Related papers: A general, efficient and robust method to calculat…
Using computer simulations, we validate a simple free energy model that can be analytically solved to predict the equilibrium size of self-limiting clusters of particles in the fluid state governed by a combination of short-range attractive…
Entropy and free-energy estimation are key in thermodynamic characterization of simulated systems ranging from spin models through polymers, colloids, protein structure, and drug-design. Current techniques suffer from being model specific,…
This report details an approach to improve the accuracy and precision of free energy difference estimates using thermodynamic integration data (slope of the free energy with respect to the switching variable lambda) and its application to…
A method is presented that reduces the number of terms of systems of linear equations (algebraic, ordinary and partial differential equations). As a byproduct these systems have a tendency to become partially decoupled and are more likely…
The microscopic origin of friction is an important topic in science and technology. To date, noteworthy aspects of it remain unsolved. In an effort to shed some light on the possible mechanisms that could give rise to the macroscopic…
In this review we focus on the determination of phase diagrams by computer simulation with particular attention to the fluid-solid and solid-solid equilibria. The calculation of the free energy of solid phases using the Einstein crystal and…
Molecular machines transduce free energy between different forms throughout all living organisms. While truly machines in their own right, unlike their macroscopic counterparts molecular machines are characterized by stochastic…
We study the equilibrium states of energy functions involving a large set of real variables, defined on the links of sparsely connected networks, and interacting at the network nodes, using the cavity and replica methods. When applied to…
Energy system models based on linear programming have been growing in size with the increasing need to model renewables with high spatial and temporal detail. Larger models lead to high computational requirements. Furthermore, seemingly…
The uniform electron gas is a key model system in the description of matter, including dense plasmas and solid state systems. However, the simultaneous occurence of quantum, correlation, and thermal effects makes the theoretical description…
Couplings of a system to other degrees of freedom (that is, environmental degrees of freedom) lead to energy dissipation when the number of environmental degrees of freedom is large enough. Here we discuss quantal treatments for such energy…
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 derive an analytic expression for the distribution of velocities of multiple interacting active particles which we test by numerical simulations. In clear contrast with equilibrium we find that the velocities are coupled to positions.…
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…
Computing phase diagrams of model systems is an essential part of computational condensed matter physics. In this paper we discuss in detail the interface pinning (IP) method for calculation of the Gibbs free energy difference between a…
We present an approach that extends the theory of targeted free energy perturbation (TFEP) to calculate free energy differences and free energy surfaces at an accurate quantum mechanical level of theory from a cheaper reference potential.…
Estimating the free energy in molecular simulation requires, implicitly or explicitly, counting how many times the system is observed in a finite region. If the simulation is biased by an external potential, the weight of the configurations…
Despite the strength of Molecular Dynamics simulations in providing insights into the microscopic details of phenomenon in many fields in materials science, physics and biology, the biggest barrier is its limited timescale which is several…
The principles behind the computation of protein-ligand binding free energies by Monte Carlo integration are described in detail. The simulation provides gas-phase binding free energies that can be converted to aqueous energies by solvation…
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…