Relevant bibliographies by topics / Molecular Interaction Maps

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  2. Dissertations / Theses
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Academic literature on the topic 'Molecular Interaction Maps'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Molecular Interaction Maps"

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Barbuti, Roberto, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini, and Aureliano Rama. "A Process Calculus for Molecular Interaction Maps." Electronic Proceedings in Theoretical Computer Science 11 (November 30, 2009): 35–49. http://dx.doi.org/10.4204/eptcs.11.3.

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Stower, Hannah. "Interaction maps for mammals." Nature Reviews Genetics 14, no. 4 (2013): 240. http://dx.doi.org/10.1038/nrg3451.

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de Souza, Natalie. "Transcription factor interaction maps." Nature Methods 7, no. 5 (2010): 344–45. http://dx.doi.org/10.1038/nmeth0510-344b.

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Kohn, Kurt W., Mirit I. Aladjem, John N. Weinstein, and Yves Pommier. "Molecular Interaction Maps of Bioregulatory Networks: A General Rubric for Systems Biology." Molecular Biology of the Cell 17, no. 1 (2006): 1–13. http://dx.doi.org/10.1091/mbc.e05-09-0824.

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A standard for bioregulatory network diagrams is urgently needed in the same way that circuit diagrams are needed in electronics. Several graphical notations have been proposed, but none has become standard. We have prepared many detailed bioregulatory network diagrams using the molecular interaction map (MIM) notation, and we now feel confident that it is suitable as a standard. Here, we describe the MIM notation formally and discuss its merits relative to alternative proposals. We show by simple examples how to denote all of the molecular interactions commonly found in bioregulatory networks. There are two forms of MIM diagrams. “Heuristic” MIMs present the repertoire of interactions possible for molecules that are colocalized in time and place. “Explicit” MIMs define particular models (derived from heuristic MIMs) for computer simulation. We show also how pathways or processes can be highlighted on a canonical heuristic MIM. Drawing a MIM diagram, adhering to the rules of notation, imposes a logical discipline that sharpens one's understanding of the structure and function of a network.
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Pommier, Y., O. Sordet, A. Rao, H. Zhang, and K. Kohn. "Targeting Chk2 Kinase: Molecular Interaction Maps and Therapeutic Rationale." Current Pharmaceutical Design 11, no. 22 (2005): 2855–572. http://dx.doi.org/10.2174/1381612054546716.

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Olsson, Tjelvar S. G., Peter A. Wood, and Colin R. Groom. "Evaluation of molecular crystal structures using full interaction maps." Acta Crystallographica Section A Foundations of Crystallography 69, a1 (2013): s75. http://dx.doi.org/10.1107/s0108767313099352.

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Kohn, Kurt W. "Molecular interaction maps as information organizers and simulation guides." Chaos: An Interdisciplinary Journal of Nonlinear Science 11, no. 1 (2001): 84. http://dx.doi.org/10.1063/1.1338126.

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Wood, Peter A., Tjelvar S. G. Olsson, Jason C. Cole, et al. "Evaluation of molecular crystal structures using Full Interaction Maps." CrystEngComm 15, no. 1 (2013): 65–72. http://dx.doi.org/10.1039/c2ce25849h.

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Walhout, Albertha J. M., and Marc Vidal. "Protein interaction maps for model organisms." Nature Reviews Molecular Cell Biology 2, no. 1 (2001): 55–63. http://dx.doi.org/10.1038/35048107.

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Griffin, James D. "Interaction maps for kinase inhibitors." Nature Biotechnology 23, no. 3 (2005): 308–9. http://dx.doi.org/10.1038/nbt0305-308.

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Dissertations / Theses on the topic "Molecular Interaction Maps"

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Obeid, Naji. "MIM-Logic : a logic for reasoning about molecular interaction maps." Toulouse 3, 2014. http://thesesups.ups-tlse.fr/2527/.

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Les séries de réactions biochimiques apparaissant au cœur d'une cellule forme ce qu'on appelle des voies métaboliques. La plupart de ces voies sont très complexes impliquant un grand nombre de protéines et d'enzymes. Une représentation logique de ces réseaux contribue au raisonnement à propos de ces voies en général, allant du fait de répondre à certaines questions, compléter des arcs et nœuds manquant, et trouver des incohérences. Dans ce contexte on propose un nouveau model logique basé sur un fragment de logique de premier ordre capable de décrire les réactions apparaissant dans des Molecular Interaction Maps. On propose aussi une méthode de déduction automatique efficace capable de répondre aux questions par déduction pour prédire les résultats des réactions et par abduction pour trouver les états des protéines et de leurs réactions. Cette méthode automatique est basée sur une procédure de traduction qui élimine les quantificateurs des formules de logique premier ordre<br>The series of biochemical reactions that occur within a cell form what we call Metabolic Pathways. Most of them can be quite intricate and involve many proteins and enzymes. Logical representations of such networks can help reason about them in general, where the reasoning can range from answering some queries, to completing missing nodes and arcs, and finding inconsistencies. This work proposes a new logical model based on a fragment of first-order logic capable of describing reactions that appear in a Molecular Interaction Maps. We also propose an efficient automated deduction method that can answer queries by deduction to predict reaction results or by abductive reasoning to find reactions and protein states. This automated deduction method is based on a translation procedure that transforms first-order formulas into quantifier free formulas
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Singh, Vidisha. "Integrative analysis and modeling of molecular pathways dysregulated in rheumatoid arthritis Computational systems biology approach for the study of rheumatoid arthritis: from a molecular map to a dynamical model RA-map: building a state-of-the-art interactive knowledge base for rheumatoid arthritis Automated inference of Boolean models from molecular interaction maps using CaSQ." Thesis, université Paris-Saclay, 2020. http://www.theses.fr/2020UPASL039.

