Computer simulation of liquid crystals

In this article we review the current status in the modelling of both thermotropic and lyotropic Liquid crystal. We discuss various coarse-graining schemes as well as simulation techniques such as Monte Carlo (MC) and Molecular dynamics (MD) simulations.In the area of MC simulations we discuss in detail the algorithm for simulating hard objects such as spherocylinders of various aspect ratios where excluded volume interaction enters in the simulation through overlap test. We use this technique to study the phase diagram, of a special class of thermotropic liquid crystals namely banana liquid crystals. Next we discuss a coarse-grain model of surfactant molecules and study the self-assembly of the surfactant oligomers using MD simulations. Finally we discuss an atomistically informed coarse-grained description of the lipid molecules used to study the gel to liquid crystalline phase transition in the lipid bilayer system.

Simulation-driven design of helmets for head impact protection using an injury-based criterion

The current paper suggests a new procedure for designing helmets for head impact protection for users such as motorcycle riders. According to the approach followed here, a helmet is mounted on a featureless Hybrid 3 headform that is used in assessing vehicles for compliance to the FMVSS 201 regulation in the USA for upper interior head impact safety. The requirement adopted in the latter standard, i.e. not exceeding a threshold HIC(d) limit of 1000, is applied in the present study as a likely criterion for adjudging the efficacy of helmets. An impact velocity of 6 m/s (13.5 mph) for the helmet-headform system striking a rigid target can probably be acceptable for ascertaining a helmet's effectiveness as a countermeasure for minimizing the risk of severe head injury. The proposed procedure is demonstrated with the help of a validated LS-DYNA model of a featureless Hybrid 3 headform in conjunction with a helmet model comprising an outer polypropylene shell to the inner surface of which is bonded a protective polyurethane foam padding of a given thickness. Based on simulation results of impact on a rigid surface, it appears that a minimum foam padding thickness of 40 mm is necessary for obtaining an acceptable value of HIC(d).

On Reducing Dynamic Web Page Construction Times

Many web sites incorporate dynamic web pages to deliver customized contents to their users. However, dynamic pages result in increased user response times due to their construction overheads. In this paper, we consider mechanisms for reducing these overheads by utilizing the excess capacity with which web servers are typically provisioned. Specifically, we present a caching technique that integrates fragment caching with anticipatory page pre-generation in order to deliver dynamic pages faster during normal operating situations. A feedback mechanism is used to tune the page pre-generation process to match the current system load. The experimental results from a detailed simulation study of our technique indicate that, given a fixed cache budget, page construction speedups of more than fifty percent can be consistently achieved as compared to a pure fragment caching approach.

Numerical simulation of nano-indentation on rough surfaces

Nano-indentation is a technique used to measure various mechanical properties like hardness, Young's modulus and the adherence of thin films and surface layers. It can be used as a quality control tool for various surface modification techniques like ion-implantation, film deposition processes etc. It is important to characterise the increasing scatter in the data measured at lower penetration depths observed in the nano-indentation, for the technique to be effectively applied. Surface roughness is one of the parameters contributing for the scatter. This paper is aimed at quantifying the nature and the amount of scatter that will be introduced in the measurement due to the roughness of the surface on which the indentation is carried out. For this the surface is simulated using the Weierstrass-Mandelbrot function which gives a self-affine fractal. The contact area of this surface with a conical indenter with a spherical cap at the tip is measured numerically. The indentation process is simulated using the spherical cavity model. This eliminates the indentation size effect observed at the micron and sub-micron scales. It has been observed that there exists a definite penetration depth in relation to the surface roughness beyond which the scatter is reduced such that reliable data could be obtained.

Algorithmic approach to simulate Hamiltonian dynamics and an NMR simulation of quantum state transfer

We propose an iterative algorithm to simulate the dynamics generated by any n-qubit Hamiltonian. The simulation entails decomposing the unitary time evolution operator U (unitary) into a product of different time-step unitaries. The algorithm product-decomposes U in a chosen operator basis by identifying a certain symmetry of U that is intimately related to the number of gates in the decomposition. We illustrate the algorithm by first obtaining a polynomial decomposition in the Pauli basis of the n-qubit quantum state transfer unitary by Di Franco et al. [Phys. Rev. Lett. 101, 230502 (2008)] that transports quantum information from one end of a spin chain to the other, and then implement it in nuclear magnetic resonance to demonstrate that the decomposition is experimentally viable. We further experimentally test the resilience of the state transfer to static errors in the coupling parameters of the simulated Hamiltonian. This is done by decomposing and simulating the corresponding imperfect unitaries.

