相关论文: Single molecule pulling with large time steps

A two-electron one-dimensional model of a heteroatomic molecule composed of two open-shell atoms is considered. Including only two electrons isolates and examines the effect that the highest occupied molecular orbital has on the Kohn-Sham…

Single-molecule force spectroscopy experiments, as well as a number of other physical systems, are governed by thermally activated transitions out of a metastable state under the action of a steadily increasing external force. The main…

We show that the smoothed particle hydrodynamics (SPH) method, used with individual time-steps in the way described in the literature, cannot handle strong explosion problems correctly. In the individual time-step scheme, particles…

Discrete Element Methods (DEM), i.e.~the simulation of many rigid particles, suffer from very stiff differential equations plus multiscale challenges in space and time. The particles move smoothly through space until they interact almost…

The mechanical unfolding of an engineered protein composed of eight domains of Ig27 is investigated by using atomic force microscopy. Exploiting a fluctuation relation, the equilibrium free energy as a function of the molecule elongation is…

Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…

We present a statistical mechanics analysis of the finite-size elasticity of biopolymers, consisting of domains which can exhibit transitions between more than one stable state at large applied force. The constant-force (Gibbs) and…

Nonequilibrium experiments of single biomolecules such as force-induced unfolding reveal details about a few degrees of freedom of a complex system. Molecular dynamics simulations can provide complementary information, but exploration of…

We carried out three-dimensional simulations, with about 1.4 million particles, of phase segregation in a low density binary fluid mixture, described mesoscopically by energy and momentum conserving Boltzmann-Vlasov equations. Using a…

A simple similarity has been proposed for kinetic (e.g., particle-in-cell) simulations of plasma transport that can effectively address the longstanding challenge of reconciling the tiny Debye length with the vast system size. This applies…

A model multilevel molecule described by two sets of rotational internal energy levels of different parity and degenerate ground states, coupled by a constant interaction, is considered, by assuming that the random collisions in a gas of…

Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…

Single-molecule stretching experiments on DNA, RNA, and other biological macromolecules opened up the possibility of an impressive progress in many fields of Life and Medical sciences. The reliability of such experiments may be crucially…

A molecular dynamics simulation of the demixing process of a binary complex plasma is analysed and the role of distinct interaction potentials is discussed by using morphological Minkowski tensor analysis of the minority phase domain growth…

Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…

Most material properties of great physical interest are directly related to nuclear dynamics, e.g. the ionic thermal conductivity, Raman/IR vibrational spectra, inelastic X-ray, and Neutron scattering. A theory able to compute from first…

This work deals with the numerical approximation of plasmas which are confined by the effect of a fast oscillating magnetic field (see \cite{Bostan2012}) in the Vlasov model. The presence of this magnetic field induces oscillations (in…

We simulate a balanced attractively interacting two-component Fermi gas in a one-dimensional lattice perturbed with a moving potential well or barrier. Using the time-evolving block decimation method, we study different velocities of the…

Cryogenic buffer gas cells have been a workhorse for the cooling of molecules in the last decades. The straightforward sympathetic cooling principle makes them applicable to a huge variety of different species. Notwithstanding this success,…

With the help of force spectroscopy, several analytical theories aim at estimating the rate coefficient of folding for various proteins. Nevertheless, a chief bottleneck lies in the fact that there is still no perfect consensus on how does…