相关论文: Single molecule pulling with large time steps

Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…

Polymers confined to a narrow channel are subject to strong entropic forces that tend to drive the molecules apart. In this study, we use Monte Carlo computer simulations to study the segregation behavior of two flexible hard-sphere…

In order to understand the nuclei which develop during the course of protein folding and unfolding, we examine phase segregation of a single heteropolymer chain which occurs in equilibrium. These segregated conformations are characterized…

The connection between work and changes in the Hamiltonian for a system with a time-dependent Hamiltonian has recently been called into question, casting doubt on the usefulness of the Jarzynski equality for calculating free energy changes.…

A system--bath (SB) model is considered to examine the Jarzynski equality in the fully quantum regime. In our previous paper [J. Chem. Phys. 153 (2020) 234107], we carried out "exact" numerical experiments using hierarchical equations of…

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…

An adpative integration technique for time advancement of particle motion in the context of coupled computational fluid dynamics (CFD) - discrete element method (DEM) simulations is presented in this work. CFD-DEM models provide an accurate…

We introduce a new way to study molecular evolution within well-established Hamilton-Jacobi formalism, showing that for a broad class of fitness landscapes it is possible to derive dynamics analytically within the $1/N$-accuracy, where $N$…

Time-dependent density functional theory, proposed recently in the context of atomic diffusion and non-equilibrium processes in solids, is tested against Monte Carlo simulation. In order to assess the basic approximation of that theory, the…

We present a new formalism to calculate phase-space acceptance in a Zeeman decelerator. Using parameters closely mimicking previous Zeeman deceleration experiments, this approach reveals a hitherto unconsidered velocity dependence of the…

We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…

In many systems, the time scales of the microscopic dynamics and macroscopic dynamics of interest are separated by many orders of magnitude. Examples abound, for instance nucleation, protein folding, and chemical reactions. For these…

The free-energy difference $\Delta F$ between two high-dimensional systems is notoriously difficult to compute, but very important for many applications, such as drug discovery. We demonstrate that an unconventional definition of work…

Applying the method from recently developed fluctuation theorems to the stochastic dynamics of single macromolecules in ambient fluid at constant temperature, we establish two Jarzynski-type equalities: (1) between the log-mean-exponential…

Recent years have witnessed major advances in our understanding of nonequilibrium processes. The Jarzynski equality, for example, provides a link between equilibrium free energy differences and finite-time, nonequilibrium dynamics. We…

One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…

Monte Carlo computer simulations are used to study the conformational free energy of a folded polymer confined to a long cylindrical tube. The polymer is modeled as a hard-sphere chain. Its conformational free energy $F$ is measured as a…

The hydration or binding free energy of a drug-like molecule is a key data for early stage drug discovery. Hundreds of thousands of evaluations are needed, which rules out the exhaustive use of atomistic simulations and free energy methods.…

The escape process from the native valley for proteins subjected to a constant stretching force is examined using a model for a Beta-barrel. For a wide range of forces, the unfolding dynamics can be treated as one-dimensional diffusion,…

Relativistic plasmas around compact objects can sometimes be approximated as being force-free. In this limit, the plasma inertia is negligible and the overall dynamics is governed by global electric currents. We present a novel numerical…