Academic literature on the topic 'Molecular simulation techniques'

Molecular dynamics (MD) simulation is a particularly useful technique in food processing. Normally, food processing techniques can be optimized to favor the creation of higher-quality, safer, more functional, and more nutritionally valuable food products. Modeling food processes through the application of MD simulations, namely, the Groningen Machine for Chemical Simulations (GROMACS) software package, is helpful in achieving a better understanding of the structural changes occurring at the molecular level to the biomolecules present in food products during processing. MD simulations can be applied to define the optimal processing conditions required for a given food product to achieve a desired function or state. This review presents the development history of MD simulations, provides an in-depth explanation of the concept and mechanisms employed through the running of a GROMACS simulation, and outlines certain recent applications of GROMACS MD simulations in the food industry for the modeling of proteins in food products, including peanuts, hazelnuts, cow’s milk, soybeans, egg whites, PSE chicken breast, and kiwifruit.

Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a `black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open-source software repository, which can be freely copied, modified and redistributed by educators. The topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.

In this study, we investigate the atomistic details of Keap1-Nrf2 inhibitors by in-depth modeling techniques, including molecular dynamics (MD) simulations, and the path-based free energy method of umbrella sampling (US). The protein–protein interaction (PPI) of Keap1-Nrf2 is implicated in several neurodegenerative diseases like cancer, diabetes, and cardiomyopathy. A better understanding of the five sub-pocket binding sites for Nrf2 (ETGE and DLG motifs) inside the Kelch domain would expedite the inhibitor design process. We selected four protein–ligand complexes with distinct co-crystal ligands and binding occupancies inside the Nrf2 binding site. We performed 100 ns of MD simulation for each complex and analyzed the trajectories. From the results, it is evident that one ligand (1VV) has flipped inside the binding pocket, whereas the remaining three were stable. We found that Coulombic (Arg483, Arg415, Ser363, Ser508, and Ser602) and Lennard–Jones (Tyr525, Tyr334, and Tyr572) interactions played a significant role in complex stability. The obtained binding free energy values from US simulations were consistent with the potencies of simulated ligands. US simulation highlight the importance of basic and aromatic residues in the binding pocket. A detailed description of the dissociation process brings valuable insight into the interaction of the four selected protein–ligand complexes, which could help in the future to design more potent PPI inhibitors.

AbstractMonte Carlo and molecular dynamics computer simulations are now able to provide detailed information concerning the structure, dynamics, and thermodynamics of pore fluids in 2:1 clays. This article will discuss interparticle interaction potentials currently available for atomistic simulations of clay-water systems, and will describe how computational techniques can be applied to modelling of clay systems. Some recent simulation studies of 2:1 clay hydration will then be reviewed. Comparison with experimental data promotes confidence in the molecular models and simulation techniques, and points to exciting future prospects.

Environmental context Computational simulations are providing an increasingly useful way to isolate specific geochemical and environmental reactions and to test how important they are to the overall rate. In this review, we summarise a few ways that one can simulate a reaction and discuss each technique’s overall strengths and weaknesses. Selected case studies illustrate how these techniques have helped to improve our understanding for geochemical and environmental problems. Abstract Methods to explore reactions using computer simulation are becoming increasingly quantitative, versatile and robust. In this review, a rationale for how molecular simulation can help build better geochemical kinetics models is first given. Some common methods are summarised that geochemists use to simulate reaction mechanisms, specifically classical molecular dynamics and quantum chemical methods and their strengths and weaknesses are also discussed. Useful tools such as umbrella sampling and metadynamics that enable one to explore reactions are discussed. Several case studies wherein geochemists have used these tools to understand reaction mechanisms are presented, including water exchange and sorption on aqueous species and mineral surfaces, surface charging, crystal growth and dissolution, and electron transfer. The effect that molecular simulation has had on our understanding of geochemical reactivity is highlighted in each case. In the future, it is anticipated that molecular simulation of geochemical reaction mechanisms will become more commonplace as a tool to validate and interpret experimental data, and provide a check on the plausibility of geochemical kinetic models.

Realistic simulation of the atomic-scale properties of complex systems has long been a goal of scientists interested in the behavior of condensed matter. Until recently, the role of atomistic simulation techniques has been to address rather idealized problems in statistical mechanics. Treatment of more realistic materials has been uncommon not because suitable approaches toward simulating such materials were unknown, but rather because the computer power available was inadequate. Recently, major advances have occurred in the complexity of systems subject to atomistic simulation, primarily due to a dramatic increase in availability of computer power. These new capabilities have driven the development of atomic-scale descriptions of real materials accurate enough for atomistic simulation of a wide range of specific materials science problems.In this section, we will outline several of the techniques used to simulate the microscopic behavior of an atomistic system. The first method introduced for atomistic simulation was the molecular dynamics technique, in which Newton's equations of motion for the individual atoms are integrated numerically for given interatomic and external forces. One of the first uses of this technique was the study, by Fermi, Pasta, and Ulam, of randomization of vibrational energy in a one-dimensional chain of atoms. Although the results of this initial application were to some extent unsatisfactory, the molecular dynamics technique has since been applied to a wide range of problems in the statistical mechanics of condensed media.

Molecular dynamics trajectories that sample from a Gibbs, or canonical, distribution can be generated by introducing a modified Hamiltonian with additional degrees of freedom as described by Nose [46]. Although this method has found widespread use in its time re-parameterized Nose-Hoover form, the lack of a Hamiltonian, and the need to 'tune' thermostatting parameters has limited, its use compared to stochastic methods. In addition, since the proof of the correct sampling is based on an ergodic assumption, thermostatting small of stiff systems often does not given the correct distributions unless the Nose-Hoover chains [43] method is used, which inherits the Nose-Hoover deficiencies noted above. More recently the introduction of the Hamiltonian Nose-Poincare method [11], where symplectic integrators can be used for improved long term stability, has renewed interest in the possibility of Hamiltonian methods which can improve dynamical sampling. This class of methods, although applicable to small systems, has applications in large scale systems with complex chemical structure, such as protein-bath and quantum-classical models.;For Nose dynamics, it is often stated that the system is driven to equilibrium through a resonant interaction between the self-oscillation frequency of the thermostat variable and a natural frequency of the underlying system. By the introduction of multiple thermostat Hamiltonian formulations, which are not restricted to chains, it has been possible to clarify this perspective, using harmonic models, and exhibit practical deficiencies of the standard Nose-chain approach. This has led to the introduction of two Hamiltonian schemes, the Nose-Poincare chains method and the Recursive Multiple Thermostat (RMT) method. The RMT method obtains canonical sampling without the stability problems encountered with chains with the advantage that the choice of Nose mass is independent of the underlying system.

