Related papers: Enhanced Sampling for Free Energy Profiles with Po…
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…
The Replica Exchange Wang-Landau Method is used to estimate the energy landscape of a polymer composed of a simple hydrophobic and polar sequence using the HP protein model. Calculations of state transitions between the energy levels of the…
Diffusion-based samplers learn to sample complex, high-dimensional distributions using energies or log densities alone, without training data. Yet, they remain impractical for molecular sampling because they are often slower than molecular…
Enhanced sampling methods such as metadynamics and umbrella sampling have become essential tools for exploring the configuration space of molecules and materials. At the same time, they have long faced a number of issues such as the…
The equilibrium state of a superfluid in a rotating cylindrical vessel is a vortex crystal -- an array of vortex lines which is stationary in the rotating frame. Experimental realisations of this behaviour typically show a sequence of…
Many problems in physics, material sciences, chemistry and biology can be abstractly formulated as a system that navigates over a complex energy landscape of high or infinite dimensions. Well-known examples include phase transitions of…
Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly exploited. Equilibrium methods such as umbrella sampling,…
The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While…
We introduce a massively parallel replica-exchange grand-canonical sampling algorithm to simulate materials at realistic conditions, in particular surfaces and clusters in reactive atmospheres. Its purpose is to determine in an automated…
Chemical reactions involve the movement of charges, and this work presents a mathematical model for describing chemical reactions in electrolytes. The model is developed using an energy variational method that aligns with classical…
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…
We study the global influence of curvature on the free energy landscape of two-dimensional binary mixtures confined on closed surfaces. Starting from a generic effective free energy, constructed on the basis of symmetry considerations and…
Normal molecular dynamics simulations are usually unable to simulate chemical reactions due to the low probability of forming the transition state. Therefore, enhanced sampling methods are implemented to accelerate the occurrence of…
Exploring the free-energy landscape along reaction coordinates or system parameters $\lambda$ is central to many studies of high-dimensional model systems in physics, e.g. large molecules or spin glasses. In simulations this usually…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
The phase field crystal (PFC) method has emerged as a promising technique for modeling materials with atomistic resolution on mesoscopic time scales. The approach is numerically much more efficient than classical density functional theory…
The free energy plays a fundamental role in descriptions of many systems in continuum physics. Notably, in multiphysics applications, it encodes thermodynamic coupling between different fields. It thereby gives rise to driving forces on the…
The paper presents amended basic map of states of chemical systems in discrete thermodynamics of chemical equilibria. Uniting two previously found basic map types in one and covering a wider range of situations, it allows us to obtain more…
We present a methodology for accelerating the estimation of the free energy from path integral Monte Carlo simulations by considering an intermediate artificial reference system where interactions are inexpensive to evaluate numerically.…
In this work, phase diagrams of a modified two-mode phase-field crystal (PFC) that show two-dimensional (2D) and three-dimensional (3D) crystallographic structures were determined by utilizing a free energy minimization method. In this…