Related papers: Approaching a parameter-free metadynamics
By drawing a parallel between metadynamics and self interacting models for polymers, we study the longtime convergence of the original metadynamics algorithm in the adiabatic setting, namely when the dynamics along the collective variables…
We propose a formulation of adaptive computation of free energy differences, in the ABF or nonequilibrium metadynamics spirit, using conditional distributions of samples of configurations which evolve in time. This allows to present a truly…
Geometric continuum models for fluid lipid membranes are considered using classical field theory, within a covariant variational approach. The approach is cast as a higher-derivative Lagrangian formulation of continuum classical field…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
In this paper, a simple case of Bayesian mechanics under the free energy principle is formulated in axiomatic terms. We argue that any dynamical system with constraints on its dynamics necessarily looks as though it is performing inference…
We present a novel method for the calculation of the energy density of states D(E) for systems described by classical statistical mechanics. The method builds on an extension of a recently proposed strategy that allows the free energy…
The ability to predict accurate thermodynamic and kinetic properties in biomolecular systems is of both scientific and practical utility. While both remain very difficult, predictions of kinetics are particularly difficult because rates, in…
We present a new derivation of the expressions for momentum and energy of a relativistic particle. In contrast to the procedures commonly adopted in textbooks, the one suggested here requires only the knowledge of the composition law for…
We introduce a novel scheme for the mechanistic investigation of solid-solid phase transitions, which we dub \textit{metashooting}. Combining transition path sampling molecular dynamics and metadynamics, this scheme allows for both a…
In his Comment [1], Philip Strasberg (PS) argues from the analysis of different examples that the framework we have presented in [2] does not recover known results of macroscopic textbook thermodynamics. Here, we show that such apparent…
We propose an adiabatic reweighting algorithm for computing the free energy along an external parameter from adaptive molecular dynamics simulations. The adaptive bias is estimated using Bayes identity and information from all the sampled…
We derive the approximate pressure profiles, density profiles, and temperature profiles of an atmosphere, also called barometric formulas. Our variant of a derivation goes beyond the common standard exercise of a thermodynamics lecture,…
A formula for the magnetostatic energy of a finite magnet is proven. In contrast to common approaches, the new energy identity does not rely on evaluation of a nonlocal boundary integral inside the magnet or the solution of an equivalent…
In this paper we propose a new formalism to map history-dependent metadynamics in a Markovian process. We apply this formalism to a model Langevin dynamics and determine the equilibrium distribution of a collection of simulations. We…
The expression of the free energy density of a classical crystalline system as a gradient expansion in terms of a set of order parameters is developed using classical density functional theory. The goal here is to extend and complete an…
The usual formulation of thermodynamics is based on the additivity of macroscopic systems. However, there are numerous examples of macroscopic systems that are not additive, due to the long-range character of the interaction among the…
Relativistic hydrodynamics of classic plasmas is derived from the microscopic model in the limit of ideal plasmas. The chain of equations is constructed step by step starting from the concentration evolution. It happens that the energy…
Building on the fundamental equation, this study revisits key thermodynamic concepts in a cohesive and innovative manner. It demonstrates the consistency of thermodynamic theory while addressing and clarifying common misconceptions and…
The origins of thermodynamics from the microscopic properties of matter have not been satisfactorily accounted for. This work presents a formulation that connects Lagrangian mechanics to thermodynamics. By using such a formulation and…
We review a recently developed micellization theory, which is based on a free-energy approach and offers several advantages over the conventional one, based on mass action and rate equations. As all the results are derived from a single…