Related papers: A Second Look at Canonical Sampling of Biomolecule…
In this work a replica exchange Monte Carlo scheme which considers an extended isobaric-isothermal ensemble with respect to pressure is applied to study hard spheres (HS). The idea behind the proposal is expanding volume instead of…
Replica exchange (RE) is one of the most popular enhanced-sampling simulations technique in use today. Despite widespread successes, RE simulations can sometimes fail to converge in practical amounts of time, e.g., when sampling around…
In complex systems with many degrees of freedom such as spin glass and biomolecular systems, conventional simulations in canonical ensemble suffer from the quasi-ergodicity problem. A simulation in generalized ensemble performs a random…
Simulation within the grand canonical ensemble is the method of choice for accurate studies of first order vapour-liquid phase transitions in model fluids. Such simulations typically employ sampling that is biased with respect to the…
Molecular dynamics simulations are widely used across chemistry, physics, and biology, providing quantitative insight into complex processes with atomic detail. However, their limited timescale of a few microseconds is a significant…
We combine replica exchange (parallel tempering) with normalizing flows, a class of deep generative models. These two sampling strategies complement each other, resulting in an efficient strategy for sampling molecular systems characterized…
We show that the acceptance probability for swaps in the parallel tempering Monte Carlo method for classical canonical systems is given by a universal function that depends on the average statistical fluctuations of the potential and on the…
Every time a chemical reaction occurs, an energy exchange between reactants and environment exists, which is defined as the enthalpy of the reaction. In the last decades, research has resulted in an increasing number of devices at the…
In this micro-canonical simulation the temperature and also the specific heat are determined as averages of expressions easy to implement. The XY-chain is studied for a test. The second order transition on a cubic lattice and the first…
We briefly review some of the scientific challenges and epistemological issues related to climate science. We discuss the formulation and testing of theories and numerical models, which, given the presence of unavoidable uncertainties in…
In finite-size scaling analyses of Monte Carlo simulations of second-order phase transitions one often needs an extended temperature/energy range around the critical point. By combining the replica-exchange algorithm with cluster updates…
An improved real-time quantum Monte Carlo procedure is presented and applied to describe the electronic transfer dynamics along molecular chains. The model consists of discrete electronic sites coupled to a thermal environment which is…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
We derive the continuous canonical distribution only by requiring the extensivity of the mean energy and the multiplicative probabilistic composition rule. The derivation is independent of the thermodynamic limit and moreover it does not…
Exchange of biochemical substances is essential way in establishing communication between bacterial cells. It is noticeable that all phases of the process are heavily influenced by perturbations of either internal or external parameters.…
Enhanced sampling algorithms have emerged as powerful methods to extend the utility of molecular dynamics simulations and allow the sampling of larger portions of the configuration space of complex systems in a given amount of simulation…
We discuss a general method of model selection from experimentally recorded time-trace data. This method can be used to distinguish between quantum and classical dynamical models. It can be used in post-selection as well as for real-time…
The replica-exchange Monte-Carlo (RXMC) method is a powerful Markov-chain Monte-Carlo algorithm for sampling from multi-modal distributions, which are challenging for conventional methods. The sampling efficiency of the RXMC method depends…
Precise temperature measurements on systems of few ultracold atoms is of paramount importance in quantum technologies, but can be very resource-intensive. Here, we put forward an adaptive Bayesian framework that substantially boosts the…
Templated copying is the central operation by which biology produces complex molecules. Cells copy sequence information from DNA to RNA and on into proteins, which are the molecules responsible for the function and regulation of cellular…