Digital Commons Network^™

Circadian Rhythmicity By Autocatalysis, Arun Mehra, Christian I. Hong, Mi Shi, Jennifer J. Loros, Jay C. Dunlap, Peter Ruoff

Dartmouth Scholarship

The temperature compensated in vitro oscillation of cyanobacterial KaiC phosphorylation, the first example of a thermodynamically closed system showing circadian rhythmicity, only involves the three Kai proteins (KaiA, KaiB, and KaiC) and ATP. In this paper, we describe a model in which the KaiA- and KaiB-assisted autocatalytic phosphorylation and dephosphorylation of KaiC are the source for circadian rhythmicity. This model, based upon autocatalysis instead of transcription-translation negative feedback, shows temperature-compensated circadian limit-cycle oscillations with KaiC phosphorylation profiles and has period lengths and rate constant values that are consistent with experimental observations.

Impact Of Local Attenuation Approximations When Estimating Correlation Length From Backscattered Ultrasound Echoes, Timothy A. Bigelow, William D. O'Brien

Timothy A. Bigelow

Estimating the characteristic correlation length of tissue microstructure from the backscattered power spectrum could improve the diagnostic capability of medical ultrasound. Previously, size estimates were obtained after compensating for source focusing, the frequency-dependent attenuation along the propagation path (total attenuation), and the frequency-dependent attenuation in the scattering region (local attenuation). In this study, the impact of approximations of the local attenuation on the scatterer size estimate was determined using computer simulations and theoretical analysis. The simulations used Gaussian impedance distributions with an effective radius of 25 μm randomly positioned in a homogeneous half-space sonified by a spherically focused source (f/1 …

Numerical Simulation And Graphical Analysis Of In Vitro Benign Tumor Growth: Application Of Single-Particle State Bosonic Matter Equation With Length Scaling, Pradip K. Biswas, Jiansen Niu, Tobias Frederico, Valentin Gogonea

Chemistry Faculty Publications

We describe the application of a non-linear single-particle state bosonic condensate equation to simulate multicellular tumor growth by treating it as a coupling of two classical wave equations with real components. With one component representing the amplitude of the cells in their volume growth phase and the other representing the amplitude of the cells in their proliferation or mitosis phase, the two components of the coupled equation feed each other during the time evolution and are coupled together through diffusion and other linear and non-linear terms. The features of quiescent and necrotic cells, which result from poor nutrient diffusion into …

Bounded Search For De Novo Identification Of Degenerate Cis-Regulatory Elements, Jonathan M. Carlson, Arijit Chakravarty, Radhika S. Khetani, Robert H. Gross

Dartmouth Scholarship

The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in practice many cis-regulatory elements are highly degenerate, precluding the use of an exhaustive word-counting strategy for their identification. While numerous methods exist for inferring base distributions using a position weight matrix, recent studies suggest that the independence assumptions inherent in the model, as well as the inability to reach a global optimum, limit this approach.

Simulations Of A New Continuous Steelmaking Process, Jorg Annie Peter, Kent D. Peaslee, D. G. C. Robertson

Materials Science and Engineering Faculty Research & Creative Works

A new continuous steelmaking process has been designed in an effort to reduce meltshop costs and increase productivity beyond the possibilities of current EAF-LMF-CC meltshops. This paper discusses possible operational performance based on industrially-verified kinetic, thermodynamic, and heat-transfer models. Dynamic simulations predict variations in steel chemistry and temperature, resulting from steel treatment and upsets. Savings in costs are projected because of increased metallic yield, lower energy requirements, more efficient use of deoxidants and alloys, fewer man-hours per ton, and decreased capital investment.

Computer Simulation Of Crowd Dynamics And Destructive Crowd Behavior, Bruce Bassi

Honors Scholar Theses

The social processes that lead to destructive behavior in celebratory crowds can be studied through an agent-based computer simulation. Riots are an increasingly common outcome of sports celebrations, and pose the potential for harm to participants, bystanders, property, and the reputation of the groups with whom participants are associated. Rioting cannot necessarily be attributed to the negative emotions of individuals, such as anger, rage, frustration and despair. For instance, the celebratory behavior (e.g., chanting, cheering, singing) during UConn’s “Spring Weekend” and after the 2004 NCAA Championships resulted in several small fires and overturned cars. Further, not every individual in the …

