Relevant bibliographies by topics / Interactive molecular simulations

Academic literature on the topic 'Interactive molecular simulations'

Author: Grafiati
Published: 25 May 2024

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Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Journal articles on the topic "Interactive molecular simulations":

1

Rapaport, D. C., and Harvey Gould. "An introduction to interactive molecular-dynamics simulations." Computers in Physics 11, no. 4 (1997): 337. http://dx.doi.org/10.1063/1.168612.

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Lanrezac, André, Benoist Laurent, Hubert Santuz, Nicolas Férey, and Marc Baaden. "Fast and Interactive Positioning of Proteins within Membranes." Algorithms 15, no. 11 (November 7, 2022): 415. http://dx.doi.org/10.3390/a15110415.

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(1) Background: We developed an algorithm to perform interactive molecular simulations (IMS) of protein alignment in membranes, allowing on-the-fly monitoring and manipulation of such molecular systems at various scales. (2) Methods: UnityMol, an advanced molecular visualization software; MDDriver, a socket for data communication; and BioSpring, a Spring network simulation engine, were extended to perform IMS. These components are designed to easily communicate with each other, adapt to other molecular simulation software, and provide a development framework for adding new interaction models to simulate biological phenomena such as protein alignment in the membrane at a fast enough rate for real-time experiments. (3) Results: We describe in detail the integration of an implicit membrane model for Integral Membrane Protein And Lipid Association (IMPALA) into our IMS framework. Our implementation can cover multiple levels of representation, and the degrees of freedom can be tuned to optimize the experience. We explain the validation of this model in an interactive and exhaustive search mode. (4) Conclusions: Protein positioning in model membranes can now be performed interactively in real time.
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Delalande, Olivier, Nicolas Férey, Gilles Grasseau, and Marc Baaden. "Complex molecular assemblies at hand via interactive simulations." Journal of Computational Chemistry 30, no. 15 (November 30, 2009): 2375–87. http://dx.doi.org/10.1002/jcc.21235.

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Lahlali, Abdelouahed, Nadia Chafiq, Mohamed Radid, Kamal Moundy, and Chaibia Srour. "The Effect of Integrating Interactive Simulations on the Development of Students’ Motivation, Engagement, Interaction and School Results." International Journal of Emerging Technologies in Learning (iJET) 18, no. 12 (June 21, 2023): 193–207. http://dx.doi.org/10.3991/ijet.v18i12.39755.

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The concept of chemical bonding and related concepts are essential topics for the fundamental understanding of chemistry courses by secondary school students. Because of the abstraction aspect, students find it difficult to understand this topic. The aim of this study is to improve students' motivation, engagement, interaction and school results by integrating interactive simulations into the teaching-learning process of chemical bonding concepts. The study was conducted in a secondary school in the Kingdom of Morocco, with a sample of 56 students in the qualifying secondary education cycle. The sample was divided into an experimental group and a control group. The experimental group is taught using more molecular models PhET simulations, while the control group follows the traditional teaching method. Using a quantitative research method with a pre- and post-test design, and an observation grid measuring students' motivation, engagement and interaction before and after the integration of interactive simulations. The data were then analysed using the IBM SPSS 25 program. The results showed that students in the experimental group working with PhET interactive simulations scored significantly higher (p<.01) than students in the control group after the post-test, thus the study showed that there is a positive correlation between students' motivation, engagement, and interaction and their school results during instruction using PhET computer simulations combined with molecular models. Therefore, the results of this study suggest that the teaching-learning of chemistry topics related to chemical bonding can be enhanced using PhET interactive simulations combined with molecular models. This research highlights the usefulness of integrating interactive simulations into the chemistry teaching-learning process.
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Dunn, Justin, and Umesh Ramnarain. "The Effect of Simulation-Supported Inquiry on South African Natural Sciences Learners’ Understanding of Atomic and Molecular Structures." Education Sciences 10, no. 10 (October 14, 2020): 280. http://dx.doi.org/10.3390/educsci10100280.

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This study investigated the effect of interactive computer simulation-supported inquiry on South African grade 8 learners’ comprehension of atoms and molecular structures. Two sample groups of 34 learners per sample group were used, one acting as a control group who were exposed to a teacher-directed pedagogy while the experimental group used simulations in inquiry-based learning as an intervention to enhance their understanding of atomic and molecular structures. Data were collected by means of conceptual tests, a questionnaire survey, and individual interviews. A statistical analysis of quantitative data gleaned from the post-test showed that the learners in the experimental group performed better than the control group learners. This reflects that the interactive simulations using in an inquiry activity impacted more favorably on the conceptual understanding of learners compared to a teacher-directed approach. The results of the questionnaire survey indicated that learners in the experimental class had a positive experience of using the simulations. They recognized that the simulations enhanced their visualization of abstract concepts, and they reflected on their efficacy in manipulating the simulation.
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Goret, G., B. Aoun, and E. Pellegrini. "MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations." Journal of Chemical Information and Modeling 57, no. 1 (January 6, 2017): 1–5. http://dx.doi.org/10.1021/acs.jcim.6b00571.

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White, Brian T., and Ethan D. Bolker. "Interactive computer simulations of genetics, biochemistry, and molecular biology." Biochemistry and Molecular Biology Education 36, no. 1 (January 2008): 77–84. http://dx.doi.org/10.1002/bmb.20152.

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Sego, T. J., James P. Sluka, Herbert M. Sauro, and James A. Glazier. "Tissue Forge: Interactive biological and biophysics simulation environment." PLOS Computational Biology 19, no. 10 (October 23, 2023): e1010768. http://dx.doi.org/10.1371/journal.pcbi.1010768.

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Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda.
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Cruz-neira, C., R. Langley, and P. A. Bash. "Interactive Molecular Modeling with Virtual Reality and Empirical Energy Simulations." SAR and QSAR in Environmental Research 9, no. 1-2 (January 1998): 39–51. http://dx.doi.org/10.1080/10629369808039148.

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McCluskey, Andrew R., James Grant, Adam R. Symington, Tim Snow, James Doutch, Benjamin J. Morgan, Stephen C. Parker, and Karen J. Edler. "An introduction to classical molecular dynamics simulation for experimental scattering users." Journal of Applied Crystallography 52, no. 3 (May 7, 2019): 665–68. http://dx.doi.org/10.1107/s1600576719004333.

