相关论文: Parallel computing and molecular dynamics of biolo…
We present a simple, and physically motivated, coarse-grained model of a lipid bilayer, suited for micron scale computer simulations. Each ~25 nm^2 patch of bilayer is represented by a spherical particle. Mimicking forces of hydrophobic…
Parallel computing has turned out to be the enabling technology to solve complex physical systems. However, the transition from shared memory, vector computers to massively parallel, distributed memory systems and, recently, to hybrid…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
Efficient implementations of the classical molecular dynamics (MD) method for Lennard-Jones particle systems are considered. Not only general algorithms but also techniques that are efficient for some specific CPU architectures are also…
Our long term goal is to execute General Purpose computation on homogeneous computing media consisting of millions of small identical Processing Elements (PE) communicating locally. We proceed by simulating the Self-Development of a Network…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
While several paths have emerged in microelectronics and computing as follow-ons to Turing architectures, and have been implemented using essentially silicon circuits, very little beyond Moore research has considered: (1) first biological…
Peripheral membrane proteins can reversibly and specifically bind to biological membranes to carry out functions such as cell signalling, enzymatic activity, or membrane remodelling. Structures of these proteins and of their lipid-binding…
This paper proposes a parallel numerical algorithm to simulate the flow and the transport in a discrete fracture network taking into account the mass exchanges with the surrounding matrix. The discretization of the Darcy fluxes is based on…
In this work, we consider alternative discretizations for PDEs which use expansions involving integral operators to approximate spatial derivatives. These constructions use explicit information within the integral terms, but treat boundary…
The paper deals with the developing of the methodological backgrounds for the modeling and simulation of complex dynamical objects. Such backgrounds allow us to perform coordinate transformation and formulate the algorithm of its usage for…
Simulating large-scale microswimmer dynamics in viscous fluid poses significant challenges due to the coupled high spatial and temporal complexity. Conventional high-performance computing (HPC) methods often address these two dimensions in…
Membrane systems represent a computational model that operates in a distributed and parallel manner, inspired by the behavior of biological cells. These systems feature objects that transform within a nested membrane structure. This…
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…
Theoretical and experimental investigations of water vapor interaction with porous materials are very needful for various fields of science and technology. Not only studies of the interaction of water vapor and porous material as a…
The numerical tools to simulate the bidomain model in cardiac electrophysiology are constantly developing due to the great clinical interest and scientific advances in mathematical models and computational power. The bidomain model consists…
Modeling membrane interactions with arbitrarily shaped colloidal particles, such as environmental micro- and nanoplastics, at the cell scale remains particularly challenging, owing to the complexity of particle geometries and the need to…
Computational determination of the equilibrium state of heterogeneous phospholipid mem-branes is a significant challenge. We wish to explore the rich phase diagram of these multi-component systems. However, the diffusion and mixing times in…
The complexities of today's materials simulations demand computer codes which are both powerful and highly flexible. A researcher should be able to readily choose different geometries, different materials and different algorithms without…
This chapter summarizes several approaches combining theory, simulation and experiment that aim for a better understanding of phenomena in lipid bilayers and membrane protein systems, covering topics such as lipid rafts, membrane mediated…