Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent λ
 L
 ≤ 2πk
 B
 T/ℏ. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.

A bound on chaos

These notes are loosely based on lectures given at the CERN Winter School on Supergravity, Strings and Gauge theories, February 2009, and at the IPM String School in Tehran, April 2009. I have focused on a few concrete topics and also on addressing questions that have arisen repeatedly. Background condensed matter physics material is included as motivation and easy reference for the high energy physics community. The discussion of holographic techniques progresses from equilibrium, to transport and to superconductivity.

https://iopscience.iop.org/article/10.1088/0264-9381/26/22/224002/pdf

Lectures on holographic methods for condensed matter physics

Journal of Statistical Mechanics: theory and experiment

Motivated by the vast string landscape, we consider the shear viscosity to entropy density ratio in conformal field theories dual to Einstein gravity with curvature square corrections. After field redefinitions these theories reduce to Gauss-Bonnet gravity, which has special properties that allow us to compute the shear viscosity nonperturbatively in the Gauss-Bonnet coupling. By tuning of the coupling, the value of the shear viscosity to entropy density ratio can be adjusted to any positive value from infinity down to zero, thus violating the conjectured viscosity bound. At linear order in the coupling, we also check consistency of four different methods to calculate the shear viscosity, and we find that all of them agree. We search for possible pathologies associated with this class of theories violating the viscosity bound.

Viscosity Bound Violation in Higher Derivative Gravity

In recent work we showed that, for a class of conformal field theories (CFT) with Gauss-Bonnet gravity dual, the shear viscosity to entropy density ratio, $\ensuremath{\eta}/s$, could violate the conjectured Kovtun-Starinets-Son viscosity bound, $\ensuremath{\eta}/s\ensuremath{\ge}1/4\ensuremath{\pi}$. In this Letter we argue, in the context of the same model, that tuning $\ensuremath{\eta}/s$ below $(16/25)(1/4\ensuremath{\pi})$ induces microcausality violation in the CFT, rendering the theory inconsistent. This is a concrete example in which inconsistency of a theory and a lower bound on viscosity are correlated, supporting the idea of a possible universal lower bound on $\ensuremath{\eta}/s$ for all consistent theories.

Viscosity Bound and Causality Violation

We holographically engineer a periodic lattice of localized fermionic impurities within a plasma medium by putting an array of probe D5-branes in the background produced by N D3-branes. Thermodynamic quantities are computed in the large N limit via the holographic dictionary. We then dope the lattice by replacing some of the D5-branes by anti-D5-branes. In the large N limit, we determine the critical temperature below which the system dimerizes with bond ordering. Finally, we argue that for the special case of a square lattice our system is glassy at large but finite N, with the low temperature physics dominated by a huge collection of metastable dimerized configurations without long-range order, connected only through tunneling events.

Holographic lattices, dimers, and glasses

Liquids relax extremely slowly on approaching the glass state. One explanation is that an entropy crisis, because of the rarefaction of available states, makes it increasingly arduous to reach equilibrium in that regime. Validating this scenario is challenging, because experiments offer limited resolution, while numerical studies lag more than eight orders of magnitude behind experimentally relevant timescales. In this work, we not only close the colossal gap between experiments and simulations but manage to create in silico configurations that have no experimental analog yet. Deploying a range of computational tools, we obtain four estimates of their configurational entropy. These measurements consistently confirm that the steep entropy decrease observed in experiments is also found in simulations, even beyond the experimental glass transition. Our numerical results thus extend the observational window into the physics of glasses and reinforce the relevance of an entropy crisis for understanding their formation.

https://www.pnas.org/content/pnas/114/43/11356.full.pdf

Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling.

Design of reliable systems must guarantee stability against input perturbations. In machine learning, such guarantee entails preventing overfitting and ensuring robustness of models against corruption of input data. In order to maximize stability, we analyze and develop a computationally efficient implementation of Jacobian regularization that increases classification margins of neural networks. The stabilizing effect of the Jacobian regularizer leads to significant improvements in robustness, as measured against both random and adversarial input perturbations, without severely degrading generalization properties on clean data.

Sho Yaida

Papers

Viscosity Bound Violation in Higher Derivative Gravity

Viscosity Bound and Causality Violation

Holographic lattices, dimers, and glasses

Configurational entropy measurements in extremely supercooled liquids that break the glass ceiling.

Robust Learning with Jacobian Regularization