Computational Methods for Locating and Analyzing Conserved Gene Regulatory DNA Elements

This thesis presents methods for locating and analyzing cis-regulatory DNA elements involved with the regulation of gene expression in multicellular organisms. The regulation of gene expression is carried out by the combined effort of several transcription factor proteins collectively binding the DNA on the cis-regulatory elements. Only sparse knowledge of the 'genetic code' of these elements exists today. An automatic tool for discovery of putative cis-regulatory elements could help their experimental analysis, which would result in a more detailed view of the cis-regulatory element structure and function. We have developed a computational model for the evolutionary conservation of cis-regulatory elements. The elements are modeled as evolutionarily conserved clusters of sequence-specific transcription factor binding sites. We give an efficient dynamic programming algorithm that locates the putative cis-regulatory elements and scores them according to the conservation model. A notable proportion of the high-scoring DNA sequences show transcriptional enhancer activity in transgenic mouse embryos. The conservation model includes four parameters whose optimal values are estimated with simulated annealing. With good parameter values the model discriminates well between the DNA sequences with evolutionarily conserved cis-regulatory elements and the DNA sequences that have evolved neutrally. In further inquiry, the set of highest scoring putative cis-regulatory elements were found to be sensitive to small variations in the parameter values. The statistical significance of the putative cis-regulatory elements is estimated with the Two Component Extreme Value Distribution. The p-values grade the conservation of the cis-regulatory elements above the neutral expectation. The parameter values for the distribution are estimated by simulating the neutral DNA evolution. The conservation of the transcription factor binding sites can be used in the upstream analysis of regulatory interactions. This approach may provide mechanistic insight to the transcription level data from, e.g., microarray experiments. Here we give a method to predict shared transcriptional regulators for a set of co-expressed genes. The EEL (Enhancer Element Locator) software implements the method for locating putative cis-regulatory elements. The software facilitates both interactive use and distributed batch processing. We have used it to analyze the non-coding regions around all human genes with respect to the orthologous regions in various other species including mouse. The data from these genome-wide analyzes is stored in a relational database which is used in the publicly available web services for upstream analysis and visualization of the putative cis-regulatory elements in the human genome.

Computational methods for the prediction of the structure and interactions of coiled-coil peptides

The past several years have seen significant advances in the development of computational methods for the prediction of the structure and interactions of coiled-coil peptides. These methods are generally based on pairwise correlations of amino acids, helical propensity, thermal melts and the energetics of sidechain interactions, as well as statistical patterns based on Hidden Markov Model (HMM) and Support Vector Machine (SVM) techniques. These methods are complemented by a number of public databases that contain sequences, motifs, domains and other details of coiled-coil structures identified by various algorithms. Some of these computational methods have been developed to make predictions of coiled-coil structure on the basis of sequence information; however, structural predictions of the oligomerisation state of these peptides still remains largely an open question due to the dynamic behaviour of these molecules. This review focuses on existing in silico methods for the prediction of coiled-coil peptides of functional importance using sequence and/or three-dimensional structural data.

Singular value decomposition based computationally efficient algorithm for rapid dynamic near-infrared diffuse optical tomography

Purpose: A computationally efficient algorithm (linear iterative type) based on singular value decomposition (SVD) of the Jacobian has been developed that can be used in rapid dynamic near-infrared (NIR) diffuse optical tomography. Methods: Numerical and experimental studies have been conducted to prove the computational efficacy of this SVD-based algorithm over conventional optical image reconstruction algorithms. Results: These studies indicate that the performance of linear iterative algorithms in terms of contrast recovery (quantitation of optical images) is better compared to nonlinear iterative (conventional) algorithms, provided the initial guess is close to the actual solution. The nonlinear algorithms can provide better quality images compared to the linear iterative type algorithms. Moreover, the analytical and numerical equivalence of the SVD-based algorithm to linear iterative algorithms was also established as a part of this work. It is also demonstrated that the SVD-based image reconstruction typically requires O(NN2) operations per iteration, as contrasted with linear and nonlinear iterative methods that, respectively, requir O(NN3) and O(NN6) operations, with ``NN'' being the number of unknown parameters in the optical image reconstruction procedure. Conclusions: This SVD-based computationally efficient algorithm can make the integration of image reconstruction procedure with the data acquisition feasible, in turn making the rapid dynamic NIR tomography viable in the clinic to continuously monitor hemodynamic changes in the tissue pathophysiology.

Additively manufactured device for dynamic culture of large arrays of 3D tissue engineered constructs

The ability to test large arrays of cell and biomaterial combinations in 3D environments is still rather limited in the context of tissue engineering and regenerative medicine. This limitation can be generally addressed by employing highly automated and reproducible methodologies. This study reports on the development of a highly versatile and upscalable method based on additive manufacturing for the fabrication of arrays of scaffolds, which are enclosed into individualized perfusion chambers. Devices containing eight scaffolds and their corresponding bioreactor chambers are simultaneously fabricated utilizing a dual extrusion additive manufacturing system. To demonstrate the versatility of the concept, the scaffolds, while enclosed into the device, are subsequently surface-coated with a biomimetic calcium phosphate layer by perfusion with simulated body fluid solution. 96 scaffolds are simultaneously seeded and cultured with human osteoblasts under highly controlled bidirectional perfusion dynamic conditions over 4 weeks. Both coated and noncoated resulting scaffolds show homogeneous cell distribution and high cell viability throughout the 4 weeks culture period and CaP-coated scaffolds result in a significantly increased cell number. The methodology developed in this work exemplifies the applicability of additive manufacturing as a tool for further automation of studies in the field of tissue engineering and regenerative medicine.

