Molecular Mechanics Simulation of Recognition Identity of tRNA~(His/GUG)

本文选用经过实验验证的碱基序列 ,用简化的方式 ,构建了被水分子和镁离子修饰的核酸序列的分子模型 ,应用分子力学模拟方法对序列进行能量优化 ,对优化后序列的构象参数、成键状况和能量数据等进行了分析。对tRNAHHis GUG的识别特性作了初步的探索 ,得到了和实验结果相近的结论。此外 ,还从能力学的角度讨论了溶剂 -溶质 -溶剂相互作用形成的网状氢键网络对核酸结构稳定性的影响 ,探讨了非Crick_WatsonGU、UU配对的能力学特征并存在于被水分子和镁离子修饰的核酸序列中的GU、UU配对情况。

Characterizing the mechanics of cultured cell monolayers.

One-cell-thick monolayers are the simplest tissues in multicellular organisms, yet they fulfill critical roles in development and normal physiology. In early development, embryonic morphogenesis results largely from monolayer rearrangement and deformation due to internally generated forces. Later, monolayers act as physical barriers separating the internal environment from the exterior and must withstand externally applied forces. Though resisting and generating mechanical forces is an essential part of monolayer function, simple experimental methods to characterize monolayer mechanical properties are lacking. Here, we describe a system for tensile testing of freely suspended cultured monolayers that enables the examination of their mechanical behavior at multi-, uni-, and subcellular scales. Using this system, we provide measurements of monolayer elasticity and show that this is two orders of magnitude larger than the elasticity of their isolated cellular components. Monolayers could withstand more than a doubling in length before failing through rupture of intercellular junctions. Measurement of stress at fracture enabled a first estimation of the average force needed to separate cells within truly mature monolayers, approximately ninefold larger than measured in pairs of isolated cells. As in single cells, monolayer mechanical properties were strongly dependent on the integrity of the actin cytoskeleton, myosin, and intercellular adhesions interfacing adjacent cells. High magnification imaging revealed that keratin filaments became progressively stretched during extension, suggesting they participate in monolayer mechanics. This multiscale study of monolayer response to deformation enabled by our device provides the first quantitative investigation of the link between monolayer biology and mechanics.

The fluid mechanics of a two-dimensional Aaberg exhaust hood

In this paper a study of the air flow pattern created by a two-dimensional Aaberg exhaust hood local ventilation system is presented. A mathematical model of the flow, in terms of the stream function ψ, is derived analytically for both laminar and turbulent injections of fluid. Streamlines and lines of constant speed deduced from the model are examined for various values of the governing dimensionless operating parameter and predictions are given as to the area in front of the hood from which the air can be sampled. The effect of the injection of fluid on the centre-line velocity of the flow is examined and a comparison of the results with the available experimental data is given. © 1992.

Experimental and numerical investigation of fracture mechanics of bitumen beams

This work presents an experimental and numerical investigation to characterise the fracture properties of pure bitumen (the binder in asphalt paving materials). The paper is divided into two parts. The first part describes an experimental study of fracture characterisation parameters of pure bitumen as determined by three-point bend tests. The second part deals with modelling of fracture and failure of bitumen by Finite Element analysis. Fracture mechanics parameters, stress intensity factor, KIC, fracture energy, GIC, and J-integral, JIC, are used for evaluation of bitumen's fracture properties. The material constitutive model developed by Ossa et al. [40,41] which was implemented into a FE code by Costanzi [18] is combined with cohesive zone models (CZM) to simulate the fracture behaviour of pure bitumen. Experimental and numerical results are presented in the form of failure mechanism maps where ductile, brittle and brittle-ductile transition regimes of fracture behaviour are classified. The FE predictions of fracture behaviour match well with experimental results. © 2012 Elsevier Ltd.

Gaussian Approximation Potential: an interatomic potential derived from first principles Quantum Mechanics

Simulation of materials at the atomistic level is an important tool in studying microscopic structure and processes. The atomic interactions necessary for the simulation are correctly described by Quantum Mechanics. However, the computational resources required to solve the quantum mechanical equations limits the use of Quantum Mechanics at most to a few hundreds of atoms and only to a small fraction of the available configurational space. This thesis presents the results of my research on the development of a new interatomic potential generation scheme, which we refer to as Gaussian Approximation Potentials. In our framework, the quantum mechanical potential energy surface is interpolated between a set of predetermined values at different points in atomic configurational space by a non-linear, non-parametric regression method, the Gaussian Process. To perform the fitting, we represent the atomic environments by the bispectrum, which is invariant to permutations of the atoms in the neighbourhood and to global rotations. The result is a general scheme, that allows one to generate interatomic potentials based on arbitrary quantum mechanical data. We built a series of Gaussian Approximation Potentials using data obtained from Density Functional Theory and tested the capabilities of the method. We showed that our models reproduce the quantum mechanical potential energy surface remarkably well for the group IV semiconductors, iron and gallium nitride. Our potentials, while maintaining quantum mechanical accuracy, are several orders of magnitude faster than Quantum Mechanical methods.

Mechanics of capillary forming of aligned carbon nanotube assemblies.

Elastocapillary self-assembly is emerging as a versatile technique to manufacture three-dimensional (3D) microstructures and complex surface textures from arrangements of micro- and nanoscale filaments. Understanding the mechanics of capillary self-assembly is essential to engineering of properties such as shape-directed actuation, anisotropic wetting and adhesion, and mechanical energy transfer and dissipation. We study elastocapillary self-assembly (herein called "capillary forming") of carbon nanotube (CNT) microstructures, combining in situ optical imaging, micromechanical testing, and finite element modeling. By imaging, we identify sequential stages of liquid infiltration, evaporation, and solid shrinkage, whose kinetics relate to the size and shape of the CNT microstructure. We couple these observations with measurements of the orthotropic elastic moduli of CNT forests to understand how the dynamic of shrinkage of the vapor-liquid interface is coupled to the compression of the forest. We compare the kinetics of shrinkage to the rate of evporation from liquid droplets having the same size and geometry. Moreover, we show that the amount of shrinkage during evaporation is governed by the ability of the CNTs to slip against one another, which can be manipulated by the deposition of thin conformal coatings on the CNTs by atomic layer deposition (ALD). This insight is confirmed by finite element modeling of pairs of CNTs as corrugated beams in contact and highlights the coupled role of elasticity and friction in shrinkage and stability of nanoporous solids. Overall, this study shows that nanoscale porosity can be tailored via the filament density and adhesion at contact points, which is important to the development of lightweight multifunctional materials.

Mechanics of indentation

The fundamental contact mechanics principles underlying nanoindentation testing techniques are reviewed. A range of material constitutive responses are covered, including elastic, plastic, and viscous deformation, and incorporating indentation of linearly viscoelastic materials and poroelastic materials. Emphasis is on routine analysis of experimental nanoindentation data, including deconvolution techniques for material properties measurements during indentation. In most cases, an analytical approach for an isotropic half-space is considered. Special cases are briefly described, including anisotropic materials, inhomogeneous composite materials and layered filmsubstrate systems. © 2011 by Pan Stanford Publishing Pte. Ltd. All rights reserved.

Automated computational modelling for solid mechanics

We present some recent developments in automated computational modelling with an emphasis on solid mechanics applications. The automation process permits an abstract mathematical model of a physical problem to be translated into computer code rapidly and trivially, and can lead to computer code which is faster than hand-written and optimised code. Crucial to the approach is ensuring that mathematical abstractions inherent in the mathematical model are inherited by the software library. © Springer Science+Business Media B.V. 2008.