Viscoelastic properties of single poly(ethylene glycol) molecules.

The viscoelastic properties of single poly(ethylene glycol) (PEG) molecules were measured by analysis of thermally and magnetically driven oscillations of an atomic force microscope (AFM) cantilever/molecule system. The molecular and monomer stiffness and friction of the PEG polymer were derived using a simple harmonic oscillator (SHO) model. Excellent agreement between the values of these two parameters obtained by the two approaches indicates the validity of the SHO model under the experimental regimes and the excellent reproducibility of the techniques. A sharp minimum in the monomeric friction is seen at around 180 pN applied force which we propose is due to a force induced change in the shape of the energy landscape describing the conformational transition of PEG from a helical to a planar state, which in turn affects the timescale of the transition and therefore modifies the measured internal friction. A knowledge of the viscoelastic response of PEG monomers is particularly important since PEG is widely used as a linker molecule for tethering groups of interest to the AFM tip in force spectroscopy experiments, and we show here that care must be exercised because of the force-dependent viscoelastic properties of these linkers.     

A new GROMOS force field for hexopyranose-based carbohydrates

A new parameter set (referred to as 45A4) is developed for the explicit-solvent simulation of hexopyranose-based carbohydrates. This set is compatible with the most recent version of the GROMOS force field for proteins, nucleic acids, and lipids, and the SPC water model. The parametrization procedure relies on: (1) reassigning the atomic partial charges based on a fit to the quantum-mechanical electrostatic potential around a trisaccharide; (2) refining the torsional potential parameters associated with the rotations of the hydroxymethyl, hydroxyl, and anomeric alkoxy groups by fitting to corresponding quantum-mechanical profiles for hexopyranosides; (3) adapting the torsional potential parameters determining the ring conformation so as to stabilize the (experimentally predominant) (4)C(1) chair conformation. The other (van der Waals and nontorsional covalent) parameters and the rules for third and excluded neighbors are taken directly from the most recent version of the GROMOS force field (except for one additional exclusion). The new set is general enough to define parameters for any (unbranched) hexopyranose-based mono-, di-, oligo- or polysaccharide. In the present article, this force field is validated for a limited set of monosaccharides (alpha- and beta-D-glucose, alpha- and beta-D-galactose) and disaccharides (trehalose, maltose, and cellobiose) in solution, by comparing the results of simulations to available experimental data. More extensive validation will be the scope of a forthcoming article. (c) 2005 Wiley Periodicals, Inc. J Comput Chem 26: 1400-1412, 2005.     

Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.     

Influence of the variable wall thickness of the sample tubes and a quartz Dewar on the EPR signal intensity in a single TE102 and double TE104 rectangular cavity

The response of a single TE₁₀₂ and double TE₁₀₄ rectangular cavity to the insertion of samples contained in tubes with variable wall thickness and a quartz Dewar into the cavity has been analyzed. A direct, indirect, and concurrent (positive or negative) “lens effect” inside the double TE₁₀₄ rectangular cavity is discussed. The experimental dependence of the EPR signal intensity on the wall thickness of the sample tube, δ, for the line-like samples with identical length of the sample material column, L=30 mm, recorded in the microwave cavity showed a directly proportional increase of the relative “lens effect” with the increase of the wall thickness of the tube in the interval, δ∈<0.1 mm, >0.5 mm. The insertion of the variable-temperature double-wall quartz Dewar (home-built, resonant frequency shift, ca. −300 MHz) into the single TE₁₀₂ rectangular cavity showed the same relative “lens effect”, with ca. 1.5-time increase of the EPR signal intensity, for a point-like sample and the line-like samples with material columns of diameter of 1 and 1.3 mm, and wall thickness of the sample tubes, δ∈<0.1 mm, >0.5 mm. The increased effect of the Dewar arises because the active volume of the quartz Dewar tube walls is always much more larger than the active volume of the sample tube wall. In the case of the double TE₁₀₄ rectangular cavity, the insertion of the quartz Dewar: (i) into the same cavity, in which the sample is present, caused a direct “lens effect”, with ca. 1.8-fold increase of the EPR signal intensity; however, (ii) into the complementary cavity, in which the sample is absent, caused an indirect “lens effect”, with ca. 0.6-fold decrease of the EPR signal intensity. With the Dewar and sample in one cavity and a large empty sample tube in the complementary cavity, a concurrent (positive or negative) “lens effect” can be observed. Thus, the possible increase/decrease of the EPR signal intensity depends on the volume ratio of the quartz Dewar tube walls and large sample tube wall inserted into the double TE₁₀₄ rectangular cavity. Each of the above phenomena may be a significant source error in quantitative EPR spectrometry unless the samples to be compared in the quantitative EPR analysis are contained in sample tubes having the same wall thickness and each EPR spectra should be recorded inside an identical quartz Dewar.     

