Related papers: ms2: A molecular simulation tool for thermodynamic…
Classical Molecular Dynamics (MD) simulations provide insight on the properties of many soft-matter systems. In some situations it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
In this paper, we develop a simulation-based approach to optimisation with multi-modal functions using slice sampling. Our method specifies the objective function as an energy potential in a Boltzmann distribution and then we use auxiliary…
Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…
Quantum-based molecular dynamics (QMD) is a highly accurate and transferable method for material science simulations. However, the time scales and system sizes accessible to QMD are typically limited to picoseconds and a few hundred atoms.…
Colliding flows are a commonly used scenario for the formation of molecular clouds in numerical simulations. Due to the thermal instability of the warm neutral medium, turbulence is produced by cooling. We carry out a two-dimensional…
We show how to evaluate mobility profiles, characterizing the transport of confined fluids under a perturbation, from equilibrium molecular simulations. The correlation functions derived with the Green-Kubo formalism are difficult to sample…
Reporting extensions of a recently developed approach to density functional theory with correct long-range be-havior (Phys. Rev. Lett. 94, 043002 (2005)). The central quantities are a splitting functional gamma[n] and a complementary…
We present SymPhas 2.0, a major update of the compile-time symbolic algebra simulation framework SymPhas for phase-field and reaction-diffusion models. This release introduces significant expansions and enhancements that enable the…
We propose and use a novel, hybrid Monte Carlo algorithm that combines configurational bias particle swaps with parallel tempering. We use this new method to simulate a standard model of a glass forming binary mixture above and below the…
Building on our previously introduced Multi-cell Monte Carlo (MC)^2 method for modeling phase coexistence, this paper provides important improvements for efficient determination of phase equilibria in solids. The (MC)^2 method uses multiple…
Molecular dynamics facilitates the simulation of a complex system to be analyzed at molecular and atomic levels. Simulations can last a long period of time, even months. Due to this cause the graphics processing units (GPUs) and multi-core…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
M2C (Multiphysics Modeling and Computation) is an open-source software for simulating multi-material fluid flows and fluid-structure interactions under extreme conditions, such as high pressures, high temperatures, shock waves, and large…
A Modified Associate Formalism is proposed for thermodynamic modelling of solution phases. The approach is free from the entropy paradox described by L\"{u}ck et al. (Z. Metallkd. 80 (1989) pp. 270--275). The model is considered in its…
Using machine learning (ML) to construct interatomic interactions and thus potential energy surface (PES) has become a common strategy for materials design and simulations. However, those current models of machine learning interatomic…
This paper presents Fossil 2.0, a new major release of a software tool for the synthesis of certificates (e.g., Lyapunov and barrier functions) for dynamical systems modelled as ordinary differential and difference equations. Fossil 2.0 is…
As with many parts of the natural sciences, machine learning interatomic potentials (MLIPs) are revolutionizing the modeling of molecular crystals. However, challenges remain for the accurate and efficient calculation of sublimation…
In conventional molecular simulation, metastable structures often survive over considerable computational time, resulting in difficulties in simulating equilibrium states. In order to overcome this difficulty, here we propose a newly…
Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…