Thesis (Ph. D.)--University of Texas at Austin, 2006. / Vita. Includes bibliographical references.

Electrostatics interaction plays a very important role in almost all biomolecular systems. The Poisson-Boltzmann equation is widely used to treat this electrostatic effect in an ionic solution. In this work, a simple mixed discrete-continuum model is considered and boundary element method is used to solve for the solution. / Singapore-MIT Alliance (SMA)

Submitted by Rodrigo De Lima Luiz (rodrigodelimaluiz@hotmail.com) on 2018-11-21T19:51:52Z No. of bitstreams: 1 DISSERTAÇÃO DEFINITIVA.pdf: 3442563 bytes, checksum: a1ec4acfa5218338bbc6cc71e90ad441 (MD5) / Approved for entry into archive by Claudia Adriana Spindola null (claudia@fct.unesp.br) on 2018-11-22T10:50:34Z (GMT) No. of bitstreams: 1 luiz_rl_me_prud.pdf: 3385709 bytes, checksum: 3b7f3df96984f568b958099cfbebbdf2 (MD5) / Made available in DSpace on 2018-11-22T10:50:34Z (GMT). No. of bitstreams: 1 luiz_rl_me_prud.pdf: 3385709 bytes, checksum: 3b7f3df96984f568b958099cfbebbdf2 (MD5) Previous issue date: 2018-10-01 / Neste trabalho, foi pesquisada uma forma alternativa de aplicação de experimentos em sala de aula, na qual os alunos foram responsáveis pela confecção deles e não meros expectadores que observaram o professor realizar a atividade experimental. Assim, os estudantes produziram, executaram e tiraram suas conclusões acerca das atividades propostas. Propôs-se, neste trabalho, a aplicação de uma sequência didática para abordar eletrostática utilizando atividades experimentais, como metodologia de aprendizagem significativa, proposta por David Ausubel. Antes da realização dos experimentos, o tema foi contextualizado através de vídeos que mostravam situações intrigantes no cotidiano dos alunos, envolvendo eletrostática. Também foi abordada a história da eletricidade com suas principais descobertas e como os conceitos científicos foram evoluindo ao longo do tempo. Em seguida, utilizando materiais de baixo custo e fáceis de serem encontrados e seguindo roteiros experimentais, os alunos construíram experimentos que permitiram a verificação dos três processos de eletrização: atrito, contato e indução. Também, verificaram a distribuição de cargas em condutores em equilíbrio eletrostático, a blindagem eletrostática e o poder das pontas. O trabalho visou despertar o interesse e motivação dos alunos nas aulas de Física, desenvolvendo suas habilidades em seguir roteiros simples, coletar e analisar dados, além de aplicar os conceitos, abordados em sala, em situações de seu cotidiano. / In this work, an alternative way of applying experiments in the classroom has been investigated, in which the students were responsible by their confections and not mere spectators who observed the teacher to perform an experimental activity. Thus, students produced, performed, and concluded on the proposed activities. It was proposed, in this work, the application of a Didactic Sequence to approach electrostatic using experimental activities, as significant learning methodology, proposed by David Ausubel. Before the experiments, the theme was contextualized through videos that showed intriguing situations in the daily life of students, involving electrostatics. It was also discussed the electricity history with its main discoveries, and how scientific concepts were developed over time. Then, using inexpensive, easy-to-find materials and following experimental script, the students constructed experiments that allowed the verification of the three electrification processes: friction, contact and induction. Also, they verified the charges distribution in conductors in electrostatic equilibrium, the electrostatic shield and the power of the tips. The aim of this work was to arouse student’s interest and motivation in physics classes, developing their skills in following simple scripts, collecting and analyzing data, and applying the concepts, addressed in the classroom, in everyday situations.

Usando geometrias do tipo ponta e plano estudou-se as características elétricas da descarga corona positiva e negativa. Mediram-se as distribuições da densidade de corrente elétrica e do campo elétrico sobre o plano coletor dos íons. São discutidos os resultados obtidos para o sistema ponta planos e para o sistema em que o campo elétrico externo é aplicado através de uma placa adicional colocada perto da ponta. Neste último caso os resultados são interpretados com um modelo teórico que supõe que os íons se movem direção perpendicular entre as placas, sob a ação de um campo constante e lateralmente sob o campo de repulsão da carga espacial. / Electric characteristics of a positive and negative corona discharge were studied for geometries of the type point and plane. The electric current density and the electric field distributions on the collector plane were measured. We discuss the results obtained with the point and plane geometry and with the geometry were a external electric field is applied by means of an additional metallic plate fixed near the point. For the latter geometry the results were interpreted by using a theoretical model in which it is assumed that the ions drift in the direction perpendicular to the plates under a constant electric field and laterally under the field of the ionic space charge.