Dissecting Trait Heterogeneity: A Comparison Of Three Clustering Methods Applied To Genotypic Data, Tricia A. Thornton-Wells, Jason H. Moore, Jonathan L. Haines

Dartmouth Scholarship

Background: Trait heterogeneity, which exists when a trait has been defined with insufficient specificity such that it is actually two or more distinct traits, has been implicated as a confounding factor in traditional statistical genetics of complex hu man disease. In the absence of de tailed phenotypic data collected consistently in combination with genetic data, unsupervised computational methodologies offer the potential for discovering underlying trait heteroge neity. The performance of three such methods – Bayesian Classification, Hyperg raph-Based Clustering, and Fuzzy k -Modes Clustering – appropriate for categorical data were comp ared. Also tested was the ability of these methods …

A Comparative Analysis Of Air-To-Ground Engagement Outcomes In The Joint Warfare System (Jwars) And The Jwars-Joint Semi-Automated Forces Federation, Melissa Anne St. Peter

Computational Modeling & Simulation Engineering Theses & Dissertations

Multi-resolution modeling is the process by which a single model is created by connecting multiple individual models to describe phenomena at different levels of resolution [1]. "When we change resolutions, replacing a detailed model by a more aggregate one, we must ask whether results are 'consistent'" [2].

There are many methods of determining if the results of two simulations are 'consistent'. However, they are very entailed and require a detailed understanding of the individual models including their functionality, algorithms, and inner workings. A straight forward and rapid way of assessing potential inconsistencies is through a statistical comparison of the model …

Mgrid: A Load-Balanced Distributed Computing Environment For The Remote Execution Of The User-Defined Matlab Code, Yuliya V. Karpievitch, Jonas S. Almeida

MUSC Faculty Journal Articles

Background: Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of …

Animal Carcinogenicity Studies: Implications For The Reach System, Andrew Knight, Jarrod Bailey, Jonathan Balcombe

Experimentation Collection

The 2001 European Commission proposal for the Registration, Evaluation and Authorisation of Chemicals (REACH) aims to improve public and environmental health by assessing the toxicity of, and restricting exposure to, potentially toxic chemicals. The greatest benefits are expected to accrue from decreased cancer incidences. Hence the accurate identification of chemical carcinogens must be a top priority for the REACH system. Due to a paucity of human clinical data, the identification of potential human carcinogens has conventionally relied on animal tests. However, our survey of the US Environmental Protection Agency’s (EPA’s) toxic chemicals database revealed that, for a majority of the …

A Multivariate Prediction Model For Microarray Cross-Hybridization, Yian A. Chen, Cheng-Chung Chou, Xinghua Lu, Elizabeth H. Slate, Konan Peck, Wenying Xu, Eberhand O. Voit, Jonas S. Almeida

MUSC Faculty Journal Articles

Background: Expression microarray analysis is one of the most popular molecular diagnostic techniques in the post-genomic era. However, this technique faces the fundamental problem of potential cross-hybridization. This is a pervasive problem for both oligonucleotide and cDNA microarrays; it is considered particularly problematic for the latter. No comprehensive multivariate predictive modeling has been performed to understand how multiple variables contribute to (cross-) hybridization. Results: We propose a systematic search strategy using multiple multivariate models [multiple linear regressions, regression trees, and artificial neural network analyses (ANNs)] to select an effective set of predictors for hybridization. We validate this approach on a …

Animal Carcinogenicity Studies: 3. Alternatives To The Bioassay, Andrew Knight, Jarrod Bailey, Jonathan Balcombe

Experimentation Collection

Conventional animal carcinogenicity tests take around three years to design, conduct and interpret. Consequently, only a tiny fraction of the thousands of industrial chemicals currently in use have been tested for carcinogenicity. Despite the costs of hundreds of millions of dollars and millions of skilled personnel hours, as well as millions of animal lives, several investigations have revealed that animal carcinogenicity data lack human specificity (i.e. the ability to identify human non-carcinogens), which severely limits the human predictivity of the bioassay. This is due to the scientific inadequacies of many carcinogenicity bioassays, and numerous serious biological obstacles, which render profoundly …

Loop Current Warming By Hurricane Wilma, Lie-Yauw Oey, Tal Ezer, Dong-Ping Wang, S. J. Fan, Xun-Qiang Yin

CCPO Publications

Hurricanes mix and cool the upper ocean, as shown here in observations and modeling of the Caribbean Sea and the Gulf of Mexico during the passage of hurricane Wilma. Curiously, the upper ocean around the Loop Current warmed prior to Wilma's entrance into the Gulf. The major cause was increased volume and heat transports through the Yucatan Channel produced by storm-induced convergences in the northwestern Caribbean Sea. Such oceanic variability may have important impacts on hurricane predictions.