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Classical molecular dynamics simulations are a common component of multi-modal analyses of scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a `black box' analysis technique. This article describes an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open-source software repository, which can be freely copied, modified and redistributed by educators. The topics covered in this OER include classical atomistic modelling, parameterizing interatomic potentials, molecular dynamics simulations, typical sources of error and some of the approaches to using simulations in the analysis of scattering data.
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Journal articles Dissertations / Theses Books

Dissertations / Theses on the topic "Interactive molecular simulations":

1

Ashe, Colin Alexander. "Interactive online simulations and curriculum for teaching and learning fundamental concepts in molecular science at the undergraduate level." Thesis, Massachusetts Institute of Technology, 2010. http://hdl.handle.net/1721.1/59212.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Materials Science and Engineering, 2010.
Includes bibliographical references (p. 213-218).
The number of research disciplines that focus, at least in part, on the atomic or molecular level is rapidly increasing. As a result, the concepts that describe the behavior of atoms and molecules, known collectively as "Molecular Science", are becoming an educational necessity for an expanding fraction of college and university students. Unfortunately, these concepts are challenging for students to learn. Because of the growing importance of these concepts and their difficulty, a project was undertaken with the goal of helping students to understand these concepts using simplified, interactive models. Students in their first year of undergraduate study were targeted. The primary goal of the project was to help students understand the so-called "energy landscape", also known as the "potential energy surface". This concept is central to Molecular Science because it contains information about both equilibrium and kinetic properties of a system. It is also widely used in textbooks and by experts for reasoning qualitatively. Interactive simulations, along with related curriculum, were created in order to help students understand the energy landscape and explore its implications. The simulations visualize simplified models, which were chosen for their analogic connection to chemical systems as well as their similarity to things with which students could intuitively relate. The primary models used were two- and three-dimensional cardboard boxes, as well as a series of platforms covered with balls. The models were simulated and visualized in Java applets. Curriculum sequences consisting of applets, exercises, and explanations were carefully constructed to present concepts in a logical order. The materials were made available online at MatDL.org, the materials pathway of the National Science Digital Library. The curriculum sequences were used as a supplemental exercise by students at Kent State University, Carnegie Mellon University (CMU), and the Massachusetts Institute of Technology (MIT). Two large assessments of student learning were conducted: one at CMU and one at MIT, involving over 400 total students. Assessment results demonstrated that using the project materials improved students' performance on the assessment tests with a greater than 99.9% degree of confidence. Free response comments indicated that students found the exercises helpful and interesting.
by Colin Alexander Ashe.
Ph.D.
2

Lanrezac, André. "Interprétation de données expérimentales par simulation et visualisation moléculaire interactive." Electronic Thesis or Diss., Université Paris Cité, 2023. http://www.theses.fr/2023UNIP7133.

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L'objectif de l'approche des simulations moléculaires interactive (Interactive Molecular Simulations - IMS) est d'observer en direct la dynamique conformationnelle d'une simulation moléculaire en cours. Le retour visuel instantané permet un suivi instructif ainsi que l'observation des changements structurels imposés par la manipulation de l'IMS par l'utilisateur. J'ai mené une étude approfondie des connaissances pour rassembler et synthétiser l'ensemble des recherches qui ont développé l'IMS. La dynamique moléculaire interactive (Interactive Molecular Dynamics - IMD) est l'un des premiers protocoles IMS qui a posé les bases du développement de cette approche. Mon laboratoire de thèse s'est inspirée de celle-ci pour développer le moteur de simulation BioSpring basé sur le modèle de réseaux élastique. Ce modèle permet de simuler la flexibilité de grands ensembles biomoléculaires et ainsi potentiellement révéler des changements à longue échelle de temps qui ne seraient pas facilement saisis par la dynamique moléculaire. Ce moteur de simulation ainsi que le logiciel de visualisation UnityMol, développé par le biais du moteur de jeu Unity3D, et liés par l'interface de communication MDDriver ont été étendus pour les faire converger vers une suite logicielle complète. Le but est de fournir à un expérimentateur, qu'il soit expert ou profane, une boîte à outils complète pour modéliser, afficher et contrôler interactivement l'ensemble des paramètres d'une simulation. L'implémentation particulière d'un tel protocole, basé sur une communication formalisée et extensible entre les différents composants, a été pensée pour pouvoir facilement intégrer de nouvelles possibilités de manipulation interactive et des jeux de données expérimentales qui s'ajouteront aux contraintes imposées à la simulation. L'utilisateur peut donc manipuler la molécule d'intérêt sous le contrôle des propriétés biophysiques intégrés dans le modèle simulé, tout en ayant la possibilité de piloter à la volée les paramètres de simulation. Aussi, un des objectifs initiaux de cette thèse était d'intégrer la gestion des contraintes d'interaction ambigües du logiciel d'amarrage biomoléculaire HADDOCK directement dans UnityMol, rendant possible l'utilisation de ces mêmes contraintes à une variété de moteurs de simulations. Un axe principal de ces recherches était de développer un algorithme de positionnement rapide et interactif de protéines dans des membranes implicite tiré d'un modèle appelé Integrative Membrane Protein and Lipid Association Method (IMPALA) développée par l'équipe de Robert Brasseur en 1998. La première étape consistait à effectuer une recherche approfondie des conditions dans lesquelles les expériences ont été réalisées à l'époque, afin de vérifier la méthode et de valider notre propre implémentation. Nous verrons qu'elle ouvre des questions intéressantes sur la manière dont on peut reproduire les expériences scientifiques. L'étape finale qui conclue cette thèse était le développement d'une nouvelle méthode universelle d'interaction lipide-protéine, UNILIPID, qui est un modèle d'incorporation interactif de protéines dans les membranes implicites. Elle est indépendante de l'échelle de représentation, peut être appliquée à des niveaux tout atomes, gros-grains jusqu'au niveau d'un grain par acide aminé. La représentation de la dernière version Martini3[6] ainsi qu'une méthode d'échantillonnage Monte-Carlo et de simulation de dynamique des corps rigides ont été spécialement intégrés à la méthode, en plus de divers outils de préparation de systèmes. En outre, UNILIPID est une approche versatile qui reproduit précisément des termes d'hydrophobicité expérimentaux pour chaque acide aminé. En plus de membranes implicites simples, je décrirai une implémentation analytique de membranes doubles ainsi qu'une généralisation à des membranes de forme arbitraire, toutes deux s'appuyant sur des applications inédites
The goal of Interactive Molecular Simulations (IMS) is to observe the conformational dynamics of a molecular simulation in real-time. Instant visual feedback enables informative monitoring and observation of structural changes imposed by the user's manipulation of the IMS. I conducted an in-depth study of knowledge to gather and synthesize all the research that has developed IMS. Interactive Molecular Dynamics (IMD) is one of the first IMS protocols that laid the foundation for the development of this approach. My thesis laboratory was inspired by IMD to develop the BioSpring simulation engine based on the elastic network model. This model allows for the simulation of the flexibility of large biomolecular ensembles, potentially revealing long-timescale changes that would not be easily captured by molecular dynamics. This simulation engine, along with the UnityMol visualization software, developed through the Unity3D game engine, and linked by the MDDriver communication interface, has been extended to converge towards a complete software suite. The goal is to provide an experimenter, whether an expert or novice, with a complete toolbox for modeling, displaying, and interactively controlling all parameters of a simulation. The particular implementation of such a protocol, based on formalized and extensible communication between the different components, was designed to easily integrate new possibilities for interactive manipulation and sets of experimental data that will be added to the restraints imposed on the simulation. Therefore, the user can manipulate the molecule of interest under the control of biophysical properties integrated into the simulated model, while also having the ability to dynamically adjust simulation parameters. Furthermore, one of the initial objectives of this thesis was to integrate the management of ambiguous interaction constraints from the HADDOCK biomolecular docking software directly into UnityMol, making it possible to use these same restraints with a variety of simulation engines. A primary focus of this research was to develop a fast and interactive protein positioning algorithm in implicit membranes using a model called the Integrative Membrane Protein and Lipid Association Method (IMPALA), developed by Robert Brasseur's team in 1998. The first step was to conduct an in-depth search of the conditions under which the experiments were performed at the time to verify the method and validate our own implementation. We will see that this opens up interesting questions about how scientific experiments can be reproduced. The final step that concluded this thesis was the development of a new universal lipid-protein interaction method, UNILIPID, which is an interactive protein incorporation model in implicit membranes. It is independent of the representation scale and can be applied at the all-atom, coarse-grain, or grain-by-grain level. The latest Martini3 representation, as well as a Monte Carlo sampling method and rigid body dynamics simulation, have been specially integrated into the method, in addition to various system preparation tools. Furthermore, UNILIPID is a versatile approach that precisely reproduces experimental hydrophobicity terms for each amino acid. In addition to simple implicit membranes, I will describe an analytical implementation of double membranes as well as a generalization to arbitrarily shaped membranes, both of which rely on novel applications
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Cardona, Amengual Javier. "Molecular simulations of the interaction of microwaves with fluids." Thesis, University of Strathclyde, 2016. http://digitool.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=27631.

