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Relevant bibliographies by topics / Monte Carlo; Molecules; Ligands

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Academic literature on the topic 'Monte Carlo; Molecules; Ligands'

Author: Grafiati

Published: 4 June 2021

Last updated: 9 February 2022

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Journal articles on the topic "Monte Carlo; Molecules; Ligands"

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Yang, Yang, Charles F. Campana, Gongzhen Cheng, Xinzhan Peng, and Malcolm E. Kenney. "The structure and properties of a sheathed, low reactivity silicon phthalocyanine and the potential for still more inert phthalocyanines." Journal of Porphyrins and Phthalocyanines 18, no. 04 (April 2014): 336–45. http://dx.doi.org/10.1142/s1088424614500060.

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The structure of a silicon phthalocyanine having a sheath composed of eight 1,4-isobutoxy, four bidentate 2,3-dibenzobarreleno substituents, and two trans-heptacyclopentylpentacyclooctasiloxy ligands has been determined by X-ray crystallography. The macrocycle in this compound is nearly completely covered by its sheath, but there is a channel in it which is large enough to give small diatomic molecules easy access to the macrocycle. In solution, transient channels exist in the sheath because of molecular vibrations. The structure of the compound also has been determined by a PM6 semi-empirical calculation. Except for one understandable difference, the results from this calculation are in good agreement with the results from the crystal determination. The van der Waals volume of the molecule has been determined from both the crystal and PM6 data by a Monte Carlo method. The amount of steric hindrance present in analogs of the compound in which its isobutoxy substituents are replaced by other alkoxy groups has been examined through calculations based on van der Waals volumes. Possible analogs of this sheathed molecule are suggested in which the sheath may be impenetrable to even small molecules and thus that are highly resistant to attack.

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Sasmal, Sukanya, Samuel C. Gill, Nathan M. Lim, and David L. Mobley. "Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics." Journal of Chemical Theory and Computation 16, no. 3 (February 14, 2020): 1854–65. http://dx.doi.org/10.1021/acs.jctc.9b01066.

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Freitas, Matheus Puggina de, and Teodorico de Castro Ramalho. "Employing conformational analysis in the molecular modeling of agrochemicals: insights on QSAR parameters of 2,4-D." Ciência e Agrotecnologia 37, no. 6 (December 2013): 485–94. http://dx.doi.org/10.1590/s1413-70542013000600001.

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A common practice to compute ligand conformations of compounds with various degrees of freedom to be used in molecular modeling (QSAR and docking studies) is to perform a conformational distribution based on repeated random sampling, such as Monte-Carlo methods. Further calculations are often required. This short review describes some methods used for conformational analysis and the implications of using selected conformations in QSAR. A case study is developed for 2,4-dichlorophenoxyacetic acid (2,4-D), a widely used herbicide which binds to TIR1 ubiquitin ligase enzyme. The use of such an approach and semi-empirical calculations did not achieve all possible minima for 2,4-D. In addition, the conformations and respective energies obtained by the semi-empirical AM1 method do not match the calculated trends obtained by a high level DFT method. Similar findings were obtained for the carboxylate anion, which is the bioactive form. Finally, the crystal bioactive structure of 2,4-D was not found as a minimum when using Monte-Carlo/AM1 and is similarly populated with another conformer in implicit water solution according to optimization at the B3LYP/aug-cc-pVDZ level. Therefore, quantitative structure-activity relationship (QSAR) methods based on three dimensional chemical structures are not fundamental to provide predictive models for 2,4-D congeners as TIR1 ubiquitin ligase ligands, since they do not necessarily reflect the bioactive conformation of this molecule. This probably extends to other systems.

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Hagan, Daniel, and Martin Hagan. "Soft Computing Tools for Virtual Drug Discovery." Journal of Artificial Intelligence and Soft Computing Research 8, no. 3 (July 1, 2018): 173–89. http://dx.doi.org/10.1515/jaiscr-2018-0012.

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AbstractIn this paper, we describe how several soft computing tools can be used to assist in high throughput screening of potential drug candidates. Individual small molecules (ligands) are assessed for their potential to bind to specific proteins (receptors). Committees of multilayer networks are used to classify protein-ligand complexes as good binders or bad binders, based on selected chemical descriptors. The novel aspects of this paper include the use of statistical analyses on the weights of single layer networks to select the appropriate descriptors, the use of Monte Carlo cross-validation to provide confidence measures of network performance (and also to identify problems in the data), the addition of new chemical descriptors to improve network accuracy, and the use of Self Organizing Maps to analyze the performance of the trained network and identify anomalies. We demonstrate the procedures on a large practical data set, and use them to discover a promising characteristic of the data. We also perform virtual screenings with the trained networks on a number of benchmark sets and analyze the results.

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Spill, Fabian, Zohar B. Weinstein, Atena Irani Shemirani, Nga Ho, Darash Desai, and Muhammad H. Zaman. "Controlling uncertainty in aptamer selection." Proceedings of the National Academy of Sciences 113, no. 43 (October 7, 2016): 12076–81. http://dx.doi.org/10.1073/pnas.1605086113.

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The search for high-affinity aptamers for targets such as proteins, small molecules, or cancer cells remains a formidable endeavor. Systematic Evolution of Ligands by EXponential Enrichment (SELEX) offers an iterative process to discover these aptamers through evolutionary selection of high-affinity candidates from a highly diverse random pool. This randomness dictates an unknown population distribution of fitness parameters, encoded by the binding affinities, toward SELEX targets. Adding to this uncertainty, repeating SELEX under identical conditions may lead to variable outcomes. These uncertainties pose a challenge when tuning selection pressures to isolate high-affinity ligands. Here, we present a stochastic hybrid model that describes the evolutionary selection of aptamers to explore the impact of these unknowns. To our surprise, we find that even single copies of high-affinity ligands in a pool of billions can strongly influence population dynamics, yet their survival is highly dependent on chance. We perform Monte Carlo simulations to explore the impact of environmental parameters, such as the target concentration, on selection efficiency in SELEX and identify strategies to control these uncertainties to ultimately improve the outcome and speed of this time- and resource-intensive process.

