No description available.

No description available.

No description available.

The present work demonstrates the application of molecular simulations (MD) in two different areas: proton transport in bulk water and estimation of the dipole moment of polar organic compounds. In both areas, relatively few successful and robust methodologies exist. In the first part, a new polarizable water model is developed for MD simulations of the proton transport process. The model was parametrized from a combination of quantum chemical calculations and experimental water properties. The model was implemented in MD simulation studies of liquid water at room temperature, as well as with excess protons. For pure water the model gave good agreement with experimental properties. The proton transport rate for a single excess proton also gave a good match with the experimental value. The water model was further extended to include chloride ions. At 0.2 M concentration the resulting density and structure agreed well with experiment, and the proton transport rate was found to be slightly reduced. The model was further extended to include multiple excess protons. For the second part of the project, an open source ab initio MD program, SIESTA, was used to perform simulations of several organic compounds which potentially have multiple stable conformations, to determine their average dipole moments. A series of methods was developed. The most robust method involved modifications to the SIESTA code and statistical analysis of the resulting configurations, in order to more accurately predict the average dipole moment. The resulting dipole moments were in good agreement with the experimental values for cases in which experimental values were reliable. Based on this study, a general method to estimate the average dipole moment of any compound is proposed.

Tesis por compendio / [ES] Los métodos de química computacional se han empleado en el estudio de materiales de zeolita aplicados a procesos de separación. Se consideró un enfoque clásico, donde los campos de fuerza se seleccionaron durante los procedimientos de benchmark entre los modelos actualmente disponibles. Los resultados obtenidos han sido validados considerando datos experimentales y se mejoró la descripción de los modelos, cuando fue posible, mediante procedimientos de parametrización. Así, los mejores modelos describieron sistemas con diferentes grados de complejidad, que fueron simulados a través de los métodos de Dinámica Molecular y Monte Carlo. La difusión y la adsorción en los microporos (bulk) y en la superficie externa de las zeolitas se pueden entender a nivel molecular. Se calculó la energía de adsorción y también se descompuso su magnitud en las contribuciones electrostática y de van der Waals. Además, fue posible observar más de cerca las interacciones anfitrión-invitado e invitado-invitado durante las trayectorias simuladas. Considerando la creciente demanda energética a nivel mundial, los biocombustibles se consideran una opción sostenible obtenida a partir de biomasa. Se han simulado con éxito los pasos del proceso experimental desarrollado por Denayer et al. para la recuperación de biobutanol a partir de una mezcla fermentada. Se modelaron los ciclos de adsorción y desorción en dos columnas zeolíticas con selectividad complementaria (tipo LTA y CHA), con sistemas de nanoláminas y considerando las principales características experimentales. Aunque las escalas de tiempo experimentales son inalcanzables para los recursos computacionales disponibles actualmente, los sistemas simulados pudieron capturar los fenómenos experimentales y fueron evaluados más a fondo a través del comportamiento microscópico de los sistemas. Un estudio experimental y computacional señaló la STW sílice pura (Si-STW) como un candidato prometedor para la separación de alcanos lineales, monoramificados y diramificados. Se probaron los isómeros C5 a C7, y el material Si-STW superó la capacidad de adsorción y selectividad de MFI de sílice pura, especialmente hacia los isómeros diramificados con átomos de carbono cuaternarios. Se calcularon las isotermas de adsorción, el calor de adsorción y el comportamiento de difusión de los hidrocarburos probados y se compararon con los resultados experimentales. Por lo tanto, las propiedades de adsorción de Si-STW pueden ser exploradas para su uso sobre el producto obtenido durante el proceso de hidromerización - que genera componentes de mayor octanaje para la mezcla de gasolina -, aumentando su número de octano. La producción de 6-kestosa para uso industrial como prebiótico y azúcar de bajo índice glucémico depende de su separación de las moléculas de sacarosa. La separación de una mezcla acuosa equimolar, que contiene sacarosa y 6-kestosa, mediante membranas zeolíticas se ha investigado a través de simulaciones de Dinámica Molecular. Una selección considerando las 253 estructuras de zeolitas reportadas, señaló los tres candidatos más prometedores (AET, ETR y DON), al evaluar el efecto de exclusión por tamaño (adsorción de sacarosa y exclusión de 6-kestosa), la movilidad de ambos azúcares dentro de las estructuras (evaluados con modelos tipo bulk), y simulando su futura aplicación como sistemas de membranas. Entre los mejores candidatos, la zeolita DON presentó una selectividad significativa para las moléculas de sacarosa, con el mayor flujo y siendo factible como material de sílice pura, igualando la composición química simulada. / [CA] Els mètodes de química computacional s'han emprat en l'estudi de materials de zeolita aplicats a processos de separació. Es va considerar un enfocament clàssic, on els camps de força es van seleccionar durant els procediments de benchmark entre els models actualment disponibles. Els resultats obtinguts han sigut validats considerant dades experimentals i es va millorar la descripció dels models, quan va ser possible, mitjançant procediments de parametrització. Així, els millors models van descriure sistemes amb diferents graus de complexitat, que van ser simulats a través dels mètodes de Dinàmica Molecular i Monte Carlo. La difusió i l'adsorció en els microporus (bulk) i en la superfície externa de les zeolites es poden entendre a nivell molecular. Es va calcular l'energia d'adsorció i també es va descompondre la seua magnitud en les contribucions electroestàtica i de van der Waals. A més, va ser possible observar més de prop les interaccions amfitrió-convidat i convidat-convidat