Molecular computations for reactions and phase transitions: applications to protein stabilization, hydrates and catalysis

In this work we have made significant contributions in three different areas of interest: therapeutic protein stabilization, thermodynamics of natural gas clathrate-hydrates, and zeolite catalysis. In all three fields, using our various computational techniques, we have been able to elucidate phenomena that are difficult or impossible to explain experimentally. More specifically, in mixed solvent systems for proteins we developed a statistical-mechanical method to model the thermodynamic effects of additives in molecular-level detail. It was the first method demonstrated to have truly predictive (no adjustable parameters) capability for real protein systems. We also describe a novel mechanism that slows protein association reactions, called the “gap effect.” We developed a comprehensive picture of methioine oxidation by hydrogen peroxide that allows for accurate prediction of protein oxidation and provides a rationale for developing strategies to control oxidation. The method of solvent accessible area (SAA) was shown not to correlate well with oxidation rates. A new property, averaged two-shell water coordination number (2SWCN) was identified and shown to correlate well with oxidation rates. Reference parameters for the van der Waals Platteeuw model of clathrate-hydrates were found for structure I and structure II. These reference parameters are independent of the potential form (unlike the commonly used parameters) and have been validated by calculating phase behavior and structural transitions for mixed hydrate systems. These calculations are validated with experimental data for both structures and for systems that undergo transitions from one structure to another. This is the first method of calculating hydrate thermodynamics to demonstrate predictive capability for phase equilibria, structural changes, and occupancy in pure and mixed hydrate systems. We have computed a new mechanism for the methanol coupling reaction to form ethanol and water in the zeolite chabazite. The mechanism at 400°C proceeds via stable intermediates of water, methane, and protonated formaldehyde.

Combatant recruitment and the outcome of war

Why do some civil wars terminate soon, with victory of one party over the other? What determines if the winner is the incumbent or the rebel group? Why do other conáicts last longer? We propose a simple model in which the power of each armed group depends on the number of combatants it is able to recruit. This is in turn a function of the relative ëdistanceíbetween group leaderships and potential recruits. We emphasize the moral hazard problem of recruitment: Öghting is costly and risky so combatants have the incentive to defect from their task. They can also desert altogether and join the enemy. This incentive is stronger the farther away the Öghter is from the principal, since monitoring becomes increasingly costly. Bigger armies have more power but less monitoring capacity to prevent defection and desertion. This general framework allows a variety of interpretations of what type of proximity matters for building strong cohesive armies ranging from ethnic distance to geographic dispersion. Di§erent assumptions about the distribution of potential Öghters along the relevant dimension of conáict lead to di§erent equilibria. We characterize these, discuss the implied outcome in terms of who wins the war, and illustrate with historical and contemporaneous case studies.

Informality in the City: a Theoretical Analysis

This thesis theoretically studies the relationship between the informal sector (both in the labor and the housing market) and the city structure.

Educación de la sexualidad, prácticas docentes y conocimientos de los estudiantes: una evaluación del Programa de Educación para la Sexualidad y Construcción de Ciudadanía (PESCC)

Este documento presenta los resultados del componente cuantitativo de la evaluación del Programa de Educación para la Sexualidad y Construcción de Ciudadanía (PESCC) del Ministerio de Educación Nacional de Colombia (MEN). Para identificar el efecto, la estrategia empírica explota la variación en la implementación del componente pedagógico del PESCC entre los colegios y la variación en el componente de fortalecimiento institucional del programa a nivel departamental. El principal hallazgo de este trabajo es que el PESCC mejora las prácticas docentes de planeación y los conocimientos de los estudiantes en servicios en salud sexual y reproductiva y en derechos humanos sexuales y reproductivos. No hay efectos significativos en otros índices de Conocimientos, Actitudes o Prácticas (CAP) de profesores o estudiantes.

Adsorció d'or i zinc amb resines impregnades XAD-2. Superfície d'Equilibri, un nou concepte per a l'adsorció

