Готові списки джерел за темами / MM simulations

Добірка наукової літератури з теми "MM simulations"

Автор: Grafiati
Опубліковано: 14 березня 2023

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Статті в журналах з теми "MM simulations"

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de la Lande, Aurélien, Aurelio Alvarez-Ibarra, Karim Hasnaoui, Fabien Cailliez, Xiaojing Wu, Tzonka Mineva, Jérôme Cuny, et al. "Molecular Simulations with in-deMon2k QM/MM, a Tutorial-Review." Molecules 24, no. 9 (April 26, 2019): 1653. http://dx.doi.org/10.3390/molecules24091653.

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deMon2k is a readily available program specialized in Density Functional Theory (DFT) simulations within the framework of Auxiliary DFT. This article is intended as a tutorial-review of the capabilities of the program for molecular simulations involving ground and excited electronic states. The program implements an additive QM/MM (quantum mechanics/molecular mechanics) module relying either on non-polarizable or polarizable force fields. QM/MM methodologies available in deMon2k include ground-state geometry optimizations, ground-state Born–Oppenheimer molecular dynamics simulations, Ehrenfest non-adiabatic molecular dynamics simulations, and attosecond electron dynamics. In addition several electric and magnetic properties can be computed with QM/MM. We review the framework implemented in the program, including the most recently implemented options (link atoms, implicit continuum for remote environments, metadynamics, etc.), together with six applicative examples. The applications involve (i) a reactivity study of a cyclic organic molecule in water; (ii) the establishment of free-energy profiles for nucleophilic-substitution reactions by the umbrella sampling method; (iii) the construction of two-dimensional free energy maps by metadynamics simulations; (iv) the simulation of UV-visible absorption spectra of a solvated chromophore molecule; (v) the simulation of a free energy profile for an electron transfer reaction within Marcus theory; and (vi) the simulation of fragmentation of a peptide after collision with a high-energy proton.
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Field, Martin J. "An Algorithm for Adaptive QC/MM Simulations." Journal of Chemical Theory and Computation 13, no. 5 (April 6, 2017): 2342–51. http://dx.doi.org/10.1021/acs.jctc.7b00099.

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Alameldeen, A. R., and D. A. Wood. "Addressing workload variability in architectural simulations." IEEE Micro 23, no. 6 (November 2003): 94–98. http://dx.doi.org/10.1109/mm.2003.1261392.

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Wymore, Troy, David W. Deerfield, Martin J. Field, John Hempel, and Hugh B. Nicholas. "Initial catalytic events in class 3 aldehyde dehydrogenase: MM and QM/MM simulations." Chemico-Biological Interactions 143-144 (February 2003): 75–84. http://dx.doi.org/10.1016/s0009-2797(02)00175-8.

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Zurek, Jolanta, Anna L. Bowman, W. Andrzej Sokalski, and Adrian J. Mulholland. "MM and QM/MM Modeling of Threonyl-tRNA Synthetase: Model Testing and Simulations." Structural Chemistry 15, no. 5 (October 2004): 405–14. http://dx.doi.org/10.1023/b:stuc.0000037896.80027.2c.

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Suh, Donghyuk, Kwangho Nam, and Wonpil Im. "CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations." Biophysical Journal 122, no. 3 (February 2023): 424a. http://dx.doi.org/10.1016/j.bpj.2022.11.2299.

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Anam, Muhammad Syaekhul, and S. Suwardi. "Hydration Structures and Dynamics of Ga3+ Ion Based on Molecular Mechanics Molecular Dynamics Simulation (Classical DM)." Indonesian Journal of Chemistry and Environment 4, no. 2 (March 10, 2022): 49–56. http://dx.doi.org/10.21831/ijoce.v4i2.48401.

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The structure and hydration dynamics of Ga3+ ion have been studied using classical Molecular Dynamics (MD) simulations. The data collection procedure includes determining the best base set, constructing 2-body and 3-body potential equations, classical molecular dynamics simulations based on 2-body potentials, classical molecular dynamics simulations based on 2-body + 3 potential-body. The trajectory file data analysis was done to obtain structural properties parameters such as RDF, CND, ADF, and dynamic properties, namely the movement of H2O ligands between hydrations shells. The results of the research indicated that the hydration complex structure of Ga(H2O)83+ and Ga(H2O)63+ was observed in molecular dynamics simulations (MM-2 body) and (MM-2 body + 3-body), respectively. The movement of H2O ligands occurs between the first and second shell or vice versa in the MD simulation of MM-2 bodies but does not occur in MD simulations of (MM-2 bodies + MM-3 bodies). Therefore, the water ligands in the first hydrated shell are stable.
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Shimada, J., T. Sakuma, K. Nakata, T. Wasiho, and T. Takada. "3K1015 BioMolecular Simulations : MD and QM/MM calculations." Seibutsu Butsuri 42, supplement2 (2002): S180. http://dx.doi.org/10.2142/biophys.42.s180_2.

