Related papers: Escaping free-energy minima
Free energies as a function of a selected set of collective variables are commonly computed in molecular simulation and of significant value in understanding and engineering molecular behavior. These free energy surfaces are most commonly…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
The dynamics of finite dimension open quantum systems is studied with the help of the simplest possible form of projection operators, namely the ones which project only onto one dimensional subspaces. The simplicity of the action of the…
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…
This thesis introduces a framework that is able to describe general many-body coarse-grained interactions. We make use of this to describe the free energy surface as a cluster expansion in terms of monomer, dimer, and trimer terms. The…
We show that the dynamics of the surface plasmon in metallic nanoparticles damped by its interaction with particle-hole excitations can be modelled by a single degree of freedom coupled to an environment. In this approach, the fast decrease…
We consider a nonlinear, free boundary fluid-structure interaction model in a bounded domain. The viscous incompressible fluid interacts with a nonlinear elastic body on the common boundary via the velocity and stress matching conditions.…
A method is presented that can find the global minimum of very complex condensed matter systems. It is based on the simple principle of exploring the configurational space as fast as possible and of avoiding revisiting known parts of this…
We address the problem of constructing accurate mathematical models of the dynamics of complex systems projected on a collective variable. To this aim we introduce a conceptually simple yet effective algorithm for estimating the parameters…
Relations between the thermodynamics and dynamics of supercooled liquids approaching a glass transition have been proposed over many years. The potential energy surface of model liquids has been increasingly studied since it provides a…
This paper introduces coordinate-independent methods for analysing multiscale dynamical systems using numerical techniques based on the transfer operator and its adjoint. In particular, we present a method for testing whether an arbitrary…
Solvent plays an important role in the relative motion of nanoscopic bodies, and the study of such phenomena can help elucidate the mechanism of hydrophobic assembly, as well as the influence of solvent-mediated effects on in vivo motion in…
We consider a hyperbolic free boundary problem by means of minimizing time discretized functionals of Crank-Nicolson type. The feature of this functional is that it enjoys energy conservation in the absence of free boundaries, which is an…
Several protocols are proposed to build continuous energy surfaces of many-body quantum systems, regarding both energy and states. The standard variational principle is augmented with constraints on state overlap, ensuring arbitrary…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
A vast array of phenomena, ranging from chemical reactions to phase transformations, are analysed in terms of a free energy surface defined with respect to a single or multiple order parameters. Enhanced sampling methods are typically used,…
Here we address a fundamental issue in surface physics: the dynamics of adsorbed molecules. We study this problem when the particle's desorption is characterized by a non Markovian process, while the particle's adsorption and its motion in…
In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations,…
We introduce a dissipative particle dynamics scheme for the dynamics of non-ideal fluids. Given a free-energy density that determines the thermodynamics of the system, we derive consistent conservative forces. The use of these effective,…
Mixed-quantum classical (MQC) methods for simulating the dynamics of molecules at metal surfaces have the potential to accurately and efficiently provide mechanistic insight into reactive processes. Here, we introduce simple two-dimensional…