Log in

Relevant bibliographies by topics / Interactive molecular simulations / Journal articles

To see the other types of publications on this topic, follow the link: Interactive molecular simulations.

Journal articles on the topic 'Interactive molecular simulations'

Author: Grafiati

Published: 25 May 2024

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'Interactive molecular simulations.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

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.

Full text

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

Abstract:

(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 t

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

Abstract:

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. T

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

Abstract:

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 quan

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

Abstract:

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.

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

APA, Harvard, Vancouver, ISO, and other styles

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.

Full text

Abstract:

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, w

APA, Harvard, Vancouver, ISO, and other styles

11

Glowacki, David R., Michael O'Connor, Gaetano Calabró, et al. "A GPU-accelerated immersive audio-visual framework for interaction with molecular dynamics using consumer depth sensors." Faraday Discuss. 169 (2014): 63–87. http://dx.doi.org/10.1039/c4fd00008k.

Full text

Abstract:

With advances in computational power, the rapidly growing role of computational/simulation methodologies in the physical sciences, and the development of new human–computer interaction technologies, the field of interactive molecular dynamics seems destined to expand. In this paper, we describe and benchmark the software algorithms and hardware setup for carrying out interactive molecular dynamics utilizing an array of consumer depth sensors. The system works by interpreting the human form as an energy landscape, and superimposing this landscape on a molecular dynamics simulation to chaperone

APA, Harvard, Vancouver, ISO, and other styles

12

Astsatryan, Hrachya, Wahi Narsisian, Eliza Gyulgyulyan, et al. "An Integrated Web-based Interactive Data Platform for Molecular Dynamics Simulations." Scalable Computing: Practice and Experience 19, no. 2 (2018): 131–38. http://dx.doi.org/10.12694/scpe.v19i2.1337.

Full text

Abstract:

The article aims to introduce an integrated web-based interactive data platform for molecular dynamic simulations using the datasets generated by different life science communities from Armenia. The suggested platform, consisting of data repository and workflow management services, is vital for current and future scientific discoveries in the life science domain. We focus on interactive data visualization workflow service as a key to perform more in-depth analyzes of research data outputs, helping to understand the problems efficiently and to consolidate the data into one collective illustrati

APA, Harvard, Vancouver, ISO, and other styles

13

Byška, J., T. Trautner, S. M. Marques, J. Damborský, B. Kozlíková, and M. Waldner. "Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization." Computer Graphics Forum 38, no. 3 (2019): 441–53. http://dx.doi.org/10.1111/cgf.13701.

Full text

APA, Harvard, Vancouver, ISO, and other styles

14

Whitworth, Karen, Sarah Leupen, Chistopher Rakes, and Mauricio Bustos. "Interactive Computer Simulations as Pedagogical Tools in Biology Labs." CBE—Life Sciences Education 17, no. 3 (2018): ar46. http://dx.doi.org/10.1187/cbe.17-09-0208.

Full text

Abstract:

Student learning in biology may be impaired by instructional environments that emphasize technical methodology over analysis. We hypothesized that time gained by experimenting with accurate computer simulations could be used to engage students in analytical, creative learning. The effects of treatments that combined a week of simulated lab instruction with a week of standard lab instruction in different order (E-to-S and S-to-E) were examined using a controlled experimental design with random assignment of lab sections and hierarchical linear modeling analysis to account for possible clusterin

APA, Harvard, Vancouver, ISO, and other styles

15

Dreher, Matthieu, Jessica Prevoteau-Jonquet, Mikael Trellet, et al. "ExaViz: a flexible framework to analyse, steer and interact with molecular dynamics simulations." Faraday Discuss. 169 (2014): 119–42. http://dx.doi.org/10.1039/c3fd00142c.

Full text

Abstract:

The amount of data generated by molecular dynamics simulations of large molecular assemblies and the sheer size and complexity of the systems studied call for new ways to analyse, steer and interact with such calculations. Traditionally, the analysis is performed off-line once the huge amount of simulation results have been saved to disks, thereby stressing the supercomputer I/O systems, and making it increasingly difficult to handle post-processing and analysis from the scientist's office. The ExaViz framework is an alternative approach developed to couple the simulation with analysis tools t

APA, Harvard, Vancouver, ISO, and other styles

16

Poppleton, Erik, Roger Romero, Aatmik Mallya, Lorenzo Rovigatti, and Petr Šulc. "OxDNA.org: a public webserver for coarse-grained simulations of DNA and RNA nanostructures." Nucleic Acids Research 49, W1 (2021): W491—W498. http://dx.doi.org/10.1093/nar/gkab324.