The various topics investigated in the course of the preparation of this thesis can by unified under the common theme of fibrous fIltration enhancement from both experimental and theoretical perspectives. Fibrous filtration is by far the most common method of gas pUrification in use today and further improvements will require a better understanding of the various mechanisms contributing to the collection of particles. The lack of agreement between experimental results and the latest theoretical models found in the literature which have been put forward to predict fIlter efficiency led to the development of a complex computer simulation of a fIltration process. The model simultaneously accounts for particle collection in the inertial impaction, interception and Brownian diffusion regimes and also recognizes that real fIlters do not consist of a simple array of fibres, but are a complex mixture of fibres positioned randomly in space. Test fIlters carefully manufactured from well characterized glass fibre components were used to challenge monosize sodium chloride aerosols. Since most of the filtration parameters are known, our model was used and directly compared with the leading theoretical models and our experimental results. The enhancement of fibrous filters by gradual clogging was investigated. The filtration characteristics; pressure drop and upstream & downstream concentrations were monitored as loading progressed. A discussion of the changes in the quality factor which was found to be dependent upon aerosol size is given. The fractal dimension of the particle deposits on individual fibres was measured and found to be dependent on the fIltration dynamics present. The fundamental forces of electrostatic filtration (Coulomb, image and polarization forces) were clearly demonstrated in a system of test aerosols and fibrous fIlters which were identical except for the amount of charges the particles and fibres contained. The size ranges in which these forces are effective were accurately measured.

The dispersion of graphene in 1,2-dichloroethane (DCE), its subsequent attachment at the water-DCE interface and the reduction of oxygen at the water-DCE interface proceeding via interfacial graphene have been investigated. Using addition of an electrolyte which screens surface charge, it was found that electrostatic repulsions play a significant role in determining the kinetic stability of lyophobic non-aqueous graphene dispersions. The onset of aggregation was determined and it was found that dispersions prepared from higher-oxygen content graphite were more stable than those prepared from lower-oxygen content graphite, indicating that oxygen content is important in determining the surface charge on graphene in non-aqueous dispersion. The presence of organic electrolyte was also found to promote assembly of graphene into a coherent film at the liquid-liquid interface. Measurement of the liquid-liquid interfacial tension and three-phase contact angle revealed that the energetics of particle attachment did not change in the presence of organic electrolyte, thus indicating a mechanism of inter-particle electrostatic repulsion minimisation through surface charge screening. Interfacial graphene was found to display a catalytic effect toward the oxygen reduction reaction at the water-DCE interface. A bipolar cell was developed which showed that this reaction occurs heterogeneously, with graphene acting as a conduit for electrons across the water-DCE interface.

