that negative cross-diffusion is enough to trigger stable Turing patterns in the RM model.

Current Topics in ESR Dating

Anne R.Skinner

Radiation Measurements (2011)

After over 25 years, the use of electron spin resonance (ESR) is well-established in dating sites of geological, paleontological and archaeological interest. Like any scientific technique, there have been changes in understanding and in methodology. Improvements have not, however, changed the observation that external dose calculations are still a significant source of uncertainty in ages. Examples from Europe, Africa and the Americans illustrate this point. For Pradayrol Cave (France), the occupation age, 330 ka, is unchallenged, making this the oldest known Neanderthal site in France. For Roc de Marsal, also in France, on the other hand, discrepancies between TL and sedimentary dose rates imply substantial differences in interpretation. In the Western Egyptian Desert, where artifacts and datable material are not well-correlated, the dating results show consistency with expectations based on global climate change, even in deflated sites. Climate change is also the question in geological studies in the Bahamas where, despite concerns about cosmic dose history, ESR dates confirm other evidence for sealevel changes. We show that an uncertain age is not the same as an impossible one.

Testing Cosmic Dose Rate Models for ESR: Dating Corals and Molluscs on San Salvador, Bahamas

Anne R.Skinner, A.E.Deely, B.A.B.Blackwell, J.E.Mylroie, J.L.Carew, and J.I.B.Blickstein

Radiation Measurements (2011)

Sealevel curves are best developed on tectonically stable coastlines like San Salvador, where eolianites preserve transgressive and regressive phases associated with Quaternary high seastands, while reef facies mark the highstands. At 11 locations around San Salvador, terrestrial mollusks (Cerion) from the eolianites, lagoonal bivalves (Codakia), and corals from the highstand deposits were dated by ESR. Volumetrically averaged sedimentary dose rates were calculated from sedimentary geochemistry and time-averaged cosmic dose rates from each sample’s current and past geologic contexts. Rice Bay Formation corals dated at 3.9 ± 0.3 to 7.1 ± 0.4 ka (OIS 1). Minimum ages for the Cockburn Town Member’s regressive phase ranged from 49 ± 6 to 75 ± 8 ka, correlating with OIS 3-4. Codakia dates showed that an OIS 5a sealevel approached modern levels at 91-78 ka. In situ corals from the Cockburn Town Reef averaged from 127 ± 6 to 138 ± 10 ka, correlating well with OIS 5e. Ages from the Reef’s rubble zones hint that some coral reefs grew as early as OIS 7, but were likely reworked during OIS 5. San Salvador preserves deposits from three mid to late Quaternary highstands above, and as many as three that closely approach, modern sealevel.

Who Used Fire 1,500,000 Years Ago?

Anne R.Skinner

Electron Paramagnetic Resonance: From Fundamental Research to Pioneering Applications, 196-197 (2009)

While many aspects of an archaeological or geological project are essential to understanding human and environmental developments, the date of a site is frequently one of the most important factors. There are several methods to determine material ages. Most people have heard of the carbon-14, ¹⁴C, method. It is based on determining the relative amount of the radioactive isotope ¹⁴C compared to the non-radioactive isotope, ¹²C. Unfortunately for investigators interested in human evolution, to the relatively short half-life of ¹⁴C, 5730±40 years, means that this method is reliable results only for samples younger than about 40,000 years. Another radiometric dating method uses the ratio of argon isotopes, ⁴⁰Ar/³⁹Ar, found in volcanic lava. While this method can date materials in the millions of years, it is, of course, limited to sites with volcanic deposits. Electron paramagnetic resonance (EPR) dating is one of the newest dating methods. The paper by Ikeya on the dating of a stalagmite (1975) is considered the first example. Currently, depending on the material being used, EPR can provide chronometric ages as young as a few thousand years and as old as several million. Therefore it assists in studies older than the ¹⁴C limit, and at sites that lack volcanic materials. Overall, the variety of materials and time periods whose chronology can be determined make EPR a significant tool in the archaeological and paleontological dating kit.

Computer Science

Distributed Application Configuration, Management, and Visualization with Plush

Jeannie.Albrecht, C.Tuttle, R.Braud, D.Dao, N.Topilski, A.C.Snoeren, and A.Vahdat

ACM Transactions on Internet Technology (TOIT)

Support for distributed application management in large-scale networked environments remains in its early stages. Although a number of solutions exist for subtasks of application deployment, monitoring, and maintenance in distributed environments, few tools provide a unified framework for application management. Many of the existing tools address the management needs of a single type of application or service that runs in a specific environment, and these tools are not adaptable enough to be used for other applications or platforms. To this end, we present the design and implementation of Plush, a fully configurable application management infrastructure designed to meet the general requirements of several different classes of distributed applications. Plush allows developers to specifically define the flow of control needed by their computations using application building blocks. Through an extensible resource management interface, Plush supports execution in a variety of environments, including both live deployment platforms and emulated clusters. Plush also uses relaxed synchronization primitives for improving fault tolerance and liveness in failure-prone environments. To gain an understanding of how Plush manages different classes of distributed applications, we take a closer look at specific applications and evaluate how Plush provides support for each.

Finding a “Kneedle” in a Haystack: Detecting Knee Points in System Behavior

Ville Satopää’11, Jeannie Albrecht, D.Irwin, and B.Raghavan

Proceedings of the Third IEEE Workshop on Simplifying Complex Networks for Practitioners (Simplex), June 2011

Computer systems often reach a point at which the relative cost to increase some tunable parameter is no longer worth the corresponding performance benefit. These “knees” typically represent beneficial points that system designers have long selected to best balance inherent trade-offs. While prior work largely uses ad hoc, system-specific approaches to detect knees, we present Kneedle, a general approach to online and offline knee detection that is applicable to a wide range of systems. We define a knee formally for continuous functions using the mathematical concept of curvature and compare our definition against alternatives. We then evaluate Kneedle’s accuracy against existing algorithms on both synthetic and real data sets, and evaluate its performance in two different applications.

Enjoying Python, processing, and Java in CS1

O.Bälter and Duane A.Bailey

ACM Inroads 1(4): 28-32 (2010)

Here we describe an introductory course in computer science where we combined Python, Processing, and core Java. The main reason for this structure was to make the initial contact with programming as gentle, enjoyable, and understandable as possible, while still having the power of graphics and sufficient Java knowledge for more advanced courses in computer science. This course was designed with a few informal pedagogical principles that facilitated the students’ abilities to learn how to learn on their own. Informal results suggest that students may be interested in a greater diversity of programming assignments.

Efficient and Precise Happens Before Race Detection

C.Flanagan and Stephen N.Freund

Communication of the ACM, 53(11), pages 93-101 (2010)

Multithreaded programs are notoriously prone to race conditions. Prior work developed precise dynamic race detectors that never report false alarms. However, these checkers employ expensive data structures, such as vector clocks (VCs) that result in significant performance overhead. This paper exploits the insight that the full generality of VCs is not necessary in most cases. That is, we can replace VCs with an adaptive lightweight representation that, for almost all operations of the target program, requires constant space and supports constant-time operations. Experimental results show that the resulting race detection algorithm is over twice as fast as prior precise race detectors, with no loss of precision.

The 1-Neighbour Knapsack Problem

G.Boradaille, Brent Heeringa, and G.Wilfong

Proceedings of the 2011 International Workshop on Combinatorial Algorithms

We study a constrained version of the knapsack problem in which dependencies between items are given by the adjacencies of a graph. In the 1-neighbour knapsack problem, an item can be selected only if at least one of its neighbours’ is also selected. We give approximation algorithms and hardness results when the nodes have both uniform and arbitrary weight and profit functions, and when the dependency graph is directed and undirected.

Heapable Sequences and Subsequences

J.Byers, Brent Heeringa, M.Mitzenmacher, and G.Zervas

Proceedings of the 2011 Workshop on Analytic Algorithms and Combinatorics

Let us call a sequence of numbers heapable if they can be sequentially inserted to form a binary tree with the heap property, where each insertion subsequent to the first occurs at a leaf of the tree, i.e. below a previously placed number. In this paper we consider a variety of problems related to heapable sequences and subsequences that do not appear to have been studied previously. Our motivation for introducing these concepts is two-fold. First, such problems correspond to natural extensions of the well-known secretary problem for hiring an organization with a hierarchical structure. Second, from a purely combinatorial perspective, our problems are interesting variations on similar longest increasing subsequence problems, a problem paradigm that has led to many deep mathematical connections.

We provide several basic results. We obtain an efficient algorithm for determining the heapability of a sequence, and also prove that the question of whether a sequence can be arranged in a complete binary heap is NP-hard. Regarding subsequences we show that, with high probability, the longest heapable subsequence of a random permutation of n numbers has length (1-o (1))n, and a subsequence of length (1-o (1))n can in fact be found online with high probability. We similarly show that for a random permutation a subsequence that yields a complete heap of size c*n for a constant c can be found with high probability. Our work highlights the interesting structure underlying this class of subsequence problems, and we leave many further interesting variations open for future work.

Searching in Dynamic Tree-Like Partial Orders

Brent Heeringa, M.C.Iordan ’09, and L.Theran

Proceedings of the 2011 Algorithms and Data Structures Symposium

We give the first data structure for the problem of maintaining a dynamic set of n elements drawn from a partially ordered universe described by a tree. We define the Line-Leaf Tree, a linear-sized data structure that supports the operations: insert; delete; test membership; and predecessor. The performance of our data structure is within an O(log w)-factor of optimal. Here w ≤ n is the width of the partial-order––a natural obstacle in searching a partial order.

Approximating Optimal Binary Decision Trees

M.Adler and Brent Heeringa

Algorithmica, April 2011- http://dx.doi.org/10.1007/s00453-011-9510-9

We give a (ln n +1)-approximation for the decision tree (DT) problem. An instance of DT is a set of m binary tests T and a set of n items X. The goal is to output a binary tree where each internal node is a test, each leaf is an item and the total external path length of the tree is minimized. Total external path length is the sum of the depths of all the leaves in the tree. DT has a long history in computer science with applications ranging from medical diagnosis to experiment design. It also generalizes the problem of finding optimal average-case search strategies in partially ordered sets. This includes several alphabetic tree problems. Our work decreases the previous upper bound on the approximation ratio by a constant factor. We provide a new analysis of the greedy algorithm that uses a simple accounting scheme to spread the cost of a tree among pairs of items split at a particular node. We conclude by showing that our upper bound also holds for the DT problem with weighted tests

Filtering Approaches for Real-Time Anti-Aliasing

J.Jimenez, D.Guiterrez, J.Yang, A.Reshetov, P.Demoreuille, T.Berghoff, C.Perthis, H.Yu, Morgan McGuire, T.Lottes, H.Malan, D.Andreev, and T.Sousa

ACM SIGGRAPH Course Notes (Proceedings of SIGGRAPH 2011), August 2011

For more than a decade, Supersample Anti-Aliasing (SSAA) and Multisample Anti-Aliasing (MSAA) have been the gold standard antialiasing solution in games. However, these techniques are not well suited for deferred shading or fixed environments like the current generation of consoles. In the last years, Industry and Academia have begun to explore alternative approaches, where anti-aliasing is performed as a post-processing step. The original, CPU-based Morphological Anti-Aliasing (MLAA) method gave birth to an explosion of real-time anti-aliasing techniques that rival MSAA. This course will cover the most relevant techniques, from the original MLAA to the latest cutting edge advancements.

