A Study of Speed of the Boundary Element Method as applied to the Realtime Computational Simulation of Biological Organs

In this work, possibility of simulating biological organs in realtime using the Boundary Element Method (BEM) is investigated. Biological organs are assumed to follow linear elastostatic material behavior, and constant boundary element is the element type used. First, a Graphics Processing Unit (GPU) is used to speed up the BEM computations to achieve the realtime performance. Next, instead of the GPU, a computer cluster is used. Results indicate that BEM is fast enough to provide for realtime graphics if biological organs are assumed to follow linear elastostatic material behavior. Although the present work does not conduct any simulation using nonlinear material models, results from using the linear elastostatic material model imply that it would be difficult to obtain realtime performance if highly nonlinear material models that properly characterize biological organs are used. Although the use of BEM for the simulation of biological organs is not new, the results presented in the present study are not found elsewhere in the literature.

REDUCING COMPUTATIONAL EFFORT IN SOLVING GEOMECHANICS PROBLEMS WITH UPPER BOUND FINITE ELEMENTS LIMIT ANALYSIS AND LINEAR OPTIMIZATION

This paper presents a simple technique for reducing the computational effort while solving any geotechnical stability problem by using the upper bound finite element limit analysis and linear optimization. In the proposed method, the problem domain is discretized into a number of different regions in which a particular order (number of sides) of the polygon is chosen to linearize the Mohr-Coulomb yield criterion. A greater order of the polygon needs to be selected only in that region wherein the rate of the plastic strains becomes higher. The computational effort required to solve the problem with this implementation reduces considerably. By using the proposed method, the bearing capacity has been computed for smooth and rough strip footings and the results are found to be quite satisfactory.

AIM-Spice Integration of a Recursive Model for Threshold Voltage Shift in Thin Film Transistors

Non-crystalline semiconductor based thin film transistors are the building blocks of large area electronic systems. These devices experience a threshold voltage shift with time due to prolonged gate bias stress. In this paper we integrate a recursive model for threshold voltage shift with the open source BSIM4V4 model of AIM-Spice. This creates a tool for circuit simulation for TFTs. We demonstrate the integrity of the model using several test cases including display driver circuits.

Computational framework to integrate the effect of antigen recognition on disease epidemiology outcome: multi-scale approach

Human Leukocyte Antigen (HLA) plays an important role, in presenting foreign pathogens to our immune system, there by eliciting early immune responses. HLA genes are highly polymorphic, giving rise to diverse antigen presentation capability. An important factor contributing to enormous variations in individual responses to diseases is differences in their HLA profiles. The heterogeneity in allele specific disease responses decides the overall disease epidemiological outcome. Here we propose an agent based computational framework, capable of incorporating allele specific information, to analyze disease epidemiology. This framework assumes a SIR model to estimate average disease transmission and recovery rate. Using epitope prediction tool, it performs sequence based epitope detection for a given the pathogenic genome and derives an allele specific disease susceptibility index depending on the epitope detection efficiency. The allele specific disease transmission rate, that follows, is then fed to the agent based epidemiology model, to analyze the disease outcome. The methodology presented here has a potential use in understanding how a disease spreads and effective measures to control the disease.

Generalized Model Predictive Static Programming and Angle-Constrained Guidance of Air-to-Ground Missiles

A new generalized model predictive static programming technique is presented for rapidly solving a class of finite-horizon nonlinear optimal control problems with hard terminal constraints. Two key features for its high computational efficiency include one-time backward integration of a small-dimensional weighting matrix dynamics, followed bya static optimization formulation that requires only a static Lagrange multiplier to update the control history. It turns out that under Euler integration and rectangular approximation of finite integrals it is equivalent to the existing model predictive static programming technique. In addition to the benchmark double integrator problem, usefulness of the proposed technique is demonstrated by solving a three-dimensional angle-constrained guidance problem for an air-to-ground missile, which demands that the missile must meet constraints on both azimuth and elevation angles at the impact point in addition to achieving near-zero miss distance, while minimizing the lateral acceleration demand throughout its flight path. Simulation studies include maneuvering ground targets along with a first-order autopilot lag. Comparison studies with classical augmented proportional navigation guidance and modern general explicit guidance lead to the conclusion that the proposed guidance is superior to both and has a larger capture region as well.

