Dissertations / Theses on the topic 'Continuum electrostatics'
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1
Xin, W. (Weidong). "Continuum electrostatics of biomolecular systems." Doctoral thesis, University of Oulu, 2008. http://urn.fi/urn:isbn:9789514287602.
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Abstract
Electrostatic interactions are very important in biomolecular systems. Electrostatic forces have received a great deal of attention due to their long-range nature and the trade-off between desolvation and interaction effects. It remains a challenging task to study and to predict the effects of electrostatic interactions in biomolecular systems. Computer simulation techniques that account for such interactions are an important tool for the study of biomolecular electrostatics.
This study is largely concerned with the role of electrostatic interactions in biomolecular systems and with developing novel models to estimate the strength of such interactions.
First, a novel formulation based upon continuum electrostatics to compute the electrostatic potential in and around two biomolecules in a solvent with ionic strength is presented. Many, if not all, current methods rely on the (non)linear Poisson-Boltzmann equation to include ionic strength. The present formulation, however, describes ionic strength through the inclusion of explicit ions, which considerably extends its applicability and validity range. The method relies on the boundary element method (BEM) and results in two very similar coupled integral equations valid on the dielectric boundaries of two molecules, respectively. This method can be employed to estimate the total electrostatic energy of two protein molecules at a given distance and orientation in an electrolyte solution with zero to moderately high ionic strength.
Secondly, to be able to study interactions between biomolecules and membranes, an alternative model partly based upon the analytical continuum electrostatics (ACE) method has been also formulated. It is desirable to develop a method for calculating the total solvation free energy that includes both electrostatic and non-polar energies. The difference between this model and other continuum methods is that instead of determining the electrostatic potential, the total electrostatic energy of the system is calculated by integrating the energy density of the electrostatic field. This novel approach is employed for the calculation of the total solvation free energy of a system consisting of two solutes, one of which could be an infinite slab representing a membrane surface.
2
Corry, Ben Alexander, and ben corry@anu edu au. "Simulation Studies of Biological Ion Channels." The Australian National University. Research School of Physical Sciences and Engineering, 2003. http://thesis.anu.edu.au./public/adt-ANU20030423.162927.
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Biological ion channels are responsible for, and regulate the
communication system in the body. In this thesis I develop, test and
apply theoretical models of ion channels, that can relate their
structure to their functional properties. Brownian dynamics
simulations are introduced, in which the motions of individual ions
are simulated as they move through the channel and in baths attached
to each end. The techniques for setting boundary conditions which
maintain ion concentrations in the baths and provide a driving
potential are tested. Provided the bath size is large enough, all
boundary conditions studied yield the same results.
¶
Continuum theories of electrolytes have previously been used to study
ion permeation. However, I show that these continuum models do not
accurately reproduce the physics taking place inside ion channels by
directly comparing the results of both equilibrium Poisson-Boltzmann
theory, and non-equilibrium Poisson-Nernst-Planck theory to
simulations. In both cases spurious shielding effects are found to
cancel out forces that play an important role in ion permeation. In
particular, the `reaction field' created by the ion entering the
narrow channel is underestimated. Attempts to correct these problems
by adding extra force terms to account for this reaction field also
fail.
¶
A model of the L-type calcium channel is presented and studied using
Brownian dynamics simulations and electrostatic calculations. The
mechanisms of permeation and selectivity are explained as the result
of simple electrostatic interactions between ions and the fixed
charges in the protein. The complex conductance properties of the
channel, including the current-voltage and current-concentration
relationships, the anomalous mole fraction behaviour between sodium
and calcium ions, the attenuation of calcium currents by monovalent
ions and the effects of mutating glutamate residues, are all
reproduced.
¶
Finally, the simulation and electrostatic calculation methods are used
to study the gramicidin A channel. It is found that the continuum
electrostatic calculations break down in this narrow channel, as the
concept of applying a uniform dielectric constant is not accurate in
this situation. Thus, the permeation properties of the channel are
examined using Brownian dynamics simulations without electrostatic
calculations. Future applications and improvements of the Brownian
dynamics simulation technique are also described.
3
Murry, Robert Lester. "Continuum electrostatic analysis of DNA bending." Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/38837.
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4
Lamb, Stephen Brian. "Enzyme immobilisation on colloidal liquid aphrons (CLAs) and the development of a continuous membrane bioreactor." Thesis, Imperial College London, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325108.
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5
Teng, Wan Dung. "Solid freeform fabrication of ceramics : continuous direct ink-jet printing and electrostatic atomization." Thesis, Brunel University, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.360823.
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6
BERNET, JULIETTE. "Consideration du solvant en modelisation moleculaire. Proposition d'un nouveau traitement analytique du modele continu du solvant, fiesta. (field integrated electrostatic approach)." Paris 7, 1997. http://www.theses.fr/1997PA077094.