The Alchemy Screen-Space Ambient Obscurance Algorithm

Morgan McGuire, B.Osman, M.Bukowski, and P.Hennessy

Proceedings of ACM SIGGRAPH and Eurographics High Performance Graphics, August 2011

Ambient obscurance (AO) produces perceptually important illumination effects such as darkened corners, cracks, and wrinkles; proximity darkening; and contact shadows. We present the AO algorithm from the Alchemy engine used at Vicarious Visions in commercial games. It is based on a new derivation of screen-space obscurance for robustness, and the insight that a falloff function can cancel terms in a visibility integral to favor efficient operations. Alchemy creates contact shadows that conform to surfaces, captures obscurance from geometry of varying scale, and provides four intuitive appearance parameters: world-space radius and bias, and aesthetic intensity and contrast. The algorithm estimates obscurance at a pixel from sample points read from depth and normal buffers. It processes dynamic scenes at HD 720p resolution in about 4.5 ms on Xbox 360 and 3 ms on NVIDIA GeForce580.

Colored Stochastic Shadow Maps

Morgan McGuire and E.Enderton

Proceedings of the ACM SIGGRAPH Symposium on Interactive 3D Graphics and Games, February 2011

This paper extends the stochastic transparency algorithm that models partial coverage to also model wavelength-varying transmission. It then applies this to the problem of casting shadows between any combination of opaque, colored transmissive, and partially covered (i.e., α-matted) surfaces in a manner compatible with existing hardware shadow mapping techniques. Colored Stochastic Shadow Maps have a similar resolution and performance profile to traditional shadow maps, however they require a wider filter in colored areas to reduce hue variation.

Subpixel Reconstruction Antialiasing

M.Chajdas, Morgan McGuire, and D.Luebke

Proceedings of the ACM SIGGRAPH Symposium on Interactive 3D Graphics and Games, February 2011

Subpixel Reconstruction Antialiasing (SRAA) combines single-pixel (1x) shading with subpixel visibility to create antialiased images without increasing the shading cost. SRAA targets deferred-shading renderers, which cannot use multisample antialiasing. SRAA operates as a post-process on a rendered image with super resolution depth and normal buffers, so it can be incorporated into an existing renderer without modifying the shaders. In this way SRAA resembles Morphological Antialiasing (MLAA), but the new algorithm can better respect geometric boundaries and has fixed runtime independent of scene and image complexity. SRAA benefits shading-bound applications. For example, our implementation evaluates SRAA in 1.8 ms (1280×720) to yield antialiasing quality comparable to 4-16x shading. Thus SRAA would produce a net speedup over super sampling for applications that spend 1 ms or more on shading; for comparison, most modern games spend 5-10 ms shading. We also describe simplifications that increase performance by reducing quality.

A Local Image Reconstruction Algorithm for Stochastic Rendering

P.Shirley, T.Aila, J.Cohen, E.Enderton, S.Laine, D.Luebke, and Morgan McGuire

Proceedings of the ACM SIGGRAPH Symposium on Interactive 3D Graphics and Games, February 2011

Stochastic renderers produce unbiased but noisy images of scenes that include the advanced camera effects of motion and defocus blur and possibly other effects such as transparency. We present a simple algorithm that selectively adds bias in the form of image space blur to pixels that are unlikely to have high frequency content in the final image. For each pixel, we sweep once through a fixed neighborhood of samples in front to back order, using a simple accumulation scheme. We achieve good quality images with only 16 samples per pixel, making the algorithm potentially practical for interactive stochastic rendering in the near future.

Stylized Rendering in Games

Morgan McGuire, H.Halen, J.F.St-Amour, A.Thibault, and B.Martel

ACM SIGGRAPH Course Notes (Proceedings of SIGGRAPH 2010), August 2010

Games like Prince of Persia and Battlefield Heroes deliver artistic visions beyond standard photo-realistic 3D. In this course, game developers teach the challenges of creating distinctive visual styles for interactive environments and some of their own solutions. Topics include the art pipeline, rendering algorithms, and integrating visuals with gameplay.

Why stylized rendering? As they matured, the visual arts (painting, sculpture, photography, and architecture) all developed new visual-abstraction mechanisms to go beyond “realism”. Recent advances in visual effects have put film and games into this transitional state. In a sense, we’re like artists at the end of the Renaissance: we’ve nearly mastered photorealism, but are only at the beginning of our discoveries about expression and perception.

Some effects are subtle, like the color shifts and post-processing in Mirror’s Edge. Others, such as the graphic-novel look of Mad World, dominate the entire rendering style. In games, real-time and interactive constraints require more efficient and robust solutions than are employed elsewhere in computer graphics. And to be successful, a stylized renderer must integrate with appropriately stylized models, animation, and audio to form a coherent virtual world and ultimately enhance game play.

Geosciences

Repeated Pulses of Vertical Methane Flux Recorded in Glacial Sediments from the Southeast Bering Sea

Mea Cook, L.D.Keigwin, D.Birgel, and K-U.Kinrichs

Paleoceanography 26, 2210 (2011)

There is controversy over the role of marine methane hydrates in atmospheric methane concentrations and climate change during the last glacial period. In this study of two sediment cores from the southeast Bering Sea (700 m and 1467 m water depth), we identify multiple episodes during the last glacial period of intense methane flux reaching the seafloor. Within the uncertainty of the radiocarbon age model, the episodes are contemporaneous in the two cores and have similar timing and duration as Dansgaard-Oeschger events. The episodes are marked by horizons of sediment containing ¹³C-depleted authigenic carbonate minerals, ¹³C-depleted archaeal and bacterial lipids, which resemble those found in ANME-1 type anaerobic methane oxidizing microbial consortia, and changes in the abundance and species distribution of benthic foraminifera. The similar timing and isotopic composition of the authigenic carbonates in the two cores is consistent with a region-wide increase in the upward flux of methane-bearing fluids. This study is the first observation outside Santa Barbara Basin of pervasive, repeated methane flux in glacial sediments. However, contrary to the “Clathrate Gun Hypothesis” [Kennett et al., 2003], these coring sites are too deep for methane hydrate destabilization to be the cause, implying that a much larger part of the ocean’s sedimentary methane may participate in climate or carbon cycle feedback at millennial time scales. We speculate that pulses of methane in these opal-rich sediments could be caused by the sudden release of overpressure in pore fluids that builds up gradually with silica diagenesis. The release could be triggered by seismic shaking on the Aleutian subduction zone caused by hydrostatic pressure increase associated with sea level rise at the start of interstadials.

Well-Ventilated Intermediate Water and Pulses of High Export Production in the NW Pacific During the Last Glaciation

Mea Cook and L.D.Keigwin

10^th International Conference on Paleoceanography (2010)

There is a sequence of laminated or dysoxic sediments observed at intermediate depth in the North Pacific from the Bolling-Allerod and the early Holocene. It is unclear whether the sediments represent an increase in export production, a decrease in ventilation of intermediate water or a combination. The timing and intensity of the oxygen depletion are spatially variable, probably as local differences in primary productivity. However, this pattern is observed in a variety of depositional settings from the Mexican margin to the Bering Sea to the Japan margin, which suggests a basin-wide mechanism at work. In a depth transect of sediment cores (939 to 4155 m water depth) from the Okhotsk Sea and Emperor Seamounts, we have measured the absolute abundance of benthic foraminifera from the LGM to the Holocene. There are narrow peaks in the abundance of Uvigerina peregrina and U. auberiana that rise an order of magnitude higher than background values. These abundance peaks probably represent times of high organic carbon flux to the seafloor, caused by either greater export production or greater preservation of exported organic carbon due to reduced ventilation. We observe peaks in Uvigerina abundance in all ten cores of this study that are radiocarbon dated with planktonic foraminifera to the very beginning of the Bolling- Allerod, 14,500 ± 200 cal BP. We observe another peak in cores from 939 to 1761 m water depth in the early Holocene, just after the end of the Younger Dryas, 11,600 ± 200 cal BP. The synchrony of the peaks and the high abundance of benthic foraminifera allow us to reconstruct the Δ¹⁴C of the water column in a snapshot at these two times by radiocarbon dating pairs of benthic and planktonic foraminifera. We find that at the beginning of the Bolling-Allerod, the water column at 1−2 km and deeper than 3 km was enriched in ¹⁴C compared to what it would have been with a modern circulation. At the beginning of the Holocene, the water column at 1−2 km is also significantly enriched in ¹⁴C, though to a lesser extent. This suggests that during the early Bolling-Allerod and early Holocene, there were pulses of high export production at times of greater ventilation of intermediate water than today.

Bering Sea Paleoceanography

Mea Cook, K.Takahashi, A.C.Ravelo, C.A.Alvarez-Zarikian, and 323 Expedition Scientists

Proceedings of the Integrated Ocean Drilling Program 323, 201 p. (2011)

Paleoclimate and paleoceanography studies present opportunities to study the dynamics of the climate system by examining how it responds to external forcing (e.g., greenhouse gases and solar radiation) and how its interacting components generate climate oscillations and abrupt changes. Paucity of data in critical regions of the Pacific such as the Bering Sea has prevented an evaluation of the role of North Pacific processes in global climate change over the last 5 million years. The Integrated Ocean Drilling Program Expedition 323 was dedicated to elucidate the history of climate and surface ocean conditions since the earliest Pliocene; characterize the history of deep ocean circulation, continental glaciation, river discharge, and sea ice; investigate linkages between this marginal sea and global processes; and constrain biogeochemical models of sub-seafloor biomass and respiration. During Expedition 323, 5741 m of sediment were drilled at seven sites in three areas: Umnak Plateau, Bowers Ridge and the Bering Sea continental slope. Water depths of coring locations ranged from 818 to 3174 m and sediment age spans 0 to 5 million years. Preliminary findings include the intensification of seasonal sea ice production 1 million years ago at the mid-Pleistocene transition, evidence of episodes of low-oxygen conditions in the Bering Sea throughout the last 5 million years, strong climate and sea level control of siliciclastic deposition, and a very large range of microbial activity as deep as 700 m below the sea floor, with notable site-to-site variations.