Full text

Abstract:

Abstract OxDNA and oxRNA are popular coarse-grained models used by the DNA/RNA nanotechnology community to prototype, analyze and rationalize designed DNA and RNA nanostructures. Here, we present oxDNA.org, a graphical web interface for running, visualizing and analyzing oxDNA and oxRNA molecular dynamics simulations on a GPU-enabled high performance computing server. OxDNA.org automatically generates simulation files, including a multi-step relaxation protocol for structures exported in non-physical states from DNA/RNA design tools. Once the simulation is complete, oxDNA.org provides an inter

APA, Harvard, Vancouver, ISO, and other styles

17

Colubri, Andrés, Molly Kemball, Kian Sani, et al. "Preventing Outbreaks through Interactive, Experiential Real-Life Simulations." Cell 182, no. 6 (2020): 1366–71. http://dx.doi.org/10.1016/j.cell.2020.08.042.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

ROBLES, MIGUEL, VILLE MUSTONEN, and KIMMO KASKI. "MOLECULAR DYNAMIC STUDY OF A SINGLE DISLOCATION IN A TWO-DIMENSIONAL LENNARD–JONES SYSTEM." International Journal of Modern Physics C 14, no. 04 (2003): 407–21. http://dx.doi.org/10.1142/s0129183103004620.

Full text

Abstract:

In this work the motion of a single dislocation in a two-dimensional triangular lattice is studied by using classical Molecular Dynamics method with the Lennard–Jones inter-atomic potential. The dislocation motion is investigated with an interactive simulation program developed to track automatically the movement of lattice defects. Constant strain and constant strain-rate deformations were applied to the system. From constant strain simulations a curve of shear stress versus dislocation velocity is obtained, showing a nonlinear power law relation. An equation of motion for the dislocation is

APA, Harvard, Vancouver, ISO, and other styles

19

Pandi, Sangavi, Langeswaran Kulanthaivel, Gowtham Kumar Subbaraj, Sangeetha Rajaram, and Senthilkumar Subramanian. "Screening of Potential Breast Cancer Inhibitors through Molecular Docking and Molecular Dynamics Simulation." BioMed Research International 2022 (June 28, 2022): 1–9. http://dx.doi.org/10.1155/2022/3338549.

Full text

Abstract:

Cyclooxygenase-2 (COX-2) is a key enzyme involved in overexpression in several human cancerous diseases including breast cancer. By performing efficient virtual screening in a series of active molecules or compounds from the Maybridge, NCI (National Cancer Institute), and Enamine databases, potential identification of COX-2 inhibitors could lead to new prognostic strategies in the treatment of breast cancer. Based on a 50% structural similitude, compounds were chosen as the inductive model of COX-2 inhibitions from these databases. Selected compounds were filtered and tested with Lipinski’s ru

APA, Harvard, Vancouver, ISO, and other styles

20

Dubois, Marc-André, Xavier Bouju, and Alain Rochefort. "Toward interactive scanning tunneling microscopy simulations of large-scale molecular systems in real time." Journal of Applied Physics 124, no. 4 (2018): 044301. http://dx.doi.org/10.1063/1.5037443.

Full text

APA, Harvard, Vancouver, ISO, and other styles

21

Marforio, Tainah Dorina, Alessandro Calza, Edoardo Jun Mattioli, Francesco Zerbetto, and Matteo Calvaresi. "Dissecting the Supramolecular Dispersion of Fullerenes by Proteins/Peptides: Amino Acid Ranking and Driving Forces for Binding to C60." International Journal of Molecular Sciences 22, no. 21 (2021): 11567. http://dx.doi.org/10.3390/ijms222111567.

