Estimation of the shear transformation zone size fin a bulk metallic glass through statistical a analysis of the first pop-in stresses during spherical nanoindentation

The size of the shear transformation zone (STZ) that initiates the elastic to plastic transition in a Zr-based bulk metallic glass was estimated by conducting a statistical analysis of the first pop-in event during spherical nanoindentation. A series of experiments led us to a successful description of the distribution of shear strength for the transition and its dependence on the loading rate. From the activation volume determined by statistical analysis the STZ size was estimated based on a cooperative shearing model. (C) 2012 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Climate change induced risk in water quality control problems

A modeling framework is presented in this paper, integrating hydrologic scenarios projected from a General Circulation Model (GCM) with a water quality simulation model to quantify the future expected risk. Statistical downscaling with a Canonical Correlation Analysis (CCA) is carried out to develop the future scenarios of hydro-climate variables starting with simulations provided by a GCM. A Multiple Logistic Regression (MLR) is used to quantify the risk of Low Water Quality (LWQ) corresponding to a threshold quality level, by considering the streamflow and water temperature as explanatory variables. An Imprecise Fuzzy Waste Load Allocation Model (IFWLAM) presented in an earlier study is then used to develop adaptive policies to address the projected water quality risks. Application of the proposed methodology is demonstrated with the case study of Tunga-Bhadra river in India. The results showed that the projected changes in the hydro-climate variables tend to diminish DO levels, thus increasing the future risk levels of LWQ. (C) 2012 Elsevier B.V. All rights reserved.

Suite of tools for statistical N-gram language modeling for pattern mining in whole genome sequences

Genome sequences contain a number of patterns that have biomedical significance. Repetitive sequences of various kinds are a primary component of most of the genomic sequence patterns. We extended the suffix-array based Biological Language Modeling Toolkit to compute n-gram frequencies as well as n-gram language-model based perplexity in windows over the whole genome sequence to find biologically relevant patterns. We present the suite of tools and their application for analysis on whole human genome sequence.

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.

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

Statistical Methods for Accelerated Life Testing with Particular Reference to Resin Impregnated Paper Bushings

Electrical failure of insulation is known to be an extremal random process wherein nominally identical pro-rated specimens of equipment insulation, at constant stress fail at inordinately different times even under laboratory test conditions. In order to be able to estimate the life of power equipment, it is necessary to run long duration ageing experiments under accelerated stresses, to acquire and analyze insulation specific failure data. In the present work, Resin Impregnated Paper (RIP) a relatively new insulation system of choice used in transformer bushings, is taken as an example. The failure data has been processed using proven statistical methods, both graphical and analytical. The physical model governing insulation failure at constant accelerated stress has been assumed to be based on temperature dependent inverse power law model.

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.

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.

Force Biased Molecular Dynamics Simulation Study of Effect of Dendrimer Generation on Interaction with DNA

We have studied the effect of dendrimer generation on the interaction between dsDNA and the PAMAM dendrimer using force biased simulation of dsDNA with three generations of dendrimer: G3, G4, and G5. Our results for the potential of mean force (PMF) and the dendrimer asphericity along the binding pathway, combined with visualization of the simulations, demonstrate that dendrimer generation has a pronounced impact on the interaction. The PMF increases linearly with increasing generation of the dendrimer. While, in agreement with previous results, we see an increase in the extent to which the dendrimer bends the dsDNA with increasing dendrimer generation, we also see that the deformation of the dendrimer is greater with smaller generation of the dendrimer. The larger dendrimer forces the dsDNA to conform to its structure, while the smaller dendrimer is forced to conform to the structure of the dsDNA. Monitoring the number of bound cations at different values of force bias distance shows the expected effect of ions being expelled when the dendrimer binds dsDNA.

Full Chemical Kinetic Simulation of Biogas Early Phase Combustion in SI Engines

This paper presents computational work on the biogas early phase combustion in spark ignition (SI) engines using detailed chemical kinetics. Specifically, the early phase combustion is studied to assess the effect of various ignition parameters such as spark plug location, spark energy, and number of spark plugs. An integrated version of the KIVA-3V and CHEMKIN codes was developed and used for the simulations utilizing detailed kinetics involving 325 reactions and 53 species The results show that location of the spark plug and local flow field play an important role. A central plug configuration, which is associated with higher local flow velocities in the vicinity of the spark plug, showed faster initial combustion. Although a dual plug configuration shows the highest rate of fuel consumption, it is comparable to the rate exhibited by the central plug case. The radical species important in the initiation of combustion are identified, and their concentrations are monitored during the early phase of combustion. The concentration of these radicals is also observed to correlate very well with the above-mentioned trend.Thus, the role of these radicals in promoting faster combustion has been clearly established. It is also observed that the minimum ignition energy required to initiate a self-sustained flame depends on the flow field condition in the vicinity of the spark plug.Increasing the methane content in the biogas has shown improved combustion.

