Dissertations / Theses on the topic 'Intermolecular model'

As the demand for high performance small electronic devices has increased, heat removal from these devices for space use is approaching critical limits. A heat pipe is a promising device to enhance the heat removal performance due to the phase change phenomena for space thermal management system. Even though a heat pipe has a big potential to remove the thermal energy from a high heat flux source, the heat removal performance of heat pipes cannot be predicted well since the first principle of evaporation has not been established. The purpose of this study is to establish a method to apply the evaporation model based on the statistical rate theory for engineering application including vapor-liquid-structure intermolecular effect. The evaporation model is applied to the heat pipe performance analysis through a pressure balance and an energy balance in the loop heat pipe.

Thesis (Ph.D)--Chemical Engineering, Georgia Institute of Technology, 2008.
Committee Chair: Gallivan, Martha A.; Committee Member: Hess, Dennis; Committee Member: Lee, Jay H.; Committee Member: Li, Mo; Committee Member: Ludovice, Pete.

Polarization plays a significant role in the physical and chemical properties of water, thus polarizable water models have been extensively evolved and studied in the past several decades. In this dissertation, two polarizable water models have been extended, and some physical properties in gas phase and condensed phase were studied and analyzed. It was verified that the out-of-plane polarization effect is of great importance in some physical properties. Besides, we proved that there are some connections between these two models, although they were derived from different methodologies. The first polarizable water model we developed was a combination of charge response kernel (CRK) method and polarizable point dipole (PPD) method. In the CRK method, a CRK matrix is defined as the second order derivative of energy with respect to the external potential at atomic sites. It is applied to represent the intensity of charge response to external environment. While in the PPD method, the polarizability tensor which is the second order derivative of energy with respect to external field at the same site, is introduced to characterize the variation of dipole moment in the presence of external perturbation. In our method, we proved that although the CRK matrix of three-site water model has 9 element, it only carries two independent variables, and these two variables only rely on the water geometry and the in-plane polarizability. Thus besides the CRK matrix located on each atomic site, an additional polarizability residing on oxygen atom specifically inducing dipole moment along the direction perpendicular to the water plane was added in our model. With the addition of the out-of-plane description, some physical properties were much enhanced. In the second polarizable water model we extended, electronegativity equalization (EE) method was employed. In this three-site water model, atomic electronegativity and hardness matrix were the first and second order derivative of energy with respect to the partial charge on atomic sites, respectively. In this method, electronegativity differs among different atom types, and the off-diagonal elements in hardness matrix are related on not only atom types but also distances among the corresponding atoms. Accordingly, the intramolecular water deformation can be included. Thus flexible polarizable water model is accessible. With flexibility, this water model is more realistic. Our model validated that more flexible parameterization and geometry could improve the physical performance. At last, we connected the second polarizable water model with the first one. Although the two polarizable models were derived from different methodologies, we proved that under one simple approximation, corresponding CRK matrix can be achieved from hardness matrix.
published_or_final_version
Chemistry
Doctoral
Doctor of Philosophy

Thesis (Ph. D.)--University of Maryland, College Park, 2007.
Thesis research directed by: Dept. of Chemistry and Biochemistry. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.

Etude de la gelification, la demixtion et des proprietes rheologiques de solutio nde galactomannane et d'alcool polyvinylique complexes par les ions borates. Etude des interactions polyol-borate par rmn du bore. Developpement d'un modele de type flory rendant compte des observations. Analogie entre la rheologie des gels reversibles (solution semidiluee de galactomannane) et celle de solution de polymere concentre