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Pranowo, Harno Dwi. "MONTE CARLO SIMULATION OF I^-, Br^-, AND Cl^- IN WATER USING AB INITIO PAIR POTENSIAL FUNCTIONS." Indonesian Journal of Chemistry 7, no. 2 (June 20, 2010): 154–59. http://dx.doi.org/10.22146/ijc.21691.

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Monte Carlo simulations were performed for I-, Br- and Cl-, in water using ab initio pair potential. The systems consisting of one anion in 215 solvent molecules have been simulated at 298 K. Anion-water pair potentials have been newly developed based on ab initio calculations of split valence basis set plus polarization quality. The structure of the solvated ion is discussed in terms of radial distribution functions, coordination number and pair potential distribution. Structural properties were investigated by means of radial distribution functions and their running integration numbers, leading for the first solvation shell to an average 12.60 H2O around I- with I--O distance of 3.74 Å and I--H distance of 2.86 Å, 11.84 H2O around Br- with Br--O distance of 3.40 Å and Br--H distance of 2.42 Å, and 10.68 H2O around Cl- with Cl--O distance of 3.20 Å and Cl--H distance of 2.24 Å, respectively. The structure of the water-anion complexes are agreed with dipole orientation. Pair energy distribution of hydrated anions showed that the pair interaction energy are increase from I-, Cl-, to Br-, namely, -6.28, -9.98 and -13.67 kcal/mol, respectively. The coordination number distribution analysis for the first solvation shell of the all hydrated anions indicated a high exchange rate for the first solvation shell ligands. Keywords: Monte Carlo simulation, halogen anion, ab initio

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Palma, Marc, and Yves Louis Pascal. "Étude théorique de la complexation des cations Pb2+ et Hg2+ par le D-talose." Canadian Journal of Chemistry 73, no. 1 (January 1, 1995): 22–40. http://dx.doi.org/10.1139/v95-005.

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Molecular modeling of interactions between D-talopyranose and D-talofuranose conformers and Pb2+ and Hg2+ cations was done in the gaseous state using the AM1 method, both with "naked" species and with some water molecules added. A complete conformational analysis of the free D-talose molecule was carried out using a Monte Carlo method (BATCHMIN program). Lower minima were identified, and the different orientations of the hydroxyl groups given. The calculated equilibrium distribution of anomers in the gaseous phase differs from that obtained experimentally in aqueous solution. This could be related to the predominance of intramolecular hydrogen bonding for the isolated molecule and intermolecular hydrogen bonding in aqueous media. In the presence of a cation, the analysis was carried out using the AM1 method for every conformation of the ligand. In the gaseous phase, Angyal's predictions are not respected. The lowest energy is represented by a flexible β-pyranosic form and some complexes are tetra or pentacoordinated. For the furanosic species, the αF forms bearing a cis-cis-cis sequence of hydroxyl groups are the less stable. Amongst the complexes of carbohydrates with metal cations in aqueous solutions, Pb2+ forms complexes and Hg2+ does not. The calculations show that, for the isolated complexes, the reverse should be true. The lesser stability in water of Hg2+ complexes with respect to Pb2+ could be interpreted in terms of (1) a more unfavourable entropic hydration effect; (2) a less favourable difference of translational entropy. A complete answer requires the dynamical study of the system in water by a Monte Carlo method. Keywords: complexes with divalent cations, D-talopyranose and D-talofuranose conformers.

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BUJOTZEK, ALEXANDER, and MARCUS WEBER. "EFFICIENT SIMULATION OF LIGAND–RECEPTOR BINDING PROCESSES USING THE CONFORMATION DYNAMICS APPROACH." Journal of Bioinformatics and Computational Biology 07, no. 05 (October 2009): 811–31. http://dx.doi.org/10.1142/s0219720009004369.

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The understanding of biological ligand–receptor binding processes is relevant for a variety of research topics and assists the rational design of novel drug molecules. Computer simulation can help to advance this understanding, but, due to the high dimensionality of according systems, suffers from the severe computational cost. Based on the framework provided by conformation dynamics and transition state theory, a novel heuristic approach of simulating ligand–receptor binding processes is introduced, which is not dependent on calculating lengthy molecular dynamics trajectories. First, the relevant portion of conformational space is partitioned with meshless methods. Then, each region is sampled separately, using hybrid Monte Carlo. Finally, the dynamical binding process is reconstructed from the static overlaps between the partial densities obtained in the sampling step. The method characterizes the metastable steps of the binding process and can yield the corresponding transition probabilities.

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Schmid, Günter, Andreas Lehnert, Ulrich Kreibig, Zbignew Adamczyk, and Peter Belouschek. "Synthese und elektronenmikroskopische Untersuchung kontrolliert gewachsener, ligandstabilisierter Goldkolloide sowie theoretische Überlegungen zur Oberflächenbelegung durch Kolloide / Synthesis and Electron Microscopic Investigation of Controlled Grown, Ligand Stabilized Gold Colloids and Theoretical Considerations on the Covering of Surfaces by Colloids." Zeitschrift für Naturforschung B 45, no. 7 (July 1, 1990): 989–94. http://dx.doi.org/10.1515/znb-1990-0713.

