Related papers: Programmable Potentials: Approximate N-body potent…
Molecular dynamics (MD) simulations involving reactive potentials can be used to model material failure. The empirical potentials which are used in such simulations are able to adapt to the atomic environment, at the expense of a…
Two-, three-, and four-boson systems are studied close to the unitary limit using potential models constructed to reproduce the minimal information given by the two-body scattering length $a$ and the two-body binding energy or virtual state…
Simulation of materials at the atomistic level is an important tool in studying microscopic structure and processes. The atomic interactions necessary for the simulation are correctly described by Quantum Mechanics. However, the…
The rich and diverse dynamics of particle-based systems ultimately originates from the coupling of their degrees of freedom via internal interactions. To arrive at a tractable approximation of such many-body problems, coarse-graining is…
Electronic nearsightedness is one of the fundamental principles governing the behavior of condensed matter and supporting its description in terms of local entities such as chemical bonds. Locality also underlies the tremendous success of…
The prediction of the three-dimensional structures of the native state of proteins from the sequences of their amino acids is one of the most important challenges in molecular biology. An essential ingredient to solve this problem within…
Previous studies have used numerical methods to optimize the hyperpolarizability of a one-dimensional quantum system. These studies were used to suggest properties of one-dimensional organic molecules, such as the degree of modulation of…
Molecular dynamics (MD) simulation, which is considered an important tool for studying physical and chemical processes at the atomic scale, requires accurate calculations of energies and forces. Although reliable energies and forces can be…
In this work, we propose a multi-scale protocol for routine theoretical studies of chemical reaction mechanisms. The initial reaction paths of our investigated systems are sampled using the Nudged-Elastic Band (NEB) method driven by a cheap…
The structural properties of fluids whose molecules interact via potentials with a hard-core plus n piece-wise constant sections of different widths and heights are derived using a (semi-analytical) rational-function approximation method.…
We describe an algorithm for constructing N-body realisations of equilibrium stellar systems. The algorithm complements existing orbit-based modelling techniques using linear programming or other optimization algorithms. The equilibria are…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Creating accurate, analytic atom--atom potentials for small organic molecules from first principles can be a time-consuming and computationally intensive task, particularly if we also require them to include explicit polarization terms,…
We have proposed an efficient parameterization method for a recent variant of the Gay-Berne potential for dissimilar and biaxial particles and demonstrated it for a set of small organic molecules. Compared to the previously proposed…
We provided a concise and self-contained introduction to molecular dynamics (MD) simulation, which involves a body of fundamentals needed for all MD users. The associated computer code, simulating a gas of classical particles interacting…
We focus on finding a coarse grained description able to reproduce the thermodynamic behavior of a molecular system by using mesoparticles representing several molecules. Interactions between mesoparticles are modelled by an interparticle…
An effective potential function is critical for protein structure prediction and folding simulation. Simplified protein models such as those requiring only $C_\alpha$ or backbone atoms are attractive because they enable efficient search of…
Theoretical studies of self-assembly processes and condensed phases in colloidal systems are often based on effective inter-particle potentials. Here we show that developing an effective potential for particles interacting with a limited…
Density functional theory offers a very accurate way of computing materials properties from first principles. However, it is too expensive for modelling large-scale molecular systems whose properties are, in contrast, computed using…
We develop a machine-learning method for coarse-graining condensed-phase molecular systems using anisotropic particles. The method extends currently available high-dimensional neural network potentials by addressing molecular anisotropy. We…