While effects of multispin modes have proven to be of utmost importance in Nuclear Magnetic Resonance spectroscopy, their roles in two intimately related fields--chemical exchange and intermolecular spin relaxation--have not been adequately explored. In a bid to improve theoretical understanding, this work presents the generalized symmetry-adapted form of the exchange superoperator, which allows for proof of the macroscopic symmetry principle. The results obtained for an $A sb2$-AB type exchange are used to explain the presence of paradoxical symmetry-forbidden signals in the spectra of parahydrogen labeled symmetric substrates such as acetylenedicarboxylic acid dimethyl ester. The implementation of the chemical exchange for the magnetic resonance simulation platform GAMMA is reported. The simulations of the novel experiment aimed at the detection of the slow intermolecular exchange through the decay of the multispin modes are presented. The exchange model is also employed to elucidate the role of intermolecular spin coherences in liquid phase. In the second part of this work, the derivation of the Redfield equations adapted for spin evolution under the time-dependent Hamiltonian is presented. The results are used to discuss the limitations of the Redfield theory as applied to relaxation measurements in the rotating frame. Rigorous spin-algebraic analysis makes it possible to establish the selection rules for the intermolecular relaxation thus clarifying the scope and the structure of relaxation coupling for the multicomponent solutions. Obtained results suggest the formulation of a Coupled Solute-Solvent Relaxation model, more compact than the complete system of Redfield equations, yet more precise than the External Random Field approach. The exact expressions for the intermolecular relaxation in AX-AB and AX-ABX type mixtures are derived and subsequently used to confirm the excellent precision of the Coupled Solute-Solvent approximation, distinctly superior to

The kinetics of reduction by free flavin semiquinones of the individual components of 1:1 complexes of yeast cytochrome c peroxidase and the cytochrome c from horse, tuna, and yeast, including several site-specific mutants of either the cytochrome c or cytochrome c peroxidase, have been studied. The orientations of the various cytochromes c within electrostatically-stabilized complexes with the peroxidase are not equivalent. This is shown by differential decreases in the rate constants for cytochrome reduction by neutral flavin semiquinones upon complexation which are in the order: tuna ≫ horse > yeast iso-2 > yeast iso-1. We have also directly measured the physiologically-significant intracomplex one-electron transfer rate constants from the ferrous cytochromes c to the peroxide-oxidized species of the peroxidase at several ionic strengths. The rate constants at low ionic strength are highly species dependent, again consistent with the contention that the orientations of the various cytochromes within the complex with CcP are not the same. Increasing the ionic strength in all cases resulted in an increase in the rate constant for the first-order process which controls electron transfer from cytochrome c to the peroxidase Compound I species of the peroxidase. When the two proteins are immobilized by covalent cross-linking, no such rate enhancement is observed, suggesting that the ionic strength effect is manifested by an increase in the number of geometric orientations between the two proteins which results in more rapid electron transfer. Similar rate enhancing effects are observed when positively charged residues on the surface of cytochrome c are converted to electrostatically neutral amino acids by site-specific mutagenesis. The effect of site-specific mutagenesis of two residues of cytochrome c peroxidase have also been studied. His-181, when converted to a glycine has little effect on the electron transfer rate constant, whereas when Trp-191 is converted to a phenylalanine no intracomplex electron transfer could be observed, indicating an obligatory role of this residue in the electron transfer process.

Le comportement conformationnel des glycannes, et donc leur flexibilite, peuvent influencer directement la reactivite chimique et l'activite biologique de ces molecules. Dans ce travail, la modelisation moleculaire d'une serie de glycannes de complexite croissante a ete realisee en utilisant plusieurs methodes d'exploration de l'espace conformationnel, dont la methode heuristique cicada, associees a differents champs de force : mm3 et amber avec plusieurs parametrisations disponibles pour les glycannes. La validation des modeles a ete apportee par des methodes theoriques de chimie quantique et des methodes experimentales telles que la resonance magnetique nucleaire et la cristallographie aux rayons x. Pour les monosaccharides, les comportements conformationnels de deux cycles furanose ont ete etudies par plusieurs methodes et les resultats ont ete compares aux structures cristallines connues. Les constantes de couplage #3j#h#-#h intracycliques ont ete calculees et comparees aux donnees de rmn. Cette approche a permis de determiner les conformations de plus basse energie ainsi que de demontrer la grande flexibilite de ces systemes. Le comportement conformationnel de la liaison glycosidique a ete etudie par modelisation moleculaire de deux disaccharides et d'un heptasaccharide. Ces etudes ont demontre la capacite de la methode cicada a explorer des espaces conformationnels tres complexes de facon rapide et efficace. Les donnees rmn et cristallographiques ont confirme l'existence des modeles de plus basse energie. Afin d'etudier les interactions proteine-glucide, un modele tridimensionnel d'un complexe entre la lectine de lathyrus ochrus et un nonasaccharide biantenne et flucosyle a ete construit. Les comportements conformationnels du nonasaccharide libre et complexe ont ete etablis en utilisant les methodes conformationnelles validees sur les molecules plus petites. Les resultats de la modelisation ont pu etre compares avec les donnees cristallographiques de plusieurs complexes lectine/oligosaccharides. Les limites des methodes de modelisation moleculaire utilisees dans cette etude sont discutees.

