A cell multipole based domain decomposition algorithm for molecular dynamics simulation of systems of arbitrary shape

2002 ◽  
Vol 144 (2) ◽  
pp. 141-153 ◽  
Author(s):  
Pasupulati Lakshminarasimhulu ◽  
Jeffry D. Madura
2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Yui Kato ◽  
Takuya Uto ◽  
Daisuke Tanaka ◽  
Kojiro Ishibashi ◽  
Akiko Kobayashi ◽  
...  

AbstractCryopreservation of cells is necessary for long periods of storage. However, some cell lines cannot be efficiently cryopreserved, even when optimized commercial cryoprotectants are employed. Previously, we found that a low-toxic synthetic zwitterion aqueous solution enabled good cryopreservation. However, this zwitterion solution could not cryopreserve some cells, such as human kidney BOSC cells, with good efficiency. Therefore, details of the cryoprotective effect of the zwitterions and optimization based on its mechanisms are required. Herein, we synthesized 18 zwitterion species and assessed the effects of the physical properties of water/zwitterion mixtures. Non-cell-permeable zwitterions can inhibit ice crystal formation extracellularly via direct interaction with water and intracellularly via dehydration of cells. However, cells that could not be cryopreserved by zwitterions were insufficiently dehydrated in the zwitterion solution. Dimethyl sulfoxide (DMSO) was combined as a cell-permeable cryoprotectant to compensate for the shortcomings of non-cell-permeable zwitterions. The water/zwitterion/DMSO (90/10/15, v/w/w) could cryopreserve different cells, for example freezing-vulnerable K562 and OVMANA cells; yielding ~1.8-fold cell viability compared to the case using a commercial cryoprotectant. Furthermore, molecular dynamics simulation indicated that the zwitterions protected the cell membrane from the collapse induced by DMSO.


Author(s):  
N. Maftouni ◽  
M. Amininasab ◽  
F. Kowsari

Nanomembrane is a very important part of living systems. Alive cells have lipid bilayer nanomembrane in liquid phase. The lateral pressure profile, or stress profile, across a cell nanomembrane is the result of the inhomogeneous nature of the interactions within a nanomembrane. It has been shown that the work exerted by the pressure profile when a protein conformational change takes place is significant, of the order of 10kBT, and that the lateral pressure profile averaged over the whole nanomembrane is modified by the inclusion of a protein. Indeed, understanding the full coupling for stress arising from protein-lipid interactions is of profound importance and calls for elucidation. Here proper ensembles for molecular dynamics simulation of inhomogeneous nanoscale system of nanomembrane-cytotoxin protein are introduced. The Virial pressure theorem together with using molecular dynamics simulation data are proposed to use to calculate pressure filed. The predicted pressure tensor of system without cytotoxin is compared with that of system including this protein. Finally deformation of nanomembrane is related to the variation of pressure tensor.


2015 ◽  
Vol 8 (4) ◽  
pp. 530-548 ◽  
Author(s):  
Li Yin ◽  
Jiming Wu ◽  
Zihuan Dai

AbstractWe develop a Lions domain decomposition algorithm based on a cell functional minimization scheme on non-matching multi-block grids for nonlinear radiation diffusion equations, which are described by the coupled radiation diffusion equations of electron, ion and photon temperatures. The L2 orthogonal projection is applied in the Robin transmission condition of non-matching surfaces. Numerical results show that the algorithm keeps the optimal accuracy on the whole computational domain, is robust enough on distorted meshes and curved surfaces, and the convergence rate does not depend on Robin coefficients. It is a practical and attractive algorithm in applying to the two-dimensional three-temperature energy equations of Z-pinch implosion simulation.


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