Related papers: curvedSpaceSim: A framework for simulating particl…
GROMACS is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest…
When they are damaged or injured, soft biological tissues are able to self-repair and heal. Mechanics is critical during the healing process, as the damaged extracellular matrix (ECM) tends to be replaced with a new undamaged ECM supporting…
We construct a model to explore the hydrodynamic interactions of active inclusions in curved biological membranes. The curved membrane is modelled as a two dimensional layer of highly viscous fluid, surrounded by external solvents of…
Modern `smart' materials have complex microscale structure, often with unknown macroscale closure. The Equation-Free Patch Scheme empowers us to non-intrusively, efficiently, and accurately simulate over large scales through computations on…
Animal cells are both encapsulated and subdivided by lipid bilayer membranes. Beyond just acting as boundaries, these membranes' shapes influence the function of cells and their compartments. Physically, membranes are two-dimensional fluids…
The Kassiopeia particle tracking framework is an object-oriented software package using modern C++ techniques, written originally to meet the needs of the KATRIN collaboration. Kassiopeia features a new algorithmic paradigm for particle…
This work presents retQSS, a novel methodology for efficient modeling and simulation of particle systems in reticulated meshed geometries. On the simulation side, retQSS profits from the discrete-event nature of Quantized State System (QSS)…
In biomimetic and biological systems, interactions between surfaces are often mediated by adhesive molecules, nanoparticles, or colloids dispersed in the surrounding solution. We present here a general, statistical-mechanical model for two…
Faceted shapes, such as polyhedra, are commonly found in systems of nanoscale, colloidal, and granular particles. Many interesting physical phenomena, like crystal nucleation and growth, vacancy motion, and glassy dynamics are challenging…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
We explore how the fundamental problems in quantum molecular dynamics can be modelled using classical simulators (emulators) of quantum computers and the actual quantum hardware available to us today. The list of problems we tackle includes…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
Simulations of quantum transport in coherent conductors have evolved into mature techniques that are used in fields of physics ranging from electrical engineering to quantum nanoelectronics and material science. The most efficient…
The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry,…
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…
We use Stokesian Dynamics simulations to study the microscopic motion of particles suspended in fluids passing through porous media. We construct model porous media with fixed spherical particles, and allow mobile ones to move through this…
Over times shorter than that required for relaxation of enthalpy, a liquid can exhibit striking heterogeneities. The picture of these heterogeneities is complex with transient patches of rigidity, irregular yet persistent, intersected by…
Quantum simulation is a leading candidate for demonstrating practical quantum advantage over classical computation, as it is believed to provide exponentially more compute power than any classical system. It offers new means of studying the…
In this paper we introduce paraglide, a visualization system designed for interactive exploration of parameter spaces of multi-variate simulation models. To get the right parameter configuration, model developers frequently have to go back…
Exploring and modeling heterogeneous elastic surfaces requires multiple interactions with the environment and a complex selection of physical material parameters. The most common approaches model deformable properties from sets of offline…