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Free-energy-based adaptive biasing methods, such as Metadynamics, the Adaptive Biasing Force (ABF) and their variants, are enhanced sampling algorithms widely used in molecular simulations. Although their efficiency has been empirically…
We present an efficient and systematically convergent approach to all-electron real-time time-dependent density functional theory (TDDFT) calculations using a mixed basis, termed as enriched finite element (EFE) basis. The EFE basis…
Grain boundary (GB) segregation models are derived for multi-principal element and high-entropy alloys (MPEAs and HEAs). Differing from classical models where one component is taken as solvent and others are considered solutes, these models…
In this study, we focus on developing efficient calibration methods via Bayesian decision-making for the family of compartmental epidemiological models. The existing calibration methods usually assume that the compartmental model is cheap…
We apply the renormalized singles (RS) Green's function in the Bethe-Salpeter equation (BSE)/$GW$ approach to predict accurate neutral excitation energies of molecular systems. The BSE calculations are performed on top of the…
We present receptor hopping and receptor swapping free energy estimation protocols based on the Alchemical Transfer Method (ATM) to model the binding selectivity of a set of ligands to two arbitrary receptors. The receptor hopping protocol,…
Approximate Bayes Computations (ABC) are used for parameter inference when the likelihood function of the model is expensive to evaluate but relatively cheap to sample from. In particle ABC, an ensemble of particles in the product space of…
Sampling useful three-dimensional molecular structures along with their most favorable conformations is a key challenge in drug discovery. Current state-of-the-art 3D de-novo design flow matching or diffusion-based models are limited to…
Bond-order potentials (BOPs) provide a local and physically transparent description of the interatomic interaction. Here we describe the efficient implementation of analytic BOPs in the BOPfox program and library. We discuss the integration…
We design and analyse variations of the classical Thompson sampling (TS) procedure for Bayesian optimisation (BO) in settings where function evaluations are expensive, but can be performed in parallel. Our theoretical analysis shows that a…
Physics-informed dynamical system models form critical components of digital twins of the built environment. These digital twins enable the design of energy-efficient infrastructure, but must be properly calibrated to accurately reflect…
Coflow is a network abstraction used to represent communication patterns in data centers. The coflow scheduling problem encountered in large data centers is a challenging $\mathcal{NP}$-hard problem. This paper tackles the scheduling…
Quantization and pruning are two effective Deep Neural Networks model compression methods. In this paper, we propose Automatic Prune Binarization (APB), a novel compression technique combining quantization with pruning. APB enhances the…
In this work, a systematic protocol is proposed to automatically parametrize implicit solvent models with polar and nonpolar components. The proposed protocol utilizes the classical Poisson model or the Kohn-Sham density functional theory…
Molecular simulations are an important tool for research in physics, chemistry, and biology. The capabilities of simulations can be greatly expanded by providing access to advanced sampling methods and techniques that permit calculation of…
We describe a simple method to determine, from ab initio calculations, the complete orientation-dependence of interfacial free energies in solid-state crystalline systems. We illustrate the method with an application to precipitates in the…
Computational load imbalance is a well-known performance issue in multiprocessor reacting flow simulations utilizing directly integrated chemical kinetics. We introduce an open-source dynamic load balancing model named DLBFoam to address…
The high computational cost of ab-initio methods limits their application in predicting electronic properties at the device scale. Therefore, an efficient method is needed to map the atomic structure to the electronic structure quickly.…
We analyze deficiencies of commonly used Coulomb approximations in Generalized Born solvation energy calculation models and report a development of a new fast surface-based method (FSBE) for numerical calculations of the solvation energy of…
A vital stage in the mathematical modelling of real-world systems is to calibrate a model's parameters to observed data. Likelihood-free parameter inference methods, such as Approximate Bayesian Computation, build Monte Carlo samples of the…