Characterization of the influence of external stimulus on protein-nucleic acid complex through multiscale computations

dc.contributor.advisor Pranav Shrotriya Gosai, Agnivo Gosai, Agnivo
dc.contributor.department Mechanical Engineering 2018-08-11T10:02:19.000 2020-06-30T03:04:34Z 2020-06-30T03:04:34Z Sun Jan 01 00:00:00 UTC 2017 2001-01-01 2017-01-01
dc.description.abstract <p>The concomitant detection, monitoring and analysis of biomolecules have assumed utmost importance in the field of medical diagnostics as well as in different spheres of biotechnology research such as drug development, environmental hazard detection and biodefense. There is an increased demand for the modulation of the biological response for such detection / sensing schemes which will be facilitated by the sensitive and controllable transmission of external stimuli. Electrostatic actuation for the controlled release/capture of biomolecules through conformational transformations of bioreceptors provides an efficient and feasible mechanism to modulate biological response. In addition, electrostatic actuation mechanism has the advantage of allowing massively parallel schemes and measurement capabilities that could ultimately be essential for biomedical applications.Experiments have previously demonstrated the unbinding of thrombin from its aptamer in presence of small positive electrode potential whereas the complex remained associated in presence of small negative potentials / zero potential. However, the nanoscale physics/chemistry involved in this process is not clearly understood. In this thesis a combination of continuum mechanics based modeling and a variety of atomistic simulation techniques have been utilized to corroborate the aforementioned experimental observations. It is found that the computational approach can satisfactorily predict the dynamics of the electrically excited aptamer-thrombin complex as well as provide an analytical model to characterize the forced binding of the complex.</p>
dc.format.mimetype application/pdf
dc.identifier archive/
dc.identifier.articleid 6532
dc.identifier.contextkey 11055586
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath etd/15525
dc.language.iso en
dc.source.bitstream archive/|||Fri Jan 14 20:42:35 UTC 2022
dc.subject.disciplines Biophysics
dc.subject.disciplines Nanoscience and Nanotechnology
dc.subject.keywords aptamer-thrombin
dc.subject.keywords biosensors
dc.subject.keywords computational biophysics
dc.subject.keywords molecular dynamics
dc.subject.keywords potential of mean force
dc.subject.keywords switchable surface
dc.title Characterization of the influence of external stimulus on protein-nucleic acid complex through multiscale computations
dc.type article
dc.type.genre thesis
dspace.entity.type Publication
relation.isAuthorOfPublication f113e15e-d444-4319-a40a-06771e6584ac
relation.isOrgUnitOfPublication 6d38ab0f-8cc2-4ad3-90b1-67a60c5a6f59 Mechanical Engineering thesis Master of Science
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