Related papers: Computing equilibrium free energies through a none…
Predicting the binding affinity between small molecules and target macromolecules while combining both speed and accuracy, is a cornerstone of modern computational drug discovery which is critical for accelerating therapeutic development.…
We show that chemically-accurate potential energy surfaces (PESs) can be generated from quantum computers by measuring only the density along an adiabatic transition between different molecular geometries. In lieu of using phase estimation,…
A general method is presented for modeling high entropy alloys as ensembles of randomly sampled, ordered configurations on a given lattice. Statistical mechanics is applied post hoc to derive the ensemble properties as a function of…
We study non-equilibrium dynamics in SYK models using quantum quench. We consider models with two, four, and higher fermion interactions ($q=2, 4$, and higher) and use two different types of quench protocol, which we call step and bump…
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…
This paper is about nonequilibrium steady states (NESS) of a class of stochastic models in which particles exchange energy with their "local environments" rather than directly with one another. The physical domain of the system can be a…
Metropolis simulations of all-atom models of peptides (i.e. small proteins) are considered. Inspired by the funnel picture of Bryngelson and Wolyness, a transformation of the updating probabilities of the dihedral angles is defined, which…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…
Quantum Gibbs state sampling algorithms generally suffer from either scaling exponentially with system size or requiring specific knowledge of spectral properties \textit{a priori}. Also, these algorithms require a large overhead of bath or…
We present an exact solution of entanglement entropy for the real-time dynamics following a quench from a thermal pure quantum (TPQ) state in an free fermion system. Contrast to the usual linear growth and saturate behavior, the…
A lattice based model of a protein is used to study the dimerization equilibrium of the GCN4 leucine zipper. Replica exchange Monte Carlo is used to determine the free energy of both the monomeric and dimeric forms as a function of…
A quantitative theory is developed, which accounts for heating artifacts in three-pulse photon echo (3PE) experiments. The heat diffusion equation is solved and the average value of the temperature in the focal volume of the laser is…
We extend the non-parametric framework of reaction coordinate optimization to non-equilibrium ensembles of (short) trajectories. For example, we show how, starting from such an ensemble, one can obtain an equilibrium free energy profile…
An investigation to optimize the application of the third-generation charge optimized many-body (COMB3) interatomic potential and associated input parameters was carried out through the study of solid-liquid interactions in classical…
The assembly of proteins in membranes plays a key role in many crucial cellular pathways. Despite their importance, characterizing transmembrane assembly remains challenging for experiments and simulations. Equilibrium molecular dynamics…
The Bethe free energy approximation provides an effective way for relaxing NP-hard problems of probabilistic inference. However, its accuracy depends on the model parameters and particularly degrades if a phase transition in the model…
We propose a new method to compute the configurational entropy of glassy systems as a function of the free energy of valleys at a given temperature, in the framework of the Stillinger and Weber approach. In this method, which we call…
We introduce a new numerical technique, namely triangular tessellation, to calculate the free energy associated with the adsorption of a colloidal particle at a flat interface. The theory and numerical scheme presented here are sufficiently…
In atomistic simulations, pseudo-dynamics relaxation schemes often exhibit better performance and accuracy in finding local minima than line-search-based descent algorithms like steepest descent or conjugate gradient. Here, an improved…
We introduce an accurate and efficient method for characterizing surface wetting and interfacial properties, such as the contact angle made by a liquid droplet on a solid surface, and the vapor-liquid surface tension of a fluid. The method…