Dins dels processos de recuperació de metalls de dissolucions diluïdes s'ha realitzat un estudi del procés d'extracció d'or i de zinc mitjançant resines amberlite XAD-2 impregnades amb sulfur de triisobutil fosfina (TIBPS) i àcid di-(2-etilhexil) fosfòric (DEHPA) respectivament. S'ha realitzat un estudi de l'equilibri de l'adsorció d'espècies metàl·liques d'aquests metalls amb les resines indicades anteriorment. Amb la metodologia emprada per a la determinació dels punts d'equilibri dels experiments en batch i en columna, s'ha vist que una única isoterma no podia descriure el fenomen global d'equilibri i que en funció de la metodologia emprada s'obtenien isotermes diferents. Es va introduir una nova variable per poder explicar el fenomen observat, i per tant, amb aquesta nova variable l'equació de la isoterma es converteix amb l'equació d'una supèrfície que s'ha definit com a Superfície d'Equilibri. S'han determinat les equacions de les Suprfícies d'Equilibri dels sistemes d'adsorció estudiats (Au(III) TIBPS/XAD-2 i Zn(II) DEHPA/XAD-2) observan una bona coincidència de tots els punts d'equilibri obtinguts sobre la superfície, així com, un bon ajust de totes les isotermes obtingudes en funció de les diferents metodologies emprades sobre les respectives superfícies d'equilibri. Aquest nou concepte generalitza el concepte d'isoterma d'un procés d'adsorció. Fimalment, s'ha plantejat un model matemàtic d'adsorció per a determinar el coeficient efectiu de difusió (De) i el coeficient de transferància de matèria (kf) per ambdós sistemes d'adsorció estudiats mitjançant l'aplicació del model de difusió de sòlid homogeni (HSDM), utilitzant com a condició de contorn en el model la isoterma de Langmuir obtinguda mitjançant els experiments en columna de llit fix i emprant també l'equació obtinguda mitjançant el nou concepte de Superfície d'Equilibri. Els resultats obtinguts són molt satisfactoris, per tant, es pot concloure que la Superfície d'Equilibri és una bona eina per a descriure l'equilibri en els processos d'adsorció d'or i zinc amb les resines amberlite XAD-2 impregnades amb TIBPS i DEHPA respectivament.

New mono- and dinuclear ruthenium complexes containing the 3,5-bis(2-pyridyl)pyrazole ligand. Synthesis, characterization and applications