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Le comportement des macromolecules biologiques est fortement influence par leur environnement d'eau et de contre-ions. En effet, ni la conformation, ni les interactions des macromolecules ne peuvent etre comprises sans tenir compte de leur environnement. La prise en compte de tels effets lors des calculs de modelisation moleculaire pose encore des problemes majeurs. L'approche la plus precise necessite une representation explicite de plusieurs milliers de molecules de solvant et ceci alourdit considerablement les calculs a effectuer. Ainsi, il est important de trouver d'autres techniques, plus rapides, mais neanmoins fiables. Une representation continue de l'environnement a travers l'equation poisson-boltzmann offre une telle possibilite. Des logiciels mis au point sur cette base ont deja fourni des resultats en bonne correlation avec des donnees experimentales dans plusieurs domaines. Un exemple de leur emploi est presente dans cette these, portant sur la modelisation de l'ouverture des bases de la double helice de l'adn. Malheureusement, l'emploi de telles techniques au sein des logiciels de simulation est limite par des temps de calculs prohibitifs. En restant dans un formalisme poisson-boltzmann, nous proposons une nouvelle approche analytique qui permet d'accelerer beaucoup les calculs et qui permettra egalement d'obtenir les derivees de l'energie electrostatique. Cette approche, denommee fiesta (field integrated electrostatic approch), evite la construction d'un maillage de l'espace ou de la surface du solute et tient compte de la polarisation du solvant a travers des sources de potentiel virtuelles situees a l'interieur du solute. L'interet de cette methodologie est confirme pas les premiers resultats obtenus sur un ensemble de molecules et de macromolecules.
7
Ritchie, Andrew William. "Quantifying electrostatic fields at protein interfaces using classical electrostatics calculations." Thesis, 2015. http://hdl.handle.net/2152/31346.
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The functional aspects of proteins are largely dictated by highly selective protein- protein and protein-ligand interactions, even in situations of high structural homology, where electrostatic factors are the major contributors to selectivity. The vibrational Stark effect (VSE) allows us to measure electrostatic fields in complex environments, such as proteins, by the introduction of a vibrational chromophore whose vibrational absorption energy is linearly sensitive to changes in the local electrostatic field. The works presented here seek to computationally quantify electrostatic fields measured via VSE, with the eventual goal of being able to quantitatively predict electrostatic fields, and therefore Stark shifts, for any given protein-interaction. This is done using extensive molecular dynamics in the Amber03 and AMOEBA force fields to generate large ensembles the GTPase Rap1a docked to RalGDS and [superscript p]²¹Ras docked to RalGDS. We discuss how side chain orientations contribute to the differential binding of different mutations of Rap1a binding to RalGDS, where it was found that a hydrogen-bonding pocket is disrupted by the mutation of position 31 from lysine to glutamic acid. We then show that multi-dimensional umbrella sampling of the probe orientations yields a wider range of accessible structures, increasing the quality of the ensembles generated. A large variety of methods for calculating electrostatic fields are presented, with Poisson- Boltzmann electrostatics yielding the most consistent, reliable results. Finally, we explore using AMOEBA for both ensemble-generation as well as the electrostatic description of atoms for field calculations, where early results suggest that the electrostatic field due to the induce dipole moment of the probe is responsible for predicting qualitatively correct Stark shifts.
8
Kuo, Shihhsien, Michael D. Altman, Jaydeep P. Bardhan, Bruce Tidor, and Jacob K. White. "Fast Methods for Simulation of Biomolecule of Electrostatics." 2003. http://hdl.handle.net/1721.1/3717.
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Biomolecular structure and interactions in aqueous environment are determined by a complicated interplay between physical and chemical forces including solvation, electrostatics, van der Waals forces, the hydrophobic effect and covalent bonding. Among them, electrostatics has been of particular interest due to its long-range nature and the tradeoff between desolvation and interaction effects [1]. In addition, electrostatic interactions play a significant role within a biomolecule as well as between biomolecules, making the balance between the two vital to the understanding of macromolecular systems. As a result, much effort has been devoted to accurate modeling and simulation of biomolecule electrostatics. One important application of this work is to compute the structure of electrostatic interactions for a biomolecule in an electrolyte solution, as well as the potential that the molecule generates in space. There are two valuable uses for these simulations. First, it provides a full picture of the electrostatic energetics of a biomolecular system, improving our understanding of how electrostatics contributes to stability, specificity, function, and molecular interaction [2]. Second, these simulations serve as a tool for molecular design, since electrostatic complementarity is an important feature of interacting molecules. Through examination of the electrostatics and potential field generated by a protein molecule, for example, it may be possible to suggest improvements to other proteins or drug molecules that interact with it, or perhaps even design new interacting molecules de novo [3]. There are two approaches in simulating a protein macromolecule in an aqueous solution with nonzero ionic strength. Discrete/atomistic approaches based on Monte-Carlo or molecular dynamics simulations treat the macromolecule and solvent explicitly at the atomic level. Therefore, an enormous number of solvent molecules are required to provide reasonable accuracy, especially when electric fields far away from macroscopic surface are of interest, leading to computational infeasibility. In this work, we adopt instead an approach based on a continuum description of the macromolecule and solvent. Although the continuum model of biomolecule electrostatics is widely used, the numerical techniques used to evaluate the model do not exploit fast solver approaches developed for analyzing integrated circuit interconnect. I will describe the formulation used for analyzing biomolecule electrostatics, and then derive an integral formulation of the problem that can be rapidly solved with precorrected-FFT method [4].Singapore-MIT Alliance (SMA)
9
Cooper, Villagran Christopher David. "Biomolecular electrostatics with continuum models: a boundary integral implementation and applications to biosensors." Thesis, 2015. https://hdl.handle.net/2144/15650.
