This archive contains spike trains simultaneously recorded from ganglion cells in the tiger salamander retina with a multi-electrode array while viewing a repeated natural movie clip. These data have been analyzed in previous papers, notably Puchalla et al. Neuron 2005 and Schneidman et al. Nature 2006.
Recent advances in experimental techniques have allowed the simultaneous recordings of
populations of hundreds of neurons, fostering a debate about the nature of the collective
structure of population neural activity. Much of this debate has focused on the
empirical findings of a phase transition in the parameter space of maximum entropy
models describing the measured neural probability distributions, interpreting this phase
transition to indicate a critical tuning of the neural code. Here, we instead focus on the
possibility that this is a first-order phase transition which provides evidence that the
real neural population is in a `structured', collective state. We show that this collective
state is robust to changes in stimulus ensemble and adaptive state. We find that the
pattern of pairwise correlations between neurons has a strength that is well within the
strongly correlated regime and does not require fine tuning, suggesting that this state is
generic for populations of 100+ neurons. We find a clear correspondence between the
emergence of a phase transition, and the emergence of attractor-like structure in the
inferred energy landscape. A collective state in the neural population, in which neural
activity patterns naturally form clusters, provides a consistent interpretation for our
Berryman, Eleanor J.; Winey, J. M.; Gupta, Yogendra M.; Duffy, Thomas S.
Stishovite (rutile-type SiO2) is the archetype of dense silicates and may occur in post-garnet eclogitic rocks at lower-mantle conditions. Sound velocities in stishovite are fundamental to understanding its mechanical and thermodynamic behavior at high pressure and temperature. Here, we use plate-impact experiments combined with velocity interferometry to determine the stress, density, and longitudinal sound speed in stishovite formed during shock compression of fused silica at 44 GPa and above. The measured sound speeds range from 12.3(8) km/s at 43.8(8) GPa to 9.8(4) km/s at 72.7(11) GPa. The decrease observed at 64 GPa reacts a decrease in the shear modulus of stishovite, likely due to the onset of melting. By 72 GPa, the measured sound speed agrees with the theoretical bulk sound speed indicating loss of all shear stiffness due to complete melting. Our sound velocity results provide direct evidence for shock-induced melting, in agreement with previous pyrometry data.
Bertelli, N; Valeo, E.J.; Green, D.L.; Gorelenkova, M.; Phillips, C.K.; Podesta, M.; Lee, J.P.; Wright, J.C.; Jaeger, E.
At the power levels required for significant heating and current drive
in magnetically-confined toroidal plasma, modification of the particle distribution
function from a Maxwellian shape is likely [T. H. Stix, Nucl. Fusion, 15 737
(1975)], with consequent changes in wave propagation and in the location and
amount of absorption. In order to study these effects computationally, both the
finite-Larmor-radius and the high-harmonic fast wave (HHFW), versions of the
full-wave, hot-plasma toroidal simulation code TORIC [M. Brambilla, Plasma Phys.
Control. Fusion 41, 1 (1999) and M. Brambilla, Plasma Phys. Control. Fusion
44, 2423 (2002)], have been extended to allow the prescription of arbitrary velocity
distributions of the form f(v||, v_perp, psi , theta). For hydrogen (H) minority heating of a
deuterium (D) plasma with anisotropic Maxwellian H distributions, the fractional
H absorption varies significantly with changes in parallel temperature but is
essentially independent of perpendicular temperature. On the other hand, for
HHFW regime with anisotropic Maxwellian fast ion distribution, the fractional
beam ion absorption varies mainly with changes in the perpendicular temperature.
The evaluation of the wave-field and power absorption, through the full wave
solver, with the ion distribution function provided by either aMonte-Carlo particle
and Fokker-Planck codes is also examined for Alcator C-Mod and NSTX plasmas.
Non-Maxwellian effects generally tends to increase the absorption with respect to
the equivalent Maxwellian distribution.
