Related papers: A Second Look at Canonical Sampling of Biomolecule…
We introduce a new update scheme to systematically improve the efficiency of parallel tempering simulations. We show that by adapting the number of sweeps between replica exchanges to the canonical autocorrelation time, the average…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
We present a study of the parallel tempering (replica exchange) Monte Carlo method, with special focus on the feedback-optimized parallel tempering algorithm, used for generating an optimal set of simulation temperatures. This method is…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Conventional simulations of complex systems in the canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble overcomes this difficulty by performing a random walk in potential energy space and other…
In the realm of statistical mechanics, it has been established that there is no distinction between the micro-canonical and canonical ensembles in the thermodynamic limit. However, this paradigm may alter when addressing statistical…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
The experimental investigation of matter under extreme densities and temperatures as they occur for example in astrophysical objects and nuclear fusion applications constitutes one of the most active frontiers at the interface of material…
We propose two efficient algorithms for configurational sampling of systems with rough energy landscape. The first one is a new method for the determination of the multicanonical weight factor. In this method a short replica-exchange…
Boson Sampling is a computational task strongly believed to be hard for classical computers, but efficiently solvable by orchestrated bosonic interference in a specialised quantum computer. Current experimental schemes, however, are still…
With the exception of superselection rules, there are no known explicit violations of the Principle of quantum Superposition. However, quantum measurement and the emergence of classicality seem to imply that the Principle of Superposition…
Thermalization of classical fields is investigated in a \phi^4 scalar field theory in 1+1 dimensions, discretized on a lattice. We numerically integrate the classical equations of motion using initial conditions sampled from various…
Advances in techniques for thermal sampling in classical and quantum systems would deepen understanding of the underlying physics. Unfortunately, one often has to rely solely on inexact numerical simulation, due to the intractability of…
The accurate interpretation of experiments with matter at extreme densities and pressures is a notoriously difficult challenge. In a recent work [T.~Dornheim et al., Nature Comm. (in print), arXiv:2206.12805], we have introduced a formally…
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
Diffusion models are a remarkably effective way of learning and sampling from a distribution $p(x)$. In posterior sampling, one is also given a measurement model $p(y \mid x)$ and a measurement $y$, and would like to sample from $p(x \mid…
It is a long-standing challenge to accurately and efficiently compute thermodynamic quantities of many-body systems at thermal equilibrium. The conventional methods, e.g., Markov chain Monte Carlo, require many steps to equilibrate. The…
Extracting the kinetic properties of a system whose dynamics depend on the pH of the environment with which it exchanges energy and atoms requires sampling the Grand Canonical Ensemble. As an alternative, we present a novel strategy that…
The use of excessively long timesteps in dissipative particle dynamics simulations may produce simulation artifacts due to the generation of configurations which are not representative of the desired canonical ensemble. The configurational…