Nanotechnology is a multidisciplinary branch of science and technology that involves a widerange of different fields such as chemistry, materials science, physics or chemical engineeringwhose goal is the production of new functional materials and devicesthrough the control of their organization at the atomic and molecular scale.
Nanotechnology has jumped from research laboratories to our daily life and today all theprogresses made in this field have been translated into direct applications in different fields being electronics and computer science and biomedicine, where the most striking advances have beendone.
What differences nanotechnology from traditional chemistry and physics can be summarized inthree points: (i) Analysis and control of the matterat the atomic and molecular level focusing in individual atoms; (ii) the appearance of novel physical properties because of the nanoscopicdimensions; (iii) the possibility of generating new complex functional systems with novelproperties.
Modeling and theory are becoming vital to designing and improving nanodevices. The intrinsicnature of nano and supramolecular scale that involves tens, hundreds and thousands of atomsmakes computational chemistry the perfect ally to design new devices and predict their properties. Computational chemistry provides the perfect tools to describe the electronic structureand the dynamic behavior, as well as the properties derived from them, through quantummechanics and classical mechanics formalisms.
The suitability of such techniques in the design and improvement of nanodevices as well as theprediction of their properties is clearly proven throughout the four blocks in which this thesis isdivided:
· Nanotubes based on natural peptide sequences
Nanotubes have gained extensive interest because of their applicability in different fieldsranging from medicine to electronics. Among nanotubes, those based on natural peptidesequences taken from some natural proteins with a tubular or fibrillar motif are gaining a
broad attention because of their high biocompatibility, the possibility of adding functionalitiesby tuning them and their potentiality to self-assemble. The enhancement of the ability to retain the tubular geometry of such structures can be achieved by substituting targeted amino acids located in the more flexible parts of the nanoconstruct by synthetic amino acids withlow conformational flexibility providing a larger rigidity to the overall structure.
· Dendronized polymers
Dendronized polymers are a specific kind of macromolecule structure that consists of a linearpolymeric backbone where dendritic units are attached regularly leading to a highly branchedthree-dimensional architecture. This fact provides dendronized polymers the peculiarity of the coexistence within the same macromolecule of three topological regions: (i) the internalbackbone; (ii) the dendron region around the backbone and (iii) the external surface. Thesemolecules have a wide range of applications in different fields such as biomedical engineering, host-guest chemistry or catalysis.
· Theoretical study of ð-conjugated systems
Conducting polymers are polymers bearing a characteristic polyconjugated nature which makethem electronic conductors. In particular thiophene-based conducting polymers have been widely studied because of their electric and nonlinear optical properties, excellent environmentalstability and relatively low cost of production. Due to the crucial role played by the electronicstructure of these systems in their relevant properties, a good knowledge of it is a key factor todesign and improve new conducting polymers. To achieve this goal QM calculations suitperfectly to get accurate estimates of such properties.
· Molecular actuators and sensors based on conducting polymers
Both experimental and computational research in nanoactuators and nanosensors are widelyreported in the literature. Among them, those based in conducting polymers are flourishingbecause of their great transport properties, electrical conductivity or rate of energy migrationwhich provide amplified sensitivity in nanosensors and a rapid response in nanoactuators. In thissense electron-rich thiophene-based oligomers and polymers combined with versatilecalix[4]arenes units are presented in the present thesis. Calix[4]arenes are synthetic macrocyclic molecules consisting of four phenol or anisole rings connected via methylene bridges that canhost different guest molecules leading to conformational rearrangement of the whole device making it useful to be employed as a sensor or actuator.

Dissertation (Ph.D.) -- Worcester Polytechnic Institute.
Keywords: Activated carbons; Hydrogen cyanide; Methyl ethyl ketone; Adsorption; Mercury; Monte-Carlo; Solvents; Molecular simulations; Zeolites; Water; Methanol; Nanopores. Includes bibliographical references (leaves 147-150).

