Related papers: Coupling different levels of resolution in molecul…
A new time discretization scheme for the numerical simulation of two-phase flow governed by a thermodynamically consistent diffuse interface model is presented. The scheme is consistent in the sense that it allows for a discrete in time…
We consider models of relativistic matter containing sharp interfaces across which the matter model changes. These models will be relevant for neutron stars with crusts, phase transitions, or for viscous boundaries where the length scale is…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…
A main task in cryo-electron microscopy single particle reconstruction is to find a three-dimensional model of a molecule given a set of its randomly oriented and positioned noisy projection-images. In this work, we propose an algorithm for…
Diffusive molecular dynamics is a novel model for materials with atomistic resolution that can reach diffusive time scales. The main ideas of diffusive molecular dynamics are to first minimize an approximate variational Gaussian free energy…
A kinetic approach for the evolution of ultracold neutral plasmas including interionic correlations and the treatment of ionization/excitation and recombination/deexcitation by rate equations is described in detail. To assess the…
A great many observables seen in intermediate energy heavy ion collisions can be explained on the basis of statistical equilibrium. Calculations based on statistical equilibrium can be implemented in microcanonical ensemble (energy and…
We extend the use of the adaptive resolution method (AdResS) in its Grand Canonical-like version (GC-AdResS) to the molecular dynamics simulation of 1,3-dimethylimidazolium chloride. We show that the partitioning of the total system in a…
Symmetry preserving difference schemes approximating second and third order ordinary differential equations are presented. They have the same three or four-dimensional symmetry groups as the original differential equations. The new…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
Metastable structures in macromolecular and colloidal systems are non-equilibrium states that often have long lifetimes and cause difficulties in simulating equilibrium. In order to escape from the long-lived metastable states, we propose a…
The Kohn-Sham (KS) equations determine, in a self-consistent way, the particle density of an interacting fermion system at thermal equilibrium. We consider a situation when the KS equations are known to have a unique solution at high…
Local master equations are a widespread tool to model open quantum systems, especially in the context of many-body systems. These equations, however, are believed to lead to thermodynamic anomalies and violation of the laws of…
Recent research has extended methods from the fields of thermodynamics and statistical mechanics into other disciplines. Most notably, one recent work creates a unified theoretical framework to understand evolutionary biology, machine…
The accurate simulation of collapsed objects requires that a huge range of spatial scales be well resolved if the result is not to be contaminated by numerically induced fragmentation. In this context, `insufficient resolution' means…
MADNESS (multiresolution adaptive numerical environment for scientific simulation) is a high-level software environment for solving integral and differential equations in many dimensions that uses adaptive and fast harmonic analysis methods…
It is shown that the partial temperatures of a homogeneous multicomponent gas mixture in the thermodynamical equilibrium cannot be equal to each other. New general solutions for equilibrium distribution functions of the multicomponent…
We consider the numerical solution of coupled volume-surface reaction-diffusion systems having a detailed balance equilibrium. Based on the conservation of mass, an appropriate quadratic entropy functional is identified and an…
Photo-induced processes are fundamental in nature, but accurate simulations are seriously limited by the cost of the underlying quantum chemical calculations, hampering their application for long time scales. Here we introduce a method…
The preparation of thermal equilibrium states is important for the simulation of condensed-matter and cosmology systems using a quantum computer. We present a method to prepare such mixed states with unitary operators, and demonstrate this…