Typical, potential-driven force fields have been usefully applied to small molecules for decades. However, complex effects such as polarisation, π systems and hydrogen bonding remain difficult to model while these effects become increasingly relevant. In fact, these complex electronic effects become crucial when considering larger biological molecules in solution. Instead, machine learning can be used to recognise patterns in chemical behaviour and predict them, sacrificing computational efficiency for accuracy and completeness of the force field. The kriging machine learning method is capable of taking the geometric features of a molecule and predicting its electrostatic properties after being trained using ab initio data of the same system. We present significant improvements in functionality, application and understanding of the kriging machine learning as part of an electrostatic force field. These improvements are presented alongside an up-scaling of the problems the force field is applied to. The force field predicts electrostatic energies for all common amino acids with a mean error of 4.2 kJmol-1 (1 kcal mol-1), cholesterol with a mean error of 3.9 kJmol-1 and a 10-alanine helix with a mean error of 6.4 kJmol-1. The kriging machine learning has been shown to work identically with charged systems, π systems and hydrogen bonded systems. This work details how different chemical environments and parameters affect the kriging model quality and assesses optimal methods for computationally-efficient kriging of multipole moments. In addition to this, the kriging models have been used to predict moments for atoms they have had no training data for with little loss in accuracy. Thus, the kriging machine learning has been shown to produce transferable models.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Molecular recognition plays an important role in biological systems. The purpose of this study was to get a better understanding of the process by incorporating computational tools.Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) method, the end-point free energy calculations provide the binding free energy the can be used to rank-order protein–ligand structures in virtual screening for compound or target identification. Free energy calculations were performed on a diverse set of 11 proteins bound to 14 small molecules was carried out for. A direct comparison was taken between the calculated free energy and the experimental isothermal titration calorimetry (ITC) data. Four and three systems in MM-GBSA and MM-PBSA calculations, respectively, reproduced the ITC free energy within 1 kcal•mol–1. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). The rank-ordering performance of MM-PBSA improved with increasing ε (ρ = 0.91 for ε = 10), but the contributions of electrostatics became significantly lower at larger ε level, suggesting that the only nonpolar and entropy components contribute to the improved results. Our previously developed scoring function, Support Vector Regression Knowledge-Based (SVRKB), resulted in excellent rank-ordering (ρ = 0.81) when applied into MD simulations. Filtering MD snapshots by prescoring protein–ligand complexes with a machine learning-based approach (SVMSP) resulted in a significant improvement in the MM-PBSA results (ε = 1) from ρ = 0.40 to ρ = 0.81. Finally, the nonpolar components in the free energy calculations showed strong correlation to the ITC free energy while the electrostatic components did not; the computed entropies did not correlate with the ITC entropy. Explicit-solvent molecular dynamics (MD) simulations offer an opportunity to sample multiple conformational states of a protein-ligand system in molecular recognition. SVMSP is a target-specific rescoring method that combines machine learning with statistical potentials. We evaluate the performance of SVMSP in its ability to enrich chemical libraries docked to MD structures. Seven proteins from the Directory of Useful Decoys (DUD) were involved in the study. We followed an innovative approach by training SVMSP scoring models using MD structures (SVMSPMD). The resulting models remarkably improved enrichment in two cases. We also explored approaches for a prior identification of MD snapshots with high enrichment power from an MD simulation in the absence of active compounds. SVMSP rescoring of protein–compound MD structures was applied for the search of small-molecule inhibitors of the mitochondrial enzyme aldehyde dehydrogenase 2 (ALDH2). Rank-ordering of a commercial library of 50,000 compounds docked to MD optimized structures of ALDH2 led to five small-molecule inhibitors. Four compounds had IC50s below 5 μM. These compounds serve as leads for the design and synthesis of more potent and selective ALDH2 inhibitors.

Achieving electrostatic control of quantum phases is at the heart of condensed matter physics allowing us to interface fundamentally different electronic orders and observe their interplay with one another. Recent investigations have revealed emergent superconductivity tuned by the electric field effect in two-dimensional (2D) semimetals and moiré heterostructures. Through electrical transport measurements, we investigate superconductivity in few-layered Td - MoTe2 in this dissertation. Given its sensitivity to the ambient, a process to encapsulate and simultaneously electrically contact the material is developed to preserve the innate properties of MoTe2. At the outset, we observe a dramatic enhancement of superconducting critical temperature (Tc) in few-layered MoTe2. Monolayer’s Tc of ∼ 7.5 K is about 60x higher than the bulk. Reflecting its relatively small Fermi surface, superconductivity is tunable with electrostatic gating andresponse to in-plane magnetic fields reveals a tilted Ising spin texture. Some 2D crystal systems exhibit a polar crystal structure resulting in a robust, nonvolatile and bistable interlayer polarization giving rise to electric-field tunable ferroelectricity. Remarkably, we show that noncentrosymmetric bilayer Td - MoTe2 exhibits such ferroelectric switching while simultaneously being a superconductor, two electronic orders conventionally thought to be incompatible with one another. Further, electrostatic doping unveils a superconductingdome. It is found that the maximum Tc is concomitant with compensated electron and hole carrier densities and vanishes when one of the Fermi pockets disappears with doping pointing towards a pairing mechanism mediated by Fermi surface nesting between electron and hole pockets. Finally, in-plane magnetotransport measurements reveal a two-fold symmetric superconductivity around the crystal axes for bilayer MoTe2. Superconductivity is maximized when magnetic field is parallel to the ?-axis of the crystal and minimized for b-axis. Although unsurprising given the ?2 crystal symmetry, these results lend further credence to the tilted Ising spin texture, as unveiled from Hc2|| measurements on the monolayer.