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18 nm Gold colloids are used as seeds for a controlled growth of 36 nm colloids which are then stabilized by P(m-C6H4SO3Na)3. These colloids can be isolated as golden leaflets and are readily soluble in water in virtually any concentration. Electron microscopic investigations prove a very small particle size distribution. X-ray powder diffraction and molecular weight determinations support the results of the electron microscopic investigations. The distance between the colloidal particles in two-dimensional layers corresponds to double-layers of phosphane ligands around each colloid, twice 1.2 nm. Isolated colloids seem to possess thicker ligand shells. A single 44 nm colloid shows a corona of about 7.2 nm thickness, corresponding to 12 phosphane layers. A quantitative description of two-dimensional packing densities is suggested using a novel theoretical model. By means of Monte Carlo simulations the two-dimensional structures are formed during the covering of supports of different geometry can be calculated.

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Russo, Anna, Pasqualina Liana Scognamiglio, Rolando Pablo Hong Enriquez, Carlo Santambrogio, Rita Grandori, Daniela Marasco, Antonio Giordano, Giacinto Scoles, and Sara Fortuna. "In Silico Generation of Peptides by Replica Exchange Monte Carlo: Docking-Based Optimization of Maltose-Binding-Protein Ligands." PLOS ONE 10, no. 8 (August 7, 2015): e0133571. http://dx.doi.org/10.1371/journal.pone.0133571.

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Dissertations / Theses on the topic "Monte Carlo; Molecules; Ligands"

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Parretti, Martin Frank. "Molecular similarity : alignment and advanced applications." Thesis, University of Oxford, 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.325831.

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Lecina, Casas Daniel. "Studying protein-ligand interactions using a Monte Carlo procedure." Doctoral thesis, Universitat de Barcelona, 2017. http://hdl.handle.net/10803/459297.

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Biomolecular simulations have been widely used in the study of protein-ligand interactions; comprehending the mechanisms involved in the prediction of binding affinities would have a significant repercussion in the pharmaceutical industry. Notwithstanding the intrinsic difficulty of sampling the phase space, hardware and methodological developments make computer simulations a promising candidate in the resolution of biophysically relevant problems. In this context, the objective of the thesis is the development of a protocol that permits studying protein-ligand interactions, in view to be applied in drug discovery pipelines. The author contributed to the rewriting PELE, our Monte Carlo sampling procedure, using good practices of software development. These involved testing, improving the readability, modularity, encapsulation, maintenance and version control, just to name a few. Importantly, the recoding resulted in a competitive cutting-edge software that is able to integrate new algorithms and platforms, such as new force fields or a graphical user interface, while being reliable and efficient. The rest of the thesis is built upon this development. At this point, we established a protocol of unbiased all-atom simulations using PELE, often combined with Markov (state) Models (MSM) to characterize the energy landscape exploration. In the thesis, we have shown that PELE is a suitable tool to map complex mechanisms in an accurate and efficient manner. For example, we successfully conducted studies of ligand migration in prolyl oligopeptidases and nuclear hormone receptors (NHRs). Using PELE, we could map the ligand migration and binding pathway in such complex systems in less than 48 hours. On the other hand, with this technique we often run batches of 100s of simulations to reduce the wall-clock time. MSM is a useful technique to join these independent simulations in a unique statistical model, as individual trajectories only need to characterize the energy landscape locally, and the global characterization can be extracted from the model. We successfully applied the combination of these two methodologies to quantify binding mechanisms and estimate the binding free energy in systems involving NHRs and tyorsinases. However, this technique represents a significant computational effort. To reduce the computational load, we developed a new methodology to overcome the sampling limitations caused by the ruggedness of the energy landscape. In particular, we used a procedure of iterative simulations with adaptive spawning points based on reinforcement learning ideas. This permits sampling binding mechanisms at a fraction of the cost, and represents a speedup of an order of magnitude in complex systems. Importantly, we show in a proof-of-concept that it can be used to estimate absolute binding free energies. Overall, we hope that the methodologies presented herein help streamline the drug design process.
Las simulaciones biomoleculares se han usado ampliamente en el estudio de interacciones proteína-ligando. Comprender los mecanismos involucrados en la predicción de afinidades de unión tiene una gran repercusión en la industria farmacéutica. A pesar de las dificultades intrínsecas en el muestreo del espacio de fases, mejoras de hardware y metodológicas hacen de las simulaciones por ordenador un candidato prometedor en la resolución de problemas biofísicos con alta relevancia. En este contexto, el objetivo de la tesis es el desarrollo de un protocolo que introduce un estudio más eficiente de las interacciones proteína-ligando, con vistas a diseminar PELE, un procedimiento de muestreo de Monte Carlo, en el diseño de fármacos. Nuestro principal foco ha sido sobrepasar las limitaciones de muestreo causadas por la rugosidad del paisaje de energías, aplicando nuestro protocolo para hacer analsis detallados a nivel atomístico en receptores nucleares de hormonas, receptores acoplados a proteínas G, tirosinasas y prolil oligopeptidasas, en colaboración con una compañía farmacéutica y de varios laboratorios experimentales. Con todo ello, esperamos que las metodologías presentadas en esta tesis ayuden a mejorar el diseño de fármacos.

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Cabeza, de Vaca López Israel. "Mapping biophysics through enhanced Monte Carlo techniques." Doctoral thesis, Universitat Politècnica de Catalunya, 2015. http://hdl.handle.net/10803/334172.