Els materials porosos s'utilitzen àmpliament en moltes branques de la ciència i tecnologia modernes com la catàlisi, la separació de mescles, la purificació de fluids i la fabricació de membranes. Per a que els sòlids porosos puguin aplicar-se amb èxit cal disposar d'una caracterització precisa de la superfície i de les propietats estructurals, així com també una bona comprensió del comportament físico-químic dels fluids dins dels porus. Alguns materials, com les zeolites, tenen estructures poroses ben definides, però d'altres, com els òxids porosos, carbons i vidres de porus controlat, són bastant amorfs. Per això, un tema clau i, sovint, complicat, és la caracterització adequada d'
aquests tipus de materials. Durant molts anys, l'adsorció de gasos s'ha emprat per estudiar les propietats de sòlids porosos, degut a que és un mètode ràpid, simple i que proporciona prou informació. Es van desenvolupar molts mètodes per extraure dades sobre la porositat i les propietats de la superfície de materials a partir d'isotermes d'adsorció. En les dues últimes dècades, amb l'ajuda dels ordinadors, cada cop més i més ràpids, l'ús de les tècniques de modelat molecular ha anat guanyant rellevància. En aquest context, l'objectiu general d'aquest treball de tesi és desenvolupar eines a escala molecular emprant la mecànica estadística i aplicant-la a la caracterització
de materials adsorbents.
Després d'una breu introducció en el tema (capítol 1), en el capítol 2 presentem una revisió de la metodologia bàsica emprada en aquest treball. En el capítol 3 hem implementat la teoria funcional de la densitat de mesures fonamentals o FMT (de l'anglès, Fundamental-Measured density functional theory), publicada per Kierlik i Rosinberg, per descriure l'adsorció de molècules Lennard-Jones en porus cilíndrics. Pel que sabem, aquest és el primer cop que la teoria s'aplica a la geometria cilíndrica. L'exactitud de la teoria en predir isotermes d'adsorció i perfils de densitat de partícules es compara amb simulacions Monte Carlo en el col·lectiu gran canònic per un rang ample de mides de porus. Aquesta comparació mostra que la concordança és molt bona en tots els casos. Addicionalment, s'ha aplicat la teoria a l'adsorció en porus plans per estudiar la influència de la geometria del porus en aquest fenomen. Els resultats indiquen que el confinament de la geometria cilíndrica introdueix diferències significatives en la forma de les isotermes d'adsorció i els perfils de densitat. Aquestes diferències són rellevants a l'hora de caracteritzar materials porosos. Els resultats indiquen que té lloc un comportament per capes en el porus cilíndric més petit que s'ha considerat, mentre que l'adsorció en un porus pla de la mateixa grandària necessita un potencial químic molt més alt per aconseguir una adsorció significant. A mida que el diàmetre del porus augmenta, la influència de la geometria es fa cada cop menys important, encara que es pot observar una certa desviació en la transició de condensació capil·lar. Addicionalment, per porus més amples, obtenim una adsorció multicapa amb condensació capil·lar a potencials químics alts, amb el mateix comportament qualitatiu observat en ambdues geometries. Quan el diàmetre assoleix el límit on els efectes de curvatura ja no són rellevants, el comportament quantitatiu del porus cilíndric es redueix al mateix que el del porus pla. La formació d'una capa fina adsorbent en mides de porus intermèdies i grans sembla correspondre a una transició de fase termodinàmica de segon ordre, per al rang de paràmetres utilitzat i les condicions termodinàmiques estudiades. No obstant, els resultats semblen indicar una interrelació entre aquest comportament i la transició pre-mullada (de la paraula anglesa prewetting) que s'observa en geometries semi-infinites, especialment al voltant del punt final crític de la línia pre-mullada. L'efecte del confinament és molt important en aquest comportament crossover (de pas). De la comparació de càlculs FMT amb resultats de la teoria funcional de la densitat no local, concloem que la FMT és una eina excel·lent per a l'estudi del comportament de fluids en geometries cilíndriques.
En el capítol 4 s'explica com hem aplicat la FMT juntament amb un mètode de regularització per estimar la distribució de mides de porus o PSD (de l'anglès, Pore-Size Distribution) de vidres porosos model. Hem escollit aquest material perquè va ser desenvolupat mitjançant tècniques de modelat molecular, i es pot comparar directament amb la teoria utilitzada en aquest treball. Un avantatge addicional d'aquests materials model, enfront els experimentals, és que, en el primer cas, la mida i forma dels porus són ben conegudes, així com també la posició dels àtoms en la superfície, esdevenint així un material perfecte per comprovar l'exactitud dels mètodes de caracterització teòrica disponibles. Com que hi ha diferents solucions de l'equació integral d'adsorció compatibles amb la isoterma d'adsorció experimental, i diversos factors poden amagar els defectes del model molecular, hem realitzat la caracterització d'una forma sistemàtica: primer hem comprovat l'exactitud de la FMT i el model de porus independent per predir les isotermes d'adsorció "experimentals" utilitzant la PSD ja coneguda per als materials. Això s'ha efectuat amb porus individuals plans i cilíndrics. En segon lloc, un cop la isoterma d'adsorció va ser reconstruïda amb èxit, vam invertir la isoterma d'adsorció integral amb un procediment de regularització. L'exactitud del mètode d'inversió s'ha comprovat també abans d'estimar la PSD de materials diferents. En últim lloc, un cop demostrat que el mètode és correcte, l'hem utilitzat per estimar la PSD de quatre materials. També hem estudiat la influència d'escollir alguns valors particulars de paràmetres moleculars per les interaccions fluid-fluid i sòlid-fluid en el comportament adsorbent d'aquests sistemes. Hem obtingut que el model de porus independent és adequat per als quatre materials investigats en aquest treball. La geometria plana sembla representar millor que la geometria cilíndrica el comportament adsorbent global. Pel que fa a la PSD obtinguda amb el nostre procediment, s'observa que les distribucions obtingudes mitjançant la inversió de la integral estan en millor concordança amb les distribucions geomètriques que les calculades amb el mètode Barrett-Joyner-Halenda (BJH). El locus del pic està situat a la mateixa mida de por, i tots ells són unimodals, mentre que les distribucions BJH mostren un màxim localitzat sistemàticament a porus més petits, estimant per sota la PSD del material, i no són unimodals. En quan a la geometria dels porus individuals que formen el material podem dir que, encara que la PSD és més ampla que les geomètriques, l'adsorció que es prediu per un conjunt de porus plans individuals està en un acord quasi quantitatiu amb la isoterma d'adsorció experimental.
Finalment, en el capítol 5 exposem com hem caracteritzat tres mostres diferents de g­alúmina, una d'elles sense tractament i les altres dues calcinades en un forn durant unes hores a 823 i 1023K. Per fer-ho hem mesurat isotermes d'adsorció de nitrogen a 77.35K en un equip Micromeretics ASAP 2000. A més, hem aprofitat les PSD's proporcionades pel programari de l'equip emprant el mètode BJH. Hem calculat isotermes teòriques mitjançant l'aproximació FMT. Hem invertit les equacions integrals d'adsorció amb el mètode de regularització i, finalment, hem obtingut les PSD's per les tres mostres d'alúmina, i les corresponents isotermes d'adsorció pels tres materials. D'aquesta forma hem observat la influència de la calcinació de l'alúmina en la seva PSD. A més, hem comprovat l'exactitud del mètode FMT/de regularització de manera sistemàtica. Quan comparem les PSD's obtingudes amb les corresponents distribucions BJH, hem verificat que, en els dos primers casos (alúmina no tractada i alúmina calcinada a 823K), el mètode BJH estima per sota la mida dels porus, proporcionant una PSD desviada cap a mides més petites. En el cas de l'alúmina calcinada a 1,023K, en la que el procés de sinterització produeix que els porus més petits desapareguin, afavorint els més grans, les PSD's del mètode BJH i les PSD's de la FMT/regularització són molt semblants. Amb això es corrobora el fet conegut de que el mètode BJH és força acurat en la regió macroporosa. Finalment, hem predit la isoterma d'adsorció d'un fluid diferent (età) a una altra temperatura (333K), en un dels materials caracteritzats (alúmina no tractada), amb l'ànim d'establir la robustesa de la PSD obtinguda. La concordança obtinguda mostra que és possible utilitzar aquest mètode de caracterització i extrapolar els resultats a altres condicions, mentre s'empri un nombre suficient de mides de porus per calcular la isoterma desitjada, i els paràmetres d'interacció sòlid-fluid es triïn adequadament.
Los materiales porosos se utilizan en muchas ramas de la ciencia y la tecnología, por ejemplo, se usan como catalizadores, en la separación de mezclas, en la purificación de fluidos, y en la fabricación de membranas. Su aplicación adecuada requiere de la caracterización precisa de sus propiedades superficiales y estructurales, además del conocimiento del comportamiento fisicoquímico de los fluidos cuando se encuentran dentro de los poros. Algunos materiales, como las zeolitas, tienen estructuras porosas bien definidas, pero otros en cambio (óxidos porosos, carbones, vidrios porosos con tamaño controlado) son bastante amorfos. Por lo tanto, una caracterización correcta de los materiales porosos es un área de estudio muy importante, la cual en algunos casos es una tarea sencilla pero en la mayoría no. Durante muchos años la adsorción de gases ha sido empleada para estudiar las propiedades de sólidos porosos, dado que es bastante fácil, simple y se puede obtener mucha información. Se han desarrollado muchos métodos para interpretar los datos experimentales y determinar la porosidad, las propiedades superficiales y la distribución de los tamaños de los poros de los materiales a partir de las isotermas de adsorción. En las dos últimas décadas, con la ayuda de las computadoras cada vez más rápidas, se ha extendido mucho el uso las técnicas de la mecánica estadística para realizar esta tarea. En este contexto, el objetivo general de esta tesis consiste en desarrollar herramientas a escala molecular utilizando la mecánica estadística para la caracterización de materiales adsorbentes.
Después de una breve introducción en el tema (capítulo 1), el capítulo 2 está dedicado a hacer una revisión de la metodología básica empleada en este trabajo. En el capítulo 3 hemos implementado la teoría funcional de la densidad de medidas fundamentales (FMT, del inglés Fundamental-Measure density functional theory) de Kierlik y Rosinberg para describir la adsorción de moléculas Lennard-Jones dentro de poros cilíndricos. Hasta donde sabemos, ésta es la primera vez que esta teoría es aplicada a geometría cilíndrica. La exactitud de la teoría en predecir las isotermas de adsorción y los perfiles de la densidad es verificada por comparación con simulaciones Monte Carlo en el colectivo Gran Canónico para un amplio intervalo de tamaños de poros, observándose una buena concordancia en todos los casos. Adicionalmente, la teoría ha sido aplicada a la adsorción en poros planos para estudiar la influencia de los poros en esta propiedad. Los resultados indican que el confinamiento de la geometría cilíndrica introduce diferencias significativas en la forma de las isotermas de adsorción y de los perfiles de la densidad. Estas diferencias son relevantes para la caracterización de los materiales porosos. Nuestros resultados indican que un comportamiento de formación de capa tiene lugar en el poro cilíndrico, mientras que la adsorción en un poro plano del mismo tamaño necesita un potencial químico mucho más alto para alcanzar una adsorción significativa. Cuando el tamaño de poro se incrementa, la influencia de la geometría se vuelve menos importante, pero aún se observa un cierto desplazamiento del lugar en el cual se da la transición de la condensación capilar. Adicionalmente, para poros más anchos, tenemos formación de multicapas con condensación capilar a potenciales químicos altos, observándose el mismo comportamiento cualitativo en ambas geometrías. Cuando el diámetro alcanza el límite en donde los efectos de la curvatura ya no son relevantes, el comportamiento cuantitativo de los poros cilíndricos y de los planos es muy similar. La formación de una fina película adsorbida a tamaños de poro grandes e intermedios parece corresponder a una transición de fase termodinámica de segundo orden, para el intervalo de parámetros usado y a las condiciones termodinámicas estudiadas. Sin embargo, los resultados encontrados parecen indicar que existe una relación entre este comportamiento y el de una transición de pre-mojado observada en geometrías semi-infinitas, especialmente en la vecindad del punto final crítico de la línea de pre-mojado. El efecto del confinamiento es muy importante en este comportamiento de transición. A partir de la comparación de los cálculos hechos con FMT y los hechos con la teoría funcional de la densidad no-local, concluimos que la FMT es una excelente herramienta para el estudio del comportamiento de los fluidos en geometrías cilíndricas confinadas.
En el capítulo 4 hemos aplicado la FMT en combinación con un método de regularización para estimar la distribución de tamaños de poros (PSD, del inglés Pore-Size Distribution) de materiales modelo que imitan a los vidrios porosos. Hemos elegido este material en particular porque fue desarrollado con técnicas de modelado molecular, y se puede hacer una comparación directa con la teoría aquí usada. Una ventaja adicional de estos materiales modelo, con respecto a los materiales reales, es que en este caso la forma y tamaño de los poros se conoce exactamente, además de que se sabe la posición de los átomos en la superficie, convirtiéndolo en un material ideal para verificar la exactitud de los métodos de caracterización teóricos disponibles. Dado que existen varias soluciones de la ecuación integral de adsorción compatibles con la isoterma de adsorción experimental, y que varios factores pueden ocultar los defectos del modelo molecular, hemos hecho la caracterización de una manera sistemática: primero hemos probado la exactitud de la FMT y del modelo de poros independientes para predecir las isotermas de adsorción "experimentales" usando la PSD geométrica ya conocida para estos materiales. Esto ha sido hecho tanto con los poros cilíndricos como con los planos. En segundo lugar, una vez que la isoterma de adsorción fue reconstruida, invertimos la isoterma integral de adsorción con un procedimiento de regularización. La exactitud del método de inversión ha sido verificado antes de estimar la PSD de los diferentes materiales. Finalmente, una vez que se ha establecido que el método es correcto, lo usamos para estimar las PSD's de estos cuatro materiales. Hemos estudiado también la influencia de elegir diferentes valores de los parámetros moleculares para la interacción fluido-fluido y para la sólido-fluido en el comportamiento de adsorción en estos sistemas. Los resultados indican que el modelo de poros independientes es adecuado para los cuatro materiales aquí investigados. La geometría plana parece representar el comportamiento de adsorción global mejor que la cilíndrica. En cuanto a lo que las PSD's obtenidas con nuestro procedimiento se refiere, las distribuciones resultantes a través de la inversión de la integral presentan una mejor concordancia con las distribuciones geométricas que las calculadas con el método Barrett-Joyner-Halenda (BJH). El máximo del pico está localizado en el mismo tamaño de poro, y las distribuciones son unimodales, mientras que las BJH's muestran un máximo sistemáticamente localizado a poros más pequeños, subestimando las PSD's del material, y éstas no son unimodales. Respecto a la geometría de los poros individuales que conforman el material, se puede decir, a pesar de que las PSD's son más dispersas que las geométricas, que la adsorción predicha por una colección de poros planos individuales tiene una concordancia casi cuantitativa con la isoterma de adsorción experimental.
Finalmente, en el capítulo 5 hemos caracterizado tres muestras diferentes de g­alúmina, una de ellas sin ningún tratamiento, y las otras dos calcinadas en un horno durante varias horas a 823 y a 1,023K. Para ello hemos medido isotermas de adsorción de nitrógeno a 77.35K en un equipo Micromeritics ASAP 2000. Adicionalmente, hemos usado las PSD's calculadas con el método BJH que proporciona el software del mismo equipo experimental para comparar. Hemos calculado las isotermas teóricas utilizando la FMT. Hemos invertido las ecuaciones integrales de adsorción con el método de regularización y, finalmente, hemos obtenido las PSD's para las tres muestras de alúmina, y las correspondientes isotermas de adsorción. De esta manera hemos podido observar la influencia de la calcinación de la alúmina en su PSD. Más aún, hemos probado la exactitud del método combinado FMT/Regularización de una manera sistemática. Cuando hemos comparado las PSD's obtenidas con las correspondientes BJH's, hemos verificado que en los dos primeros casos (alúmina sin tratamiento y alúmina calcinada a 823K) el método BJH subestima el tamaño de los poros, dando PSD's desplazadas a tamaños de poros más pequeños. En el caso de la alúmina calcinada a 1,023K, en la cual el proceso de sinterización ha producido la desaparición de los poros más pequeños en beneficio de los grandes, las PSD's BJH y las PSD's FMT/Regularización son muy similares. Con esto corroboramos el hecho conocido de que el método BJH es bastante exacto en la región de los macroporos. Para terminar, hemos predicho la isoterma de adsorción de un fluido diferente (etano) a una temperatura también diferente (333K) en uno de los materiales caracterizados (alúmina sin tratar) con la idea de comprobar sí la PSD obtenida es transferible a otras condiciones o no. La concordancia observada muestra que es posible usar este método de caracterización y extrapolar los resultados a otras condiciones, procurando que se utilice un número suficiente de tamaños de poro diferentes para calcular la isoterma deseada, y se elijan bien los parámetros de interacción sólido-fluido.
Porous materials are widely used in many branches of modern science and technology, such as catalysis, separation of mixtures, purification of fluids and fabrication of membranes. A successful application of porous solids requires a precise characterization of their surface and structural properties, as well as a good understanding of the physical and chemical behavior of fluids inside the pores. Some materials, such as zeolites, have well defined porous structures, but others, such as porous oxides, carbons and controlled-porous glasses, are quite amorphous. Therefore, a proper characterization of this kind of materials is an important topic, and more often than not, a complicated one. For many years, gas adsorption has been used to study properties of porous solids, since it is fast, simple and informative. Many methods were developed to extract information about porosity and surface properties of materials from adsorption isotherm data. In the last two decades, with the aid of the increasingly faster computers, the use of molecular modeling techniques has been gaining relevance. In this context, the general objective of this thesis is to develop tools at the molecular level using statistical mechanics for the characterization of adsorbent materials.
After a brief introduction on the topic (chapter 1), chapter 2 is devoted to a review of the basic methodology employed in this work. In chapter 3 we have implemented the Fundamental-Measure density functional theory (FMT) due to Kierlik and Rosinberg to describe the adsorption of Lennard-Jones molecules in cylindrical pores. To our best knowledge, this is the first time that this theory is applied to a cylindrical geometry. The accuracy of the theory in predicting adsorption isotherms and density profiles is checked by comparison with Grand Canonical Monte Carlo simulations for a wide range of pore sizes, showing very good agreement in all cases. In addition, the theory has been applied to the adsorption in slit-like pores to study the influence of the pore geometry on this property. The results indicate that the confinement of the cylindrical geometry introduces significant differences in the shape of the adsorption isotherms and density profiles. These differences are relevant for the characterization of porous materials. Our results indicate that a layering behavior takes place in the smallest cylindrical pore considered, while the adsorption in a planar pore of the same size needs a much higher chemical potential to achieve a significant adsorption. As the pore size increases, the influence of the geometry becomes less important, although a certain shift in the capillary condensation transition can still be observed. Additionally, for wider pores, we obtain multilayer adsorption with capillary condensation at high chemical potentials, with the same qualitative behavior observed for both geometries. When the diameter size reaches the limit where the curvature effects are not of further relevance, the cylindrical pores reduce to the same quantitative behavior of the slit-like pores. The formation of a thin adsorbed layer at intermediate and large pore sizes seems to correspond to a second order thermodynamic phase transition, for the range of parameters used and the thermodynamic conditions studied. However, the results found seem to indicate some relationship between this behavior and the prewetting transition observed in semi-infinite geometries, especially in the vicinity of the critical end point of the prewetting line. The effect of the confinement is very important in this crossover behavior. From the comparison of Fundamental-Measure density functional theory calculations versus non-local density functional theory results, we conclude that the FMT is an excellent tool for the study of the behavior of fluids in confined
cylindrical geometries.
In chapter 4 we have applied the FMT in conjunction with a regularization method to estimate the pore-size distribution (PSD) of model porous glasses. We have chosen this particular material because it was developed with molecular modeling techniques, and a direct comparison can be made with the theory used here. An additional advantage of these model materials, versus experimental ones, is that in this case the size and shape of the pores is well known, as well as the position of the atoms in the surface, making it a perfect material to check the accuracy of the theoretical characterization methods available. Since there are several solutions of the adsorption integral equation compatible with the experimental adsorption isotherm, and several factors can hide defects of the molecular model, we have done the characterization in a systematic manner: we have first checked the accuracy of the FMT and the independent pore model for predicting the "experimental" adsorption isotherms using the geometrical PSD already known for the materials. This has been done with individual cylindrical and slit-like pores. Secondly, once the adsorption isotherm was successfully reconstructed, we inverted the integral adsorption isotherm with a regularization procedure. The accuracy of the inversion method has also been checked before estimating the PSD of the different materials. Finally, once the method has been proved to be correct, we used it to estimate the PSD of four materials. We have also studied the influence of choosing different values of molecular parameters for the fluid-fluid and the solid-fluid interaction on the adsorption behavior of these systems. We have obtained that the independent pore model is adequate for the four materials investigated here. The slit-like geometry seems to represent the overall adsorption behavior better than the cylindrical geometry. As far as the PSD obtained with our procedure is concerned, the distributions obtained by inversion of the integral are in better agreement with the geometrical distributions than the ones calculated with the Barrett-Joyner-Halenda (BJH) method. The locus of the peak is at the same pore size, and all of them are unimodal, while the BJH distributions show a maximum systematically located at smaller pores, underestimating the PSD of the material, and they are not unimodal. Regarding the geometry of the individual pores that form the material, we can say that, although the PSD is broader than the geometrical ones, the adsorption predicted by a collection of individual slit-like pores is in almost quantitative agreement with the "experimental" adsorption isotherm.
Finally, in chapter 5 we have characterized three different samples of g­alumina, one of them without treatment and the others two calcined in a furnace during several hours at 823 and 1,023K. For this we have measured adsorption isotherms of nitrogen at 77.35K in a Micromeritics ASAP 2000 apparatus. Additionally, we have used the PSD's provided by the software of the experimental equipment using the BJH method. We have calculated theoretical isotherms by the FMT approach. We have inverted the adsorption integral equations with the regularization method and, finally, we have obtained the PSD's for our three samples of alumina, and the corresponding adsorption isotherms. In this way we have observed the influence of the calcination of alumina on its PSD. Moreover, we have tested the accuracy of the FMT/Regularization method in a systematic way. When we compared the PSD's obtained with the corresponding BJH distributions, we verified that in the two first cases (untreated alumina and alumina calcined at 823K) the BJH method underestimated the size of the pores, giving PSD's shifted to smaller sizes. In the case of alumina calcined at 1,023K, in which the sintering process has produced the disappearance of the smallest pores, favoring the wider ones, the BJH PSD's and the FMT/regularization PSD's perform very similar. With this, we corroborated the known fact that the BJH method is quite accurate in the macroporous region. Finally, we have predicted an adsorption isotherm of a different fluid (ethane) at a different temperature (333K) in one of the characterized materials (untreated alumina) with the aim of establishing the robustness of the PSD obtained. The agreement obtained shows that it is possible to use this characterization method and extrapolate the results at other conditions, provided that a enough number of different pore sizes are used to calculate the desirable isotherm, and the solid-fluid interaction parameters are well chosen.

