Literatura académica sobre el tema "QM/MM simulations"
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Artículos de revistas sobre el tema "QM/MM simulations"
Suh, Donghyuk, Kwangho Nam y Wonpil Im. "CHARMM-GUI QM/MM interfacer for the hybrid QM/MM molecular dynamics simulations". Biophysical Journal 122, n.º 3 (febrero de 2023): 424a. http://dx.doi.org/10.1016/j.bpj.2022.11.2299.
Texto completoKulkarni, Prajakta U., Harshil Shah y Vivek K. Vyas. "Hybrid Quantum Mechanics/Molecular Mechanics (QM/MM) Simulation: A Tool for Structure-Based Drug Design and Discovery". Mini-Reviews in Medicinal Chemistry 22, n.º 8 (mayo de 2022): 1096–107. http://dx.doi.org/10.2174/1389557521666211007115250.
Texto completoWatanabe, Hiroshi C. y Qiang Cui. "Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations". Journal of Chemical Theory and Computation 15, n.º 7 (16 de mayo de 2019): 3917–28. http://dx.doi.org/10.1021/acs.jctc.9b00180.
Texto completode 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, n.º 9 (26 de abril de 2019): 1653. http://dx.doi.org/10.3390/molecules24091653.
Texto completoKönig, Gerhard, Frank Pickard, Jing Huang, Walter Thiel, Alexander MacKerell, Bernard Brooks y Darrin York. "A Comparison of QM/MM Simulations with and without the Drude Oscillator Model Based on Hydration Free Energies of Simple Solutes". Molecules 23, n.º 10 (19 de octubre de 2018): 2695. http://dx.doi.org/10.3390/molecules23102695.
Texto completoLiang, Dongyue, Jiewei Hong, Dong Fang, Joseph W. Bennett, Sara E. Mason, Robert J. Hamers y Qiang Cui. "Analysis of the conformational properties of amine ligands at the gold/water interface with QM, MM and QM/MM simulations". Physical Chemistry Chemical Physics 20, n.º 5 (2018): 3349–62. http://dx.doi.org/10.1039/c7cp06709g.
Texto completoYang, Wei, Ryan Bitetti-Putzer y Martin Karplus. "Chaperoned alchemical free energy simulations: A general method for QM, MM, and QM/MM potentials". Journal of Chemical Physics 120, n.º 20 (22 de mayo de 2004): 9450–53. http://dx.doi.org/10.1063/1.1738106.
Texto completoChalmet, S., D. Rinaldi y M. F. Ruiz-López. "A QM/MM/continuum model for computations in solution: Comparison with QM/MM molecular dynamics simulations". International Journal of Quantum Chemistry 84, n.º 5 (2001): 559–64. http://dx.doi.org/10.1002/qua.1410.
Texto completoShimada, J., T. Sakuma, K. Nakata, T. Wasiho y 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.
Texto completoSolt, Iván, Petr Kulhánek, István Simon, Steven Winfield, Mike C. Payne, Gábor Csányi y Monika Fuxreiter. "Evaluating Boundary Dependent Errors in QM/MM Simulations". Journal of Physical Chemistry B 113, n.º 17 (30 de abril de 2009): 5728–35. http://dx.doi.org/10.1021/jp807277r.
Texto completoTesis sobre el tema "QM/MM simulations"
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.
Texto completoVárnai, 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.
Texto completoRanaghan, 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.
Texto completoMartins, 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.
Welke, Kai [Verfasser] y 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.
Texto completoPatel, Chandan. "Hybrid molecular simulations of oxidative complex lesions". Thesis, Lyon, École normale supérieure, 2013. http://www.theses.fr/2013ENSL0835.
Texto completoDNA 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
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.
Texto completoRedox 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
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.
Texto completoRossich, 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.
Texto completoIn 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
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.
Texto completoCapítulos de libros sobre el tema "QM/MM simulations"
Steinbrecher, Thomas y Marcus Elstner. "QM and QM/MM Simulations of Proteins". En Methods in Molecular Biology, 91–124. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_5.
