Related papers: Programmable Potentials: Approximate N-body potent…
A new potential energy surface (PES) and dynamical study are presented of the reactive process between H2CO + OH towards the formation of HCO + H2O and HCOOH + H. In this work a source of spurious long range interactions in symmetry adapted…
Ab initio electronic structure methods give accurate results for small systems, but do not scale well to large systems. Chemical insight tells us that molecular functional groups will behave approximately the same way in all molecules,…
A fundamental objective of materials modeling is identifying atomic structures that align with experimental observables. Conventional approaches for disordered materials involve sampling from thermodynamic ensembles and hoping for an…
We address the two main questions relevant to microscopic nuclear structure calculations starting from a free NN potential. These concern the accuracy of these kinds of calculations and the extent to which they depend on the potential used…
Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale. In general, an accurate parametrization…
Realistic modeling of ionic systems necessitates taking explicitly account of many-body effects. In molecular dynamics simulations, it is possible to introduce explicitly these effects through the use of additional degrees of freedom. Here…
Coarse-graining (CG) is a systematic reduction of the number of degrees of freedom (DOF) used to describe a system of interest. CG can be thought of as a projection on coarse-grained DOF and is therefore dependent on the functions used to…
A 3D Cellular Automaton model developed by the authors to deal with the dynamics of N-body interactions has been adapted to investigate the head-on collision of two identical bound clusters of particles, and the ensuing process of…
Bosonic two-dimensional self-bound clusters consisting of $N$ atoms interacting through additive van der Waals potentials become unbound at a critical mass m*(N); m*(N) has been predicted to be independent of the size of the system.…
Machine learned chemical potentials have shown great promise as alternatives to conventional computational chemistry methods to represent the potential energy of a given atomic or molecular system as a function of its geometry. However,…
We present a quantitative, multi-scale coarse-grained model of DNA coated colloids. The parameters of this model are transferable and are solely based on experimental data. As a test case, we focus on nano-sized colloids carrying…
We have developed a multi-objective optimization (MOO) procedure to construct modified-embedded-atom-method (MEAM) potentials with minimal manual fitting. This procedure has been applied successfully to develop a new MEAM potential for…
Recent findings suggest that humans deploy cognitive mechanism of physics simulation engines to simulate the physics of objects. We propose a framework for bots to deploy probabilistic programming tools for interacting with intuitive…
Using the formalism of extended N=4 supersymmetric quantum mechanics we consider the procedure of the construction of multi-well potentials. We demonstrate the form-invariance of Hamiltonians entering the supermultiplet, using the presented…
The electrostatic potential in the neighborhood of a biomolecule can be computed thanks to the non-linear divergence-form elliptic Poisson-Boltzmann PDE. Dedicated Monte-Carlo methods have been developed to solve its linearized version (see…
Interacting particle systems play a key role in science and engineering. Access to the governing particle interaction law is fundamental for a complete understanding of such systems. However, the inherent system complexity keeps the…
We consider a self-propelled particle system which has been used to describe certain types of collective motion of animals, such as fish schools and bird flocks. Interactions between particles are specified by means of a pairwise potential,…
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective…
In this paper, we utilized generative models, and reformulate it for problems in molecular dynamics (MD) simulation, by introducing an MD potential energy component to our generative model. By incorporating potential energy as calculated…
Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…