Related papers: Programmable Potentials: Approximate N-body potent…

An analytical description of polymer melts and their mixtures as liquids of interacting soft colloidal particles is obtained from liquid-state theory. The derived center-of-mass pair correlation functions with no adjustable parameters…

Simulations of complex physical systems are typically realized by discretizing partial differential equations (PDEs) on unstructured meshes. While neural networks have recently been explored for surrogate and reduced order modeling of PDE…

We analytically derive the lower bound of the total conformational energy of a protein structure by assuming that the total conformational energy is well approximated by the sum of sequence-dependent pairwise contact energies. The condition…

I review the quantum theory of the electron moving in a random environment. First, the quantum mechanics of individual particles scattered on a random potential is discussed. The quantum-mechanical description is extended to many-body…

Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…

We present an approach for calculating coarse-grained angle-resolved effective pair potentials for uniaxial molecules. For integrating out the intramolecular degrees of freedom we apply umbrella sampling and steered dynamics techniques in…

DNA-functionalized particles have great potential for the design of complex self-assembled materials. The major hurdle in realizing crystal structures from DNA-functionalized particles is expected to be kinetic barriers that trap the system…

Deep potentials for molecular dynamics (MD) achieve first-principles accuracy at much lower computational cost. However, their use in large length- and time-scale simulations is limited by their lower speeds compared to analytical atomistic…

The central approximation made in classical molecular dynamics simulation of materials is the interatomic potential used to calculate the forces on the atoms. Great effort and ingenuity is required to construct viable functional forms and…

Ligand coated nanoparticles are complex objects consisting of a metallic or semiconductor core with organic ligands grafted on their surface. These organic ligands provide stability to a nanoparticle suspension. In solutions, the effective…

The simulation of borosilicate glasses is challenging due to the composition and temperature dependent coordination state of boron atoms. Here, we present a newly developed machine learning optimized classical potential for molecular…

Physical reasoning is a core aspect of intelligence in animals and humans. A central question is what model should be used as a basis for reasoning. Existing work considered models ranging from intuitive physics and physical simulators to…

We present an algorithm for quickly generating multiple realizations of N-body simulations to be used, for example, for cosmological parameter estimation from surveys of large-scale structure. Our algorithm uses a new method to resample the…

A numerical method using implicit surface representations is proposed to solve the linearized Poisson-Boltzmann equations that arise in mathematical models for the electrostatics of molecules in solvent. The proposed method used an implicit…

Compartmentalised biochemical reactions are a ubiquitous building block of biological systems. The interplay between chemical and compartmental dynamics can drive rich and complex dynamical behaviors that are difficult to analyse…

Recent advances in machine-learned interatomic potentials largely benefit from the atomistic representation and locally invariant many-body descriptors. It was however recently argued that including three- (or even four-) body features is…

We introduce a class of interatomic potential models that can be automatically generated from data consisting of the energies and forces experienced by atoms, derived from quantum mechanical calculations. The resulting model does not have a…

A number of problems arise when long-range forces, such as those governed by Bessel functions, are used in particle-particle simulations. If a simple cut-off for the interaction is used, the system may find an equilibrium configuration at…

Different steps leading to the new functional for pairing based on natural orbitals and occupancies proposed in ref. [D. Lacroix and G. Hupin, arXiv:1003.2860] are carefully analyzed. Properties of quasi-particle states projected onto good…

We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…