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La polyarthrite rhumatoïde (PR) est unemaladie auto-immune complexe qui entraîne uneinflammation synoviale et une hyperplasie pouvantprovoquer une érosion osseuse et une destruction ducartilage dans les articulations. L'étiologie de la PR restepartiellement inconnue, mais elle implique de multiplescascades de signalisation croisées et l'expression demédiateurs pro-inflammatoires. Dans la première partie demon projet de doctorat, nous présentons un effortsystématique pour construire une base de connaissancessur la PR, entièrement annotée et validée par des experts.Cette carte de la PR illustre les voies moléculaires et designalisation importantes impliquées dans la maladie. Latransduction du signal est systématiquement représentéedes récepteurs au noyau en utilisant la représentationstandard de notation graphique en biologie des systèmes(SBGN). La curation manuelle est basée sur des critèresstricts et spécifique aux études sur l'homme, limitantl'apparition de faux positifs sur la carte. Cette carte peutservir de base de connaissances interactive pour la maladiemais aussi de tableau pour la visualisation des donnéesomiques. De plus, c’est une excellente base pour ledéveloppement d'un modèle informatique. La naturestatique de la carte PR pourrait fournir une compréhensionrelativement limitée du comportement émergeant dusystème dans différentes conditions. La modélisationinformatique pourra révéler les propriétés dynamiques duréseau par le biais de perturbations in silico et peut êtreutilisée pour tester et prédire des hypothèses.Dans la deuxième partie du projet, nous présentons unpipeline permettant la construction automatisée d'un grandmodèle booléen, à partir d'une carte d'interactionsmoléculaires. Pour cela, nous avons développé l'outilCaSQ (CellDesigner as SBML-qual), qui automatise laconversion des cartes moléculaires en modèles booléensexécutables basés sur la topologie et la sémantique descartes. Le modèle booléen résultant pourrait être utilisépour des simulations in silico afin de reproduire lecomportement biologique connu du système et de prédirede nouvelles cibles thérapeutiques. Pour l'analyse deperformance de l’outil, nous avons utilisé différentescartes et modèles de maladies en mettant l'accent sur lagrande carte moléculaire de la PR.Dans la troisième partie du projet, nous présentons nosefforts pour créer un modèle dynamique (booléen) àgrande échelle pour les synoviocytes de type fibroblastede polyarthrite rhumatoïde (RA-FLS). Parmi denombreuses cellules de l'articulation et du systèmeimmunitaire impliquées dans la pathogenèse de la PR, lesRA-FLS joue un rôle important dans l'initiation et laperpétuation de l'inflammation articulaire destructrice.Les RA-FLS expriment des cytokinesimmunomodulatrices, des molécules d'adhésion et desenzymes de modélisation matricielle. De plus, les RAFLSprésentent des taux de prolifération élevés et unphénotype résistant à l'apoptose. Les RA-FLS peuventégalement se comporter comme les principaux moteurs del'inflammation, et les thérapies dirigées contre les RA FLSpourraient devenir une approche complémentaire auximmunothérapies. Le défi est de prédire les conditionsoptimales qui favoriseraient l'apoptose des RA FLS,limiteraient l'inflammation, ralentiraient le taux deprolifération et minimiseraient l'érosion osseuse et ladestruction du cartilage<br>Rheumatoid arthritis (RA) is a complexautoimmune disease that results in synovial inflammationand hyperplasia leading to bone erosion and cartilagedestruction in the joints. The aetiology of RA remainspartially unknown, yet, it involves a variety of intertwinedsignalling cascades and the expression of pro-inflammatorymediators. In the first part of my PhD project, we present asystematic effort to construct a fully annotated, expertvalidated, state of the art knowledge-base for RA. The RAmap illustrates significant molecular and signallingpathways implicated in the disease. Signal transduction isdepicted from receptors to the nucleus systematically usingthe systems biology graphical notation (SBGN) standardrepresentation. Manual curation based on strict criteria andrestricted to only human-specific studies limits theoccurrence of false positives in the map. The RA map canserve as an interactive knowledge base for the disease butalso as a template for omic data visualization and as anexcellent base for the development of a computationalmodel. The static nature of the RA map could provide arelatively limited understanding of the emerging behaviorof the system under different conditions. Computationalmodeling can reveal dynamic network properties throughin silico perturbations and can be used to test and predictassumptions.In the second part of the project, we present a pipelineallowing the automated construction of a large Booleanmodel, starting from a molecular interaction map. For thispurpose, we developed the tool CaSQ (CellDesigner asSBML-qual), which automates the conversion ofmolecular maps to executable Boolean models based ontopology and map semantics. The resulting Booleanmodel could be used for in silico simulations to reproduceknown biological behavior of the system and to furtherpredict novel therapeutic targets. For benchmarking, weused different disease maps and models with a focus onthe large molecular map for RA.In the third part of the project we present our efforts tocreate a large scale dynamical (Boolean) model forrheumatoid arthritis fibroblast-like synoviocytes (RAFLS).Among many cells of the joint and of the immunesystem involved in the pathogenesis of RA, RA FLS playa significant role in the initiation and perpetuation ofdestructive joint inflammation. RA-FLS are shown toexpress immuno-modulating cytokines, adhesionmolecules, and matrix-modelling enzymes. Moreover,RA-FLS display high proliferative rates and an apoptosisresistantphenotype. RA-FLS can also behave as primarydrivers of inflammation, and RA FLS-directed therapiescould become a complementary approach to immunedirectedtherapies. The challenge is to predict the optimalconditions that would favour RA FLS apoptosis, limitinflammation, slow down the proliferation rate andminimize bone erosion and cartilage destruction
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West, Adam Geoffrey. "Molecular interactions of the MADS-box transcription factors." Thesis, University of Newcastle Upon Tyne, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.362415.

