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The superposition of atomic potentials (SAP) approach has recently been shown to be a simple and efficient way to initialize electronic structure calculations [S. Lehtola, J. Chem. Theory Comput. 15, 1593 (2019)]. Here, we study the…
This paper gives a systematic method for constructing an N-body potential, approximating the true potential, that accurately captures meso-scale behavior of the chemical or biological system using pairwise potentials coming from…
Electrocardiographic imaging (ECGI) aims to non-invasively reconstruct activation maps of the heart from temporal body surface potentials. While most existing approaches rely on inverse and optimization techniques that may yield…
Detailed experimental data for physisorption potential-energy curves of H2 on low-indexed faces of Cu challenge theory. Recently, density-functional theory has been developed to also account for nonlocal correlation effects, including van…
An overview of computational methods to describe high-dimensional potential energy surfaces suitable for atomistic simulations is given. Particular emphasis is put on accuracy, computability, transferability and extensibility of the methods…
Local field potentials (LFPs) sampled with extracellular electrodes are frequently used as a measure of population neuronal activity. However, relating such measurements to underlying neuronal behaviour and connectivity is non-trivial. To…
The G-protein coupled receptors EP2 and EP4 both transduce the signal of the lipid messenger Prostaglandin E2 (PGE2). Changes in the cell response to PGE2 can have important effects on immunity and development of diseases, however, a…
In this paper we develop theoretical analysis and numerical reconstruction techniques for the solution of an inverse boundary value problem dealing with the nonlinear, time-dependent monodomain equation, which models the evolution of the…
This paper presents revised calculations for the Maki parameters $\kappa_{1}$ and $\kappa_{2}$ and the pair potential $\Delta({\bf r})$ of s-wave type-II superconductors near the upper critical field $H_{c2}$ with arbitrary impurity…
A general set of methods is presented for calculating chemical potentials in solid and liquid mixtures using {\em ab initio} techniques based on density functional theory (DFT). The methods are designed to give an {\em ab initio} approach…
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…
In this work we characterize an initial van der Waals adduct in the potential energy surface of reaction between cyanoacetylene HC3N and the cyano radical. The geometry of the CN-HC3N adduct has been optimized through calculations employing…
Catheter ablation has limited therapeutic efficacy against non-paroxysmal atrial fibrillation (AF), and electrophysiological studies using mapping catheters have been applied to evaluate the AF substrate. However, many of these approaches…
We propose a boundary element method for the accurate solution of the cell-by-cell bidomain model of electrophysiology. The cell-by-cell model, also called Extracellular-Membrane-Intracellular (EMI) model, is a system of reaction-diffusion…
The circulatory system, comprising the heart and blood vessels, is vital for nutrient transport, waste removal, and homeostasis. Traditional computational models often treat cardiac electromechanics and blood flow dynamics separately,…
Excitable membranes are an important type of nonlinear dynamical system and their study can be used to provide a connection between physical and biological circuits. We discuss two models of excitable membranes important in cardiac and…
Multi-electrode arrays covering several square millimeters of neural tissue provide simultaneous access to population signals such as extracellular potentials and spiking activity of one hundred or more individual neurons. The…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
We propose a simple scheme to construct composition-dependent interatomic potentials for multicomponent systems that when superposed onto the potentials for the pure elements can reproduce not only the heat of mixing of the solid solution…
The relationship between blood flow and neuronal activity is widely recognized, with blood flow frequently serving as a surrogate for neuronal activity in fMRI studies. At the microscopic level, neuronal activity has been shown to influence…