La drépanocytose est une maladie génétique qui se caractérise par des globules rouges en forme de faucille. Chez les personnes atteintes de drépanocytose, ces globules rouges (GR) adhèrent à l’endothélium vasculaire et provoquent ainsi une vaso-occlusion. Ce phénomène s’explique par la surexpression de la protéine Lutheran (Lu) à la surface des globules rouges falciformes qui se lie fortement à la Laminine (Ln) 511/521 exprimée par l’endothélium vasculaire enflammé. Le but de cette étude est d’identifier un inhibiteur d’interaction protéine-protéine (PPI) qui possède une forte probabilité de liaison à Lu afin d’inhiber l’interaction Lu-Ln 511/521. Un criblage virtuel de 1 295 678 composés ciblant la protéine Lu a été réalisé. La validation préalable d’un protocole de scoring a été envisagée sur la protéine CD80 qui présente un site de liaison avec des caractéristiquestopologiques et physico-chimiques similaires au site de liaison prédit sur Lu ainsi que plusieurs ligands avec des constantes d’affinité connues. Ce protocole contient différentes étapes de sélection basées sur les affinités calculées (scores), des simulations de dynamique moléculaire et les propriétés moléculaires. Un protocole de scoring fiable a été validé sur CD80 avec le programme de docking DOCK6 et les fonctions de scoring XSCORE et MM-PBSA ainsi qu’avec la méthode decalcul FMO. L’application de ce protocole sur Lu a permis d’obtenir deux ligands validés par des tests in vitro qui font l’objet d’un dépôt de brevet. La fonction de scoring XSCORE a permis d’identifier neuf autres ligands qui semblent aussi être des candidats prometteurs pour inhiber l’interaction Lu-Ln 511/521
Drepanocytosis is a genetic blood disorder characterized by red blood cells that assume an abnormal sickle shape. In the pathogenesis of vaso-occlusive crises of sickle cell disease, red blood cells bind to the vascular endothelium and promote vaso-occlusion. At the surface of these sickle red blood cells, the overexpressed protein Lutheran (Lu) strongly interacts with the Laminin (Ln) 511/521.The aim of this study was to identify a protein-protein interaction (PPI) inhibitor with a highprobability of binding to Lu for the inhibition of the Lu-Ln 511/521 interaction. A virtual screening was performed with 1 295 678 compounds that target Lu. Prior validation of a robust scoring protocol was considered on the protein CD80 because this protein has a binding site with similar topological and physico-chemical characteristics and it also has a series of ligands with known affinity constants. This protocol consisted of multiple filtering steps based on calculated affinities (scores), molecular dynamics simulations and molecular properties. A robust scoring protocol was validated on the protein CD80 with the docking program DOCK6 and the scoring functions XSCORE and MM-PBSA and also with the FMO method. This protocol was applied to the protein Lu and we found two compounds that were validated by in vitro studies. The protection of these ligands by a patent is under process. Nine other compounds were identified by the scoring functionXSCORE and seem to be promising candidates for inhibiting the Lu-Ln 511/521 interaction

