Related papers: Accurate Estimation of Solvation Free Energy Using…
Aims. We use Hermite splines to interpolate pressure and its derivatives simultaneously, thereby preserving mathematical relations between the derivatives. The method therefore guarantees that thermodynamic identities are obeyed even…
Multi-fidelity simulation is a widely used strategy to reduce the computational cost of many-query numerical simulation tasks such as uncertainty quantification, design space exploration, and design optimization. The reduced basis approach…
An interpolation method to evaluate magnetic fields given unstructured, scattered magnetic data is presented. The method is based on the reconstruction of the global magnetic field using a superposition of orthogonal functions. The…
We propose an algorithm for molecular dynamics or Monte Carlo simulations that uses an interpolation procedure to estimate potential energy values from energies and gradients evaluated previously at points of a simplicial mesh. We chose an…
In the molecular dynamics calculations for the free energy of ions and ionic molecules, we often encounter wet charged molecular systems where electrical neutrality condition is broken. This causes a problem in the evaluation of…
We devise automated workflows for the calculation of Helmholtz and Gibbs free energies and their temperature and pressure dependence and provide the corresponding computational tools. We employ non-equilibrium thermodynamics for evaluating…
Interacting defect systems are ubiquitous in materials under realistic scenarios, yet gaining an atomic-level understanding of these systems from a computational perspective is challenging - it often demands substantial resources due to the…
The accurate prediction of solvation free energy is of significant importance as it governs the behavior of solutes in solution. In this work, we apply a variety of machine learning techniques to predict and analyze the alchemical free…
In this paper, we propose a new trigonometric interpolation algorithm and establish relevant convergent properties. The method adjusts an existing trigonometric interpolation algorithm such that it can better leverage Fast Fourier Transform…
Recently, nanofluidics experiments have been used to characterize the behavior of single DNA molecules confined to narrow slits etched with arrays of nanopits. Analysis of the experimental data relies on analytical estimates of the…
We introduce a new paradigm for immersed finite element and isogeometric methods based on interpolating function spaces from an unfitted background mesh into Lagrange finite element spaces defined on a foreground mesh that captures the…
We present a simulation protocol that allows for efficient sampling of the degrees of freedom of a solute in explicit solvent. The protocol involves using a non-equilibrium umbrella sampling method, in this case the recently developed…
Harmonic calculations based on density-functional theory are generally the method of choice for the description of phonon spectra of metals and insulators. The inclusion of anharmonic effects is, however, delicate as it relies on…
We present a novel method to model and calculate deformation fields between shapes embedded in $\mathbb{R}^D$. Our framework combines naturally interpolating the two input shapes and calculating correspondences at the same time. The key…
Extracting equilibrium information from nonequilibrium measurements is a challenge task of great importance in understanding the thermodynamic properties of physical, chemical, and biological systems. The discovery of the Jarzynski equality…
In some fields such as Mathematics Mechanization, automated reasoning and Trustworthy Computing etc., exact results are needed. Symbolic computations are used to obtain the exact results. Symbolic computations are of high complexity. In…
The enrichment formulation of double-interpolation finite element method (DFEM) is developed in this paper. DFEM is first proposed by Zheng \emph{et al} (2011) and it requires two stages of interpolation to construct the trial function. The…
Free energies play a central role in many descriptions of equilibrium and non-equilibrium properties of solids. Continuum partial differential equations (PDEs) of atomic transport, phase transformations and mechanics often rely on first and…
For nonlinear reduced-order models, especially for those with non-polynomial nonlinearities, the computational complexity still depends on the dimension of the original dynamical system. As a result, the reduced-order model loses its…
Immersed boundary methods are high-order accurate computational tools used to model geometrically complex problems in computational mechanics. While traditional finite element methods require the construction of high-quality boundary-fitted…