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Solt, Iván, Petr Kulhánek, István Simon, Steven Winfield, Mike C. Payne, Gábor Csányi, and Monika Fuxreiter. "Evaluating Boundary Dependent Errors in QM/MM Simulations." Journal of Physical Chemistry B 113, no. 17 (April 30, 2009): 5728–35. http://dx.doi.org/10.1021/jp807277r.

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Morzan, Uriel N., Diego J. Alonso de Armiño, Nicolás O. Foglia, Francisco Ramírez, Mariano C. González Lebrero, Damián A. Scherlis, and Darío A. Estrin. "Spectroscopy in Complex Environments from QM–MM Simulations." Chemical Reviews 118, no. 7 (March 21, 2018): 4071–113. http://dx.doi.org/10.1021/acs.chemrev.8b00026.

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Більше джерел

Дисертації з теми "MM simulations"

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Shaw, Katherine E. "Testing QM/MM Methods Using Free Energy Simulations." Thesis, University of Bristol, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.525442.

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Várnai, Csilla. "Adaptive QM/MM simulations for reactions in solution." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609933.

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Ranaghan, Kara Elizabeth. "Analysis of key effects in enzyme-catalysed reactions by QM/MM simulations." Thesis, University of Bristol, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.432942.

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Patel, Chandan. "Hybrid molecular simulations of oxidative complex lesions." Thesis, Lyon, École normale supérieure, 2013. http://www.theses.fr/2013ENSL0835.

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L'ADN est en permanence exposé à un grand nombre d'événements dommageables déclenchées par des agents endogènes et exogènes. De nombreux travaux expérimentaux ont fourni des informations cruciales sur les propriétés structurelles et la réparation de certains des lésions de l'ADN. Cependant, il manque une vision mécanistique ou énergétique sur leur formation. La biochimie computationnelle a émergé comme un outil puissant pour comprendre les réactions biochimiques et les propriétés électroniques de systèmes complexes.Dans cette thèse, nous étudions la formation de lésions complexes intra-brin et inter-brin. Ces lésions tandem constituent une puissant menace à l'intégrité du génome, en raison de leur haute fréquence mutagenique. Tout d'abord, nous discutons l'attaque d'une liaison covalente entre un radical pyrimidinique. En comparant avec les bases isolees, nos simulations hybrides Car-Parrinello demontrent que la reactivité de la thymine et de la cytosine radicalaires sont inversees dans l'environnement B-helical. De plus, nos resultats montrent egalement une deformation plus importante pour la lesion G[8-5]C.Nous rationalisons également la plus grande réactivité des cytosines par rapport aux purines vers la formation multi-etapes de lésions complexes inter-brins par condensation avec un site C4' abasique. Ces résultats bases sur des simulations avec solvatation explicite et combines a la théorie de la fonctionnelle de la densité sont en accord avec les données expérimentales
DNA is continuously exposed to a vast number of damaging events triggered by endogenous and exogenous agents. Numerous experimental studies have provided key information regarding structural properties of some of the DNA lesions and their repair. However, they lack in mechanistic or energetic information pertaining to their formation. Computational Biochemistry has emerged as a powerful tool to understand biochemical reactions and electronic properties of large systems.In this thesis we study the formation of inter- and intra-strand cross-links. These tandem lesions pose a potent threat to genome integrity, because of their high mutagenic frequency. First, we discuss the formation of complex defects which arise from the attack of a pyrimidine radical onto guanine. In comparison with the reactivity of isolated nucleobases, our hybrid Car-Parrinello Molecular Dynamics simulations reveal that the reactivity of hydrogen-abstracted thymine and cytosine is reversed within a B-helix environment. Further, our data also suggest a more severe distortion of the B-helix for G[8-5]C.Second, we rationalize the higher reactivity of cytosine vs. purines toward the multistep formation of inter-strand crosslinks with a C4' oxidized a basic site, which is in qualitative agreement with experiments on isolated nucleobases, using explicit solvent simulations combined to density functional theory
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Martins, Ernane de Freitas. "QM/MM simulations of electronic transport properties for DNA sensing devices based on graphene." Universidade Estadual Paulista (UNESP), 2018. http://hdl.handle.net/11449/154328.

