相关论文: Single molecule pulling with large time steps
We perform molecular dynamics simulations of a supported molecular thin film. By varying thickness and temperature, we observe anisotropic mobility as well as strong gradients of both the vibrational motion and the structural relaxation…
We present Cahn-Hilliard and Allen-Cahn numerical integration algorithms that are unconditionally stable and so provide significantly faster accuracy-controlled simulation. Our stability analysis is based on Eyre's theorem and unconditional…
We propose a time discretization scheme for a class of ordinary differential equations arising in simulations of fluid/particle flows. The scheme is intended to work robustly in the lubrication regime when the distance between two particles…
We demonstrate experimentally that, applying optimal protocols which drive the system between two equilibrium states characterized by a free energy difference $\Delta F$, we can maximize the probability of performing the transition between…
Molecular dynamics simulation is used to investigate the crystallization of a classical two-dimensional electron system, in which electrons interact with the Coulomb repulsion. From the positional and the orientational correlation…
In recent years single molecule force spectroscopy has opened a new avenue to provide profiles of the complex energy landscape of biomolecules. In this field, quantitative analyses of the data employing sound theoretical models, have played…
We describe a novel coarse-grained simulation method for modelling the dynamics of globular macromolecules, such as proteins. The macromolecule is treated as a continuum that is subject to thermal fluctuations. The model includes a…
A system of a solvated canonical B-DNA of 12 base pairs with the specified sequence is initially equilibrated in a state of zero external force $f$ acting on it. After equilibration, a switching experiment is performed over the system by…
Brownian dynamics simulations are used to study the detachment of a particle from a substrate. Although the model is simple and generic, we attempt to map its energy, length and time scales onto a specific experimental system, namely a bead…
We present a new method for simulating crystal growth by energetic beam deposition. The method combines a Kinetic Monte-Carlo simulation for the thermal surface diffusion with a small scale molecular dynamics simulation of every single…
Jarzynski's equality provides an elegant and powerful tool to directly compute differences in free energy in Monte Carlo simulations and it can be readily extended to lattice gauge theories to compute a large set of physically interesting…
A multilevel approach to sample the potential energy surface in a path integral formalism is proposed. The purpose is to reduce the required number of ab initio evaluations of energy and forces in ab initio path integral molecular dynamics…
The Jarzynski equality and the fluctuation theorem relate equilibrium free energy differences to non-equilibrium measurements of the work. These relations extend to single-molecule experiments that have probed the finite-time thermodynamics…
The past two decades witnessed important developments in the field of non-equilibrium statistical mechanics. Among these developments, the Jarzynski equality, being a milestone following the landmark work of Clausius and Kelvin, stands out.…
We introduce a method for classical trajectory calculations to simulate collisions between atoms and large rigid asymmetric-top molecules. Using this method, we investigate the formation of molecule-helium complexes in buffer-gas cooling…
The weighted ensemble (WE) simulation strategy provides unbiased sampling of non-equilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady state behavior.…
We study the motion of an overdamped colloidal particle in a time-dependent non-harmonic potential. We demonstrate the first law-like balance between applied work, exchanged heat, and internal energy on the level of a single trajectory. The…
We present a new time-stepping criterion for N-body simulations that is based on the true dynamical time of a particle. This allows us to follow the orbits of particles correctly in all environments since it has better adaptivity than…
Large molecular dynamics simulations (millions of atoms, tens of microseconds, thousands of processors) hit the strong scalability wall: simulation on twice as many processors does not take half the time. Inspired by large N-body space…
The excess free energy of a molecular cluster is a key quantity in models of the nucleation of droplets from a metastable vapour phase; it is often viewed as the free energy arising from the presence of an interface between the two phases.…