durant les trajectòries simulades. Considerant la creixent demanda energètica a nivell mundial, els biocombustibles es consideren una opció sostenible obtinguda a partir de biomassa. S'han simulat amb èxit els passos del procés experimental desenvolupat per Denayer et al. per a la recuperació de biobutanol a partir d'una mescla fermentada. Es van modelar els cicles d'adsorció i desorció en dues columnes de zeolites amb selectivitat complementària (tipus LTA i CHA), amb sistemes de nanoláminas i considerant les principals característiques experimentals. Encara que les escales de temps experimentals són inassolibles per als recursos computacionals disponibles actualment, els sistemes simulats van poder capturar els fenòmens experimentals i van ser avaluats més a fons a través del comportament microscòpic dels sistemes. Un estudi experimental i computacional va assenyalar la STW sílice pura (Si-STW) com un candidat prometedor per a la separació d'alcans lineals, monoramificats i diramificats. Es van provar els isòmers C5 a C7, i el material Si-STW va superar la capacitat d'adsorció i selectivitat de MFI de sílice pura, especialment cap als isòmers diramificats amb àtoms de carboni quaternaris. Es van calcular les isotermes d'adsorció, la calor d'adsorció i el comportament de difusió dels hidrocarburs provats i es van comparar amb els resultats experimentals. Per tant, les propietats d'adsorció de Si-STW poden ser explorades per al seu ús sobre el producte obtingut durant el procés de hidromerització - que genera components de major octanatge per a la mescla de gasolina -, augmentant el seu número d'octà. La producció de 6-kestosa per a ús industrial com a prebiòtic i sucre de baix índex glucèmic depén de la seua separació de les molècules de sacarosa. La separació d'una mescla aquosa equimolar que conté sacarosa i 6-kestosa mitjançant membranes de zeolites s'ha investigat amb simulacions de Dinàmica Molecular. Una selecció considerant les 253 estructures de zeolites reportades, va assenyalar els tres candidats més prometedors (AET, ETR i DON), en avaluar l'efecte d'exclusió per grandària (adsorció de sacarosa i exclusió de 6-kestosa), la mobilitat de tots dos sucres dins de les estructures (avaluats amb models tipus bulk), i simulant la seua futura aplicació com a sistemes de membranes. Entre els millors candidats, la zeolita DON va presentar una selectivitat significativa per a les molècules de sacarosa, amb el major flux i sent factible com a material de sílice pura, igualant la composició química simulada. / [EN] Computational chemistry methods have been employed in the study of zeolite materials applied to separation processes. A classical approach was considered, where the force fields were selected during benchmark procedures among the models currently available. The obtained results have been validated considering experimental data, and models description was improved, when possible, by parameterization procedures. Thus, the best models described systems with different degrees of complexity, that were simulated through Molecular Dynamics and Monte Carlo methods. Diffusion and adsorption in zeolites' micropores (bulk) and external surface could be understood at a molecular level. The adsorption energy was calculated, and its magnitude also decomposed into the electrostatic and van der Waals contributions. Besides, a closer look into the host-guest and guest-guest interactions could be done during the trajectories simulated. Considering the growing energetic demand worldwide, biofuels are considered a sustainable option obtained from biomass. The steps of the experimental process developed by Denayer et al. for biobutanol recovery from a fermented mixture have been successfully simulated. Both adsorption and desorption cycles in two zeolitic columns with complementary selectivity (LTA and CHA-type) were modeled as nanosheet systems, considering the main experimental features. Although the experimental time scales are unreachable for the current computational resources available, the systems simulated could capture the experimental phenomena, and were further evaluated through the microscopic behavior of the systems. An experimental and computational study pointed pure silica STW (Si-STW) as a promising candidate for the separation of linear, monobranched and dibranched alkanes. C5 to C7 isomers were tested, and Si-STW material outperformed pure silica MFI adsorption capacity and selectivity, specially towards the dibranched isomers with quaternary carbon atoms. Adsorption isotherms, heat of adsorption and the diffusional behavior of the tested hydrocarbons have been calculated, and compared with the experimental results. Thus, Si-STW adsorptive properties can be further explored for its usage over the product obtained during the hydromerisation process - that generates higher-octane components for gasoline mixture -, increasing its octane number. The production of 6-kestose for industrial usage as prebiotic and low-glycemic sugar is dependent on its separation from sucrose molecules. The separation of an equimolar aqueous mixture, containing sucrose and 6-kestose, by zeolitic membranes have been investigated through Molecular Dynamics simulations. A screening considering the 253 zeolites structures reported, pointed out the three most promising candidates (AET, ETR and DON), by evaluating the size exclusion effect (adsorption of sucrose and exclusion of 6-kestose), the mobility of both sugars inside the frameworks (evaluated with bulk models), and simulating their future application as membrane systems. Among the best candidates, DON framework presented a significant selectivity for sucrose molecules, with the largest flux, and being feasible as a pure silica material, matching the chemical composition simulated. / This work was supported by Generalitat Valenciana (GVA) predoctoral fellowship GRISOLIAP/2019/084. We also thank GVA for PROMETEO/2021/077 project and ASIC-UPV and SGAI-CSIC for the use of computational facilities. We acknowledge the Spanish Ministry of Sciences, Innovation and Universities (MCIU), State Research Agency (AEI), and the European Fund for Regional Development (FEDER) for their funding via project RTI2018-101784-B-I00 and Program Severo Ochoa SEV-2016-0683 / Misturini, A. (2022). Mixture Separations with Zeolites: Molecular View on Adsorptive Processes [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/191433 / Compendio