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Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Nanotechnology is an important and very active area of research contributing to many different fields. The development of new devices applied to personalized medicine is one of its applications. When we desire to develop new devices many effort are done, including experimental and theoretical investigations. The theoretical/computational physics can enormously contribute to this area, since the simulations can reveal the working mechanism in these systems being possible to understand and propose new devices with improved performance. We present an extensive theoretical investigation of the electronic transport properties of graphene-based devices for DNA sensing. We have used a hybrid methodology which combines quantum mechanics and molecular mechanics, the so called QM/MM method, coupled to electronic transport calculations using non-equilibrium Green’s functions. First, we studied graphene in solution in order to understand the effects of polarization on the electronic and transport properties under different salt concentrations. We also stud- ied graphene with Stone-Wales defect in pure water. For these systems we tested a simple polarization model based on rigid rods. Our analysis were also done over different QM/MM partitions including explicit water molecules in the quantum part. Our results showed that the inclusion of the solvent in the electronic transport calculations for graphene decreases the total transmission, showing the important role played by the water. Our results also showed that the electronic transport properties of graphene do not suffer significant changes as we increase the salt concentration in the solution. The inclusion of polarization effects in graphene, despite changing the structuring of water molecules that make up the first solvation shell of graphene, do not significantly affect the electronic transport through graphene. We then studied DNA sequencing devices. First we focused on sequencing using a nanopore between topological line defects in graphene. Our results showed that sequencing DNA with high selectivity and sensitivity using these devices appears possible. We also address nanogap in graphene. For this we looked at the effects of water on electronic transport by using different setups for the QM/MM partition. We showed that the inclusion of water molecules in the quantum part increases the electronic transmission in several orders of magnitude, also showing the fundamental role played by water in tunneling devices. The electronic transport simulations showed that the proposed device has the potential to be used in DNA sequencing, presenting high selectivity and sensitivity. We propose an graphene-based biochip for sequence-specific detection of DNA strands. The main idea of this sort of device is to detect hybridization of single-stranded DNA, forming double-stranded DNA. We showed that the vertical DNA adsorption, either through an anchor molecule (pyrene) or using the nucleotide itself as anchor, do not present good results for detection, since the signals for the single and double strands are quite similar. For the case of horizontal DNA adsorption on graphene our results indicated that the two signals can be distinguishable, showing promising potential for sensitivity and selectivity.
Nanotecnologia é uma importante e muito ativa área de pesquisa contribuindo para muitos campos diferentes. O desenvolvimento de novos dispositivos aplicados à medicina personalizada é uma de suas aplicações. Quando desejamos desenvolver novos dispositivos muitos esforços são feitos, incluindo investigações experimentais e teóricas. A Física teórica/computacional pode contribuir enormemente com esta área, já que simulações podem revelar o mecanismo de funcionamento nesses sistemas tornando possível entender e propor novos dispositivos com desempenho melhorado. Nós apresentamos uma extensa investigação teórica das propriedades de transporte eletrônico de dispositivos baseados em grafeno para sensoriamento de DNA. Utilizamos uma metodologia híbrida que combina mecânica quântica e mecânica molecular, o chamado método QM/MM, acoplado a cálculos de transporte eletrônico utilizando funções de Green fora do equilíbrio. Primeiramente nós estudamos grafeno em solução de modo a entender os efeitos de polarização nas propriedades eletrônica e de transporte em diferentes concentrações de sal. Também estudamos grafeno com defeito Stone-Wales em água pura. Para esses sistemas, testamos um modelo de polarização simples baseado em bastões rígidos. Nossas análises também foram feitas em diferentes partições QM/MM incluindo moléculas de água explícitas na parte quântica. Nossos resultados mostraram que a inclusão do solvente nos cálculos de transporte eletrônico para o grafeno diminui a transmissão total, mostrando o papel fundamento desempenhado pelo água. Nossos resultados também mostraram que as propriedades de transporte eletrônico do grafeno não sofrem mudanças significativas na medida em que aumentamos a concentração de sal na solução. A inclusão de efeitos de polarização em grafeno, apesar de mudar a estruturação das moléculas de água que compõem a primeira camada de solvatação do grafeno, não afeta significativamente o transporte eletrônico através do grafeno. Nós, então, estudamos dispositivos para sequenciamento de DNA. Focamos primeira- mente no sequenciamento usando nanoporo entre defeitos de linha topológicos no grafeno. Nossos resultados mostraram que o sequenciamento de DNA com alta seletividade e sensitividade usando esses dispositivos se mostra possível. Nós também abordamos nanogap em grafeno. Para tal, avaliamos os efeitos da água no transporte eletrônico utilizando diferentes configurações para a partição QM/MM. Mostramos que a inclusão de moléculas de água na parte quântica aumenta a transmissão eletrônica em várias ordens de grandeza, também mostrando o papel fundamental desempenhado pela água em dispositivos de tunelamento. As simulações de transporte eletrônico mostraram que o dispositivo proposto tem o potencial de ser usado em sequenciamento de DNA, apresentando alta seletividade e sensitividade. Propusemos um biochip baseado em grafeno para detecção de sequências específicas de fitas de DNA. A ideia principal desta classe de dispositivos é detectar a hibridização da fita simples de DNA, formando a fita dupla de DNA. Mostramos que a adsorção vertical de DNA, seja utilizando uma molécula âncora (pireno) ou utilizando o próprio nucleotídio como âncora, não apresenta bons resultados para detecção, já que os sinais para as fitas simples e dupla são bem próximos. Para o caso da adsorção horizontal de DNA em grafeno nossos resultados indicaram que os dois sinais podem ser distinguíveis, mostrando potencial promissor para sensitividade e seletividade.
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6

Welke, Kai [Verfasser], and M. [Akademischer Betreuer] Elstner. "QM/MM Simulations of Channelrhodopsins - Elucidating Structure and Spectroscopic Properties / Kai Welke. Betreuer: M. Elstner." Karlsruhe : KIT-Bibliothek, 2013. http://d-nb.info/1047383446/34.

