Non-equilibrium Relations for Spin Glasses with Gauge Symmetry

We study the applications of non-equilibrium relations such as the Jarzynski equality and fluctuation theorem to spin glasses with gauge symmetry. It is shown that the exponentiated free-energy difference appearing in the Jarzynski equality reduces to a simple analytic function written explicitly in terms of the initial and final temperatures if the temperature satisfies a certain condition related to gauge symmetry. This result is used to derive a lower bound on the work done during the non-equilibrium process of temperature change. We also prove identities relating equilibrium and non-equilibrium quantities. These identities suggest a method to evaluate equilibrium quantities from non-equilibrium computations, which may be useful to avoid the problem of slow relaxation in spin glasses.Comment: 8 pages, 2 figures, submitted to JPS

Testing Error Correcting Codes by Multicanonical Sampling of Rare Events

The idea of rare event sampling is applied to the estimation of the performance of error-correcting codes. The essence of the idea is importance sampling of the pattern of noises in the channel by Multicanonical Monte Carlo, which enables efficient estimation of tails of the distribution of bit error rate. The idea is successfully tested with a convolutional code

Simulation of Lattice Polymers with Multi-Self-Overlap Ensemble

A novel family of dynamical Monte Carlo algorithms for lattice polymers is proposed. Our central idea is to simulate an extended ensemble in which the self-avoiding condition is systematically weakened. The degree of the self-overlap is controlled in a similar manner as the multicanonical ensemble. As a consequence, the ensemble --the multi-self-overlap ensemble-- contains adequate portions of self-overlapping conformations as well as higher energy ones. It is shown that the multi-self-overlap ensemble algorithm reproduce correctly the canonical averages at finite temperatures of the HP model of lattice proteins. Moreover, it outperforms massively a standard multicanonical algorithm for a difficult example of a polymer with 8-stickers. Alternative algorithm based on exchange Monte Carlo method is also discussed.Comment: 5 Pages, 4 Postscript figures, uses epsf.st

Nonequilibrium work on spin glasses in longitudinal and transverse fields

We derive a number of exact relations between equilibrium and nonequilibrium quantities for spin glasses in external fields using the Jarzynski equality and gauge symmetry. For randomly-distributed longitudinal fields, a lower bound is established for the work done on the system in nonequilibrium processes, and identities are proven to relate equilibrium and nonequilibrium quantities. In the case of uniform transverse fields, identities are proven between physical quantities and exponentiated work done to the system at different parts of the phase diagram with the context of quantum annealing in mind. Additional relations are given, which relate the exponentiated work in quantum and simulated (classical) annealing. It is also suggested that the Jarzynski equality may serve as a guide to develop a method to perform quantum annealing under non-adiabatic conditions.Comment: 17 pages, 5 figures, submitted to JPS

A List Referring Monte Carlo Method for Lattice Glass Models

We present an effcient Monte-Carlo method for lattice glass models which are characterized by hard constraint conditions. The basic idea of the method is similar to that of the $N$-fold way method. By using a list of sites into which we can insert a particle, we avoid trying a useless transition which is forbidden by the constraint conditions. We applied the present method to a lattice glass model proposed by Biroli and M{\'e}zard. We first evaluated the efficiency of the method through measurements of the autocorrelation function of particle configurations. As a result, we found that the efficiency is much higher than that of the standard Monte-Carlo method. We also compared the efficiency of the present method with that of the $N$-fold way method in detail. We next examined how the efficiency of extended ensemble methods such as the replica exchange method and the Wang-Landau method is inflnuenced by the choice of the local update method. The results show that the efficiency is considerably improved by the use of efficient local update methods. For example, when the number of sites $N_{\rm site}$ is 1024, the ergodic time $\tau_{\rm E}$ of the replica exchange method in the grand-canonical ensemble, which is the average round-trip time of a replica in chemical-potential space, with the present local update method is more than $10^2$ times shorter than that with the standard local update method. This result shows that the efficient local update method is quite important to make extended ensemble methods more effective.Comment: 16 pages, 21 figures; 1 subsection, 1 appendix, and 5 figures are added, abstract is changed, 1 figure is remove

