Related papers: A tutorial for mesoscale computer simulations of l…
The application of machine learning (ML) techniques, especially neural networks, has seen tremendous success at processing images and language. This is because we often lack formal models to understand visual and audio input, so here neural…
A coarse-grained computational model is used to investigate the effect of a fluctuating fluid membrane on the dynamics of patchy-particle assembly into virus capsid-like cores. Results from simulations for a broad range of parameters are…
Soft particles at fluid interfaces play an important role in many aspects of our daily life, such as the food industry, paints and coatings, and medical applications. Analytical methods are not capable of describing the emergent effects of…
Recently, the application of machine learning models has gained momentum in natural sciences and engineering, which is a natural fit due to the abundance of data in these fields. However, the modeling of physical processes from simulation…
A new method is presented for mesoscopic simulations of particle dispersions in liquid crystal solvents. It allows efficient first-principle simulations of the dispersions involving many particles with many-body interactions mediated by the…
We present a stochastic phase-field model for multicomponent lipid bilayers that explicitly accounts for the quasi-two-dimensional hydrodynamic environment unique to a thin fluid membrane immersed in aqueous solution. Dynamics over a wide…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
The purpose of this paper is to study the shapes and stabilities of bio-membranes within the framework of exterior differential forms. After a brief review of the current status in theoretical and experimental studies on the shapes of…
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…
As a complementary tool to laboratory experiments, discrete numerical simulation, applied to granular materials, provides valuable information on the grain and contact scale microstructure, thereby enabling one to better understand the…
The task of accurately locating fluid phase boundaries by means of computer simulation is hampered by problems associated with sampling both coexisting phases in a single simulation run. We explain the physical background to these problems…
Coarse-grained molecular dynamics (CGMD) is a technique developed as a concurrent multiscale model that couples conventional molecular dynamics (MD) to a more coarse-grained description of the periphery. The coarse-grained regions are…
Computational Fluid Dynamics (CFD) is a major sub-field of engineering. Corresponding flow simulations are typically characterized by heavy computational resource requirements. Often, very fine and complex meshes are required to resolve…
The biological function of membranes is closely related to their softness, which is often studied through the membranes' thermally-driven fluctuations. The analysis commonly assumes that the relaxation rate of a pure bending deformation is…
We propose a methodology to measure the mechanical properties of membranes from their fluctuations and apply this to optical microscopy measurements of giant unilamellar vesicles of lipids. We analyze the effect of the projection of thermal…
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…
The present work presents a density-functional microscopic model of soft biological tissue. The model was based on a prototype molecular structure from experimentally resolved collagen peptide residues and water clusters and has the…
Sintering, as a thermal process at elevated temperature below the melting point, is widely used to bond contacting particles into engineering products such as ceramics, metals, polymers, and cemented carbides. Modelling and simulation as…
Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping…
The separation between molecular and mesoscopic length and time scales poses a severe limit to molecular simulations of mesoscale phenomena. We describe a hybrid multiscale computational technique which address this problem by keeping the…