Dynamic nature of proteins - interpretation of residual dipolar couplings

Protein conformations and dynamics can be studied by nuclear magnetic resonance spectroscopy using dilute liquid crystalline samples. This work clarifies the interpretation of residual dipolar coupling data yielded by the experiments. It was discovered that unfolded proteins without any additional structure beyond that of a mere polypeptide chain exhibit residual dipolar couplings. Also, it was found that molecular dynamics induce fluctuations in the molecular alignment and doing so affect residual dipolar couplings. The finding clarified the origins of low order parameter values observed earlier. The work required the development of new analytical and computational methods for the prediction of intrinsic residual dipolar coupling profiles for unfolded proteins. The presented characteristic chain model is able to reproduce the general trend of experimental residual dipolar couplings for denatured proteins. The details of experimental residual dipolar coupling profiles are beyond the analytical model, but improvements are proposed to achieve greater accuracy. A computational method for rapid prediction of unfolded protein residual dipolar couplings was also developed. Protein dynamics were shown to modulate the effective molecular alignment in a dilute liquid crystalline medium. The effects were investigated from experimental and molecular dynamics generated conformational ensembles of folded proteins. It was noted that dynamics induced alignment is significant especially for the interpretation of molecular dynamics in small, globular proteins. A method of correction was presented. Residual dipolar couplings offer an attractive possibility for the direct observation of protein conformational preferences and dynamics. The presented models and methods of analysis provide significant advances in the interpretation of residual dipolar coupling data from proteins.

Analysis of Dynamic Heterogeneity in a Glass Former from the Spatial Correlations of Mobility

The growth of characteristic length scales associated with dynamic heterogeneity in glass-forming liquids is investigated in an extensive computational study of a four-point, time-dependent structure factor defined from spatial correlations of mobility, for a model liquid for system sizes extending up to 351 232 particles, in constant-energy and constant-temperature ensembles. Our estimates for dynamic correlation lengths and susceptibilities are consistent with previous results from finite size scaling. We find scaling exponents that are inconsistent with predictions from inhomogeneous mode coupling theory and a recent simulation confirmation of these predictions.

Active vibration suppression of beams with discrete actuators using optimal dynamic inversion

Most of the structural elements like beams, cables etc. are flexible and should be modeled as distributed parameter systems (DPS) to represent the reality better. For large structures, the usual approach of 'modal representation' is not an accurate representation. Moreover, for excessive vibrations (possibly due to strong wind, earthquake etc.), external power source (controller) is needed to suppress it, as the natural damping of these structures is usually small. In this paper, we propose to use a recently developed optinial dynamic inversion technique to design a set of discrete controllers for this purpose. We assume that the control force to the structure is applied through finite number of actuators, which are located at predefined locations in the spatial domain. The method used in this paper determines control forces directly from the partial differential equation (PDE) model of the system. The formulation has better practical significance, both because it leads to a closed form solution of the controller (hence avoids computational issues) as well as because a set of discrete actuators along the spatial domain can be implemented with relative ease (as compared to a continuous actuator).

A study of symbolic processing and computational aspects in helicopter dynamics

Even research models of helicopter dynamics often lead to a large number of equations of motion with periodic coefficients; and Floquet theory is a widely used mathematical tool for dynamic analysis. Presently, three approaches are used in generating the equations of motion. These are (1) general-purpose symbolic processors such as REDUCE and MACSYMA, (2) a special-purpose symbolic processor, DEHIM (Dynamic Equations for Helicopter Interpretive Models), and (3) completely numerical approaches. In this paper, comparative aspects of the first two purely algebraic approaches are studied by applying REDUCE and DEHIM to the same set of problems. These problems range from a linear model with one degree of freedom to a mildly non-linear multi-bladed rotor model with several degrees of freedom. Further, computational issues in applying Floquet theory are also studied, which refer to (1) the equilibrium solution for periodic forced response together with the transition matrix for perturbations about that response and (2) a small number of eigenvalues and eigenvectors of the unsymmetric transition matrix. The study showed the following: (1) compared to REDUCE, DEHIM is far more portable and economical, but it is also less user-friendly, particularly during learning phases; (2) the problems of finding the periodic response and eigenvalues are well conditioned.