Simulation of Potential and Electric Field Profiles for transmission line Insulators

Since the end of second world war, extra high voltage ac transmission has seen its development. The distances between generating and load centres as well as the amount of power to be handled increased tremendously for last 50 years. The highest commercial voltage has increased to 765 kV in India and 1,200 kV in many other countries. The bulk power transmission has been mostly performed by overhead transmission lines. The dual task of mechanically supporting and electrically isolating the live phase conductors from the support tower is performed by string insulators. Whether in clean condition or under polluted conditions, the electrical stress distribution along the insulators governs the possible flashover, which is quite detrimental to the system. Hence the present investigation aims to study accurately, the field distribution for various types of porcelain/ceramic insulators (Normal and Antifog discs) used for high-voltage transmission. The surface charge simulation method is employed for the field computation. A comparison on normalised surface resistance, which is an indicator for the stress concentration under polluted condition, is also attempted.

Simulation of surface and volume stress for high voltage transmission insulators

The bulk of power transmission from the generating stations to the load centres is carried through overhead lines. The distances involved could span several hundreds of kilometres. To minimize line losses, power transmission over such long distances is carried out at high voltages (several hundreds of kV). A network of outdoor lines operating at different voltages has been found to be the most economical method of power delivery. The disc insulators perform dual task of mechanically supporting and electrically isolating the live phase conductors from the support tower. These insulators have to perform under various environmental conditions; hence the electrical stress distribution along the insulators governs the possible flashover, which is quite detrimental to the system. In view of this the present investigation aims to simulate the surface electric field stress on different types of porcelain/ceramic insulators; both normal and anti-fog type discs which are used for high voltage transmission/distribution systems are considered. The surface charge simulation method is employed for the field computation to simulate potential, electric field, surface and bulk/volume stress.

Mutations in hpyAVIBM, C5 cytosine DNA methyltransferase from Helicobacter pylori result in relaxed specificity

The genome of Helicobacter pylori is rich in restrictionmodification (RM) systems. Approximately 4% of the genome codes for components of RM systems. hpyAVIBM, which codes for a phase-variable C5 cytosine methyltransferase (MTase) from H. pylori, lacks a cognate restriction enzyme. Over-expression of M.HpyAVIB in Escherichia coli enhances the rate of mutations. However, when the catalytically inactive F9N or C82W mutants of M.HpyAVIB were expressed in E. coli, mutations were not observed. The M.HpyAVIB gene itself was mutated to give rise to different variants of the MTase. M.HpyAVIB variants were purified and differences in kinetic properties and specificity were observed. Intriguingly, purified MTase variants showed relaxed substrate specificity. Homologues of hpyAVIBM homologues amplified and sequenced from different clinical isolates showed similar variations in sequence. Thus, hpyAVIBM presents an interesting example of allelic variations in H. pylori where changes in the nucleotide sequence result in proteins with new properties.

Conformational dynamics of HIV-1 protease: a comparative molecular dynamics simulation study with multiple amber force fields

Flap dynamics of HIV-1 protease (HIV-pr) controls the entry of inhibitors and substrates to the active site. Dynamical models from previous simulations are not all consistent with each other and not all are supported by the NMR results. In the present work, the er effect of force field on the dynamics of HIV-pr is investigated by MD simulations using three AMBER force fields ff99, ff99SB, and ff03. The generalized order parameters for amide backbone are calculated from the three force fields and compared with the NMR S2 values. We found that the ff99SB and ff03 force field calculated order parameters agree reasonably well with the NMR S2 values, whereas ff99 calculated values deviate most from the NMR order parameters. Stereochemical geometry of protein models from each force field also agrees well with the remarks from NMR S2 values. However, between ff99SB and ff03, there are several differences, most notably in the loop regions. It is found that these loops are, in general, more flexible in the ff03 force field. This results in a larger active site cavity in the simulation with the ff03 force field. The effect of this difference in computer-aided drug design against flexible receptors is discussed.