Full text

Abstract:

Molecular dynamics simulations were used to quantitatively investigate the interactions between the twenty proteinogenic amino acids and C60. The conserved amino acid backbone gave a constant energetic interaction ~5.4 kcal mol−1, while the contribution to the binding due to the amino acid side chains was found to be up to ~5 kcal mol−1 for tryptophan but lower, to a point where it was slightly destabilizing, for glutamic acid. The effects of the interplay between van der Waals, hydrophobic, and polar solvation interactions on the various aspects of the binding of the amino acids, which were g

APA, Harvard, Vancouver, ISO, and other styles

22

Gauthier, Andrea. "Game and Simulation Stimulate Conceptual Change about Molecular Emergence in Different Ways, with Potential Cultural Implications." Education Sciences 14, no. 4 (2024): 366. http://dx.doi.org/10.3390/educsci14040366.

Full text

Abstract:

Many undergraduate students hold robust misconceptions about the emergent nature of molecular processes, believing them to be directed rather than random. Interactive simulations might help transform such misconceptions by visualizing stochastic processes in a time-independent medium and enabling students to manipulate the environment to test their naïve hypotheses. Furthermore, game-based learning (GBL) might enhance the effectiveness of such simulations by promoting productive negativity (PN), i.e., learning from failure. In a randomized controlled trial with pre-test, post-test and delayed

APA, Harvard, Vancouver, ISO, and other styles

23

Yang, Jiantao, and Tairen Sun. "Finite-Time Interactive Control of Robots with Multiple Interaction Modes." Sensors 22, no. 10 (2022): 3668. http://dx.doi.org/10.3390/s22103668.

Full text

Abstract:

This paper proposes a finite-time multi-modal robotic control strategy for physical human–robot interaction. The proposed multi-modal controller consists of a modified super-twisting-based finite-time control term that is designed in each interaction mode and a continuity-guaranteed control term. The finite-time control term guarantees finite-time achievement of the desired impedance dynamics in active interaction mode (AIM), makes the tracking error of the reference trajectory converge to zero in finite time in passive interaction mode (PIM), and also guarantees robotic motion stop in finite

APA, Harvard, Vancouver, ISO, and other styles

24

Torrens-Fontanals, Mariona, Alejandro Peralta-García, Carmine Talarico, Ramon Guixà-González, Toni Giorgino, and Jana Selent. "SCoV2-MD: a database for the dynamics of the SARS-CoV-2 proteome and variant impact predictions." Nucleic Acids Research 50, no. D1 (2021): D858—D866. http://dx.doi.org/10.1093/nar/gkab977.

Full text

Abstract:

Abstract SCoV2-MD (www.scov2-md.org) is a new online resource that systematically organizes atomistic simulations of the SARS-CoV-2 proteome. The database includes simulations produced by leading groups using molecular dynamics (MD) methods to investigate the structure-dynamics-function relationships of viral proteins. SCoV2-MD cross-references the molecular data with the pandemic evolution by tracking all available variants sequenced during the pandemic and deposited in the GISAID resource. SCoV2-MD enables the interactive analysis of the deposited trajectories through a web interface, which

APA, Harvard, Vancouver, ISO, and other styles

25

Sellis, Diamantis, Dimitrios Vlachakis, and Metaxia Vlassi. "Gromita: A Fully Integrated Graphical user Interface to Gromacs 4." Bioinformatics and Biology Insights 3 (January 2009): BBI.S3207. http://dx.doi.org/10.4137/bbi.s3207.

Full text

Abstract:

Gromita is a fully integrated and efficient graphical user interface (GUI) to the recently updated molecular dynamics suite Gromacs, version 4. Gromita is a cross-platform, perl/tcl-tk based, interactive front end designed to break the command line barrier and introduce a new user-friendly environment to run molecular dynamics simulations through Gromacs. Our GUI features a novel workflow interface that guides the user through each logical step of the molecular dynamics setup process, making it accessible to both advanced and novice users. This tool provides a seamless interface to the Gromacs

APA, Harvard, Vancouver, ISO, and other styles

26

Abdi, Sayed Aliul Hasan, Amena Ali, Shabihul Fatma Sayed, et al. "Morusflavone, a New Therapeutic Candidate for Prostate Cancer by CYP17A1 Inhibition: Exhibited by Molecular Docking and Dynamics Simulation." Plants 10, no. 9 (2021): 1912. http://dx.doi.org/10.3390/plants10091912.