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This thesis is focused on the study of molecular interactions at the atomistic detail and is divided into one introductory chapter and four chapters referencing different problems and methodological approaches. All of them are focused on the development and improvement of computational Monte Carlo algorithms to study, in an efficient manner, the behavior of these systems at a classical molecular mechanics level. The four biophysical problems studied in this thesis are: induced fit docking between protein-ligand and between DNA-ligand to understand the binding mechanism, protein stretching response, and generation/ scoring of protein-protein docking poses. The thesis is organized as follows: First chapter corresponds to the state of the art in computational methods to study biophysical interactions, which is the starting point of this thesis. Our in-house PELE algorithm and the main standard methods such as molecular dynamics will be explained in detail. Chapter two is focused on the main PELE modifications to add new features, such as the addition of a new force field, implicit solvent and an anisotropic network specific for DNA simulation studies. We study, compare and validate the conformations generated by six representative DNA fragments with the new PELE features using molecular dynamics as a reference. Chapter three is devoted to applying the new methods implemented and tested in PELE to study protein-ligand interactions and DNA-ligand interactions using four systems. First, we study the porphyrin binding to Gun4 protein combining PELE and molecular dynamics simulations. Besides, we provide a docking pose that has been corroborated by a new crystal structure published during the revision process of the submitted study showing the accuracy of our predictions. In the second project, we use our improved version of PELE to generate the first structural model of an alpha glucose 1,6-bisphosphate substrate bound to the human Phosphomannomutase 2 demonstrating that this ligand can adopt two low-energy orientations. The third project is the study of DNA-ligand interactions for three cisplatin drugs where we evaluate the binding free energy using Markov state models. We show excellent results respect another free energy methods studied with molecular dynamics. The last project is the study of the daunomycin DNA intercalator where we simulate and study the binding process with PELE. Chapter four is focused on the computational study of force extension profiles during the protein unfolding. We added a dynamic harmonic constraint following a similar procedure applied in steered molecular dynamics to our Monte Carlo approach to fix or pull some selected atoms forcing the protein unfolding in a defined direction. We implement and compare with steered molecular dynamics this technique with Ubiquitin and Azurin proteins. Moreover, we add this feature to a well-known algorithm called MCPRO from William Jorgensen¿s group at YALE University to evaluate the free energy associated to the unfolding of the deca-alanine system. Chapter five corresponds to the introduction of a multiscale approach to study protein-protein docking. A coarse-grained model will be combined with a Monte Carlo exploration reducing the degrees of freedom to generate thousands of protein-protein poses in a quick way. Poses produced by this procedure will be refined and ranked through a protonation, hydrogen bond optimization, and minimization protocol at the all-atom representation to identify the best poses. I present two test cases where this procedure has been applied showing a good accuracy in the predictions: tryptogalinin and ferredoxin/flavodoxin systems.
Aquesta tesi es centra en l'estudi de les interaccions moleculars amb detall atomic i es divideix en un capítol d'introducció i quatre capítols que fan referència a diferents problemes i enfocaments metodològics. Tots ells se centren en el desenvolupament i millora dels algoritmes computacionals de Monte Carlo per estudiar, de manera eficient, el comportament d'aquests sistemes a un nivell mecànica molecular clàssica. Els quatre problemes biofísics estudiats en aquesta tesi són: acoblament induït entre la proteïna-lligand i entre DNA-lligant per comprendre el mecanisme d'unió, resposta de les proteïnes a l'estirament, i la generació/puntuació d'acoblament entre poses proteïna-proteïna. La tesi s'organitza de la següent manera: El primer capítol correspon a l'estat de l'art en mètodes computacionals per estudiar les interaccions biofísiques, que és el punt de partida d'aquesta tesi. El nostre PELE algoritme i els principals mètodes estàndard com ara la dinàmica molecular s'explicaran en detall. El capítol dos es centra en les principals modificacions PELE per afegir noves característiques, com ara l'addició d'un nou camp de força, solvent implícit i modes normals per aquests estudis de simulació d'ADN. Es fa un estudi, comparació i validació de les conformacions generades per sis fragments d'ADN representatius amb PELE utilitzant dinàmica molecular com a referència. El tercer capítol està dedicat a l'aplicació dels nous mètodes implementats i provats en PELE per estudiar les interaccions proteïna-lligand i la interacció lligand-DNA utilitzant quatre sistemes. En primer lloc, se estudia la unió a proteïnes GUN4 combinant PELE i simulacions de dinàmica molecular. A més, es proposa un acoblament que ha sigut corroborat per una nova estructura cristal·lina publicada durant el procés de revisió de l'estudi mostrant l'exactitud de les nostres prediccions. En el segon projecte, hem utilitzat la nostra versió millorada de PELE per generar el primer model estructural d'una glucosa alfa substrat 1,6-bisfosfat unit a la fosfomanomutasa humana 2, que demostra que aquest lligant pot adoptar dues orientacions de baiza energia. El tercer projecte és l'estudi de les interaccions d'ADN lligant per tres medicaments cisplatí on se avalua l'energia lliure d'unió utilitzant Markov States Models. Es mostren excel·lents resultats respecte d'altres mètodes d'energia lliure estudiats amb dinàmica molecular. L'últim projecte és l'estudi de l'intercalador d'ADN anomenat daunomicina on es simula i estudia el procés d'unió amb PELE. El capítol 4 es centra en l'estudi computacional dels perfils d'extensió de la força durant el desplegament de la proteïna. Hem afegit una restricció harmònica dinàmica seguint un procediment similar al aplicat en dinàmica molecular en el nostre algoritme Monte Carlo per fixar o moure alguns àtoms seleccionats obligant a desplegar la proteïna en una direcció definida. Aquesta tècnica s'ha implementat i comparat amb dinàmica molecular per les proteïnes ubiquitina i azurin. D'altra banda, hem afegit aquesta modificació a un algoritme ben conegut anomenat MCPRO del grup de William Jorgensen a la Universitat de Yale per avaluar l'energia lliure associada al desplegament del sistema deca alanina. El capítol cinc correspon a la introducció d'un enfocament multiescala per estudiar l'acoblament proteïna-proteïna. Un model de gra gruixut es combinat amb una exploració Monte Carlo per reduir els graus de llibertat i generar milers de poses proteïna-proteïna d'una manera ràpida. Les poses produides per aquest procediment es perfeccionan i evaluan a través d'una protonació, optimització d'enllaços d'hidrogen, i minimització a escala atòmica per identificar les millors poses. Es presenten dos casos de prova on s'ha aplicat aquest procediment que mostra una bona precisió en les prediccions: tryptogalinin i ferredoxina / flavodoxina systems.