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Bost, Pierre. "Decoding cellular communications and interactions between immune cells by using single-cell approaches." Electronic Thesis or Diss., Sorbonne université, 2020. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2020SORUS020.pdf.

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Les communications cellulaires sont indispensables au bon fonctionnement des organismes multicellulaires, notamment pour s’adapter à un environnement changeant en permanence. Les cellules du système immunitaire n’échappent pas à cette règle mais les interactions entre cellules immunitaires restent peu connues et compliquée à étudier. La récente apparition des technologies de séquençage dites ‘cellules uniques’ représente une opportunité unique pour étudier ces communications. Dans cette thèse, différentes approches expérimentales et analytiques ont été développées pour étudier ces communications à une échelle de cellules uniques. Ces stratégies ont ensuite été appliquées à différents contextes pathologiques, incluant le COVID-19, la maladie d’Alzheimer ou une immunisation par des pathogènes inactivés, et ont permis d’identifier des voies de communications cellulaires jusqu’ici inconnues ou mal comprises. Néanmoins, l’efficacité de ces approches est limitée par l’absence d’informations sur la localisation des cellules et des travaux supplémentaires intégrant ce genre de données est essentiel pour aller plus loin dans la dissection des communications entre cellules immunitaires<br>Cellular communications are essential to the proper functioning of multi-cellular organisms, particularly in order to adapt to a constantly changing environment. The cells of the immune system are no exception to this rule, but the interactions between immune cells remain little known and complicated to study. The recent emergence of 'single cell' sequencing technologies represents a unique opportunity to study these communications. In this thesis, different experimental and analytical approaches have been developed to study these communications on a single cell scale. These strategies were then applied to different disease contexts, including COVID-19, Alzheimer's disease or immunisation with inactivated pathogens, and identified previously unknown or poorly understood cellular communication pathways. However, the effectiveness of these approaches is limited by the lack of information on cell location and further work integrating such data will be essential to go further in the dissection of immune cell communications
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Profantova, Barbora. "Molecular mechanisms of DNA regulatory segment recognition by mads box family transcription factors." Thesis, Paris 6, 2014. http://www.theses.fr/2014PA066436/document.

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Cette thèse concerne les propriétés physico-chimiques des " Boîtes MADS ", séquences de liaison de facteurs de transcription déterminantes pour la formation de complexes avec des segments de régulation de l'ADN comportant des séquences spécifiques nommées " Boîtes CArG ". Des études ont aussi été menées sur certains segments bien choisis des Boîtes MADS et quelques-uns de leurs analogues mutés. Un large choix d'approches spectroscopiques a été employé pour ces études : absorption électronique, dichroïsme circulaire, fluorescence et diffusion Raman. Des approches performantes d'analyse multivariée ont été utilisées pour le traitement des résultats expérimentaux. Les trois tyrosines de la Boîte MADS, situées dans des environnements de charge et d'hydrophobicité différents, ont été utilisées comme marqueurs spectroscopiques intrinsèques. Les principaux résultats de ce travail concernent les caractéristiques de structures, flexibilités et équilibres acido-basiques de la Boîte MADS et de ses différents segments<br>The thesis deals with physico-chemical properties of the MADS box, binding domain of transcription factors, which are important for the formation of complexes with the DNA regulatory segment bearing the CArG box. The study was performed also on model oligopeptides, selected segments of the MADS box and their analogues with a point mutation. A wide range of spectroscopic techniques was employed, namely absorption, circular dichroism, fluorescence and Raman spectroscopies. Advanced approaches including multivariate methods were used for data processing. The three tyrosines of the MADS box located in amino-acid vicinities of different charge and hydrophobicity, were used as intrinsic spectroscopic probes. The obtained characteristics of the MADS box and its segments structural arrangement, flexibility and acid-base equilibria are the main results of the work
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Martineau, Eric. "Modeling Peptide-binding Interactions and Polymer-binding Interactions and their Role in Mass Spectrometry." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/24197.