Full text

Abstract:

Morusflavone, a flavonoid from Morus alba L., was evaluated for its interactive ability and stability with CYP17A1, in comparison with abiraterone, which is a Food and Drug Administration (FDA)-approved CYP17A1 inhibitor. CYP17A1 inhibition is an important therapeutic target for prostate cancer. The CHAMM36 force field was used to perform molecular dynamics (MD) simulations in this study. The results show that Morusflavone has significant interactive ability and stability for CYP17A1, in comparison with abiraterone. The final interaction energies for the Morusflavone–CYP17A1 and abiraterone–CY

APA, Harvard, Vancouver, ISO, and other styles

27

Loya, Adil, Antash Najib, Fahad Aziz, Asif Khan, Guogang Ren, and Kun Luo. "Comparative molecular dynamics simulations of thermal conductivities of aqueous and hydrocarbon nanofluids." Beilstein Journal of Nanotechnology 13 (July 7, 2022): 620–28. http://dx.doi.org/10.3762/bjnano.13.54.

Full text

Abstract:

The addition of metal oxide nanoparticles to fluids has been used as a means of enhancing the thermal conductive properties of base fluids. This method formulates a heterogeneous fluid conferred by nanoparticles and can be used for high-end fluid heat-transfer applications, such as phase-change materials and fluids for internal combustion engines. These nanoparticles can enhance the properties of both polar and nonpolar fluids. In the current paper, dispersions of nanoparticles were carried out in hydrocarbon and aqueous-based fluids using molecular dynamic simulations (MDS). The MDS results h

APA, Harvard, Vancouver, ISO, and other styles

28

Allain, Ariane, Isaure Chauvot de Beauchêne, Florent Langenfeld, Yann Guarracino, Elodie Laine, and Luba Tchertanov. "Allosteric pathway identification through network analysis: from molecular dynamics simulations to interactive 2D and 3D graphs." Faraday Discuss. 169 (2014): 303–21. http://dx.doi.org/10.1039/c4fd00024b.

Full text

Abstract:

Allostery is a universal phenomenon that couples the information induced by a local perturbation (effector) in a protein to spatially distant regulated sites. Such an event can be described in terms of a large scale transmission of information (communication) through a dynamic coupling between structurally rigid (minimally frustrated) and plastic (locally frustrated) clusters of residues. To elaborate a rational description of allosteric coupling, we propose an original approach – MOdular NETwork Analysis (MONETA) – based on the analysis of inter-residue dynamical correlations to localize the

APA, Harvard, Vancouver, ISO, and other styles

29

Clarke, Kenneth A. "Microcomputer Simulations of Mechanical Properties of Skeletal Muscle for Undergraduate Classes." Alternatives to Laboratory Animals 15, no. 3 (1988): 183–87. http://dx.doi.org/10.1177/026119298801500303.

Full text

Abstract:

In a previous paper, the development of interactive simulations of neurophysiology experiments for undergraduate classes was described. Similar voltage/time displays are used in other areas of undergraduate physiology classes and could therefore be simulated in this way. One such area is in the study of the mechanical properties of muscle, in which a transducer is used to translate muscle length or tension changes into voltages. This paper describes the development and class use of interactive simulations of experiments using isometric recordings from isolated frog muscle.

APA, Harvard, Vancouver, ISO, and other styles

30

Molza, A. E., N. Férey, M. Czjzek, et al. "Innovative interactive flexible docking method for multi-scale reconstruction elucidates dystrophin molecular assembly." Faraday Discuss. 169 (2014): 45–62. http://dx.doi.org/10.1039/c3fd00134b.

Full text

Abstract:

At present, our molecular knowledge of dystrophin, the protein encoded by the DMD gene and mutated in myopathy patients, remains limited. To get around the absence of its atomic structure, we have developed an innovative interactive docking method based on the BioSpring software in combination with Small-angle X-ray Scattering (SAXS) data. BioSpring allows interactive handling of biological macromolecules thanks to an augmented Elastic Network Model (aENM) that combines the spring network with non-bonded terms between atoms or pseudo-atoms. This approach can be used for building molecular asse

APA, Harvard, Vancouver, ISO, and other styles

31

Nakano, Aiichiro, Rajiv K. Kalia, Priya Vashishta, et al. "Scalable Atomistic Simulation Algorithms for Materials Research." Scientific Programming 10, no. 4 (2002): 263–70. http://dx.doi.org/10.1155/2002/203525.

