Archive

25 March 2015, Volume 32 Issue 2 Previous Issue    Next Issue

---

For Selected:

Download Citations EndNote Ris BibTeX

Toggle Thumbnails

Select

Electrostatic Calculation in Biomolecular Modeling PENG Bo, LI Hanlin, LU Benzhuo 2015, 32(2): 127-159.  DOI: O242;O244;O561.4 Abstract ( )   PDF (1339KB) ( )   Biological systems could be investigated at molecular level by simulating interactions of molecules.Among various molecular interaction,electrostatic interaction is of central importance to understand solvation properties of biomolecules,and to explain solvation effects such as folding,binding,enzyme catalysis and so on.In this work,Poisson-Boltzmann model for biomolecular solvation calculation is reviewed,including background,development,theories,numerical calculations and applications in molecular biology.Besides,as an approximated model,generalized Born model is discussed.

Select

Simulation of Gas-Liquid Two-Phase Flows with Discontinuous Galerkin Method GUO Hongping, OUYANG Jie 2015, 32(2): 160-168.  DOI: O24 Abstract ( )   PDF (2898KB) ( )   A unified discontinuous Galerkin finite element framework on unstructured grids is developed to simulate gas-liquid twophase flows.In the framework,interior penalty discontinuous Galerkin (IPDG) method is employed to discretize imcompressible Navier-Stokes equations,while Runge-Kutta discontinuous Galerkin (RKDG) method is used to solve Level Set equation.Lid-driven cavity flow is simulated to validate IPDG method.Numerical results of bubble rising indicate the approach can be used to complex twophase flows with low computational efforts and simple implement.Moreover,RKDG method can effectively track deformations of interface without reinitialization.

Select

High Performance GPU Parallel Computing of Gas Dynamic by Direct Simulation Monte Carlo HE Yongxiang, LIU Xin, ZHAO Haibo 2015, 32(2): 169-176.  DOI: O356 Abstract ( )   PDF (2662KB) ( )   Parallel computing of direct simulation Monte Carlo (DSMC) based on compute unified device architecture (CUDA) is developed and improved data transmission in multi-GPU parallel computing is devoted to promote parallel efficiency.A two-dimensional Couette flow and lid-driven cavity flow by CPU,single GPU and double GPU parallel computing are simulated,respectively.Precision of results by GPU is consistent with that by CPU and speedup ratio can reach to 10~30 by single GPU acceleration and 40~60 by double GPU acceleration.Speedup efficiency by multi-GPU is approximated to 100%.

Select

Numerical Simulation of Water Flooding Development in Low Permeability Reservoirs with a Discrete Fracture Model SUN Jingjing, HUANG Zhaoqin, YAO Jun, LI Aifen, WANG Daigang 2015, 32(2): 177-185.  DOI: TE319 Abstract ( )   PDF (5418KB) ( )   A discrete fracture model is used to simulate water flooding in low permeability reservoirs considering nonlinear flow characteristic of matrix system.At first,we reduce dimension of fractures and propose a mathematical model.On this basis,unstructured grid and control volume finite difference method are applied to numerical computation considering complex geometry of fractures.Accuracy of simulator is validated through a simple example.At last,two water-injection tests are performed to analyze effect of different non-Darcy flow models.

Select

Heat Current Calculation in Equilibrium Molecular Dynamics Simulations of Thermal Conductivity YE Zhenqiang, CAO Bingyang, LI Yuanwei 2015, 32(2): 186-194.  DOI: TK124 Abstract ( )   PDF (2109KB) ( )   Unified and succinct heat current formulations for Lennard-Jones,Stillinger-Weber and Tersoff potentials are derived.Heat current formulations for Tersoff potential from literature are reanalyzed.It was found that some of them are identical with the derivation,while the others,which are not in conformity with the study,need to be modified.Effects of potential partition coefficient on calculated thermal conductivity are also investigated.It shows that different partitions of pair potential may lead to a maximum variation of about 10%,while effect for triplet part is insignificant.In addition,a larger noise and fluctuation of heat current autocorrelation function was found in exclusive partition method,indicating that it may cause large calculation errors.

Select

Three-Dimensional Temperature Field Reconstruction with Acoustics Based on Regularized SVD Algorithm WANG Ran, AN Liansuo, SHEN Guoqing, ZHANG Shiping 2015, 32(2): 195-201.  DOI: O551.2 Abstract ( )   PDF (2461KB) ( )   For reconstruction of three-dimensional temperature field in furnace of power plant boiler,a mathematical model based on acoustic theory was constructed.Two regularization algorithms based on Singular Value Decomposition (SVD) algorithm were proposed.Three typical temperature fields were simulated.Anti-noise ability of algorithms was tested by Gaussian noise with standard deviations.It indicates that regularized SVD algorithm is able to solve severely ill-posed reconstruction problems.Reconstruction temperature field reflects accurately temperature distributions,and algorithms have good anti-noise ability.TSVD regularization algorithm with faster reconstruction speed and better anti-noise ability is suitable for power plant boiler with complicated combustion.

Select

Compressive Sensing for Electromagnetic Scattering from Random Surface WANG Haibo, HUANG Wenhua, BA Tao, YANG Zhiqiang 2015, 32(2): 202-206.  DOI: O44;TM15 Abstract ( )   PDF (3192KB) ( )   Harmonic functions are selected as basis,and scattering source is rebuild by orthogonal matching pursuit algorithm (OMP),which is observed by random matrix.Scattering far field patterns calculated by CS-OMP and LU decomposition agree well.