Computational Study of the Formation of Short Centrosymmetric N-center dot center dot center dot S Supramolecular Synthon and Related Weak Interactions in Crystalline 1,2,4-Triazoles

A comprehensive analysis of the crystal packing and the energetic features of a series of four biologically active molecules belonging to the family of substituted 4-(benzylideneamino)-3-(4-fluoro-3-phenoxyphenyl)-1H-1,2,4-triazole-5-(4 H)-thione derivatives have been performed based on the molecular conformation and the supramolecular packing. This involves the formation of a short centrosymmetric R-2(2)(8) NH...S supramolecular synthon in the solid state, including the presence of CH...S, CH...O, CH...N, CH...F, CH...Cl, CF...FC, CCl...ClC, and CH...pi intermolecular interactions along with pp stacking to evaluate the role of noncovalent interactions in the crystal. The presence of such synthons has a substantial contribution toward the interaction energy (-18 to -20 kcal/mol) as obtained from the PIXEL calculation, wherein the Coulombic and polarization contribution are more significant than the dispersion contribution. The geometrical characteristics of such synthons favor short distance, and the population of related molecules having these geometries is rare as has been obtained from the Cambridge Structural Database (CSD). Furthermore, their interaction energies have been compared with those present in our molecules in the solid state. The topological characteristics of the NH...S supramolecular synthon, in addition to related weak interactions, CH...N, CH...Cl, CF...FC, and CCl...ClC, have been estimated using the quantum theory of atoms in molecules (QTAIM). In addition, an analysis of the Hirshfeld surface and associated fingerprint plots of these four molecules also have provided a platform for the evaluation of the contribution of different atom...atom contacts, which contribute toward the packing of the molecules in solids.

Effect of alkyl substituents in BODIPYs: a comparative DFT computational investigation

Random changes in the alkyl substitution patterns of fluorescent dyes, e.g. BODIPYs, are often accompanied by significant changes in their photophysical properties. To understand such alterations in properties in closely related molecular systems, a comparative DFT (density functional theory) computational investigation was performed in order to comprehend the effects of alkyl substitution in controlling the structural and electronic nature of BODIPY dyes. In this context, a systematic strategy was utilized, considering all possible outcomes of constitutionally-isomeric molecules to understand the alkyl groups' effects on the BODIPY molecules. Four different computational methods {i.e. B3LYP/631G(d); B3LYP/6-311++ G(d,p); wb97xd/6-311++ G(d,p) and mpw1pw91/6-311++ G(d,p)} were employed to rationalize the agreement of the trends associated with the molecular properties. In line with experimental observations, it was found that alkyl substituents in BODIPY dyes situated at 3/5-positions effectively participate in stabilization as well as planarization of such molecules. Screening of all the possible isomeric molecular systems was used to understand the individual properties and overall effects of the typical alkyl substituents in controlling several basic properties of such BODIPY molecules.

Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

Background: mIHF belongs to a subfamily of proteins, distinct from E. coli IHF. Results: Functionally important amino acids of mIHF and the mechanism(s) underlying DNA binding, DNA bending, and site-specific recombination are distinct from that of E. coli IHF. Conclusion: mIHF functions could contribute beyond nucleoid compaction. Significance: Because mIHF is essential for growth, the molecular mechanisms identified here can be exploited in drug screening efforts. The annotated whole-genome sequence of Mycobacterium tuberculosis revealed that Rv1388 (Mtihf) is likely to encode for a putative 20-kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or the organization of the mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg-170, Arg-171, and Arg-173, which might be involved in DNA binding, and a conserved proline (Pro-150) in the tight turn. The phenotypic sensitivity of Escherichia coli ihfA and ihfB strains to UV and methyl methanesulfonate could be complemented with the wild-type Mtihf but not its alleles bearing mutations in the DNA-binding residues. Protein-DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, binds with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes DNA compaction into nucleoid-like or higher order filamentous structures. We therefore propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Faster computation of the Karhunen-Loeve expansion using its domain independence property