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The interaction of electromagnetic radiation with matter has led to a large number of interesting applications. The propagation of electromagnetic waves within materials is described by Maxwell’s equations. However, the fundamental understanding of the causes of the response of the material, defined by constitutive relations for its complex, frequency-dependent dielectric constant, can only be achieved through the study of processes occurring at the molecular scale. The fluctuation-dissipation theorem relates the frequency-dependent dielectric constant of a material to equilibrium fluctuations in its dipole moment. This fact can be used to determine dielectric properties from equilibrium molecular dynamics simulations for frequencies covering the microwave region of the electromagnetic spectrum (300 MHz – 300 GHz). In this work, the ability of current force fields to predict dielectric spectra of one component systems and mixtures is examined, showing accurate results when compared with experimental data for the systems under consideration. Additionally, the influence of temperature on the dielectric spectra is analysed, yielding equally satisfactory results. In the particular case of ethanol/water mixtures, the estimation of dielectric spectra at intermediate concentrations using molecular dynamics simulations outperforms the traditional use of mixing rules. The simulations of these systems reveal the importance of collaborative processes between groups of molecules, such as hydrogen bond networks, in the overall dielectric response. The reduction of the contribution of these processes as temperature increases confirms the weakening of these networks at high temperatures. The predicted dielectric properties are used in a heating model to estimate temperature profiles in microwave heating processes. Unexpected results are obtained which reveal the need for accurate determination of the electric field distribution within the workload in order to obtain representative heating profiles. In contrast, penetration depths are accurately determined from dielectric properties generated through molecular simulations.
4

Bryson, Kevin. "Molecular simulation of DNA and its interaction with polyamines." Thesis, University of York, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.297070.

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França, João. "Solid-liquid interaction in ionanofluids. Experiments and molecular simulation." Thesis, Université Clermont Auvergne‎ (2017-2020), 2017. http://www.theses.fr/2017CLFAC077.

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L'un des principaux domaines de recherche en chimie et en ingénierie chimique implique l'utilisation de liquides ioniques et de nanomatériaux comme alternatives à de nombreux produits chimiques et processus chimiques, comme ce dernier étant actuellement considérés comme non respectueux de l'environnement. Leur utilisation potentiel comme nouveaux fluides de transfert de chaleur et matériaux de stockage de chaleur, qui peuvent obéir à la plupart des principes de la chimie verte, nécessite l'étude expérimentale et théorique des mécanismes de transfert de chaleur dans les fluides complexes comme les ionanofluides. Le but de cette thèse était d'étudier les ionanofluides, qui consistent en la dispersion de nanomatériaux dans un liquide ionique.Le premier objectif de ce travail était de mesurer les propriétés thermophysiques des liquides ioniques et ionanofluides, à savoir la conductivité thermique, la viscosité, la densité et la capacité thermique dans une gamme de température comprise entre -10 et 150 ºC et à pression atmosphérique. Dans ce sens, les propriétés thermophysiques d'un ensemble considérable de liquides ioniques et d'ionanofluides ont été mesurées, avec un accent particulier sur la conductivité thermique des fluides. Les liquides ioniques étudiés étaient [C2mim][EtSO4], [C4mim][(CF3SO2)2N], [C2mim][N(CN)2], [C4mim][N(CN)2], [C4mpyr][N(CN)2], [C2mim][SCN], [C4mim][SCN], [C2mim][C(CN)3], [C4mim][C(CN)3], [P66614][N(CN)2], [P66614][Br] et leurs suspensions avec 0.5% et 1% w/w de nanotubes de carbone multi-parois (MWCNTs - de l'anglais multi-walled carbon nanotubes). Les résultats obtenus montrent qu'il y a une augmentation substantielle de la conductivité thermique du fluide de base due à la suspension du nanomatériau, en considérant les deux fractions massiques. Cependant, l'amélioration varie de manière significative lorsqu'on considère différents liquides ioniques de base, avec une gamme comprise entre 2 et 30%, avec une température croissante. Ce fait rend plus difficile l'unification des informations obtenues afin d'obtenir un modèle permettant de prédire l'amélioration de la conductivité thermique. Les modèles actuellement utilisé pour calculer la conductivité thermique des nanofluides présentent des valeurs considérablement sous-estimées par rapport aux valeurs expérimentales, en partie à cause des considérations sur le rôle de l'interface solide-liquide sur le transport de la chaleur.En ce qui concerne la densité, l'impact de l'ajout de MWCNTs sur la densité du fluide de base est très faible, variant entre 0.25% et 0.5% pour 0.5% w/w et 1% w/w MWCNTs, respectivement. Cela était assez attendu et est dû à la différence considérable de densité entre les deux types de matériaux. Cependant, la viscosité était la propriété pour laquelle les valeurs les plus élevées d' augmentation ont été vérifiées, allant de 28 à 245% pour les deux fractions massiques de MWCNT. La capacité calorifique était la seule des quatre propriétés mentionnées ci-dessus à ne pas être étudiée dans ce travail en raison de problèmes techniques avec le calorimètre à utiliser. Néanmoins, la quantité de données recueillies sur les propriétés thermophysiques restantes était extensif. On pense que ce dernier contribue de manière significative à une base de données croissante des propriétés des liquides ioniques et des ionanofluides, tandis que en fournissant un aperçu de la variation des propriétés obtenues à partir de la suspension de MWCNTs dans des liquides ioniques.(...)
One of the main areas of research in chemistry and chemical engineering involves the use of ionic liquids and nanomaterials as alternatives to many chemical products and chemical processes, as the latter are currently considered to be environmentally non-friendly. Their possible use as new heat transfer fluids and heat storage materials, which can obey to most principles of green chemistry or green processing, requires the experimental and theoretical study of the heat transfer mechanisms in complex fluids, like the ionanofluids. It was the purpose of this dissertation to study ionanofluids, which consist on the dispersion of nanomaterials in an ionic liquid.The first objective of this work was to measure thermophysical properties of ionic liquids and ionanofluids, namely thermal conductivity, viscosity, density and heat capacity in a temperature range between -10 e 150 ºC and at atmospherical pressure. In this sense, the thermophysical properties of a considerable set of ionic liquids and ionanofluids were measured, with particular emphasis on the thermal conductivity of the fluids. The ionic liquids studied were [C2mim][EtSO4], [C4mim][(CF3SO2)2N], [C2mim][N(CN)2], [C4mim][N(CN)2], [C4mpyr][N(CN)2], [C2mim][SCN], [C4mim][SCN], [C2mim][C(CN)3], [C4mim][C(CN)3], [P66614][N(CN)2], [P66614][Br] and their suspensions with 0.5% and 1% w/w of multi-walled carbon nanotubes (MWCNTs). The results obtained show that there is a substantial enhancement of the thermal conductivity of the base fluid due to the suspension of the nanomaterial, considering both mass fractions. However, the enhancement varies significantly when considering different base ionic liquids, with a range between 2 to 30%, with increasing temperature. This fact makes it more difficult to unify the obtained information in order to obtain a model that allows predicting the enhancement of the thermal conductivity. Current models used to calculate the thermal conductivity of nanofluids present values that are considerably underestimated when compared to the experimental ones, somewhat due to the considerations on the role of the solid-liquid interface on heat transport.Considering density, the impact from the addition of MWCNTs on the base fluid’s density is very low, ranging between 0.25% and 0.5% for 0.5% w/w and 1% w/w MWCNTs, respectively. This was fairly expected and is due to the considerable difference in density between both types of materials. However, viscosity was the property for which the highest values of enhancement were verified, ranging between 28 and 245% in both mass fractions of MWCNTs. The heat capacity was the only of the four properties mentioned above not to be studied in this work due to technical issues with the calorimeter to be used. Nevertheless, the amount of data collected on the remainder thermophysical properties was extensive. It is believed that the latter contributes meaningfully to a growing database of ionic liquids and ionanofluids’ properties, while providing insight on the variation of said properties obtained from the suspension of MWCNTs in ionic liquids.The second objective of this work consisted on the development of molecular interaction models between ionic liquids and highly conductive nanomaterials, such as carbon nanotubes and graphene sheets. These models were constructed based on quantum calculations of the interaction energy between the ions and a cluster, providing interaction potentials. Once these models were obtained, a second stage on this computational approach entailed to simulate, by Molecular Dynamics methods, the interface nanomaterial/ionic liquid, in order to understand the specific interparticle/molecular interactions and their contribution to the heat transfer. This would allow to study both structural properties, such as the ordering of the ionic fluid at the interface, and dynamic ones, such as residence times and diffusion. (...)
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Gacek, Sobieslaw Stanislaw. "Molecular dynamics simulation of shock waves in laser-material interaction." [Ames, Iowa : Iowa State University], 2009.