Elemental analysis of substances made of heavy elements and detection of light elements in heavy matrices are difficult by means of photon transmission techniques. Neutrons have been used in this work, taking unique advantage of their absorption and scattering properties, to detect the structure of industrial and biological objects made of strongly-neutron scattering or absorbing materials, or to study objects combining of high and low neutron cross section materials. The most convenient matrices and impurities amenable to neutron inspection were searched by obtaining expressions for minimum detectable mass and length fraction of elements in an object. Formulae to calculate the minimum required number of neutrons to detect an impurity in a matrix have also been developed. The optimum sample thickness to be investigated with a minimum number of neutrons is likewise derived. Calculations have been carried out for the minimum detectable mass fraction of hydrogen in a number of sample matrices of industrial interest and of elements in a water matrix highlighting the differences with photon attenuation measurements. Results are presented for three neutron energies cold (0.001 eV), thermal (0.025 eV), and fast (14 MeV); concentrations in the parts per million range are demonstrated. Fast neutrons were used because of their high penetration ability, in order to study bulk industrial and biological samples and for their adequacy in detection of light elements such as H, C, N and O in large objects. An attempt to simulate fast neutron transmission tomographs of biological samples was made using the MORSE-CGA Monte-Carlo code. The code was used to calculate transmission of multienergetic U-235 fast fission neutron source in a complex geometry for industrial and biological applications. A fast neutron collimator for radiography, a collimator for brain tomography and a tomography chamber were simulated to design a technique to estimate the effect of scattered neutrons in practical tomography. The macroscopic cross section and mean free path of neutrons for the media of the heterogeneous matrices were also obtained by using microscopic cross sections of elements from the DLC-100G package. Using a multienergetic source provided an opportunity to determine the optimum neutron energy for examination of objects. The analysis required establishing a technique to calculate the fraction of neutrons in each energy group for the 100 group structure of the DLC-100G package. Finally the simulated neutron tomographic images were reconstructed by using the neutron transmission data for different angles of the object, and reconstructing them by the filtered back projection technique. In non-destructive evaluation of medical organs by fast neutron simulation tomography the simulated tomography of prototype biological objects were able to distinguish brain in skull, bone-marrow in bone and bone in soft tissue with good contrast up to 0.42. These results are valuable to identify developing cystic lesions and daughter cyst within the marrow vascular spaces, solid bony tumors, aberrant masses in the facial bone, tumor in spine or other bone marrow abnormalities. In studying component characterisation of industrial objects non-destructively by fast neutron tomography a 3mm diameter duct containing engine-oil was detected at 40 cm depth inside an aluminium combustion engine with a remarkable contrast of 0.35. The minimum detectable mass of oil in aluminium for an optimum neutron energy was 0.1mg/g with a similar result for iron.