Select

A High Precision Algorithm for Intersection in Laser Ray Tracing Simulation YANG Rong, HANG Xudeng, ZHAI Chuanlei, LI Shuanggui, QI Jin, LI Jinghong 2015, 32(2): 207-213.  DOI: O242.1 Abstract ( )   PDF (1516KB) ( )   We analyze non-physical solutions in laser ray tracing simulation.With a system of nonlinear equations,a new algorithm for intersection is presented.A special preconditioner is used to improve numerical stability.The algorithm is suitable for any intersectant condition.Numerical experiments show that the algorithm has better precision and adaptability.Simulation in LARED code shows good performance.

Select

Time Correlation and Neutron Multiplicity Counting Measurement in Numerical Experiment Platform on Verification Technologies ZHU Jianyu, XIE Wenxiong, LI Gang, ZHANG Songbai, DENG Li 2015, 32(2): 213-219.  DOI: O571.33 Abstract ( )   PDF (2911KB) ( )   We set up a numerical experiment platform.It consolidates codes used to simulate warhead verification technologies of passive neutron,passive γ ray,active neutron,active high-energy photon and delayed neutron methods.Two functions on simulating time-dependent coincidence and neutron multiplicity counter measurements were added to the platform.They are carried out by DTB code and NMC code.This paper introduces development and validation of the programs,including theory and program flow.Two numerical experiments are designed to validate the program.The platform provides systematic data to support statistical analysis on nuclear warhead verification technologies

Select

Theoretical Study on Structure Stability and Magnetic Properties of (OsH2)n(n=1-5) Clusters ZHANG Xiurong, LUO Min, GUO Wenlu 2015, 32(2): 220-228.  DOI: O641 Abstract ( )   PDF (5218KB) ( )   Geometrical optimizations of (OsH2)n(n=1-5) clusters are carried out by using density functional calculation with generalized gradient approximation (GGA) in which electronic spin multiplicities are adequately considered.Ground-state structures of clusters are obtained with optimized geometries' total energy and frequency.For each ground state structure,average binding energy,second-order differences of total energies,magnetic moment and density of states are investigated.It shows that (OsH2)n(n=1-5) clusters tend to form three-dimensional structures.Interaction between H and Os is strong and (OsH2)4 is more stable than its neighbors.Only ground-state geometry of (OsH2)5 displays anti-ferromagnetic coupling.Magnetic moment is mainly provided by osmium atoms and is dominant from contributions of d orbitals.

Select

Quantum Transport in Hetero-material-gate CNTFETs with Gate Underlap:A Numerical Study WANG Wei, ZHANG Lu, LI Na, YANG Xiao, ZHANG Ting, YUE Gongshu 2015, 32(2): 229-239.  DOI: O484.3 Abstract ( )   PDF (3845KB) ( )   Effects of gate underlap on electronic properties of conventional single-material-gate CNTFET (C-CNTFET) and heteromaterial-gate CNTFET (HMG-CNTFET) are investigated theoretically in a quantum kinetic model.The model is based on twodimensional non-equilibrium Green's functions (NEGF) solved self-consistently with Poisson's equations.It shows that intrinsic cutoff frequency of C-CNTFETs reaches a few THz.In addition,a comparison study was performed about C-and HMG-CNTFETs.Calculated results show that,C-CNTFETs with longer underlap have better switching speed but less on/off current ratios.For HMG-CNTFET,gate underlap improves sub-threshold performance and switching delay times,and decreases output conductance significantly.

Select

Physical Model for Ionizing Radiation Damage in Partially Depleted SOI Transistors HE Baoping, LIU Minbo, WANG Zujun, YAO Zhibin, HUANG Shaoyan, SHENG Jiangkun, XIAO Zhigang 2015, 32(2): 240-246.  DOI: TN386.1 Abstract ( )   PDF (2392KB) ( )   For physical process of holes trapped in oxide and interface trap buildup induced by proton,physical models of oxide trapped charge and interface trap charge in partially depleted SOI transistors after ionizing radiation exposure are proposed.Relations between oxide trapped charge density or interface trap charge density and radiation dose are described well.These models are validated by radiation experiments.It shows that within confines of experimental dose,oxide trapped charge density induced by radiation rays depends negative exponential on radiation dose.Results for high total dose as annealing is taken into account exhibits excellent agreement with experimental data.Interface trap charge density induced by radiation rays is linear in dose within confines of experimental dose.

Select

Compression of Jammed States of Two-dimensional Frictionless Particles ZHANG Xinggang, HU Lin 2015, 32(2): 247-252.  DOI: O414.2 Abstract ( )   PDF (2145KB) ( )   Numerical simulation is conducted to investigate two-dimensional frictionless disks under isotropic compression.Results with different simulation conditions are contrasted.It shows that monodisperse system is easier to crystallize.Its critical packing fraction φC and critical mean contact number ZC are larger than bidisperse system.On J point,relations of packing fraction increment Δφ to mean contact number increment ΔZ and average overlap δ are almost irrelevant to simulation conditions.Relation of pressure P and packing fraction increment Δφ is only determined by interaction form.These relationships can be fitted very well by power functions.