The goal of this work is to reduce the cost of computing the coefficients in the Karhunen-Loeve (KL) expansion. The KL expansion serves as a useful and efficient tool for discretizing second-order stochastic processes with known covariance function. Its applications in engineering mechanics include discretizing random field models for elastic moduli, fluid properties, and structural response. The main computational cost of finding the coefficients of this expansion arises from numerically solving an integral eigenvalue problem with the covariance function as the integration kernel. Mathematically this is a homogeneous Fredholm equation of second type. One widely used method for solving this integral eigenvalue problem is to use finite element (FE) bases for discretizing the eigenfunctions, followed by a Galerkin projection. This method is computationally expensive. In the current work it is first shown that the shape of the physical domain in a random field does not affect the realizations of the field estimated using KL expansion, although the individual KL terms are affected. Based on this domain independence property, a numerical integration based scheme accompanied by a modification of the domain, is proposed. In addition to presenting mathematical arguments to establish the domain independence, numerical studies are also conducted to demonstrate and test the proposed method. Numerically it is demonstrated that compared to the Galerkin method the computational speed gain in the proposed method is of three to four orders of magnitude for a two dimensional example, and of one to two orders of magnitude for a three dimensional example, while retaining the same level of accuracy. It is also shown that for separable covariance kernels a further cost reduction of three to four orders of magnitude can be achieved. Both normal and lognormal fields are considered in the numerical studies. (c) 2014 Elsevier B.V. All rights reserved.

Computational design of model Re/Ru bearing Ni-base superalloys

It is well established that Re and Ru additions to Ni-base superalloys result in improved creep performance and phase stability. However, the role of Re and Ru and their synergetic effects are not well understood, and the first step in understanding these effects is to design alloys with controlled microstructural parameters. A computational approach was undertaken in the present work for designing model alloys with varying levels of Re and Ru. Thermodynamic and first principles calculations were employed complimentarily to design a set of alloys with varying Re and Ru levels, but which were constrained by constant microstructural parameters, i.e., phase fractions and lattice misfit across the alloys. Three ternary/quaternary alloys of type Ni-Al-xRe-yRu were thus designed. These compositions were subsequently cast, homogenized and aged. Experimental results suggest that while the measured volume fraction matches the predicted value in the Ru containing alloy, volume fraction is significantly higher than the designed value in the Re containing alloys. This is possibly due to errors in the thermodynamic database used to predict phase fraction and composition. These errors are also reflected in the mismatch between predicted and measured values of misfit.

Spatio-temporal correlations in aqueous systems: computational studies of static and dynamic heterogeneity by 2D-IR spectroscopy

Local heterogeneity is ubiquitous in natural aqueous systems. It can be caused locally by external biomolecular subsystems like proteins, DNA, micelles and reverse micelles, nanoscopic materials etc., but can also be intrinsic to the thermodynamic nature of the aqueous solution itself (like binary mixtures or at the gas-liquid interface). The altered dynamics of water in the presence of such diverse surfaces has attracted considerable attention in recent years. As these interfaces are quite narrow, only a few molecular layers thick, they are hard to study by conventional methods. The recent development of two dimensional infra-red (2D-IR) spectroscopy allows us to estimate length and time scales of such dynamics fairly accurately. In this work, we present a series of interesting studies employing two dimensional infra-red spectroscopy (2D-IR) to investigate (i) the heterogeneous dynamics of water inside reverse micelles of varying sizes, (ii) supercritical water near the Widom line that is known to exhibit pronounced density fluctuations and also study (iii) the collective and local polarization fluctuation of water molecules in the presence of several different proteins. The spatio-temporal correlation of confined water molecules inside reverse micelles of varying sizes is well captured through the spectral diffusion of corresponding 2D-IR spectra. In the case of supercritical water also, we observe a strong signature of dynamic heterogeneity from the elongated nature of the 2D-IR spectra. In this case the relaxation is ultrafast. We find remarkable agreement between the different tools employed to study the relaxation of density heterogeneity. For aqueous protein solutions, we find that the calculated dielectric constant of the respective systems unanimously shows a noticeable increment compared to that of neat water. However, the `effective' dielectric constant for successive layers shows significant variation, with the layer adjacent to the protein having a much lower value. Relaxation is also slowest at the surface. We find that the dielectric constant achieves the bulk value at distances more than 3 nm from the surface of the protein.

