Related papers: Analyzing and biasing simulations with PLUMED
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
Accurate, yet computationally efficient energy functions are essential for state-of-the art molecular dynamics (MD) studies of condensed phase systems. Here, a generic workflow based on a combination of machine learning-based and empirical…
Computer simulations of inhomogeneous soft matter systems often require accurate methods for computing the local pressure. We present a simple derivation, based on the virial relation, of two equivalent expressions for the local (atomistic)…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
We review and discuss recent advances in the simulation of bulk critical phenomena in model fluids. In particular we emphasise the extensions to finite-size scaling theory needed to cope with the lack of symmetry between coexisting fluid…
Massively-parallel molecular dynamics simulation is applied to systems containing electrolytes, vapour-liquid interfaces, and biomolecules in contact with water-oil interfaces. Novel molecular models of alkali halide salts are presented and…
Incorporating computational fluid dynamics in the design process of jets, spacecraft, or gas turbine engines is often challenged by the required computational resources and simulation time, which depend on the chosen physics-based…
Many applications of computational fluid dynamics require multiple simulations of a flow under different input conditions. In this paper, a numerical algorithm is developed to efficiently determine a set of such simulations in which the…
A dynamical system involving a driven pendulum filled with liquid, is analyzed in the present paper series. The study of such a system is conducted in order to understand energy dissipation resulting from the shallow water sloshing and…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
A new approach to simulating warm and hot dense matter that combines density functional theory based calculations of the electronic structure to classical molecular dynamics simulations with pair interaction potentials is presented. The new…
Despite the significant role of turbomachinery in fluid-based energy transfer, precise simulation of rotating solid objects with complex geometry is a challenging task. In the present study, the volume penalization method (VPM) is combined…
Analyzing large volumes of high-dimensional data requires dimensionality reduction: finding meaningful low-dimensional structures hidden in their high-dimensional observations. Such practice is needed in atomistic simulations of complex…
Efficient simulations of quantum evolutions of spin-1/2 systems are relevant for ensemble quantum computation as well as in typical NMR experiments. We propose an efficient method to calculate the dynamics of an observable provided that the…
Metaheuristic algorithms, widely used for solving complex non-convex and non-differentiable optimization problems, often lack a solid mathematical foundation. In this review, we explore how concepts and methods from kinetic theory can offer…
We present a method which extends Monte Carlo studies to situations that require a large dynamic range in particle number. The underlying idea is that, in order to calculate the collisional evolution of a system, some particle interactions…
In this paper a new multiscale modeling technique is proposed. It relies on a recently introduced measure-theoretic approach, which allows to manage the microscopic and the macroscopic scale under a unique framework. In the resulting…
Molecular dynamics simulations are used to model the thermal properties of a fluid containing solid nanoparticles (nanofluid). The flexibility of molecular simulation allows us to consider the effects of particle mass, particle-particle and…