Analysis of a micro–macro acceleration method with minimum relative entropy moment matching

We analyse convergence of a micro–macro acceleration method for the simulation of stochastic differential equations with time-scale separation. The method alternates short bursts of path simulations with the extrapolation of macroscopic state variables forward in time. After extrapolation, a new microscopic state is constructed, consistent with the extrapolated macroscopic state, that minimises the perturbation caused by the extrapolation in a relative entropy sense. We study local errors and numerical stability of the method to prove its convergence to the full microscopic dynamics when the extrapolation time step tends to zero and the number of macroscopic state variables tends to infinity.     

Unravelling the Enigma of Nonoxidative Conversion of Methane on Iron Single-Atom Catalysts

The direct, nonoxidative conversion of methane on a silica-confined single-atom iron catalyst is a landmark discovery in catalysis, but the proposed gas-phase reaction mechanism is still open to discussion. Here, we report a surface reaction mechanism by computational modeling and simulations. The activation of methane occurs at the single iron site, whereas the dissociated methyl disfavors desorption into gas phase under the reactive conditions. In contrast, the dissociated methyl prefers transferring to adjacent carbon sites of the active center (Fe₁©SiC₂), followed by C−C coupling and hydrogen transfer to produce the main product (ethylene) via a key −CH−CH₂ intermediate. We find a quasi Mars–van Krevelen (quasi-MvK) surface reaction mechanism involving extracting and refilling the surface carbon atoms for the nonoxidative conversion of methane on Fe₁©SiO₂ and this surface process is identified to be more plausible than the alternative gas-phase reaction mechanism.     

Molecular insight for the role of key residues of calreticulin in its binding activities: A computational study

Calreticulin (CRT) is localized to and has functions in multiple cellular compartments, including the cell surface, the endoplasmic reticulum, and the extracellular matrix. Mutagenesis studies have identified several residues on a concave β-sheet surface of CRT critical for CRT binding to carbohydrate and other proteins/peptides. How the mutations of these key residues in CRT affect the conformation and dynamics of CRT, further influencing CRT binding to carbohydrates and other proteins to signal the important biological activities remain unknown. In this study, we investigated the effect of three key point mutations (C105A, C137A and W319A) on CRT conformation and dynamics via atomistic molecular dynamics simulations. Results show that these three key residues mutations induced the changes of CRT local backbone flexibility and secondary structure of CRT N-domain, which could further affect CRT’s binding activity. C137A mutation led to dramatic decrease of the overall size of CRT due to the P-domain fold back to the globular domain and formed new inter-domain contacts, which can cause blockage of CRT’s binding with other large substrates. Furthermore, for CRT concave β-strand surface patch containing lectin binding site, CRT C105A, C137A and W319A point mutation resulted in the changes in solvent accessible surface area, key residues’ side chain atom positions and dynamical correlated motions between residues. All these changes could directly affect CRT binding behavior. Results of this study provide molecular and structural insights into understanding the role of key residues of CRT in its binding behavior.     

Coarse‐grained A‐graft‐B model of poly(lactic acid) for molecular dynamics simulations

A mesoscopic model of poly(lactic acid) is developed where the polymer is represented as an A‐graft‐B chain with monomer units consisting of two covalently connected beads. A coarse‐graining algorithm is proposed to convert an atomistic model of PLA into a coarse‐grained one. The developed model is based on atomistic simulations of oligolactides to take into account terminal groups correctly. It was used for coarse‐grained simulations of polylactide. Gyration radii and end to end distances of polymer chains as well as the density of the polymer melt are shown to be in a good agreement with those obtained from atomistic simulations. The thermal expansion coefficients of the OLA melts calculated using the coarse‐grained model are in reasonable agreement with those obtained from all‐atom molecular dynamics. The model provides a 17‐fold speedup compared with atomistic calculations. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 604–612     

Simulation of the inherent turbulence and wake interaction inside an infinitely long row of wind turbines

The turbulence in the interior of a wind farm is simulated using large eddy simulation and the actuator line technique implemented in the Navier–Stokes equations. The simulations are carried out for an infinitely long row of turbines simulated by applying cyclic boundary conditions at the inlet and outlet. The simulations investigate the turbulence inherent to the wind turbines as no ambient turbulence or shear is added to this idealised case. The simulated data give insight into the performance of the wind turbines operating in the wake of others as well as details on key turbulent quantities. One of the key features of wakes behind wind turbines is the dynamic wake meandering, which is shown to be related to the wind turbine spacing and the vortex shedding from the turbine as a bluff body. The flow is analysed and reconstructed by applying proper orthogonal decomposition.     