COMPUTATIONAL MODELING OF A MULTI-LAYERED PIEZO-COMPOSITE BEAM MADE UP OF MFC

The Variational Asymptotic Method (VAM) is used for modeling a coupled non-linear electromechanical problem finding applications in aircrafts and Micro Aerial Vehicle (MAV) development. VAM coupled with geometrically exact kinematics forms a powerful tool for analyzing a complex nonlinear phenomena as shown previously by many in the literature 3 - 7] for various challenging problems like modeling of an initially twisted helicopter rotor blades, matrix crack propagation in a composite, modeling of hyper elastic plates and various multi-physics problems. The problem consists of design and analysis of a piezocomposite laminate applied with electrical voltage(s) which can induce direct and planar distributed shear stresses and strains in the structure. The deformations are large and conventional beam theories are inappropriate for the analysis. The behavior of an elastic body is completely understood by its energy. This energy must be integrated over the cross-sectional area to obtain the 1-D behavior as is typical in a beam analysis. VAM can be used efficiently to approximate 3-D strain energy as closely as possible. To perform this simplification, VAM makes use of thickness to width, width to length, width multiplied by initial twist and strain as small parameters embedded in the problem definition and provides a way to approach the exact solution asymptotically. In this work, above mentioned electromechanical problem is modeled using VAM which breaks down the 3-D elasticity problem into two parts, namely a 2-D non-linear cross-sectional analysis and a 1-D non-linear analysis, along the reference curve. The recovery relations obtained as a by-product in the cross-sectional analysis earlier are used to obtain 3-D stresses, displacements and velocity contours. The piezo-composite laminate which is chosen for an initial phase of computational modeling is made up of commercially available Macro Fiber Composites (MFCs) stacked together in an arbitrary lay-up and applied with electrical voltages for actuation. The expressions of sectional forces and moments as obtained from cross-sectional analysis in closed-form show the electro-mechanical coupling and relative contribution of electric field in individual layers of the piezo-composite laminate. The spatial and temporal constitutive law as obtained from the cross-sectional analysis are substituted into 1-D fully intrinsic, geometrically exact equilibrium equations of motion and 1-D intrinsic kinematical equations to solve for all 1-D generalized variables as function of time and an along the reference curve co-ordinate, x(1).

A literature survey on the real-time computational simulation of biological organs

This paper lists some references that could in some way be relevant in the context of the real-time computational simulation of biological organs, the research area being defined in a very broad sense. This paper contains 198 references.

System reliability of randomly vibrating structures: Computational modeling and laboratory testing

The problem of determination of system reliability of randomly vibrating structures arises in many application areas of engineering. We discuss in this paper approaches based on Monte Carlo simulations and laboratory testing to tackle problems of time variant system reliability estimation. The strategy we adopt is based on the application of Girsanov's transformation to the governing stochastic differential equations which enables estimation of probability of failure with significantly reduced number of samples than what is needed in a direct simulation study. Notably, we show that the ideas from Girsanov's transformation based Monte Carlo simulations can be extended to conduct laboratory testing to assess system reliability of engineering structures with reduced number of samples and hence with reduced testing times. Illustrative examples include computational studies on a 10 degree of freedom nonlinear system model and laboratory/computational investigations on road load response of an automotive system tested on a four post Lest rig. (C) 2015 Elsevier Ltd. All rights reserved.

Modeling Ultrasonic NDE and Guided Wave based Structural Health Monitoring

Structural Health Monitoring (SHM) systems require integration of non-destructive technologies into structural design and operational processes. Modeling and simulation of complex NDE inspection processes are important aspects in the development and deployment of SHM technologies. Ray tracing techniques are vital simulation tools to visualize the wave path inside a material. These techniques also help in optimizing the location of transducers and their orientation with respect to the zone of interrogation. It helps in increasing the chances of detection and identification of a flaw in that zone. While current state-of-the-art techniques such as ray tracing based on geometric principle help in such visualization, other information such as signal losses due to spherical or cylindrical shape of wave front are rarely taken into consideration. The problem becomes a little more complicated in the case of dispersive guided wave propagation and near-field defect scattering. We review the existing models and tools to perform ultrasonic NDE simulation in structural components. As an initial step, we develop a ray-tracing approach, where phase and spectral information are preserved. This enables one to study wave scattering beyond simple time of flight calculation of rays. Challenges in terms of theory and modelling of defects of various kinds are discussed. Various additional considerations such as signal decay and physics of scattering are reviewed and challenges involved in realistic computational implementation are discussed. Potential application of this approach to SHM system design is highlighted and by applying this to complex structural components such as airframe structures, SHM is demonstrated to provide additional value in terms of lighter weight and/or longevity enhancement resulting from an extension of the damage tolerance design principle not compromising safety and reliability.