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7

Gillet, Natacha. "Simulations Numériques de Transferts Interdépendants d’Electrons et de Protons dans les Protéines." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112159/document.

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Les processus d’oxydo-réduction impliquant des molécules organiques se retrouvent très fréquemment dans les protéines. Ces réactions comprennent généralement des transferts d’électrons et de protons qui se traduisent dans le bilan réactionnel par des transferts couplés proton-électron, des transferts simples d’hydrogène, d’hydrure... Une des principales méthodes pour élucider ces mécanismes est fournie par l'évaluation de grandeurs thermodynamiques et cinétiques. Expérimentalement, ces informations sont cependant obtenues avec une résolution temporelle souvent limitée à la milli/microseconde. Les simulations numériques présentées ici complètent, à des échelles de temps plus courtes (femto, pico, nanosecondes), ces données expérimentales. Il existe de nombreuses méthodes de simulations dédiées à l’étude de mécanismes redox dans les protéines combinant la description quantique des réactifs (QM) nécessaire à l’étude des changements d’états électroniques et la description classique de l’environnement (MM), l'échantillonnage de conformations se faisant grâce à des simulations de dynamique moléculaire (MD). Ces méthodes diffèrent par la qualité de la description du mécanisme réactionnel et le coût en temps de calcul. L’objectif de cette thèse est d’étudier les mécanismes de différents processus impliquant des transferts de protons et d’électrons en recherchant à chaque fois les outils adaptés. Elle comporte trois parties : i) l’évaluation de potentiels redox de cofacteurs quinones ; ii) la description du mécanisme d’oxydation du L-lactate dans l’enzyme flavocytochrome b2 ; iii) la décomposition d’un transfert formel d’hydrure entre deux flavines au sein de la protéine EmoB. Dans le cas du calcul des potentiels redox, nous utilisons une méthode notée QM+MM où la description électronique se fait en phase gaz au niveau DFT tandis que les simulations de MD s’effectuent classiquement. Nous appliquons l’approximation de réponse linéaire (ARL) pour décrire la réponse du système aux étapes de changement d’état de protonation ou d’oxydation de la fonction quinone ce qui aboutit au calcul du potentiel redox théorique. Nous avons ainsi pu établir une courbe de calibration des résultats théoriques en fonction des données expérimentales, confirmant la validité de l'ARL pour les cofacteurs quinones dans l’eau. La méthode a été étendue à la protéine MADH mais les limites de l’ARL ont été atteintes du fait des fluctuations importantes de l’environnement. L’étude de l’oxydation du L-lactate en pyruvate repose sur le calcul de surfaces d'énergie libre au niveau AM1/MM. Ces surfaces sont obtenues à l’aide de simulations de MD biaisées puis corrigées à l’aide de calculs d’énergies DFT. Différents chemins de réactions impliquant les transferts d’un proton et d’un hydrure du substrat vers une histidine et une flavine respectivement ont pu être identifiés. Ces transferts peuvent être séquentiels ou concertés suivant la conformation du site actif ou les mutations effectuées. Les surfaces concordent avec les effets observés expérimentalement. Les barrières obtenues restent cependant supérieures à celles attendues ouvrant la voie à d’autres simulations. La décomposition du mécanisme de transfert d’hydrure en transfert d’électron et d’atome d’hydrogène s’appuie sur de longues simulations classiques et des calculs d’énergies au niveau DFT contrainte (cDFT)/MM. La DFT contrainte permet de décrire les états diabatiques associés au transfert d’électron à différents stades du transfert d’hydrogène. En appliquant l’ARL, nous pouvons construire des paraboles correspondant aux états diabatiques et déterminer la séquence des évènements de transfert d'électron et d’hydrogène. La comparaison entre milieux protéique et aqueux nous a permis d’établir que le rôle de la protéine dans le transfert d'hydrure global est de bloquer le transfert d’électron en l’absence du transfert d’hydrogène empêchant ainsi la formation de flavines semi-réduites
Redox processes involving organic molecules are ubiquitous in proteins. They generally imply global reactions such as Proton Coupled Electron Transfers, hydrogen atom or hydride transfers which can be decomposed into both electrons and proton transfers. Kinetic and thermodynamic information leads to a better understanding of these mechanisms. However, experiments are often limited to a milli- or microsecond timescales. We present here numerical simulations allowing modeling at shorter timescales (femto, pico or nanosecond) to complete experimental data. Many numerical methods combine quantum description (QM) of the active center and classical description (MM) of the environment to describe redox transformations into biological media. Molecular dynamics (MD) simulations allowed a conformational sampling of the global system. Nevertheless, depending on their level of description of the QM part, the methods can cost more or less CPU time to get a good conformational sampling. In this thesis, we have studied different redox mechanisms involving both proton and electron transfers with a particular care paid to the balance between quality of the electronic description and of conformational sampling. For each mechanism, the coupled proton and electron transfers are investigated differently. This manuscript thus falls into three parts: i) the evaluation of the redox potentials quinone derivatives ; ii) the mechanistic description of the L-lactate oxidation into pyruvate in the flavocytochrome b2 enzyme; iii) decomposition of the formal hydride transfer occurring between two flavins in EmoB protein. A QM+MM scheme is chosen to evaluate redox potential of quinone cofactors: the electronic behavior is described at DFT level in gas phase while classical MDs provide a large conformational sampling of the molecule and its environment. Deprotonation and oxidation free energies are estimated by applying the linear response approximation (LRA). We finally get a theoretical value of the redox potential for different quinocofactors in water and a calibration curve of these theoretical results in function of experimental data. This curve allowed predictions of quinone redox potentials in water with a good accuracy (less than 0.1 eV). We also try our method on the MADH protein containing a Tryptophan Tryptophilquinone cofactor. However, because of great fluctuations of the environment, the LRA is not suitable for this system. This underlines the limits of our methodology. The oxidation of L-lactate to pyruvate is described by free energy surfaces obtained at AM1/MM level. Biased MDs provide the AM1/MM profile which is then corrected at DFT level. Several reactions pathways have been noticed. They consist in sequential or concerted transfers of a proton from L-lactate to a histidine and a hydride from L-lactate to a flavin cofactor. The coupling between the two transfers depends on the conformation of the active site or on the mutations. The obtained surfaces fit qualitatively the experimental data but the theoretical activation barriers are too high. Other simulations must be explored: different methods, other mechanism... Finally, a combination of long classical MDs and constrained DFT (cDFT)/MM are employed to decompose a hydride transfer between two flavins into one hydrogen atom and one electron transfer. cDFT methodology allow us to describe diabatic states associated to the electron transfer during the hydrogen atom transfer. Applying the LRA, we can build parabola of the diabatic and determine the sequence of the two transfers. The comparison of our results in the EmoB protein or in aqueous medium shows that the protein allows the electron transfer only if the hydrogen atom transfer is happening. By this way, no semi-reduced flavin is created
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8

