Related papers: Coupling different levels of resolution in molecul…
Lattice Boltzmann simulations have been very successful in simulating liquid-gas and other multi-phase fluid systems. However, the underlying second order analysis of the equation of motion has long been known to be insufficient to…
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 molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
When applied to binary solutions, thermal gradients lead to the generation of concentration-gradients and thus to inhomogeneous systems. While being known for more than 150 years, the molecular origins for this phenomenon are still debated,…
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a…
Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms,…
Thermodynamic simulation of chemical and metallurgical systems is the only method to predict their equilibrium composition and is the most important application of chemical thermodynamics. The conventional strategy of simulation is always…
In this work, we provide a detailed theoretical analysis, supported by numerical tests, of the reliability of the adaptive resolution simulation (AdResS) technique in sampling the Grand Canonical ensemble. We demonstrate that the correct…
Numerical computations have become a pillar of all modern quantitative sciences. Any computation involves modeling--even if often this step is not made explicit--and any model has to neglect details while still being physically accurate.…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…
The simulation of open molecular systems requires explicit or implicit reservoirs of energy and particles. Whereas full atomistic resolution is desired in the region of interest, there is some freedom in the implementation of the…
Accurate simulations of atomistic systems from first principles are limited by computational cost. In high-throughput settings, machine learning can reduce these costs significantly by accurately interpolating between reference…
Cosmic structure simulations have improved enormously over the past decade, both in terms of the resolution which can be achieved, and with the addition of hydrodynamic and other techniques to formerly purely gravitational methods. This is…
A large number of powerful, high-quality, and open-source simulation packages exist to efficiently perform molecular dynamics simulations, and their prevalence has greatly accelerated discoveries across a wide range of scientific domains.…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
The earliest molecular dynamics simulations relied on solving the Newtonian or equivalently the Hamiltonian equations of motion for a system. While pedagogically very important as the total energy is preserved in these simulations, they…
Simulations that couple different classical molecular models in an adaptive way by changing the number of degrees of freedom on the fly, are available within reasonably consistent theoretical frameworks. The same does not occur when it…
Quantum thermodynamics with open systems is often based on the quantum optical weak-coupling master equation or on operational repeated interaction models, whereas early works on thermalisation and on decoherence theory were mostly…
Machine learning models have emerged as a very effective strategy to sidestep time-consuming electronic-structure calculations, enabling accurate simulations of greater size, time scale and complexity. Given the interpolative nature of…
Classical molecular dynamics simulations of hydrogen plasmas have been performed with emphasis on the analysis of equilibration process. Theoretical basis of simulation model as well as numerically relevant aspects -- such as the proper…