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dc.contributor.authorCooper Villagran, Christopher Daviden_US
dc.date.accessioned2016-04-08T17:38:33Z
dc.date.available2016-04-08T17:38:33Z
dc.date.issued2015
dc.identifier.urihttps://hdl.handle.net/2144/15650
dc.description.abstractThe implicit-solvent model uses continuum electrostatic theory to represent the salt solution around dissolved biomolecules, leading to a coupled system of the Poisson-Boltzmann and Poisson equations. This thesis uses the implicit-solvent model to study solvation, binding and adsorption of proteins. We developed an implicit-solvent model solver that uses the boundary element method (BEM), called PyGBe. BEM numerically solves integral equations along the biomolecule-solvent interface only, therefore, it does not need to discretize the entire domain. PyGBe accelerates the BEM with a treecode algorithm and runs on graphic processing units. We performed extensive verification and validation of the code, comparing it with experimental observations, analytical solutions, and other numerical tools. Our results suggest that a BEM approach is more appropriate than volumetric based methods, like finite-difference or finite-element, for high accuracy calculations. We also discussed the effect of features like solvent-filled cavities and Stern layers in the implicit-solvent model, and realized that they become relevant in binding energy calculations. The application that drove this work was nano-scale biosensors-- devices designed to detect biomolecules. Biosensors are built with a functionalized layer of ligand molecules, to which the target molecule binds when it is detected. With our code, we performed a study of the orientation of proteins near charged surfaces, and investigated the ideal conditions for ligand molecule adsorption. Using immunoglobulin G as a test case, we found out that low salt concentration in the solvent and high positive surface charge density leads to favorable orientations of the ligand molecule for biosensing applications. We also studied the plasmonic response of localized surface plasmon resonance (LSPR) biosensors. LSPR biosensors monitor the plasmon resonance frequency of metallic nanoparticles, which shifts when a target molecule binds to a ligand molecule. Electrostatics is a valid approximation to the LSPR biosensor optical phenomenon in the long-wavelength limit, and BEM was able to reproduce the shift in the plasmon resonance frequency as proteins approach the nanoparticle.en_US
dc.language.isoen_US
dc.subjectBiophysicsen_US
dc.subjectBiosensorsen_US
dc.subjectBoundary element methoden_US
dc.subjectImplicit solventen_US
dc.subjectPoisson-Boltzmannen_US
dc.subjectProtein electrostaticsen_US
dc.subjectTreecodeen_US
dc.titleBiomolecular electrostatics with continuum models: a boundary integral implementation and applications to biosensorsen_US
dc.typeThesis/Dissertationen_US
dc.date.updated2016-03-12T07:14:04Z
etd.degree.nameDoctor of Philosophyen_US
etd.degree.leveldoctoralen_US
etd.degree.disciplineMechanical Engineeringen_US
etd.degree.grantorBoston Universityen_US


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