Hydrodynamic Fractionation of Zircon Age Populations

Ronadh Cox, R.L.Lawrence, R.W.Mapes, and D.S.Coleman

Geological Society of America Bulletin 123, 295-305 (2011)

Zircons in transport in the modern Amazon River range from coarse silt to medium sand. Older grains are smaller on average: Mesozoic and Cenozoic grains have average equivalent spherical diameter (ESD) 122 ± 42 µm (lower fine sand), whereas grains >2000 Ma have average ESD 67 ± 14 µm (upper coarse silt). As a full Wentworth size class separates the two values, zircons in these age populations are hydraulically distinct. Five samples representing different hydrodynamic microenvironments of a single dune present significantly different detrital zircon age spectra, apparently the result of hydraulic processes. Peak mismatch (age peaks failing to overlap at 2σ level), is the most common disparity; but age populations present in some samples are missing from other samples. The lack of correspondence among the samples appears to exceed that attributable to random sampling. We conclude that hydrodynamic fractionation of zircons and zircon age populations does occur. Zircon size should therefore be taken into consideration in detrital zircon provenance analysis.

Hydrocode Modeling of Impacts at Europa

Ronadh Cox and A.W.Bauer’11

42^nd Lunar and Planetary Science Conference, abstract 1123 (2011)

Previous hydrocode simulations (e.g. [1]) have shown that impacts of sufficient energy could break through Europa’s ice crust to the water layer that probably underlies it [2], and this provides limiting criteria for formation of first-order (non-penetrating) craters [3]. But as the first-order crater population on Europa is small (24 known ≥ 10 km [4]), and as estimates of ice thickness (< 1 km to a few 10s of km [5, 6]) intersect with the penetration capabilities of likely impactors [3], it’s necessary to think broadly about a range of possible impact outcomes, and especially about the potential effects of large impacts or impacts into areas of thinner crust. We report here results of hydrocode simulations that provide constraints on ice penetration—both second and third order—for crust thicknesses and impact energies within the range of those expected at Europa.

Geomorphology of Chaos Areas on Europa

Ronadh Cox and Andrew T.Mikell ’09

42^nd Lunar and Planetary Science Conference, abstract 1128 (2011)

Chaos areas on Europa—regions where the surface has been disrupted, with blocks of remnant crust set in a hummocky matrix of slushy appearance—are poorly understood, and no satisfactory explanation for their formation has yet been presented. One of the proposed interpretations is that impact penetration could create holes in the ice layer, exposing underlying water; and while it’s clear that not all questions can be answered with current data, ongoing analysis and simulations continue to suggest that this may be a viable hypothesis. We present here GIS analysis of chaos area geomorphology. The geometry of chaos areas on Europa matches predictions from impact experiments, and their distribution corresponds to that expected for an ecliptic impactor population.

Hydrocode Modeling of Ice-Penetrating Impacts on Jupiter’s Moon, Europa

Ronadh Cox, Aaron W.Bauer’11, and V.J.Bray

Geological Society of America Abstracts with Programs 42, 304 (2010)

Geological, gravitational, and magnetic-field evidence indicates a subsurface water ocean at relatively shallow depth beneath Europa’s ice crust. If ice thickness is ≤20 km (indicated by crater depth:diameter ratios and lithostatic stress constraints), impacts of sufficient energy could break through to the underlying water. Using the iSALE hydrocode, we have produced 2-D numerical simulations of impacts at Europa to assess the likelihood of impact penetration of the ice crust. Preliminary results indicate that a 620 m diameter comet at 15 km/s penetrates crust up to 6 km thick, and a 2.9 km bolide at 15 km/s penetrates 20 km thick crust. These impacts are energetically equivalent to 26 km/s impacts of bolides 430 m and 2 km, respectively. Penetrating impacts produce a water-filled breach extending fully through the ice, with the water comprising both impact-melted crust and exposed water under-layer. In some cases unbelted blocks of ice—ejecta that have fallen back into the opening cavity—persist as rafts in the water. Calculated recurrence intervals at Europa (from equations of Zahnle et al. 2003; Icarus, v. 163) are ≈2 m.y. for a 420 m and ≈10 m.y. for a 2 km comet. So even if ice thicknesses are substantial (≈ 20 km), our simulations suggest that impact penetration at Europa is likely, and may be a regular occurrence. Chaos terrain—where crust has been destroyed and underlying water appears to have been exposed—is unique to Europa, and may be the geomorphologic expression of such events.

Cosmogenic ¹⁰Be Analysis of River Sands Provides Background Erosion Rates for Madagascar

Ronadh Cox, P.Bierman, E.O.Perry, and A.F.M.Rakotondrazafy

Geological Society of America Abstracts with Programs 42, 418 (2010)

Madagascar is considered one of the world’s most ravaged landscapes, with inferred erosion rates 100-1000 m/m.y. Lavakas—saprolite gullies of the central highlands—are cited as evidence of catastrophic anthropogenic degradation. But this picture is based on few data, mostly from bare-plot runoff and short-term estuary sedimentation records. There are no long-term (>1 yr) stream-sediment gauge data. Cosmogenic ¹⁰Be in quartz sand from rivers provides quantitative constraints on regional erosion rates at millenial timescales for specific geomorphologic settings. Data from 32 rivers spanning Madagascar from W to E indicate variable erosion rates of 3-76 m/m.y. The results challenge conventional interpretations of the role of lavakas in Malagasy erosion. Perhaps most surprising is the result that rates from lavaka-hosting watersheds are all <20 m/m.y. In strong contrast, the 6 highest erosion rates (30-76 m/m.y.) are all measured from zero-lavaka watersheds: i.e. high natural erosion rates occur in the absence of lavakas. These data provide a time-integrated background from which to interpret erosion in Madagascar’s varied environments, and show that erosion—although most dramatically expressed in the lavaka-bearing highlands—may be greatest in coastal lowlands.

Quaternary Slope Sediments and Paleosoils in the Colorado Front Range – Process and Age

David P.Dethier, J.Voelkel, J.Huber, and M.Leopold

Geological Society of America Abstracts with Programs 42(5), 469 (2010)

The subalpine to montane zones of the Colorado Front Range, U.S.A., are characterized by the abundance of stratified slope deposits exhibiting depths > 1 m and recurring sediment characteristics within the respective strata complexes. Apart from the initial description by Leopold et al. (2008a), they have not been investigated up to now in terms of either their genesis or age. First OSL dating attempts demonstrate the general applicability of the dating method in this context and render last glacial ages ranging between 40 and 12 ka. Across a landscape transect stretching W-E from the subalpine zone east of the Continental Divide (tree line at Niwot Ridge) to the zone of the Foot Hills at the border with the Great Plains (Boulder), representative profiles are investigated with regards to hypsometric differences in stratification, sediment characteristics and morphodynamics. Most notably the montane zone of the Colorado Front Range is characterized by a lack of a considerable number of paleoclimatically interpretable geoarchives due to its semiarid climatic conditions. Additionally the slope sediments provide a basis for discussing the position of the permafrost line during the LGM. Therefore the state of the art project contributes a novel approach to the reconstruction of paleoenvironments and paleoclimates across the various altitudinal zones of the Colorado Front Range.

Using the Accumulation of CBD-Extractable Iron and Clay to Estimate Soil and Landform Age, Front Range, Colorado

David P.Dethier and P.Birkeland

Geological Society of America Abstracts with Programs 42(5), 364 (2010)

In transport-limited environments, the color (oxidized Fe) and clay content of regolith, particularly soil horizons, provide a basis for estimating the exposure age of surficial deposits and associated landforms. We were interested in quantifying soil properties at several classic Front Range glacial and hillslope localities; here we use extractable iron and clay content to estimate soil age or residence time at undated sites. We measured citrate-buffered dithionite (CBD)-extractable Fe (Fe_d) concentrations in ~ 140 samples of fresh rock, saprolite, morainal and colluvial materials and soil horizons from the Boulder Creek catchment and nearby areas; clay content was measured on ~90 samples. Fresh rocks contain < 1% Fe_d and < 5% clay. As bedrock and surficial deposits age, Fe_d and clay accumulate from weathering and dustfall. Holocene regolith contains small amounts of Fe_d and clay; soils developed on early Holocene cirque deposits locally contain 1.5% Fe_d and 8% clay. Concentrations mainly are higher in soils on older glacial deposits (Pinedale and Bull Lake age) and are still higher on hillslopes beyond the glacial limit, where colluvium may be >130 kyr. Clay and Fe_d contents are positively correlated (r²=0.46), but scatter in the data likely reflects the influence of variable parent material, local climate, dustfall and landscape stability. Maximum profile concentration and the total mass of Fe_d in soil and in an underlying buried soil in Lefthand Canyon suggest that colluvium has accumulated episodically over >100 kyr. Another red soil developed in colluvium on an old surface near Ward appears even older. In contrast, at Gordon Gulch, one of the Boulder Creek CZO catchments developed on what appears to be a stable surface, Fe_d and clay concentrations suggest that soils mainly are of Pinedale age. In the absence of radiometric ages, the accumulation of Fe_d and clay in various soils provides a useful chronofunction for 10³ to ~10⁶ yrs with a strong dependence on climate.

Assessing the Hydrologic Impact of Land-Use Change in Upper Gordon Gulch, a Small Upland Catchment in the Arapaho National Forest, Colorado

David P.Dethier and Eirik M.Buraas ’09

Geological Society of America Abstracts with Programs 42(5), 351 (2010)

Assessing the hydrologic impacts of future land management on National Forest land is important because increases in low-permeability areas (roads, trails, logged areas) produce higher peak discharges during high intensity precipitation events. The cumulative impact of such land-use changes is significant in areas such as the upland catchments of the Front Range, where forested land helps to buffer the effects of intense summer thunderstorms. We used the upper Gordon Gulch catchment (0.94 km²), part of the Boulder Creek Critical Zone Observatory in Arapaho National Forest, to measure and model the effect of precipitation intensity and land-use change on peak discharge.

We measured soil infiltration rates and soil compaction (dynamic cone penetrometer), analyzed soil samples, and estimated 1-hr precipitation intensities for recurrence intervals ranging from 0.5 to 500 years using local precipitation data. Infiltration rates reflect regolith properties and recent human impacts. Our measurements show that rates are correlated (p-value <0.05) with field values for soil compaction and with laboratory values for soil texture and loss-on-ignition (LOI). Estimated precipitation intensities and measured infiltration rates show that precipitation in most areas of the catchment will flow through soil layers and sandy regolith and as groundwater toward surface channels.

We modeled peak flows for upper Gordon Gulch using Kineros 2, a GIS-based, distributed property runoff model (Semmens et al., 2008) and the Rational Runoff Technique. Model runs suggest that a substantial fraction of peak discharge originates from roads and trails, logged areas and rock outcrops, which collectively comprise < 10% of the catchment. Peak discharge values modeled using Kineros 2 exceed 1 m³s^-1km^-2 for the 100-year storm only if basin impermeable area increases to >10% or if large portions of the basin burn. Our results suggest that planners should carefully consider and model possible hydrologic effects from cumulative land-use change in the National Forest. The local variation and range in soil properties also indicate that catchment-scale hydrologic models require detailed, locally measured data to contribute useful information to planners of National Forest land.