The Equations of State (EoSs) ranging from cubic equations to theoretically-based molecular models are of great practical application in the modeling of physical properties of real fluids In particular, the molecular EoSs based on statistical mechanics and supported by molecular simulations are of special interest due to their ability to represent the fluid properties using only a few substance-dependent parameters with physical meaning, in principle, statistical mechanics provide theories for calculating the thermodynamics and structure of a fluid given its Intermolecular potential function. The focus in this study is on Perturbation theories for chain molecules whose reference system constitutes non-bonded segments.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Peptídeos antimicrobianos são moléculas biologicamente ativas que, geralmente, tem as membranas fosfolipídicas como alvo primário. Resultados de diferentes técnicas experimentais têm sugerido que esses peptídeos permeabilizam as membranas pela formação de poros. Parte dos peptídeos caracterizados apresentam especificidade de disrupção para membranas de bactérias, em detrimento das membranas dos hospedeiros. Essa característica tem atraído a atenção da comunidade científica internacional, porque indica que estas moléculas podem ser modelos para o desenvolvimento de novos antibióticos, portanto o entendimento do mecanismo de ação, ou seja, do mecanismo de formação de poro, tem extrema importância. Simulações por Dinâmica Molecular foram produzidas para investigarmos o impacto que peptídeos antimicrobianos da família Mastoparano tem sobre membranas lipídicas modelo. Dois cenários foram explorados: (i) de baixa concentração peptídeo/lipídeo, P/L=1/128, que consistia de simulações fine-grained das interações de um peptídeo com uma bicamada pura de 128 lipídeos aniônicos (POPG) ou zwiteriônicos (POPC); (ii) de alta concentração, P/L=1/21, que abordava as interações de seis peptídeos com uma bicamada mista de 128 lipídeos POPC/POPG (1/1) usando uma modelagem coarse-grained. Tomando o peptídeo MP1 como caso paradigmático, verificamos que em baixo P/L é possível sugerir que sua característica seletiva surge da capacidade de coordenar e perturbar maior número de lipídeos em membrana aniônica comparada à neutra. Essa capacidade fica acentuada nas simulações com membrana mista, onde a atração dos lipídeos aniônicos pelos peptídeos catiônicos guiou a separação local e a formação de domínios de lipídeos aniônicos, o que facilitou o afinamento local da membrana e a formação de poro transmembrânico. Esses achados ajudam a explicar como peptídeos
Antimicrobial peptides are biologically active molecules that, usually, have the phospholipid membranes as a primary target. Results from different experimental techniques have suggested these peptides permeabilize membranes by the pore formation. Part of the characterized peptides have specificity of disruption for bacterial membranes, instead of host membrane. This feature has attracted the attention of the international scientific community, because it indicates that these molecules can be models for the development of novel antibiotics, so understanding the mechanism of action, ie, the mechanism of pore formation, is extremely important. Molecular dynamics simulations were performed to investigate the impact of antimicrobial peptides from the Mastoparano family have on model lipid membranes. Two scenarios were explored: (i) of low peptide/lipid concentration, P/L=1/128, which consisted of fine-grained simulations of the interactions of a peptide with a pure bilayer of 128 anionic (POPG) or zwitterionic (POPC) lipids; (ii) of high concentration, P/L=1/21, which addressed the interactions of six peptides with a mixed bilayer of 128 POPC/POPG (1/1) lipids, using a coarse-grained modeling. Taking the MP1 peptide as a paradigmatic case, we found that in low P/L is possible to suggest that its selective feature arises of its ability to coordinate and disturb large number of lipids in the anionic membrane compared to neutral one. This ability is accentuated in simulations with mixed membrane, where the attraction of the anionic lipids by the cationic peptides led to the local segregation and formation of POPG lipid domains, which facilitated the local thinning of the membrane and the formation of transmembrane pore. These findings help to explain how short peptides, such as MP1, are able of forming pores in a membrane whose thickness is larger than the length of the peptide

