Related papers: Multidimensional replica-exchange method for free-…
We describe the study of thermodynamics of materials using replica-exchange Wang-Landau (REWL) sampling, a generic framework for massively parallel implementations of the Wang-Landau Monte Carlo method. To evaluate the performance and…
One reason that free energy difference calculations are notoriously difficult in molecular systems is due to insufficient conformational overlap, or similarity, between the two states or systems of interest. The degree of overlap is…
The emergence and understanding of new design paradigms that exploit flow induced mechanical instabilities for propulsion or energy harvesting demands robust and accurate flow structure interaction numerical models. In this context, we…
An improved weighting algorithm applied to hadron showers has been developed for a fine grained LAr calorimeter. The new method uses tabulated weights which depend on the density of energy deposited in individual cells and in a surrounding…
We introduce a reweighting technique which allows for a continuous sampling of temperatures in a single simulation and employ it to compute the temperature dependence of the QCD topological susceptibility at high temperatures. The method…
We use thermodynamic perturbation theory to calculate the free energies and resulting phase diagrams of binary systems of spherical colloidal particles and interacting polymer coils in good solvent within an effective one-component…
We compute the free energy at all temperatures for the spherical pure $p$-spin models from the generalized Thouless-Anderson-Palmer representation. This is the first example of a mixed $p$-spin model for which the free energy is computed in…
Inspired by the recent development on calculating the free energy change via a relaxation process [Nat. Phys. 14, 842 (2018)], we investigate the role of heat released in an irreversible relaxation following a large perturbation. Utilizing…
In this thesis we examine methodologies for determining free energy differences (FEDs) of phases via Monte Carlo simulation. We identify and address three generic issues that arise in FED calculations; the choice of representation, the…
Thermal density functional theory calculations often use the Mermin-Kohn-Sham scheme, but employ ground-state approximations to the exchange-correlation (XC) free energy. In the simplest solvable nontrivial model, an asymmetric Hubbard…
This paper develops a novel change point identification method for high-dimensional data using random projections. By projecting high-dimensional time series into a one-dimensional space, we are able to leverage the rich literature for…
We propose a new Monte Carlo method for efficiently sampling trajectories with fixed initial and final conditions in a system with discrete degrees of freedom. The method can be applied to any stochastic process with local interactions,…
We present a novel implementation of the parallel tempering Monte Carlo method in a multicanonical ensemble. Multicanonical weights are derived by a self-consistent iterative process using a Boltzmann inversion of global energy histograms.…
The computational treatment of many-electron systems capable of exchanging {electrons and nuclei} with the environment represents one of the outermost frontiers in simulation methodology. The exchanging process occurs in a large variety of…
We apply a recently developed adaptive algorithm that systematically improves the efficiency of parallel tempering or replica exchange methods in the numerical simulation of small proteins. Feedback iterations allow us to identify an…
Computing the equilibrium properties of complex systems, such as free energy differences, is often hampered by rare events in the dynamics. Enhanced sampling methods may be used in order to speed up sampling by, for example, using high…
We present a new method for investigating first-order phase transitions using Monte Carlo simulations. It relies on the multiple-histogram method and uses solely histograms of individual phases. In addition, we extend the method to include…
Thermodynamic integration (TI) offers a rigorous method for estimating free-energy differences by integrating over a sequence of interpolating conformational ensembles. However, TI calculations are computationally expensive and typically…
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…
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,…