Yang, Xuchun. "Probing the Photochemistry of Rhodopsin Through Population Dynamics Simulations." Bowling Green State University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=bgsu1563553836632515.

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9

Tamura, Kouichi. "Atomistically Deciphering Functional Large Conformational Changes of Proteins with Molecular Simulations." 京都大学 (Kyoto University), 2016. http://hdl.handle.net/2433/215334.

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10

Rossich, Molina Estefanía. "Addressing the reactivity of biomolecules in the gas phase : coupling tandem mass spectrometry with chemical dynamics simulations." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLE043.

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Durant cette thèse, nous avons abordé l'étude de la réactivité en phase gazeuse des biomolécules. L’avènement des techniques d’ionisation douces telle que l’ionisation par éléctronébulisation, a rendu possible ces dernières années, la formation d'ions en phase gazeuse sans dégrader la biomolécule étudiée.La Dissociation Induite par Collision (CID) est un cas particulier de spectrométrie de masse en tandem, que nous avons utilisée durant ce travail. Le principe du CID est d'activer les modes rovibrationnelles d’un système moléculaire ionique par collision avec un gaz inerte, ce qui augmente la probabilité de fragmentation de l'ion. Bien qu'étant une technique très utile d'un point de vue analytique, la spectrométrie de masse en tandem ne donne pas d'informations sur les mécanismes des réactions se produisant dans la cellule de collision; afin d’obtenir ces informations, les simulations de dynamique chimiques apparaissent comme un outil satisfaisant. En effet, en utilisant la dynamique directe, nous évitons ainsi d'explorer la totalité de la surface d'énergie potentielle, qui devient compliquée lors de l’étude d’édifices moléculaires de grande taille. Etant donné que les simulations de dynamique chimiques sont limitées à de courtes échelles, de l’ordre de la dizaine de picosecondes, nous avons également employé la théorie unimoléculaire RRKM (Rice-Ramsperger-Kassel-Marcus) pour étudier la réactivité à des temps plus longs, en vue de comprendre les processus réactionnels se produisant à l’issue du processus de relaxation vibrationnelle intramoléculaire (IVR). Durant ce travail de thèse, nous avons choisi d'étudier comme système modèle de base nucléique la molécule d'uracile. Par ailleurs,nous avons aussi étudié la réactivité en phase gazeuse de sucres (cellobiose, maltose et gentiobiose), qui ont été au préalable dérivatisés afin de localiser la charge sur la molécule et ainsi simplifier l’étude théorique associée
In the present thesis, we address the study of the reactivity of biomolecules in the gasphase.The advent of soft ionization techniques such as electrospray ionization, made possible, in the last years, the gentle formation of ions in the gas phase without breaking the molecule understudy.Collision Induced Dissociation (CID) is aparticular case of tandem mass spectrometrydynamics simulations are pointed like asatisfactory tool. Using direct dynamics weavoid exploring the whole potential energysurface, which becomes really complicatedwhen dealing with big molecules.Since chemical dynamics simulations arerestricted to the short time scale reactivity,typically ~10ps, we make use of the Rice–Ramsperger–Kassel–Marcus (RRKM)unimolecular theory to study the reactivity atUniversité Paris-SaclayEspace Technologique / Immeuble DiscoveryRoute de l’Orme aux Merisiers RD 128 / 91190 Saint-Aubin, Francethat we use in the present thesis. The aim of CIDis to activate the rovibrational modes of an ionicmolecular system by collisions with an inert gas,increasing the probability of the ion of beingfragmented.Despite being a really useful technique, tandemmass spectrometry does not give informationabout the mechanisms of the reactions takingplace in the collision cell; in order to obtain suchinformation, chemicallonger time scales to understand reaction pathsthat take place after intramolecular vibrationrelaxation (IVR).In the present thesis we have chosen to study asmodel system of nucleobase the uracil molecule.Furthermore, we also studied the gas-phase reactivity of carbohydrates (cellobiose, maltose and gentiobiose), which were preliminarily derivatized in order to simplify the charge localization, and consequently the theoretical study
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Частини книг з теми "MM simulations"