Internal Structure of the Green Lake 5 Rock Glacier, Colorado Front Range, USA

David P.Dethier, M.Leopold, M.W.Williams, N.Caine, and J.Völkel

Permafrost and Periglacial Process 22(2), 107-119 (2011)

Information about the internal structure of rock glaciers is needed to understand their reaction to ongoing climate warming. Three different geophysical techniques — shallow seismic refraction, ground-penetrating radar (GPR) and electrical resistivity tomography — were used to develop a detailed subsurface model of the Green Lake 5 rock glacier in the Colorado Front Range, USA. Below a thin zone of fine sediments and soils (0.7 – 1-m thickness; 0 – 20 kΩm and 320 – 370 ms^-1), a 1 – 3-m thick zone with low p-wave velocities (790 – 820 ms^-1) and high electrical resistivity (20 – 100 kΩm) is interpreted as the ice-free, blocky active layer with large void spaces. The data corroborate strong reflections of the GPR signals, which travel at this depth at 0.11 m ns^-1. A third layer that extends from depths of 1 – 3 m to about 5 m is characterised by lower electric resistivities (5 – 20 kΩm) and has lower electromagnetic wave velocities (0.65 m ns^-1), representing unfrozen, finer and wetter sediments. At around 5-m depth, the measured physical parameters change drastically (vp = 3200 – 3300 ms^-1, 50 – 150 kΩm, vGPR = 0.15 m ns^-1), showing an ice-rich permafrost zone above the bedrock. This model of the internal structure was used to evaluate an existing hydrological flowpath model based on the hydrochemical properties of water outflow from the rock glacier.

Mineralogic and Geochemical Changes from Alteration of Granitic Rocks, Boulder Creek Catchment, Colorado

David P.Dethier and D.J.Bove

Vadoze Zone Journal (in press, 2011)

In the critical zone of the upland Boulder Creek (Colorado) catchment, a weathered mantle consisting of 3 to 10 m of oxidized bedrock, saprolite, and mobile regolith (grus and soil), overlies fresh and locally hydrothermally altered bedrock that is exposed beneath a low-relief surface. Saprolite forms from isovolumetric alteration of primary rock materials to secondary minerals by percolating water; mobile regolith includes rock materials in transport downslope, mixed by a variety of biologic and physical processes. Analysis of vadose-zone samples by petrographic, ICP-MS and XRD techniques demonstrates that weathering of Precambrian Boulder Creek Granodiorite and Silver Plume Granite has formed small amounts of clay and iron oxides. Bulk geochemical changes during alteration are minor except in the transformation of saprolite to regolith, which is enriched in neoformed minerals. In saprolite, the alteration sequence is plagioclase>biotite>microcline>quartz. Quantitative XRD analysis shows that smectite + kaolinite form < 10% of the rock in weathered samples and that smectite is absent and kaolinite + illite comprise >15 percent of the rock at several hydrothermally altered sites. Iron oxide and hydroxide minerals such as goethite and hematite have formed by weathering and by hydrothermal alteration. Hydrothermal alteration of granodiorite to saprolite at the Hurricane Hill site resulted in substantial losses of CaO, MgO and Na₂O, Sr and metals such as Cd and Pb, and enrichment in K₂O and the trace elements Cs, Sb and W. At four critical- zone profiles studied in detail: (1) increases in kaolinite, smectite and Fe-oxides and decreases in magnetite concentration due to weathering are significant if fresh rock is compared to regolith; (2) illite is enriched in soil; (3) minor amounts of clay minerals are inherited from fresh rock; and (4) clay minerals and Fe-oxides are abundant only in hydrothermally altered saprolite. Some of the apparent enrichment of secondary minerals in weathered profiles likely results from dustfall and from material mixed into mobile regolith from heterogeneous bedrock sources. If some portion of the clay minerals in regolith and some fraction of dissolved material leaving Boulder Creek catchments are exotic, rates of clay and Fe-oxide formation in the Boulder Creek area must be slow and the alteration of granitic rocks during the conversion of saprolite to regolith may be driven mainly by volume expansion in this cool, continental climate.

Self-Efficacy Rocks! A Comparison of Student Affect and Performance in Physical Geology Courses

Lisa A.Gilbert and others

Geological Society of America Abstracts with Programs 42(5), 191 (2010)

The GARNET (Geoscience Affective Research Network) project examines the connection between student learning and the affective domain, which includes student motivations, values, attitudes and learning strategies. A key question is the influence of the affective domain on course grade. In 2008-2009, nine participating instructors at four institutions administered the Motivated Strategies for Learning Questionnaire (MSLQ; Pintrich et al., 1993) at the beginning and end of the course. A total of 326 students fully participated and consented to use of their data. We compared the students’ course grades to their MSLQ results and found that three of the MSLQ subscales were significantly correlated to students’ percentile rankings within their classes: Self-Efficacy (positive correlation), Time and Study Environment (positive correlation), and Rehearsal (negative correlation), with Self-Efficacy being the most important. All of these correlations held true for both pre-course and post-course MSLQ scores, although the correlations were stronger for the post-course scores.

In 2009-2010, we repeated the procedure with 14 instructors at seven institutions. The grade distributions were statistically identical for four of these instructors, so we focused on these instructors and used grade rather than percentile rank as our measure of student performance. A total of 351 of these instructors’ students completed both pre- and post-course surveys and consented to use of their data. We again found a strong correlation between Self-Efficacy and student grade. Other subscales showed significant but weaker correlations. On the pre-course survey, students’ scores on the Effort Regulation scale showed a positive correlation with their grades. On the post-course survey, students’ scores on the Intrinsic Goal Orientation scale and the Test Anxiety scale were negatively correlated with their course grades.

Students with high self-efficacy are confident that they can understand class material, do well on assignments and exams, and master the skills taught in the course. Instructors striving to improve student performance in introductory geology classes may wish to try to improve students’ self-efficacy.

Retention in Geosciences: What Influences Students to Continue Beyond an Introductory Undergraduate Course?

Lisa A.Gilbert and others

Geological Society of America Abstracts with Programs 42(5), 584 (2010)

Students decide to enroll in introductory geoscience courses for a variety of reasons, most commonly to fulfill a general education requirement. At the conclusion of their introductory geoscience course, we asked students whether they planned to take another geology course. Over 800 students were surveyed from 7 institutions and 14 different instructors (public and private universities and colleges) for demographic and affective characteristics. We used the Motivated Strategies for Learning Questionnaire (Pintrich et al., 1993) as part of GARNET Project (Geoscience Affective Research Network) to determine student motivations (e.g., goal orientation and control beliefs) and learning strategies (e.g., study methods, critical thinking, and metacognition). We also collected demographic, performance, and interest information from the students, both at the beginning and end of the semester.

Preliminary analysis indicates that students from under-represented race/ethnicity groups and female students tend to have a lower interest in continuing with another geology course. Students with a low prior interest in science and those enrolling to fulfill a general education requirement are less likely to continue. In addition, those students who perceive it will be an easy course are less likely to plan to take another geology course. Students who enter the course with high intrinsic motivation and task value leave the course with a higher likelihood of taking another geoscience course. Additionally, students who show the largest drop in motivational scores during the introductory course also leave with a low interest for continuing. Students at the beginning of the semester who are hesitant to commit to a science degree are somewhat more likely to indicate interest in pursuing a science degree after taking introductory geology. Further, undecided majors were more likely to say they planned to take another geology course than students who had declared any major, even more than students from other STEM fields. Our initial results suggest that geoscience majors may more likely come from students with initial high scores in motivation and those that have not yet declared a major.

The Little Engine that Could—Less Prior Knowledge but High Self-Efficacy is Equivalent to Greater Prior Knowledge and Low Self-Efficacy

Lisa A.Gilbert and others

Geological Society of America Abstracts with Programs 42(5), 191 (2010)

Does a student entering a geology course at a specific ability level (on the basis of past performance and prior knowledge) but greater confidence in their capability to be successful, end up with a higher score in class than a student who has similar ability but lower initial self-confidence? We analyzed survey results from students in introductory physical geology classes in regard to prior knowledge, records of student success, self-efficacy, and performance (grade). Based on previous findings, we hypothesized that regardless of ability, the students who entered the class with higher self-efficacy (belief in their ability to be successful in the course) would earn higher grades than those with low self-efficacy.

We administered pre- and post-course Motivated Strategies for Learning Questionnaires (MSLQ; Pintrich et al, 1993) in introductory geology classes taught by 14 instructors at seven colleges and universities as part of a larger study of student affect (GARNET). We compared the MSLQ scores for more than 800 students to final class scores. Self-efficacy was measured by one of 15 subscales that make up the MSLQ. A step-wise multiple regression of matched pairs of student responses reveals that student performance is most strongly correlated with their score on the self-efficacy subscale on this larger database.

One could argue that high self-efficacy may simply reflect a student’s previous knowledge. In an effort to determine whether our data merely showed that more capable students do better than less capable students, we analyzed data from groups of students with similar prior knowledge. Students in this mini-study were almost exclusively freshmen who were members of two 95-person classes at a large public university in the Southeastern U.S. Student aptitude was measured on the basis of their GPA scores, and their results on a standard entry exam (GCI) and students were divided into groups of high (upper quartile), medium, and low (lower quartile) scores. We further divided these groups on the basis of self-efficacy. In individual aptitude groups, the high self-efficacy students earned higher grades than students with low self-efficacy scores. Further, students with low GCI or GPA scores but high self-efficacy earned the same grade as students with high GCI or GPA scores and low self-efficacy.

The Influence of Instructional Methods on Student Motivation, Attitudes, Values, Self Confidence and Work Effort

Lisa A.Gilbert and others

Geological Society of America Abstracts with Programs 42(5), 584 (2010)

Student motivation, values, attitudes, learning regulation and other components of the affective domain both promote and limit learning. For example, multiple studies have demonstrated that some aspects of student motivation have more significant influences on college student learning (reflected by grades and concept inventories) than does student ability measured by standardized test results. Different approaches to instruction may (1) directly promote different amounts of learning, and (2) change student affect, further promoting or limiting learning.

The GARNET study investigated the influence of the affective domain on >800 students in introductory geology classes taught by 14 instructors at 7 colleges/universities. The most significant affective characteristics that predict student success upon entering a course are student confidence (self-efficacy) and willingness to work hard and persist (effort regulation). During a semester, both of these change, almost always in a negative direction regardless of the specific school/class/instructor.