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As a first project, collision-induced dissociation experiments were carried out using electrospray ionisation mass spectrometry on gas phase complexes involving different poly(methylmetacrylate) oligomers with three amino acids: glycine, leucine, and phenylalanine. After acquiring breakdown diagrams, RRKM modeling was used to fit the experimental data in order to obtain the 0 K activation energy and the entropy of activation. These thermodynamic data were then used to understand the competing dissociation channels observed (except for gas phase complexes involving glycine that had only one dissociation channel). Molecular dynamics simulated annealing calculations were carried on the gas phase complexes to understand further the energetic and entropic effects involved as well as the 3D conformation of these complexes. Valuable insight information was found on the 3D conformations, on a qualitative level. Using rotational constants and vibrational harmonic frequencies, it was possible to evaluate the entropy variation between the experimentally observed competing channels. Reasonable agreement was found between the experimental and theoretical variations of entropies. Finally, the proton affinity of poly(methylmetacrylate) oligomers is being discussed. Even though no absolute values for the proton affinity were found, the experimental and computational results help to understand the variation that accompanies the oligomers length. The second project presents the development an efficient and reproducible screening method for identifying low molecular weight compounds that bind to amyloid beta peptides (Abeta) peptides using electrospray ionization mass spectrometry (ESI-MS). Low molecular weight (LMW) compounds capable of interacting with soluble Abeta may be able to modulate/inhibit the Abeta aggregation process and serve as potential disease-modifying agents for Alzheimer’s disease. The present approach was used to rank the binding affinity of a library of compounds to Abeta1-40 peptide. The results obtained show that low molecular weight compounds bind similarly to Abeta1-42, Abeta1-40, as well as Abeta1-28 peptides and they underline the critical role of Abeta peptide charge motif in binding at physiological pH. Finally, some elements of structure-activity relationship (SAR) involved in the binding affinity of homotaurine to soluble Abeta peptides are discussed. As a third project, the gas phase binding of small molecules to the Abeta1-40 peptide generated by electrospray ionization has been explored with collision-induced dissociation mass spectrometry and kinetic rate theory. This project presents a simple procedure used to theoretically model the experimental breakdown diagrams for the Abeta1-40 peptide complexed with a series of aminosulfonate small molecules, namely homotaurine, 3-cyclohexylamino-2-hydroxy-1-propanesulfonic acid (CAPSO), 3-(1,3,4,9-tetrahydro-2H-beta-carbolin-2-yl) propane-1-sulfonic acid, 3-(1,3,4,9-tetrahydro-2H-beta-carbolin-2-yl)butane-1-sulfonic acid, and 3-(cyclohexylamino) propane-1-sulfonic acid. An alternative method employing an extrapolation procedure for the microcanonical rate constant, k(E), is also discussed.
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Collier, Miranda. "Small heat shock protein interactions with in vivo partners." Thesis, University of Oxford, 2018. http://ora.ox.ac.uk/objects/uuid:24cf8041-c82d-4bc4-87a7-0ae7e38f1879.

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Small heat-shock proteins (sHsps) are part of a broad cellular sys- tem that functions to maintain a stable proteome under stress. They also perform a variety of regulatory roles at physiological conditions. Despite the multitude of sHsp targets, their interactions with partners are not well understood due to highly dynamical structures. In this thesis, I apply a variety of biophysical and structural approaches to examine distinct interactions made by the abundant human sHsps αβ-crystallin and Hsp27. First, I find that αβ-crystallin binds a cardiac-specific domain of the muscle sarcomere protein titin. A cardiomyopathy-causative variant of αβ-crystallin is shown to disrupt this interaction, with demonstrated implications for tissue biomechanics. Next, I investigate the conformation and unfolding behaviour of another sarcomere-associated protein, filamin C, finding support for the hypothesis that it is mechanosensitive. This leads into an interrogation of the interaction between filamin C and Hsp27, which we find is modulated by phosphorylation of Hsp27. This modulation only manifests during filamin C unfolding, pointing toward a protective chaperoning mode against over-extension during mechanical stress. This finding is bolstered by up-regulation and interaction of both proteins in a mouse model of heart failure. I establish a system for similar studies of a third sHsp, cvHsp, which is muscle-specific and implicated in various myopathies but scantly understood at the molecular level compared to αβ-crystallin and Hsp27. Finally, I probe the stoichiometries and kinetics of complexes formed between αβ-crystallin and Hsp27 themselves, which co-assemble into a highly polydisperse ensemble. This involved the development of a high-resolution native mass spectrometry method for disentangling heterogeneous systems. Together these findings add to our understanding of the roles and mechanisms of ATP-independent molecular chaperones.
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Cheng, Guilong. "Unraveling Macro-Molecular Machinery by Mass Spectrometry: from Single Proteins to Non-Covalent Protein Complexes." Diss., The University of Arizona, 2007. http://hdl.handle.net/10150/195466.

