New algorithms for computing field of vision over 2d grids, evan debenham. In this dissertation, we propose algorithms that accelerate molecular simulations by clustering particles into rigid bodies. The rest of the thesis is dedicated to the rsync algorithm which provides a novel method of ef. Modeling of molecular evolution and maximum likelihood inference of molecular phylogeny. Part ii of this dissertation is done under his supervision, andalthough he had no of. Optimization algorithms applied to large petri nets by ahmed tarek, b. Pdf an indexed bibliography of genetic algorithm theses. In this dissertation we will address two topics in bioinformatics. Extracting scales of measurement automatically from biomedical text with special emphasis on comparative and superlative scales, sara baker.
Uncovering the complexities associated with promoting health. Molecular imaging plays an important role for development of systems biomedicine, which noninvasively extracts pictorial information on physiological and pathological activities at the cellular and molecular levels. An algorithm of that kind was devised in 2014 by gillespie and coworkers. Initial evidence on the association between municipal audit committees, governance and internal controls, pamela jean strickland. Reconstruction methods for optical molecular tomography.
Our algorithm, implemented in the phylogenetic software. Optical molecular tomography is an emerging area of molecular imaging. Over the past decade, novel algorithms have been developed both for analyzing biological. First, we describe a fast and e ective stochastic search algorithm to nd maximumlikelihood phylogenies. This algorithm has been developed for md anderson using a multidisciplinary approach considering circumstances particular to md andersons specific patient population, services and structure, and clinical information. Attractor molecular signatures and their applications for. In order to place the study in ita proper context and perspcctivq the historical development of nomenclature is first discussed, aa well as other related aspects of the chemical information pmblcm. We show what components make up genetic algorithms and how. However, data analysis to extract valuable information from the nanoscale measurement data remained as a major challenge. The principal motivation of protein design is to circumvent the functional repertoire of natural proteins and create new classes of enzymes for therapeutic and industrial purposes.
The parallel algorithm uses an efficient novel parallel bucket sort. It is easy to follow for a scientist entering the field and at the same time contains overview of most critical topics in md simulation. The central theme of our approach revolves around abstracting a complex biological process as a collection of discrete, interacting molecular entities driven in time by a set. An algorithm for translating chemical names to molecular. Unfortunately, they still remain computationally challenging. A comparison of two different prophylactic dose regimens of low molecular weight heparin in bariatric surgery.
According to websites, for example his authors biography in the huffington post dr. I certify that i have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of doctor of philosophy. The crystal and molecular structures of selected organic. It has been a pleasure to work with him during my visits. The chapters dealing with molecular sequences will mainly focus on the development of novel algorithms. To support queries for models in this domain, it will be useful to collect information on the source of molecular data used by specific predictive models and on the type of clinical outcomes that these models predict. To browse dissertations and theses by academic department or program, please go to the schools, colleges, and departments page please click on the submissions guidelines link in the sidebar for more information about submitting your dissertation questions about the submission process. The crystal and molecular structures of selected organic and organometalllc compounds and an algorithm for empirical absorption correction by barbara ann karcher a dissertation submitted to the graduate faculty in partial fulfillment of the requirements for the degree of doctor of philosophy department. This requires performing global optimization over a highdimensional search space.
Fast algorithm for joint reconstruction of ancestral amino. We give a simple sequential algorithm to solve this problem and an efficient parallel version of the algorithm. Rooney, timothy edward, an application of clustering and cluster update methods to boiler sensor prediction and casebasedreasoning to boiler repair. This book is an excellent introduction to the field of molecular dynamics simulation. An overview of algorithms important to computational structural biology that addresses such topics as nmr and design and analysis of proteins. A property based approach to integrated process and molecular design fadwa tahra eljack a dissertation submitted to the graduate faculty of auburn university in partial fulfillment of the requirements for the degree of doctor of philosophy auburn, alabama may 10, 2007. In this dissertation, we present a networkcentric modeling and simulation approach to systematically study the stochastic dynamics of cellular processes at a molecular level.
This dissertation discusses, explains, and demonstrates a new algorithm for translating chetica 1 nomenclature into molecular formulas. An examination of jail reentry in a nonmetropolitan county. Evolutionary dynamics in molecular populations of ligase ribozymes, carolina diaz arenas. Theoretical study of anharmonic vibrational modes and. A dynamic programming algorithm is developed for maximumlikelihood reconstruction of the set of all ancestral amino acid sequences in a phylogenetic. This dissertation is the culmination of many long years of work and would absolutely not be possible without the support of my advisor, professor angela violi, who has challenged and guided me in the exploration of my research with her considerable expertise and force of will. Computer science theses and dissertations computer science. Nsu theses and dissertations nova southeastern university. The pennsylvania state university the graduate school. Venous thromboembolism vte prophyhlaxis for hospitalized. Genetic algorithms gas have become popular as a means of solving hard combinatorial optimization problems.
Molecular formulas of several hundred randomly selected chemicals were calculated successfully, verifying the linguistic analyses and the logic of the canputer program. A read is counted each time someone views a publication summary such as the title, abstract, and list of authors, clicks on a figure, or views or downloads the fulltext. Understanding molecular simulation, second edition. Daniel thomas gillespie 15 august 1938 19 april 2017 was a physicist who is best known for his derivation in 1976 of the stochastic simulation algorithm ssa, also called the gillespie algorithm. Singlemolecule electrical characterization reveals the events occurring at the nanoscale, which provides guidelines for molecular materials and devices. An introduction to genetic algorithms jenna carr may 16, 2014 abstract genetic algorithms are a type of optimization algorithm, meaning they are used to nd the maximum or minimum of a function. The contributions of this thesis are centered around new algorithms for bipartite matching prob lems, in which, surprisingly, graph sparsi cation plays a major role, and ecient algorithms for constructing sparsi ers in modern data models. Understanding molecular simulation from algorithms to applications daan frenkel fom institute for atomic and molecular physics, amsterdam, the netherlands department of chemical engineering, faculty of sciences university of amsterdam amsterdam, the netherlands berend smit department of chemical engineering faculty of sciences university of amsterdam.
