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Full-Text Articles in Physical Sciences and Mathematics
Accurate And Robust Mechanical Modeling Of Proteins, Naomi Fox
Accurate And Robust Mechanical Modeling Of Proteins, Naomi Fox
Open Access Dissertations
Through their motion, proteins perform essential functions in the living cell. Although we cannot observe protein motion directly, over 68,000 crystal structures are freely available from the Protein Data Bank. Computational protein rigidity analysis systems leverage this data, building a mechanical model from atoms and pairwise interactions determined from a static 3D structure. The rigid and flexible components of the model are then calculated with a pebble game algorithm, predicting a protein's flexibility with much more computational efficiency than physical simulation. In prior work with rigidity analysis systems, the available modeling options were hard-coded, and evaluation was limited to case …
Multiscale Modeling Of Human Addiction: A Computational Hypothesis For Allostasis And Healing, Yariv Z. Levy
Multiscale Modeling Of Human Addiction: A Computational Hypothesis For Allostasis And Healing, Yariv Z. Levy
Open Access Dissertations
This dissertation presents a computational multiscale framework for predicting behavioral tendencies related to human addiction. The research encompasses three main contributions. The first contribution presents a formal, heuristic, and exploratory framework to conduct interdisciplinary investigations about the neuropsychological, cognitive, behavioral, and recovery constituents of addiction. The second contribution proposes a computational framework to account for real-life recoveries that are not dependent on pharmaceutical, clinical, and counseling support. This exploration relies upon a combination of current biological beliefs together with unorthodox rehabilitation practices, such as meditation, and proposes a conjecture regarding possible cognitive mechanisms involved in the recovery process. Further elaboration …
Discovery Of Complex Regulatory Modules From Expression Genetics Data, Manjunatha Jagalur
Discovery Of Complex Regulatory Modules From Expression Genetics Data, Manjunatha Jagalur
Open Access Dissertations
Mapping of strongly inherited classical traits have been immensely helpful in understanding many important traits including diseases, yield and immunity. But some of these traits are too complex and are difficult to map. Taking into consideration gene expression, which mediates the genetic effects, can be helpful in understanding such traits. Together with genetic variation data such data-set is collectively known as expression genetics data. Presence of discrete and continuous variables, observed and latent variables, availability of partial causal information, and under-specfied nature of the data make expression genetics data computationally challenging, but potentially of great biological importance. In this dissertation …