Indiana University-Purdue University Indianapolis (IUPUI) / Protein malfunction can cause human diseases, which makes the protein a target in the process of drug discovery. In-depth knowledge of how protein functions can widely contribute to the understanding of the mechanism of these diseases. Protein functions are determined by protein structures and their dynamic properties. Protein dynamics refers to the constant physical movement of atoms in a protein, which may result in the transition between different conformational states of the protein. These conformational transitions are critically important for the proteins to function. Understanding protein dynamics can help to understand and interfere with the conformational states and transitions, and thus with the function of the protein. If we can understand the mechanism of conformational transition of protein, we can design molecules to regulate this process and regulate the protein functions for new drug discovery. Protein Dynamics can be simulated by Molecular Dynamics (MD) Simulations. The MD simulation data generated are spatial-temporal and therefore very high dimensional. To analyze the data, distinguishing various atomic interactions within a protein by interpreting their 3D coordinate values plays a significant role. Since the data is humongous, the essential step is to find ways to interpret the data by generating more efficient algorithms to reduce the dimensionality and developing user-friendly visualization tools to find patterns and trends, which are not usually attainable by traditional methods of data process. The typical allosteric long-range nature of the interactions that lead to large conformational transition, pin-pointing the underlying forces and pathways responsible for the global conformational transition at atomic level is very challenging. To address the problems, Various analytical techniques are performed on the simulation data to better understand the mechanism of protein dynamics at atomic level by developing a new program called Probing Long-distance interactions by Tapping into Paired-Distances (PLITIP), which contains a set of new tools based on analysis of paired distances to remove the interference of the translation and rotation of the protein itself and therefore can capture the absolute changes within the protein. Firstly, we developed a tool called Decomposition of Paired Distances (DPD). This tool generates a distance matrix of all paired residues from our simulation data. This paired distance matrix therefore is not subjected to the interference of the translation or rotation of the protein and can capture the absolute changes within the protein. This matrix is then decomposed by DPD using Principal Component Analysis (PCA) to reduce dimensionality and to capture the largest structural variation. To showcase how DPD works, two protein systems, HIV-1 protease and 14-3-3 σ, that both have tremendous structural changes and conformational transitions as displayed by their MD simulation trajectories. The largest structural variation and conformational transition were captured by the first principal component in both cases. In addition, structural clustering and ranking of representative frames by their PC1 values revealed the long-distance nature of the conformational transition and locked the key candidate regions that might be responsible for the large conformational transitions. Secondly, to facilitate further analysis of identification of the long-distance path, a tool called Pearson Coefficient Spiral (PCP) that generates and visualizes Pearson Coefficient to measure the linear correlation between any two sets of residue pairs is developed. PCP allows users to fix one residue pair and examine the correlation of its change with other residue pairs. Thirdly, a set of visualization tools that generate paired atomic distances for the shortlisted candidate residue and captured significant interactions among them were developed. The first tool is the Residue Interaction Network Graph for Paired Atomic Distances (NG-PAD), which not only generates paired atomic distances for the shortlisted candidate residues, but also display significant interactions by a Network Graph for convenient visualization. Second, the Chord Diagram for Interaction Mapping (CD-IP) was developed to map the interactions to protein secondary structural elements and to further narrow down important interactions. Third, a Distance Plotting for Direct Comparison (DP-DC), which plots any two paired distances at user’s choice, either at residue or atomic level, to facilitate identification of similar or opposite pattern change of distances along the simulation time. All the above tools of PLITIP enabled us to identify critical residues contributing to the large conformational transitions in both HIV-1 protease and 14-3-3σ proteins. Beside the above major project, a side project of developing tools to study protein pseudo-symmetry is also reported. It has been proposed that symmetry provides protein stability, opportunities for allosteric regulation, and even functionality. This tool helps us to answer the questions of why there is a deviation from perfect symmetry in protein and how to quantify it.