Texto completoMuslim, Abdul-Mueed, Jonathan P. McNamara, Hoda Abdel-Aal, Ian H. Hillier y Richard A. Bryce. "QM/MM Simulations of Carbohydrates". En ACS Symposium Series, 186–202. Washington, DC: American Chemical Society, 2006. http://dx.doi.org/10.1021/bk-2006-0930.ch010.
Texto completoGroenhof, Gerrit. "Introduction to QM/MM Simulations". En Methods in Molecular Biology, 43–66. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-017-5_3.
Texto completoLevi, Gianluca. "Computational Details of the QM/MM BOMD Simulations". En Springer Theses, 125–41. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-28611-8_10.
Texto completoBucher, Denis, Fanny Masson, J. Samuel Arey y Ursula Röthlisberger. "Hybrid QM/MM Simulations of Enzyme-Catalyzed DNA Repair Reactions". En Quantum Biochemistry, 517–35. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2010. http://dx.doi.org/10.1002/9783527629213.ch17.
Texto completoMehmood, Rimsha y Heather J. Kulik. "Quantum-Mechanical/Molecular-Mechanical (QM/MM) Simulations for Understanding Enzyme Dynamics". En Methods in Molecular Biology, 227–48. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1826-4_12.
Texto completoRothlisberger, U. y P. Carloni. "Drug-Target Binding Investigated by Quantum Mechanical/Molecular Mechanical (QM/MM) Methods". En 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.
Texto completoLiu, Haiyan. "QM/MM Energy Functions, Configuration Optimizations, and Free Energy Simulations of Enzyme Catalysis". En 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.
Texto completoMartins-Costa, Marilia T. C. y Manuel F. Ruiz-López. "Advances in QM/MM Molecular Dynamics Simulations of Chemical Processes at Aqueous Interfaces". En 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.
Texto completoLodola, Alessio, Donatella Callegari, Laura Scalvini, Silvia Rivara y Marco Mor. "Design and SAR Analysis of Covalent Inhibitors Driven by Hybrid QM/MM Simulations". En Methods in Molecular Biology, 307–37. New York, NY: Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0282-9_19.
Texto completoActas de conferencias sobre el tema "QM/MM simulations"
Xenides, Demetrios, Bernhard R. Randolf, Theodore E. Simos y George Maroulis. "Ab Initio QM∕MM Simulations of Water and Hydrated Cations". En 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.
Texto completoLin, Jung-Hsin. "Abstract 1660: Unraveling isoform selectivities of a broad class of HDAC inhibitors with QM/MM molecular dynamics simulations". En Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-1660.
Texto completoSilva Teixeira, Carla S., Sergio F. Sousa y Nuno M. F. S. A. Cerqueira. "Molecular dynamic simulations and QM/MM studies addressed to build an active Tryptophan Synthase model. A critical enzyme to treat tuberculosis". En 2019 IEEE 6th Portuguese Meeting on Bioengineering (ENBENG). IEEE, 2019. http://dx.doi.org/10.1109/enbeng.2019.8692492.
Texto completoAsada, Toshio, Kanta Ando y Shiro Koseki. "Efficient approach to obtain free energy gradient using QM/MM MD simulation". En INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2015 (ICCMSE 2015). AIP Publishing LLC, 2015. http://dx.doi.org/10.1063/1.4938813.
Texto completoElstner, M., M. Hoffmann, M. Wanko, George Maroulis y Theodore E. Simos. "Simulation of Proton Transfer Processes and Excited-State Properties in Proteins with QM∕MM Methods". En Computational Methods in Science and Engineering. AIP, 2007. http://dx.doi.org/10.1063/1.2827035.
Texto completoTongraar, Anan, Bernd M. Rode, Theodore E. Simos y George Maroulis. "Preferential Solvation and Dynamics of Ions Solvated in Mixed Solvents: Insights from QM∕MM MD Simulation Approach". En 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/10.1063/1.2836244.
Texto completoInformes sobre el tema "QM/MM simulations"
Schutt, Timothy y Manoj Shukla. Predicting the impact of aqueous ions on fate and transport of munition compounds. Engineer Research and Development Center (U.S.), agosto de 2021. http://dx.doi.org/10.21079/11681/41481.
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