Full text

Abstract:

A suite of scalable atomistic simulation programs has been developed for materials research based on space-time multiresolution algorithms. Design and analysis of parallel algorithms are presented for molecular dynamics (MD) simulations and quantum-mechanical (QM) calculations based on the density functional theory. Performance tests have been carried out on 1,088-processor Cray T3E and 1,280-processor IBM SP3 computers. The linear-scaling algorithms have enabled 6.44-billion-atom MD and 111,000-atom QM calculations on 1,024 SP3 processors with parallel efficiency well over 90%. production-qua

APA, Harvard, Vancouver, ISO, and other styles

32

Hokkanen, J. E. "Visual simulations, artificial animals and virtual ecosystems." Journal of Experimental Biology 202, no. 23 (1999): 3477–84. http://dx.doi.org/10.1242/jeb.202.23.3477.

Full text

Abstract:

This review is about a field that does not traditionally belong to biological sciences. A branch of computer animation has its mission to create active self-powered objects living artificial lives in the theoretical biology zone. Selected work, of particular interest to biologists, is presented here. These works include animated simulations of legged locomotion, flexible-bodied animals swimming and crawling, artificial fish in virtual ecosystems, automated learning of swimming and the evolution of virtual creatures with respect to morphology, locomotion and behaviour. The corresponding animati

APA, Harvard, Vancouver, ISO, and other styles

33

Rusu, Victor H., Denys E. S. Santos, Marcelo D. Poleto, et al. "Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations." Journal of Chemical Information and Modeling 60, no. 12 (2020): 5923–27. http://dx.doi.org/10.1021/acs.jcim.0c01168.

Full text

APA, Harvard, Vancouver, ISO, and other styles

34

Ertl, Thomas, Michael Krone, Stefan Kesselheim, Katrin Scharnowski, Guido Reina, and Christian Holm. "Visual analysis for space–time aggregation of biomolecular simulations." Faraday Discuss. 169 (2014): 167–78. http://dx.doi.org/10.1039/c3fd00156c.

Full text

Abstract:

Conducting a current through a nanopore allows for the analysis of molecules inside the pore because a current modulation caused by the electrostatic properties of the passing molecules can be measured. This mechanism shows great potential for DNA sequencing, as the four different nucleotide bases induce different current modulations. We present a visualisation approach to investigate this phenomenon in our simulations of DNA within a nanopore by combining state-of-the-art molecular visualisation with vector field illustration. By spatial and temporal aggregation of the ions transported throug

APA, Harvard, Vancouver, ISO, and other styles

35

Stone, John E., Ryan McGreevy, Barry Isralewitz, and Klaus Schulten. "GPU-accelerated analysis and visualization of large structures solved by molecular dynamics flexible fitting." Faraday Discuss. 169 (2014): 265–83. http://dx.doi.org/10.1039/c4fd00005f.

Full text

Abstract:

Hybrid structure fitting methods combine data from cryo-electron microscopy and X-ray crystallography with molecular dynamics simulations for the determination of all-atom structures of large biomolecular complexes. Evaluating the quality-of-fit obtained from hybrid fitting is computationally demanding, particularly in the context of a multiplicity of structural conformations that must be evaluated. Existing tools for quality-of-fit analysis and visualization have previously targeted small structures and are too slow to be used interactively for large biomolecular complexes of particular inter

APA, Harvard, Vancouver, ISO, and other styles

36

Dewhurst, David G., Guy J. Brown, and Anthony S. Meehan. "Microcomputer Simulations of Laboratory Experiments in Physiology." Alternatives to Laboratory Animals 15, no. 4 (1988): 280–89. http://dx.doi.org/10.1177/026119298801500403.

Full text

Abstract:

Three interactive computer-assisted learning programs based on simulations of simple experiments in physiology (frog sciatic nerve, frog sciatic nerve-gastrocnemius muscle and frog heart) are described. The programs use experimental data to generate realistic, high-resolution graphic simulations of results and present these either on a simulated oscilloscope or on a continuously scrolling display to simulate a chart recorder. Students can thus conduct an experiment and take measurements directly from the monitor, as they would in the real situation. The programs fulfil most of the main objecti

APA, Harvard, Vancouver, ISO, and other styles

37

Woods, Christopher J., Maturos Malaisree, Julien Michel, Ben Long, Simon McIntosh-Smith, and Adrian J. Mulholland. "Rapid decomposition and visualisation of protein–ligand binding free energies by residue and by water." Faraday Discuss. 169 (2014): 477–99. http://dx.doi.org/10.1039/c3fd00125c.