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Hedman, Fredrik. "Algorithms for Molecular Dynamics Simulations." Doctoral thesis, Stockholm University, Department of Physical, Inorganic and Structural Chemistry, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1008.

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Methods for performing large-scale parallel Molecular Dynamics(MD) simulations are investigated. A perspective on the field of parallel MD simulations is given. Hardware and software aspects are characterized and the interplay between the two is briefly discussed.

A method for performing ab initio MD is described; the method essentially recomputes the interaction potential at each time-step. It has been tested on a system of liquid water by comparing results with other simulation methods and experimental results. Different strategies for parallelization are explored.

Furthermore, data-parallel methods for short-range and long-range interactions on massively parallel platforms are described and compared.

Next, a method for treating electrostatic interactions in MD simulations is developed. It combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform---ENUF for short. The method scales as N log N, where N is the number of charges in the system. ENUF has a behavior very similar to Ewald summation and can be easily and efficiently implemented in existing simulation programs.

Finally, an outlook is given and some directions for further developments are suggested.

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Marchi, Davide. "Multiscale modelling of organic molecules interacting with solids." Doctoral thesis, Università del Piemonte Orientale, 2022. http://hdl.handle.net/11579/144038.

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This Ph.D. thesis concerns the application of computational chemistry methods to molecular systems of interest, in collaboration with experimental research groups. The bulk of the work was focused on self-assembled monolayers (SAM) of thiol molecules on gold surfaces. SAMs are of central interest in surface science; they are studied for potential applications, among others, in nanolithography, biosensing, and electronics. The nature of the sulfur/gold interface is still debated: although it is commonly held that the –SH moiety dissociates to form a covalent S-Au bond, several studies report SAMs of undissociated thiols. To get insights on this point, we combined density functional theory (DFT) and molecular dynamics (MD) simulations to study in detail the thermodynamics of SAM formation on gold surfaces, using 7-mercapto-4-methylcoumarin (MMC) and 3-mercaptopropionic acid (MPA) as model molecules. The chemical potential of a thiol molecule in the SAM was computed by MD thermodynamic integration as a function of the SAM density; the maximum SAM densities for MMC and MPA in dissociated and undissociated form were computed and compared with experimental results.
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Hermansson, Anders. "Calculating Ligand-Protein Binding Energies from Molecular Dynamics Simulations." Thesis, KTH, Skolan för kemivetenskap (CHE), 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-170722.

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Indications that existing parameter sets of extended Linear Interaction Energy (LIE) models are transferable between lipases from Rhizomucor Miehei and Thermomyces Lanigunosus in complex with a small set of vinyl esters are demonstrated. By calculat- ing energy terms that represents the cost of forming cavities filled by the ligand and the complex we can add them to a LIE model with en established parameter set. The levels of precision attained will be comparable to those of an optimal fit. It is also demonstrated that the Molecular Mechanics/Poisson Boltzmann Surface Area (MM/PBSA) and Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) methods are in- applicable to the problem of calculating absolute binding energies, even when the largest source of variance has been reduced.
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Gehrcke, Jan-Philip. "Investigation of the interleukin-10-GAG interaction using molecular simulation methods." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-163205.

