Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 9 of 9 for “"DNA model"”.
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DT-DNA: Devising a DNA Paradigm for Modeling Health Digital Twins
… of DTs was a key motivation behind the model introduced in this thesis for building health digital twins of citizens. In contrast with DTs that have been developed in more industrial fields, this type of digital twins modeling necessitates protecting each citizen's unique identity while …
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Computational tools for modeling and measuring chromosome structure
DNA conformation within cells has many important biological implications, but there are challenges both in modeling DNA due to the need for specialized techniques, and experimentally since tracing out in vivo conformations is currently impossible. This thesis contributes two computational projects …
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Critical role of histone tail entropy in nucleosome unwinding
… long-lasting genome stability while keeping the DNA accessible to protein molecules. Using a transferable protein-DNA model and advanced sampling techniques, we investigated the stability and dynamics of the nucleosome by determining the free energy cost of its DNA unwinding. Simulation results …
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Manipulation of 3D knotted polygons
… The random polygons themselves are a simple model of long polymer chains. (A DNA molecule is one example of a polymer.)</p> <p>This software architecture includes "building blocks" which specify the actual manipulations and computations to be performed, and a structural framework which allows …
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Stability of Nucleic Acid Secondary Structures and Their Contribution to Gene Expression
… encoded in the bacterio-opsin gene {bop) (1). DNA sequence analysis and predictive folding algorithms suggest that the first twenty-five bases of the bop gene mRNA can form a secondary structural element (a "stem-loop"). Using biophysical methods, the goal was to determine if the stem-loop …
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Ab initio computational applications to complex biomolecular systems
… related systems ― including water and DNA molecules ― have been studied using ab initio (first-principles) methods. By investigating the properties of water as the preliminary step, the hydrogen bond (HB) interactions, which play important roles in biomolecules, were better understood …
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Quantitative all-atom and coarse-grained molecular dynamics simulation studies of DNA
… genetic information for all life on earth—DNA—is a polymer with unusual physical properties. The mechanical and electrostatic properties of DNA are utilized extensively by cells in the replication, regular maintenance, and expression of their genetic material. This can be illustrated by …
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Maximum Entropy Optimization: a General Approach to Study Ordered and Disordered Proteins Reveals Key Features of Protein Phase Separation
… to predict their microstructures. Computational modeling could provide high-resolution structural characterizations of these condensates and help uncover physicochemical interactions that dictate their stability. However, the presence of both ordered and disordered domains in these proteins …
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Interactions between nucleoid associated proteins and DNA in the presence of mechanical and chemical forces
"The way that DNA is organized within a cell controls its physiological behavior. DNA must be condensed in order to fit into the much smaller cell, but must also be accessible to proteins responsible for biological processes. Architectural proteins assist with this large-scale arrangement of DNA to …