First, the effect of transition metal oxide (e.g., V2O5, Co2O3, etc.) on the physical properties (e.g., density, glass transition temperature (Tg), optical properties and mechanical properties) and chemical durability of a simplified borosilicate nuclear waste glass was investigated. Adding V2O5 in borosilicate nuclear waste glasses decreases the Tg, while increasing the fracture toughness and chemical durability, which benefit the future formulation of nuclear waste glasses. Second, structural study of ZrO2/SiO2 substitution in silicate/borosilicate glasses was systematically conducted by molecular dynamics (MD) simulation and the quantitative structure-property relationships (QSPR) analysis to correlate structural features with measured properties. Third, for bioactive glass formulation, mixed-network former effect of B2O3 and SiO2 on the structure, as well as the physical properties and bioactivity were studied by both experiments and MD simulation. B2O3/SiO2 substitution of 45S5 and 55S5 bioactive glasses increases the glass network connectivity, correlating well with the reduction of bioactivity tested in vitro. Lastly, the effect of optical dopants on the optimum analytical performance on atom probe tomography (APT) analysis of borosilicate glasses was explored. It was found that optical doping could be an effective way to improve data quality for APT analysis with a green laser assisted system, while laser spot size is found to be critical for optimum performance. The combined experimental and simulation approach adopted in this dissertation led to a deeper understanding of complex borosilicate glass structures and structural origins of various properties.

No description available.