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Glycosaminoglycans (GAGs) are linear polysaccharides, built of periodically occurring disaccharide units. GAGs are ubiquitous in the extracellular matrix (ECM), where they exhibit multifarious biological activities. This diversity arises from - among others - their ability to interact with and regulate a large number of proteins, such as cytokines, chemokines, and growth factors. As of the huge variety in their chemical configuration, GAGs are further sub-classified into different types (heparin, for instance, is one of these sub-classes). Hence, GAGs are a diverse class of molecules, which surely contributes to the broadness of their spectrum of biological functions. Through varying arrangements of sulfate groups and different types of saccharide units, individual GAG molecules can establish specific atomic contacts to proteins. One of the best-studied examples is antithrombin-heparin, whose biologically relevant interaction requires a specific pentasaccharide sequence. It is valid to assume, however, that various proteins are yet to be discovered whose biological functions are in some way affected by GAGs. In other cases, and this is true for the cytokine interleukin-10 (IL-10), there are already experimental indications for a biologically relevant protein-GAG interaction, but the details are still obscure and the fundamental molecular interaction mechanism has still not been clarified. IL-10 has been shown to bind GAGs. So far, however, no structural detail about IL-10-GAG interaction is known. Function-wise, IL-10 is mainly considered to be immunosuppressive and therefore anti-inflammatory, but it in fact has the pleiotropic ability to influence the immune system in both directions, i.e. it constitutes a complex regulation system on its own. Therefore, the role of GAGs in this system is potentially substantial, but is yet to be clarified. In vitro experiments have yielded indications for GAGs being able to modulate IL-10\'s biological function, and obviously IL-10 and GAGs are simultaneously present in the ECM. This gives rise to the assumption that IL-10-GAG interaction is of biological significance, and that understanding the impact of GAGs on IL-10 biology is important - from the basic research point of view, but also for the development of therapies, potentially involving artificially designed ECMs. A promising approach for obtaining knowledge about the nature of IL-10-GAG interaction is its investigation on the structural level, i.e. the identification and characterization of the molecular interaction mechanisms that govern the IL-10-GAG system. In this PhD project it was my goal to reveal structural and molecular details about IL-10-GAG interaction with theoretical and computational means, and with the help of experiments performed by collaborators in the framework of the Collaborative Research Centre DFG Transregio 67. For achieving this, I developed three methods for the in silico investigation of protein-GAG systems in general and subsequently applied them to the IL-10-GAG system. Parts of that work have been published in scientific journals, as outlined further below. I proposed and validated a systematic approach for predicting GAG binding regions on a given protein, based on the numerical simulation and analysis of its Coulomb potential. One advantage of this method is its intrinsic ability to provide clues about the reliability of the resulting prediction. Application of this approach to IL-10 lead to the observation that its Coulomb attraction for GAGs is significantly weaker than in case of exemplary protein-GAG systems (such as FGF2-heparin). Still, a distinct IL-10-GAG binding region centered on the residues R102, R104, R106, R107 of the human IL-10 sequence was identified. This region can be assumed to play a major role in IL-10-GAG interaction, as described in chapter 3. Molecular docking methods are used to generate binding mode predictions for a given receptor-ligand system. In chapter 4, I clarify the importance of data clustering as an essential step for post-processing docking results and present a clustering methodology optimized for GAG molecules. It allows for a reproducible analysis, enabling systematic comparisons among different docking studies. The approach has become standard procedure in our research group. It has been applied in a variety of studies, and served as an essential tool for studying IL-10-GAG interaction, as described in chapter 3. Motivated by the shortcomings of classical docking approaches, especially with respect to protein-GAG systems, I worked on the development of a molecular dynamics-based docking method with less radical approximations than usually applied in classical docking. The goal was to make the computational model properly account for the special physical properties of GAGs, and to include the effects of receptor flexibility and solvation. The methodology was named Dynamic Molecular Docking (DMD) and published in the Journal of Chemical Information and Modeling-together with a validation study. The subsequent application of DMD in a variety of studies required enormous amounts of computational resources. For tackling this challenge, I established a graphics processing unit-based high-performance computing environment in our research group and developed a software framework for reliably performing DMD studies on this hardware, as well as on other computing resources of the TU Dresden. The investigation of the IL-10-GAG system via DMD was focused on the IL-10-GAG binding region predicted earlier, and made heavy usage of the optimized clustering approach named above. An important result of this endeavor is that IL-10's amino acid residue R107 significantly stands out compared to all other residues and supposedly plays a particularly important role in IL-10-GAG recognition. The collaboration with the NMR laboratory of Prof. Daniel Huster at the Universität Leipzig was fruitful: I post-processed nuclear Overhauser effect data and obtained heparin structure models, which revealed that IL-10-heparin interaction has a measurable impact on the backbone structure of the heparin molecule. These results were published in Glycobiology. In chapter 8, I propose two different scenarios about how GAG-binding to IL-10 might affect its biological function, based on the findings made in this thesis project. In conclusion, a set of methods has been developed, all of which are generically applicable for the investigation of protein-GAG systems. Regarding the IL-10-GAG system, valuable structural insights for increasing the understanding about its molecular mechanisms were derived. These observations pave the way towards unraveling GAG-mediated bioactivity of IL-10, which may then be specifically exploited, for instance in artificial ECMs for improved wound healing.
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Books on the topic "Interactive molecular simulations":

1

Gabriele, Cruciani, ed. Molecular interaction fields: Applications in drug discovery and ADME prediction. Weinheim: Wiley-VCH, 2005.

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Ruth, Nussinov, and Schreiber Gideon, eds. Computational protein-protein interactions. Boca Raton: CRC Press/Taylor & Francis, 2009.

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Takao, Kumazawa, Kruger Lawrence, and Mizumura Kazue, eds. The polymodal receptor: A gateway to pathological pain. Amsterdam: Elsevier, 1996.

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Folkers, Gerd, Raimund Mannhold, Hugo Kubinyi, and Gabriele Cruciani. Molecular Interaction Fields: Applications in Drug Discovery and ADME Prediction. Wiley & Sons, Incorporated, John, 2006.

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Folkers, Gerd, Raimund Mannhold, Hugo Kubinyi, and Gabriele Cruciani. Molecular Interaction Fields: Applications in Drug Discovery and ADME Prediction. Wiley-VCH Verlag GmbH, 2006.

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(Editor), Wolfgang Alt, Mark Chaplain (Editor), Michael Griebel (Editor), and Jürgen Lenz (Editor), eds. Polymer and Cell Dynamics: Multiscale Modeling and Numerical Simulations (Mathematics and Biosciences in Interaction). Birkhäuser Basel, 2003.

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Molecular interaction fields: Applications in drug discovery and ADME prediction. Weinheim, DE: Wiley-VCH, 2006.

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(Editor), Gabriele Cruciani, Raimund Mannhold (Series Editor), Hugo Kubinyi (Series Editor), and Gerd Folkers (Series Editor), eds. Molecular Interaction Fields: Applications in Drug Discovery and ADME Prediction (Methods and Principles in Medicinal Chemistry). Wiley-VCH, 2006.

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Falconi, Mattia, Arvind Ramanathan, and James Leland Olds, eds. Interaction of Biomolecules and Bioactive Compounds with the SARS-CoV-2 Proteins: Molecular Simulations for the fight against Covid-19. Frontiers Media SA, 2022. http://dx.doi.org/10.3389/978-2-88976-575-1.