Results from two sections of Introductory Geology at the University of North Dakota show profound effects of different teaching styles on similar groups of students. One class (A) was a traditional lecture class with student grades primarily based on two one-hour exams and a final. The other (B) was more learner centered, involving in-class group activities, projects, homework, and significantly less emphasis on lecture and exams. Although final letter grade distribution was about the same for both classes, numerical scores differed (max=80, avg=68 for A; max=100, avg=86 for B). For students in class A, confidence and work habits declined markedly during the semester, and test anxiety grew. For students in class B, confidence and habits declined only slightly, and test anxiety decreased.

The ways we teach our class, evaluate student learning, and assign grades have significant impact on student affect and may have implications beyond our immediate classroom. Students have greater self-efficacy, work harder and persist in the face of difficulty, and have less test anxiety in student-centered classes. Consequently they have the potential to learn more, and have better motivation, values, attitudes, and learning regulation when they leave the classroom.

Examination of the Motivation and Learning Strategies of Underrepresented Students in Introductory Geosciences

Lisa A.Gilbert and others

Geological Society of America Abstracts with Programs 42(5), 338 (2010)

The GARNET (Geoscience Affective Research Network) project examines the connection between student affect (attitudes, motivation, values, and regulation of learning) and geoscience learning outcomes. We examined how demographic characteristics relate to the motivation and learning strategies of under-represented students entering introductory geology courses at different institutions. Participating instructors used the Motivated Strategies for Learning Questionnaire (MSLQ; Pintrich et al., 1993) to investigate how aspects of the affective domain varied for students from under-represented populations.

One obstacle to understanding how to address increasing diversity in the geosciences is the dearth of data about the experience of students in introductory geoscience classes. Introductory courses are considered a gateway to recruiting majors. Student affect can influence ongoing student learning, enrollment in subsequent classes, and the potential for a student to select a geoscience major. Affect may be more critical for under-represented students due to stereotype impressions.

Students from under-represented populations reported lower intrinsic and extrinsic motivation when entering our classes. The implication of this finding is that under-represented students begin with a lower motivation to achieve and learn the content. In this analysis, we examine a larger number of under-represented students across a more diverse transect of institutions (large university, community college and private colleges) from beginning to the end of the semester. Preliminary results indicate that many of the factors that affect Caucasian students also affect under-represented students, however they start the course as distinctly different statistical populations. Across different student demographic groups a decline in self-efficacy (confidence in learning) during a semester occurs. Under-represented students begin the semester with a lower average self-efficacy than the Caucasian students. The amount of effort that students are willing to put into a class displays a similar trend, with under-represented students entering with lower scores. These findings have important implications for their success in the course as well as their decisions to enroll in future geoscience classes.

Role of Gender in Student Affect in Introductory Physical Geology Courses at Multiple Institutions

Lisa A.Gilbert and others

Geological Society of America Abstracts with Programs 42(5), 191 (2010)

Are female students in your class more motivated, more confident, or more anxious about their performance than male students? As a part of the GARNET (Geosciences Affective Research NETwork) project we identify differences between the genders regarding incoming motivation, attitudes, values and learning strategies, and how those components change during the course of semester in introductory physical geology class.

GARNET collected student responses to the MSLQ (Motivated Strategies for Learning Questionnaire; Pintrich et al., 1993) at the beginning and end of the semester for the 2009/2010 academic year. Respondents represent 539 males and 607 females from 14 classes in 7 institutions ranging from research universities to community colleges. Responses in the 15 subscales of the MSLQ and various demographic data were statistically analyzed to characterize pre-instruction affect and the shift in affect during the course of the semester.

Incoming attitudes between the genders are significantly different in cognitive and metacognitive strategies (e.g. memorization, critical thinking), self-efficacy, test anxiety, time and study environment, and effort regulation. Females report less confidence (self-efficacy) in their ability to succeed in the course, have higher test anxiety, but record higher scores on most learning/cognitive strategies then their male peers at the beginning of semester. Shifts in value components (e.g. intrinsic goal orientation), self-efficacy, critical thinking, metacognition and elaboration strategies were significantly different between the genders. Female students recorded negative shifts in multiple scales (e.g., self-efficacy, task value, critical thinking). In contrast, males showed some negative shifts (e.g., self-efficacy) but increased their scores in several subscales (e.g., intrinsic goal orientation, critical thinking).

The differences in attitudinal shifts between the genders throughout the course of a single semester could have implications on the likelihood of recruiting female students into geology. Despite similar course grades, female students reported that they were statistically less likely to take additional classes beyond the introductory geology course compared to the male peers.

Geoscience Affective Research Network: Researching Student Attitudes, Motivations, Values and Regulation of Learning in Introductory Geoscience Courses

Lisa A.Gilbert and others

Geological Society of America Abstracts with Programs 42(5), 585 (2010)

Concerns about ensuring a scientifically literate society and the continued supply of able scientists are particularly relevant to the geosciences. At a time when college and university enrollments are climbing, geoscience enrollments are in decline. Though there are many resources available to instructors for improving student cognitive strategies (e.g., analytical and critical thinking), there is relatively little guidance available for addressing student affect (personal characteristics that influence student learning and attitudes toward science). Few previous studies have explored the relationship between student cognition and affect in college science classrooms, especially in the geosciences. The Geoscience Affective Research NETwork (GARNET) is an NSF-funded study that aims to explore the connections between instruction, student affect (attitudes, motivations, values, and regulation of learning) and geoscience learning. Results to date have documented significant differences in student affect and learning gains in introductory geoscience courses at multiple institutions; both have important implications for how we teach. Best practices that have the potential to improve student affect and learning outcomes have also been identified.

GARNET seeks broad participation by introductory geoscience instructors from community colleges, private liberal arts colleges, and public universities to investigate student affect and learning. Students enrolled in participating courses will complete some or all of the Motivated Strategies for Learning Questionnaire (MSLQ). Additionally, in some cases, student learning gains may be measured using the Geoscience Concept Inventory (GCI) and the learning environment may be characterized using the Reformed Teaching Observation Protocol (RTOP). Instructors will also have materials and guidance for using a range of teaching interventions that can improve student learning and affect in their classes. Instructors will receive information about student learning gains, affective characteristics, and the learning environment, all with the goal of promoting better student learning, retaining students in the geosciences, and improving instructor satisfaction.

Tracking Silurian Eustasy: Alignment of Empirical Evidence or Pursuit of Deductive Reasoning?

Markes E.Johnson

Palaeogeography, Palaeoclimatology, Palaeoecology 296, 276-284 (2010)

Sea level is not static, but liable to fluctuations due to addition or subtraction of water in the world’s oceans, as well as changes to the shape and holding capacity of ocean basins. Relative changes in sea level are well supported by the rock record on a regional scale. Whether or not global (eustatic) changes are evident and how frequently they occurred during any given interval of time is a matter of contention among stratigraphers. Opinions have evolved over the last century with arguments based on refinements in biostratigraphy, chemostratigraphy, radiometric dating, and conceptual advances in sequence stratigraphy derived from technological advances in seismic stratigraphy. In 1936, the Pulsation Theory of A.W. Grabau attributed to Paleozoic strata a global history of 11 highstands distributed through a sequence with 21 subdivisions. In 1977, Peter Vail and associates from the Exxon Production Research Company independently interpreted a similar Paleozoic history showing 10 second-order highstands but distributed over 19 subdivisions. Vail’s approach was model-based and followed a deductive path, while Grabau’s was based on inductive reasoning. Recent refinements in a Paleozoic sea-level curve by Haq and Schutter are based on the same deductive approach taken by the Vail group, but pinned to patterns in sequence stratigraphy. Drawing on the Silurian System as a Paleozoic sample, the timing, frequency, and magnitude of sea-level highstands deduced by Haq and Schutter are compared with those promulgated by the author from the mid-1980s onward using empirical evidence more in line with Grabau’s methodology. Both apply the concept of geographic reference areas, but Haq and Schutter identify 50% more Silurian highstands over an interval lasting 27.7 million years. Eight out of 10 Silurian highstands identified by this author match or overlap 8 out of 15 highstands recognized by Haq and Schutter. At issue is which, if any, qualify as eustatic signals with respect to current databases for biostratigraphic correlation. Evaluation is based on evidence reviewed from Iowa, New York, Norway, Estonia, and Austria in the paleogeographic context of three independent Silurian continents.

Ichnofacies and Microbial Build-Ups on Late Miocene Rocky Shores from Minorca (Balearic Islands), Spain

Markes E.Johnson, B.G.Baarli, A.Santos, and E.Mayoral

Facies 57, 255-265 (2011)

Angular unconformites between Jurassic and Miocene strata are exposed in the sea cliffs of Cala Cigonya on the northwest coast of Menorca in the Balearic Islands of Spain. The geological discontinuities represent rocky shores on opposite sides of a former headland with 15 m of topographic relief. On the east flank, Jurassic dolomite is overlain by Upper Miocene (Tortonian to Messinian) breccia and laminated limestone. Here, a partially exhumed dolomite surface records Miocene bivalve borings of the ichnospecies Gastrochaenolites torpedo and G. lapidicus that achieved a density of >1,000 borings/m². Other associated traces include sponge borings (Entobia isp.) and polychaete borings (Caulostrepsis isp.). A breccia deposit 0.8 m thick was derived from the underlying dolomite and angular clasts still retain evidence of bivalve borings. Above follows a succession of laminated limestone beds more than 5 m thick, including some levels with dome-shaped stromatolites and other horizons with reworked dolomite clasts. Thin-section analysis of the laminated limestone reveals dark and light couplets 0.2 mm thick consistent with microbial origins. In contrast, the west flank was buried by coarse sandstone and laminated sediments. Here, dwelling structures of regular echinoids (Circolites kotoncensis) are the dominant traces preserved on the dolomite surface, reaching a maximum density of 66 borings/m². Associated borings include Entobia geometrica as well as rare traces of Gastrochaenolites isp. and Trypanites isp. Notable for the absence of a basal Miocene breccia, the west flank is interpreted as a sheltered rocky shore coeval with an exposed rocky shore on the east flank. Today, heavy surf on the north coast of Menorca is related to the Tramontana winds that blow out of Spain during winter months.  Similar atmospheric circulation patterns must have prevailed during the Late Miocene, but the replacement of ichnofacies by microbial build-ups resulted from increased salinity during the Messinian crisis.

