完全匹配层吸收边界在2D3V等离子体粒子模拟中的实现

基于Berenger完全匹配层的基本思想,导出了高斯单位制下2维完全匹配层吸收介质的控制方程及参数设置方法,并进行了数值验证和参数优化。依据所得结论编制了相应的吸收边界模块加入到2D3V等离子体粒子模拟程序PLASIM中,取得了良好的吸收效果。基于完全匹配层吸收边界的实现,在小窗口内对超强激光预脉冲与低密度等离子体的长时间相互作用过程进行了模拟研究,结果表明:激光强度和作用时间是影响等离子体密度改变的重要因素,超强激光其长时间的预脉冲可以通过有质动力的累积效应在低密度等离子体中引起较大的密度变化。     

质子束在等离子体中传输的粒子模拟

用粒子模拟程序研究了长脉冲质子束在等离子体中的传输特性,模拟结果表明,等离子体可以明显改善质子束的空间传输特性,大尺度的等离子体相对于等离子体层可以实现较长距离的稳定传输。研究发现,在实现长距离传输时,等离子体波会对质子束密度有较大的调制作用,严重影响质子束的传输性质,同时通过优化束密度分布可以有效减弱等离子体波的激发,实现束较稳定的传输。     

First-principles investigation of the electronic structure and magnetism of eskolaite

The electronic structure and magnetism of eskolaite are studied by using first-principles calculations where the on-site Coulomb interaction and the exchange interaction are taken into account and the LSDA+U method is used. The calculated energies of magnetic configurations are very well fitted by the Heisenberg Hamiltonian with interactions in five neighbour shells; interaction with two nearest neighbours is found to be dominant. The Néel temperature is calculated in the spin-3/2 pair-cluster approximation. It is found that the measurements are in good agreement with the calculations of lattice parameters, density of states, band gap, local magnetic moment, and the Néel temperature for the values of U and J that are close to those obtained within the constrained occupation method. The band gap is of the Mott--Hubbard type.     

Stochasticity in the yeast mating pathway

We report stochastic simulations of the yeast mating signal transduction pathway. The effects of intrinsic and external noise, the influence of cell-to-cell difference in the pathway capacity, and noise propagation in the pathway have been examined. The stochastic temporal behaviour of the pathway is found to be robust to the influence of inherent fluctuations, and intrinsic noise propagates in the pathway in a uniform pattern when the yeasts are treated with pheromones of different stimulus strengths and of varied fluctuations. In agreement with recent experimental findings, extrinsic noise is found to play a more prominent role than intrinsic noise in the variability of proteins. The occurrence frequency for the reactions in the pathway are also examined and a more compact network is obtained by dropping most of the reactions of least occurrence.     

非等温广义牛顿流体的无网格模拟

基于原始变量法,将RPIM推广到非等温广义牛顿流动问题的求解.为了减少未知量的个数,压力和速度采用罚函数方法耦合;同时采用积分降阶技术以保证获得满意的数值解.数值实验结果表明,采用罚函数法处理速度和压力在无网格方法中同样适用,且RPIM用于非等温广义牛顿流动问题的求解时具有易施加本质边界条件、计算精度高和收敛性较快的优点.     

Molecular Dynamics Simulation of Temperature-dependent Flexibility of Thermophilic Xylose Isomerase

The complex model of Thermus thermophilus xylose isomerase （TtXI） with D-xylose was constructed, and molecular dynamics （MD） simulations were carried out at 300 and 360 K for 10 ns by NAMD2.5. The radius of gyration （Rg）, subunit interactions, and residue flexibility were analyzed. The results show that residues 60-69, 142-148, 169-172, and 332-340 have high flexibility at 300 and 360 K. Residues with higher flexibility at 360 K than that at 300 K can mainly be divided into two groups： one locates in the helix-loophelix region consisting of residues 55-80 in catalytic domain; the other at subunit interfaces. The Rg of catalytic domain at 360 K shows 0.16 A higher than that at 300 K, but Rg of small C-terminal domain has no obvious difference. The results indicate that enhanced Rg of catalytic domain may lead to the intense motion of the active site of TtXI and promote the D-xylose isomization reaction. Eight hydrogen bonds and five ion pairs are reduced at subunit interfaces at 360 K compared with 300 K, that may be the main reason for the decrease in rigidity and increase in activity at high temperature of TtXI. This result also help to explain the cold-adaption phenomenon of TtXI E372G mutant reported previously. Our results reveal the relationship between temperature and structure flexibility of TtXI, and play an important role in understanding the thermostability of thermophile protein with multiple subunits.     