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Presented in this dissertation are studies of protein dynamics and protein/protein interactions using solution phase hydrogen/deuterium exchange in combination with mass spectrometry (HXMS). In addition, gas phase fragmentation behaviors of deuterated peptides are investigated, with the purpose of increasing resolution of the HXMS. In the area of single protein dynamics, two protein systems are studied. Studies on the cytochrome c2 from Rhodobacter capsulatus indicate its domain stability to be similar to that of the horse heart cytochrome c. Further comparison of the exchange kinetics of the cytochrome c2 in its reduced and oxidized state reveals that the so-called hinge region is destabilized upon oxidation. We also applied a similar approach to investigate the conformational changes of photoactive yellow protein when it is transiently converted from the resting state to the signaling state. The central &amp;#946;-sheet of the protein is shown to be destabilized upon photoisomerization of the double bond in the chromophore. Another equally important question when it comes to understanding how proteins work is the interactions between proteins. To this end, two protein complexes are subjected to studies by solution phase hydrogen deuterium exchange and mass spectrometry. In the case of LexA/RecA interaction, both proteins show decreases in their extents of exchange upon complex formation. The potential binding site in LexA was further mapped to the same region that the protein uses to cleave itself upon interacting with RecA. In the sHSP/MDH system, hydrogen/deuterium exchange experiments revealed regions within sHSP-bound MDH that were significantly protected against exchange under heat denaturing condition, indicative of a partially unfolded state. Hydrogen/deuterium exchange therefore provides a way of probing low resolution protein structure within protein complexes that have a high level of heterogeneity. Finally, the feasibility of increasing resolution of HXMS by gas phase peptide fragmentation is investigated by using a peptide with three prolines near the C-terminus. Our data show that deuterium migration indeed occurs during the collision activated dissociation process. Caution is required when interpreting the MS/MS spectra as a way of pinpointing the exact deuterium distribution within peptides.
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Platt, Sean P. "Interactions of the Naphthalene Radical Cation with Polar and Unsaturated Molecules in the Gas Phase." VCU Scholars Compass, 2016. http://scholarscompass.vcu.edu/etd/4210.

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Characterizing the interactions of solvent molecules with ions is fundamental in understanding the thermodynamics of solution chemistry. These interactions are difficult to observe directly in solution because the number of solvent molecules far exceed that of ions. This lend the gas phase to be the ideal medium in the study ion-solvent interactions on a molecular level. Ionized polycyclic aromatic hydrocarbon (PAH) molecules can readily form hydrogen bonds with neutral solvent molecules in aqueous and interstellar medium. Previous research has been done for stepwise solvation of small molecules such as benzene+, pyridine, and phenylacetylene. The similarity in these results show that these organic ions can be considered prototypical model systems for aromatic ion-neutral solvent interactions. The goal of this dissertation is to demonstrate that naphthalene can act as a prototypical model of PAH ions for ion-solvent interactions. Two types of experiments are considered throughout this dissertation using ion mobility mass spectrometry: (1) ion-neutral equilibrium thermochemistry and (2) mobility measurements. For thermochemistry experiments, the naphthalene radical cation was injected into the drift cell containing helium and/or neutral solvent vapor and the enthalpy and entropy changes were measured by varying the drift cell temperature and measuring the equilibrium constants. The results of these studies showed that small polar molecules bind to naphthalene with similar energy based on the measured by the enthalpy changes. Unsaturated aliphatic molecules behave similarly, but with much lower binding energy. Aromatic ions tend to bind to the naphthalene with lower binding energy than that observed with the benzene ion. The results for small polar molecules were compared to similar studies using the phenyl cation. The second series of experiments required the coexpansion of the naphthalene and benzene or pyridine. Injecting theses dimers into the drift cell allowed the measurement of reduced mobility on the dimers at a series of temperatures. These were used to calculate the average collision cross section and thus give insight in to the structure of these aromatic dimers. Structures were determined by comparing these results to those predicted by DFT calculations.
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Sawyer, Holly Ann. "Investigation of the effect of intra-molecular interactions on the gas-phase conformation of peptides as probed by ion mobility-mass spectrometry, gas-phase hydrogen/deuterium exchange, and molecular mechanics." Texas A&M University, 2004. http://hdl.handle.net/1969.1/3093.