Monsoon circulation interaction with Western Ghats orography under changing climate - Projection by a 20-km mesh AGCM

In this study, the authors have investigated the likely future changes in the summer monsoon over the Western Ghats (WG) orographic region of India in response to global warming, using time-slice simulations of an ultra high-resolution global climate model and climate datasets of recent past. The model with approximately 20-km mesh horizontal resolution resolves orographic features on finer spatial scales leading to a quasi-realistic simulation of the spatial distribution of the present-day summer monsoon rainfall over India and trends in monsoon rainfall over the west coast of India. As a result, a higher degree of confidence appears to emerge in many aspects of the 20-km model simulation, and therefore, we can have better confidence in the validity of the model prediction of future changes in the climate over WG mountains. Our analysis suggests that the summer mean rainfall and the vertical velocities over the orographic regions of Western Ghats have significantly weakened during the recent past and the model simulates these features realistically in the present-day climate simulation. Under future climate scenario, by the end of the twenty-first century, the model projects reduced orographic precipitation over the narrow Western Ghats south of 16A degrees N that is found to be associated with drastic reduction in the southwesterly winds and moisture transport into the region, weakening of the summer mean meridional circulation and diminished vertical velocities. We show that this is due to larger upper tropospheric warming relative to the surface and lower levels, which decreases the lapse rate causing an increase in vertical moist static stability (which in turn inhibits vertical ascent) in response to global warming. Increased stability that weakens vertical velocities leads to reduction in large-scale precipitation which is found to be the major contributor to summer mean rainfall over WG orographic region. This is further corroborated by a significant decrease in the frequency of moderate-to-heavy rainfall days over WG which is a typical manifestation of the decrease in large-scale precipitation over this region. Thus, the drastic reduction of vertical ascent and weakening of circulation due to `upper tropospheric warming effect' predominates over the `moisture build-up effect' in reducing the rainfall over this narrow orographic region. This analysis illustrates that monsoon rainfall over mountainous regions is strongly controlled by processes and parameterized physics which need to be resolved with adequately high resolution for accurate assessment of local and regional-scale climate change.

Simulation of Influence of Bilayer Melting on Dynamics and Thermodynamics of Interfacial Water

We investigate the effect of bilayer melting transition on thermodynamics and dynamics of interfacial water using molecular dynamics simulation with the two-phase thermodynamic model. We show that the diffusivity of interface water depicts a dynamic crossover at the chain melting transition following an Arrhenius behavior until the transition temperature. The corresponding change in the diffusion coefficient from the bulk to the interface water is comparable with experimental observations found recently for water near 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) vesicles Phys. Chem. Chem. Phys. 13, 7732 (2011)]. The entropy and potential energy of interfacial water show distinct changes at the bilayer melting transition, indicating a strong correlation in the thermodynamic state of water and the accompanying first-order phase transition of the bilayer membrane. DOI: 10.1103/PhysRevLett.110.018303

SEU Tolerant Robust Memory Cell Design

The implementation of semiconductor circuits and systems in nano-technology makes it possible to achieve high speed, lower voltage level and smaller area. The unintended and undesirable result of this scaling is that it makes integrated circuits susceptible to soft errors normally caused by alpha particle or neutron hits. These events of radiation strike resulting into bit upsets referred to as single event upsets(SEU), become increasingly of concern for the reliable circuit operation in the field. Storage elements are worst hit by this phenomenon. As we further scale down, there is greater interest in reliability of the circuits and systems, apart from the performance, power and area aspects. In this paper we propose an improved 12T SEU tolerant SRAM cell design. The proposed SRAM cell is economical in terms of area overhead. It is easy to fabricate as compared to earlier designs. Simulation results show that the proposed cell is highly robust, as it does not flip even for a transient pulse with 62 times the Q(crit) of a standard 6T SRAM cell.