Nonlinear hydrodynamics of a hard-sphere fluid near the glass transition

We conduct a numerical study of the dynamic behavior of a dense hard-sphere fluid by deriving and integrating a set of Langevin equations. The statics of the system is described by a free-energy functional of the Ramakrishnan-Yussouff form. We find that the system exhibits glassy behavior as evidenced through a stretched exponential decay and a two-stage relaxation of the density correlation function. The characteristic times grow with increasing density according to the Vogel-Fulcher law. The wave-number dependence of the kinetics is extensively explored. The connection of our results with experiment, mode-coupling theory, and molecular-dynamics results is discussed.

Particle filters for structural system identification using multiple test and sensor data: A combined computational and experimental study

The problem of structural system identification when measurements originate from multiple tests and multiple sensors is considered. An offline solution to this problem using bootstrap particle filtering is proposed. The central idea of the proposed method is the introduction of a dummy independent variable that allows for simultaneous assimilation of multiple measurements in a sequential manner. The method can treat linear/nonlinear structural models and allows for measurements on strains and displacements under static/dynamic loads. Illustrative examples consider measurement data from numerical models and also from laboratory experiments. The results from the proposed method are compared with those from a Kalman filter-based approach and the superior performance of the proposed method is demonstrated. Copyright (C) 2009 John Wiley & Sons, Ltd.

Dynamic structure factors of a dense mixture

We compute the dynamic structure factors of a dense binary liquid mixture. These describe dynamics on molecular length scales, where structural relaxation is important. We find that the presence of a few large particles in a dense fluid of small particles slows down the dynamics considerably. We also observe a deep narrowing of the spectrum for a disordered mixture composed of a nearly equal packing of the two species. In contrast, a few small particles diffuse easily in the background of a dense fluid of large particles. We expect our results to describe neutron scattering from a dense mixture.

Active vibration suppression of beams with discrete actuators using optimal dynamic inversion

Most of the structural elements like beams, cables etc. are flexible and should be modeled as distributed parameter systems (DPS) to represent the reality better. For large structures, the usual approach of 'modal representation' is not an accurate representation. Moreover, for excessive vibrations (possibly due to strong wind, earthquake etc.), external power source (controller) is needed to suppress it, as the natural damping of these structures is usually small. In this paper, we propose to use a recently developed optimal dynamic inversion technique to design a set of discrete controllers for this purpose. We assume that the control force to the structure is applied through finite number of actuators, which are located at predefined locations in the spatial domain. The method used in this paper determines control forces directly from the partial differential equation (PDE) model of the system. The formulation has better practical significance, both because it leads to a closed form solution of the controller (hence avoids computational issues) as well as because a set of discrete actuators along the spatial domain can be implemented with relative ease (as compared to a continuous actuator)

Dynamic stiffness matrix of a general cable element

A computational scheme for determining the dynamic stiffness coefficients of a linear, inclined, translating and viscously/hysteretically damped cable element is outlined. Also taken into account is the coupling between inplane transverse and longitudinal forms of cable vibration. The scheme is based on conversion of the governing set of quasistatic boundary value problems into a larger equivalent set of initial value problems, which are subsequently numerically integrated in a spatial domain using marching algorithms. Numerical results which bring out the nature of the dynamic stiffness coefficients are presented. A specific example of random vibration analysis of a long span cable subjected to earthquake support motions modeled as vector gaussian random processes is also discussed. The approach presented is versatile and capable of handling many complicating effects in cable dynamics in a unified manner.

Vibration and Stability of Fluid Conveying Pipes with Stochastic Parameters

Flexible cantilever pipes conveying fluids with high velocity are analysed for their dynamic response and stability behaviour. The Young's modulus and mass per unit length of the pipe material have a stochastic distribution. The stochastic fields, that model the fluctuations of Young's modulus and mass density are characterized through their respective means, variances and autocorrelation functions or their equivalent power spectral density functions. The stochastic non self-adjoint partial differential equation is solved for the moments of characteristic values, by treating the point fluctuations to be stochastic perturbations. The second-order statistics of vibration frequencies and mode shapes are obtained. The critical flow velocity is-first evaluated using the averaged eigenvalue equation. Through the eigenvalue equation, the statistics of vibration frequencies are transformed to yield critical flow velocity statistics. Expressions for the bounds of eigenvalues are obtained, which in turn yield the corresponding bounds for critical flow velocities.

Numerical simulations of fracture initiation in ductile solids under mode I, dynamic loading

In this paper, an overview of some recent computational studies by the authors on ductile crack initiation under mode I, dynamic loading is presented. In these studies, a large deformation finite element procedure is employed along with the viscoplastic version of the Gurson constitutive model that accounts for the micro-mechanical processes of void nucleation, growth and coalescence. A three-point bend fracture specimen subjected to impact, and a single edge notched specimen loaded by a tensile stress pulse are analysed. Several loading rates are simulated by varying the impact speed or the rise time and magnitude of the stress pulse. A simple model involving a semi-circular notch with a pre-nucleated circular hole situated ahead of it is considered. The growth of the hole and its interaction with the notch tip, which leads to plastic strain and porosity localization in the ligament connecting them, is simulated. The role of strain-rate dependence on ductile crack initiation at high loading rates, and the specimen geometry effect on the variation of dynamic fracture toughness with loading rate are Investigated.