Se han sintetizado dos nuevos complejos mononucleares de Ru, con formula [RuCl2(Hbpp)(dmso)2], a partir de la reacción entre [RuCl2(dmso)4] y Hbpp (3,5-bis(2-piridil)pirazola). El hecho que sólo tres de los seis posibles estereoisómeros se obtengan a partir de esta reacción, se ha racionalizado en base a factores estructurales y electrónicos. Estos complejos se han caracterizado de forma estructural, espectroscópica y electroquímica. En acetonitrilo en medio básico, el isómero trans,cis-[RuCl2(Hbpp)(dmso)2] da lugar a procesos de isomerización de enlace de un ligando dmso cuando el Ru(II) se oxida a Ru(III). Las constantes termodinámicas y cinéticas para el proceso se han determinado por voltametria cíclica. La irradiación de trans,cis-[RuCl2(Hbpp)(dmso)2] y cis(out),cis-[RuCl2(Hbpp)(dmso)2] con luz UV o solar da lugar a reacciones de fotosustitución de un ligando dmso por una molécula de acetonitrilo para dar un nuevo compuesto el cual ha sido caracterizado en solución por técnicas espectroscópicas y electroquímicas. Ambos complejos resultan catalizadores útiles en la transferencia de hidrógeno de isopropanol a acetofenona, obteniéndose 1-feniletanol como único producto y un 42.1% de conversión (36.1 ciclos metálicos) a 80ºC con el isómero trans,cis-[RuCl2(Hbpp)(dmso)2], que resulta significativamente más eficaz que el complejo cis(out),cis-[RuCl2(Hbpp)(dmso)2]. La reacción de cis(out),cis-[RuCl2(Hbpp)(dmso)2] con trpy (2,2':6',2"-terpiridina) da lugar a los dos isómeros geométricos del complejo [Ru(Hbpp)(trpy)(Cl)]+, el in y el out. Estos complejos se han aislado y caracterizado por técnicas estructurales, espectroscópicas y electroquímicas. Estos cloro complejos han sido utilizados como precursores para la síntesis de los complejos análogos con ligandos aqua (in,out-[Ru(Hbpp)(trpy)(H2O)]2+) y piridina (in,out-[Ru(Hbpp)(trpy)(py)]2+), los cuales también han sido aislados y caracterizados. Las propiedades ácido-base de los aqua complejos, y del complejo out-py se han estudiado detalladamente por voltametria cíclica y mediante valoraciones espectrofotométricas ácido-base. El tratamiento matemático de los datos así obtenidos nos ha permitido determinar los valores de pKa para los distintos equilibrios de protonación de los complejos en los estados de oxidación II y III. El complejo out-aqua ha demostrado ser un buen catalizador para la oxidación electroquímica del alcohol benzílico, presumiblemente a benzaldehido. La constante de velocidad de segundo orden para el proceso ha sido determinada como 17.1 M-1 s-1, por simulación matemática. El dímero con un puente cloro, [Ru2Cl(bpp)(trpy)2]2+ ha sido preparado por dos rutas sintéticas diferentes. El dímero análogo con un puente acetato se ha obtenido por reacción del cloro dímero con un exceso de acetato sódico. El dímero con dos ligandos aqua [Ru2(bpp)(trpy)2(OH2)2]3+ puede obtenerse por hidrólisis ácida del complejo con un acetato puente o por hidrólisis básica del complejo con un puente cloro. Estos complejos han sido caracterizados por técnicas estructurales, espectroscópicas y electroquímicas. Las soluciones del dímero con dos ligandos aqua en medio ácido resultan inestables a la coordinación de aniones de la solución con el tiempo. Las propiedades ácido-base del dímero con dos aguas coordinadas han sido estudiadas por voltametria cíclica y mediante experimentos de electrólisis a potencial controlado. El pKa para la desprotonación de uno de los ligandos aqua ha sido determinado mediante una valoración espectrofotométrica ácido-base como 6.7. Este valor tan bajo de pKa se atribuye a la formación de la entidad {Ru2O2H3}, favorable termodinámicamente. Los espectros UV-vis para los distintos estados de oxidación del aqua dímero, de RuIIRuII a RuIIIRuIV, han sido obtenidos por oxidación química y electroquímica del complejo. Se han llevado a cabo estudios cinéticos de la oxidación, paso a paso, de RuII,II a RuIV,IV , y se han determinado las constantes de oxidación de segundo orden para los distintos procesos de oxidación. La capacidad del aqua dímero en la oxidación del agua a oxígeno molecular ha sido investigada en solución homogénea utilizando CeIV como oxidante. La evolución de oxígeno se ha demostrado por cromatografia de gases. Se ha obtenido una eficiencia del 73% y 18.6 ciclos catalíticos, cuando 1.83 x 10-6 moles de dímero se han mezclado con un exceso de 100 equivalentes de cerio. El dímero con dos aguas cataliza también la oxidación del agua de forma heterogénea, con el complejo adsorbido sobre una membrana de nafion, aunque la eficiencia es menor. Se ha propuesto un mecanismo intramolecular para la reacción de oxidación del agua. Consiste en la oxidación a 4 electrones del dímero, de RuII,II a RuIV,IV, el cual reacciona con el agua para formar oxígeno y revierte nuevamente al estado de oxidación II,II. Este modelo es consistente con estudios catalíticos de la evolución de oxígeno en función de las concentraciones de cerio y catalizador, llevados a cabo en solución ácida homogénea, que demuestran que la oxidación a 4 electrones del agua se encuentra catalizada por una sola molécula de complejo bajo concentraciones elevadas de cerio. La constante de pseudo-primer-orden para la evolución de oxígeno tiene un valor de 1.4 x 10-2 s-1, que es uno de los valores de constante más elevados obtenidos hasta la fecha. Desafortunadamente, el aqua dímero se desactiva durante el proceso de catálisis dando lugar a una especie naranja, la cual estamos actualmente tratando de caracterizar.

Self-Fulfilling Crises in the Eurozone: An Empirical Test. CEPS Working Document No. 366, 22 June 2012

This paper tests the hypothesis that government bond markets in the eurozone are more fragile and more susceptible to self-fulfilling liquidity crises than in stand-alone countries. We find evidence that a significant part of the surge in the spreads of the PIGS countries (Portugal, Ireland, Greece and Spain) in the eurozone during 2010-11 was disconnected from underlying increases in the debt-to-GDP ratios and fiscal space variables, and was the result of negative self-fulfilling market sentiments that became very strong since the end of 2010. We argue that this can drive member countries of the eurozone into bad equilibria. We also find evidence that after years of neglecting high government debt, investors became increasingly worried about this in the eurozone, and reacted by raising the spreads. No such worries developed in stand-alone countries despite the fact that debt-to-GDP ratios and fiscal space variables were equally high and increasing in these countries.

Sudden stratospheric warmings as noise-induced transitions

Sudden stratospheric warmings (SSWs) are usually considered to be initiated by planetary wave activity. Here it is asked whether small-scale variability (e.g., related to gravity waves) can lead to SSWs given a certain amount of planetary wave activity that is by itself not sufficient to cause a SSW. A highly vertically truncated version of the Holton–Mass model of stratospheric wave–mean flow interaction, recently proposed by Ruzmaikin et al., is extended to include stochastic forcing. In the deterministic setting, this low-order model exhibits multiple stable equilibria corresponding to the undisturbed vortex and SSW state, respectively. Momentum forcing due to quasi-random gravity wave activity is introduced as an additive noise term in the zonal momentum equation. Two distinct approaches are pursued to study the stochastic system. First, the system, initialized at the undisturbed state, is numerically integrated many times to derive statistics of first passage times of the system undergoing a transition to the SSW state. Second, the Fokker–Planck equation corresponding to the stochastic system is solved numerically to derive the stationary probability density function of the system. Both approaches show that even small to moderate strengths of the stochastic gravity wave forcing can be sufficient to cause a SSW for cases for which the deterministic system would not have predicted a SSW.

Analysis and application of ichnofabrics

Bioturbation at all scales, which tends to replace the primary fabric of a sediment by the ichnofabric (the overall fabric of a sediment that has been bioturbated), is now recognised as playing a major role in facies interpretation. The manner in which the substrate may be colonized, and the physical, chemical and ecological controls (grainsize, sedimentation rate, oxygenation, nutrition, salinity, ethology, community structure and succession), together with the several ways in which the substrate is tiered by bioturbators, are the factors and processes that determine the nature of the ichnofabric. Eleven main styles of substrate tiering are described, ranging from single, pioneer colonization to complex tiering under equilibria, their modification under environmental deterioration and amelioration, and diagenetic enhancement or obscuration. Ichnofabrics may be assessed by four attributes: primary sedimentary factors, Bioturbation Index (BI), burrow size and frequency, and ichnological diversity. Construction of tier and ichnofabric constituent diagrams aid visualization and comparison. The breaks or changes in colonization and style of tiering at key stratal surfaces accentuate the surfaces, and many reflect a major environmental shift of the trace-forming biota. due to change in hydrodynamic regime (leading to non-deposition and/or erosion and/or lithification), change in salinity regime, or subaerial exposure. The succession of gradational or abrupt changes in ichnofabric through genetically related successions, together with changes in colonization and tiering across event beds, may also be interpreted in terms of changes in environmental parameters. It is not the ichnotaxa per se that are important in discriminating between ichnofabrics, but rather the environmental conditions that determine the overall style of colonization. Fabrics composed of different ichnotaxa (and different taphonomies) but similar tier structure and ichnoguild may form in similar environments of different age or different latitude. Appreciation of colonization and tiering styles places ancient ichnofabrics on a sound processrelated basis for environmental interpretation. (C) 2002 Elsevier Science B.V. All rights reserved.

Managing invasive alien species with professional and hobby farmers: insights from ecological-economic modelling

Biosecurity is a great challenge to policy-makers globally. Biosecurity policies aim to either prevent invasions before they occur or to eradicate and/or effectively manage the invasive species and diseases once an invasion has occurred. Such policies have traditionally been directed towards professional producers in natural resource based sectors, including agriculture. Given the wide scope of issues threatened by invasive species and diseases, it is important to account for several types of stakeholders that are involved. We investigate the problem of an invasive insect pest feeding on an agricultural crop with heterogeneous producers: profit-oriented professional farmers and utility-oriented hobby farmers. We start from an ecological-economic model conceptually similar to the one developed by Eiswerth and Johnson [Eiswerth, M.E. and Johnson, W.S., 2002. Managing nonindigenous invasive species: insights from dynamic analysis. Environmental and Resource Economics 23, 319-342.] and extend it in three ways. First, we make explicit the relationship between the invaded state carrying capacity and farmers' planting decisions. Second, we add another producer type into the framework and hence account for the existence of both professional and hobby fanners. Third, we provide a theoretical contribution by discussing two alternative types of equilibria. We also apply the model to an empirical case to extract a number of stylised facts and in particular to assess: a) under which circumstances the invasion is likely to be not controllable; and b) how extending control policies to hobby farmers could affect both types of producers. (C) 2008 Elsevier B.V. All rights reserved.

Structural and equilibrium studies on mixed ligand complexes of Co(II), Ni(II), Cu(II) and Zn(II) with N-(2-benzimidazolyl)methyliminodiacetic acid and typical N,N donor ligands

Mixed ligand complexes: [Co(L)(bipy)] (.) 3H(2)O (1), [Ni(L)(phen)] (.) H2O (2), [Cu(L)(phen)] (.) 3H(2)O (3) and [Zn(L)(bipy)] (.) 3H(2)O (4), where L2- = two -COOH deprotonated dianion of N-(2-benzimidazolyl)methyliminodiacetic acid (H(2)bzimida, hereafter, H,L), bipy = 2,2' bipyridine and phen = 1,10-phenanthroline have been isolated and characterized by elemental analysis, spectral and magnetic measurements and thermal studies. Single crystal X-ray diffraction studies show octahedral geometry for 1, 2 and 4 and square pyramidal geometry for 3. Equilibrium studies in aqueous solution (ionic strength I = 10(-1) mol dm(-3) (NaNO3), at 25 +/- 1 degrees C) using different molar proportions of M(II):H2L:B, where M = Co, Ni, Cu and Zn and B = phen, bipy and en (ethylene diamine), however, provides evidence of formation of mononuclear and binuclear binary and mixed ligand complexes: M(L), M(H-1L)(-), M(B)(2+), M(L)(B), M(H-1L)(B)(-), M-2(H-1L)(OH), (B)M(H-1L)M(B)(+), where H-1L3- represents two -COOH and the benzimidazole NI-H deprotonated quadridentate (O-, N, O-, N), or, quinquedentate (O-, N, O-, N, N-) function of the coordinated ligand H,L. Binuclear mixed ligand complex formation equilibria: M(L)(B) + M(B)(2+) = (B)M(H-1L)M(B)(+) + H+ is favoured with higher pi-acidity of the B ligands. For Co(II), Ni(II) and Cu(II), these equilibria are accompanied by blue shift of the electronic absorption maxima of M(II) ions, as a negatively charged bridging benzimidazolate moiety provides stronger ligand field than a neutral one. Solution stability of the mixed ligand complexes are in the expected order: Co(II) < Ni(II) < Cu(II) > Zn(II). The Delta logK(M) values are less negetive than their statistical values, indicating favoured formation of the mixed ligand complexes over the binary ones. (c) 2005 Elsevier B.V. All rights reserved.

Recent work on entropically-driven ring-opening polymerizations: some potential applications

The entropically-driven ring-opening polymerization of macrocyclic monomers (> ca. 14 ring atoms per repeat unit) and/or macrocyclic oligomers is a relatively new method of polymer synthesis that exploits the well-known phenomenon of ring-chain equilibria. It attracts interest because of its novel features. For example, these ring-opening polymerizations emit no volatiles and little or no heat. This review considers the principles of entropically-driven ring-opening polymerizations, gives selected examples and discusses potential applications. The latter include micromolding, high throughput syntheses and the synthesis of supramolecular polymers. Copyright (c) 2005 John Wiley T Sons, Ltd.

Competing edge networks

We introduce a model for a pair of nonlinear evolving networks, defined over a common set of vertices, sub ject to edgewise competition. Each network may grow new edges spontaneously or through triad closure. Both networks inhibit the other’s growth and encourage the other’s demise. These nonlinear stochastic competition equations yield to a mean field analysis resulting in a nonlinear deterministic system. There may be multiple equilibria; and bifurcations of different types are shown to occur within a reduced parameter space. This situation models competitive peer-to-peer communication networks such as BlackBerry Messenger displacing SMS; or instant messaging displacing emails.

Inequality, intergenerational mobility and redistributive policies under endogenous information

This paper presents a dynamic model to study how different levels of information about the root determinants of wealth (luck versus effort) can impact inequality and intergenerational mobility through societal beliefs, individual choices and redistributive policies. To my knowledge, the model presented is the first dynamicmodel in which skills are stochastic and both beliefs and voted redistribution are determined endogenously. The model is able to explain a number of empirical facts. Large empirical evidence shows that the difference in the political support for redistribution appears to reflect differences in the social perceptions regarding the determinants of individual wealth and the underlying sources of income inequality. Moreover the beliefs about the determinants of wealth impact individual choices of effort and therefore the beliefs about the determinants of wealth impact inequality and mobility both through choices of effort and redistributive policies. The model generates multiple equilibria (US versus Europe-type) which may account for the observed features not only in terms of societal beliefs and redistribution but also in terms of perceived versus real mobility and inequality.

Evaluating the alternatives

In this article, I study the impacts of a specific incentives-based approach to safety regulation, namely the control of quality through sampling and threatening penalties when quality fails to meet some minimum standard. The welfare-improving impacts of this type of scheme seem high and are cogently illustrated in a recent contribution by Segerson, which stimulated many of the ideas in this paper. For this reason, the reader is referred to Segerson for a background on some of the motivation, and throughout, I make an effort to indicate differences between the two approaches. There are three major differences. First, I dispense with the calculus as much as possible, seeking readily interpreted, closedform solutions to illustrate the main ideas. Second, (strategically optimal, symmetric) Nash equilibria are the mainstay of each of the current models. Third, in the uncertainquality- provision equilibria, each of the Nash suppliers chooses the level of the lower bound for quality as a control and offers a draw from its (private) distribution in a contribution to the (public) pool of quality.