Symmetry-breaking in local Lyapunov exponents

Integrable dynamical systems, namely those having as many independent conserved quantities as freedoms, have all Lyapunov exponents equal to zero. Locally, the instantaneous or finite time Lyapunov exponents are nonzero, but owing to a symmetry, their global averages vanish. When the system becomes nonintegrable, this symmetry is broken. A parallel to this phenomenon occurs in mappings which derive from quasiperiodic Schr?dinger problems in 1-dimension. For values of the energy such that the eigenstate is extended, the Lyapunov exponent is zero, while if the eigenstate is localized, the Lyapunov exponent becomes negative. This occurs by a breaking of the quasiperiodic symmetry of local Lyapunov exponents, and corresponds to a breaking of a symmetry of the wavefunction in extended and critical states. Received 25 October 2001 / Received in final form 8 December 2001 Published online 2 October 2002 RID="a" ID="a"e-mail: r.ramaswamy@mail.jnu.ac.in     

Palladium island growth on Ni(111) Stochastic classical trajectory — ghost atom calculations

We generalize previous stochastic classical trajectory-ghost atom calculations for describing palladium deposition onto the Ni(111) surface between 0.1 and 0.5 monolayers. The growth evolves through two-dimensional islands. The islands are formed following the downward funneling mechanism. Surface temperature does not affect the island growth.     

Terfenol-D/PZT磁电复合材料的磁电相位移动研究

采用粘合法制备了叠层结构的块体Terfenol-D/PZT磁电复合材料,测量了不同频率下的磁电回线,采用新的极坐标下的方式做图.从极坐标下的磁电回线中可以看出,随直流磁场的变化,非谐振频率下的磁电相位发生了轻微移动,移动幅度随频率的增加而增加;而在谐振频率下,伴随着巨磁电效应,磁电相位发生了显著移动,移动幅度达到了近90°.与粉末Terfenol-D/环氧树脂/PZT磁电复合材料对比之后表明,非谐振频率下块体Terfenol-D/PZT的磁电相位移动主要由涡流引起;而谐振频率下大幅度相位移动则主要来源于Terfenol-D的磁致弹性变化.     

一类具有免疫时滞的病毒动力学模型的稳定性分析

建立和分析了一类具有CTL免疫反应且带有免疫时滞的病毒动力学模型.讨论了系统解的有界性,并获得了无病平衡点全局渐近稳定以及正平衡点稳定的条件.最后借助Matlab对模型进行了数值模拟.     

Optimal control applied on an HIV‐1 within‐host model

The treatment of human immunodeficiency virus (HIV) remains a major challenge, even if significant progress has been made in infection treatment by ‘drug cocktails’. Nowadays, research trend is to minimize the number of pills taken when treating infection. In this paper, an HIV‐1 within host model where healthy cells follow a simple logistic growth is considered. Basic reproduction number of the model is calculated using next generation matrix method, steady states are derived; their local, as well as global stability, is discussed using the Routh–Hurwitz criteria, Lyapunov functions and the Lozinskii measure approach. The optimal control policy is formulated and solved as an optimal control problem. Numerical simulations are performed to compare several cases, representing a treatment by Interleukin2 alone, classical treatment by multitherapy drugs alone, then both treatments at the same time. Objective functionals aim to (i) minimize infected cells quantity; (ii) minimize free virus particles number; and (iii) maximize healthy cells density in blood. Copyright © 2015 John Wiley & Sons, Ltd.