Engagement of CF3 Group in N-H center dot center dot center dot F-C Hydrogen Bond in the Solution State: NMR Spectroscopy and MD Simulation Studies

Unambiguous evidence for the engagement of CF3 group in N-H center dot center dot center dot F-C hydrogen bond in a low polarity solvent, the first observation of its kind, is reported. The presence of such weak molecular interactions in the solution state is convincingly established by one and two-dimensional H-1, F-19, and natural abundant N-15 NMR spectroscopic studies. The strong and direct evidence is derived by the observation of through-space couplings, such as, (1h)J(FH), (1h)J(FN), and (2h)J(FF), where the spin polarization is transmitted through hydrogen bond. In an interesting example of a molecule containing two CF3 groups getting simultaneously involved in hydrogen bond, where hydrogen bond mediated couplings are not reflected in the NMR spectrum, F-19-F-19 NOESY experiment yielded confirmatory evidence. Significant deviations in the strengths of (1)J(NH), variable temperature, and the solvent induced perturbations yielded additional support. The NMR results are corroborated by both DFT calculations and MD simulations, where the quantitative information on different ways of involvement of fluorine in two and three centered hydrogen bonds, their percentage of occurrences, and geometries have been obtained. The hydrogen bond interaction energies have also been calculated.

On the dynamic contact angle in simulation of impinging droplets with sharp interface methods

Effects of dynamic contact angle models on the flow dynamics of an impinging droplet in sharp interface simulations are presented in this article. In the considered finite element scheme, the free surface is tracked using the arbitrary Lagrangian-Eulerian approach. The contact angle is incorporated into the model by replacing the curvature with the Laplace-Beltrami operator and integration by parts. Further, the Navier-slip with friction boundary condition is used to avoid stress singularities at the contact line. Our study demonstrates that the contact angle models have almost no influence on the flow dynamics of the non-wetting droplets. In computations of the wetting and partially wetting droplets, different contact angle models induce different flow dynamics, especially during recoiling. It is shown that a large value for the slip number has to be used in computations of the wetting and partially wetting droplets in order to reduce the effects of the contact angle models. Among all models, the equilibrium model is simple and easy to implement. Further, the equilibrium model also incorporates the contact angle hysteresis. Thus, the equilibrium contact angle model is preferred in sharp interface numerical schemes.

A THREE-WHEELED MOBILE ROBOT FOR TRAVERSING UNEVEN TERRAIN WITHOUT SLIP: SIMULATION AND EXPERIMENTS

A wheeled mobile robot (WMR) can move on uneven terrains without slip if the wheels are allowed to tilt laterally. This paper deals with the analysis, design and experimentations with a WMR where the wheels can tilt laterally. The wheels of such a WMR must be equipped with two degrees of freedom suspension mechanism. A prototype three-wheeled mobile robot is fabricated with a two degree-of-freedom suspension mechanism. Simulations show that the three-wheeled mobile robot can traverse uneven terrains with very little slip and experiments with the prototype on a representative uneven terrain confirm that the slip is significantly reduced.

Simulation of length-preserving motions of flexible one dimensional oObjects using optimization

During the motion of one dimensional flexible objects such as ropes, chains, etc., the assumption of constant length is realistic. Moreover,their motion appears to be naturally minimizing some abstract distance measure, wherein the disturbance at one end gradually dies down along the curve defining the object. This paper presents purely kinematic strategies for deriving length-preserving transformations of flexible objects that minimize appropriate ‘motion’. The strategies involve sequential and overall optimization of the motion derived using variational calculus. Numerical simulations are performed for the motion of a planar curve and results show stable converging behavior for single-step infinitesimal and finite perturbations 1 as well as multi-step perturbations. Additionally, our generalized approach provides different intuitive motions for various problem-specific measures of motion, one of which is shown to converge to the conventional tractrix-based solution. Simulation results for arbitrary shapes and excitations are also included.