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Lin, Fei Berlinsky A. J. Kallin C. Sørensen Erik S. "A quantum Monte Carlo study on the fullerene molecules and solids." *McMaster only, 2006.

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Parker, S. D. "Monte Carlo modelling of Case I and Case II solvent diffusion in polymers." Thesis, University of Surrey, 1999. http://epubs.surrey.ac.uk/843853/.

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The development of two original Monte Carlo models of solvent diffusion into a polymer is described. Employing a coarse grained model of a polymer solution on a regular lattice, the dynamic properties of both the solvent and polymer molecules can be observed. The "Simple" Monte Carlo model reliably reproduces Case I dynamics, but no departure from this is seen for any reasonable model parameters. This "Simple" Monte Carlo model is unable to reproduce Case II diffusion dynamics. One reason for this is that in this Monte Carlo model the processes of solvent diffusion and polymer relaxation are entirely independent processes. In this thesis it is suggested that a simple Monte Carlo model of this type will always produce Case I diffusion dynamics. The dynamic algorithm described in this work relies on simple instantaneous molecular motions between neighbouring lattice sites. It is shown that a diffusion process based on these motions is purely concentration dependent, relying only on the current state of the system. To use the Monte Carlo method to simulate Case II diffusion dynamics, the diffusion process is made time dependent by incorporating a history dependent model of diffusion first proposed by Crank (CRANK 1953). In this "History Dependent" Monte Carlo model the motions of both the solvent and the polymer are no longer instantaneous, but occur at a rate that approaches equilibrium by a first order process governed by a relaxation time characteristic of the viscoelastic relaxation of the polymer. This "History Dependent" Monte Carlo model successfully simulates most of the features of Case II diffusion and also demonstrates a return to Case I diffusion in the limit of long times. Unlike many models of Case II diffusion, this Monte Carlo model is able to simultaneously model the microscopic motions of both the solvent and the polymer molecules. This novel feature demonstrates the formation of a discontinuous moving boundary between the rubbery polymer and the glassy polymer that is typical of Case II diffusion dynamics.

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Lin, Haiping. "Simulations of chiral ordering of achiral molecules by Density Functional Theory and Monte Carlo." Thesis, University of Liverpool, 2008. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.490915.

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The self-organization of organic molecules on metal surfaces can play a crucial role in various subjects of science such as electrochemistry and heterogeneous catalysis. However, their practical applications have been suffering from lack of atomic scale understanding of the ordering behavior. Theoretically, however, the description of the self-assembly processes has been limited by the inability of microscopic models to account for the interplay of all elementary processes at realistic temperatures and pressures. In this work, we take the succinate molecules and Cu(1IO) surface as a model system to study the nature of the asymmetric self-assembly behavior of the achiral adsorbates on an achiral surface. In the first step, density-functional theory (DFT) is used to accurately characterize the molecule-surface system on the microscopic level. The obtained energetics is then employed to parameterize a lattice gas Hamiltonian, which subsequently allows to address the mesoscopic ordering behavior at finite temperatures by means of ~v1onte Carlo simulations. Two well-defined ordered structures have appeared in the rvlonte Carlo simulations. The (5 0, 3 2) structure has been confirmed to be the ground state configuration by direct DFT calculations. This structure has not been reported before and it can be the ordering configuration observed in some STrvI experiments. By summing up all the calculations, the nature of the self-organization behavior of succinate molecules on Cu(llO) is attributed to the indirect lateral interactions of the adsorbates. This result may provide a new understanding of designing two dimensional periodic architectures on metal surfaces. Supplied by The British Library - 'The world's knowledge'

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Suewattana, Malliga. "Monte Carlo simulations of ferroelectric crystal growth and molecular electronic structure of atoms and molecules." W&M ScholarWorks, 2005. https://scholarworks.wm.edu/etd/1539623487.

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In this thesis, we explore two stochastic techniques to study properties of materials in realistic systems. Specifically, the kinetic Monte Carlo (KMC) method is utilized to study the crystal growth process of ferroelectric materials and the quantum Monte Carlo (QMC) approach is used to investigate the ground state properties of atoms and molecules.;In the growth simulations, we study the growth rates and chemical ordering of ferroelectric alloys using an electrostatic model with long-range Coulomb interactions. Crystal growth is characterized by thermodynamic processes involving adsorption and evaporation, with solid-on-solid restrictions and excluding diffusion. A KMC algorithm is formulated to simulate this model efficiently in the presence of long-range interactions. The growth process is simulated as a function of temperature, chemical composition, and substrate orientation. We carried out the simulations on two heterovalent binaries, those of the NaCl and the Ba(Mg1/3Nb2/3))O3(BMN) structures. Compared to the simple rocksalt ordered structures, ordered BMN grows only at very low temperatures and only under finely tuned conditions. For materials with tetravalent compositions, such as (1-x)Ba(Mg 1/3Nb2/3))O3 + x BaZrO3 (BMN-BZ), the model does not incorporate tetravalent ions at low-temperature, exhibiting a phase-separated ground state instead. at higher temperatures, tetravalent ions can be incorporated, but the resulting crystals show no chemical ordering in the absence of diffusive mechanisms.;In the second part of the thesis, we present results from an auxiliary field quantum Monte Carlo (AFQMC) study of ground state properties, in particular dissociation and ionization energy, of second-row atoms and molecules. The method projects the many-body ground state from a trial wavefunction by random walks in the space of Slater determinants. The Hubbard-Stratonovich transformation is employed to decouple the Coulomb interaction between electrons. A trial wave function is used in the approximation to control the "phase problem". We also carry out Hartree-Fock (HF) and Density Functional Theory (DFT) calculations for comparison to AFQMC results and to serve as starting wavefunctions for our AFQMC calculations. Results of dissociation energy are in excellent agreement with experimental values. Ionization energy errors are somewhat larger than those of other methods. We conclude with a discussion of several possible sources of error as well as a direction for the improvement.

