Related papers: A combined on-the-fly/interpolation procedure for …
Modelling has become a third distinct line of scientific enquiry, alongside experiments and theory. Molecular dynamics (MD) simulations serve to interpret, predict and guide experiments and to test and develop theories. A major limiting…
The equilibrium phase behavior of microphase-forming systems is notoriously difficult to obtain because of the extended metastability of their modulated phases. In this paper we present a systematic simulation methodology for studying…
The system-level dynamics of multivalent biomolecular interactions can be simulated using a rule-based kinetic Monte Carlo method in which a rejection sampling strategy is used to generate reaction events. This method becomes inefficient…
Techniques for simulating molecules whose conformations satisfy constraints are presented. A method for selecting appropriate moves in Monte Carlo simulations is given. The resulting moves not only obey the constraints but also maintain…
The current capacity of computers makes it possible to perform simulations of small systems with portable, explicit-solvent potentials achieving high degree of accuracy. However, simplified models must be employed to exploit the behaviour…
We present a systematic framework for shortening and automating molecular dynamics equilibration through improved position initialization methods and uncertainty quantification analysis, using the Yukawa one-component plasma as an exemplar…
Constructing more expressive ansatz has been a primary focus for quantum Monte Carlo, aimed at more accurate \textit{ab initio} calculations. However, with more powerful ansatz, e.g. various recent developed models based on neural-network…
Proposed here is a dynamic Monte-Carlo algorithm that is efficient in simulating dense systems of long flexible chain molecules. It expands on the configurational-bias Monte-Carlo method through the simultaneous generation of a large set of…
We discuss the efficiency of Monte Carlo methods in solving continuum radiative transfer problems. The sampling of the radiation field and convergence of dust temperature calculations in the case of optically thick clouds are both studied.…
Molecular simulations in an open environment, involving ion exchange, are necessary to study various systems, from biosystems to confined electrolytes. However, grand-canonical simulations are often computationally demanding in condensed…
We present a formalism of the transition matrix Monte Carlo method. A stochastic matrix in the space of energy can be estimated from Monte Carlo simulation. This matrix is used to compute the density of states, as well as to construct…
We present an elementary and self-contained account of the analogies existing between classical diffusion and the imaginary-time evolution of quantum systems. These analogies are used to develop a new quantum simulation method which allows…
A prescription is presented for the interpolation between multi-dimensional distribution templates based on one or multiple model parameters. The technique uses a linear combination of templates, each created using fixed values of the…
Simulation studies are used to evaluate and compare the properties of statistical methods in controlled experimental settings. In most cases, performing a simulation study requires knowledge of the true value of the parameter, or estimand,…
A Monte Carlo simulator is presented to reproduce data of nucleus-nucleus interactions at high energies. The program is designed in a microscopic point of view, where the cascade approach is applied. Moreover, each nucleon from both the…
A Monte Carlo simulation program is presented which can be used to determine the small-$x$ evolution of a heavy onium using Mueller's colour dipole formulation, giving the full distribution of dipoles in rapidity and impact parameter.…
Due to a hard dependency between time steps, large-scale simulations of gas using the Direct Simulation Monte Carlo (DSMC) method proceed at the pace of the slowest processor. Scalability is therefore achievable only by ensuring that the…
Understanding the spatio-temporal evolution of radiolytic species created by high-energy electrons in water underpins key applications from radiotherapy and nuclear safety to environmental processing and electron microscopy. Here, using the…
Quantum Monte Carlo methods find fruitful application in large shell model problems. These methods reduce the imaginary-time many-body evolution operator to a coherent superposition of one-body evolutions in a fluctuating one-body field;…
We present a generic reweighting method for nonequilibrium Markov processes. With nonequilibrium Monte Carlo simulations at a single temperature, one calculates the time evolution of physical quantities at different temperatures, which…