An image encryption scheme combining chaos with cycle operation for DNA sequences

An image encryption scheme is proposed using high-dimensional chaotic systems and cycle operation for DNA sequences. In the scheme, the pixels of the original image are encoded randomly with the DNA coding rule controlled by a key stream produced from Chen’s hyper-chaos. In addition to confusion on the DNA sequence matrix with Lorenz system, a cycle operation for DNA sequences is projected to diffuse the pixel values of the image. In order to enhance the diffusion effect, a bitwise exclusive-OR operation is carried out for the decoded matrices with a binary key stream, and then the cipher-image is obtained. Simulation results demonstrate that the proposed image encryption scheme with acceptable robustness is secure against exhaustive attack, statistical attack and differential attack.     

Pattern formation in a nonequilibrium phase transition for a generalized Burgers–Fisher equation

A nonequilibrium phase transition of a generalized Burgers–Fisher equation describing biological pattern formation with a periodic boundary condition is examined. In the presence of a weak external force, some approximate bifurcation solutions near a critical point and new spatially periodic patterns are obtained by using the perturbation method in an infinite-dimensional space. The result shows that the external force delays the bifurcation.     

Auto‐Tandem Cooperative Catalysis Using Phosphine/Palladium: Reaction of Morita–Baylis–Hillman Carbonates and Allylic Alcohols

Auto‐tandem catalysis (ATC), in which a single catalyst promotes two or more mechanistically different reactions in a cascade pattern, provides a powerful strategy to prepare complex products from simple starting materials. Reported here is an unprecedented auto‐tandem cooperative catalysis (ATCC) for Morita–Baylis–Hillman carbonates from isatins and allylic carbonates using a simple Pd(PPh₃)₄ precursor. Dissociated phosphine generates phosphorus ylides and the Pd leads to π‐allylpalladium complexes, and they undergo a γ‐regioselective allylic–allylic alkylation reaction. Importantly, a cascade intramolecular Heck‐type coupling proceeds to finally furnish spirooxindoles incorporating a 4‐methylene‐2‐cyclopentene motif. Experimental results indicate that both Pd and phosphine play crucial roles in the catalytic Heck reaction. In addition, the asymmetric versions with either a chiral phosphine or chiral auxiliary are explored, and moderate results are obtained.     

2D Monoelemental Germanene Quantum Dots: Synthesis as Robust Photothermal Agents for Photonic Cancer Nanomedicine

As a new family member of the emerging two‐dimensional (2D) monoelemental materials (Xenes), germanene has shown promising advantages over the prototypical 2D Xenes, such as black phosphorus (BP) and graphene. However, efficient manufacture of novel germanene nanostructures is still a challenge. Herein, a simple top‐down approach for the liquid‐exfoliation of ultra‐small germanene quantum dots (GeQDs) is presented. The prepared GeQDs possess an average lateral size of about 4.5 nm and thickness of about 2.2 nm. The functionalized GeQDs were demonstrated to be robust photothermal agents (PTAs) with outstanding photothermal conversion efficacy (higher than those of graphene and BPQDs), superior stability, and excellent biocompatibility. As a proof‐of‐principle, 2D GeQDs‐based PTAs were used in fluorescence/photoacoustic/photothermal‐imaging‐guided hyperpyrexia ablation of tumors. This work could expand the application of 2D germanene to the field of photonic cancer nanomedicine.