364 research outputs found
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)
We describe AlphaFold, the protein structure prediction system that was entered by the group A7D in CASP13 Submissions were made by three free-modelling methods which combine the predictions of three neural networks. All three systems were guided by predictions of distances between pairs of residues produced by a neural network. Two systems assembled fragments produced by a generative neural network, one using scores from a network trained to regress GDT_TS. The third system shows that simple gradient descent on a properly constructed potential is able to perform on-par with more expensive traditional search techniques and without requiring domain segmentation. In the CASP13 free-modelling assessors' ranking by summed z-scores, this system scored highest with 68.3 vs 48.2 for the next closest group. (An average GDT_TS of 61.4.) The system produced high-accuracy structures (with GDT_TS scores of 70 or higher) for 11 out of 43 free-modelling domains. Despite not explicitly using template information, the results in the template category were comparable to the best performing template-based methods
Improved protein structure prediction using potentials from deep learning
Protein structure prediction can be used to determine the three-dimensional shape of a protein from its amino acid sequence1. This problem is of fundamental importance as the structure of a protein largely determines its function2; however, protein structures can be difficult to determine experimentally. Considerable progress has recently been made by leveraging genetic information. It is possible to infer which amino acid residues are in contact by analysing covariation in homologous sequences, which aids in the prediction of protein structures3. Here we show that we can train a neural network to make accurate predictions of the distances between pairs of residues, which convey more information about the structure than contact predictions. Using this information, we construct a potential of mean force4 that can accurately describe the shape of a protein. We find that the resulting potential can be optimized by a simple gradient descent algorithm to generate structures without complex sampling procedures. The resulting system, named AlphaFold, achieves high accuracy, even for sequences with fewer homologous sequences. In the recent Critical Assessment of Protein Structure Prediction5 (CASP13)—a blind assessment of the state of the field—AlphaFold created high-accuracy structures (with template modelling (TM) scores6 of 0.7 or higher) for 24 out of 43 free modelling domains, whereas the next best method, which used sampling and contact information, achieved such accuracy for only 14 out of 43 domains. AlphaFold represents a considerable advance in protein-structure prediction. We expect this increased accuracy to enable insights into the function and malfunction of proteins, especially in cases for which no structures for homologous proteins have been experimentally determined7
ADAPTIVE OPTICS IMAGING OF VHS 1256-1257: A LOW MASS COMPANION TO A BROWN DWARF BINARY SYSTEM
Recently, Gauza et al. (2015) reported the discovery of a companion to the
late M-dwarf, VHS J125601.92-125723.9 (VHS 1256-1257). The companion's absolute
photometry suggests its mass and atmosphere are similar to the HR 8799 planets.
However, as a wide companion to a late-type star, it is more accessible to
spectroscopic characterization. We discovered that the primary of this system
is an equal-magnitude binary. For an age Myr the A and B components
each have a mass of , and the b component
has a mass of , making VHS 1256-1257 only the third brown
dwarf triple system. There exists some tension between the spectrophotometric
distance of pc and the parallax distance of pc. At
12.7 pc VHS1256-1257 A and B would be the faintest known M7.5 objects, and are
even faint outliers among M8 types. If the larger spectrophotmetric distance is
more accurate than the parallax, then the mass of each component increases. In
particular, the mass of the b component increases well above the deuterium
burning limit to and the mass of each binary
component increases to . At 17.1 pc, the UVW
kinematics of the system are consistent with membership in the AB~Dor moving
group. The architecture of the system resembles a hierarchical stellar multiple
suggesting it formed via an extension of the star-formation process to low
masses. Continued astrometric monitoring will resolve this distance uncertainty
and will provide dynamical masses for a new benchmark system.Comment: Accepted to ApJ
Measurement of higher cumulants of net-charge multiplicity distributions in AuAu collisions at GeV
We report the measurement of cumulants () of the net-charge
distributions measured within pseudorapidity () in AuAu
collisions at GeV with the PHENIX experiment at the
Relativistic Heavy Ion Collider. The ratios of cumulants (e.g. ,
) of the net-charge distributions, which can be related to volume
independent susceptibility ratios, are studied as a function of centrality and
energy. These quantities are important to understand the quantum-chromodynamics
phase diagram and possible existence of a critical end point. The measured
values are very well described by expectation from negative binomial
distributions. We do not observe any nonmonotonic behavior in the ratios of the
cumulants as a function of collision energy. The measured values of and can be directly compared to lattice
quantum-chromodynamics calculations and thus allow extraction of both the
chemical freeze-out temperature and the baryon chemical potential at each
center-of-mass energy.Comment: 512 authors, 8 pages, 4 figures, 1 table. v2 is version accepted for
publication in Phys. Rev. C as a Rapid Communication. Plain text data tables
for the points plotted in figures for this and previous PHENIX publications
are (or will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Transverse energy production and charged-particle multiplicity at midrapidity in various systems from to 200 GeV
Measurements of midrapidity charged particle multiplicity distributions,
, and midrapidity transverse-energy distributions,
, are presented for a variety of collision systems and energies.
