Computer Simulation of Liquid Crystal Films

Abstract

We present the results of extensive Monte Carlo simulations of liquid crystal films of various thicknesses. A simple nearest-neighbour lattice model, the Lebwohl-Lasher model, is employed, with periodic boundaries in two directions and free, planar, surfaces in the third. Particular attention is devoted to locating the temperature of the order-disorder (nematic-isotropic) phase transition. Weak first-order behaviour apparently persists in systems as thin as 8 layers across, but below this the transition cannot be detected. The shift of the transition temperature from its bulk value approaches the expected asymptotic linear dependence on inverse thickness, but significant deviations from this are seen for films of 10 layers thickness and less. These results enable an accurate estimate to be made of the bulk phase transition temperature in the thermodynamic limit, and the result is consistent with that extrapolated from systems with full periodic boundaries.     

Modelling and simulation of the adsorption of the lipase from Geotrichum sp. on hydrophobic interaction columns

The Langmuir model fitted well the adsorption isotherms of lipase on the hydrophobic resin. The model parameters, Q_m and k_d, were affected by NaCl concentration: Q_m increased from 31 to 80 U g^–1 resin, and k_d changed from 9.4 to 3 U ml^–1. Column modelling and the simulation data were compared with the experimental data with good agreement. The highest achieved column efficiency was 71%.     

Structural basis for GroEL-assisted protein folding from the crystal structure of (GroEL-KMgATP)14 at 2.0A resolution

Nucleotide regulates the affinity of the bacterial chaperonin GroEL for protein substrates. GroEL binds protein substrates with high affinity in the absence of ATP and with low affinity in its presence. We report the crystal structure of (GroEL-KMgATP)(14) refined to 2.0 A resolution in which the ATP triphosphate moiety is directly coordinated by both K(+) and Mg(2+). Upon the binding of KMgATP, we observe previously unnoticed domain rotations and a 102 degrees rotation of the apical domain surface helix I. Two major consequences are a large lateral displacement of, and a dramatic reduction of hydrophobicity in, the apical domain surface. These results provide a basis for the nucleotide-dependent regulation of protein substrate binding and suggest a mechanism for GroEL-assisted protein folding by forced unfolding.     

CFD Simulation of Fish-like Body Moving in Viscous Liquid

The study of fish-like bodies moving in liquid is an interesting and challenging research subject in the fields of biolocomotion and biomimetics. Typically the effect of tail oscillation on fluid flow around such a body is highly unsteady, generating vortices and requiring detailed analysis of fluid-structure interactions. An understanding of the complexities of such flows is of interest not only to biologists but also to engineers interested in developing vehicles capable of emulating the high performance of fish propulsion and manoeuvring. In the present study, a computational fluid dynamic （CFD） simulation of a three-dimensional biomimetic fish-like body has been developed to investigate the fluid flows around this body when moving in a viscous liquid. A parametric analysis of the variables that affect the flow surrounding the body is presented, along with flow visualisations, in an attempt to quantify and qualify the effect that these variables have on the performance of the body. The analysis provided by the unsteady transient simulation of a fish-like body has allowed the flow surrounding a fish-like body undergoing periodic oscillations to be studied. The simulation produces a motion of the tail in the （x, y） plane, with the tail oscillating as a rigid body in the form of a sinusoidal wave.     

Braking Performance of a Biomimetic Squid-Like Underwater Robot

In this study, the braking performance of the undulating fin propulsion system of a biomimetic squid-like underwater robot was investigated through free run experiment and simulation of the quasi-steady mathematical model. The quasi-steady equations of motion were solved using the measured and calculated hydrodynamic forces and compared with free-run test results. Various braking strategies were tested and discussed in terms of stopping ability and the forces acting on the stopping stage. The stopping performance of the undulating fin propulsion system turned out to be excellent considering the short stopping time and short stopping distance. This is because of the large negative thrust produced by progressive wave in opposite direction. It was confirmed that the undulating fin propulsion system can effectively perform braking even in complex underwater explorations.     

Preparation of a robust biocatalyst of d-amino acid oxidase on sepabeads supports using the glutaraldehyde crosslinking method

In this work different protocols to immobilize d-amino acid oxidase (DAAO) on sepabeads were assayed (ionic adsorption on different supports and covalent attachment using glutaraldehyde), studying the stability of the final preparations. The highest stability was achieved by the treatment with glutaraldehyde of DAAO adsorbed on Sepabeads EA (a commercial aminated support having ethylendiamine groups). In fact, this derivative was six times more stable than the enzyme adsorbed only by ionic interaction and much more stable than the soluble enzyme. The effect of the nature of the amino groups in the support was then analyzed. DAAO adsorbed on sepabeads coated with polyethylenimine (PEI) yielded a higher stability than the preparation on Sepabeads EA. The treatment with glutaraldehyde of DAAO adsorbed on Sepabeads PEI yielded the best results in terms of stability, being 200 times more stable than DAAO adsorbed onto Sepabeads EA. The effects of polyethylenimine size and glutaraldehyde concentration were also studied. sepabeads coated with 25 kDa polyethylenimine and treatment with 0.5% glutaraldehyde solution were the optimal parameters regarding the stability (the half life time was 9 h at 56° C, 600 times more stable than the soluble enzyme). Moreover, the optimal derivative showed a maximum load capacity of 15 mg/g of support. This derivative seems to fulfill the requirements for industrial applications.     

Large Neural Network Simulations on Multiple Hardware Platforms

To efficiently simulate very large networks of interconnected neurons, particular consideration has to be given to the computer architecture being used. This article presents techniques for implementing simulators for large neural networks on a number of different computer architectures. The neuronal simulation task and the computer architectures of interest are first characterized, and the potential bottlenecks are highlighted. Then we describe the experience gained from adapting an existing simulator, SWIM, to two very different architectures–vector computers and multiprocessor workstations. This work lead to the implementation of a new simulation library, SPLIT, designed to allow efficient simulation of large networks on several architectures. Different computer architectures put different demands on the organization of both data structures and computations. Strict separation of such architecture considerations from the neuronal models and other simulation aspects makes it possible to construct both portable and extendible code.     

Molecular Dynamics Simulation of Behaviours of Non-Polar Droplets Merging and Interactions with Hydrophobic Surfaces

This paper presents a molecular dynamics simulation of the behaviours of non-polar droplets merging and also the fluid molecules interacting with a hydrophobic surface. Such behaviours and transport phenomena are popular in general microchannel flow boiling and two-phase flow. The droplets are assumed to be composed of Lennards-Jones type molecules. Periodic boundary conditions are applied in three coordinate directions of a 3-D system, where there exist two liquid droplets and their vapour. The two droplets merge when they come within the prescribed small distance. The merging of two droplets apart from each other at different initial distances is tested and the possible larger （or critical） non-dimensional distance, in which droplets merging can occur, is discussed. The evolution of the merging process is simulated numerically by employing the Molecular Dynamics （MD） method. For interactions with hydrophobic solid wall, a system with fluid confined between two walls is used to study the wetting phenomena of fluid and solid wall. The results are compared with those of hydrophilic wall to show the unique characteristics of hydrophobic interactions by microscopic methods.