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Nussinov, Ruth. Computational Protein-Protein Interactions. CRC, 2009.

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Book chapters on the topic "Interactive molecular simulations":

1

Kamberaj, Hiqmet. "Python Interactive GUI for CHARMM Software Package." In Computer Simulations in Molecular Biology, 183–208. Cham: Springer Nature Switzerland, 2023. http://dx.doi.org/10.1007/978-3-031-34839-6_9.

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Lejdfors, Calle, Malek O. Khan, Anders Ynnerman, and Bo Jönsson. "GISMOS: Graphics and Interactive Steering of MOlecular Simulations." In Lecture Notes in Computational Science and Engineering, 154–64. Berlin, Heidelberg: Springer Berlin Heidelberg, 2000. http://dx.doi.org/10.1007/978-3-642-57313-2_17.

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Botello-Smith, Wesley M., and Yun Lyna Luo. "Concepts, Practices, and Interactive Tutorial for Allosteric Network Analysis of Molecular Dynamics Simulations." In Methods in Molecular Biology, 311–34. New York, NY: Springer US, 2021. http://dx.doi.org/10.1007/978-1-0716-1394-8_17.

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Tsukanov, Alexey A., and Olga Vasiljeva. "Nanomaterials Interaction with Cell Membranes: Computer Simulation Studies." In Springer Tracts in Mechanical Engineering, 189–210. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-60124-9_9.

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AbstractThis chapter provides a brief review of computer simulation studies on the interaction of nanomaterialswith biomembranes. The interest in this area is governed by the variety of possible biomedical applications of nanoparticles and nanomaterials as well as by the importance of understanding their possible cytotoxicity. Molecular dynamics is a flexible and versatile computer simulation tool, which allows us to research the molecular level mechanisms of nanomaterials interaction with cell or bacterial membrane, predicting in silico their behavior and estimating physicochemical properties. In particular, based on the molecular dynamics simulations, a bio-action mechanism of two-dimensional aluminum hydroxide nanostructures, termed aloohene, was discovered by the research team led by Professor S. G. Psakhie, accounting for its anticancer and antimicrobial properties. Here we review three groups of nanomaterials (NMs) based on their structure: nanoparticles (globular, non-elongated), (quasi)one-dimensional NMs (nanotube, nanofiber, nanorod) and two-dimensional NMs (nanosheet, nanolayer, nanocoated substrate). Analysis of the available in silico studies, thus can enable us a better understanding of how the geometry and surface properties of NMs govern the mechanisms of their interaction with cell or bacterial membranes.
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Lim, Kap, and James N. Herron. "Molecular Simulation of Protein-PEG Interaction." In Poly(Ethylene Glycol) Chemistry, 29–56. Boston, MA: Springer US, 1992. http://dx.doi.org/10.1007/978-1-4899-0703-5_3.

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Hünenberger, P. H., and W. F. van Gunsteren. "Empirical classical interaction functions for molecular simulation." In Computer Simulation of Biomolecular Systems, 3–82. Dordrecht: Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-017-1120-3_1.

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Schmitt, S., S. Stephan, B. Kirsch, J. C. Aurich, H. M. Urbassek, and H. Hasse. "Molecular Dynamics Simulation of Cutting Processes: The Influence of Cutting Fluids at the Atomistic Scale." In Proceedings of the 3rd Conference on Physical Modeling for Virtual Manufacturing Systems and Processes, 260–80. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-35779-4_14.

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AbstractMolecular dynamics simulations are an attractive tool for studying the fundamental mechanisms of lubricated machining processes on the atomistic scale as it is not possible to access the small contact zone experimentally. Molecular dynamics simulations provide direct access to atomistic process properties of the contact zone of machining processes. In this work, lubricated machining processes were investigated, consisting of a workpiece, a tool, and a cutting fluid. The tool was fully immersed in the cutting fluid. Both, a simple model system and real substance systems were investigated. Using the simplified and generic model system, the influence of different process parameters and molecular interaction parameters were systematically studied. The real substance systems were used to represent specific real-world scenarios. The simulation results reveal that the fluid influences mainly the starting phase of an atomistic level cutting process by reducing the coefficient of friction in this phase compared to a dry case. After this starting phase of the lateral movement, the actual contact zone is mostly dry. For high pressure contacts, a tribofilm is formed between the workpiece and the cutting fluid, i.e. a significant amount of fluid particles is imprinted into the workpiece crystal structure. The presence of a cutting fluid significantly reduces the heat impact on the workpiece. Moreover, the cutting velocity is found to practically not influence the coefficient of friction, but significantly influences the dissipation and, therefore, the temperature in the contact zone. Finally, the reproducibility of the simulation method was assessed by studying replica sets of simulations of the model system.
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Corongiu, G., M. Aida, M. F. Pas, and E. Clementi. "Molecular Dynamics Simulations with ab initio Interaction Potentials." In Modem Techniques in Computational Chemistry: MOTECC-91, 847–919. Dordrecht: Springer Netherlands, 1991. http://dx.doi.org/10.1007/978-94-011-3032-5_21.

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Kumar, Veerendra, and Shivani Yaduvanshi. "Protein-Protein Interaction Studies Using Molecular Dynamics Simulation." In Methods in Molecular Biology, 269–83. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-3147-8_16.

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Yamashita, Takefumi. "Molecular Dynamics Simulation for Investigating Antigen–Antibody Interaction." In Computer-Aided Antibody Design, 101–7. New York, NY: Springer US, 2022. http://dx.doi.org/10.1007/978-1-0716-2609-2_4.

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Conference papers on the topic "Interactive molecular simulations":

1

Vanderveken, D. J., G. Baudoux, D. P. Vercauteren, and F. Durant. "KEMIT: Interactive Computer-Aided Molecular Design Using the PHIGS+Standard: Applications to Biomolecules." In Advances in biomolecular simulations. AIP, 1991. http://dx.doi.org/10.1063/1.41332.

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Lietsch, Stefan, Christoph Laroque, and Henning Zabel. "Computational Steering of Interactive Material Flow Simulations." In ASME 2008 International Design Engineering Technical Conferences and Computers and Information in Engineering Conference. ASMEDC, 2008. http://dx.doi.org/10.1115/detc2008-49405.

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In this paper we present the integration of computational steering techniques into the interactive material flow simulation d3FACT insight. This kind of simulation differs from traditional, long running High Performance Computing (HPC) simulations such as Computational Fluid Dynamics (CFD) or Molecular Dynamics in many aspects. One very important aspect is that these simulations run in (soft) real-time, thus the corresponding visualization needs to be updated after every step of the simulation. In turn, this allows to let changes, made through the visualization, impact the actual simulation and again, to see the effects in visualization. To allow this kind of control over the simulation and to further provide a flexible basis to integrate several instances of simulation, visualization and steering components, we used and enhanced a self-developed computational steering platform, which fits best for the needs of highly interactive and distributed simulations. Thereby we are able to realize multi-user and comparative scenarios which were not possible in this field of simulations before.
3

Parulek, Julius, Cagatay Turkay, Nathalie Reuter, and Ivan Viola. "Implicit surfaces for interactive graph based cavity analysis of molecular simulations." In 2012 IEEE Symposium on Biological Data Visualization (BioVis). IEEE, 2012. http://dx.doi.org/10.1109/biovis.2012.6378601.