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Ion mobility-mass spectrometry (IM-MS), gas-phase hydrogen/deuterium (H/D) exchange ion molecule reactions and molecular modeling provide complimentary information and are used here for the characterization of peptide ion structure, including fine structure detail (i.e., cation-&#960; interactions, &#946;-turns, and charge solvation interactions). IM-MS experiments performed on tyrosine containing tripeptides show that the collision cross-sections of sodiated, potassiated and doubly sodiated species of gly-gly-tyr are smaller than that of the protonated species, while the cesiated and doubly cesiated species are larger. Conversely, all of the alkali-adducted species of try-gly-gly have collision cross-sections that are larger than that of the protonated species. The protonated and alkali metal ion adducted (Na+, K+ and Cs+) species of bradykinin and bradykinin fragments 1-5, 1-6, 1-7, 1-8, 2-7, 5-9 and 2-9 were also studied using IM-MS and the alkali metal ion adducts of these species were found to have cross-sections very close to those of the protonated species. Additionally, multiple peak features observed in the ATDs of protonated bradykinin fragments 1-5, 1-6 and 1-7 are conserved upon alkali metal ion adduction. It was observed from gas-phase H/D ion molecule reactions that alkali adducted species exchange slower and to a lesser extent than protonated species in the tyrosine- and arginine-containing peptides. Experimental and computational results are discussed in terms of peptide ion structure, specifically the intra-molecular interactions present how those interactions change upon alkali salt adduction, as well as with the sequence of the peptide. Additionally, IM-MS data suggests the presence of a compact conformation of bradykinin fragment 1-5 (RPPGF) when starting from organic solvent conditions. As water is added stepwise to methanolic solutions, a more extended conformation is populated. When the starting solution is composed of &#8776;90% water, two distinct mobility profiles are observed as well as a shoulder, indicating the presence of three gas-phase conformations for RPPGF. Gas-phase H/D exchange of [M+H]+ ions prepared from aqueous solvents show a bi-exponential decay, whereas samples prepared from organic solvents show a single exponential decay. The effect of solvent on gas-phase peptide ion structure, i.e., solution-phase memory effects, is discussed and gas-phase structures are compared to know solution-phase structures.
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Books on the topic "Molecular Interaction Maps"

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Niessen, Wilfried M. A., and Jeroen Kool. Analyzing Biomolecular Interactions by Mass Spectrometry. Wiley-VCH Verlag GmbH, 2015.

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Niessen, Wilfried M. A., and Jeroen Kool. Analyzing Biomolecular Interactions by Mass Spectrometry. Wiley & Sons, Incorporated, John, 2015.

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Divan, Aysha, and Janice Royds. Molecular Biology. Oxford University Press, 2016. http://dx.doi.org/10.1093/actrade/9780198723882.001.0001.

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Molecular biology is the story of the molecules of life, their relationships, and how these interactions are controlled. Its applications are wide and growing; the power of molecular biology can now be harnessed to treat diseases, solve crimes, map human history, and produce genetically modified organisms and crops. Starting with the building blocks established by Darwin, Wallace, and Mendel, and the discovery of the structure of DNA in 1953, Molecular Biology: A Very Short Introduction considers the wide range of applications for molecular biology today, including the development of new drugs and DNA fingerprinting, and looks forward to two key areas of evolving research: personalized medicine and synthetic biology.
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Book chapters on the topic "Molecular Interaction Maps"

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Alliot, Jean-Marc, Robert Demolombe, Luis Fariñas del Cerro, Martín Diéguez, and Naji Obeid. "Abductive Reasoning on Molecular Interaction Maps." In Interactions Between Computational Intelligence and Mathematics. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-74681-4_4.

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Demolombe, Robert, Luis Fariñas del Cerro, and Naji Obeid. "A Logical Model for Molecular Interaction Maps." In Logical Modeling of Biological Systems. John Wiley & Sons, Inc., 2014. http://dx.doi.org/10.1002/9781119005223.ch3.

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Barbuti, Roberto, Daniela Lepri, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini, and Aureliano Rama. "Simulation of Kohn’s Molecular Interaction Maps through Translation into Stochastic CLS+." In Perspectives of Systems Informatics. Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-642-11486-1_6.

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Krallinger, Martin, and Alfonso Valencia. "Applications of Text Mining in Molecular Biology, from Name Recognition to Protein Interaction Maps." In Data Analysis and Visualization in Genomics and Proteomics. John Wiley & Sons, Ltd, 2005. http://dx.doi.org/10.1002/0470094419.ch4.

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Koudriavtsev, Andrei, Reginald F. Jameson, and Wolfgang Linert. "Molecular Interactions." In The Law of Mass Action. Springer Berlin Heidelberg, 2001. http://dx.doi.org/10.1007/978-3-642-56770-4_5.

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Ryan, Colm, Gerard Cagney, Nevan Krogan, Pádraig Cunningham, and Derek Greene. "Imputing and Predicting Quantitative Genetic Interactions in Epistatic MAPs." In Methods in Molecular Biology. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-276-2_17.

