Relevant bibliographies by topics / Interactive molecular simulations

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  1. Journal articles

Academic literature on the topic 'Interactive molecular simulations'

Author: Grafiati
Published: 25 May 2024

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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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2

Lanrezac, André, Benoist Laurent, Hubert Santuz, Nicolas Férey, and Marc Baaden. "Fast and Interactive Positioning of Proteins within Membranes." Algorithms 15, no. 11 (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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3

Delalande, Olivier, Nicolas Férey, Gilles Grasseau, and Marc Baaden. "Complex molecular assemblies at hand via interactive simulations." Journal of Computational Chemistry 30, no. 15 (2009): 2375–87. http://dx.doi.org/10.1002/jcc.21235.

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4

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 (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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5

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 (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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6

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 (2017): 1–5. http://dx.doi.org/10.1021/acs.jcim.6b00571.

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7

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

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8

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 (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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9

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 (1998): 39–51. http://dx.doi.org/10.1080/10629369808039148.

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10

McCluskey, Andrew R., James Grant, Adam R. Symington, et al. "An introduction to classical molecular dynamics simulation for experimental scattering users." Journal of Applied Crystallography 52, no. 3 (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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