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Muslim, Abdul-Mueed, Jonathan P. McNamara, Hoda Abdel-Aal, Ian H. Hillier, and Richard A. Bryce. "QM/MM Simulations of Carbohydrates." In ACS Symposium Series, 186–202. Washington, DC: American Chemical Society, 2006. http://dx.doi.org/10.1021/bk-2006-0930.ch010.

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Groenhof, Gerrit. "Introduction to QM/MM Simulations." In Methods in Molecular Biology, 43–66. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_3.

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Steinbrecher, Thomas, and Marcus Elstner. "QM and QM/MM Simulations of Proteins." In Methods in Molecular Biology, 91–124. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_5.

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Levi, Gianluca. "Computational Details of the QM/MM BOMD Simulations." In Springer Theses, 125–41. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-28611-8_10.

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Bucher, Denis, Fanny Masson, J. Samuel Arey, and Ursula Röthlisberger. "Hybrid QM/MM Simulations of Enzyme-Catalyzed DNA Repair Reactions." In Quantum Biochemistry, 517–35. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2010. http://dx.doi.org/10.1002/9783527629213.ch17.

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Mehmood, Rimsha, and Heather J. Kulik. "Quantum-Mechanical/Molecular-Mechanical (QM/MM) Simulations for Understanding Enzyme Dynamics." In Methods in Molecular Biology, 227–48. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1826-4_12.

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Rothlisberger, U., and P. Carloni. "Drug-Target Binding Investigated by Quantum Mechanical/Molecular Mechanical (QM/MM) Methods." In Computer Simulations in Condensed Matter Systems: From Materials to Chemical Biology Volume 2, 449–79. Berlin, Heidelberg: Springer Berlin Heidelberg, 2006. http://dx.doi.org/10.1007/3-540-35284-8_17.

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Zhang, Xiaohua, Horacio Péréz-Sánchez, and Felice C. Lightstone. "Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach." In Bioinformatics and Biomedical Engineering, 584–93. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-16480-9_56.

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Liu, Haiyan. "QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis." In Challenges and Advances in Computational Chemistry and Physics, 331–53. Dordrecht: Springer Netherlands, 2010. http://dx.doi.org/10.1007/978-90-481-3034-4_12.

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Martins-Costa, Marilia T. C., and Manuel F. Ruiz-López. "Advances in QM/MM Molecular Dynamics Simulations of Chemical Processes at Aqueous Interfaces." In Challenges and Advances in Computational Chemistry and Physics, 303–24. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-21626-3_11.

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Тези доповідей конференцій з теми "MM simulations"

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Llorach, Gerard, Giso Grimm, Maartje M. E. Hendrikse, and Volker Hohmann. "Towards Realistic Immersive Audiovisual Simulations for Hearing Research." In MM '18: ACM Multimedia Conference. New York, NY, USA: ACM, 2018. http://dx.doi.org/10.1145/3264869.3264874.

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Castro, Juan D., Sahitya Singh, Akshaj Arora, Sara Louie, and Damir Senic. "Enabling Safe Autonomous Vehicles by Advanced mm-Wave Radar Simulations." In 2019 IEEE/MTT-S International Microwave Symposium - IMS 2019. IEEE, 2019. http://dx.doi.org/10.1109/mwsym.2019.8700843.

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Xenides, Demetrios, Bernhard R. Randolf, Theodore E. Simos, and George Maroulis. "Ab Initio QM∕MM Simulations of Water and Hydrated Cations." In COMPUTATIONAL METHODS IN SCIENCE AND ENGINEERING: Theory and Computation: Old Problems and New Challenges. Lectures Presented at the International Conference on Computational Methods in Science and Engineering 2007 (ICCMSE 2007): VOLUME 1. AIP, 2007. http://dx.doi.org/10.1063/1.2836243.

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Robertson, C. W., A. R. Young, K. Ronald, A. W. Cross, and C. G. Whyte. "Studies involving simulations of a mm-wave cusp-gun gyro-TWA." In 2013 6th UK, Europe, China Millimeter Waves and THz Technology Workshop (UCMMT). IEEE, 2013. http://dx.doi.org/10.1109/ucmmt.2013.6641536.

