Related papers: Improved Adaptive Resolution Molecular Dynamics Si…
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between…
We propose a new model for the description of complex granular particles and their interaction in molecular dynamics simulations of granular material in two dimensions. The grains are composed of triangles which are connected by deformable…
The recently proposed Hamiltonian Adaptive Resolution Scheme (H-AdResS) allows to perform molecular simulations in an open boundary framework. It allows to change on the fly the resolution of specific subset of molecules (usually the…
This chapter describes the application of constrained geometric simulations for prediction of antibody structural dynamics. We utilize constrained geometric simulations method FRODAN, which is a low computational complexity alternative to…
The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows one to treat a molecular system with different levels of resolution depending on the location of the molecules. The construction of a Hamiltonian based on the this idea…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
Molecular Dynamics simulations are becoming a powerful tool for examining and predicting atomic and molecular processes in various environment. The present review shows how, in the fields of plasma physics, chemistry and interactions with…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present…
Coarse-grained models are a core computational tool in theoretical chemistry and biophysics. A judicious choice of a coarse-grained model can yield physical insight by isolating the essential degrees of freedom that dictate the…
Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…
In recent years, a few multiple-resolution modelling strategies have been proposed, in which functionally relevant parts of a biomolecule are described with atomistic resolution, while the remainder of the system is concurrently treated…
Numerous molecular systems, including solutions, proteins, and composite materials, can be modeled using mixed-resolution representations, of which the quantum mechanics/molecular mechanics (QM/MM) approach has become the most widely used.…
Coarse-graining has become an area of tremendous importance within many different research fields. For molecular simulation, coarse-graining bears the promise of finding simplified models such that long-time simulations of large-scale…
Molecular dynamics simulations are a cornerstone in science, allowing to investigate from the system's thermodynamics to analyse intricate molecular interactions. In general, to create extended molecular trajectories can be a…
Developing accurate and efficient coarse-grained representations of proteins is crucial for understanding their folding, function, and interactions over extended timescales. Our methodology involves simulating proteins with molecular…
Developing physics-based models for molecular simulation requires fitting many unknown parameters to diverse experimental datasets. Traditionally, this process is piecemeal and difficult to reproduce, leading to a fragmented landscape of…
Due to the wide range of timescales that are present in macromolecular systems, hierarchical multiscale strategies are necessary for their computational study. Coarse-graining (CG) allows to establish a link between different system…
A method for adaptive model order reduction for nonsmooth discrete element simulation is developed and analysed in numerical experiments. Regions of the granular media that collectively move as rigid bodies are substituted with rigid bodies…
Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to…