Yes / The adsorption of three homo-tripeptides, HHH, YYY, and SSS, at the aqueous Au interface is investigated, using molecular dynamics simulations. We find that consideration of surface facet effects, relevant to experimental conditions, opens up new questions regarding interpretations of current experimental findings. Our well-tempered metadynamics simulations predict the rank ordering of the tripeptide binding affinities at aqueous Au(111) to be YYY > HHH > SSS. This ranking differs with that obtained from existing experimental data which used surface-immobilized Au nanoparticles as the target substrate. The influence of Au facet on these experimental findings is then considered, via our binding strength predictions of the relevant amino acids at aqueous Au(111) and Au(100)(1 × 1). The Au(111) interface supports an amino acid ranking of Tyr > HisA ≃ HisH > Ser, matching that of the tripeptides on Au(111), while the ranking on Au(100) is HisA > Ser ≃ Tyr ≃ HisH, with only HisA showing non-negligible binding. The substantial reduction in Tyr amino acid affinity for Au(100) vs Au(111) offers one possible explanation for the experimentally observed weaker adsorption of YYY on the nanoparticle-immobilized substrate compared with HHH. In a separate set of simulations, we predict the structures of the adsorbed tripeptides at the two aqueous Au facets, revealing facet-dependent differences in the adsorbed conformations. Our findings suggest that Au facet effects, where relevant, may influence the adsorption structures and energetics of biomolecules, highlighting the possible influence of the structural model used to interpret experimental binding data. / Air Office of Scientific Research, Grant No. FA9550-12-1-0226

No description available.

CO₂ injection in oil reservoirs provides the dual benefit of increasing oil recovery as well as sequestration. Compositional simulations using phase behavior calculations are used to model miscibility and estimate oil recovery. The injected CO₂, however, is known to react with brine. The precipitation and dissolution reactions, especially with carbonate rocks, can have undesirable consequences. The geochemical reactions can also change the mole numbers of components and impact the phase behavior of hydrocarbons. A Gibbs free energy framework that integrates phase equilibrium computations and geochemical reactions is presented in this dissertation. This framework uses the Gibbs free energy function to unify different phase descriptions - Equation of State (EOS) for hydrocarbon components and activity coefficient model for aqueous phase components. A Gibbs free energy minimization model was developed to obtain the equilibrium composition for a system with not just phase equilibrium (no reactions) but also phase and chemical equilibrium (with reactions). This model is adaptable to different reservoirs and can be incorporated in compositional simulators. The Gibbs free energy model is used for two batch calculation applications. In the first application, solubility models are developed for acid gases (CO₂ /H2 S) in water as well as brine at high pressures (0.1 - 80 MPa) and high temperatures (298-393 K). The solubility models are useful for formulating acid gas injection schemes to ensure continuous production from contaminated gas fields as well as for CO₂ sequestration. In the second application, the Gibbs free energy approach is used to predict the phase behavior of hydrocarbon mixtures - CO₂ -nC₁₄ H₃₀ and CH₄ -CO₂. The Gibbs free energy model is also used to predict the impact of geochemical reactions on the phase behavior of these two hydrocarbon mixtures. The Gibbs free energy model is integrated with flow using operator splitting to model an application of cation exchange reactions between aqueous phase and the solid surface. A 1-D numerical model to predict effluent concentration for a system with three cations using the Gibbs free energy minimization approach was observed to be faster than an equivalent stoichiometric approach. Analytical solutions were also developed for this system using the hyperbolic theory of conservation laws and are compared with experimental results available at laboratory and field scales. / text

No / By extending the cleaving method to molecular systems, we perform direct calculations of the ice Ih-water interfacial free energy for the TIP4P model. The values for the basal, prism, and f11 20g faces are 23:3 0:8 mJm 2, 23:6 1:0 mJm 2, and 24:7 0:8 mJm 2, respectively. The closeness of these values implies a minimal role of thermodynamic factors in the anisotropic growth of ice crystals. These results are about 20% lower than the best experimental estimates. However, the Turnbull coefficient is about 50% higher than for real water, indicating a possible limitation of the TIP4P model in describing freezing. / EPSRC

Dengue é uma doença tropical negligenciada que atualmente ameaça mais da metade da população mundial e representa custo anual de bilhões de dólares para as áreas afetadas. Avanços recentes na elucidação estrutural de proteínas humanas e vitais contribuíram para o entendimento do ciclo de replicação vital e das interações vírus-hospedeiro a nível molecular. Em particular, a camada mais externa do vírus é composta por 180 monômeros da glicoproteína do envelope. Cada um desses monômeros apresenta duas glicosilações que são reconhecidas por lectinas cuja atividade depende de Ca2+. A interação entre o vírus e essas lectinas favorece a infecção ou o aparecimento de sintomas mais severos. Neste trabalho aplicamos simulações de dinâmica molecular e métodos de estimativa de afinidade para avançar nosso conhecimento sobre os mecanismos moleculares do reconhecimento de glicosilações high-mannose pelas lectinas DC-SIGN e MR, ambas já experimentalmente validadas como alvos biológicos para desenvolvimento de novos antivirais. Adicionalmente, através de virtual screening usando um conjunto de programas de implementação própria e uma biblioteca de moléculas já aprovadas para uso como fármacos, encontramos uma molécula (lohexol) que apresenta alto potencial de interação com ambos os receptores. Embora testes experimentais ainda sejam necessários para validar esse achado, nossos resultados sugerem que essa molécula, e eventualmente moléculas similares, podem agir como inibidor da infecção do vírus da Dengue por um mecanismo duplo. / Dengue is a tropical neglected disease that currently threatens more than half the world\'s population and represents a yearly cost of billions of dollars to the affected areas. Recent advances in the elucidation of 3D structures of human and viral proteins has contributed to the understanding of the viral replication cycle and virus-host interactions at the molecular level. In particular, the outermost layer of the virus is composed by 180 monomers of the envelope glycoprotein. Each one of these monomers displays two glycosylations that are recognized by lectins which have Ca2+-dependent activity. The interaction between the virus and these lectins favors infection or severe disease onset. In this work we apply molecular dynamics simulations and affinity estimation methods to advance our knowledge about the molecular mechanisms underlying the recognition of the high-mannose glycosylation by the DC-SIGN and MR lectins, both of which are already validated as targets for the development of new antivirals against Dengue. Additionally, by running virtual screening assays using a set of programs implemented by us and a library containing molecules which are already approved to be used as drugs, we found one molecule (lohexol) which presents high potential of interaction with both receptors. Although experimental testing is still necessary to validate this finding, our results suggest that this molecule, and eventually similar ones, can act as an inhibitor of the Dengue virus infection by a dual mechanism.

