Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces

We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an all-atom molecular dynamics (MD) description for specific atomistic details in the vicinity of the functional surface, with a dissipative particle dynamics (DPD) approach that captures mesoscopic hydrodynamics in the domain away from the functional surface. In order to achieve a seamless transition in dynamic properties we endow the MD simulation with a DPD thermostat, which is validated against experimental results by modeling water at different temperatures. We then validate the MD-DPD coupling method for transient Couette and Poiseuille flows, demonstrating that the concurrent MD-DPD coupling can resolve accurately the continuum-based analytical solutions. Subsequently, we simulate shear flows over polydimethylsiloxane (PDMS)-grafted surfaces (polymer brushes) for various grafting densities, and investigate the slip flow as a function of the shear stress. We verify that a "universal" power law exists for the sliplength, in agreement with published results. Having validated the MD-DPD coupling method, we simulate time-dependent flows past an endothelial glycocalyx layer (EGL) in a microchannel. Coupled simulation results elucidate the dynamics of EGL changing from an equilibrium state to a compressed state under shear by aligning the molecular structures along the shear direction. MD-DPD simulation results agree well with results of a single MD simulation, but with the former more than two orders of magnitude faster than the latter for system sizes above one micron.Comment: 11 pages, 12 figure

Discovering Key Unknowns for Tungsten-Hydrogen-Helium Plasma Material Interactions Using Molecular Dynamics

Molecular dynamics simulations have been used to study plasma material interactions to better understand the performance of a tungsten divertor. A tendril-like geometry was modeled to study the diffusion of helium in nanotendrils and its relation to fuzz growth. The tendrils remain stable throughout the simulation and a modified helium release mechanism is found that allows the helium retention to reach a steady state within the tendril. The helium retention within the tendril inversely depends on the surface to volume ratio. There is limited diffusion deep into the tendril and extrapolating the flux calculated to experimentally relevant time scales indicates that helium diffusion is not sufficient to drive fuzz growth. Helium implantation near a grain boundary, but not directly on the grain boudary itself, was performed. Helium behavior within the implantation zone is consistent with previous simulations of helium in defect-free tungsten. Some helium diffuses to the grain boundary where it forms small helium clusters but virtually no helium atoms diffuse over the grain boundary. The sink strength of the grain boundary and helium bubbles are calculated and the values are comparable, indicating that the grain boundary sink strength only matters at the beginning of the simulation before the helium bubbles form. Simulations of hydrogen and helium were performed to assess the interaction between the two gas atom species in tungsten. Simulations of small subsurface mixed hydrogen-helium bubbles indicate that hydrogen diffuses to the helium bubble periphery region and becomes trapped there. A binding energy of 2 eV is calculated. Modeling of hydrogen implantation in helium pre-implanted tungsten were performed and the presence of helium modifies the depth distribution and blocks the deeper diffusion of hydrogen when compared with hydrogen implantation in pure tungsten. This could potentially have a significant impact on tritium retention and material performance

Cues to opening mechanisms from in silico electric field excitation of cx26 hemichannel and in vitro mutagenesis studies in HeLa transfectans

Connexin channels play numerous essential roles in virtually every organ by mediating solute exchange between adjacent cells, or between cytoplasm and extracellular milieu. Our understanding of the structure-function relationship of connexin channels relies on X-ray crystallographic data for human connexin 26 (hCx26) intercellular gap junction channels. Comparison of experimental data and molecular dynamics simulations suggests that the published structures represent neither fully-open nor closed configurations. To facilitate the search for alternative stable configurations, we developed a coarse grained (CG) molecular model of the hCx26 hemichannel and studied its responses to external electric fields. When challenged by a field of 0.06 V/nm, the hemichannel relaxed toward a novel configuration characterized by a widened pore and an increased bending of the second transmembrane helix (TM2) at the level of the conserved Pro87. A point mutation that inhibited such transition in our simulations impeded hemichannel opening in electrophysiology and dye uptake experiments conducted on HeLa tranfectants. These results suggest that the hCx26 hemichannel uses a global degree of freedom to transit between different configuration states, which may be shared among the whole connexin family

Graphitization of amorphous carbon by swift heavy ion impacts: Molecular dynamics simulation

Stable C-C bonds existing in several sp hybridizations place carbon thin films of different structural compositions amongst the materials most tolerant to radiation damage, for applications in extreme environments. One of such applications, solid state electron stripper foils for heavy-ion accelerators, requires the understanding of the structural changes induced by high-energy ion irradiation. Tolerance of carbon structure to radiation damage, thermal effects and stress waves due to swift heavy ion impacts defines the lifetime and operational efficiency of the foils. In this work, we analyze the consequences of a single swift heavy ion impact on two different amorphous carbon structures by means of molecular dynamic simulations. The structures are constructed by using two different recipes to exclude the correlation of the evolution of sp2-to-sp3 hybridization with the initial condition. Both initial structures contain approximately 60% of sp2-bonded carbon atoms, however, with different degree of clustering of atoms with sp3 hybridization. We simulate the swift heavy ion impact employing an instantaneous inelastic thermal spike model. The analysis of changes in density, bonding content and the number and size of carbon primitive rings reveals graphitization of the material within the ion track, with higher degree of disorder in the core and more order in the outer shell. Simulated track dimensions are comparable to those observed in small angle x-ray scattering measurements of evaporation-deposited amorphous carbon stripper foils irradiated by 1.14 GeV U ions.Katharina Kupka gratefully acknowledges support by BMBF (contract No. 05P12RDRBL) and HGS-HIRe Graduate School. W.R., H.V. and K.N. acknowledge funding from the Academy of Finland project HISCON. We also thank the CSC-IT Center for Science Ltd for generous grants of computer time. PK acknowledges the Australian Research Council for financial support. Part of this research was undertaken on the SAXS/WAXS beamline at the Australian Synchrotron