Methodology for Pavement Design Reliability and Back Analysis Using Markov Chain Monte Carlo Simulation

Given the increasing cost of designing and building new highway pavements, reliability analysis has become vital to ensure that a given pavement performs as expected in the field. Recognizing the importance of failure analysis to safety, reliability, performance, and economy, back analysis has been employed in various engineering applications to evaluate the inherent uncertainties of the design and analysis. The probabilistic back analysis method formulated on Bayes' theorem and solved using the Markov chain Monte Carlo simulation method with a Metropolis-Hastings algorithm has proved to be highly efficient to address this issue. It is also quite flexible and is applicable to any type of prior information. In this paper, this method has been used to back-analyze the parameters that influence the pavement life and to consider the uncertainty of the mechanistic-empirical pavement design model. The load-induced pavement structural responses (e.g., stresses, strains, and deflections) used to predict the pavement life are estimated using the response surface methodology model developed based on the results of linear elastic analysis. The failure criteria adopted for the analysis were based on the factor of safety (FOS), and the study was carried out for different sample sizes and jumping distributions to estimate the most robust posterior statistics. From the posterior statistics of the case considered, it was observed that after approximately 150 million standard axle load repetitions, the mean values of the pavement properties decrease as expected, with a significant decrease in the values of the elastic moduli of the expected layers. An analysis of the posterior statistics indicated that the parameters that contribute significantly to the pavement failure were the moduli of the base and surface layer, which is consistent with the findings from other studies. After the back analysis, the base modulus parameters show a significant decrease of 15.8% and the surface layer modulus a decrease of 3.12% in the mean value. The usefulness of the back analysis methodology is further highlighted by estimating the design parameters for specified values of the factor of safety. The analysis revealed that for the pavement section considered, a reliability of 89% and 94% can be achieved by adopting FOS values of 1.5 and 2, respectively. The methodology proposed can therefore be effectively used to identify the parameters that are critical to pavement failure in the design of pavements for specified levels of reliability. DOI: 10.1061/(ASCE)TE.1943-5436.0000455. (C) 2013 American Society of Civil Engineers.

Modified Newton, rank-1 Broyden update and rank-2 BFGS update methods in helicopter trim: A comparative study

Nonlinear equations in mathematical physics and engineering are solved by linearizing the equations and forming various iterative procedures, then executing the numerical simulation. For strongly nonlinear problems, the solution obtained in the iterative process can diverge due to numerical instability. As a result, the application of numerical simulation for strongly nonlinear problems is limited. Helicopter aeroelasticity involves the solution of systems of nonlinear equations in a computationally expensive environment. Reliable solution methods which do not need Jacobian calculation at each iteration are needed for this problem. In this paper, a comparative study is done by incorporating different methods for solving the nonlinear equations in helicopter trim. Three different methods based on calculating the Jacobian at the initial guess are investigated. (C) 2011 Elsevier Masson SAS. All rights reserved.

Eulerian two-phase flow simulation and experimental validation of semisolid slurry generation process using cooling slope

Experimental and numerical studies of slurry generation using a cooling slope are presented in the paper. The slope having stainless steel body has been designed and constructed to produce semisolid A356 Al alloy slurry. The pouring temperature of molten metal, slope angle of the cooling slope and slope wall temperature were varied during the experiment. A multiphase numerical model, considering liquid metal and air, has been developed to simulate the liquid metal flow along the cooling channel using an Eulerian two-phase flow approach. Solid fraction evolution of the solidifying melt is tracked at different locations of the cooling channel following Schiel's equation. The continuity, momentum and energy equations are solved considering thin wall boundary condition approach. During solidification of the melt, based on the liquid fraction and latent heat of the alloy, temperature of the alloy is modified continuously by introducing a modified temperature recovery method. Numerical simulations has been carried out for semisolid slurry formation by varying the process parameters such as angle of the cooling slope, cooling slope wall temperature and melt superheat temperature, to understand the effect of process variables on cooling slope semisolid slurry generation process such as temperature distribution, velocity distribution and solid fraction of the solidifying melt. Experimental validation performed for some chosen cases reveals good agreement with the numerical simulations.