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Biased sampling in molecular dynamics simulations overcomes timescale limitations and delivers free-energy landscapes, essential to understand complex atomistic phenomena. However, when applied across diverse systems and processes, biasing…
A three dimensional parallel implementation of Multiscale Mixed Methods based on non-overlapping domain decomposition techniques is proposed for multi-core computers and its computational performance is assessed by means of numerical…
Byte Pair Encoding (BPE) is a widely used tokenization algorithm, whose tokens cannot extend across pre-tokenization boundaries, functionally limiting it to representing at most full words. The BoundlessBPE and SuperBPE algorithms extend…
The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics, and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
We assess the applicability of Alchemical Perturbation Density Functional Theory (APDFT) for quickly and accurately estimating deprotonation energies. We have considered all possible single and double deprotonations in one hundred small…
The Atom-Calibrated Basis-set Extrapolation (ACBE) method is introduced as a robust approach for extrapolating MP2 correlation energies from small basis sets. Unlike conventional extrapolation techniques, ACBE incorporates system- and…
Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…
Hybrid density functional theory (DFT) remains intractable for large periodic systems due to the demanding computational cost of exact exchange. We apply the tensor hypercontraction (THC) (or interpolative separable density fitting)…
Semidefinite programming (SDP) is widely acknowledged as one of the most effective methods for deriving the tightest lower bounds of the optimal power flow (OPF) problems. In this paper, an enhanced semidefinite relaxation model that…
The biological functions of proteins often depend on dynamic structural ensembles. In this work, we develop a flow-based generative modeling approach for learning and sampling the conformational landscapes of proteins. We repurpose highly…
First-order fully implicit as well as implicit--explicit schemes for coupled elliptic-parabolic systems are discussed in [Ern and Meunier, ESAIM: M2AN, 2009] and [Altmann et al., Math.\ Comp., 2021], respectively. The extension of the…
Biomolecular electrostatics is key in protein function and the chemical processes affecting it. Implicit-solvent models via the Poisson-Boltzmann (PB) equation provide insights with less computational cost than atomistic models, making…
Semiconductor device models are essential to understand the charge transport in thin film transistors (TFTs). Using these TFT models to draw inference involves estimating parameters used to fit to the experimental data. These experimental…
Calculating free energy differences is a topic of substantial interest and has many applications including molecular docking and hydration, solvation, and binding free energies which is used in computational drug discovery. However, in…
We present an efficient \textit{ab initio} method for calculating the electronic structure and total energy of strongly correlated electron systems. The method extends the traditional Gutzwiller approximation for one-particle operators to…
Reduced density matrix functional theory (RDMFT) calculations are usually implemented in a decoupled manner, where the orbital and occupation optimizations are repeated alternately. Typically, orbital updates are performed using the unitary…
This paper presents a new boundary integral equation (BIE) method for simulating particulate and multiphase flows through periodic channels of arbitrary smooth shape in two dimensions. The authors consider a particular system---multiple…
As battery technologies advance toward higher stability and energy density, the need for extensive cell-level testing across various component configurations becomes critical. To evaluate performance and understand the operating principles…
We present our blind predictions for the Statistical Assessment of the Modeling of Proteins and Ligands (SAMPL), 9th challenge, focusing on binding of WP6 (carboxy-pillar[6]arene) with ammonium/diammonium cationic guests. Host-guest binding…