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Petit, Andrew S. "Monte Carlo Methods for the Study of the Ro-Vibrational States of Highly Fluxional Molecules." The Ohio State University, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=osu1366136698.

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Cleland, Deidre Mary. "The initiator full configuration interaction quantum Monte Carlo method : development and applications to molecular systems." Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610385.

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Ferrando, Nicolas. "Potentiels intermoléculaires et algorithmes de monte carlo : application à l'étude des composés oxygénés." Thesis, Paris 11, 2011. http://www.theses.fr/2011PA112080/document.

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Ce travail de thèse a pour but de proposer des potentiels d'interaction et des méthodologies pour prédire, au travers de simulations Monte Carlo, les équilibres et propriétés de phases de systèmes oxygénés rencontrés dans les procédés de conversion de la biomasse. Le potentiel AUA4 a ainsi été étendu aux alcools, éthers, cétones, aldéhydes et esters carboxyliques. Une attention particulière a été portée à la transférabilité de ce champ de forces, afin de pouvoir simuler de manière prédictive un grand nombre de molécules oxygénées. Différentes propriétés d'équilibre de corps purs sont correctement prédites (masses volumiques, pressions de saturation, enthalpies de vaporisation, propriétés critiques, tensions de surface, structure de la phase liquide). De nombreux mélanges ont également été simulés dans le pseudo-ensemble point de bulle, qui a été étendu aux molécules polaires dans le cadre de ce travail. Les résultats de simulation de mélanges complexes comme des bioessences ont été validés par l'acquisition de nouvelles mesures expérimentales. Enfin, une nouvelle méthodologie pour le calcul des interactions électrostatiques intramoléculaires a été mise au point dans ce travail pour la simulation de molécules oxygénées multifonctionnelles (polyols, éthers de glycol, composés aromatiques oxygénés). L'utilisation de cette méthode, qui permet d'éviter l'emploi de paramètres empiriques additionnels, conduit à des résultats très encourageants, ce qui laisse entrevoir de nombreuses perspectives pour la prédiction de propriétés de mélanges industriels complexes
The goal of this thesis work is to propose interaction potentials and numerical methods to predict through Monte Carlo simulations the phase equilibrium and properties of oxygenated systems involved in biomass conversion processes. The AUA4 potential was therefore extended to alcohols, ethers, ketones, aldehydes and carboxylic esters. A special care was paid to the transferability of this force field to allow the predictive simulation of a large number of oxygenated compounds. Various equilibrium properties of pure compounds are correctly predicted (densities, saturation pressures, vaporization enthalpies, critical properties, surface tensions, liquid phase structure). Many mixtures have also been simulated in the bubble point pseudo-ensemble which was extended in this work to polar molecules. The simulation results of complex mixtures such as biofuels have been validated through new experimental data acquisition. Finally, a new methodology for the intramolecular electrostatic energy interaction has been developed in this work to simulate multifunctional oxygenated molecules (polyols, glycol ethers, oxygenated aromatic compounds). The use of this method, which allows to avoid the use of additional empirical parameters, leads to promising results, giving thus future opportunities to predict properties of complex mixtures of industrial interest

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Books on the topic "Monte Carlo; Molecules; Ligands"

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Filippi, Claudia. Multiconfiguration wavefunctions for quantum Monte Carlo calculations of first-row diatomic molecules. Ithaca, N.Y: Cornell Theory Center, Cornell University, 1996.

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Allen, Michael P., and Dominic J. Tildesley. Monte Carlo methods. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198803195.003.0004.

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The estimation of integrals by Monte Carlo sampling is introduced through a simple example. The chapter then explains importance sampling, and the use of the Metropolis and Barker forms of the transition matrix defined in terms of the underlying matrix of the Markov chain. The creation of an appropriately weighted set of states in the canonical ensemble is described in detail and the method is extended to the isothermal–isobaric, grand canonical and semi-grand ensembles. The Monte Carlo simulation of molecular fluids and fluids containing flexible molecules using a reptation algorithm is discussed. The parallel tempering or replica exchange method for more efficient exploration of the phase space is introduced, and recent advances including solute tempering and convective replica exchange algorithms are described.

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Allen, Michael P., and Dominic J. Tildesley. Advanced Monte Carlo methods. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198803195.003.0009.

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This chapter describes the ways in which the Monte Carlo importance sampling method may be adapted to improve the calculation of ensemble averages, particularly those associated with free energy differences. These approaches include umbrella sampling, non-Boltzmann sampling, the Wang–Landau method, and nested sampling. In addition, a range of special techniques have been developed to accelerate the simulation of flexible molecules, such as polymers. These approaches are illustrated with scientific examples and program code. The chapter also explains the analysis of such simulations using techniques such as weighted histograms, and acceptance ratio calculations. Practical advice on selection of methods, parameters, and the direction in which to make comparisons, are given. Monte Carlo methods for modelling phase equilibria and chemical reactions at equilibrium are described.

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(Contributor), H. R. Brown, C. Creton (Contributor), C. Y. Hui (Contributor), W. H. Jo (Contributor), E. J. Kramer (Contributor), K. Suematsu (Contributor), and J. S. Yang (Contributor), eds. Molecular Simulation/Fracture/Gel Theory (Advances in Polymer Science). Springer, 2001.

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R, Brown H., ed. Molecular simulation, fracture, gel theory. Berlin: Springer, 2002.

