Related papers: Computing three-dimensional densities from force d…
Implicit electron-density solvation models based on joint density-functional theory offer a computationally efficient solution to the problem of calculating thermodynamic quantities of solvated systems from firstprinciples quantum…
Three-dimensional turbulence is usually studied experimentally by using a spatially localized forcing at large scales (e.g. via rotating blades or oscillating grids), often in a deterministic way. Here, we report an original technique where…
Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…
We present an extension of our recently introduced molecular density functional theory of water [G. Jeanmairet et al., J. Phys. Chem. Lett. 4, 619, 2013] to the solvation of hydrophobic solutes of various sizes, going from angstroms to…
We present results on the accurate one-dimensional (1D) modeling of simple atomic and molecular systems excited by strong laser fields. We use atomic model potentials that we derive from the corrections proposed earlier using the reduced…
We introduce a method for calculating the probability density function (PDF) of a turbulent density field in three dimensions using only information contained in the projected two-dimensional column density field. We test the method by…
Two of the most challenging tasks in molecular simulation consist in capturing the properties of systems with long-range interactions (e.g. electrolyte solutions) as well as systems containing large molecules such as hydrogels. For the…
We derive and analyze a simplified formulation of the numerical viscosity terms appearing in the expression of the numerical fluxes associated to several High-Resolution Shock-Capturing schemes. After some algebraic pre-processing, we give…
We present an amelioration of current known algorithms for optimal spectral partitioning problems. The idea is to use the advantage of a representation using density functions while decreasing the computational time. This is done by…
One of the fundamental problems in machine learning is the estimation of a probability distribution from data. Many techniques have been proposed to study the structure of data, most often building around the assumption that observations…
We present a brief review of the classical density functional theory of atomic and molecular fluids. We focus on the application of the theory to the determination of the solvation properties of arbitrary molecular solutes in arbitrary…
Dense 3D visual mapping estimates as many as possible pixel depths, for each image. This results in very dense point clouds that often contain redundant and noisy information, especially for surfaces that are roughly planar, for instance,…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
The Kohn-Sham scheme of density functional theory is one of the most widely used methods to solve electronic structure problems for a vast variety of atomistic systems across different scientific fields. While the method is fast relative to…
In transitions between different environmental settings, a molecular system inevitably undergoes a range of detectable changes, and the ability to accurately simulate such responses, e.g., in the form of shifts to molecular energies,…
Simulation involves predicting responses of a physical system. In this article, we simulate opto-acoustic signals generated in a three-dimensional volume due to absorption of an optical pulse. A separable computational model is developed…
Emerging sampling algorithms based on normalizing flows have the potential to solve ergodicity problems in lattice calculations. Furthermore, it has been noted that flows can be used to compute thermodynamic quantities which are difficult…
In this paper we present a new method, which allows for the construction of triangular isosurfaces from three-dimensional data sets, such as 3D image data and/or numerical simulation data that are based on regularly shaped, cubic lattices.…
Large high-dimensional datasets are becoming more and more popular in an increasing number of research areas. Processing the high dimensional data incurs a high computational cost and is inherently inefficient since many of the values that…
The major uncertainties in studies of the multi-scale structure of the Universe arise not from observational errors but from the variety of legitimate definitions and detection methods for individual structures. To facilitate the study of…