El objetivo de esta tesis se centra en el estudio de la transferencia de electrones (ET), una de las reacciones más simples y cruciales en bioquímica. Para dichos procesos, obtener información directa de los factores que lo promueves, asi como del camino de transferencia electronica, no es una tarea trivial. Dicha información a un nivel de conocimiento detallado atómico y electrónico, sin embargo, es muy valiosa en términos de una mejor comprensión del ciclo enzimático, que podría conducir, por ejemplo, a un diseño más eficaz de inhibidores. El objetivo principal de esta tesis es el desarrollo de una metodología para el estudio cuantitativo de la ET en los sistemas biológicos. En este sentido, hemos desarrollado un nuevo método para obtener el camino de transferencia electrónico, llamado QM/MM e-­‐ Pathway, que se puede aplicar en sistemas complejos con ET de largo alcance. El método se basa en una búsqueda sucesiva de residuos importantes para la ET, utilizando la modificación de la región quantica en métodos mixtos QM/MM, y siguiendo la evolución de la densidad de espín dentro de la zona de transferencia. Hemos demostrado la utilidad y la aplicabilidad del algoritmo en el complejo P450cam/Pdx, identificando el papel clave de la Arg112 (en P450cam) y del Asp48 (en Pdx), ambos conocidos en la literatura. Además de obtener caminos de ET, hemos cuantificado su importancia en términos del acoplamiento electrónico entre el dador y aceptor para los diferentes caminos. En este sentido, se realizaron dos estudios de la influencia del solvente y de la temperatura en el acoplamiento electrónico para sistemas modelo oligopéptidos. Ambos estudios revelaron que los valores del acoplamiento electrónico fluctúan fuertemente a lo largo de las trayectorias de dinámica molecular obtenidas, y el mecanismo de transferencia de electrones se ve ampliamente afectado por el espacio conformacional del sistema. La combinación del QM/MM e-­‐pathway y de los cálculos de acoplamiento electronico fueron utilizados finalmente para investigar la ET en el complejo CCP/Cytc. Nuestros hallazgos indican el papel fundamental del Trp191 en localizar un estadio intermedio para la transferencia electronica, así como el camino ET principal que incluye Ala194, Ala193, Gly192 y Trp191. Ambos hallazgos fueron confirmados a través de la literatura. Los resultados obtenidos para el muestro de manios de ET, junto con su evaluación a través de cálculos de acoplamiento electrónico, sugieren un enfoque sencillo y prometedor para investigar ET de largo alcance en proteínas.
The focus of this PhD thesis lies on electron transfer (ET) processes, belonging to the simplest but most crucial reactions in biochemistry. Getting direct information of the forces driving the process and the actual electron pathway is not a trivial task. Such atomic and electronic detailed information, however, is very valuable in terms of a better understanding of the enzymatic cycle, which might lead, for example, to more efficient protein inhibitor design. The main objective of this thesis was the development of a methodology for the quantitative study of ET in biological systems. In this regard, we developed a novel approach to map long-­‐range electron transfer pathways, called QM/MM e-­‐Pathway. The method is based on a successive search for important ET residues in terms of modifying the QM region following the evolution of the spin density of the electron (hole) within a given transfer region. We proved the usefulness and applicability of the algorithm on the P450cam/Pdx complex, indicating the key role of Arg112 of P450cam and Asp48 of Pdx for its ET pathway, both being known to be important from the literature. Besides only identifying the ET pathways, we further quantified their importance in terms of electronic coupling of donor and acceptor incorporating the particular pathway residues. Within this regard, we performed two systematic evaluations of the underlying reasons for the influence of solvent and temperature onto electronic coupling in oligopeptide model systems. Both studies revealed that electronic coupling values strongly fluctuate throughout the molecular dynamics trajectories obtained, and the mechanism of electron transfer is affected by the conformational space the system is able to occupy. Combining both ET mapping and electronic coupling calculations, we finally investigated the electron transfer in the CcP/Cytc complex. Our findings indicate the key role of Trp191 being the bridge-­‐localized state of the ET as well as the main pathway consisting of Ala194, Ala193, Gly192 and Trp191 between CcP and Cytc. Both findings were confirmed through the literature. Moreover, our calculations on several snapshots state a nongated ET mechanism in this protein complex. The methodology developed along this thesis, mapping ET pathways together with their evaluation through electronic coupling calculations, suggests a straightforward and promising approach to investigate long-­‐range ET in proteins.

