Related papers: Free energy reconstruction from steered dynamics w…
Biased sampling methods such as the Temperature Accelerated Sliced Sampling (TASS), which can explore high dimensional collective variable (CV) space, is of great interest in free energy calculations. Such methods can efficiently sample…
Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to…
The Jarzynski equality allows the calculation of free-energy differences using values of work measured from nonequilibrium trajectories. The number of trajectories required to accurately estimate free-energy differences in this way grows…
Massless scalar electrodynamics is studied at high temperature and zero chemical potential. I derive the free energy to order $\lambda^2$, $\lambda e^2$ and $e^4$ by effective field theory methods. The first step consists of the…
It has been a long challenge to analytically construct the quantitative temperature-dependent multi-well free-energy landscape over the space of order parameters describing phase transitions and associated critical phenomena. Here we…
We reconstruct the Equation of State of Dark Energy (EoS) from current data using a non-parametric approach where, rather than assuming a specific time evolution of this function, we bin it in time. We treat the transition between the bins…
Using a model-independent low-energy effective field theory, we calculate the free energy of three-dimensional antiferromagnets in a combination of mutually perpendicular external magnetic and staggered fields at the…
We present studies of the potential energy landscape of selected binary Lennard-Jones thirteen atom clusters. The effect of adding selected impurity atoms to a homogeneous cluster is explored. We analyze the energy landscapes of the studied…
In this work the free energy of solid phases is computed for the Lennard-Jones potential and for a model of NaCl. The free energy is evaluated through the Einstein crystal/molecule methodologies using the Molecular Dynamics programs:…
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…
Free energy perturbation (FEP) is frequently used to evaluate the free energy change of a biological process, e.g. the drug binding free energy or the ligand solvation free energy. Due to the sampling inefficiency, FEP is often employed…
We propose a new Monte Carlo algorithm for the free energy calculation based on configuration space sampling. We implement this algorithm for Ising model. Comparison with the exact free energy shows an excellent agreement. We analyse the…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
A promising method for calculating free energy differences Delta F is to generate non-equilibrium data via ``fast-growth'' simulations or experiments -- and then use Jarzynski's equality. However, a difficulty with using Jarzynski's…
We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
With the traditional equilibrium molecular simulations, it is usually difficult to efficiently visit the whole conformational space in complex systems, which are separated into some metastable conformational regions by high free energy…
Defining the energy function as the negative logarithm of the density, we explore the energy landscape of a distribution via the tree of sublevel sets of its energy. This tree represents the hierarchy among the connected components of the…
Variational Autoencoders (VAEs) typically rely on a probabilistic decoder with a predefined likelihood, most commonly an isotropic Gaussian, to model the data conditional on latent variables. While convenient for optimization, this choice…
We consider the Farey fraction spin chain in an external field $h$. Utilising ideas from dynamical systems, the free energy of the model is derived by means of an effective cluster energy approximation. This approximation is valid for…