Included are distributions for AuAu collisions at ,
130, 62.4, 39, 27, 19.6, 14.5, and 7.7 GeV, CuCu collisions at
and 62.4 GeV, CuAu collisions at
GeV, UU collisions at GeV,
Au collisions at GeV, HeAu collisions at
GeV, and collisions at
GeV. Centrality-dependent distributions at midrapidity are presented in terms
of the number of nucleon participants, , and the number of
constituent quark participants, . For all collisions
down to GeV, it is observed that the midrapidity data
are better described by scaling with than scaling with . Also presented are estimates of the Bjorken energy density,
, and the ratio of to ,
the latter of which is seen to be constant as a function of centrality for all
systems.Comment: 706 authors, 32 pages, 20 figures, 34 tables, 2004, 2005, 2008, 2010,
2011, and 2012 data. v2 is version accepted for publication in Phys. Rev.
Systematic study of charged-pion and kaon femtoscopy in AuAu collisions at =200 GeV
We present a systematic study of charged pion and kaon interferometry in
AuAu collisions at =200 GeV. The kaon mean source radii
are found to be larger than pion radii in the outward and longitudinal
directions for the same transverse mass; this difference increases for more
central collisions. The azimuthal-angle dependence of the radii was measured
with respect to the second-order event plane and similar oscillations of the
source radii were found for pions and kaons. Hydrodynamic models qualitatively
describe the similar oscillations of the mean source radii for pions and kaons,
but they do not fully describe the transverse-mass dependence of the
oscillations.Comment: 499 authors, 27 pages, 13 figures, and 11 tables. v2 is the version
accepted for publication in Phys. Rev. C. Plain text data tables for the
points plotted in figures for this and previous PHENIX publications are (or
will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Measurements of elliptic and triangular flow in high-multiplicity HeAu collisions at GeV
We present the first measurement of elliptic () and triangular ()
flow in high-multiplicity HeAu collisions at
GeV. Two-particle correlations, where the particles have a large separation in
pseudorapidity, are compared in HeAu and in collisions and
indicate that collective effects dominate the second and third Fourier
components for the correlations observed in the HeAu system. The
collective behavior is quantified in terms of elliptic and triangular
anisotropy coefficients measured with respect to their corresponding
event planes. The values are comparable to those previously measured in
Au collisions at the same nucleon-nucleon center-of-mass energy.
Comparison with various theoretical predictions are made, including to models
where the hot spots created by the impact of the three He nucleons on the
Au nucleus expand hydrodynamically to generate the triangular flow. The
agreement of these models with data may indicate the formation of low-viscosity
quark-gluon plasma even in these small collision systems.Comment: 630 authors, 9 pages, 4 figures, 2 tables. v2 is the version accepted
for publication by Physical Review Letters. Plain text data tables for the
points plotted in figures for this and previous PHENIX publications are (or
will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Measurements of double-helicity asymmetries in inclusive production in longitudinally polarized collisions at GeV
We report the double helicity asymmetry, , in inclusive
production at forward rapidity as a function of transverse momentum
and rapidity . The data analyzed were taken during
GeV longitudinally polarized collisions at the Relativistic Heavy Ion
Collider (RHIC) in the 2013 run using the PHENIX detector. At this collision
energy, particles are predominantly produced through gluon-gluon
scatterings, thus is sensitive to the gluon polarization
inside the proton. We measured by detecting the decay
daughter muon pairs within the PHENIX muon spectrometers in the
rapidity range . In this kinematic range, we measured the
to be ~(stat)~~(syst). The
can be expressed to be proportional to the product of the
gluon polarization distributions at two distinct ranges of Bjorken : one at
moderate range where recent RHIC data of jet and
double helicity spin asymmetries have shown evidence for significant gluon
polarization, and the other one covering the poorly known small- region . Thus our new results could be used to further
constrain the gluon polarization for .Comment: 335 authors, 10 pages, 4 figures, 3 tables, 2013 data. Version
accepted for publication by Phys. Rev. D. Plain text data tables for the
points plotted in figures for this and previous PHENIX publications are (or
will be) publicly available at http://www.phenix.bnl.gov/papers.htm
Upsilon (1S+2S+3S) production in d+Au and p+p collisions at sqrt(s_NN)=200 GeV and cold-nuclear matter effects
The three Upsilon states, Upsilon(1S+2S+3S), are measured in d+Au and p+p
collisions at sqrt(s_NN)=200 GeV and rapidities 1.2<|y|<2.2 by the PHENIX
experiment at the Relativistic Heavy-Ion Collider. Cross sections for the
inclusive Upsilon(1S+2S+3S) production are obtained. The inclusive yields per
binary collision for d+Au collisions relative to those in p+p collisions
(R_dAu) are found to be 0.62 +/- 0.26 (stat) +/- 0.13 (syst) in the gold-going
direction and 0.91 +/- 0.33 (stat) +/- 0.16 (syst) in the deuteron-going
direction. The measured results are compared to a nuclear-shadowing model,
EPS09 [JHEP 04, 065 (2009)], combined with a final-state breakup cross section,
sigma_br, and compared to lower energy p+A results. We also compare the results
to the PHENIX J/psi results [Phys. Rev. Lett. 107, 142301 (2011)]. The rapidity
dependence of the observed Upsilon suppression is consistent with lower energy
p+A measurements.Comment: 495 authors, 11 pages, 9 figures, 5 tables. Submitted to Phys. Rev.
C. Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
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