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According to the Jarzynski theorem, equilibrium free energy differences can be calculated from the statistics of work carried out during non-equilibrium transformations. Although exact, this approach can be plagued by large statistical…
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,…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
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…
A common approach to study nucleation rates is the estimation of free-energy barriers. This usually requires knowledge about the shape of the forming droplet, a task that becomes notoriously difficult in macromolecular setups starting with…
A central endeavor of thermodynamics is the measurement of free energy changes. Regrettably, although we can measure the free energy of a system in thermodynamic equilibrium, typically all we can say about the free energy of a…
Recent very large molecular dynamics simulations of homogeneous nucleation with $(1-8) \cdot 10^9$ Lennard-Jones atoms [Diemand et al. J. Chem. Phys. {\bf 139}, 074309 (2013)] allow us to accurately determine the formation free energy of…
Locating transition states is crucial for investigating transition mechanisms in wide-ranging phenomena, from atomistic to macroscale systems. Existing methods, however, can struggle in problems with a large number of degrees of freedom,…
Lennard-Jones clusters, while an easy system, have a significant number of non equivalent configurations that increases rapidly with the number of atoms in the cluster. Here, we aim at determining the cluster partition function; we use the…
We perform, with the help of cloud computing resources, extensive Langevin simulations which provide free energy estimates for unbiased three dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to…
We evaluate the grand potential of a cluster of two molecular species, equivalent to its free energy of formation from a binary vapour phase, using a nonequilibrium molecular dynamics technique where guide particles, each tethered to a…
We use Bayesian inference and nested sampling to develop a non-parametric method to reconstruct the primordial power spectrum $P_{\mathcal{R}}(k)$ from Large Scale Structure (LSS) data. The performance of the method is studied by applying…
We develop a novel data-driven approach to the inverse problem of classical statistical mechanics: given experimental data on the collective motion of a classical many-body system, how does one characterise the free energy landscape of that…
We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of 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…
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…
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…
Studies in atomic-scale modeling of surface phase equilibria often focus on temperatures near zero Kelvin due to the challenges in calculating the free energy of surfaces at finite temperatures. The Bayesian-inference-based nested sampling…
A method is presented for Bayesian model selection without explicitly computing evidences, by using a combined likelihood and introducing an integer model selection parameter $n$ so that Bayes factors, or more generally posterior odds…