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Jamieson-Binnie, Alexander D., Michael B. O'Connor, Jonathan Barnoud, Mark D. Wonnacott, Simon J. Bennie, and David R. Glowacki. "Narupa iMD: A VR-Enabled Multiplayer Framework for Streaming Interactive Molecular Simulations." In SIGGRAPH '20: Special Interest Group on Computer Graphics and Interactive Techniques Conference. New York, NY, USA: ACM, 2020. http://dx.doi.org/10.1145/3388536.3407891.

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Kim, BoHung, Ali Beskok, and Tahir Cagin. "Molecular Dynamics Simulations of Thermal Interactions in Nanoscale Liquid Channels." In ASME 2008 International Mechanical Engineering Congress and Exposition. ASMEDC, 2008. http://dx.doi.org/10.1115/imece2008-67448.

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Molecular Dynamics (MD) simulations of nano-scale flows typically utilize fixed lattice crystal interactions between the fluid and stationary wall molecules. This approach cannot properly model thermal exchange at the wall-fluid interface. Therefore, we use an interactive thermal wall model that can properly simulate the flow and heat transfer in nano-scale channels. Using the interactive thermal wall, Fourier law of heat conduction is verified for the 3.24 nm channel, while the thermal conductivity obtained from Fourier law is verified using the predictions of Green-Kubo theory. Moreover, temperature jumps at the liquid/solid interface, corresponding to the well known Kapitza resistance, are observed. Using systematic studies thermal resistance length at the interface is characterized as a function of the surface wettability, thermal oscillation frequency, wall temperature and thermal gradient. An empirical model for the thermal resistance length, which could be used as the jump-coefficient of a Navier boundary condition, is developed.
6

Zhao, Ruijie, Yunfei Chen, Kedong Bi, Meihui Lin, and Zan Wang. "A Modified Thermal Boundary Resistance Model for FCC Structures." In ASME 2009 Second International Conference on Micro/Nanoscale Heat and Mass Transfer. ASMEDC, 2009. http://dx.doi.org/10.1115/mnhmt2009-18175.

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A modified lattice-dynamical model is proposed to calculate the thermal boundary resistance at the interface between two fcc lattices. The nonequilibrium molecular dynamics (MD) simulation is employed to verify the theoretical calculations. In our physical model, solid crystal argon is set at the left side and the right side structure properties are tunable by setting the atomic mass and the interactive energy strength among atoms with different values. In the case of mass mismatch, the predictions of the lattice-dynamical (LD) model agree well at low temperature while the calculations of the diffuse mismatch model (DMM) based on the detailed phonon dispersion agree well at high temperature with the MD simulations. The modified LD model, considering a partially specular and partially diffuse phonon scattering, can explain the simulations reasonably in the whole temperature rage. The good agreement between the theoretical calculations and the simulations may be attributed to that phonon scattering mechanisms are dominated by elastic scattering at the perfect interfaces. In the case of interactive energy strength mismatch, the simulations are under the predictions of both the theoretical models, which may be attributed to the fact that this mismatch can bring about an outstanding contribution to opening up an inelastic channel for heat transfer at the interfaces.
7

Enemark, So̸ren, Marco A. Deriu, and Monica Soncini. "Mechanical Properties of Tubulin Molecules by Molecular Dynamics Simulations." In ASME 8th Biennial Conference on Engineering Systems Design and Analysis. ASMEDC, 2006. http://dx.doi.org/10.1115/esda2006-95674.

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The basic unit in microtubules is αβ-tubulin, a hetero-dimer consisting of an α- and a β-tubulin monomer. The mechanical characteristics of the dimer as well as of the individual monomers may be used to obtain new insight into the microtubule tensile properties. In the present work we evaluate the elastic constants of each of the monomers and the interaction force between them by means of molecular dynamics simulations. Molecular models of α-, β-, and αβ-tubulin were developed starting from the 1TUB.pdb structure from the RSCB database. Simulations were carried out in a solvated environment using explicit water molecules. In order to measure the monomers’ elastic constants, simulations were performed by mimicking experiments carried out with atomic force microscopy. A different approach was used to determine the interaction force between the α- and β-monomers using 8 different monomer configurations based on different inter-monomer distances. The obtained results show an elastic constant value for α-tubulin of 3.4–3.9 N/m, while for the β-tubulin the elastic constant was measured to be 1.8–2.4 N/m. The maximum interaction force between the monomers was estimated to be 11.2 nN. In perspective, these outcomes will allow exchanging atomic level description with key mechanical features enabling microtubule characterisation by continuum mechanics approach.
8

Darbandi, Masoud, Hossein Reza Abbasi, Moslem Sabouri, and Rasool Khaledi-Alidusti. "Simulation of Heat Transfer in Nanoscale Flow Using Molecular Dynamics." In ASME 2010 8th International Conference on Nanochannels, Microchannels, and Minichannels collocated with 3rd Joint US-European Fluids Engineering Summer Meeting. ASMEDC, 2010. http://dx.doi.org/10.1115/fedsm-icnmm2010-31065.

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We investigate heat transfer between parallel plates separated by liquid argon using two-dimensional molecular dynamics (MD) simulations incorporating with 6–12 Lennard-Jones potential between molecule pairs. In molecular dynamics simulation of nanoscale flows through nanochannels, it is customary to fix the wall molecules. However, this approach cannot suitably model the heat transfer between the fluid molecules and wall molecules. Alternatively, we use thermal walls constructed from the oscillating molecules, which are connected to their original positions using linear spring forces. This approach is much more effective than the one which uses a fixed lattice wall modeling to simulate the heat transfer between wall and fluid. We implement this idea in analyzing the heat transfer in a few cases, including the shear driven and poiseuille flow with specified heat flux boundary conditions. In this method, the work done by the viscous stress (in case of shear driven flow) and the force applied to the fluid molecules (in case of poiseuille flow) produce heat in the fluid, which is dissipated from the nanochannel walls. We present the velocity profiles and temperature distributions for the both chosen test cases. As a result of interaction between the fluid molecules and their adjacent wall molecules, we can clearly observe the velocity slip in the velocity profiles and the temperature jump in the cross-sectional temperature distributions.
9

Xie, Jian-Fei, and Bing-Yang Cao. "Molecular Dynamics Study on Fluid Flow in Nanochannels With Permeable Walls." In ASME 2016 5th International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/mnhmt2016-6421.

