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Articles 1 - 4 of 4
Full-Text Articles in Molecular Biology
Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra
Three-Dimensional Ideal Gas Reference State Based Energy Function, Avdesh Mishra
University of New Orleans Theses and Dissertations
Energy functions are found to be a key of protein structure prediction. In this work, we propose a novel 3-dimensional energy function based on hydrophobic-hydrophilic properties of amino acid where we consider at least three different possible interaction of amino acid in a 3-dimensional sphere categorized as hydrophilic versus hydrophilic, hydrophobic versus hydrophobic and hydrophobic versus hydrophilic. Each of these interactions are governed by a 3-dimensional parameter alpha used to model the interaction and 3-dimensional parameter beta used to model weight of contribution. We use Genetic Algorithm (GA) to optimize the value of alpha, beta and Z-score. We obtain three …
Developing An Application For Evolutionary Search For Computational Models Of Cellular Development, Nicolas Scott Cornia
Developing An Application For Evolutionary Search For Computational Models Of Cellular Development, Nicolas Scott Cornia
Boise State University Theses and Dissertations
VPEvolve is a free and open source application that utilizes a Visual Programming Environment (VPE) for the setup of the Genetic Algorithm (GA), for optimization of computational models. Specifically, the User Interface uses connected glyphs to represent the genetic operators of mutation, reproduction, fitness and selection. These glyphs give the user an intuitive way to set the parameters for the GA, and better visualization of the population's flow through these operators.
VPEvolve is currently being developed alongside research being done in Biocomputing to create models of cellular regeneration based on the regenerative properties of Planaria or flatworms. Since these models …
Up Regulation Of Heat Shock Protein 70b (Hsp70b) And Ssa1 In Chlamydomonas Reinhardtii Via Hsp70a-Rbcs2 And Psad Promoter, B. Kirtley Amos
Up Regulation Of Heat Shock Protein 70b (Hsp70b) And Ssa1 In Chlamydomonas Reinhardtii Via Hsp70a-Rbcs2 And Psad Promoter, B. Kirtley Amos
Theses and Dissertations--Biosystems and Agricultural Engineering
Fabrication of effective algae cultivation systems adjacent to coal-fired power plants to fixate waste CO2 would represent a sizable step towards achieving a carbon neutral energy cycle. However, emission gas would elevate the algal cultivation system temperature and decreases its pH without expensive preprocessing. Increased temperature and acidity constitutes a profound stress on the algae. Although stressed algae produce heat shock proteins (HSPs) that promote protein folding and protect against stress, the ordinary biological response is insufficient to protect against coal flue gas. Experimental upregulation of HSPs could make algae respond to the stress caused by high temperatures and …
Ex Vivo Dna Cloning, Adam B. Fisher
Ex Vivo Dna Cloning, Adam B. Fisher
Theses and Dissertations
Genetic engineering of microbes has developed rapidly along with our ability to synthesize DNA de novo. Yet, even with decreasing DNA synthesis costs there remains a need for inexpensive, rapid and reliable methods for assembling synthetic DNA into larger constructs or combinatorial libraries. While technological advances have resulted in powerful techniques for in vitro and in vivo assembly of DNA, each suffers inherent disadvantages. Here, an ex vivo DNA cloning suite using crude cellular lysates derived from E. coli is demonstrated to amplify and assemble DNA containing small sequence homologies. Further, the advantages of an ex vivo approach are …