相关论文: Free-energy landscapes in magnetic systems from me…
We present a simple model system with four hard disks moving in a circular region for which free energy landscapes can be directly calculated and visualized in two and three dimensions. We construct several energy landscapes for our system…
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantities associated with simplified models of proteins, and thus…
We propose a metadynamics-based (MetaD-based) approach for constructing the free energy surface (FES) of vacancy dynamics in crystals. In this approach, the vacancy FES can be constructed without explicitly defining a unique vacancy…
Magnetic vortices in soft ferromagnetic nano-disks have been extensively studied for at least several decades both for their fundamental (as a "live" macroscopic realization of a field theory model of an elementary particle) as well as…
The equilibrium free energy landscape of off-lattice model heteropolymers as a function of an internal coordinate, namely the end-to-end distance, is reconstructed from out-of-equilibrium steered molecular dynamics data. This task is…
The equilibrium state of a superfluid in a rotating cylindrical vessel is a vortex crystal -- an array of vortex lines which is stationary in the rotating frame. Experimental realisations of this behaviour typically show a sequence of…
In the free energy landscape picture of glassy systems, the slow dynamics characteristic of these systems is believed to be due to the existence of a complicated free-energy landscape with many local minima. We show here that for a…
The dynamics of highly magnetized plasmas in extreme astrophysical environments are effectively modeled by Force-Free Electrodynamics (FFE), a framework essential for studying objects like neutron stars and accreting black holes. The…
Various methods achieving importance sampling in ensembles of nonequilibrium trajectories enable to estimate free energy differences and, by maximum-likelihood post-processing, to reconstruct free energy landscapes. Here, based on Bayes…
We report a systematic and accurate approach for deriving the bulk free energy surface (FES), a function of temperature, polarization, and strain, from the first-principles density functional theory (DFT) of proper ferroelectrics. The core…
The spin dynamics are calculated for a model system consisting of magnetically soft, layered nanomagnets, in which two ferromagnetic (F) cylindrical dots, each with a magnetic vortex ground state, are separated by a non-magnetic spacer (N).…
We present a simulation technique to evaluate the most important quantity for nucleation processes: the nucleation barrier, i.e. the free energy of formation of the critical cluster. The method is based on stabilizing a small cluster by…
By quenching into the metastable region of the three-dimensional Ising model, we investigate the paths that the magnetization (energy) takes as a function of time. We accumulate the magnetization (energy) paths into time-dependent…
Properties of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form are investigated numerically. A considerable number of glassy local…
Ab initio metadynamics enables extracting free-energy landscapes having the accuracy of first principles electronic structure methods. We introduce an interface between the PLUMED code that computes free-energy landscapes and…
The topography of the free energy landscape in phase space of a dense hard sphere system characterized by a discretized free energy functional of the Ramakrishnan-Yussouff form is investigated numerically using a ``microcanonical'' Monte…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
Energy landscapes are high-dimensional surfaces representing the dependence of system energy on variable configurations, which determine crucially the system's emergent behavior but are difficult to be analyzed due to their high-dimensional…
A magnetic vortex has attracted significant attention since it is a topologically stable magnetic structure in a soft magnetic nanodisk. Many studies have been devoted to understanding the nature of magnetic vortex in isolated systems. Here…
The information-encoding molecules RNA and DNA form a combinatorially large set of secondary structures through nucleic acid base pairing. Thermodynamic prediction algorithms predict favoured, or minimum free energy (MFE), secondary…