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Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…
We have investigated the potential energy surfaces for alanine chains consisting of three and six amino acids. For these molecules we have calculated potential energy surfaces as a function of the Ramachandran angles Phi and Psi, which are…
Electronically-active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from $\pi$-conjugated oligopeptides composed of an aromatic core…
A molecular dynamics simulation is performed to investigate spatial scale of low energy excitation (LEE) in a single linear chain of united atoms. The self part of the dynamic structure function, $S_\mathrm{S}(q,\omega)$, is obtained in a…
We study motility-induced phase separation~(MIPS) in active AB binary mixtures undergoing the chemical reaction $A \rightleftharpoons B$. Starting from the evolution equations for the density fields $\rho_i(\vec r, t)$ describing MIPS, we…
Oxide-water interfaces govern a wide range of physical and chemical processes fundamental to many fields like catalysis, geochemistry, corrosion, electrochemistry, and sensor technology. Near solid oxide surfaces, water behaves differently…
Although molten carbonates only represent, at most, a very minor phase in the Earth's mantle, they are thought to be implied in anomalous high-conductivity zones in its upper part (70-350 km). Besides the high electrical conductivity of…
New, high-precision measurements of the 3He(e,e'p) reaction using the A1 collaboration spectrometers at the Mainz microtron MAMI are presented. These were performed in parallel kinematics at energy transfers below the quasi-elastic peak,…
Experiments measuring contact formation between a probe and quencher in disordered chains provide information on the fundamental dynamical timescales relevant to protein folding, but their interpretation usually relies on simplified…
Simulating interactions between non-spherical colloidal particles is computationally challenging due to the complex dependency of forces and energies on their geometry. We introduce and evaluate both descriptor-based and end-to-end models…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is…
Electron heating and mixing during asymmetric reconnection are studied with a 3D kinetic simulation that matches plasma parameters from Magnetospheric Multiscale (MMS) spacecraft observations of a magnetopause diffusion region. The mixing…
Metriplectic systems are learned from data in a way that scales quadratically in both the size of the state and the rank of the metriplectic data. Besides being provably energy conserving and entropy stable, the proposed approach comes with…
We have simulated Edwards-Anderson (EA) as well as Sherrington-Kirkpatrick systems of L^3 spins. After averaging over large sets of EA system samples of 3 =< L =< 10, we obtain accurate numbers for distributions p(q) of the overlap…
Accurate, yet computationally efficient energy functions are essential for state-of-the art molecular dynamics (MD) studies of condensed phase systems. Here, a generic workflow based on a combination of machine learning-based and empirical…
In this paper, a hybrid quasi-static atomistic simulation method at finite temperature is developed, which combines the advantages of MD for thermal equilibrium and atomic-scale finite element method (AFEM) for efficient equilibration. Some…
Radiation transport codes require accurate nuclear cross sections to compute particle fluences inside shielding materials. The Tripathi semi-empirical reaction cross section, which includes over 60 parameters tuned to nucleon-nucleus (NA)…
Molecular dynamics (MD) simulations of ions (K$^+$, Na$^+$, Ca$^{2+}$ and Cl$^-$) in aqueous solutions are investigated. Water is described using the SPC/E model. A stochastic coarse-grained description for ion behaviour is presented and…
The system of three ${}^4\mathrm{He}$ atoms with realistic interactions is studied in the momentum-space framework. It is demonstrated that short and long-range difficulties encountered in the coordinate-space calculations can be reliably…