Molecular dynamics study on the phase diagrams of linear and branched chain molecules

The particle transfer molecular dynamics is used to study the phase equilibria of linear and branched chain molecules. The scaling of the critical temperature versus chain length is obtained and the critical densities are found to decrease with increasing chain length, which are in agreement with the results of experiment and theory. The phase diagrams of the linear and the branched chain molecules nearly overlap with each other. Moreover, the radial distribution functions of linear and branched chain molecules in gas phase are very similar, but in the liquid phase, they are different for different kinds of chains.

Effect of annealing on the viscoelastic and viscoplastic responses of low-density polyethylene

Two series of tensile tests with constant crosshead speeds (ranging from 5 to 200 mm/min) and tensile relaxation tests (at strains from 0.03 to 0.09) were performed on low-density polyethylene in the subyield region of deformations at room temperature. Mechanical tests were carried out on nonannealed specimens and on samples annealed for 24 h at the temperatures T = 50, 60, 70, 80, and 100 degreesC. Constitutive equations were derived for the time-dependent response of semicrystalline polymers at isothermal deformations with small strains. A polymer is treated as an equivalent heterogeneous network of chains bridged by temporary junctions (entanglements, physical crosslinks, and lamellar blocks). The network is thought of as an ensemble of mesoregions linked with each other. The viscoelastic behavior of a polymer is modeled as a thermally induced rearrangement of strands (separation of active strands from temporary junctions and merging of dangling strands with the network). The viscoplastic response reflects sliding of junctions in the network with respect to their reference positions driven by macrostrains. Stress-strain relations involve five material constants that were found by fitting the observations.

The viscoelastic and viscoplastic behavior of low-density polyethylene

Three series of tensile tests with constant cross-head speeds (ranging from 5 to 200 mm/min), tensile relaxation tests (at strains from 0.03 to 0.09) and tensile creep tests (at stresses from 2.0 to 6.0 MPa) are performed on low-density polyethylene at room temperature. Constitutive equations are derived for the time-dependent response of semicrystalline polymers at isothermal deformation with small strains. A polymer is treated as an equivalent heterogeneous network of chains bridged by temporary junctions (entanglements, physical cross-links and lamellar blocks). The network is thought of as an ensemble of meso-regions linked with each other. The viscoelastic behavior of a polymer is modelled as thermally-induced rearrangement of strands (separation of active strands from temporary junctions and merging of dangling strands with the network). The viscoplastic response reflects mutual displacement of meso-domains driven by macro-strains. Stress-strain relations for uniaxial deformation are developed by using the laws of thermodynamics. The governing equations involve five material constants that are found by fitting the observations. Fair agreement is demonstrated between the experimental data and the results of numerical simulation.

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

The study of associations between two biomolecules is the key to understanding molecular function and recognition. Molecular function is often thought to be determined by underlying structures. Here, combining a single-molecule study of protein binding with an energy-landscape-inspired microscopic model, we found strong evidence that biomolecular recognition is determined by flexibilities in addition to structures. Our model is based on coarse-grained molecular dynamics on the residue level with the energy function biased toward the native binding structure ( the Go model). With our model, the underlying free-energy landscape of the binding can be explored. There are two distinct conformational states at the free-energy minimum, one with partial folding of CBD itself and significant interface binding of CBD to Cdc42, and the other with native folding of CBD itself and native interface binding of CBD to Cdc42. This shows that the binding process proceeds with a significant interface binding of CBD with Cdc42 first, without a complete folding of CBD itself, and that binding and folding are then coupled to reach the native binding state.