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

Vor dem Hintergrund zukünftiger Sensoren, basierend auf dem piezoresistiven Effekt von einwandigen Kohlenstoffnanoröhren (SWCNT), werden in dieser Arbeit umfangreiche Ergebnisse zum mechanischen Verhalten von Grenzflächen zwischen SWCNTs und edlen Metallen am Beispiel von Pd und Au präsentiert. Im Fokus steht dabei die Synergie von rechnerischen und experimentellen Methoden Molekulardynamik (MD), nanoskalige Tests und Analytik , um (1) mit guter Genauigkeit maximale Kräfte von gezogenen SWCNTs, welche in Metall eingebettet sind, vorauszuberechnen und (2) einen wertvollen Beitrag zum Verständnis der zu Grunde liegenden Fehlermechanismen zu liefern. Es wurde ein MDModell eines in eine einkristalline Matrix eingebetteten SWCNTs mit Randbedingen eines Auszugsversuchs entwickelt. Mit diesem Modell können Kraft-Weg-Beziehungen und Energieverläufe für einen quasistatischen verschiebungsgesteuerten Auszugsversuch errechnet werden. Das Modell liefert kritische Kräfte bei Versagen des Systems. Des Weiteren können mit diesem Modell der Einfluss des SWCNT-Typus, der Einbettungslänge, der Temperatur, von intrinsischen Defekten und Oberflächengruppen (SFGs) auf das Grenzflächenverhalten untersucht werden. Zum Vergleich wurden kritische Kräfte experimentell durch in situ Auszugsversuche in einem Rasterelektronenmikroskop bestimmt. Es wurde eine sehr gute Übereinstimmung von rechnerischen und experimentellen Daten festgestellt. Der vorherrschende Fehler im Experiment ist der SWCNT-Bruch, jedoch wurden auch einige SWCNT-Auszüge beobachtet. Mit Hilfe der MD-Simulationen wurde gefunden, dass die SFGs als kleine Anker in der umgebenden metallischen Matrix wirken und somit die maximalen Kräfte signifikant erhöhen. Diese Grenzflächenverstärkung kann Zugspannungen verursachen, die genügend hoch sind, so dass SWCNT-Bruch initiert wird. Im Gegensatz dazu zeigten Simulationen von Auszugstests mit idealen SWCNTs nur kleine Auszugskräfte, welche meistens unabhängig von der Einbettungslänge des SWCNTs sind. Dieses Verhalten wird mit einer inkommensurablen Konfiguration der Kristallstrukturen an der Grenzfläche von SWCNTs und der einbettenden Edelmetalle interpretiert. Zur Qualifizierung der Existenz von carboxylatischen Oberflächengruppen auf dem genutzten SWCNT-Material wurden analytische Untersuchungen mittels Fluoreszenzmarkierung von Oberflächengruppen durchgeführt. In Übereinstimmung mit Literaturstellen zum gesicherten Nachweis von SFGs, bedingt durch technologische Behandlungen, weisen diese Experimente stark auf das Vorhandensein von carboxylatischen Oberflächengruppen auf dem genutzten SWCNT-Material hin. Demnach kann der dominante SWCNT-Bruch Fehler durch die Grenzflächenverstärkung auf Grund von SFGs erklärt werden. / In the light of future sensors, that are based upon the piezoresistive effect of singlewalled carbon nanotubes (SWCNTs), this work presents comprehensive results of studies on the mechanical behavior of interfaces between SWCNTs and noble metals using the examples of Pd and Au. With this contribution, the focus is on a synergy between computational and experimental approaches involving molecular dynamics (MD) simulations, nanoscale testing, and analytics (1) to predict to a good degree of accuracy maximum forces of pulled SWCNTs embedded in a noble metal matrix and (2) to provide valuable input to understand the underlying mechanisms of failure. A MD model of a SWCNT embedded in a single crystalline matrix with pull-out test boundary conditions was developed. With this model, force-displacement relations and energy evolutions for a quasi-static displacement controlled test can be computed. The model provides critical forces for failure of the system. Furthermore, the influence of SWCNT type, embedding length, temperature, intrinsic defects and surface functional groups (SFGs) on the interface behavior can be studied using this model. For comparison, critical forces were experimentally determined by conducting pull-out tests in situ, inside a scanning electron microscope. A very good agreement of computational and experimental values was discovered. The dominant failure mode in the experiment was a SWCNT rupture, although several pull-out failures were also observed. From MD simulations, it was found that SFGs act as small anchors in the metal matrix and significantly enhance the maximum forces. This interface reinforcement can lead to tensile stresses sufficiently high to initiate SWCNT rupture. In contrast, pull-out test simulations of ideal SWCNTs show only small pull-out forces, which are mostly independent on SWCNT embedding length. This behavior is interpreted with an incommensurate configuration of crystal structures at the interface between SWCNTs and embedding noble metals. To qualify the existence of carboxylic SFGs on the used SWCNT material, an analytical investigation by means of fluorescence labeling of surface species was performed. In agreement with literature reports on the secured verification of SFGs due to necessary technological treatments, these experiments strongly indicate the presence of carboxylic SFGs on the used SWCNT material. Thus, the dominant SWCNT rupture failure is explained with an interface reinforcement by SFGs.