Heating magnetically confined plasmas using waves in the ion-cyclotron range of frequencies typically requires coupling these waves over a steep density gradient. This process has produced an unexpected and deleterious phenomenon on the National Spherical Torus eXperiment (NSTX): a prompt loss of wave power along magnetic field lines in front of the antenna to the divertor. Understanding this loss may be key to achieving effective heating and expanding the operational space of NSTX-Upgrade. Here, we propose that a new type of mode, which conducts a significant fraction of the total wave power in the low-density peripheral plasma, is driving these losses. We demonstrate the existence of such modes, which are distinct from surface modes and coaxial modes, in a cylindrical cold-plasma model when a half wavelength structure fits into the region outside the core plasma. The latter condition generalizes the previous hypothesis regarding the occurence of the edge losses and may explain why full-wave simulations predict these losses in some cases but not others. If valid, this condition implies that outer gap control is a potential strategy for mitigating the losses in NSTX-Upgrade in addition to raising the magnetic field or influencing the edge density.
Kim, E.-W.; Bertelli, N.; Johnson, J.R.; Valeo, E.; Hosea, J.; Perkins, R.
We illustrate the capabilities of a recently developed two-dimensional full wave code (FW2D) in space and tokamak plasmas by adopting various values of density, magnetic field configuration and strength as well as boundary shape. As example, we first showed fast compressional wave propagation in the inner magnetosphere is dramatically modified by a plasmaspheric plume at Earth's magnetosphere. The results show that wave energy is trapped in the plume showing a leaky eigenmode-like structure with plume, which is similar to the detected magnetosonic waves. We also performed simulations of high harmonic fast waves in the scrape-off layer (SOL) plasmas of the National Spherical Torus eXperiment (NSTX)/NSTX-Upgrade. Comparison the results with previous full-wave simulations show that although the FW2D code uses a cold plasma approximation, the electric field and the fraction of the power losses in the SOL plasmas show excellent consistency and agreement with the previous full wave simulations performed by the AORSA code.
Taylor, Jenny A.; Bratton, Benjamin P.; Sichel, Sophie R.; Blair, Kris M.; Jacobs, Holly M.; DeMeester, Kristen E.; Kuru, Erkin; Gray, Joe; Biboy, Jacob; VanNieuwenhze, Michael S.; Vollmer, Waldemar; Grimes, Catherine L.; Shaevitz, Joshua W.; Salama, Nina R.
Helical cell shape is necessary for efficient stomach colonization by Helicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. We show that the helical centerline pitch and radius of wild-type H. pylori cells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of short pulses with either N-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape.
Monitoring the attention of others is fundamental to social cognition. Most of the literature on the topic assumes that our social cognitive machinery is tuned specifically to the gaze direction of others as a proxy for attention. This standard assumption reduces attention to an externally visible parameter. Here we show that this assumption is wrong and a deeper, more meaningful representation is involved. We presented subjects with two cues about the attentional state of a face: direction of gaze and emotional expression. We tested whether people relied predominantly on one cue, the other, or both. If the traditional view is correct, then the gaze cue should dominate. Instead, people employed a variety of strategies, some relying on gaze, some on expression, and some on an integration of cues. We also assessed people’s social cognitive ability using two, independent, standard tests. If the traditional view is correct, then social cognitive ability, as assessed by the independent tests, should correlate with the degree to which people successfully use the gaze cue to judge the attention state of the face. Instead, social cognitive ability correlated best with the degree to which people successfully integrated the cues together, instead of with the use of any one specific cue. The results suggest a rethink of a fundamental component of social cognition: monitoring the attention of others involves constructing a deep model that is informed by a combination of cues. Attention is a rich process and monitoring the attention of others involves a similarly rich representation.
Hill, K. W.; Gao, L.; Kraus, B. F.; Bitter, M.; Efthimion, P. C.; Pablant, N. A.; Schneider, M. B.; Thorn, D. B.; Chen, H.; Kauffman, R. L.; Liedahl, D. A.; MacDonald, M. J.; MacPhee, A. G.; Scott, H. A.; Stoupin, S.; Doron, R.; Stambulchik, E.; Maron, Y.; Lahmann, B.
