Related papers: Polarisable force fields: What do they add in biom…
Molecular simulations provide a powerful means to unravel the complex relationships between network architecture and the mechanical response of polymer networks, with a particular emphasis on rupture and fracture phenomena. Although…
The interfaces between metal electrodes and liquid electrolytes are prototypical in electrochemistry. That is why it is crucial to have a molecular and dynamical understating of such interfaces for both electrical properties and chemical…
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…
This document attempts to clarify potential confusion regarding electrostatics calculations, specifically in the context of biomolecular structure and specifically as regards the units typically used to contour/visualize isopotential…
Molecular dynamics (MD) simulation techniques are widely used for various natural science applications. Increasingly, machine learning (ML) force field (FF) models begin to replace ab-initio simulations by predicting forces directly from…
A short overview about the potential of polarized beams at future colliders is given. In particular the baseline design for polarized beams at the ILC is presented and the physics case for polarized $e^-$ and $e^+$ is discussed. In order to…
In recent years, cell-based assays have been frequently used in molecular interaction analysis. Cell-based assays complement traditional biochemical and biophysical methods, as they allow for molecular interaction analysis, mode of action…
Machine learning (ML) has emerged as a pervasive tool in science, engineering, and beyond. Its success has also led to several synergies with molecular dynamics (MD) simulations, which we use to identify and characterize the major…
While biological crystallization processes have been studied on the microscale extensively, models addressing the mesoscale aspects of such phenomena are rare. In this work, we investigate whether the phase-field theory developed in…
The structural dynamics of macromolecules is important for most microbiological processes, from protein folding to the origins of neurodegenerative disorders. Noninvasive measurements of these dynamics are highly challenging. Recently,…
Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off…
To address the computational challenges of ab initio molecular dynamics and the accuracy limitations of empirical force fields, the introduction of machine learning force fields has proven effective in various systems including metals and…
To exclude collisions leading to the overlap of finite-sized charged particles in molecular dynamics (MD) simulations in systems like complex (dusty) plasmas, we developed a scheme to generate a pair interaction force functionally depending…
A brief review of modeling and simulation methods for a study of polymers at interfaces is provided. When studying truly multiscale problems as provided by realistic polymer systems, coarse graining is practically unavoidable. In this…
A proper treatment of electrostatic interactions is crucial for the accurate calculation of forces in computer simulations. Electrostatic interactions are typically modeled using Ewald based methods, which have become one of the…
The dynamics of phase transitions plays a crucial r\^ole in the so-called interface between high energy particle physics and cosmology. Many of the interesting results generated during the last fifteen years or so rely on simplified…
Both classical and quantum electrodynamics predict the existence of dipole-dipole long-range electrodynamic intermolecular forces; however, these have never been hitherto experimentally observed. The discovery of completely new and…
Simulating protein-membrane interactions is an important and dynamic area of research. A proper definition of electrostatic forces on membrane surfaces is necessary for developing electromechanical models of protein-membrane interactions.…
We discuss the Lattice Boltzmann-Particle Dynamics (LBPD) multiscale paradigm for the simulation of complex states of flowing matter at the interface between Physics, Chemistry and Biology. In particular, we describe current large-scale…
Multi-component polymer mixtures are ubiquitous in biological self-organization but are notoriously difficult to study computationally. Plagued by both slow single molecule relaxation times and slow equilibration within dense mixtures,…