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Here, we provide an overview of theoretical approaches to semiflexible polymers and their networks. Such semiflexible polymers have large bending rigidities that can compete with the entropic tendency of a chain to crumple up into a random…
Background: Monte Carlo simulations of diffusion are commonly used as a model validation tool as they are especially suitable for generating the diffusion MRI signal in complicated tissue microgeometries. New method: Here we describe the…
Using the specific model of a system of like charged ions confined between two planar like charged surfaces, we compare the predictions for the energy and density profile of four simulation methods available to treat the long range Coulomb…
Biological systems exploit self-assembly to create complex structures whose arrangements are finely controlled from molecular to mesoscopic level. Herein we report an example of using fully synthetic systems that mimic two levels of…
Quantum spin rings represent fundamental model systems that exhibit distinctive quantum phenomena-such as quantum critical behavior and quasiparticle excitations-arising from their periodic boundary conditions and enhanced quantum…
Aiming to understand real-world hierarchical networks whose degree distributions are neither power law nor exponential, we construct a hybrid clique network that includes both homogeneous and inhomogeneous parts, and introduce an…
This paper gives an overview of the particle transport theory essentials, the basics of particle-material interaction simulation, physical quantities needed to simulate particle transport and interactions in materials, Monte Carlo…
Microgels are colloidal-scale particles individually made of crosslinked polymer networks that can swell and deswell in response to external stimuli, such as changes to temperature or pH. Despite a large amount of experimental activities on…
The study of networks plays a crucial role in investigating the structure, dynamics, and function of a wide variety of complex systems in myriad disciplines. Despite the success of traditional network analysis, standard networks provide a…
We present computer simulations of a realistic model of microgels. Unlike the regular network frameworks usually assumed in the simulation literature, we model and simulate a realistic and efficient synthesis route, mimicking cross-linking…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
We develop the hybrid Monte Carlo method for simulations of single off-lattice polymer chains. We discuss implementation and choice of simulation parameters in some detail. The performance of the algorithm is tested on models for…
The structure of surfaces and interfaces of silica (SiO2) is investigated by large scale molecular dynamics computer simulations. In the case of a free silica surface, the results of a classical molecular dynamics simulation are compared to…
Disordered networks of semiflexible filaments are common support structures in biology. Familiar examples include fibrous matrices in blood clots, bacterial biofilms, and essential components of cells and tissues of plants, animals, and…
Bilayer graphene has been a subject of intense study in recent years. We extend a structural phase field crystal method to include an external potential from adjacent layer(s), which is generated by the corresponding phase field and changes…
We consider two (2D) and three (3D) dimensional granular systems exposed to compression, and ask what is the influence of the number of physical dimensions on the properties of the interaction networks that spontaneously form as these…
Simulation is often used to evaluate the relevance of a Directing Program of Production (PDP) or to evaluate its impact on detailed sc\'enarii of scheduling. Within this framework, we propose to reduce the complexity of a model of…
An innovative image analysis technique is proposed to process real solar cell pictures, identify grains and grain boundaries in polycrystalline Silicon, and finally generate finite element meshes. Using a modified intrinsic cohesive zone…
In this perspective, we examine three key aspects of an end-to-end pipeline for realistic cellular simulations: reconstruction and segmentation of cellular structures; generation of cellular structures; and mesh generation, simulation, and…
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed…