McKee Minute September 2014

The September 2014 McKee Minute features several books on kitchen inspiration such as The Smitten Kitchen Cookbook by Deb Perelman, resources for money management, and a spotlight on social work

Calculations of isobaric phase enthalpy differences for binary systems from vapor-liquid equilibrium data

Equations relating isobaric vapor-liquid equilibrium data to heats of vaporization are useful in testing the thermodynamic consistency of experimental VLE data and in the design of distillation equipment. Several researchers have proposed such equations based on the Gibbs-Duhem equation. At low pressures, simplified versions of these equations were successfully used to test the consistency of published VLE and enthalpy data. At high pressures, equilibrium phase enthalpy differences were calculated from rigorous equations using a modified form of the Redlich-Kwong equation to calculate fugacity coefficients. As expected, the relative error of using the simplified equations was found to increase with increasing pressure

An experimental study of condenser scoops

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Naval Architecture and Marine Engineering, 1938.MIT copy bound with: Main power plant for a destroyer leader / Antonio Marin, Manuel E. Giménez Figueroa -- Powering of ships / John S. Haponik -- Head loss in gate and angle stop valves / L. W. Schutz, A. M. Main, Jr. -- Castellated stiffeners for bulkheads / John C. Proctor and Harlan Turner, Jr.Includes bibliographical references (leaf 29).by Lyndon Crawford, Virgil G. Hall.B.S

Discovering Jewish Studies Collections in Academic Libraries: A Practical Guide

The U.S. colleges and universities offering non-sectarian educational programs in Jewish Studies rely on the support of their academic libraries for research materials and library services. For college libraries which use Library of Congress Classification scheme, it is a common practice to integrate studies resources into their general library collections. Since Jewish Studies sources span a vast number of subjects within all major disciplines, shelving integration leads to the dispersion of all relevant sources and such dispersion in turn leads to a variety of problems for library professionals and library users. For collection development librarians the problems range from lack of information about collection\u27s size, strengths or weaknesses, and for library users interested in browsing the collection, dispersion of subjects creates a major roadblock. This practical guide aims at providing a solution to such problems. By identifying all relevant Library of Congress call numbers and the corresponding Library of Congress subject headings, the guide offers a simplified access to Jewish Studies sources in general library collections. It is arranged by four major discipline: Arts & Humanities, Social Sciences, Sciences, and General Works & Bibliographies. Within each discipline, specific LC call number ranges and corresponding subjects are listed. The subjects are further subdivided and precisely identified. The guide will assist collection development librarians, library liaisons, grants and fundraising professionals and especially the Jewish Studies faculty and students, in identifying and locating relevant sources

Kinase deoxyribozymes

Nature has developed the use of proteins and RNA as enzymes, while DNA is used for the storage and transfer of genetic information. Proteins and RNA are biopolymers that can fold into specific secondary and tertiary structures to enable catalysis. Considering the structural similarity to RNA, single-stranded DNA should also be able to form complex structures capable of catalyzing reactions. DNA catalysts have not been identified in nature, but in vitro selection has led to the identification of DNA catalysts for a variety of chemical reactions. Identification of new catalysts favors the use of DNA for multiple reasons. Amplification of functional DNA sequences is directly possible using natural polymerases, whereas amplification of RNA requires an additional reverse transcription step and amplification of proteins is not possible. The total number of possible sequences is smaller for nucleic acids (4n, where n is the number of residues) than for proteins (20n). Within this sequence space a large number of random nucleic acid sequences will fold into secondary and tertiary structures unlike proteins which require specific amino acid sequences to form complex structures. Therefore, in vitro selection experiments to identify DNA catalysts will cover a large portion of sequence space, and a large fraction of the covered space will contain structured DNA sequences with the potential to be catalytically active. The ease of synthesis and stability of DNA compared to RNA or proteins also provides an advantage for its use as a catalyst. Natural post-translational modifications (PTMs) are important in biological systems. PTMs modulate protein activity resulting in rapid changes to cellular processes. Studying the role of specific PTMs is often limited to the ability to generate site-specific post-translationally modified proteins of interest. Phosphorylation of amino acid side chains is an abundant natural PTM that is essential for cellular function. Protein kinases, which catalyze phosphorylation, are often motif specific. Engineering these natural kinases to change motif requirements is challenging and often results in decreased substrate specificity. To identify new catalysts for the site-specific phosphorylation of a desired protein the use of DNA as a catalytic biomolecule is advantageous because an initially random population of DNA sequences does not have substrate biases, and DNA is a large biopolymer with the possibility to interact specifically with the substrates. Both ribozymes and deoxyribozymes have been identified to catalyze the phosphorylation of oligonucleotides. However, previous efforts to identify kinase deoxyribozymes to catalyze the phosphorylation of amino acid side chains were unsuccessful because the -thiophosphoryl donor used was not stable in the selection conditions. As described herein, a new in vitro selection method was developed using a previously identified deoxyribozyme to separate the active deoxyribozymes from the inactive DNA sequences. This method led to the identification of the first kinase deoxyribozymes capable of phosphorylating tyrosine residues within a tethered peptide substrate using a bound 5′-triphosphorylated RNA oligonucleotide as the phosphoryl donor. Separate selection experiments were performed using 1 mM GTP as the phosphoryl donor. The identified DNA catalysts are able to phosphorylate tyrosine within a peptide substrate and require only low micromolar concentrations of GTP. Site-specific modification of proteins is often desired. Most deoxyribozymes identified to modify peptide substrates have been identified using peptide substrates containing the reactive residue flanked by alanine residues. Peptide sequences derived from natural proteins contain a variety of amino acid residues with diverse functional groups that could be a point of interaction between the peptide substrate and DNA catalyst. Selection experiments were performed with biologically derived peptide sequences to identify tyrosine kinase deoxyribozymes with the ability to phosphorylate peptides sequence-specifically. Of the three peptide substrates evaluated the use of one led to deoxyribozymes that are peptide motif-specific, the second peptide led to deoxyribozymes with partial peptide sequence-selectivity, and the third did not lead to the identification of deoxyribozymes. The identification of peptide motif-specific deoxyribozymes demonstrates that DNA catalysts can interact specifically with peptide substrates, and individual DNA enzymes can interact with the same peptide substrate in a different manner. The ability to phosphorylate substrates that are free in solution is desired. However, previously identified kinase deoxyribozymes are unable to phosphorylate untethered peptide substrates. Original efforts increased the length of the tether between the peptide substrate and DNA anchor to mimic a peptide free in solution. These selection experiments did not lead to deoxyribozymes, and further analysis of other deoxyribozymes with untethered peptide reactivity suggests the long tethers may interfere with catalysis. Further efforts have focused on the incorporation of hydrophobic modifications into the DNA catalysts to improve peptide binding. DNA aptamers containing hydrophobic modifications have improved protein binding. Increased binding affinity between the peptide substrate and DNA catalyst may enable untethered peptide reactivity. While initial efforts focused on tyrosine phosphorylation, serine phosphorylation is also abundant in nature. Serine kinase deoxyribozymes have been identified to phosphorylate serine within tightly tethered peptide substrates using 5′-triphosphorylated RNA as the phosphoryl donor. Subsequent efforts to increase the tether length or use ATP as the phosphoryl donor were unsuccessful. Efforts to improve DNA catalysts with the ability to phosphorylate serine include using biologically derived peptide sequences to increase interactions between the deoxyribozyme and peptide substrate, and incorporating catalytically participatory modifications into the DNA enzymes

Fortegnelse over person- og godsvogner : normalt spor : gjelder fra 1ste juli 1950 (erstatter den tilsvarende fortegnelse av 1ste juli 1948)

Tjenesteskrifter utgitt av Norges statsbaner, Hovedstyret Trykk nr. 745

The Ethynyl Hydrogen Bond

The nature and properties of the hydrogen bond are discussed with special reference to the ethynyl hydrogen bond. Proof is given of the electron accepting capacity of the C-H group and of the electron donating capacity of the "pi" electron system of aromatic rings. The theory of the calorimetries spectroscopic and diffraction methods of studying the hydrogen bond are discussed in detail especially as it applies to the investigations discussed in this thesis. An investigation of the ethynyl hydrogen bond was conducted in which the chief acatylenic electron acceptor used was benzoyl acetylene. Instruments were constructed for a calorimetric study of the ethynyl hydrogen bond, the apparatus being checked for accuracy by determining the heat of solution of potassium chloride in water. Heats of mixing of benzoyl acetylene in a variety of solvents were obtained and from these the enthalpy of hydrogen bond formation between the benzoyl acetylene and the active solvents was obtained. An infrared investigation of benzoyl acetylene and phenyl acetylene in a wide variety of solvents was carried out, the frequency shifts, half band widths and maximum intensities of the bands being noted. This indicated the wide range of compounds capable of hydrogen bonding and also provided evidence of bonding to the "pi" electron system of aromatic compounds as distinct from bonding to particular electronegative atoms. A quantitative study of benzoyl acetylene in benzene, various methylated benzenes and in n-butyl ether was carried out allowing the determination of association constants and degrees of association. This was repeated at a variety of temperatures allowing the calculation of hydrogen bond strengths. Results obtained using the infrared technique were found to be subject to considerable error. A quantitative study of benazoyl acetylene in the same solvents as above was carried out using the nuclear magnetic resonance method. This provided a very accurate method of determining association constants and degrees of association. It was intended to carry out temperature studies using this technique but this was impossible due to non-delivery of equipment. This method was also applied to the study of 1:4 dichlorobut-2-yne and propargyl chloride in benzene-cyclohexane mixtures and indicated the probable existence of hydrogen bonds between the methylene protons of these molecules and the "pi" electrons of benzene. An X-ray diffraction investigation of the ethynyl hydrogen bond was carried out with Dr. G. Ferguson. For this purpose ortho-bromobesasoylacetylene was prepared and photographed. A two-dimensional Fourier map of the molecule is shown and the first accurate measurement of a known C=H...O hydrogen bond is given

Energy characterization and comfort conditions in Rafael De La Hoz’s social housing in Córdoba. Scenarios for improvement

La reducción del impacto global del proceso edificatorio en el entorno medioambiental y la búsqueda de una mayor eficiencia energética han promovido la investigación en medidas que limiten el consumo energético, así como la adopción de soluciones técnicas adecuadas para el desarrollo sostenible y la mejora de la habitabilidad en los edificios. En España, el 61 % del parque residencial existente presenta deficiencias respecto a los estándares energéticos actuales, al haberse construido anteriormente a la primera normativa en materia de acondicionamiento térmico de los edificios, la Norma Básica de la Edificación "Condiciones Térmicas en los Edificios", NBE CT 79. Así pues, se considera una línea prioritaria actuar para mejorar energética y ambientalmente este importante parque residencial. La presente tesis doctoral tiene como voluntad establecer un protocolo de análisis del parque residencial existente, respondiendo a los tres objetivos generales planteados, con objeto de incrementar la información disponible acerca del estado actual de estos edificios como paso previo a acometer cualquier actuación de mejora en ellos, valorando el nivel de bienestar térmico en el interior de viviendas situadas en clima mediterráneo a partir de modelos empíricos de enfoque adaptativo, con objeto de cuantificar la mejora que estos edificios podrían obtener si se aplicaran estrategias pasivas estándar de rehabilitación energética que mermaran la falta de confort térmico, así como la demanda de energía primaria y las emisiones de CO2 asociadas. En concreto, este protocolo de análisis se aplica en el parque edificado de vivienda social entre 1950-1980 en Córdoba, ciudad situada en el área sur del arco mediterráneo español, y se centra principalmente, en la obra del arquitecto Rafael de la Hoz, ya que supuso un paradigma del Movimiento Moderno en el desarrollo de este tipo residencial. El análisis ambiental y energético del parque edificado se desarrolla a través un enfoque bottom-up mediante tres niveles: un nivel de detalle 1, a escala territorial, centrado en la promoción, donde se aborda la caracterización arquitectónica y constructiva mediante la clasificación tipológica de los edificios y la definición de las soluciones constructivas de su envolvente térmica; un nivel de detalle 2, enfocado a nivel de bloque, en el que se desarrolle la caracterización energética de los edificios analizados a partir de la información obtenida en el nivel previo, y se cuantifique su nivel de emisiones de CO2 y demanda anual de energía primaria; y un nivel de detalle 3, a escala de vivienda, en el que se recopila información del estado actual de los edificios mediante la realización de ensayos in situ (termografía, permeabilidad al aire de la envolvente térmica de los edificios) y la monitorización de variables ambientales y energéticas, en tres viviendas pertenecientes a tres barriadas de vivienda social de Rafael de la Hoz, representativas de este parque residencial, seleccionadas tras el análisis estadístico de la información obtenida en los niveles previos. Gracias a la recopilación de información bajo condiciones de uso y ocupación reales, la investigación desarrollada salva las diferencias entre el comportamiento simulado de los modelos energéticos y el comportamiento energético real de los casos de estudio, permitiendo validar el potencial de mejora de los edificios analizados mediante la implementación de los modelos energéticos con estrategias pasivas estándar de rehabilitación centradas en la envolvente térmica de los edificios, que posibiliten el bienestar térmico en las viviendas, además de contribuir a reducir la demanda de energía primaria y las emisiones de CO2 de este sector residencial. Para finalizar el ciclo de análisis, se transponen los escenarios de mejora evaluados en las viviendas, a los niveles de detalle a escala territorial y urbana (1 y 2), para cuantificar la mejora obtenida en términos globales. Además de cuantificar el comportamiento ambiental y el consumo y demanda energéticos en los casos de estudio monitorizados, la presente tesis doctoral se centra en el estudio de las condiciones interiores de las viviendas analizadas, y si éstas realmente pueden proporcionar un nivel razonable de confort térmico y bienestar a los usuarios. Generalmente, los estándares actuales se centran en modelos estáticos de evaluación de confort y las regulaciones locales en materia de eficiencia energética prescriben unos rangos muy restrictivos, lo cual genera un uso casi obligado de sistemas activos de climatización para mantener las condiciones interiores dentro de los rangos de confort. Por el contrario, el modelo adaptativo ofrece una evaluación más realista del bienestar térmico, garantizando una menor necesidad del uso de equipos activos en el mantenimiento del confort interior, ya que el edificio se mantiene en régimen de libre evolución durante más tiempo, sin necesidad de activar los sistemas de calefacción o refrigeración. Dada la naturaleza empírica de las ecuaciones de confort adaptativo, se plantea un análisis de la aplicabilidad de dos modelos pertenecientes a estudios experimentales y a estándares internacionales, de forma que se logre un ajuste de dicho modelo a climas Mediterráneos de la zona climática B4 (Csa), como es el caso de Córdoba. En concreto, el Estándar 55 de ASHRAE, de aplicación internacional, y el Estándar MM de Barbadilla- Martin et al. (2017), desarrollado en la misma zona climática que el parque edificado objeto de estudio se emplearán para desarrollar la evaluación y el diagnóstico de las condiciones de falta de confort térmico en el parque residencial a través de este tipo de enfoque dinámico. Los escenarios e hipótesis de intervención que se plantean para la actualización de este parque residencial se centran en la incorporación de aislamiento térmico en la parte opaca de la envolvente térmica, la mejora de las características térmicas de vidrios y carpinterías, así como de la permeabilidad de los huecos, y la implementación en las viviendas de un sistema de ventilación higrorregulable de caudal variable. El análisis individual de cada estrategia de actuación deriva en la definición de una propuesta integral de mejora cuya aplicación ofrece un significativo incremento de las condiciones de bienestar térmico en el interior de las viviendas, aproximando las temperaturas al rango de confort térmico establecido por el modelo adaptativo ajustado (20,9 ºC en invierno y 30 ºC en verano) hasta alcanzar un 100 % de horas ocupadas de bienestar térmico en algunos casos. La estrategia integral de mejora es aplicable en actuaciones de conjunto a nivel urbano y territorial que engloben edificaciones con características constructivas similares, consiguiendo de esta forma una reducción del 30 % de las emisiones de CO2 y un 40 % de la demanda anual de energía primaria del sector edificado a escala global. La voluntad de contribuir a aumentar el conocimiento acerca del parque residencial de la zona mediterránea ha dado pie a la generación de una base de datos asociada a un Sistema de Información Geográfica, en la que se ha incorporado toda la información relativa a la identificación, definición y análisis de las características morfológicas, constructivas y energéticas del parque residencial. Dicha base de datos georreferenciada se presenta como una herramienta de almacenamiento, análisis y manipulación de la información relativa al estado actual de este parque residencial, posibilitando la accesibilidad y el manejo de esta información a entidades y organismos encargados de la redacción de planes especiales de rehabilitación energética del parque residencial obsoleto.Current intentions to reduce the environmental global impact and a higher energy efficiency of the building sector have encouraged research on energy conservation measures and concrete actions suitable for sustainable development and the improvement of habitability conditions in buildings. In Spain, 61 % of the existing residential stock shows a deficient energy performance regarding prevailing energy standards, due to the fact that they were built before the first regulation on thermal conditions in buildings, the NBE-CT 79. Hence, improving this important amount of existing housing stock from the energy and environmental angle is a preferential issue to matter. This doctoral thesis pursues to set up a protocol for analysing the existing residential stock, by answering to three main aims, to increase the available data on the current state of these buildings as a previous step to intervene on them with any kind of upgrading action, to assess the level of thermal well-being inside the dwellings located under Mediterranean weather conditions by means of adaptive approach-based empirical models, to quantify their potential for improvement through the application of passive standard energy retrofit strategies that lessen the lack of thermal comfort, as well as shorten the annual energy demand and the associated CO2 emissions. In particular, the analysis protocol is applied to the existing social housing stock built between 1950-1980 in Córdoba, a city from the southern area of the Spanish Mediterranean arc, mainly focusing in the work of the Spanish architect Rafael de la Hoz, who entailed an architectural paradigm of Modern Movement by fostering the development of this sort of residential buildings. The environmental and energy assessment of the building stock is developed through a three-level bottomup approach: a detail level 1, at a territorial extent, centred in a promotion scale, which deals with the architectural and constructive characterization of the buildings, by their typological classification and the definition of the constructive solutions employed in their thermal envelope; a detail level 2, targeted to a building scale, which runs an energy characterization of the analysed buildings from the gathered information in the previous level, and quantifies their CO2 emissions and primary energy annual demand; a detail level 3, at a dwelling scale, in which a compilation of data about the current state of the buildings is gathered by means of in situ tests (infrared thermography and air-tightness of the outer parts of the buildings’ thermal envelope) and the monitoring of environmental and energy parameters, in three dwellings that belong to three social housing neighbourhoods made by Rafael de la Hoz, which turn to be representative of the investigated building stock after running a statistical analysis in previous levels. Thanks to the data collection under real use and occupancy conditions, the present research bridges the gaps between energy models simulation results and the energy performance of real case-study units. This allows to validate the potential of improvement of the studied buildings by way of passive standard energy retrofit strategies applied on the thermal envelope of the energy models that foresee an increase on thermal comfort in the dwellings, alongside with the decrease of primary energy demand and the CO2 emissions of this housing sector. To close the cycle, the scenarios for improvement assessed on the dwellings are transposed to urban and territorial scale detail levels (1 and 2), to quantify the obtainable benefits in global terms. In addition to the environmental and energy consumption and demand evaluation of monitored case-study dwellings, this doctoral thesis focus on the assessment of indoor conditions in them, and whether they really provide the users with a reasonable thermal comfort and well-being level. Usually, current energy standards and local regulations base thermal well-being requisites on a steady-state basis, and prescribe very narrow comfort temperature ranges, that imply a compulsory use of conditioning active systems (HVAC) to keep indoor temperatures between the threshold. On the contrary, the adaptive model offers a more realistic approach to thermal well-being, guaranteeing a lower need to use active equipment in maintaining indoor comfort, inasmuch the building runs in free-floating regime for longer hour, without needing the activation of HVAC systems. Given the empirical nature of the adaptive comfort equations, the applicability of two models that belong to experimental research and appear in international standards are examined, in order to set an adjusted model to Mediterranean weather conditions from Spanish B4 climate zone (Csa), as is the case of Córdoba. Particularly, ASHRAE Standard 55, with international scope of application, and Barbadilla-Martin et al. (2017) Standard MM, developed in the same climate zone as the analysed buildings, will be employed in the assessment and diagnosis of the lack of comfort in the considered housing stock by way of the adaptive approach. Hypothetical scenarios of intervention for the upgrading of this residential stock are targeted to the addition of thermal insulation in the opaque parts of the thermal envelope, implementing window glazing and joinery with improved thermal characteristics, together with more air-tight windows, and the incorporation of a mechanical ventilation system with a hygroregulable air-flow adjusted to occupancy needs. The individual analysis of each strategy leads to the formulation of an all-inclusive proposal that provides with a significant increase of thermal well-being inside the dwellings, bringing indoor temperatures closer to temperature ranges set by the adjusted adaptive comfort model (20.9 ºC in winter and 30 ºC in summer) achieving a 100 % of occupancy hours of thermal well-being. The all-inclusive strategy can be applied at urban and territorial levels of intervention concerning buildings that share similar constructive characteristics and obtaining a 30 % reduction of CO2 emissions and a 40 % decrease of primary energy annual demand in the building sector at a global scale. The aim to fill the gap of knowledge about the existing Mediterranean housing stock has led to the generation of a data base associated to a Geographic Information System, in which all the recorded data on the identification, definition and analysis of morphological, constructive and energy aspects of the residential stock has been organized and stored. The geographic data base is hereby presented as a tool for storing, analysing and data mining the current state of the residential stock, making it user-friendly and accessible to key stakeholders in charge of the development of energy retrofitting urban plans to upgrade these obsolete buildings

The role of dynamic hydrogen bond networks in protonation coupled dynamics of retinal proteins

Hydrogen bonds (H-bonds) are an essential interaction in membrane proteins. Embedded in complex hydrated lipid bilayers, intramolecular interactions through the means of hydrogen bonding networks are often crucial for the function of the protein. Internal water molecules that occupy stable sites inside the protein, or water molecules that visit transiently from the bulk, can play an important role in shaping local conformational dynamics forming complex networks that bridge regions of the protein via water-mediated hydrogen bonds that can function as wires for the transferring of protons as a part of the protein’s function. For example, the membrane-embedded channelrhodopsins which are found in archaea are proteins that couple light induced isomerization of a retinal chromophore with proton transfer reactions and passive flow of cations through their pore. I contributed to the development of a new algorithm package that features a unique approach to H-bond analyses. I performed analyses of long Molecular Dynamics (MD) trajectories of channelrhodopsin variants embedded in hydrated lipid membranes and large data sets of static structures, to detect and dissect dynamic hydrogen-bond networks. The photocycle of channelrhodopsins begins with absorption and isomerization of the retinal from an all-trans state to a 13-cis state and followed by the deprotonation of the Schiff base. Thus, the retinal is found in the epicenter of the analyses. Through the use of 2-dimensional graphs of the protein H-bond networks I identified protein groups potentially important for the proton transfer activity. Local dynamics are highly affected by point mutations of amino acids important for function. The interior of channelrhodopsin C1C2 hosts extensive networks of protein and H-bonded-water molecules, and a never reported before, network that can bridge transiently the two retinal chromophores in channelrhodopsin dimers. In a recently identified inward proton pump, AntR, I applied centrality measures on MD trajectories of the homology model I generated, to assess the communication of the amino acid residues within the networks. I detected a frequently sampled long water chain that connects the retinal with a candidate proton acceptor, as well as a conserved serine in the vicinity of the retinal chromophore plays a significant role in the connectivity and communication of the H-bond networks upon isomerization. A similar water bridge is sampled in independent simulations of ChR2, where a participant for the proton donor group connects to the 13-cis,15-anti retinal. Proton transfer reactions often take place through certain amino acids, forming patterns. I analyzed H-bond patterns or motifs in large hand-curated datasets of static structures of α-transmembrane helix proteins, organized according to the superfamilies they belong, their function and an alternative classification method. The presence of motifs in TM proteins is tightly related to their families/superfamilies of the host protein and their position along the membrane normal.Wasserstoffbrücken (H-Brücke) sind eine wesentliche Wechselwirkung in Membranproteinen. Eingebettet in komplexe hydratisierte Lipiddoppelschichten sind intramolekulare Wechselwirkungen über Wasserstoffbrückenbindungsnetzwerke oft entscheidend für die Funktion des Proteins. Interne Wassermoleküle, die stabile Stellen im Inneren des Proteins besetzen, oder Wassermoleküle, die vorübergehend aus der Masse zu Besuch kommen, können eine wichtige Rolle bei der Gestaltung der lokalen Konformationsdynamik spielen, indem sie komplexe Netzwerke bilden, die Regionen des Proteins über wasservermittelte Wasserstoffbrückenbindungen überbrücken, die als Drähte für den Transfer von Protonen als Teil der Proteinfunktion funktionieren können. Die in Archaeen vorkommenden, in die Membran eingebetteten Kanalrhodopsine sind beispielsweise Proteine, die die lichtinduzierte Isomerisierung eines Retinachromophors mit Protonentransferreaktionen und dem passiven Fluss von Kationen durch ihre Pore verbinden. Ich habe an der Entwicklung eines neuen Algorithmuspakets mitgewirkt, das einen einzigartigen Ansatz für H-Bindungsanalysen bietet. Ich habe lange Molekulardynamik-Trajektorien von Kanalrhodopsine-Varianten, die in hydratisierte Lipidmembranen eingebettet sind, sowie große Datensätze statischer Strukturen analysiert, um dynamische Wasserstoffbrücken-bindungsnetzwerke zu erkennen und zu zerlegen. Der Photozyklus der Kanalrhodopsine beginnt mit der Absorption und Isomerisierung des Retinals von einem all-trans-Zustand zu einem 13-cis-Zustand, gefolgt von der Deprotonierung der Schiff-Base. Somit steht das Retinal im Mittelpunkt der Analysen. Durch die Verwendung von 2-dimensionalen Graphen der Protein- H-Brückenetzwerke identifizierte ich Proteingruppen, die für die Protonentransferaktivität wichtig sein könnten. Die lokale Dynamik wird durch Punktmutationen der für die Funktion wichtigen Aminosäuren stark beeinflusst. Das Innere von Kanalrhodopsine C1C2 beherbergt ausgedehnte Netzwerke von Protein- und H-Brücke-Wassermolekülen und ein bisher unbekanntes Netzwerk, das die beiden retinalen Chromophore in Kanalrhodopsine-Dimeren vorübergehend überbrücken kann. In einer kürzlich identifizierten Protonenpumpe, AntR, wendete ich Zentralitätsmaße auf MD-Trajektorien des von mir erstellten Homologiemodells an, um die Kommunikation der Aminosäurereste innerhalb der Netzwerke zu bewerten. Ich fand, dass eine häufig gesampelte lange Wasserkette, die das Retinal mit einem Protonenakzeptor verbindet, sowie ein konserviertes Serin in der Nähe des Retinal-Chromophors eine wichtige Rolle bei der Konnektivität und Kommunikation der H-Brückesnetzwerke bei der Isomerisierung spielt. Eine ähnliche Wasserbrücke ist in unabhängigen Simulationen von Kanalrhodopsine-2 zu finden, wo ein Teilnehmer für die Protonendonorgruppe mit dem 13-cis,15-anti-Retinal verbunden ist. Protonenübertragungsreaktionen finden oft über bestimmte Aminosäuren statt und bilden Muster. Ich analysierte H-Brückemuster oder -motive in großen, von Hand kuratierten Datensätzen statischer Strukturen von α-Transmembranhelix-Proteinen, geordnet nach den Superfamilien, zu denen sie gehören, ihrer Funktion und einer alternativen Klassifizierungsmethode. Das Vorhandensein von Motiven in TM-Proteinen steht in engem Zusammenhang mit ihren Familien/Superfamilien des Wirtsproteins und ihrer Position entlang der Membrannormale