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Manjeet, Kaur, and Sunita Yadav. "Role of Mapks During Plant-Insect Interaction." In Plant-Pest Interactions: From Molecular Mechanisms to Chemical Ecology. Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-15-2467-7_5.

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Tsvetkov, Philipp O., Romain La Rocca, Soazig Malesinski, and François Devred. "Characterization of Microtubule-Associated Proteins (MAPs) and Tubulin Interactions by Isothermal Titration Calorimetry (ITC)." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9179-2_12.

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Joshi, Sonali. "MAPK Interacting Protein Kinase 1 and 2 (Mnk1 and Mnk2)." In Encyclopedia of Signaling Molecules. Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-67199-4_101722.

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Joshi, Sonali. "MAPK Interacting Protein Kinase 1 and 2 (Mnk1 and Mnk2)." In Encyclopedia of Signaling Molecules. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4614-6438-9_101722-1.

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Conference papers on the topic "Molecular Interaction Maps"

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Bortolussi, Luca, Simone Fonda, and Alberto Policriti. "Constraint-Based Simulation of Biological Systems Described by Molecular Interaction Maps." In 2007 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2007). IEEE, 2007. http://dx.doi.org/10.1109/bibm.2007.31.

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Shuang-Kou Chen, Bo-Chu Wang, Wen-Zhang Huang, and Shan-bu Gao. "Molecular dynamics simulation of the interaction between Maps and Cu(100) surface." In 2010 2nd Conference on Environmental Science and Information Application Technology (ESIAT). IEEE, 2010. http://dx.doi.org/10.1109/esiat.2010.5568296.

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França, Erick Guimarães, Waleska Renata Pereira Costa, Eduardo de Faria Franca, and Carlos Alberto de Oliveira. "COMPORTAMENTO DE FTALOCIANINA LIPOSSOMAL NO CONTEXTO DA DINÂMICA MOLECULAR." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol2020173.

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Since the early 1990s, hydrated phospholipid bilayers have been studied using computational modeling methods. In this context, the simulation of the behavior of lipid biomembranes is a promising area, not only for its applications in the understanding of cell membranes, but also for its application to several drug delivery systems widely used and studied during the last decades. Is this worj performed computational simulations of lipid membranes added or not with cholesterol and zinc phthalocyanine, to obtain membrane density values, zinc phthalocyanine side diffusion, system and drug atomic mobility and density maps of the system using GROMACS. Liposomes with suitable ratio between free cholesterol and esterified cholesterol and phospholipids showed encapsulation rates of approximately 80%. In conclusion, The interaction of photosensitizers with free cholesterol influences their spatial disposition in the bi-layers and is directly related to the cell mortality rate.
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Stack, M. M., J. Rodling, and M. T. Mathew. "Micro-Abrasion-Corrosion Mapping of Bio-Materials: Some New Perspectives." In World Tribology Congress III. ASMEDC, 2005. http://dx.doi.org/10.1115/wtc2005-64156.

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Recent developments in the studies of micro-abrasion have resulted in the construction of mechanistic maps where the change in micro-abrasion is presented as a function of the main tribological parameters. However, in many practical situations where micro-abrasion occurs, the environment tends to be corrosive. In such cases, the interaction of micro-abrasion and corrosion is of interest because the combined interaction may lead to “synergistic” or “antagonistic” effects, where corrosion may have a deleterious or beneficial effect in modifying the mechanical properties of the surface. In this paper, the micro-abrasion of a Co-Cr specimen against an ultra high molecular weight polyethylene (UHMWPE) ball was studied in Ringers solution. The effects of applied load at a range of electrochemical potentials were investigated. Atomic force and scanning electron microscopy techniques were used to identify the extent of wear and the role of the corrosion film on the micro-abrasion rate enabling the various wear, corrosion and the interactive effects to be evaluated for the system. The results showed that various micro-abrasion-corrosion mechanisms could be identified in active and passive conditions. These were used to generate micro-abrasion-corrosion mechanism maps showing the change in mechanism as functions of load and applied potential and the extent of interaction between the wear and the corrosion processes was demonstrated on such maps. Possible uses of the generic form of these maps to identify micro-abrasion-corrosion mechanisms in other bio-medical applications are addressed in this paper.
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Xie, Jian-Fei, and Bing-Yang Cao. "Molecular Dynamics Study on Fluid Flow in Nanochannels With Permeable Walls." In ASME 2016 5th International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/mnhmt2016-6421.

