Related papers: Initial estimate for minimum energy pathways and t…
Accurate orientation estimation is a crucial component of 3D molecular structure reconstruction, both in single-particle cryo-electron microscopy (cryo-EM) and in the increasingly popular field of cryo-electron tomography (cryo-ET). The…
For interacting electrons in solids, Heisenberg's equation is used to calculate the distribution in energy of transitions induced by adding an electron to an atomic-like spin orbital. This is the projected density of transitions which…
We develop a new scheme for determining molecular partial atomic charges (PACs) with external electrostatic potential (ESP) closely mimicking that of the molecule. The PACs are the "minimal corrections" to a reference-set of PACs necessary…
We perform calculations of the {3D} finite-temperature homogeneous electron gas (HEG) in the warm-dense regime ({r_{s} \equiv (3/4\pi n)^{1/3}a_{B}^{- 1} = 1.0- 40.0} and {\Theta \equiv T/T_{F} = 0.0625- 8.0}) using restricted path integral…
In this work, a generic rigorous Bayesian formalism is introduced to predict the most likely path of any ion crossing a medium between two detection points. The path is predicted based on a combination of the particle scattering in the…
We consider partially observable Markov decision processes (POMDPs) with a set of target states and positive integer costs associated with every transition. The traditional optimization objective (stochastic shortest path) asks to minimize…
Choosing a nonlinear state estimator for an application often involves a trade-off between local optimality (such as provided by an extended Kalman filter) and (almost-/semi-) global asymptotic stability (such as provided by a constructive…
In the present work we detail how the many-body potential energy landscape of interatomic potentials for carbon can be explored by utilising the nested sampling algorithm, allowing the calculation of their pressure-temperature phase diagram…
Path integral calculations of equilibrium isotope effects and isotopic fractionation are expensive due to the presence of path integral discretization errors, statistical errors, and thermodynamic integration errors. Whereas the…
Outer sphere electron transfer rates can be calculated from simulation data by sampling the equilibrium statistics of the canonical reaction coordinate -- the vertical energy gap. For these calculations, electron transfer is typically…
Characterizing the entropy of a system is a crucial, and often computationally costly, step in understanding its thermodynamics. It plays a key role in the study of phase transitions, pattern formation, protein folding and more. Current…
A recently developed method, introduced in Phys. Rev. Lett. 94 (2005) 180403, Phys. Rev. B 72 (2005) 064302, Phys. Lett. A 344 (2005) 84, systematically improved the convergence of generic path integrals for transition amplitudes. This was…
A theoretical method for the estimation of cross sections and rates for excitation and charge transfer processes in low-energy hydrogen atom collisions with neutral atoms, based on an asymptotic two-electron model of ionic-covalent…
In this paper we present a method for simulating the response of microstrip detectors to minimum ionizing particles, making use of a program for field calculation, a program for carrier drift and SPICE for circuit response. A knowledge of…
When a system is driven out of equilibrium by a time-dependent protocol that modifies the Hamiltonian, it follows a nonequilibrium path. Samples of these paths can be used in nonequilibrium work theorems to estimate equilibrium quantities,…
Approximating marginals of a graphical model is one of the fundamental problems in the theory of networks. In a recent paper a method was shown to construct a variational free energy such that the linear response estimates, and maximum…
This paper introduces an approach for detecting differences in the first-order structures of spatial point patterns. The proposed approach leverages the kernel mean embedding in a novel way by introducing its approximate version tailored to…
Molecular dynamics is a powerful tool for studying the thermodynamics and kinetics of complex molecular events. However, these simulations can rarely sample the required time scales in practice. Transition path sampling overcomes this…
A new simulation approach of field evaporation is presented. The model combines classical electrostatics with molecular dynamics (MD) simulations. Unlike previous atomic-level simulation approaches, our method does not rely on an…
We present a message-passing algorithm to solve the edge disjoint path problem (EDP) on graphs incorporating under a unique framework both traffic optimization and path length minimization. The min-sum equations for this problem present an…