Rhodolith Transport and Immobilization on a Vvolcanically Active Rocky Shore: Middle Miocene at Cabeço das Laranjas on Ilhéu de Cima (Madeira Archipelago, Portugal)

Markes E.Johnson, C.M.da Silva, A.Santos, B.G.Baarli, M.Cachão, E.J.Mayoral, A.C.Rebelo and J.Ledesma-Vázquez

Palaeogeography, Palaeoclimatology, Palaeoecology 300, 113-127 (2011)

Extraordinary deposits of fossil rhodoliths occur at the Cabeço das Laranjas (Portuguese ~ Hill of the Oranges) in a small fault block at the northwest end of Ilhéu de Cima off Porto Santo in the Madeira Archipelago. Stratigraphic repetitions of densely packed rhodolith beds up to 2.6 m thick are associated with a receding rocky shoreline, and are interpreted as the result of hurricanes. The initial storm deposit sits unconformably on basalt and eroded basalt boulders associated with tuff and volcaniclatic breccia. Approximately 90,000 rhodoliths of Middle Miocene age (14 – 15 Ma) are exposed on the upper surface of the initial deposit over a 450-m² shelf exhumed from the hill’s southeast side. Ranging in diameter from ≤ 3 cm to 20 cm, many of the rhodoliths generated by crustose coralline red algae are now iron stained and resemble a mass of oranges in gross appearance. Sea stacks and large boulders rise through the thick basal rhodolith bed to form small catchment areas that held the deposit in place after the storm’s passage. The succeeding rhodolith deposits are variably separated by layers with mixed carbonate and volcanic sand, pure volcanic lapilli, and volcaniclastic tephra mixed with tuff showing swaley cross-stratification. Three out of four rhodolith beds are truncated against the flank of the adjoining rocky shore. Only the youngest (fourth) rhodolith layer is fully exposed around the perimeter of the hill and can be shown to cross a basalt barrier that is traceable for 70 m in cross section as an erosional ramp dipping from 6º to 8º southeast. The entire fossil-rich sequence is capped by a basalt flow showing columnar disjunction. Based on thin-section analysis, three genera of coralline red algae are recognized in the basal rhodolith deposit: Sporolithon, Lithothamnion, and Neogoniolithon. Associated biodiversity is low, represented by 16 kinds of marine invertebrates dominated by encrustations and borings on the rhodoliths and very few free body fossils. The Madeira region of the North Atlantic may have been susceptible to major cyclonic storms immediately after the Middle Miocene Climate Optimum, when a northward shift of the Inter-tropical Convergence Zone was stimulated by a steeper temperature gradient in the southern hemisphere related to expansion of continental glaciers on Antarctica.

Miocene Intertidal Zonation on a Volcanically Active Shoreline: Porto Santo in the Madeira Archipelago (Portugal)

Markes E.Johnson, A.G.Santos, E.J.Mayoral, C.M.da Silva, M.Cacháo, and B.G.Baarli

Lethaia 44, 26-32 (2011)

Short-term biological colonization on hardgrounds perturbed by volcanic and local tectonic events is a topic, as yet, poorly explored on basaltic shorelines of oceanic islands. A Miocene sea cliff on Ilhéu de Cima off Porto Santo in the Madeira Archipelago of Portugal provides a case study showing intertidal zonation with two types of barnacles, serpulid worm tubes, two coral species, epifaunal bivalves, and the traces of endolithic bivalves. Large barnacles (Balanus sp.) and serpulids are limited to the upper 40 cm of a 160-cm high basalt cliff. Small barnacles, possibly the same species, extend to the base. The upper half includes the corals Isophyllastrea orbignyana and Tarbellastraea reussiana, to which many small, coral-inhabiting barnacles of Ceratoconcha costata are fixed.  Borings identified as Gastrochaenolites torpedo appear through the bottom two-thirds of the cliff face. Rarely, G. lapidicus is exposed in longitudinal section with borings up to 4.5 cm deep in solid basalt. Epifaunal bivalves, such as Spondylus sp., are limited to a middle zone. Associated with the sea cliff is an outer platform on which a multitude of T. reussiana colonies occur in growth position. The corals exhibit planar erosion over a 180-m² area. The shelf was faulted and cut by a basalt dike prior to the brief recolonization of I. orbignyana, found attached to low fault scarps. Habitation of the sea cliff was facilitated by rising sea level, but abruptly terminated by burial under volcanoclastic ejecta.

Adding Structures to 3-D Geologic Maps

Paul Karabinos

Geological Society of America, Abstracts with Programs 42(5), 208 (2010)

Combining geologic maps and cross-sections into traditional block diagrams is a time-tested and effective way to portray the structure of a region and to illustrate how maps and cross-sections work together; block diagrams are especially valuable for non-specialists. The inherent power of block diagrams is dramatically increased by software that can create interactive 3-D models of a region, which can be rotated, panned, and zoomed by the user. Particularly useful software options include Midland Valley’s MOVE 2010 powerful modeling package, ESRI’s GIS-based applications, Google Earth, and Google SketchUp. The best way to create virtual block diagrams is to combine the individual strengths of two or more applications, and merge the results into a single 3-D model.

The most effective 3-D models drape geologic maps on topography and show how the maps and cross-sections connect at the topographic surface. Creating models in segments gives the user flexibility to ‘turn off’ individual portions of the surface to sequentially reveal multiple cross-sections. Such models help students and non-specialists visualize geologic structures, and provide geologists with a valuable tool for assessing the validity of geologic interpretations.

Even the best 3-D virtual block diagrams can be challenging for a non-specialist to interpret and understand. Basic concepts such as bedding and strike and dip are unfamiliar to most non-geologists. Adding structures and textures to geologic maps can clarify these fundamental concepts. For example, ArcGlobe can portray the strike and dip of bedding of different units as color-coded 3-D ‘wafers’ that protrude above the surface and are precisely oriented to match the orientation of beds. Structures such as plunging folds become readily apparent using this technique.

Another approach is to use the astonishing flexibility and power of Google SketchUp to accurately model geologic structures in real-world coordinates and export the results to either Google Earth or ArcGlobe. These accurately constructed and located models of geologic structures can be integrated with geologic maps, and are particularly effective for showing how bedrock geology affects the topography of a region.

Evidence for Complex Mid-Crustal Flow in the Northern Appalachians from Regional Garnet Inclusion and Zoning Patterns

Paul Karabinos

Geological Society of America, Abstracts with Programs 42(5), 237 (2010)

Garnet-bearing pelitic and mafic schists are common in VT. Rosenfeld (1968) described garnets with two-stage growth histories from the Neoproterozoic Gassetts Schist in the Chester dome, and argued that the first-stage cores were Taconic and that the second-stage rims were Acadian. Thompson et al. (1977) suggested that both stages could have grown during a single prograde event that included an intermediate garnet-consuming reaction.

Garnets that grew in two stages are widespread in VT. Many contain zoning reversals indicating that garnet was partially resorbed during the growth hiatus. Rutile inclusions are common in garnet cores but absent in the rims and matrix indicating that the first growth stage occurred under higher pressure conditions than the second.

The hiatus in garnet growth is texturally linked to the formation of a new cleavage and does not correlate with metamorphic grade. The wide variation in grade of rocks containing two-stage garnets indicates that the hiatus cannot be attributed to an intermediate garnet consuming reaction during a single event. Two isograd maps, one for each stage of garnet growth, show that the grade during the second growth stage is consistently higher than the first, but there is a striking spatial correlation between the highest-grade areas during each stage. This suggests that both growth episodes occurred during a single orogeny, rather than separated by 80 m.y. The age of peak metamorphism is well constrained to be 380 Ma. Further, inclusions patterns and mineral chemistry indicate ca. 3 kbars of decompression during garnet growth. Thus, the hiatus in garnet growth was triggered by a tectonic event that altered the P-T conditions at a particular mid-crustal level.

In contrast, Sil. and Dev. pelitic and mafic schist samples contain garnets with simple zoning patterns and no evidence for two stages of growth. Metamorphism in these rocks occurred during increasing P. The spatial distribution of distinctive garnet zoning and inclusion patterns is consistent with structural evidence for a high-strain zone with normal displacement that separates structurally lower rocks with complex garnets from higher rocks with simple garnets. Structurally lower rocks were extruded northward and upward into Sil. and Dev. nappes that were transported westward during the Acadian orogeny.

Preferred Orientation of Cobbles and Boulders in Unstrained Alluvial Fan Deposits: Implications for Rf-Phi Analysis of Deformed Conglomerates

Paul Karabinos and Lisa Merkhofer’11

Geological Society of America, Abstracts with Programs 42(5), 208 (2010)

Deformed conglomerates are commonly used for strain analysis because clasts can be approximated as ellipses. The Rf-φ method uses the orientation and axial ratio of elliptical objects to estimate finite strain, but it assumes an initially random orientation of clast long axes. This assumption has been tested in sandstones, but not in cobble and boulder-sized conglomerates. In sandstones, initially preferred orientations of long axes can significantly affect estimated strain values and can be difficult to detect (Patterson and Yu, 1993).

Our work focused on undeformed conglomerates in the Deerfield Basin in MA. The Jurassic Sugarloaf Arkose and Mount Toby Conglomerate were deposited near a normal fault at the eastern margin of the basin. We measured 13 joint faces from 3 large outcrops. Exposures include both clast and matrix supported fabrics. Clast size ranges from pebble to boulder, and clasts are angular to well rounded. Each outcrop contains one or two joint faces parallel to bedding and two to four faces approximately perpendicular to bedding.

We used a Gigapan mount to take high-resolution photographs of the joint faces. We included a 2×1 m grid to correct for image distortion using Photoshop. We imported the photos into Geoshear, a strain analysis program (Karabinos and Warren, 2010). Using Geoshear, clasts are digitized and both Cartesian and polar Rf-φ plots created. We measured an average of 247 clasts on each surface, ranging from 85 to 955 clasts.

In faces perpendicular to bedding, Rf-φ plots show an initially preferred orientation of long axes parallel to bedding, and clasts with higher axial ratios are more likely to be oriented parallel to bedding; this is the so-called ‘delta’ configuration of Elliott (1970). Rf-φ plots for faces parallel to bedding showed no preferred orientation of clast long axes. The virtual tools allowed us to measure numerous clasts directly from rock faces, and to create a visual record of our measurements readily available for review by other geologists. Geoshear also allows us to run deformation “experiments” to evaluate how accurately we can estimate strain imposed on samples with an initially preferred orientation, and thereby assess the importance of preferred orientations in typical conglomerates.

Integrating Geologic Maps and Cross Sections in an Interactive 3-D Environment

Paul Karabinos

Geological Society of America Penrose Conference, 2011

Traditional geologic maps and cross sections are common, time-tested, and effective ways to portray the structure of a region, but are best appreciated by experienced geologists. Textbooks integrate maps and cross sections into static perspective block diagrams to help students visualize basic concepts in structural geology. The inherent power of block diagrams, however, is dramatically increased by software that can create interactive 3-D models of a region, which can be rotated, panned, and zoomed by the user. The best way to create virtual block diagrams is to combine the individual strengths of dedicated GIS software with Google SketchUp and Earth, and merge the results into a single 3-D model.

Effective 3-D models drape geologic maps on topography and show how the maps and cross-sections connect at the topographic surface. Creating models in segments gives the user flexibility to ‘turn off’ individual portions of the surface to sequentially reveal multiple cross-sections. Such models help students and non-specialists visualize geologic structures, and provide geologists with a valuable tool for assessing the validity of geologic interpretations. It is even possible to construct cross sections in a 3-D environment using SketchUp.

