Related papers: Efficient sampling in complex materials at finite …
A densely packed granular system is an example of an out-of-equilibrium system in the jammed state. It has been a longstanding problem to determine whether this class of systems can be described by concepts arising from equilibrium…
We propose a method for efficient simulations in extended ensembles, useful, e.g., for the study of problems with complex energy landscapes and for free energy calculations. The main difficulty in such simulations is the estimation of the a…
For quantum many-body systems in one dimension, computational complexity theory reveals that the evaluation of ground-state energy remains elusive on quantum computers, contrasting the existence of a classical algorithm for temperatures…
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…
Quantum thermodynamic process involves manipulating and controlling quantum states to extract energy or perform computational tasks with high efficiency. There is still no efficientgeneral method to theoretically quantify the effect of the…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Sampling from flat energy or density distributions has proven useful in equilibrating complex systems with large energy barriers. Several thermostats and barostats are presented to sample these flat distributions by molecular dynamics.…
Integrated tempering sampling (ITS) method is an approach to enhance the sampling over a broad range of energies and temperatures in computer simulations. In this paper, a new version of integrated tempering sampling method is proposed. In…
The link between the energy surface of bulk systems and their dynamical properties is generally difficult to establish. Using the activation-relaxation technique (ART nouveau), we follow the change in the barrier distribution of a model of…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
At low temperatures, dynamics in amorphous silicon occurs through a sequence of discrete activated events that locally reorganize the topological network. Using the activation-relaxation technique, a data base containing over 8000 such…
Ensuring a satisfactory statistical convergence of anharmonic thermodynamic properties requires sampling of many atomic configurations, however the methods to obtain those necessarily produce correlated samples, thereby reducing the…
We investigate the effective temperature of a harmonic chain whose two ends are coupled to two baths at different temperatures. We propose to take the weighted average temperature as the effective temperature of the system. The weight…
Simulating the nonequilibrium dynamics of thermal states is a fundamental problem across scales from high energy to condensed matter physics. Quantum computers may provide a way to solve this problem efficiently. Preparing a thermal state…
In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy…
The weighted ensemble (WE) method, an enhanced sampling approach based on periodically replicating and pruning trajectories in a set of parallel simulations, has grown increasingly popular for computational biochemistry problems, due in…
Warm dense matter (WMD) describes an intermediate phase, between condensed matter and classical plasmas, found in natural and man-made systems. In a laboratory setting, WDM needs to be created dynamically. It is typically laser or…
Matrix element reweighting is a powerful experimental technique widely employed to maximize the amount of information that can be extracted from a collider data set. We present a procedure that allows to automatically evaluate the weights…
We develop a perturbation theory of quantum (and classical) master equations with slowly varying parameters, applicable to systems which are externally controlled on a time scale much longer than their characteristic relaxation time. We…
We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…