Related papers: Free energy reconstruction from steered dynamics w…
The multistate Bennett acceptance ratio (MBAR) method is a prevalent approach for computing free energies of thermodynamic states. In this work, we introduce BayesMBAR, a Bayesian generalization of the MBAR method. By integrating…
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 PhD thesis, we explore and apply methods inspired by the free energy principle to two important areas in machine learning and neuroscience. The free energy principle is a general mathematical theory of the necessary…
Enhanced sampling techniques have become an essential tool in computational chemistry and physics, where they are applied to sample activated processes that occur on a time scale that is inaccessible to conventional simulations. Despite…
We describe a first-principles statistical mechanics method to calculate the free energies of crystalline alloys that depend on temperature, composition, and strain. The approach relies on an extension of the alloy cluster expansion to…
Jarzynski's equality [1] allows us to investigate free energy landscapes (FELs) by constructing distributions of work performed on a system from an initial ensemble of states to final states. This work is experimentally measured by…
Studying the structure of systems in nonequilibrium steady states necessitates tools that quantify population shifts and associated deformations of equilibrium free energy landscapes under persistent currents. Within the framework of…
We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity…
We consider a simple model to describe the widths of the mode locked intervals for the critical circle map. Using two different partitions of the rational numbers, based on Farey series and Farey tree levels respectively, we calculate the…
We report our studies of the potential energy surface (PES) of selected binary Lennard-Jones clusters. The effect of adding selected impurity atoms to a homogeneous cluster is explored. Inherent structures and transition states are found by…
To validate the second-by-second dynamics of turbines in field experiments, it is necessary to accurately reconstruct the winds going into the turbine. Current time-resolved inflow reconstruction techniques estimate wind behavior in…
Free energy profiles serve as a fundamental bridge between microscopic atomic fluctuations and macroscopic thermodynamic observables. Estimating the free energy profile along a reaction coordinate, referred to as the potential of mean force…
Phase diagrams serve as a highly informative tool for materials design, encapsulating information about the phases that a material can manifest under specific conditions. In this work, we develop a method in which Bayesian inference is…
Thermodynamic phase transitions, a central concept in physics and chemistry, are typically controlled by an interplay of enthalpic and entropic contributions. In most cases, the estimation of the enthalpy in simulations is straightforward…
Free energy differences are a central quantity of interest in physics, chemistry, and biology. We develop design principles that improve the precision and accuracy of free energy estimators, which has potential applications to screening for…
We propose a biochemical model providing the kinetic and energetic descriptions of the processivity dynamics of kinesin and dinein molecular motors. Our approach is a modified version of a well known model describing kinesin dynamics and…
A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…
We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…
Any coarse-grained description of a nonequilibrium system should faithfully represent its latent irreversible degrees of freedom. However, standard dimensionality reduction methods typically prioritize accurate reconstruction over physical…
A first-principles based methodology for efficiently and accurately finding thermodynamically stable and metastable atomic structures is introduced and benchmarked. The approach is demonstrated for gas-phase metal-oxide clusters in…