Related papers: Escaping free-energy minima
We present a ``coarse molecular dynamics'' approach and apply it to studying the kinetics and thermodynamics of a peptide fragment dissolved in water. Short bursts of appropriately initialized simulations are used to infer the deterministic…
In this paper we combine two powerful computational techniques, well-tempered metadynamics and time lagged independent component analysis. The aim is to develop a new tool for studying rare events and exploring complex free energy…
Within a density matrix approach for nuclear many--body system, it is derived non--Markovian Langevin equations of motion for nuclear collective parameters, where memory effects are defined by memory time. The developed stochastic approach…
Many enhanced sampling techniques rely on the identification of a number of collective variables that describe all the slow modes of the system. By constructing a bias potential in this reduced space one is then able to sample efficiently…
The general problem of dissipation in macroscopic large-amplitude collective motion and its relation to energy diffusion of intrinsic degrees of freedom of a nucleus is studied. By applying the cranking approach to the nuclear many body…
A variety of methods are developed for characterising the free energy landscapes of continuum, Landau-type free energy models. Using morphologies of lipid vesicles and a multistable liquid crystal device as examples, I show that the methods…
We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to…
The aging dynamics of a simple model glass is numerically investigated observing how it takes place in the potential energy landscape $V$. Partitioning the landscape in basins of minima of $|\nabla V|^2$, we are able to elucidate some…
The present paper proposes an adaptive biasing potential for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells…
To address the time-scale limitations in molecular dynamics (MD) simulations, numerous enhanced sampling methods have been developed to expedite the exploration of complex free energy landscapes. A commonly employed approach accelerates the…
Friction is a phenomenon that manifests across all spatial and temporal scales, from the molecular to the macroscopic scale. It describes the dissipation of energy from the motion of particles or abstract reaction coordinates and arises in…
We address the problem of constructing accurate mathematical models of the dynamics of molecular systems projected on a collective variable. To this aim we introduce an algorithm optimizing the parameters of a standard or generalized…
Nanoparticles with different surface morphologies that straddle the interface between two immiscible liquids are studied via molecular dynamics simulations. The methodology employed allows us to compute the interfacial free energy at…
Nanodevices exploiting quantum effects are critically important elements of future quantum technologies (QT), but their real-world performance is strongly limited by decoherence arising from local `environmental' interactions. Compounding…
We introduce a new method to simulate the physics of rare events. The method, an extension of the Temperature Accelerated Molecular Dynamics, comes in use when the collective variables introduced to characterize the rare events are either…
Metadynamics is a commonly used and successful enhanced sampling method. By the introduction of a history dependent bias which depends on a restricted number of collective variables(CVs) it can explore complex free energy surfaces…
Free energies play a central role in characterising the behaviour of chemical systems and are among the most important quantities that can be calculated by molecular dynamics simulations. Solvation free energies in various organic solvents,…
In this work, I propose a statistical mechanical framework, for the evaluation of the free energy in molecular systems, by "deleting" all the molecules in a "single" step. The approach can be considered as the statistical mechanics…
We apply well-established concepts of Langevin sampling to derive a new class of algorithms for the efficient computation of free energy differences of fluctuating particles embedded in a 'fast' membrane, i.e., a membrane that…
We propose a new method for the problems of computing free energy and surface pressure for various statistical mechanics models on a lattice $\Z^d$. Our method is based on representing the free energy and surface pressure in terms of…