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Phipps, A. R., A. J. MacLachlan, C. W. Robertson, I. V. Konoplev, A. D. R. Phelps, and A. W. Cross. "PIC simulations and experimental design of a Cherenkov mm-wave source." In 2013 38th International Conference on Infrared, Millimeter, and Terahertz Waves (IRMMW-THz 2013). IEEE, 2013. http://dx.doi.org/10.1109/irmmw-thz.2013.6665535.

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Uhlig, W. Casey, Paul R. Berning, Peter T. Bartkowski, and Matthew J. Coppinger. "Electrically-Launched mm-sized Hypervelocity Projectiles." In 2019 15th Hypervelocity Impact Symposium. American Society of Mechanical Engineers, 2019. http://dx.doi.org/10.1115/hvis2019-016.

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Abstract A series of experiments and simulations were performed as proof of concept that an electrically powered research gun could propel small cylindrical projectiles to hypervelocities. Although small-caliber electrothermal accelerators and other electromagnetic launch systems have been utilized for some years for laboratory hypervelocity impact and other studies [1-5], we developed a simple, reproducible device that allows impact studies and direct comparison to magnetohydrodynamic (MHD) simulations for design considerations, efficiency improvements, and validation studies. This work focusses on 4.8 mm cylindrical 7075-T6 aluminum projectiles with a length to diameter ratio of one (nominally a mass of 0.24 grams) and a 150-mm long, 25-mm outer-diameter 4043 steel barrel with a 4.8-mm diameter bore and 9.5-mm chamber that acts as the electrical cathode. The anode consists of a 6.3-mm diameter copper rod that is reduced to 2.9 mm then tapered to a point with the tip length over diameter ratio (L/D) varying from 2 to 5. The tip is placed at the chamber/bore junction. The copper anode is insulated by a polyethylene sleeve and epoxy surrounding the electrode such that the arc initiates only at the very tip. A 191 μF capacitor was used as the power source for all experiments. The applied voltage was varied from 10 kV to 20 kV, and the resulting inductance of the system varied from approximately 320 nH to 450 nH (due to varying separation in the copper transmission lines). Fits to the current pulse using an LRC circuit resulted in resistance on the order of 10 mΩ to 15 mΩ. Typically the portion of the electrical pulse responsible for the bulk of the acceleration of the projectile occurs within the first 15 μs; however, the projectile is accelerated during the entirety of the time it remains in the barrel, which is on the order of 40 μs to 50 μs.
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Madjar, A., Z. Turski, and Yifei Li. "GaN HEMT Performance - Measurements and Simulations of a 3.6 mm Device from Cree." In Proceedings of the 36th European Microwave Conference. IEEE, 2006. http://dx.doi.org/10.1109/eumc.2006.281471.

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Matalatala, Michel, Margot Deruyck, Emmeric Tanghe, Luc Martens, and Wout Joseph. "Simulations of beamforming performance and energy efficiency for 5G mm-wave cellular networks." In 2018 IEEE Wireless Communications and Networking Conference (WCNC). IEEE, 2018. http://dx.doi.org/10.1109/wcnc.2018.8377212.

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Reniers, A. C. F., Q. Liu, M. H. A. J. Herben, and A. B. Smolders. "Review of the accuracy and precision of mm-wave antenna simulations and measurements." In 2016 10th European Conference on Antennas and Propagation (EuCAP). IEEE, 2016. http://dx.doi.org/10.1109/eucap.2016.7481973.

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Madjar, A., Z. Turski, and Yifei Li. "GaN HEMT Performance - Measurements and Simulations of a 3.6 mm Device from Cree." In 1st European Microwave Integrated Circuits Conference. IEEE, 2006. http://dx.doi.org/10.1109/emicc.2006.282689.

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Звіти організацій з теми "MM simulations"

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Schutt, Timothy, and Manoj Shukla. Predicting the impact of aqueous ions on fate and transport of munition compounds. Engineer Research and Development Center (U.S.), August 2021. http://dx.doi.org/10.21079/11681/41481.

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A model framework for natural water has been developed using computational chemistry techniques to elucidate the interactions between solvated munition compounds and eight common ions in naturally occurring water sources. The interaction energies, residence times, coordination statistics, and surface preferences of nine munition related compounds with each ion were evaluated. The propensity of these interactions to increase degradation of the munition compound was predicted using accelerated replica QM/MM simulations. The degradation prediction data qualitatively align with previous quantum mechanical studies. The results suggest that primary ions of interest for fate and transport modeling of munition compounds in natural waters may follow the relative importance of SO₄²⁻, Cl⁻ ≫ HCO₃⁻, Na⁺, Mg²⁺ > Ca²⁺, K⁺, and NH₄⁺.
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Aursjø, Olav, Aksel Hiorth, Alexey Khrulenko, and Oddbjørn Mathias Nødland. Polymer flooding: Simulation Upscaling Workflow. University of Stavanger, November 2021. http://dx.doi.org/10.31265/usps.203.

