Related papers: Efficient sampling in complex materials at finite …
While the dynamics of many complex systems is dominated by activated events, there are very few simulation methods that take advantage of this fact. Most of these procedures are restricted to relatively simple systems or, as with the…
The dynamics of many atomic systems is controlled by activated events taking place on a time scale which is long compared to that associated with thermal vibrations. This often places problems of interest outside the range of standard…
Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective…
We investigate the theoretical foundations of the simulated tempering method and use our findings to design efficient algorithms. Employing a large deviation argument first used for replica exchange molecular dynamics [Plattner et al., J.…
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…
While recent work towards the development of tight-binding and ab-initio algorithms has focused on molecular dynamics, Monte Carlo methods can often lead to better results with relatively little effort. We present here a multi-step Monte…
Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies…
Jamming is a common feature of out of equilibrium systems showing slow relaxation dynamics. Here we review our efforts in understanding jamming in granular materials using experiments and computer simulations. We first obtain an estimation…
Temperature Accelerated Sliced Sampling (TASS) is an efficient method to compute high dimensional free energy landscapes. The original TASS method employs the Weighted Histogram Analysis Method (WHAM) which is an iterative post-processing…
Umbrella sampling is an efficient method for the calculation of free energy changes of a system along well-defined reaction coordinates. However, when multiple parallel channels along the reaction coordinate or hidden barriers in directions…
We describe a method that focuses sampling effort on a user-defined selection of a large system, which can lead to substantial decreases in computational effort by speeding up the calculation of nonbonded interactions. A naive approach can…
We present an efficient sampling method for computing a partition function and accelerating configuration sampling. The method performs a random walk in the $\lambda$ space, with $\lambda$ being any thermodynamic variable that characterizes…
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…
Understanding the thermodynamic properties of quantum systems is essential for developing energy-efficient quantum technologies. In this regard, this work explores the application of quantum computational methods to study the quantum…
The recently introduced nested sampling algorithm allows the direct and efficient calculation of the partition function of atomistic systems. We demonstrate its applicability to condensed phase systems with periodic boundary conditions by…
We review a selection of methods for performing enhanced sampling in molecular dynamics simulations. We consider methods based on collective variable biasing and on tempering, and offer both historical and contemporary perspectives. In…
The equations of the temperature-accelerated molecular dynamics (TAMD) method for the calculations of free energies and partition functions are analyzed. Specifically, the exponential convergence of the law of these stochastic processes is…
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…
Fast and accurate sampling method is in high demand, in order to bridge the large gaps between molecular dynamic simulations and experimental observations. Recently, integrated tempering enhanced sampling method (ITS) has been proposed and…
Using very long molecular dynamics simulation runs, temperature protocols spanning up to five orders of magnitude in time-scales are performed to investigate thermally activated structural relaxation in a model amorphous solid. The…