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Book chapters on the topic "Monte Carlo; Molecules; Ligands"

1

Mavrantzas, V. G. "Monte Carlo Simulation of Chain Molecules." In Handbook of Materials Modeling, 2583–97. Dordrecht: Springer Netherlands, 2005. http://dx.doi.org/10.1007/978-1-4020-3286-8_137.

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Mavrantzas, V. G. "Monte Carlo Simulation of Chain Molecules." In Handbook of Materials Modeling, 2583–97. Dordrecht: Springer Netherlands, 2005. http://dx.doi.org/10.1007/1-4020-3286-2_137.

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Hart, Trevor N., and Randy J. Read. "Multiple-Start Monte Carlo Docking of Flexible Ligands." In The Protein Folding Problem and Tertiary Structure Prediction, 71–108. Boston, MA: Birkhäuser Boston, 1994. http://dx.doi.org/10.1007/978-1-4684-6831-1_3.

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March, N. H. "Quantum Monte Carlo Calculation of Correlation Energy." In Electron Correlation in Molecules and Condensed Phases, 75–105. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4899-1370-8_5.

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Cano, Joan, and Yves Journaux. "Monte Carlo Simulation: A Tool to Analyse Magnetic Properties." In Magnetism: Molecules to Materials, 189–222. Weinheim, Germany: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/9783527620548.ch6d.

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Schmidt, K. E., Jiong Xiang, and J. W. Moskowitz. "Monte Carlo Calculations of Atoms, Molecules, and Ions." In Recent Progress in Many-Body Theories, 305–14. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4615-3466-2_20.

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Cano, Joan, and Yves Journaux. "Monte Carlo Simulation: A Tool to Analyse Magnetic Properties." In Magnetism: Molecules to Materials V, 189–222. Weinheim, FRG: Wiley-VCH Verlag GmbH & Co. KGaA, 2005. http://dx.doi.org/10.1002/3527604383.ch6.

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Jeitler, M. "Monte-Carlo Modeling of Epithermal Effects in Muon-Catalyzed dt Fusion." In Muonic Atoms and Molecules, 137–46. Basel: Birkhäuser Basel, 1993. http://dx.doi.org/10.1007/978-3-0348-7271-3_13.

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McCoy, Anne B., Charlotte E. Hinkle, and Andrew S. Petit. "Studying Properties of Floppy Molecules Using Diffusion Monte Carlo." In ACS Symposium Series, 145–55. Washington, DC: American Chemical Society, 2012. http://dx.doi.org/10.1021/bk-2012-1094.ch012.

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Anderson, James B. "Quantum Monte Carlo: Atoms, Molecules, Clusters, Liquids, and Solids." In Reviews in Computational Chemistry, 133–82. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2007. http://dx.doi.org/10.1002/9780470125908.ch3.

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Conference papers on the topic "Monte Carlo; Molecules; Ligands"

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Gupta, Vijay K., and Charles D. Eggleton. "A Numerical Method for Coupling Nano-Scale Molecular Binding With Mesoscale Cellular Deformation." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-13296.

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Cell adhesion plays a pivotal role in diverse biological processes, including inflammation and thrombosis. Changes in cell adhesion can be the defining event in a wide range of diseases, including cancer, osteoporosis, atherosclerosis, and arthritis. Cells are exposed constantly to hemodynamic/hydrodynamic forces and the balance between the dispersive hydrodynamic forces and the adhesive forces generated by the interactions of membrane-bound receptors and their ligands determines cell adhesion. The ultimate objective of our work is to develop software that can simulate the adhesion of cells colliding under hydrodynamic forces that can be used to investigate the complex interplay among the physical mechanisms and scales involved in the adhesion process. Here, we review the development of a multi-scale model combining Monte-Carlo models of molecular binding with the Immersed Boundary Method for cellular-hydrodynamic interactions. This model predicted for the first time that the rolling of more compliant cells is relatively smoother and slower compared to cells with stiffer membranes, due to increased cell-substrate contact area. At the molecular level, we show that the average number of bonds per cell as well as per single microvillus decreases with increasing membrane stiffness. The numerical model was modified to compare the effects of different kinetic models of molecular binding on cell rolling. Simulations predict that the catch-slip bond behavior and to a lesser extent bulk cell deformation are responsible for the shear threshold phenomenon. In bulk flow, shear rate has been shown to critically affect the kinetics and receptor specificity of cell-cell interactions. We are currently simulating the adhesion of two PMN cells in quiescent conditions and the exposing the cells to external pulling forces and shear flow in order to investigate the behavior of the nano-scale molecular bonds to forces applied at the cellular scale.

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Cholewiak, G., Joachim Stelzer, and L. Longa. "Antiferroelectric smectic ordering of dipolar molecules from Monte Carlo simulations." In Liquid Crystals, edited by Jolanta Rutkowska, Stanislaw J. Klosowicz, Jerzy Zielinski, and Jozef Zmija. SPIE, 1998. http://dx.doi.org/10.1117/12.299966.

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Tyagi, Pawan, and Christopher D’Angelo. "A Monte Carlo Study of Molecular Spintronics Devices." In ASME 2013 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/imece2013-62413.