Even the best 3-D virtual block diagrams can be challenging for students to interpret and understand. Basic concepts such as bedding and strike and dip are unfamiliar to most non-geologists. SketchUp can be used to add visual cues to maps and show the intersection of unconformities, faults, and plunging folds with the topographic surface. These accurately constructed and located models of geologic structures can be exported to Google Earth, and are particularly effective for showing how bedrock geology affects the topography of a region.

An Emsian Age for the Goshen Formation in the Connecticut Valley-Gaspe Trough in Massachusetts

Paul Karabinos

Geological Society of America, Abstracts with Programs 43, 160 (2011)

The Devonian Goshen Formation is the westernmost unit in the Connecticut Valley-Gaspe Trough (CVGT) in MA. Equivalent rocks in VT are called the Northfield Formation. The Goshen Formation is the only Devonian unit in MA in contact with Ordovician rocks west of the CVGT and around the Shelburne Falls, Goshen, Granville, and Woronoco domes. This contact relationship suggested to Hatch et al. (1988) that the Goshen Formation is predominantly older than the Waits River Formation. However, they noted the lithologic similarity between the Goshen Formation and the Royalton belt of the Devonian Gile Mountain Formation in VT, which is demonstrably younger than the Waits River Formation. The age range of the Waits River Formation is approximately 423 Ma (Aleinikoff and Karabinos, 1990) to at least 415 Ma (McWilliams et al., 2010).

The Goshen Formation commonly contains graded beds that delineate numerous upright folds in the central part of the outcrop belt, where a younger member (Dgq) is defined by a greater percentage of micaceous quartzite beds. We discovered several beds within the Dgq member of the Goshen Formation near Cummington, MA, that we interpret as volcanic in origin. Prismatic, colorless zircons extracted from a 1.5 m thick felsic layer yield a SHRIMP Concordia Age of 405 ± 4 Ma (11 of 15 analyses). This age is indistinguishable from ages of 407 ± 3 Ma from a metarhyolite in the Meetinghouse Slate Member of the Gile Mountain Formation (Rankin and Tucker, 2009) and 409 ± 5 Ma from volcanic zircons extracted from a quartzite bed in the Royalton belt of the Gile Mountain Formation (McWilliams et al., 2010).

Our data show that the Dgq member of the Goshen Formation is the same age as the Royalton belt and the Meetinghouse Slate Member of the Gile Mountain Formation, and that they are all younger than the Waits River Formation. Assuming that the older part of the Goshen Formation in MA and the equivalent Northfield Formation in VT are not significantly older than the volcanic bed we dated, the youngest units in the CVGT occur along both the western and eastern margins, and the older Waits River Formation occupies the central part of the trough. Also, sedimentation in the CVGT appears to have been active from ca. 423 to at least 405 Ma, which constrains tectonic models of terrane accretion in the northern Appalachians.

Quaternary Intertidal Deposits Intercalated with Volcanic Rocks on Isla Sombrero Chino in the Galápagos Islands (Ecuador)

Paul Karabinos, Markes E.Johnson, and V.Mendia

Journal of Coastal Research 26(4), 762-768 (2010)

A stratigraphic succession composed of limestone intercalated with volcanic ash and basalt capped by a conglomerate of mixed limestone and basalt cobbles was deposited in a trough-shaped depression approximately 25 m wide and 50 m long to a thickness of 1.62 m on the southwest side of Isla Sombrero Chino in the Galápagos Islands of Ecuador. Two layers of well-cemented calcarenite up to 20 cm thick accumulated as beach deposits with bioclasts of gastropods dominated by the Galápagos Periwinkle (Nodilittorina galapagiensis), a representative of the Beaded Hoofshell (Hipponix grayanus), broken crab fragments, and bird bones. Crustacean remains most likely belong to the Sally Lightfoot Crab (Graspus graspus). The bird bones are attributed to Audubon’s Shearwater (Puffinus iherminieri). Distinctly intertidal in origin, such a mixed assemblage of invertebrates and vertebrates is unusual, and the association with basalt flows is seldom met in the rock record. The pristine state of the volcanic cone on Sombrero Chino is consistent with a ³He exposure age of 13 ± 0.8 ka. The age of the basalt-limestone sequence is unknown but must be younger than the ³He exposure age. The basalt-limestone sequence is elevated approximately 3 to 4 m above current sea level. This implies that the intertidal limestone was deposited during an interval of higher sea level or, more likely, was uplifted by magmatic inflation. Such intertidal deposits, in conjunction with more precise dating, have the potential to constrain the history of relative sea-level change during island growth and isostatic subsidence related to volcanism and lithospheric cooling. Intertidal deposits of the kind reported here also help to distinguish between monogenetic as opposed to polygenetic history for volcanic islands.

From Rodinia to Pangea: The Lithotectonic Record of the Appalachian Region

Paul Karabinos, R.P.Tollo, M.J.Bartholomew, and J.P.Hibbard, editors

Geological Society of America Memoir 206, 956 p. (2010)

The Appalachians constitute one of Earth’s major tectonic features and have served as a springboard for innovative geologic thought for more than 170 years. This volume contains 36 original papers reporting the results of research performed throughout nearly the entire length and breadth of the Appalachian region, including all major provinces and geographical areas. Memoir 206 was designed to commemorate the (near-) fortieth anniversary of the publication of the classic Studies of Appalachian Geology volumes that appeared just prior to the application of plate tectonic concepts to the region. Contributions concerning structural evolution, sedimentation, stratigraphy, magmatic processes, metamorphism, tectonics, and terrane accretion illustrate the wide range of ongoing research in the area and collectively serve to mark the considerable progress in scientific thought that has occurred during the past four decades.

Mathematics and Statistics

The Spiral Index of Knots

Colin Adams, W.George, R.Hudson, R.Morrison, L.Starkston, S.Taylor, and O.Turanova

Mathematical Proceedings of the Cambridge Philosophical Societ, 149(2), 297-315 (2010)

In this paper, we introduce two new invariants that are closely related to Milnor’s curvature-torsion invariant. The first, a particularly natural invariant called the spiral index of a knot, captures the number of local maxima in a knot projection that is free of inflection points. This invariant is sandwiched between the bridge and braid index of a knot, and captures more subtle properties. The second invariant, the projective superbridge index, provides a method of counting the greatest number of local maxima that occur in a given projection. In addition to investigating the relationships among these invariants, we use them to classify all those knots for which Milnor’s curvature-torsion invariant is 6pi.

Looking Backward

Colin Adams

Mathematical Intelligencer 32(3), (2010)

What happens to someone who is hypnotized to sleep and reawakens 100 years later in their expectation of the present day world, and finds a mathematical paradise?

A Forgivably Flat Classic, review of Flatland

Colin Adams

American Scientist 98(6), 498-500 (2010)

A review of the classic book “Flatland” in a new edition

Group Therapy

Colin Adams

Mathematical Intelligencer 32(4), (2010)

How does group therapy work for a group of mathematicians who know group theory?

Hardy and Ramanujan

Colin Adams

Mathematical Intelligence 33(1), (2011)

A more detailed account of the enigmatic relationship between Hardy and Ramanujan

Leonhard Euler and Seven Bridges of Konigsberg

Colin Adams

Mathematical Intelligencer 33(2), (2011)

The true story of how Leonhard Euler became the greatest bridge stroller problem solver in history

Arithmetic from an Advanced Perspective: An Introduction to the Adeles

Edward B.Burger

Pro Mathematica 24, 9-54 (2010)

Here we offer an introduction to the adele ring over the field of rational numbers Q and highlight some of its beautiful algebraic and topological structure. We then apply this rich structure to revisit some ancient results of number theory and place them within this modern context as well as make some new observations. We conclude by indicating how this theory enables us to extend the basic arithmetic of Q to the more subtle, complicated, and interesting setting of an arbitrary number field k.

Deformations of Bordered Surfaces and Convex Polytopes

Satyan Devadoss, T.Heath and C.Vipismakul

Notices of the American Mathematical Society 58, 530-541 (2011)

We provide a combinatorial framework to understand how surfaces with boundary can deform, and then proceed to classify all such deformations which have polytopal structures.

Pseudograph Associahedra

Satyan Devadoss, M.Carr and S.Forcey

Journal of Combinatorial Theory, Series A 118, 2035-2055 (2011)

Given an arbitrary finite graph (with loops and multiple edges), we construct a polytope which captures the connectedness of the graph.

Discrete and Computational Geometry

Satyan Devadoss and J.O’Rourke

Princeton University Press (2011)

This textbook bridges the gap between discrete geometry of pure mathematics and computational geometry of data-driven computer science, at an undergraduate level. It includes traditional topics such as convex hulls, triangulations, and Voronoi diagrams, as well as advanced material such as curve reconstruction, quasigeodesics, and Dehn invariants.

Stats: Data and Models, 3^rd Edition

Richard DeVeaux, P.Velleman and D.Bock

Pearson Education (2010)

Simultaneous Confidence Bounds for Relative Risks in Multiple Comparisons to Control

Bernhard Klingenberg

Statistics in Medicine 29, 3232-3244 (2010)

We discuss the construction of asymptotic simultaneous upper confidence limits that jointly bound relative risks formed by comparing several treatments to a control. Motivated by a vaccine study, we investigate the performance of several methods under such settings. Inverting the minimum of score statistics, together with estimating the correlation matrix of these statistics under the null gives simultaneous coverage rates closest to the nominal level. In typical settings of vaccine studies, this method proves to be the most powerful of the ones considered, but computationally simpler alternatives are also worth exploring when the number of comparisons is large. Simultaneous lower and two-sided confidence intervals are also considered. All procedures can be implemented and evaluated using freely available and general R code.

Formal Fibers of Unique Factorization Domains

Susan Loepp, A.Boocher, M.Daub, R.Johnson, H.Lindo, and P.Woodard

Canadian Journal of Mathematics 62, 721-736 (2010)

In this paper, the authors construct unique factorization domains such that most of the formal fibers of these integral domains are geometrically regular. In addition, they construct unique factorization domains containing many ideals for which tight closure and completion do not commute.

A Unitary Test of the L-Functions Ratios Conjecture

Steven J.Miller, J.Goes, S.Jackson’10, D.Montague, K.Ninsuwan, R.Peckner and Thuy Pham’11

Journal of Number Theory 130, 2238-2258 (2010)

We verify the L-function Ratios Conjecture’s predictions for the unitary family of all Dirichlet L-functions with prime conductor; we show square-root agreement between prediction and number theory if the support of the Fourier transform of the test function is in (-1, 1), and for support up to (-2, 2) we show agreement up to a power savings in the family’s cardinality. The interesting feature in this family (which has not surfaced in previous investigations) is determining what is and what is not a diagonal term in the Ratios recipe.