Topographic Influence On Overflow Dynamics: Idealized Numerical Simulations And The Faroe Bank Channel Overflow, Tal Ezer

CCPO Publications

Properties of the North Atlantic Deep Water (NADW) depend on mixing that occurs in the Denmark Strait (DS) and the Faroe Bank Channel (FBC) overflow regions. How the sill's topography in those regions may affect mixing processes and downstream variability is thus investigated using a high-resolution terrain-following ocean model. Model results agree with observations that show enhanced mixing and entrainment downstream from the sill; however, mixing seems to occur over a longer distance downstream from the FBC sill and more abruptly downstream from the DS sill. Sensitivity experiments with various FBC sill widths demonstrate that the narrow sill is responsible …

Modeling Of The Effects Of Athermal Flow Strength And Activation Energy For Dislocation Glide On The Nanoindentation Creep Of Nickel Thin Film At Room Temperature

A.S. Md Abdul Haseeb

Nanoindentation creep behaviour of nickel at room temperature has been modeled based on the obstacle-controlled dislocation glide mechanism. Using the model, the effects of two important materials parameters viz. the activation free energy required by dislocation to overcome an obstacle without any aid from external stress, ΔF and the athermal flow strength, τ0, which is the flow strength of solids at 0 K are systematically studied. It has been found that ΔF plays a dominant role in room temperature creep properties of nickel. The role of ΔF is particularly dominant in determining the time dependent deformation. On the other hand, …

Computational Modeling To Predict Mechanical Function Of Joints: Validations And Applications Of Lower Leg Simulations, Peter C. Liacouras

Theses and Dissertations

Computational models of musculoskeletal joints and limbs can provide useful information about joint mechanics. Validated models can be used as a predictive device for understanding joint function and serve as a clinical tool for predicting the outcome of surgical procedures. A new computational modeling approach was developed for simulating joint kinematics that are dictated by bone/joint anatomy, ligamentous constraints, and applied loading.Three-dimensional computational models of the lower leg were created. Model development involved generating three-dimensional surfaces from CT images, followed by importing these surfaces into SolidWorks and COSMOSMotion. ThroughSolidWorks and COSMOSMotion, each bone surface was created into a solid object …

Teaching Lean Manufacturing Concepts Using Physical Simulations Within Engineering Technology Program, Alok Verma

Engineering Technology Faculty Publications

Physical Simulations have a proven record as a teaching tool. Concepts that are often hard to grasp are made easy by the use of physical simulation activities. The constructivism learning theory suggests that people learn better by actively participating in the process of learning. Effectiveness of simulation-based learning is well recognized. According to the Encyclopedia of Educational Technology, "Simulation-based learning involves the placement of a student into a realistic scenario or situation. The student is then responsible for any changes that occur as a result of their decisions." The computer integrated manufacturing course in the mechanical engineering technology program was …

Design Factors For The Communication Architecture Of Distributed Discrete Event Simulation Systems, Catharine Mcintire Hoaglund

Theses Digitization Project

The purpose of the thesis was to investigate the influence communication architecture decisions have on the performance of a simulation system with distributed components. In particular, the objective was to assess the relative importance of factors affecting reliability and variability of an external data interface to the performance of the simulation, as compared to factor within the simulation itself.

Modeling Of The Effects Of Athermal Flow Strength And Activation Energy For Dislocation Glide On The Nanoindentation Creep Of Nickel Thin Film At Room Temperature

A.S. Md Abdul Haseeb

Nanoindentation creep behaviour of nickel at room temperature has been modeled based on the obstacle-controlled dislocation glide mechanism. Using the model, the effects of two important materials parameters viz. the activation free energy required by dislocation to overcome an obstacle without any aid from external stress, ΔF and the athermal flow strength, τ0, which is the flow strength of solids at 0 K are systematically studied. It has been found that ΔF plays a dominant role in room temperature creep properties of nickel. The role of ΔF is particularly dominant in determining the time dependent deformation. On the other hand, …