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Molecular spintronics devices (MSDs) are capable of harnessing the controllable transport and magnetic properties of molecular device elements and are highly promising candidates for revolutionizing computer logic and memory. These advanced MSD can enable the next generation of instrumentation and control devices for the wide range of mechanical engineering systems. A MSD is typically produced by placing magnetic molecule(s) between the two ferromagnetic electrodes. Recent experimental studies show that some magnetic molecules produced unprecedented strong exchange couplings between the two ferromagnetic electrodes, leading to intriguing magnetic and transport properties in a MSD. Future development of MSDs will critically depend on obtaining an in-depth understanding of the molecule induced exchange coupling, and its impact on MSD’s switchability, functional temperature range, stability etc. However, the large size of MSD systems and unsuitable device designs are the two biggest hurdles in theoretical and experimental studies of magnetic attributes produced by molecules in a MSD. This research theoretically studies the MSD by performing Monte Carlo simulations (MCS). The effect of magnetic molecule induced exchange coupling was studied at different temperature and for different device sizes — represented by a 2D Ising model. Our MCS shows that thermal energy of the MSD strongly influenced the molecular coupling effect. We studied the effect of a wide range of molecule-metal electrode couplings on the fundamental properties of MSDs. If molecules induced exchange coupling increased beyond a threshold limit a MSD acquired dramatically new attributes. Our MCS exhibited that the transition points in MSD’s magnetic properties was the interplay of temperature and molecular coupling strength. These simulations will allow the understanding of fundamental device mechanisms behind the functioning of novel MSDs. Our MSD model represents a myriad of magnetic molecules and ferromagnets combinations promising for realizing experimental MSDs. These MCS will also assist in designing new class of MSDs with desired attributes for advanced computers and control systems.

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Nakamura, Hirosi, Keiji Yamada, and Masao Doi. "Monte Carlo study on a model Langmuir monolayer of hard-rod molecules." In The 8th tohwa university international symposium on slow dynamics in complex systems. AIP, 1999. http://dx.doi.org/10.1063/1.58500.

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GRUNER, M. E., S. SIL, and P. ENTEL. "MONTE CARLO STUDY OF THE MAGNETOELASTIC PROPERTIES OF FE-NI CLUSTERS." In From Atoms, Molecules and Clusters in Complex Environment to Thin Films and Multilayers. WORLD SCIENTIFIC, 2000. http://dx.doi.org/10.1142/9789812793652_0015.

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Das, Ankan, Sandip K. Chakrabarti, Kinsuk Acharyya, and Sonali Chakrabarti. "A Monte-Carlo simulation of the production of hydrogen molecules on grain surfaces." In FIRST INTERNATIONAL CONFERENCE ON CHEMICAL EVOLUTION OF STAR FORMING REGION AND ORIGIN OF LIFE: Astrochem2012. AIP, 2013. http://dx.doi.org/10.1063/1.4812617.

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Ong, Yi Hong, Andrew Q. Li, and Timothy C. Zhu. "Monte Carlo investigation of the effect of skin tissue optical properties on detected Cherenkov emission." In Molecular-Guided Surgery: Molecules, Devices, and Applications V, edited by Brian W. Pogue and Sylvain Gioux. SPIE, 2019. http://dx.doi.org/10.1117/12.2509854.

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Naglic, Peter, Yevhen Zelinskyi, Boštjan Likar, Franjo Pernuš, and Miran Bürmen. "From Monte Carlo simulations to efficient estimation of optical properties for spatial frequency domain imaging." In Molecular-Guided Surgery: Molecules, Devices, and Applications V, edited by Brian W. Pogue and Sylvain Gioux. SPIE, 2019. http://dx.doi.org/10.1117/12.2510195.

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Saha, Sanjoy, Li Shi, and Ravi S. Prasher. "Monte Carlo Simulation of Phonon Backscattering in a Nanowire." In ASME 2006 International Mechanical Engineering Congress and Exposition. ASMEDC, 2006. http://dx.doi.org/10.1115/imece2006-15668.

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Surface roughness can play a large role in phonon transport in nanoscale devices. Phonon scattering at a surface is often treated to be either specular, diffusive, or partially specular and partially diffuse. The observation of backscattering of gas molecules on a surface has led us to speculate that under certain conditions strong phonon backscattering can occur at a surface. Such backscattering is usually not taken into account in phonon transport simulation. In this work, Monte Carlo simulation of phonon transport is employed to investigate whether phonon backscattering can occur at the surface of a silicon nanowire with V-shaped surface roughness of various sizes.

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McCoy, Anne, Andrew Petit, Melanie Marlett, and Jason Ford. "SIMULTANEOUS EVALUATION OF MULTIPLE ROTATIONALLY EXCITED STATES OF FLOPPY MOLECULES USING DIFFUSION MONTE CARLO." In 69th International Symposium on Molecular Spectroscopy. Urbana, Illinois: University of Illinois at Urbana-Champaign, 2014. http://dx.doi.org/10.15278/isms.2014.rc01.

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Reports on the topic "Monte Carlo; Molecules; Ligands"

1

Brown, W. R. Quantum Monte Carlo for vibrating molecules. Office of Scientific and Technical Information (OSTI), August 1996. http://dx.doi.org/10.2172/414375.

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Barnett, R. N. Quantum Monte Carlo for atoms and molecules. Office of Scientific and Technical Information (OSTI), November 1989. http://dx.doi.org/10.2172/7040202.

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Engelhardt, Larry. Quantum Monte Carlo Calculations Applied to Magnetic Molecules. Office of Scientific and Technical Information (OSTI), January 2006. http://dx.doi.org/10.2172/892729.

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Hammond, B. Monte Carlo for the electronic structure of molecules. Office of Scientific and Technical Information (OSTI), November 1988. http://dx.doi.org/10.2172/6224360.

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Chang, C., and M. A. Morales. Auxiliary-Field Quantum Monte Carlo Simulations of Strongly-Correlated Molecules and Solids. Office of Scientific and Technical Information (OSTI), November 2016. http://dx.doi.org/10.2172/1335769.

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Prabhat, Mr, Dmitry Zubarev, and Jr ,. William A. Lester. Statistical Exploration of Electronic Structure of Molecules from Quantum Monte-Carlo Simulations. Office of Scientific and Technical Information (OSTI), December 2010. http://dx.doi.org/10.2172/1016359.

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