椭球粒子声辐射力计算及分析

针对水下椭球粒子,以声散射理论为基础,采用分波序列的方法,建立了椭球粒子声辐射力的理论计算模型。进而根据声辐射力计算公式,以刚性椭球粒子和液体椭球粒子为例,计算并分析不同Bessel波束作用下椭球粒子的轴向声辐射力函数特征。数值仿真计算结果表明,对于刚性椭球粒子,扁平椭球粒子相对于细长椭球粒子更有助于激发负声辐射力;对于液体椭球粒子,细长椭球粒子相对于扁平椭球粒子更加容易产生负声辐射力;对于不同介质的椭球粒子,不同的入射波束激发的负声辐射力的效果也存在明显的差异。该结果为复杂的尺寸和介质粒子声操控技术提供了理论的可行性。     

Sublimation and Diffusion Kinetics of 2,4,6-Trinitrotoluene (TNT) Single Crystals by Atomic Force Microscopy (AFM)

In this article, we report the in-situ nanoscale experimental measurement of sublimation rates, activation energy of sublimation, and diffusion coefficients of 2,4,6-trinitrotoluene (TNT) single crystals in air using atomic force microscopy (AFM). The crystals were prepared by slow evaporation at 5 °C using acetone-dissolved TNT. The mass loss was calculated by monitoring the shrinkage of the surface area of layered islands formed on the surface of the TNT crystals due to sublimation upon isothermal heating at temperatures below the melting point. The results suggest the sublimation process occurs via two-dimensional detachment of TNT molecules from the non-prominent facets on the crystal surface which imitates the nucleation and crystal growth process. Sublimation rates are one order of magnitude smaller than previously reported values. However, the calculated activation energy (112.15 ± 3.2 kJ/mol) and temperature-dependent sublimation rates agree well with the reported values for TNT thin films and microcrystals determined by UV-vis absorbance spectroscopy and quartz crystal microscopy (QCM) (90–141 kJ/mol). The average diffusion coefficient is (4.35 × 10^–6 m²/s) which is within the range of the reported theoretical values with an average of 5.59 × 10^–6 m²/s, and about 25% less than that determined using thermogravimetric analysis for powder TNT.     

Folding Free Energy Determination of an RNA Three-Way Junction Using Fluctuation Theorems

Nonequilibrium work relations and fluctuation theorems permit us to extract equilibrium information from nonequilibrium measurements. They find application in single-molecule pulling experiments where molecular free energies can be determined from irreversible work measurements by using unidirectional (e.g., Jarzynski’s equality) and bidirectional (e.g., Crooks fluctuation theorem and Bennet’s acceptance ratio (BAR)) methods. However, irreversibility and the finite number of pulls limit their applicability: the higher the dissipation, the larger the number of pulls necessary to estimate ΔG within a few kBT. Here, we revisit pulling experiments on an RNA three-way junction (3WJ) that exhibits significant dissipation and work-distribution long tails upon mechanical unfolding. While bidirectional methods are more predictive, unidirectional methods are strongly biased. We also consider a cyclic protocol that combines the forward and reverse work values to increase the statistics of the measurements. For a fixed total experimental time, faster pulling rates permit us to efficiently sample rare events and reduce the bias, compensating for the increased dissipation. This analysis provides a more stringent test of the fluctuation theorem in the large irreversibility regime.     

双旋转附属圆柱对主圆柱尾流控制的影响

基于Fluent软件平台,采用数值模拟方法对非稳态圆柱体结构尾流流动特性进行了研究。对在Re=50～200范围内,双旋转附属圆柱的转速对主圆柱体尾流流动特性的影响进行了分析。研究结果表明:随着附属圆柱旋转速率的增加,主圆柱体表面所受阻力系数平均值与均方根值、升力系数均方根值均会减小。同时,旋转速率的变化对柱体结构表面压力分布的影响显著,压力系数在附属圆柱的位置产生了跳跃性变化。另外,当附属圆柱转速达到临界值时,尾流涡街变窄,涡脱落现象消失,并且系统的能量效率到达最佳状态。     

Ir(111)表面石墨烯中缺陷的原子结构确认

识别和解析石墨烯中缺陷的精确原子结构是研究不同类型缺陷的物化特性,实现石墨烯物性调控的前提,可以为在原子尺度研究石墨烯缺陷的构效关系提供重要的实验依据.本文结合扫描隧道显微镜(STM)和原子力显微镜(AFM)确认了在Ir(111)表面生长的石墨烯中自发形成的缺陷,以及通过离子轰击方法在石墨烯中引入的多种缺陷结构,包括单空位缺陷、非六元环拓扑结构以及石墨烯层下的基底缺陷.     

力法去弹性支座多余约束的一种处理方式

针对带弹性支座多余约束结构力法计算问题,在分析弹性支座计算特点基础上,提出一种解除弹性支座固定支点约束、保留完整弹簧作为基本结构一部分的去弹性支座多余约束处理思路,一方面便于利用原结构弹簧固定支点处已知的零位移条件建立形式统一、意义明确的力法典型方程,方程系数和自由项均为基本结构中弹簧解除约束点处的绝对位移;另一方面弹簧变形对计算的影响限于主系数,将弹簧看作附着于基本结构的轴力单元,主系数可由杆件弯曲变形产生的主位移与弹性支座柔度系数叠加得到。解除支座固定支点的去多余约束方式对拉压弹性支座、转动弹性支座及刚性支座均适用,可规范力法求解过程和提高计算效率。