A dissertation in computer science submitted to the graduate faculty of texas tech university in partial fulfillment of the requirements for the degree of doctor of philosophy approved accepted interim dean of the graduate school aust, 2001. The running time of our algorithm scales linearly with the number of sequences and thus can be applied to a practically unlimited number of sequences. Probabilistic models for gene silencing data defense. To date, no fast algorithm exists for joint reconstruction.
An algorithm for translating chemical names to molecular formulas. Medical image segmentation using a genetic algorithm, payel ghosh dissertation pdf. What has been the shortest phd dissertation online, in. A model for field deployment of wireless sensor networks wsns within the domain of microclimate habitat monitoring, mark a. Algorithms for molecular biology publishes articles on novel algorithms for biological sequence and structure analysis, phylogeny reconstruction, and combinatorial algorithms and machine learning. Algorithms in structural molecular biology the mit press. Dissertations of the computational molecular biology department.
For molecular medicine predictive models dissertation. The rsync algorithm was a direct result of my work on parallel. Automatic classification of singlemolecule charge transport. Aminobutyric acid a receptor gabaar to alleviate inflammation for asthma and neuropathic pain pdf. An alignmentfree computational tool for analyzing and visualizing dna sequences interrelationships, rallis karamichalis. Understanding molecular simulation from algorithms to applications daan frenkel fom institute for atomic and molecular physics, amsterdam, the netherlands department of chemical engineering, faculty of sciences university of amsterdam amsterdam, the netherlands berend smit department of chemical engineering faculty of sciences university of. Genetic algorithms gas perform global optimization by starting from an initial population of structures a methods and applications of crystal structure prediction. To browse dissertations and theses by academic department or program, please go to the schools. High multiplicity strip packing, andrew blochhansen. Dan boneh i certify that i have read this dissertation and that, in my opinion, it is fully adequate in scope and quality as a dissertation for the degree of doctor of philosophy. Using the tools of information technology to understand the molecular machinery of the cell offers both challenges and opportunities to computational scientists. Philip steven low and his commercial site, he claims he authored a 1 page phd thesis tedmed authors biography philip low states at the salk, dr. Molecular and cellular biology theses and dissertations. Theses and dissertations university of wisconsin milwaukee.
Prognostic molecular factors and algorithms in diffuse. The goal of molecular crystal structure prediction csp is to find all the plausible polymorphs for a given molecule. An investigation of molecular pathways to aid in therapeutic development for neurofibromatosis type 2. The link is a simple text searching algorithmtridgell and hawking 1996. I also provide a polynomial time algorithm that approximates the optimal solution to within a factor of olog2n.
Evolutionary niching in the gator genetic algorithm for. Pdf adaptive algorithms for molecular simulation semantic. Prognostic molecular factors and algorithms in diffuse large. A new algorithm for primer design, debanjan guha roy. An empirical investigation of the economic value of information security management system standards, babak shoraka. Attractor molecular signatures and their applications for prognostic biomarkers weiyi cheng this dissertation presents a novel data mining algorithm identifying molecular signatures, called attractor metagenes, from large biological data sets. Observe that the last few years are most incomplete in the database. Hawley, eric thomas 201905 neurofibromatosis type 2 nf2 is an autosomal dominant cancer predisposition in which loss of heterozygosity at the nf2 gene locus leads to the development of tumors of neural crest derived origin, most. Shaffer, data structures and algorithm analysis in. Interdisciplinary graduate program in molecular and cellular biology. Computer science theses and dissertations computer. Prognostic molecular factors and algorithms in diffuse large bcell lymphoma heidi nyman department of oncology helsinki university central hospital university of helsinki, finland and molecular and cancer biology programme, biomedicum helsinki university of helsinki, finland academic dissertation. Here, we provide a new efficient algorithm for joint ml ancestral reconstruction. The first part of this chapter briefly traces their history, explains the basic.
We first study several neighborsearch algorithms for large rigid bodies, and show that hierarchybased algorithms may. Algorithms for the description of molecular sequences. Theoretical study of anharmonic vibrational modes and couplings with the vscf algorithm mehdi bounouar a dissertation submitted to the technische universit. Nor would it possible without my close collaborator. Molecular algorithms 269 a turing machine consists of very simple components. Olson, dustin, chemical selfassembly strategies toward the design of molecular electronic circuits pdf. It is often interesting to find the substrings of length k that appear most frequently in a given string. It also presents a computational model for combining such signatures to create prognostic biomarkers. Diffusion is therefore modeled much more accurately in the svta than in. Duong, khanh linh 2014, molecular and cellular basis of hematopoietic stem cells maintenance and differentiation. Molecular simulations have become an essential tool in biology, chemistry and physics. An algorithm for translating directly frnm chemical names to molecular formulas is described, fire validity nf the algcmithm was tested both manually and hy computer. Called the smallvoxel tracking algorithm svta, it subdivides the system volume into voxels that are smaller than the reactant molecules, and hence much smaller than the voxels used in the rdssa.
Oyefusi, adebola, active polymeric materials for 3d shaping and sensing. The last two chapters of this dissertation represent the initiation of a novel line research concerned with the adaptation of tools from symbolic dynamics and thermodynamic formalism to the study of dna sequences. Graduate thesis or dissertation algorithms for string. Stochastic simulation of carbonaceous nanoparticle.
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