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There are many issues to consider when implementing polymer flooding offshore. On the practical side one must handle large volumes of polymer in a cost-efficient manner, and it is crucial that the injected polymer solutions maintain their desired rheological properties during transit from surface facilities and into the reservoir. On the other hand, to predict polymer flow in the reservoir, one must conduct simulations to find out which of the mechanisms observed at the pore and core scales are important for field behavior. This report focuses on theoretical aspects relevant for upscaling of polymer flooding. To this end, several numerical tools have been developed. In principle, the range of length scales covered by these tools is extremely wide: from the nm (10-9 m) to the mm (10-3 m) range, all the way up to the m and km range. However, practical limitations require the use of other tools as well, as described in the following paragraphs. The simulator BADChIMP is a pore-scale computational fluid dynamics (CFD) solver based on the Lattice Boltzmann method. At the pore scale, fluid flow is described by classical laws of nature. To a large extent, pore scale simulations can therefore be viewed as numerical experiments, and they have great potential to foster understanding of the detailed physics of polymer flooding. While valid across length scales, pore scale models require a high numerical resolution, and, subsequently, large computational resources. To model laboratory experiments, the NIORC has, through project 1.1.1 DOUCS, developed IORCoreSim. This simulator includes a comprehensive model for polymer rheological behavior (Lohne A. , Stavland, Åsen, Aursjø, & Hiorth, 2021). The model is valid at all continuum scales; however, the simulator implementation is not able to handle very large field cases, only smaller sector scale systems. To capture polymer behavior at the full field scale, simulators designed for that specific purpose must be used. One practical problem is therefore: How can we utilize the state-of-the-art polymer model, only found in IORCoreSim, as a tool to decrease the uncertainty in full field forecasts? To address this question, we suggest several strategies for how to combine different numerical tools. In the Methodological Approach section, we briefly discuss the more general issue of linking different scales and simulators. In the Validation section, we present two case studies demonstrating the proposed strategies and workflows.
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Thomas, William C. User instructions and technical details for 500 mm GHP simulation programs. Gaithersburg, MD: National Institute of Standards and Technology, July 2018. http://dx.doi.org/10.6028/nist.gcr.18-016.

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Benjamin, Kelly J., and John Starkenberg. Simulating Sympathetic Detonation of 105-mm Artillery Projectiles with CTH. Fort Belvoir, VA: Defense Technical Information Center, June 1997. http://dx.doi.org/10.21236/ada326855.

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Walsh, Kenneth P. Computer Simulation of a 155-mm Projectile in a Scat Gun Assembly. Fort Belvoir, VA: Defense Technical Information Center, September 2008. http://dx.doi.org/10.21236/ada487480.

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Payne, Nicholas, Pasquale Carlucci, and Mark Mellini. Modeling and Simulation of Engraving and Gun Launch of a 40-mm Sensor Grenade. Fort Belvoir, VA: Defense Technical Information Center, November 2008. http://dx.doi.org/10.21236/ada491473.

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Birk, Avi, and Douglas E. Kooker. A Novel Soft Recovery System for the 155-mm Projectile and Its Numerical Simulation. Fort Belvoir, VA: Defense Technical Information Center, April 2001. http://dx.doi.org/10.21236/ada393357.

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Coffee, Terence P., Gloria P. Wren, and Walter F. Morrison. A Comparison between Experiment and Simulation for Concept VIC regenerative Liquid Propellant Guns. 2. 105 mm. Fort Belvoir, VA: Defense Technical Information Center, April 1990. http://dx.doi.org/10.21236/ada222588.

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Gast, Ronald, Eric Kathe, Michael Gully, Robert Durocher, Kenneth Olsen, and Steven Pigliavento. Design, Testing, and Simulation of an Experimental 105-mm M35 Fire Out-of-Battery (FOOB) Direct Fire Gun. Fort Belvoir, VA: Defense Technical Information Center, September 2003. http://dx.doi.org/10.21236/ada417401.

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Fuchs, Marcel, Jerry Hatfield, Amos Hadas, and Rami Keren. Reducing Evaporation from Cultivated Soils by Mulching with Crop Residues and Stabilized Soil Aggregates. United States Department of Agriculture, 1993. http://dx.doi.org/10.32747/1993.7568086.bard.

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Field and laboratory studies of insulating properties of mulches show that the changes they produce on the heat balance and the evaporation depend not only on the intrinsic characteristics of the material but also on the structure of air flow in boundary layer. Field measurements of the radiation balance of corn residue showed a decrease of reflectivity from 0.2 to 0.17 from fall to spring. The aerodynamic properties of the atmospheric surface layer were turbulent, with typical roughness length of 12 to 24 mm. Evaporation from corn residue covered soils in climate chambers simulating the diurnal course of temperature in the field were up to 60% less than bare soil. Wind tunnel studies showed that turbulence in the atmospheric boundary layer added a convective component to the transport of water vapor and heat through the mulches. The decreasing the porosity of the mulch diminished this effect. Factors increasing the resistance to vapor flow lowering the effect of wind. The behavior of wheat straw and stabilized soil aggregates mulches were similar, but the resistance to water of soil aggregate layer with diameter less than 2 mm were very large, close to the values expected from molecular diffusion.
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