Related papers: Absolute free energies estimated by combining pre-…
The remarkable accuracy and versatility of single-molecule techniques make possible new measurements that are not feasible in bulk assays. Among these, the precise estimation of folding free energies using fluctuation theorems in…
The partition function with ring diagrams at finite temperature is exactly caluclated by using contour integrals in the complex energy plane. It contains a pole part with temperature and momentum dependent mass and a phase shift part…
We describe a self-contained procedure to evaluate the free energy of liquid and solid phases of an alloy system. The free energy of a single-element solid phase is calculated with thermodynamic integration using the Einstein crystal as the…
The free energy of globular protein chain is considered to be a functional defined on smooth curves in three dimensional Euclidean space. From the requirement of geometrical invariance, together with basic facts on conformation of helical…
Gradients in free energies are the driving forces of physical and biochemical systems. To predict free energy differences with high accuracy, Molecular Dynamics (MD) and other methods based on atomistic Hamiltonians conduct sampling…
Atomistic simulations are employed to demonstrate the existence of a well-defined thermodynamic phase transformation between grain boundary (GB) phases with different atomic structures. The free energy of different interface structures for…
Quantum-mechanical analysis based on an exact sum rule is used to extract an semiclassical angle-dependent energy function for transition metal ions in biomolecules. The angular dependence is simple but different from existing classical…
We present a method to approximate partition functions of quantum systems using mixed-state quantum computation. For positive semi-definite Hamiltonians, our method has expected running-time that is almost linear in $(M/(\epsilon_{\rm…
Predicting crystal nucleation is among the most significant long--standing challenges in condensed matter. In the system most studied (hard sphere colloids), the comparison between experiments performed using static light scattering and…
This work presents the implementation of a fragment-based, quantum-centric supercomputing workflow for computing molecular electronic structure using quantum hardware. The workflow is applied to predict the relative energies of two…
Using the entropy $S$ as a reaction coordinate, we determine the free energy barrier associated with the formation of a liquid droplet from a supersaturated vapor for atomic and molecular fluids. For this purpose, we develop the $\mu VT-S$…
The analytical gradient for periodic systems is presented, for the case of metallic systems. The total energy and the free energy are computed on the Hartree-Fock or density functional level, with the wave function being expanded in terms…
This dissertation develops, for several families of statistical mechanical and random growth models, techniques for analyzing infinite-volume asymptotics. In the statistical mechanical setting, we focus on the low-temperature phases of spin…
We consider the statistical mechanics of a classical particle in a one-dimensional box subjected to a random potential which constitutes a Wiener process on the coordinate axis. The distribution of the free energy and all correlation…
We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using the pre-calculated statistical libraries…
We review a recently developed micellization theory, which is based on a free-energy approach and offers several advantages over the conventional one, based on mass action and rate equations. As all the results are derived from a single…
Accurate calculations of solvation free energies remain a central challenge in molecular simulations, often requiring extensive sampling and numerous alchemical intermediates to ensure sufficient overlap between phase-space distributions of…
Starting for the Stillinger and Weber expression for the free energy of supercooled liquids, we extend the free energy to the case in which two time scales separate and the system is in quasi-equilibrium. The concept of an effective…
The alternative replica technique which involve summation over all integer momenta of the partition function and which does not require analytic continuation to non-integer values of the replica parameter $n$ is discussed. In terms of this…
By using results of highly accurate computations of the total energies of a large number of few-electron atoms we construct a few interpolation formulas which can be used to approximate the total energies of bound atomic states. In our…