Molecular Dynamics (MD) simulation is a versatile methodology that has found many applications in materials science, chemistry and biology. In biology, the models employed range from mixed quantum mechanical and fully atomistic to united atom and continuum mechanical. These systems are evolved in discrete time by solving Newton’s equations of motion at each time step. The numerical methods currently in use limit the step size of a typical all atom simulation to 1 femtosecond. This step size limitation means that many steps need to be taken in order to reach biologically relevant time scales. At each time step, an evaluation of the forces on each atom must be performed resulting in heavy computational loads. This work investigates the use of implicit integration methods in MD. Implicit integration methods have been proven superior to their explicit counterparts in classical mechanical simulation, with which MD has many similarities. Longer time steps reduce the number of force evaluations that must be performed and the corresponding computational load. Herein we present results that compare implicit integration techniques with the current standard for molecular dynamics, the explicit velocity Verlet integration scheme. Total energy conservation is used as a metric for evaluating the dependability of simulations in the microcanonical ensemble. In order to understand the nature of the problem, several long simulations were run and analyzed by performing a Fourier analysis on the position, velocity and acceleration signals. Lastly, several methods for improving the viability of implicit integration methods are considered including replacing the Jacobian used in the Quasi-Newton method with a constant, diagonal mass matrix, evaluating the Jacobian infrequently and finding a better prediction of the system configuration to improve the convergence of the Quasi-Newton method.