Orientador: José Roberto Ruggiero
Banca: Pedro Geraldo Pascutti
Banca: José Maria Pires
Banca: Alexandre Suman de Araújo
Banca: Sabrina Thais Broggio Costa
Resumo: Peptídeos antimicrobianos são moléculas biologicamente ativas que, geralmente, tem as membranas fosfolipídicas como alvo primário. Resultados de diferentes técnicas experimentais têm sugerido que esses peptídeos permeabilizam as membranas pela formação de poros. Parte dos peptídeos caracterizados apresentam especificidade de disrupção para membranas de bactérias, em detrimento das membranas dos hospedeiros. Essa característica tem atraído a atenção da comunidade científica internacional, porque indica que estas moléculas podem ser modelos para o desenvolvimento de novos antibióticos, portanto o entendimento do mecanismo de ação, ou seja, do mecanismo de formação de poro, tem extrema importância. Simulações por Dinâmica Molecular foram produzidas para investigarmos o impacto que peptídeos antimicrobianos da família Mastoparano tem sobre membranas lipídicas modelo. Dois cenários foram explorados: (i) de baixa concentração peptídeo/lipídeo, P/L=1/128, que consistia de simulações fine-grained das interações de um peptídeo com uma bicamada pura de 128 lipídeos aniônicos (POPG) ou zwiteriônicos (POPC); (ii) de alta concentração, P/L=1/21, que abordava as interações de seis peptídeos com uma bicamada mista de 128 lipídeos POPC/POPG (1/1) usando uma modelagem coarse-grained. Tomando o peptídeo MP1 como caso paradigmático, verificamos que em baixo P/L é possível sugerir que sua característica seletiva surge da capacidade de coordenar e perturbar maior número de lipídeos em membrana aniônica comparada à neutra. Essa capacidade fica acentuada nas simulações com membrana mista, onde a atração dos lipídeos aniônicos pelos peptídeos catiônicos guiou a separação local e a formação de domínios de lipídeos aniônicos, o que facilitou o afinamento local da membrana e a formação de poro transmembrânico. Esses achados ajudam a explicar como peptídeos
Abstract: Antimicrobial peptides are biologically active molecules that, usually, have the phospholipid membranes as a primary target. Results from different experimental techniques have suggested these peptides permeabilize membranes by the pore formation. Part of the characterized peptides have specificity of disruption for bacterial membranes, instead of host membrane. This feature has attracted the attention of the international scientific community, because it indicates that these molecules can be models for the development of novel antibiotics, so understanding the mechanism of action, ie, the mechanism of pore formation, is extremely important. Molecular dynamics simulations were performed to investigate the impact of antimicrobial peptides from the Mastoparano family have on model lipid membranes. Two scenarios were explored: (i) of low peptide/lipid concentration, P/L=1/128, which consisted of fine-grained simulations of the interactions of a peptide with a pure bilayer of 128 anionic (POPG) or zwitterionic (POPC) lipids; (ii) of high concentration, P/L=1/21, which addressed the interactions of six peptides with a mixed bilayer of 128 POPC/POPG (1/1) lipids, using a coarse-grained modeling. Taking the MP1 peptide as a paradigmatic case, we found that in low P/L is possible to suggest that its selective feature arises of its ability to coordinate and disturb large number of lipids in the anionic membrane compared to neutral one. This ability is accentuated in simulations with mixed membrane, where the attraction of the anionic lipids by the cationic peptides led to the local segregation and formation of POPG lipid domains, which facilitated the local thinning of the membrane and the formation of transmembrane pore. These findings help to explain how short peptides, such as MP1, are able of forming pores in a membrane whose thickness is larger than the length of the peptide
Doutor