Towards an Average Version of the Birch and Swinnerton-Dyer Conjecture

Steven J.Miller and J.Goes

Journal of Number Theory 130, 2341-2358 (2010)

We find non-trivial upper and lower bounds for the average number of normalized zeros in intervals on the order of 1/ log N_E (which is the expected scale). Our results may be interpreted as providing further evidence in support of the Birch and Swinnerton-Dyer conjecture, as well as the Katz-Sarnak density conjecture from random matrix theory (as the number of zeros predicted by random matrix theory lies between our upper and lower bounds).

Explicit Constructions of Infinite Families of MSTD Sets (with Dan Scheinerman) Additive Number Theory: Festschrift in Honor of the Sixtieth Birthday of Melvyn B. Nathanson

Steven J.Miller, D.Chudnovsky and G.Chudnovsky, eds.

Springer-Verlag (2010)

We present a new construction that yields a family of sum-dominated sets in {1, 2, …, r} of size C 2^r / r⁴ for a fixed, non-zero constant C; our family is significantly denser than previous constructions.

The Lowest Eigenvalue of Jacobi Random Matrix Ensembles and Painleve VI

Steven J.Miller, E.Duenez, D.K.Huynh, J.Keating and N.Snaith

Journal of Physics A: Mathematical and Theoretical 43, 405204 (27 pp) (2010)

We present two complementary methods, each applicable in a different range, to evaluate the distribution of the lowest eigenvalue of random matrices in a Jacobi ensemble.

An Orthogonal Test of the L-Functions Ratios Conjecture, II

Steven J.Miller and D.Montague

Acta Arithmetica 146, 53-90 (2011)

We prove the accuracy of the Ratios Conjectures prediction for the 1-level density of families of cuspidal newforms of constant sign (up to square-root agreement for support in (-1, 1), and up to a power savings in (-2, 2)), and discuss the arithmetic significance of the lower order terms. This is the most involved test of the Ratios Conjectures predictions to date, as it is known that the error terms dropped in some of the steps do not cancel, but rather contribute a main term! Specifically, these are the non-diagonal terms in the Petersson formula, which lead to a Bessel-Kloosterman sum which contributes only when the support of the Fourier transform of the test function exceeds (-1, 1).

Effective Equidistribution and the Sato-Tate Law for Families of Elliptic Curves

Steven J.Miller and R.Murty

Journal of Number Theory 131(1), 25-44 (2011)

We provide effective bounds on the family of all elliptic curves and one-parameter families of elliptic curves modulo p (for p prime tending to infinity) obeying the Sato-Tate Law.

Isoperimetric Sets of Integers

Steven J.Miller, F.Morgan, Edward Newkirk ’09, Lori Pedersen, Deividas Seferis ‘09

Mathematics Magazine 84, 37-42 (2011)

The celebrated isoperimetric theorem says that the circle provides the least-perimeter way to enclose a given area. I n this note we discuss a generalization.

An Elliptic Curve Family Test of the Ratios Conjecture

Steven J.Miller, D.K.Huynh and Ralph Morrison’10

Journal of Number Theory 131, 1117-1147 (2011)

We compare the L-Function Ratios Conjectures prediction with number theory for the family of quadratic twists of a fixed elliptic curve with prime conductor, and show agreement in the 1-level density.

Demand-Driven Scheduling of Movies in a Multiplex

Steven J.Miller, J.Eliashberg and C.B.Weinberg

Newsletter of the European Marketing Academy (October 2010)

Summary of Silver-Scheduler paper in honor of it receiving the IJRM Best Paper Award for 2009

Stable Constant Constant Mean Curvature Hypersurfaces are Area Minimizing in Small L¹ Neighborhoods

Frank Morgan and A.Ros

Interfaces Free Boundaries, 151-155 (2010)

We prove that a strictly stable constant-mean-curvature hypersurface in a smooth manifold of dimension less than or equal to 7 is uniquely homologically area minimizing for fixed volume in a small L¹ neighborhood.

Isoperimetric Sequences

Frank Morgan, Steven J.Miller, Edward Newkirk ‘09, Lori Pedersen, Deividas Seferis ‘09

Math Magazine 84, 37-42 (2011)

We generalize the isoperimetric problem from geometry to numbers.

Rebalance Every (15000/V)^1/3 Years

Frank Morgan and W.Filkins

SSRN (2010)

An original formula for how often to rebalance investments

The Log-Convex Density Conjecture

Frank Morgan, C.Houdré, M.Ledoux, E.Milman, and M.Milman, eds.

Concentration, Functional Inequalities and Isoperimetry (Proc. Intl. Wkshp., Florida Atlantic Univ., Oct./Nov. 2009) Contemporary Mathematics 545, Amer. Math. Soc. (2011)

A short exposition of a conjecture on when balls about the origin are isoperimetric in Rⁿ with density

Mixing on Rank-One Transformations

Cesar E.Silva and D.Creutz ’03

Studia Mathematica 199(1), 43-72 (2010)

We prove mixing on rank-one transformations is equivalent to “the uniform convergence of ergodic averages (as in the mean ergodic theorem) over subsequences of partial sums.” In particular, all polynomial staircase transformations are mixing.

Dynamics of the p-adic Shift and Applications

Cesar E.Silva, J.Kingsbery ’06, A.Levin, and A.Preygel

Discrete and Continuous Dynamical Systems 30(1), 209-218 (2011)

There is a natural continuous realization of the one-sided Bernoulli shift on the p-adic integers as the map that shifts the coefficients of the p-adic expansion to the left. We study this map’s Mahler power series expansion. We prove strong results on p-adic valuations of the coefficients in this expansion, and show that certain natural maps (including many polynomials) are in a sense small perturbations of the shift. As a result, these polynomials share the shift map’s important dynamical properties. This provides a novel approach to an earlier result of the authors.

Digraph Representations of Rational Functions Over the p-adic Numbers

Cesar E.Silva and H.Diao

P-adic Numbers, Ultrametric Analysis, and Applications 3(1), 23-38 (2011)

In this paper, we construct a digraph structure on p-adic dynamical systems defined by rational functions. We study the conditions under which the functions are measure-preserving, invertible and isometric, ergodic, and minimal on invariant subsets, by means of graph theoretic properties.

Physics

A Two Length Scale Polymer Theory for RNA Loop Free Energies and Helix Stacking

Daniel P.Aalberts and Nagarajan Nandagopol ’09

RNA, 16, 1350-1355 (2010)

The reliability of RNA secondary structure predictions is subject to the accuracy of the underlying free energy model. Mfold and other RNA folding algorithms are based on the Turner model, whose weakest part is its formulation of loop free energies, particularly for multibranch loops. RNA loops contain single-strand and helix-crossing segments, so we develop an enhanced two-length freely jointed chain theory and revise it for self-avoidance. Our resulting universal formula for RNA loop entropy has fewer parameters than the Turner/Mfold model, and yet simulations show that the standard errors for multibranch loop free energies are reduced by an order of magnitude. We further note that coaxial stacking decreases the effective length of multibranch loops and provides, surprisingly, an entropic stabilization of the ordered configuration in addition to the enthalpic contribution of helix stacking. Our formula is in good agreement with measured hairpin free energies. We find that it also improves the accuracy of folding predictions.

A Vision for Photoisomerization

Daniel P.Aalberts and H.F.Stabenau ’02

Physica A 389, 2981-2986

We propose a simple physical mechanism to explain the ultrafast first step of vision, a photoinduced cis to trans rotation of retinal. In the ground state, the torsional stability of π bonds is countered by Coulomb interactions acting between the π lobes; the torsional dependence for Coulomb interactions is absent in the often-used Ohno approximation, but restored with our formula. After photoexcitation, the bonding weakens causing the destabilizing terms to dominate. The twist in the ground state due to steric interactions surrounding the 11-cis bond increases the initial torque and thus the speed of the reaction.

 

Arbitrary Control of Entanglement between Two Superconducting Resonators

Frederick W.Strauch, K.Jacobs, and R.W.Simmonds

Physical Review Letters 105, 050501 (July 27, 2010)

We present a method to synthesize an arbitrary quantum state of two superconducting resonators. This state-synthesis algorithm utilizes a coherent interaction of each resonator with a tunable artificial atom to create entangled quantum superpositions of photon number (Fock) states in the resonators. We theoretically analyze this approach, showing that it can efficiently synthesize NOON states, with large photon numbers, using existing technology.

 

Parallel State Transfer and Efficient Quantum Routing on Quantum Networks

Christopher Chudzicki’10 and Frederick W.Strauch

Physical Review Letters 105, 260501 (December 22, 2010)

We study the routing of quantum information in parallel on multidimensional networks of tunable qubits and oscillators. These theoretical models are inspired by recent experiments in superconducting circuits. We show that perfect parallel state transfer is possible for certain networks of harmonic oscillator modes. We extend this to the distribution of entanglement between every pair of nodes in the network, finding that the routing efficiency of hypercube networks is optimal and robust in the presence of dissipation and finite bandwidth.

Neutrino mass, sneutrino dark matter, and signals of lepton flavor violation in the MRSSM

A.Kumar, David Tucker-Smith, and N.Weiner

JHEP 1009, 111 (2010)

We study the phenomenology of mixed-sneutrino dark matter in the Minimal R-symmetric Supersymmetric Standard Model (MRSSM). Mixed sneutrinos fit naturally within the MRSSM, as the smallness (or absence) of neutrino Yukawa couplings singles out sneutrino A-terms as the only ones not automatically forbidden by R-symmetry. We perform a study of randomly generated sneutrino mass matrices and find that (i) the measured value of ΩDM is well within the range of typical values obtained for the relic abundance of the lightest sneutrino, (ii) with small lepton-number-violating mass terms for the right-handed sneutrinos, random matrices satisfying the ΩDM constraint have a decent probability of satisfying direct detection constraints, and much of the remaining parameter space will be probed by upcoming experiments, (iii) the lepton-number-violating mass terms radiatively generate appropriately small Majorana neutrino masses, with neutrino oscillation data favoring a mostly sterile lightest sneutrino with a dominantly μ/τ-flavored active component, and (iv) a sneutrino LSP with a significant μ component can lead to striking signals of e-μ flavor violation in dilepton invariant-mass distributions at the LHC.

Muonic hydrogen and MeV forces

David Tucker-Smith and I.Yavin

Phys.Rev D83, 10172(R) (2011)

We explore the possibility that a new interaction between muons and protons is responsible for the discrepancy between the CODATA value of the proton radius and the value deduced from the measurement of the Lamb shift in muonic hydrogen. We show that a new force carrier with roughly MeV mass can account for the observed energy shift as well as the discrepancy in the muon anomalous magnetic moment. However, measurements in other systems constrain the couplings to electrons and neutrons to be suppressed relative to the couplings to muons and protons, which seems challenging from a theoretical point of view. One can nevertheless make predictions for energy shifts in muonic deuterium, muonic helium, and true muonium under the assumption that the new particle couples dominantly to muons and protons.