An Ultrasonic Powder Consolidation is an additive manufacturing technique that utilizes high-frequency vibrations to consolidate micro/nano powder materials to fully dense and near to net-shaped parts. Unlike traditional powder consolidation techniques such as sintering, shock wave-based and pressure-based processes, the consolidation during Ultrasonic Powder Consolidation process happens at relatively low temperatures and pressures within few seconds or less. Ultrasonic Powder Consolidation process presents several inherent advantages including low power consumption, low cost and zero thermal stresses on the consolidated parts. Experimental studies have shown that Ultrasonic Powder Consolidation process is capable of successfully consolidating powders of metals and metal-matrix composites. While Ultrasonic Powder Consolidation process promises several potential applications, the mechanism of bond formation between the consolidated metal powders is not completely understood. This research uses Molecular Dynamics simulation technique to investigate the underlying bond formation and consolidation mechanisms involved in Ultrasonic Powder Consolidation process. The research also explores the effects of critical process parameters including vibration frequency, amplitude and initial temperature on the quality of the consolidated part. The study found that high-frequency vibrations cause high interfacial stresses resulting in acoustic softening and high plastic deformation of the nanoparticles. The study revealed that the overall atomistic temperature does not exceed the melting point of the material. The study also found that the vibration amplitude and frequency played a significant role in the consolidation process. Finally, the simulation study showed that the high-frequency vibration leads to large plastic deformations at ultra-high shear strain rates causing the interfacial atoms to interlock with each other resulting in high densification and consolidation. The results of this study would augment the ongoing experimental studies on Ultrasonic Powder Consolidation process which would help realize the promised potentials of this low temperature – low-pressure consolidation technique.

Our group uses di-alkyl carbocyanine dyes to detect force-induced membrane perturbation in mechanotransduction studies (Butler et al 2000). These dyes are also used extensively in single molecule spectroscopic techniques to infer dynamics of native membrane lipids. However, the precise distribution and orientation of the dye in a bilayer and how well the dye dynamics mimic native lipid dynamics are not known. Thus we present the results of a 40 nanosecond molecular dynamics simulation of a fully hydrated bilayer containing 0, 2, or 4 molecules of 1,1′-dioctadecyl-3,3,3′,3′-tetramethylindocarbocyanine perchlorate (DiI-C18) and 128 molecules of dipalmitoylphosphatidyl choline (DPPC).

Molecular dynamics is the simulation method that is most amenable to the length and time scales of nanotribological experiments. The ability to track the individual motion of every atom in simulations has led to a detailed understanding of the underlying physics that is difficult to extract from experiment. While significant progress has been made in simulations over the past two decades, computational issues still limit the types of problems that can be approached, and the detailed understanding that results. Here we discuss recent advances in molecular dynamics simulations that push the bounds of simulation size, velocity, and chemistry. These state of the art simulation techniques have made great strides in allowing detailed comparisons to experimental results. These advances will be placed in context by addressing the barriers that remain and where future progress lies.

An effective simulation technique for describing the spreading properties of molecularly thin lubricant films on magnetic disks has been developed. We propose a molecular precipitation method that can simulate initial molecule arrangement of the films dip-coated onto the disks. Reptation and Rouse models as the model of the molecular motion, and molecular insertion and molecular precipitation methods as the method for putting molecules in initial positions were compared. From the results of the spreading profiles and diffusion coefficients, it has been revealed that the molecular precipitation method combined with the Rouse model is effective in simulating the spreading of the lubricant films.