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The 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.
10
Kloppmann, Edda [Verfasser]. "Structure-function relationship of archaeal rhodopsin proteins analyzed by continuum electrostatics / presented by Edda Kloppmann." 2010. http://d-nb.info/1004286023/34.
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11
Corry, Ben Alexander. "Simulation Studies of Biological Ion Channels." Phd thesis, 2002. http://hdl.handle.net/1885/46252.
Full textAbstract:
Biological ion channels are responsible for, and regulate the communication system in the body. In this thesis I develop, test and apply theoretical models of ion channels, that can relate their structure to their functional properties. Brownian dynamics simulations are introduced, in which the motions of individual ions are simulated as they move through the channel and in baths attached to each end. The techniques for setting boundary conditions which maintain ion concentrations in the baths and provide a driving potential are tested. Provided the bath size is large enough, all boundary conditions studied yield the same results. ...
12
Essigke, Timm [Verfasser]. "A continuum electrostatic approach for calculating the binding energetics of multiple ligands / presented by Timm Essigke." 2008. http://d-nb.info/988380617/34.
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13
El-Ballouli, Ala’a O. "Continuous-Flow Synthesis and Materials Interface Engineering of Lead Sulfide Quantum Dots for Photovoltaic Applications." Diss., 2016. http://hdl.handle.net/10754/611210.
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Harnessing the Sun’s energy via the conversion of solar photons to electricity has emerged as a sustainable energy source to fulfill our future demands. In this regard, solution-processable, size-tunable PbS quantum dots (QDs) have been identified as a promising active materials for photovoltaics (PVs). Yet, there are still serious challenges that hinder the full exploitation of QD materials in PVs. This dissertation addresses two main challenges to aid these QDs in fulfilling their tremendous potential in PV applications.
First, it is essential to establish a large-scale synthetic technique which maintains control over the reaction parameters to yield QDs with well-defined shape, size, and composition. Rigorous protocols for cost-effective production on a scale are still missing from literature. Particularly, previous reports of record-performance QD-PVs have been based on small-scale, manual, batch syntheses. One way to achieve a controlled large-scale synthesis is by reducing the reaction volume to ensure uniformity. Accordingly, we design a droplet-based continuous-flow synthesis of PbS QDs. Only upon separating the nucleation and growth phases, via a dual-temperature-stage reactor, it was possible to achieve high-quality QDs with high photoluminescence quantum yield (50%) in large-scale. The performance of these QDs in a PV device was comparable to batch-synthesized QDs, thus providing a promise in utilizing automated synthesis of QDs for PV applications.
Second, it is crucial to study and control the charge transfer (CT) dynamics at QD interfaces in order to optimize their PV performance. Yet, the CT investigations based on PbS QDs are limited in literature. Here, we investigate the CT and charge separation (CS) at size-tunable PbS QDs and organic acceptor interfaces using a combination of femtosecond broadband transient spectroscopic techniques and steady-state measurements. The results reveal that the energy band alignment, tuned by the quantum confinement, is a key element for efficient CT and CS processes. Additionally, the presence of interfacial electrostatic interaction between the QDs and the acceptors facilitates CT from large PbS QD (bandgap < 1 eV); thus enabling light-harvesting from the broad near-infrared solar spectrum range.
The advances in this work – from automated synthesis to charge transfer studies – pave new pathways towards energy harvesting from solution-processed nanomaterials.
14
Truchon, Jean-François. "Modéliser la polarisation électronique par un continuum diélectrique intramoléculaire vers un champ de force polarisable pour la chimie bioorganique." Thèse, 2008. http://hdl.handle.net/1866/6551.
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Haas, Alexander H. [Verfasser]. "Investigation of coupled electron and proton transfer in the quinol:fumarate reductase from Wolinella succinogenes with electrochemically induced FTIR and VIS difference spectroscopy and multiconformation continuum electrostatic calculations / von Alexander H. Haas." 2005. http://d-nb.info/974441740/34.
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