Related papers: Absolute free energies estimated by combining pre-…
Quantum embedding is an appealing route to fragment a large interacting quantum system into several smaller auxiliary `cluster' problems to exploit the locality of the correlated physics. In this work we critically review approaches to…
Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is…
Approximate molecular calculations via standard Kohn-Sham Density Functional Theory are exactly reproduced by performing self-consistent calculations on isolated fragments via Partition Density Functional Theory [Phys. Rev. A 82, 024501…
An expression is derived for the free energy of nonideal atomic plasma, which corresponds to exact asymptotic expansions. The analytical dependence of correction for the interaction of free charges on the partition function of atom is…
The massively parallel computation of absolute binding free energy with a well-equilibrated system (MP-CAFEE) has been developed [H. Fujitani, Y. Tanida, M. Ito, G. Jayachandran, C. D. Snow, M. R. Shirts, E. J. Sorin, and V. S. Pande, J.…
Free energy calculation is critical in predictive tasks such as protein folding, docking and design. However, rigorous calculation of free energy change is prohibitively expensive in these practical applications. The minimum potential…
Using molecular simulation, we determine Ginzburg-Landau free energy functions for molecular fluids. To this aim, we extend the Expanded Wang-Landau method to calculate the partition functions, number distributions and Landau free energies…
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…
We present exact calculations of the partition function $Z$ of the $q$-state Potts model and its generalization to real $q$, the random cluster model, for arbitrary temperature on $n$-vertex ladder graphs with free, cyclic, and M\"obius…
We present a new method to evaluate vibrational free energies of atomic systems without a priori specification of an interatomic potential. Our model-agnostic approach leverages descriptors, high-dimensional feature vectors of atomic…
The equilibrium properties of particles adsorption is investigated theoretically. The model relies on a free energy formulation which allows to generalize the Maxwell-Boltzmann description to solutions for which the bulk volume fraction of…
We develop a quantum algorithm for estimating the free energy as well as the total Gibbs state of interacting quantum Coulomb gases and molecular systems in dimensions $d \in \{2,3\}$ at finite temperature. These systems lie beyond the…
We have derived several relations, which allow the evaluation of the system free energy changes in the leading order in $\hbar^{2}$ along classically generated trajectories. The results are formulated in terms of purely classical…
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…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
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…
Fluctuation relations allow for the computation of equilibrium properties, like free energy, from an ensemble of non-equilibrium dynamics simulations. Computing them for quantum systems, however, can be difficult, as performing dynamic…
We review uses of the generalized-ensemble algorithms for free-energy calculations in protein folding. Two of the well-known methods are multicanonical algorithm and replica-exchange method; the latter is also referred to as parallel…
Comparison of free energies between different phases and different compositions underlies the prediction of alloy phase diagrams. To allow direct comparison, consistent reference points for the energies or enthalpies are required, and the…
In the long-time pursuit of the solution to calculate the partition function (or free energy) of condensed matter, Monte-Carlo-based nested sampling should be the state-of-the-art method, and very recently, we established a direct integral…