Related papers: Lambda-ABF: Simplified, Portable, Accurate and Cos…

We present ALFRED: a virtual memory abstraction that resolves the dichotomy between volatile and non-volatile memory in intermittent computing. Mixed-volatile microcontrollers allow programmers to allocate part of the application state onto…

This paper presents a load balancing strategy for reaction rate evaluation and chemistry integration in reacting flow simulations. The large disparity in scales during combustion introduces stiffness in the numerical integration of the PDEs…

To reduce complexity and achieve scalable performance in high-dimensional black-box settings, we propose a distributed method for nonconvex derivative-free optimization of continuous variables with an additively separable objective, subject…

We introduce Attention Free Transformer (AFT), an efficient variant of Transformers that eliminates the need for dot product self attention. In an AFT layer, the key and value are first combined with a set of learned position biases, the…

We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or "lambda-path" technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof…

The competition between evolution time, interaction strength, and temperature challenges our understanding of many-body quantum systems out-of-equilibrium. Here we consider a benchmark system, the Hubbard dimer, which allows us to explore…

The computational cost of stiff chemical kinetics remains a dominant bottleneck in reacting-flow simulation, yet hybrid integration strategies are typically driven by hand-tuned heuristics or supervised predictors that make myopic decisions…

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in…

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 introduce a flexible, scalable Bayesian inference framework for nonlinear dynamical systems characterised by distinct and hierarchical variability at the individual, group, and population levels. Our model class is a generalisation of…

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…

We propose a refined scheme of deriving an effective low-energy Hamiltonian for materials with strong electronic Coulomb correlations beyond density functional theory (DFT). By tracing out the electronic states away from the target degrees…

We present the Alchemical Transfer with Coordinate Swapping (ATS) method to enable the calculation of the relative binding free energies between large congeneric ligands and single-point mutant peptides to protein receptors with the…

Comprehension of metabolic pathways is considerably enhanced by metabolic flux analysis (MFA-ILE) in isotope labeling experiments. The balance equations are given by hundreds of algebraic (stationary MFA) or ordinary differential equations…

Kernel-based machine learning regression algorithms (MLRAs) are potentially powerful methods for being implemented into operational biophysical variable retrieval schemes. However, they face difficulties in coping with large training…

We present an extensive set of surface and chemisorption energies calculated using state of the art many-body perturbation theory. In the first part of the paper we consider ten surface reactions in the low coverage regime where…

We present a new method to compute free energies at a quantum mechanical (QM) level of theory from molecular simulations using cheap reference potential energy functions, such as force fields. To overcome the poor overlap between the…

A software package, called DFTBaby, is published, which provides the electronic structure needed for running non-adiabatic molecular dynamics simulations at the level of charge-consistent tight-binding DFT. A long-range correction is…

An accurate description of nonadiabatic dynamics of molecular species on metallic surfaces poses a serious computational challenge associated with a multitude of closely-spaced electronic states. We propose a mixed quantum-classical scheme…

Accurate free-energy calculations are essential for predicting thermodynamic properties and phase stability, but existing methods are limited: phonon-based approaches neglect anharmonicity and liquids, while molecular dynamics (MD) is…