Equilibrium Sampling From Nonequilibrium Dynamics

We present some applications of an Interacting Particle System (IPS) methodology to the field of Molecular Dynamics. This IPS method allows several simulations of a switched random process to keep closer to equilibrium at each time, thanks to a selection mechanism based on the relative virtual work induced on the system. It is therefore an efficient improvement of usual non-equilibrium simulations, which can be used to compute canonical averages, free energy differences, and typical transitions paths

Large random correlations in individual mean field spin glass samples

We argue that complex systems must possess long range correlations and illustrate this idea on the example of the mean field spin glass model. Defined on the complete graph, this model has no genuine concept of distance, but the long range character of correlations is translated into a broad distribution of the spin-spin correlation coefficients for almost all realizations of the random couplings. When we sample the whole phase space we find that this distribution is so broad indeed that at low temperatures it essentially becomes uniform, with all possible correlation values appearing with the same probability. The distribution of correlations inside a single phase space valley is also studied and found to be much narrower.Comment: Added a few references and a comment phras

Evidence for the double degeneracy of the ground-state in the 3D ±J\pm J spin glass

A bivariate version of the multicanonical Monte Carlo method and its application to the simulation of the three-dimensional $\pm J$ Ising spin glass are described. We found the autocorrelation time associated with this particular multicanonical method was approximately proportional to the system volume, which is a great improvement over previous methods applied to spin-glass simulations. The principal advantage of this version of the multicanonical method, however, was its ability to access information predictive of low-temperature behavior. At low temperatures we found results on the three-dimensional $\pm J$ Ising spin glass consistent with a double degeneracy of the ground-state: the order-parameter distribution function $P(q)$ converged to two delta-function peaks and the Binder parameter approached unity as the system size was increased. With the same density of states used to compute these properties at low temperature, we found their behavior changing as the temperature is increased towards the spin glass transition temperature. Just below this temperature, the behavior is consistent with the standard mean-field picture that has an infinitely degenerate ground state. Using the concept of zero-energy droplets, we also discuss the structure of the ground-state degeneracy. The size distribution of the zero-energy droplets was found to produce the two delta-function peaks of $P(q)$.Comment: 33 pages with 31 eps figures include

Parallel Excluded Volume Tempering for Polymer Melts

We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts which makes use of both parallel tempering and large scale Monte Carlo moves. The method is based upon simulating a set of systems in parallel, each of which has a slightly different repulsive core potential, such that a thermodynamic path from full excluded volume to an ideal gas of random walks is generated. While each system is run with standard stochastic dynamics, resulting in an NVT ensemble, we implement the parallel tempering through stochastic swaps between the configurations of adjacent potentials, and the large scale Monte Carlo moves through attempted pivot and translation moves which reach a realistic acceptance probability as the limit of the ideal gas of random walks is approached. Compared to pure stochastic dynamics, this results in an increased efficiency even for a system of chains as short as $N = 60$ monomers, however at this chain length the large scale Monte Carlo moves were ineffective. For even longer chains the speedup becomes substantial, as observed from preliminary data for $N = 200$

Enhanced and effective conformational sampling of protein molecular systems for their free energy landscapes

Protein folding and protein–ligand docking have long persisted as important subjects in biophysics. Using multicanonical molecular dynamics (McMD) simulations with realistic expressions, i.e., all-atom protein models and an explicit solvent, free-energy landscapes have been computed for several systems, such as the folding of peptides/proteins composed of a few amino acids up to nearly 60 amino-acid residues, protein–ligand interactions, and coupled folding and binding of intrinsically disordered proteins. Recent progress in conformational sampling and its applications to biophysical systems are reviewed in this report, including descriptions of several outstanding studies. In addition, an algorithm and detailed procedures used for multicanonical sampling are presented along with the methodology of adaptive umbrella sampling. Both methods control the simulation so that low-probability regions along a reaction coordinate are sampled frequently. The reaction coordinate is the potential energy for multicanonical sampling and is a structural identifier for adaptive umbrella sampling. One might imagine that this probability control invariably enhances conformational transitions among distinct stable states, but this study examines the enhanced conformational sampling of a simple system and shows that reasonably well-controlled sampling slows the transitions. This slowing is induced by a rapid change of entropy along the reaction coordinate. We then provide a recipe to speed up the sampling by loosening the rapid change of entropy. Finally, we report all-atom McMD simulation results of various biophysical systems in an explicit solvent