Related papers: Coupling different levels of resolution in molecul…
A method for integrating the chemical equations associated with nuclear combustion at high temperature is presented and extensively checked. Following the idea of E. M\"uller, the feedback between nuclear rates and temperature was taken…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Equilibrium sampling of biomolecules remains an unmet challenge after more than 30 years of atomistic simulation. Efforts to enhance sampling capability, which are reviewed here, range from the development of new algorithms to…
In adaptive resolution simulations, molecular fluids are modeled employing different levels of resolution in different subregions of the system. When traveling from one region to the other, particles change their resolution on the fly. One…
Quantum simulation of chemical systems is one of the most promising near-term applications of quantum computers. The variational quantum eigensolver, a leading algorithm for molecular simulations on quantum hardware, has a serious…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the…
The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry,…
In this paper, we investigate the use of variational quantum algorithms for simulating the thermodynamic properties of dinuclear metal complexes. Our study highlights the potential of quantum computing to transform advanced simulations and…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
The characterisation of the atomic and molecular hydrogen content of high-redshift galaxies is a major observational challenge that will be addressed over the coming years with a new generation of radio telescopes. We investigate this…
We model the dynamics of a closed quantum system brought out of mechanical equilibrium, undergoing a non-driven, spontaneous, thermodynamic transformation. In particular, we consider a quantum particle in a box with a moving and insulating…
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 perform molecular-dynamics simulations of a molecular system in supercooled states for different values of inertia parameters to provide evidence that the long-time dynamics depends only on the equilibrium structure. This observation is…
The recent results attained from a thermodynamically conceived numerical scheme applied on wave propagation in viscoelastic/rheological solids are generalized here, both in the sense that the scheme is extended to four spacetime dimensions…
Our understanding of the physics of biological molecules, such as proteins and DNA, is limited because the approximations we usually apply to model inert materials are not in general applicable to soft, chemically inhomogeneous systems. The…
Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…
Particle-based shape modeling (PSM) is a family of approaches that automatically quantifies shape variability across anatomical cohorts by positioning particles (pseudo landmarks) on shape surfaces in a consistent configuration. Recent…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Considering turbulence is crucial to understanding clouds. However, covering all scales involved in the turbulent mixing of clouds with their environment is computationally challenging, urging the development of simpler models to represent…