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This paper presents the fluid flow in nanochannels with permeable walls using the molecular dynamics (MD) simulations. A three-dimensional Couette flow has been carried out to investigate the effect of the permeable surface on the fluid density distributions and the slip velocity. The ordering layer of molecules is constructed near the smooth surface but it was destroyed by the permeable ones resulting in the density drop in porous wall. The fluid density in porous wall is large under strong fluid-structure interaction (FSI) and it is decreased under weak FSI. The negative slip is observed for fluid flow past solid walls under strong FSI, no-slip under medium FSI and positive slip under weak FSI whatever it is smooth or porous. Moreover, the largest slip velocity and slip length occur on the smooth surface of solid wall. As predicted by Maxwell theory, the molecule is bounced back when it impinges on the smooth surface. The molecules, however, can reside in porous wall by replacing the molecules that are trapped in the pores. Moreover, the molecule can escape from the pore and enter the channel becoming a free molecule. After travelling for a period time in the channel, the molecule can enter the pore again. During the molecular movement, the momentum exchange has been implemented not only between fluid molecules and wall but also between the fluid molecules themselves in the pore, and the multi-collision between fluid molecules takes place. The reduced slip velocity at the porous wall results in the larger friction coefficient compared to the smooth surface wall. The molecular boundary condition predicted by Maxwell theory on the smooth surface is no longer valid for flow past the permeable surface, and a novel boundary condition should be introduced.
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Banerjee, Soumik. "Molecular Simulation of the Self-Agglomeration of Carbon Nanostructures in Various Chemical Environments." In ASME 2012 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/imece2012-89697.

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Self-assembly of carbon nanostructures in solutions provides a cost-effective means to synthesize uniform vertically-aligned nanostructures with specific morphologies including shapes such as wires, sheets and spherical particles. In addition to facilitating the synthesis of bulk carbon nanomaterial, a complete understanding of the agglomeration mechanics also provides a means to deposit uniform layers of carbon nanostructures on top of substrates to produce molecularly-tailored composites with specific mechanical properties. Self-assembly is a complex dynamical process that involves the interaction between the nanoparticle precursors, the transport properties of the individual precursor molecules as well as the precursor-solvent interactions. Depending on the chemical nature of the solvent used during the process various nanostructures of varying shapes and morphologies can be synthesized starting from individual buckyballs and nanotubes. However, despite its wide range of applications, there is a lack of understanding of the self-assembly of carbon nanoparticles. Some of the key factors that govern the agglomeration process are the π-π interaction of the aromatic carbon nanostructures and their interaction with the solvent molecules. A predictive model for self-assembly, that relates the above parameters to the morphology, therefore needs to account for the specific molecular interactions. We present molecular simulation results that incorporate the above effects and shows that the nature of association of the nanoparticle precursors determines the shape and size of the agglomerate. Furthermore, our results show the dependency of the agglomerate size on the concentration of precursors as well as the ambient temperature.

Reports on the topic "Interactive molecular simulations":

1

Hill, Christian. International Atomic and Molecular Code Centres Network: Database Services for Radiation Damage in Nuclear Materials. IAEA Nuclear Data Section, January 2020. http://dx.doi.org/10.61092/iaea.agtk-r4gy.

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The International Code Centres Network (CCN) is a group of experts developing codes and models for atomic, molecular and plasma-surface interaction data relevant to fusion applications. Variable subsets of the group are brought together by the IAEA Atomic and Molecular Data (AMD) Unit in order to discuss computational and scientific issues associated with code developments. At the 6th Technical Meeting described in this report, 11 experts in the field of Molecular Dynamics (MD) simulations of radiation damage reviewed CascadesDB, a database of atomic configurations generated by MD simulations of collision cascades. This database is developed and hosted by the AMD Unit and provides a central repository for the results of MD simulations of the evolution of a material’s structure following an impact by a high energy particle. Further plans to extend and enhance CascadesDB, and to establish a new database resource, DefectDB, containing density functional theory calculations of defect structures were also discussed.
2

Hill, C. Summary Report of the 7th Biennial Technical Meeting of the Code Centres Network of the International Atomic and Molecular Code Centres Network: Database Services for Radiation Damage in Nuclear Materials. IAEA Nuclear Data Section, October 2021. http://dx.doi.org/10.61092/iaea.25ex-cn8n.

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The International Code Centres Network (CCN) is a group of experts developing codes and models for atomic, molecular and plasma-surface interaction data relevant to fusion applications. Variable subsets of the group are brought together by the IAEA Atomic and Molecular Data (AMD) Unit in order to discuss computational and scientific issues associated with code developments. At the 7th Technical Meeting described in this report, which was held virtually from 18 – 20 October 2021, 18 experts in the field of Density Functional Theory (DFT) and Molecular Dynamics (MD) simulations of radiation damage reviewed the status of and proposed developments to the DefectDB and CascadesDB databases. These services, which are hosted by the AMD Unit, provide a central repository for the results of computational simulations of the evolution of a material’s structure following an impact by a high energy particle.
3

Parra, José G., Jesús Roa, and Arnaldo Armado. Exploration of the molecular interaction of a humic acid model with the water by means of molecular dynamics simulations. Peeref, March 2023. http://dx.doi.org/10.54985/peeref.2303p4473663.

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Matthews, Lisa, Guanming Wu, Robin Haw, Timothy Brunson, Nasim Sanati, Solomon Shorser, Deidre Beavers, Patrick Conley, Lincoln Stein, and Peter D'Eustachio. Illuminating Dark Proteins using Reactome Pathways. Reactome, October 2022. http://dx.doi.org/10.3180/poster/20221027matthews.

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Abstract:
Diseases are often the consequence of proteins or protein complexes that are non-functional or that function improperly. An active area of research has focused on the identification of molecules that can interact with defective proteins and restore their function. While 22% percent of human proteins are estimated to be druggable, less than fifteen percent are targeted by FDA-approved drugs, and the vast majority of untargeted proteins are understudied or so-called "dark" proteins. Elucidation of the function of these dark proteins, particularly those in commonly drug-targeted protein families, may offer therapeutic opportunities for many diseases. Reactome is the most comprehensive, open-access pathway knowledgebase covering 2585 pathways and including 14246 reactions, 11088 proteins, 13984 complexes, and 1093 drugs. Placing dark proteins in the context of Reactome pathways provides a framework of reference for these proteins facilitating the generation of hypotheses for experimental biologists to develop targeted experiments, unravel the potential functions of these proteins, and then design drugs to manipulate them. To this end, we have trained a random forest with 106 protein/gene pairwise features collected from multiple resources to predict functional interactions between dark proteins and proteins annotated in Reactome and then developed three scores to measure the interactions between dark proteins and Reactome pathways based on enrichment analysis and fuzzy logic simulations. Literature evidence via manual checking and systematic NLP-based analysis support predicted interacting pathways for dark proteins. To visualize dark proteins in the context of Reactome pathways, we have also developed a new website, idg.reactome.org, by extending the Reactome web application with new features illustrating these proteins together with tissue-specific protein and gene expression levels and drug interactions.

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