Temperature dependence of the distribution of the first passage time: Results from discontinuous molecular dynamics simulations of an all-atom model of the second beta-hairpin fragment of protein G

More than 22 000 folding kinetic simulations were performed to study the temperature dependence of the distribution of first passage time (FPT) for the folding of an all-atom Go-like model of the second beta-hairpin fragment of protein G. We find that the mean FPT (MFPT) for folding has a U (or V)-shaped dependence on the temperature with a minimum at a characteristic optimal folding temperature T-opt*. The optimal folding temperature T-opt* is located between the thermodynamic folding transition temperature and the solidification temperature based on the Lindemann criterion for the solid. Both the T-opt* and the MFPT decrease when the energy bias gap against nonnative contacts increases. The high-order moments are nearly constant when the temperature is higher than T-opt* and start to diverge when the temperature is lower than T-opt*. The distribution of FPT is close to a log-normal-like distribution at T* greater than or equal to T-opt*. At even lower temperatures, the distribution starts to develop long power-law-like tails, indicating the non-self-averaging intermittent behavior of the folding dynamics. It is demonstrated that the distribution of FPT can also be calculated reliably from the derivative of the fraction not folded (or fraction folded), a measurable quantity by routine ensemble-averaged experimental techniques at dilute protein concentrations.

Studies of electrochemical quantized capacitance charging of surface ensembles of silver nanoparticles

CTAB-stabilized silver nanoparticles were synthesized by NaBH4 reduction. The as-prepared nanoparticles can be self-assembled on 3-mercaptopropionic acid (MPA) modified gold electrode, which was supported strongly by XPS measurements. Exceptional long-term stability of the as-prepared colloidal silver aqueous solution and the desorption of silver nanoparticle ensemble on MPA after alcohol rinsing proved that these CTAB molecules adsorbed on silver core formed interdigitated bilayer structure. DPV and differential capacitance measurements were performed to characterize the as-prepared silver nanoparticle ensemble. and the interesting quantized capacitance charging behaviors were observed.

Surface sediment diatoms from the western Pacific marginal seas and their correlation to environmental variables

Diatom data of 192 surface sediment samples from the marginal seas in the western Pacific together with modern summer and winter sea surface temperature and salinity data were analyzed. The results of canonical correspondence analysis show that summer sea-surface salinity (SSS) is highly positively correlated with winter SSS and so is summer sea-surface temperature (SST) with winter SST. The correlations between SSSs and SSTs are less positively correlated, which may be due to interactions of regional current pattern and monsoon climate. The correlations between diatom species, sample sites and environmental variables concur with known diatom ecology and regional oceanographic characters. The results of forward selection of the environmental variables and associated Monte Carlo permutation tests of the statistical significance of each variable suggest that summer SSS and winter SST are the main environmental factors affecting the diatom distribution in the area and therefore preserved diatom data from down core could be used for reconstructions of summer SSS and winter SST in the region.

Effective response of a non-linear composite in external AC electric field

A general effective response is proposed for nonlinear composite media, which obey a current field relation of the form J = sigmaE + chi\E\(2) E when an external alternating current (AC) electrical field is applied. For a sinusoidal applied field with finite frequency omega, the effective constitutive relation between the current density and electric field can be defined as, = sigma(e) + chi(e) <\E(x, omega, t)\(2) E(x, omega, t)> + (. . .), where sigma(e) and chi(e) are the general effective linear and nonlinear conductive responses, respectively. The angled brackets <(. . .)> denotes the ensemble average. As two examples, we have investigated the cylindrical and spherical inclusions embedded in a host and also derived the formulae of the general effective linear and nonlinear conductive responses in dilute limit. For higher volume fraction of inclusions, we have proposed a nonlinear effective medium approximation (EMA) method to estimate the general effective response of nonlinear composites in external AC field. Furthermore, the effective nonlinear responses at harmonics are predicted by using the general effective response. (C) 2002 Elsevier Science B.V. All rights reserved.

A hybrid coupled ocean-atmosphere model and ENSO prediction study

A hybrid coupled ocean-atmosphere model is designed, which consists of a global AGCM and a simple anomaly ocean model in the tropical Pacific. Retroactive experimental predictions initiated in each season from 1979 to 1994 are performed. Analyses indicate that: (1) The overall predictive capability of this model for SSTA over the central-eastern tropical Pacific can reach one year, and the error is not larger than 0.8 degrees C. (2) The prediction skill depends greatly on the season when forecasts start. However, the phenomenon of SPB (spring prediction barrier) is not found in the model. (3) The ensemble forecast method can effectively improve prediction results. A new initialization scheme is discussed.