Numerical data used to draw the figures in the manuscript
Using a recently installed impurity powder dropper (IPD), boron powder (< 150 μm) was injected into lower single null (LSN) L-mode discharges in WEST. IPDs possibly enable real-time wall conditioning of the plasma-facing components and may help to facilitate H-mode access in the full-tungsten environment of WEST. The discharges in this experiment featured Ip = 0.5 MA, BT = 3.7 T, q95 = 4.3, tpulse = 12–30 s, ne,0 ~ 4×1019 m-2, and PLHCD ~ 4.5 MW. Estimates of the deuterium and impurity particle fluxes, derived from a combination of visible spectroscopy measurements and their corresponding S/XB coefficients, showed decreases of ~ 50% in O+, N+, and C+ populations during powder injection and a moderate reduction of these low-Z impurities (~ 50%) and W (~ 10%) in the discharges that followed powder injection. Along with the improved wall conditions, WEST discharges with B powder injection observed improved confinement, as the stored energy WMHD, neutron rate, and electron temperature Te increased significantly (10–25% for WMHD and 60–200% for the neutron rate) at constant input power. These increases in confinement scale up with the powder drop rate and are likely due to the suppression of ion temperature gradient (ITG) turbulence from changes in Zeff and/or modifications to the electron density profile.
This distribution compiles numerous physical properties for 2,585 intrinsically disordered proteins (IDPs) obtained by coarse-grained molecular dynamics simulation. This combination comprises "Dataset A" as reported in "Featurization strategies for polymer sequence or composition design by machine learning" by Roshan A. Patel, Carlos H. Borca, and Michael A. Webb (DOI: 10.1039/D1ME00160D). The specific IDP sequences are sourced from version 9.0 of the DisProt database. The simulations were performed using the LAMMPS molecular dynamics engine. The interactions used for simulation are obtained from R. M. Regy , J. Thompson , Y. C. Kim and J. Mittal , Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins, Protein Sci., 2021, 1371 —1379.
This distribution contains experimentally measured data for the extent of retained enzyme activity post thermal stressing for three distinct enzymes: glucose oxidase, lipase, and horseradish peroxidase. The data is used to form conclusions and develop machine learning models as reported in the publication "Machine Learning on a Robotic Platform for the Design of Polymer-Protein Hybrids" by Matthew Tamasi, Roshan Patel, Carlos Borca, Shashank Kosuri, Heloise Mugnier, Rahul Upadhya, N. Sanjeeva Murthy, Michael Webb*, and Adam Gormley. Details regarding the experimental protocols are reported in the aforementioned paper but are briefly discussed in the README.
Gilson, Erik; Lee, H; Bortolon, A; Choe, W; Diallo, A; Hong, SH; Lee, HM; Maingi, R; Mansfield, DK; Nagy, A; Park, SH; Song, IW; Song, JI; Yun, SW; Nazikian, R
Results from KSTAR powder injection experiments, in which tens of milligrams of boron nitride (BN) were dropped into low-power H-mode plasmas, show an improvement in wall conditions in subsequent discharges and, in some cases, a reduction or elimination of edge-localized modes (ELMs). Injected powder is distributed by the plasma flow and is deposited on the wall and, over the course of several discharges, was observed to gradually reduce recycling by 33%, and decrease both the ELM amplitude and frequency. This is the first demonstration of the use of BN for ELM mitigation. In all of these experiments, an Impurity Powder Dropper (IPD) was used to introduce precise, controllable amounts of the materials into ELMy H-mode KSTAR discharges. The plasma duration was between 10 s and 15 s, 𝐼𝑝 = 500 kA, 𝐵𝑇 = 1.8 T, 𝑃NBI = 1.6 MW, and 𝑃ECH = 0.6 MW. Plasma densities were between 2 and 3 × 1019 m−3. In all cases, the pre-fill and startup gas-fueling was kept constant, suggesting that the decrease in baseline D𝛼 emission is in fact due to a reduction in recycling. The results presented herein highlight the viability of powder injection for intra-shot and between-shot wall conditioning.
In this paper we present initial simulations of pedestal control by Lithium Granule Injection (LGI) in NSTX. A model for small granule ablation has been implemented in the M3D-C1 code , allowing the simulation of realistic Lithium granule injections. 2D simulations in NSTX L-mode and H-mode plasmas are done and the effect of granule size, injection angle and velocity on the pedestal gradient increase are studied. For H-mode cases, the amplitude of the local pressure perturbation caused by the granules is highly dependent on the solid granule size. In our simulations, reducing the granule injection velocity allows one to inject more particles at the pedestal top.