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This paper presents the fluid flow in nanochannels with permeable walls using the molecular dynamics (MD) simulations. A three-dimensional Couette flow has been carried out to investigate the effect of the permeable surface on the fluid density distributions and the slip velocity. The ordering layer of molecules is constructed near the smooth surface but it was destroyed by the permeable ones resulting in the density drop in porous wall. The fluid density in porous wall is large under strong fluid-structure interaction (FSI) and it is decreased under weak FSI. The negative slip is observed for fluid flow past solid walls under strong FSI, no-slip under medium FSI and positive slip under weak FSI whatever it is smooth or porous. Moreover, the largest slip velocity and slip length occur on the smooth surface of solid wall. As predicted by Maxwell theory, the molecule is bounced back when it impinges on the smooth surface. The molecules, however, can reside in porous wall by replacing the molecules that are trapped in the pores. Moreover, the molecule can escape from the pore and enter the channel becoming a free molecule. After travelling for a period time in the channel, the molecule can enter the pore again. During the molecular movement, the momentum exchange has been implemented not only between fluid molecules and wall but also between the fluid molecules themselves in the pore, and the multi-collision between fluid molecules takes place. The reduced slip velocity at the porous wall results in the larger friction coefficient compared to the smooth surface wall. The molecular boundary condition predicted by Maxwell theory on the smooth surface is no longer valid for flow past the permeable surface, and a novel boundary condition should be introduced.
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Costa, Rogério F., Antônio S. N. Aguiar, Igor D. Borges, et al. "The influence of Chloride Shift Position on hydroxychlorochalcone." In VIII Simpósio de Estrutura Eletrônica e Dinâmica Molecular. Universidade de Brasília, 2020. http://dx.doi.org/10.21826/viiiseedmol202037.

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This work describes molecular structures of chalcones 2'-Hydroxy-4',6'-dimethyl-2-chlorochalcone and 2'-Hydroxy-4',6'-dimethyl-4-chlorochalcone and overlap of these structures in order to detect the change in planarity. The Hirshfeld Surface analysis to investigate when the position of the atom the chlorine in the aromatic ring is changed and how does this change influence in the properties of the organic compound. The geometric molecular were obtained through the DFT/M06-2X/6-311++G(2d, 2p) theory level. Frontier Molecular Orbital, NBO and MEP map were determined, in order to observe the information related to charge transfer in the molecule. The interactions between the molecules were verified with the aid of QTAIM.
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Zhu, Taishan, and Wenjing Ye. "Gas-Phase Heat Transfer From a Heated Microcantilever Inside a Vacuum Enclosure." In ASME 2009 Second International Conference on Micro/Nanoscale Heat and Mass Transfer. ASMEDC, 2009. http://dx.doi.org/10.1115/mnhmt2009-18469.

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The modeling of heat transfer inside a vacuum packaged MEMS devices has been performed by several researchers mostly through Monte Carlo simulations. In this work, we employ an analytical approach to study the heat transport of gas inside a high vacuum enclosure. In this pressure range, the interaction between gas molecules is negligible compared to their interaction with the walls, and hence the gas is treated as the free-molecule gas. The heated cantilever is modeled as a uniform beam with a rectangular cross section located at a certain distance away from the bottom wall which could represent a substrate in the real device. To account for various situations, the temperatures of the surrounding walls are allowed to be different from each other and different from that of the beam and the substrate. The temperature contour and the heat flux are obtained from the analytical approach. A molecular simulation code based on the direct simulation Monte Carlo (DSMC) has been developed and employed to validate the analytical results and excellent agreements have been obtained. The effects of incomplete thermal accommodation are also investigated. It is anticipated that the developed analytical solutions would be very valuable to the design of Pirani sensors and other MEMS devices utilizing micro heaters, for example, the thermal sensing atomic force microscope.
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FERRIN, THOMAS E., and EILEEN T. KRAEMER. "MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 1998. http://dx.doi.org/10.1142/9789814447300_0033.

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KRAEMER, EILEEN T., and THOMAS E. FERRIN. "MOLECULES TO MAPS: TOOLS FOR VISUALIZATION AND INTERACTION IN COMPUTATIONAL BIOLOGY." In Proceedings of the Pacific Symposium. WORLD SCIENTIFIC, 1999. http://dx.doi.org/10.1142/9789814447331_0019.

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Chen, Liang, and Satish Kumar. "Thermal Transport in Graphene Supported on Copper." In ASME 2012 Third International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/mnhmt2012-75075.

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The present study investigates the thermal transport in suspended graphene and graphene supported on copper substrate using equilibrium molecular dynamics simulations, Green-Kubo method and relaxation time approximation (RTA) approach. The thermal coupling between graphene and copper substrate was investigated by varying the interaction strength between the carbon atoms and Cu atoms at the interface. The contribution of different phonon modes to the thermal conductivity of suspended and supported graphene was analyzed in order to elucidate the graphene-substrate thermal interactions. The thermal conductivity of graphene decreases with the increasing strength of the interfacial interaction. The analysis shows that the interactions with copper substrate can reduce the thermal conductivity by up to 44%. The decrease of thermal conductivity is primarily due to the suppression of contribution from out-of-plane acoustic (ZA) phonons in the large wave vector region.
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Reports on the topic "Molecular Interaction Maps"

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Jarrold, Caroline C. Probing Metal Cluster and Metal Oxide Cluster Interactions with Organo-Sulfur and Organo-Phosphorous Molecules using Mass Spectrometry and Anion PES. Defense Technical Information Center, 2002. http://dx.doi.org/10.21236/ada425154.

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