One in eight woman develop breast cancer in the United States of America and is the most common type of cancer in the world. Breast cancer has the highest rate of death compared to any other form of cancer. Triple Negative Breast Cancer (TNBC) is the most lethal type of breast cancer, which is the most fatal of all breast cancer types. TNBC is onerous to treat since it lacks all the three most commonly targeted hormones and receptors. Current patients afflicted with TNBC are treated with platinum core chemotherapeutics, namely Cisplatin. Despite the anticancer effects shown by Cisplatin, TNBC attenuates its effect and develops a resistance eventually, which results in reoccurrence of TNBC after few years. Hence there is a demand for effective and alternative ways to treat TNBC. To inhibit the TNBC cell proliferation, blocking the key glycolytic enzyme Lactase Dehydrogenase B (LDHB) is studied and validated. Galloflavin (GF), a proven LDHB inhibitor is utilized in this series of studies and analysis. In addition, Electrochemotherapy, which involves the application of electrical pulses (EP) were utilized to enhance the uptake of GF. The combination of Electrochemotherapy (ECT) with LDHB is a novel way to treat TNBC to produce an alternative to traditional chemotherapy. EP+GF will be subjected onto TNBC cells at various concentrations and pulse parameters. The purpose of this study is to test the effect of alternative chemotherapeutic drug delivery methods for TNBC patients for decrease in mortality rate and improve quality of life. Results indicate TNBC cell viability is the least for EP+GF treatments and the maximum Reactive Oxygen Species (ROS) levels and a maximum decrease in Glucose and Lactate uptake for EP+GF treatments relative to control. Immunoblotting studies indicate the inhibition of LDHB is the most on EP+GF treatments, indicating that this could be a novel modality to treat TNBC.

The virial equation of state p = ρRT[ 1 + B(T) ρ + C(T) ρ2 + · · ·] for high pressure and density gases is used for computing chemical equilibrium properties and mixture compositions of strong shock and detonation waves. The second and third temperature-dependent virial coefficients B(T) and C(T) are included in tabular form in computer codes, and they are evaluated by polynomial interpolation. A very accurate numerical integration method is presented for computing B(T) and its derivatives for tables, and a sophisticated method is introduced for interpolating B(T) more accurately and efficiently than previously possible. Tabulated B(T) values are non-uniformly distributed using an adaptive grid, to minimize the size and storage of the tables and to control the maximum relative error of interpolated values. The methods introduced for evaluating B(T) apply equally well to the intermolecular potentials of Lennard-Jones in 1924, Buckingham and Corner in 1947, and Rice and Hirschfelder in 1954.

Dissertação de mest., Química (Química Orgânica), Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2011
Ao longo da história recente, a sacarina e seus derivados, pseudosacarinas, tornaram-se alvo de intensa investigação. Dado o crescente interesse revelado pelas pseudosacarinas, propôs-se neste trabalho, a síntese e caracterização estrutural de três exemplos desses compostos: 3-Metoxi-1,2-benzisotiazole 1,1-dióxido (MBID), N-Metil-1,2-benzisotiazole-3-amina 1,1-dióxido (MeBAD) e N,N-Dimetil-1,2-benzisotiazole-3-amina 1,1-dióxido (DiMeBAD). Posteriormente à sua síntese, os compostos foram submetidos a experiências de espectroscopia de IV em matrizes de gases nobres, onde a amostra é submetida a temperaturas extremamente baixas (≈20 K) e mantida em concentrações muito reduzidas, permitindo assim uma boa aproximação ao seu estado isolado no estado gasoso. A caracterização/interpretação teórica dos compostos foi efectuada com base em métodos computacionais assentes nos princípios da mecânica quântica, tendo sido efectuados cálculos ab initio e DFT. Com base nos resultados deste conjunto de cálculos realizado foi possível aferir que para esta família de compostos era necessário, para uma eficiente descrição vibracional, a consideração de bases de funções fortemente polarizadas. A reactividade dos compostos sintetizados também foi alvo de atenção, especialmente a evidência da isomerização térmica do tipo Chapman. Dos três compostos estudados, o rearranjo térmico de tipo Chapman só foi verificado experimentalmente no MBID. Surpreendentemente foi constatado que este, para além de ocorrer no estado líquido, pode também ocorrer no estado sólido. Mecanisticamente propõe-se que o processo de isomerização térmica do MBID ocorra por uma via intermolecular, segundo um modelo “Quase-Simultâneo”, onde a transferência dos grupos metilo entre duas moléculas (do átomo de oxigénio para o átomo de azoto do anel heteroaromático) ocorre quase simultaneamente.