Algorithm Studies on How to Obtain a Conditional Nonlinear Optimal Perturbation (CNOP)

The conditional nonlinear optimal perturbation (CNOP), which is a nonlinear generalization of the linear singular vector (LSV), is applied in important problems of atmospheric and oceanic sciences, including ENSO predictability, targeted observations, and ensemble forecast. In this study, we investigate the computational cost of obtaining the CNOP by several methods. Differences and similarities, in terms of the computational error and cost in obtaining the CNOP, are compared among the sequential quadratic programming (SQP) algorithm, the limited memory Broyden-Fletcher-Goldfarb-Shanno (L-BFGS) algorithm, and the spectral projected gradients (SPG2) algorithm. A theoretical grassland ecosystem model and the classical Lorenz model are used as examples. Numerical results demonstrate that the computational error is acceptable with all three algorithms. The computational cost to obtain the CNOP is reduced by using the SQP algorithm. The experimental results also reveal that the L-BFGS algorithm is the most effective algorithm among the three optimization algorithms for obtaining the CNOP. The numerical results suggest a new approach and algorithm for obtaining the CNOP for a large-scale optimization problem.

东中国海区域海浪同化系统设计与研究

针对目前海浪同化中没有适合东中国海区的业务应用系统，以及缺乏集合卡尔曼滤波方法（Ensemble Kalman Filter，EnKF）的应用的现状，设计了东中国海区域海浪同化系统。首先比较了目前常用的各种资料同化方法，指出各种同化方法的实质都是一种滤波过程，并选取最优插值方法（Optimal Interpolation，OI）和EnKF方法开展同化试验，动力模式选取WAVEWATCH III，观测资料为Topex/Poseidon卫星高度计观测波高。然后用观测法研究了模式预报误差协方差的统计性质，指出误差相关距离尺度在3°至6°之间。最后用22001号浮标观测资料验证了两个同化系统2000年8月的有效波高计算值，结果表明OI方案的同化系统对有效波高的均方根误差减少了9.0%，系统运行稳定，可应用于业务化部门；EnKF方案的同化系统在集合样本数为50的情况下，对有效波高的均方根误差减少了6.0%，用EnKF方法同化有效波高是可行的。

Genetic mapping of size-related quantitative trait loci (QTL) in the bay scallop (Argopecten irradians) using AFLP and microsatellite markers

We constructed genetic linkage maps for the bay scallop Argopecten irradians using AFLP and microsatellite markers and conducted composite interval mapping (CIM) of body-size-related traits. Three hundred seventeen AFLP and 10 microsatellite markers were used for map construction. The female parent map contained 120 markers in 15 linkage groups, spanning 479.6 cM with an average interval of 7.0 cM. The male parent map had 190 markers in 17 linkage groups, covering 883.8 cM at 7.2 cM per marker. The observed coverage was 70.4% for the female and 81.1% for the male map. Markers that were distorted toward the same direction were closely linked to each other on the genetic maps, suggesting the presence of genes important for survival. Six size-related traits, shell length, shell height, shell width, total weight, soft tissue weight, and shell weight, were measured for QTL mapping. The size data were significantly correlated with each other. We subjected the data, log transformed firstly, to a principle component analysis and use the first principle component for QTL mapping. CIM analysis revealed one significant QTL (LOD=2.69, 1000 permutation, P<0.05) in linkage group 3 on the female parent map. The mapping of size-related QTL in this study raises the possibility of improving the growth of bay scallops through marker-assisted selection. (c) 2007 Published by Elsevier B.V.

资源受限单机动态调度的并行GA算法研究

研究资源受限系统动态调度问题,针对时序约束问题提出一种并行遗传算法(PGA)。给出满足排序优先次序约束的一种基因编码方法;采用不破坏优先级可行性的交叉操作,并予以证明;建立一种并行处理机制,使搜索避免出现局优现象。在技术允许情况下,单机动态调度引入抢占式加工方式,会一定程度上提高系统的性能。通过仿真试验验证,并行GA算法可兼顾优化效果和计算效率,解决单机动态调度问题。