Related papers: A Second Look at Canonical Sampling of Biomolecule…
A comprehensive description of molecular electron transfer reactions is essential for our understanding of fundamental phenomena in bio-energetics and molecular electronics. Experimental studies of molecular systems in condensed-phase…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
In complex systems with many degrees of freedom such as peptides and proteins there exist a huge number of local-minimum-energy states. Conventional simulations in the canonical ensemble are of little use, because they tend to get trapped…
This paper is concerned with tuning friction and temperature in Langevin dynamics for fast sampling from the canonical ensemble. We show that near-optimal acceleration is achieved by choosing friction so that the local quadratic…
Speculative sampling is a popular technique for accelerating inference in Large Language Models by generating candidate tokens using a fast draft model and accepting or rejecting them based on the target model's distribution. While…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
Many experimentally-accessible, finite-sized interacting quantum systems are most appropriately described by the canonical ensemble of statistical mechanics. Conventional numerical simulation methods either approximate them as being coupled…
It is often difficult to quantitatively determine if a new molecular simulation algorithm or software properly implements sampling of the desired thermodynamic ensemble. We present some simple statistical analysis procedures to allow…
We propose a new multi-scale molecular dynamics simulation method which can achieve high accuracy and high sampling efficiency simultaneously without aforehand knowledge of the coarse grained (CG) potential and test it for a biomolecular…
We develop a novel method of replica-exchange molecular dynamics (REMD) simulation, mass-scaling REMD (MSREMD) method, which improves trajectory accuracy at high temperatures, and thereby contributes to numerical stability. In addition, the…
Recently, there has been a growing interest in the usage of mm-scale composites of plasmonic nanoparticles for enhancing the rates of chemical reactions; the effect was shown recently to be predominantly associated with the elevated…
Characterizing exoplanetary atmospheres via Bayesian retrievals requires assuming some chemistry model, such as thermochemical equilibrium or parameterized abundances. The higher-resolution data offered by upcoming telescopes enables more…
Heat transfer can differ distinctly at the nanoscale from that at the macroscale. Recent advancement in computational and experimental techniques has enabled a large number of interesting observations and understanding of heat transfer…
We introduce and illustrate a number of performance measures for rare-event sampling methods. These measures are designed to be of use in a variety of expanded ensemble techniques including parallel tempering as well as infinite and partial…
Realistic simulations of experiments at large scale photon facilities, such as optical laser laboratories, synchrotrons, and free electron lasers, are of vital importance for the successful preparation, execution, and analysis of these…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…
We discuss the application of techniques of quantum estimation theory and quantum metrology to thermometry. The ultimate limit to the precision at which the temperature of a system at thermal equilibrium can be determined is related to the…
The simulation of rare events is one of the key problems in atomistic simulations. Towards its solution a plethora of methods have been proposed. Here we combine two such methods metadynamics and inte-grated tempering sampling. In…
When addressing the thermodynamics of finite-sized systems, one must specify whether one wants to fix conserved charges to a sharp value or whether one is content to fix their thermodynamic average. In other words, contrary to the…