Related papers: Single molecule pulling with large time steps
We study self-avoiding walks on the square lattice restricted to a square box of side $L$ weighted by a length fugacity without restriction of their end points. This models a confined polymer in dilute solution. The model admits a phase…
Abridged. Kinetic plasma simulations are nowadays commonly used to study a wealth of non-linear behaviours and properties in laboratory and space plasmas. In particular, in high-energy physics and astrophysics, the plasma usually evolves in…
This article describes nonequilibrium techniques for the calculation of free energies of solids using molecular dynamics (MD) simulations. These methods provide an alternative to standard equilibrium thermodynamic integration methods and…
A molecular level analysis of segmental trajectories obtained from molecular dynamics simulations is used to obtain the full relaxation time spectrum in aging polymer glasses subject to three different deformation protocols. As in…
Hypothesis A prototypical modelling approach is required for a full characterisation of the static and equilibrium dynamical properties of confined ionic liquids (ILs), in order to gain predictive power of properties that are difficult to…
We consider paths of a one-dimensional simple random walk conditioned to come back to the origin after L steps (L an even integer). In the 'pinning model' each path \eta has a weight \lambda^{N(\eta)}, where \lambda>0 and N(\eta) is the…
Extracting equilibrium information from nonequilibrium measurements is a challenge task of great importance in understanding the thermodynamic properties of physical, chemical, and biological systems. The discovery of the Jarzynski equality…
Molecular dynamics computer simulations are used to investigate thedynamics of a binary mixture of charged (Yukawa) particles with a size-ratio of 1:5. We find that the system undergoes a phase transition where the large particles…
Understanding the influence of activity on dense amorphous assemblies is crucial for biological processes such as wound healing, embryogenesis, or cancer progression. Here, we study the effect of self-propulsion forces of amplitude $f_0$…
Through experimental investigation into the behaviour of a polar dielectric working fluid, an ideal quasi-thermodynamic cycle has been established. Particular stages of this cycle are described in terms of a condensed-matter analogue of the…
We have developed and implemented a new quantum molecular dynamics approximation that allows fast and accurate simulations of dense plasmas from cold to hot conditions. The method is based on a carefully designed orbital-free implementation…
We consider several solitons moving in a slowly varying external field. We show that the effective dynamics obtained by restricting the full Hamiltonian to the finite dimensional manifold of $ N$-solitons (constructed when no external field…
The force-assisted desorption kinetics of a macromolecule from adhesive surface is studied theoretically, using the notion of tensile (Pincus) blobs, as well as by means of Monte-Carlo (MC) and Molecular Dynamics (MD) simulations. We show…
Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational…
We study analytically and by means of an off-lattice bead-spring dynamic Monte Carlo simulation model the adsorption kinetics of a single macromolecule on a structureless flat substrate in the regime of strong physisorption. The underlying…
We derive the differential equation describing the time evolution of the work probability distribution function of a stochastic system which is driven out of equilibrium by the manipulation of a parameter. We consider both systems described…
The Jarzynski equality allows the calculation of free-energy differences using values of work measured from nonequilibrium trajectories. The number of trajectories required to accurately estimate free-energy differences in this way grows…
The sequence-dependent folding landscapes of nucleic acid hairpins reflect much of the complexity of biomolecular folding. Folding trajectories, generated using single molecule force clamp experiments by attaching semiflexible polymers to…
Accurate phase diagram calculation from molecular dynamics requires systematic treatment and convergence of statistical averages. In this work we propose a Gaussian process regression based framework for reconstructing the free energy…
Phase-field methods offer a versatile computational framework for simulating large-scale morphological evolution. However, the applicability and predictability of phase-field models are inherently limited by their ad hoc nature, and there…