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Understanding the mechanisms of hydrogen embrittlement (HE) is essential for advancing next-generation high-strength steels, thereby motivating the development of highly accurate machine-learning interatomic potentials (MLIPs) for the Fe-H…
We present a family of alchemical perturbation potentials that enable the calculation of hydration free energies of small to medium-sized molecules in a concerted single alchemical coupling step instead of the commonly used sequence of two…
To further develop accurate and large-scale simulations of electrochemical interfaces, we propose a unified explicit electric potential framework to simultaneously predict atomic forces and electron density distributions. The framework…
The thesis is aimed to solve the template-free protein folding problem by tackling two important components: efficient sampling in vast conformation space, and design of knowledge-based potentials with high accuracy. We have proposed the…
Protein rigidity and flexibility can be analyzed accurately and efficiently using the program FIRST. Previous studies using FIRST were designed to analyze the rigidity and flexibility of proteins using a single static (snapshot) structure.…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
The accurate estimation of free energy differences between two states is a long-standing challenge in molecular simulations. Traditional approaches generally rely on sampling multiple intermediate states to ensure sufficient overlap in…
Possible crystalline modifications of chemical compounds at low temperatures correspond to local minima of the energy landscape. Determining these minima via simulated annealing is one method for the prediction of crystal structures, where…
Structure-based protein design has attracted increasing interest, with numerous methods being introduced in recent years. However, a universally accepted method for evaluation has not been established, since the wet-lab validation can be…
This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology…
Rare decays of the Z boson provide a sensitive probe for physics beyond the Standard Model (SM). This study investigates the $e^{+}e^{-} \to Z \to \nu\bar{\nu}\gamma$ process within the context of the Tera-Z programmes at future colliders…
We present a novel inference algorithm for arbitrary, binary, undirected graphs. Unlike loopy belief propagation, which iterates fixed point equations, we directly descend on the Bethe free energy. The algorithm consists of two phases,…
High-entropy alloys (HEAs) exhibit exceptional catalytic performance due to their complex surface structures. However, the vast number of active binding sites in HEAs, as opposed to conventional alloys, presents a significant computational…
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…
We report a scalable Fortran implementation of the phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) and demonstrate its excellent performance and beneficial scaling with respect to system size. Furthermore, we investigate…
We present the Time of Flight Fixed by Energy Estimation (TOFFEE) as a measure of the fission chain dynamics in subcritical assemblies. TOFFEE is the time between correlated gamma rays and neutrons, subtracted by the estimated travel time…
Computing vibrational free energies ($F_{vib}$) and entropies ($S_{vib}$) has posed a long standing challenge to the high-throughput ab initio investigation of finite temperature properties of solids. Here we use machine-learning techniques…
When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe…
We calculate binding energies of four molecular solids using the Hartree-Fock (HF) and second-order M{\o}ller-Plesset perturbation theory (MP2). We obtain the energies within many-body expansion (MBE) as well as using periodic boundary…
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.…