Thesis advisor: Udayan Mohanty / Computational research can play a crucial component in the discovery of unique biochemical phenomena, from answering fundamental questions about molecular function and structure to the modeling of designed pharmaceuticals to cure many debilitating illnesses. Here computational methods are employed to examine the exquisite role that magnesium ions play in stabilizing ribosomal subunits responsible for protein translation and to analyze the potential of a proposed anticancer drug for a pathway that is impaired in the majority of human cancer cases. / Thesis (BS) — Boston College, 2011. / Submitted to: Boston College. College of Arts and Sciences. / Discipline: College Honors Program. / Discipline: Chemistry.

Rubbing alignment is widely used in display industry, Rubbing cause anisotropy in rubbed polyimide thin film influence the alignment of Liquid Crystal. The major part of this article is to analyze surface optical anisotropy of rubbed polyimide thin film. RAS signals and surface free energies of rubbed polyimide thin film with different rubbing strength are measured, and relationship between anisotropy of surface and rubbing strength is discussed. The mechanism of alignment can be understood by this work. Reflection Anisotropy Spectroscopy (RAS) has been used in Semiconductor as a tool to monitor crystal growth for many years. RAS is a non-contact and non-destructive measurement method. It only measures the difference of two orthogonal complex reflection signals and optical anisotropy of surface. It¡¦s very sensitive to the anisotropy of surface. In the current studies, RAS has been used to detect surface anisotropy of rubbed polymer. We measured the surface free energy of the rubbed polyimide thin films. It has been found that surface free energy is of anisotropy due to the application of mechanical rubbing to the polymer surface. Pretilt angle influences the alignment of liquid crystals. The molecule orientation of PI surface and anisotropy of rubbed PI surface effect pretilt angle¡CPretilt angles measured by pretilt angle measurement system compare with RAS signals. RAS signals, anisotropy of surface free energies, and pretilt angles are increasing with increasing rubbing strength.

Discotic liquid crystals (DLCs), which consist of disc-like molecules, are known to be able to form nematic and columnar mesophases through self-assembly. Because of the high electric charge mobility in one-dimension, DLCs are found to have uses in making electronic and photonic devices, such as organic light emitting diode, photovoltaic and molecular wires. In order to achieve better performance of these applications, it is essential to obtain the desired alignment of the DLCs. The purpose of this study is to investigate the stacking of disk-like molecules and to control their alignment. The materials used in the present studies are HDBP-8 and LC10. In this thesis, we will show that the stack of disk-like molecules is strongly influenced by temperature. We will also discuss how the molecules stacking is influenced by surface free energy. The disk-like molecules tend to stack with face-on when the surface free energy of the substrates is high. On a surface with lower surface free energy, molecules tend to stack with edge-up. In the latter part of the research, substrates are specially treated to have different surface free energies, and molecular stack on these substrates is observed.

Cytochrome c oxidase couples the reduction of dioxygen to proton pumping against an electrochemical gradient. The D-channel provides the principal uptake pathway for protons. A water chain is thought to mediate the relay of protons through the D-channel, but it is interrupted at N139 in all crystallographic structures. Here, free energy simulations are used to examine the proton uptake pathway in the wild type and in single-point mutants N139V and N139A, where reduction and pumping is compromised. A general approach for the calculation of water occupancy in protein cavities is presented and demonstrates that combining efficient sampling algorithms with long simulation times is required to achieve statistical convergence of equilibrium properties in the protein interior. The relative population of conformational and hydration states of the D-channel is characterized. Results shed light onto the role of N139 in the mechanism of proton uptake and clarify the physical basis for inactive phenotypes.

Cytochrome c oxidase couples the reduction of dioxygen to proton pumping against an electrochemical gradient. The D-channel provides the principal uptake pathway for protons. A water chain is thought to mediate the relay of protons through the D-channel, but it is interrupted at N139 in all crystallographic structures. Here, free energy simulations are used to examine the proton uptake pathway in the wild type and in single-point mutants N139V and N139A, where reduction and pumping is compromised. A general approach for the calculation of water occupancy in protein cavities is presented and demonstrates that combining efficient sampling algorithms with long simulation times is required to achieve statistical convergence of equilibrium properties in the protein interior. The relative population of conformational and hydration states of the D-channel is characterized. Results shed light onto the role of N139 in the mechanism of proton uptake and clarify the physical basis for inactive phenotypes.