Related papers: A pathway towards proper modeling of physical prop…

Simulation schemes that allow to change molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surrounding introduce conceptual problems of thermodynamic consistency. In this work we present…

A scattering model is developed for ultracold molecular collisions, which allows inelastic processes, chemical reactions, and complex formation to be treated in a unified way. All these scattering processes and various combinations of them…

Using molecular simulation to aid in the analysis of neutron reflectometry measurements is commonplace. However, reflectometry is a tool to probe large-scale structures, and therefore the use of all-atom simulation may be irrelevant. This…

We develop a multiscale hybrid scheme for simulations of soft condensed matter systems, which allows one to treat the system at the particle level in selected regions of space, and at the continuum level elsewhere. It is derived…

The microscopic structure of several amorphous substances often reveals complex patterns such as medium- or long-range order, spatial heterogeneity, and even local polycrystallinity. To capture all these features, models usually incorporate…

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…

Ab initio methods for electronic structure of molecules have reached a satisfactory accuracy for calculation of static properties, but remain too expensive for quantum dynamical calculations. We propose an efficient semiclassical method for…

In recent years the machine learning techniques have shown a great potential in various problems from a multitude of disciplines, including materials design and drug discovery. The high computational speed on the one hand and the accuracy…

Recent advances in (scanning) transmission electron microscopy have enabled routine generation of large volumes of high-veracity structural data on 2D and 3D materials, naturally offering the challenge of using these as starting inputs for…

When addressing spatial biological questions using mathematical models, symmetries within the system are often exploited to simplify the problem by reducing its physical dimension. In a reduced-dimension model molecular movement is…

A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…

Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…

Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…

The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…

We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…

Atomic scale simulations are a key element of modern science in that they allow to understand, and even predict, complex physical or chemical phenomena on the basis of the fundamental laws of nature. Among the different existing atomic…

Chemical space which encompasses all stable compounds is unfathomably large and its dimension scales linearly with the number of atoms considered. The success of machine learning methods suggests that many physical quantities exhibit…

Molecular dynamics (MD) is a widely-used tool for simulating the molecular and materials properties. It is a common wisdom that molecular dynamics simulations should obey physical laws and, hence, lots of effort is put into ensuring that…

A new approach for integration of motion in many-body systems of interacting polyatomic molecules is proposed. It is based on splitting time propagation of pseudo-variables in a modified phase space, while the real translational and…

Ab initio simulations are capable of providing detailed information of material behavior at the nanoscale. Simulating experimentally relevant situations is, however, often computationally intense. Using hybrid approaches between ab initio…