Full text

Abstract:

Recent advances in computational hardware, software and algorithms enable simulations of protein–ligand complexes to achieve timescales during which complete ligand binding and unbinding pathways can be observed. While observation of such events can promote understanding of binding and unbinding pathways, it does not alone provide information about the molecular drivers for protein–ligand association, nor guidance on how a ligand could be optimised to better bind to the protein. We have developed the waterswap (C. J. Woods et al., J. Chem. Phys., 2011, 134, 054114) absolute binding free energy

APA, Harvard, Vancouver, ISO, and other styles

38

Zou, Rui, Yubin Liu, Jie Zhao, and Hegao Cai. "A Framework for Human-Robot-Human Physical Interaction Based on N-Player Game Theory." Sensors 20, no. 17 (2020): 5005. http://dx.doi.org/10.3390/s20175005.

Full text

Abstract:

In order to analyze the complex interactive behaviors between the robot and two humans, this paper presents an adaptive optimal control framework for human-robot-human physical interaction. N-player linear quadratic differential game theory is used to describe the system under study. N-player differential game theory can not be used directly in actual scenerie, since the robot cannot know humans’ control objectives in advance. In order to let the robot know humans’ control objectives, the paper presents an online estimation method to identify unknown humans’ control objectives based on the rec

APA, Harvard, Vancouver, ISO, and other styles

39

Zhang, Yuqi, Li Chen, Xiaoyu Wang, et al. "Interactive Mechanism of Potential Inhibitors with Glycosyl for SARS-CoV-2 by Molecular Dynamics Simulation." Processes 9, no. 10 (2021): 1749. http://dx.doi.org/10.3390/pr9101749.

Full text

Abstract:

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a type of Ribonucleic Acid (RNA) coronavirus and it has infected and killed many people around the world. It is reported that the receptor binding domain of the spike protein (S_RBD) of the SARS-CoV-2 virus is responsible for attachment to human angiotensin converting enzyme II (ACE2). Many researchers are attempting to search potential inhibitors for fighting SARS-CoV-2 infection using theoretical or experimental methods. In terms of experimental and theoretical research, Cefuroxime, Erythromycin, Lincomycin and Ofloxacin are the

APA, Harvard, Vancouver, ISO, and other styles

40

Jungck, John R., Holly Gaff, and Anton E. Weisstein. "Mathematical Manipulative Models: In Defense of “Beanbag Biology”." CBE—Life Sciences Education 9, no. 3 (2010): 201–11. http://dx.doi.org/10.1187/cbe.10-03-0040.

Full text

Abstract:

Mathematical manipulative models have had a long history of influence in biological research and in secondary school education, but they are frequently neglected in undergraduate biology education. By linking mathematical manipulative models in a four-step process—1) use of physical manipulatives, 2) interactive exploration of computer simulations, 3) derivation of mathematical relationships from core principles, and 4) analysis of real data sets—we demonstrate a process that we have shared in biological faculty development workshops led by staff from the BioQUEST Curriculum Consortium over th

APA, Harvard, Vancouver, ISO, and other styles

41

Stevens, Ron, David F. Johnson, and Amy Soller. "Probabilities and Predictions: Modeling the Development of Scientific Problem-Solving Skills." Cell Biology Education 4, no. 1 (2005): 42–57. http://dx.doi.org/10.1187/cbe.04-03-0036.

Full text

Abstract:

The IMMEX (Interactive Multi-Media Exercises) Web-based problem set platform enables the online delivery of complex, multimedia simulations, the rapid collection of student performance data, and has already been used in several genetic simulations. The next step is the use of these data to understand and improve student learning in a formative manner. This article describes the development of probabilistic models of undergraduate student problem solving in molecular genetics that detailed the spectrum of strategies students used when problem solving, and how the strategic approaches evolved wi

APA, Harvard, Vancouver, ISO, and other styles

42

Tieleman, D. P., B. I. Sejdiu, E. A. Cino, et al. "Insights into lipid-protein interactions from computer simulations." Biophysical Reviews 13, no. 6 (2021): 1019–27. http://dx.doi.org/10.1007/s12551-021-00876-9.

Full text

Abstract:

Abstract Lipid-protein interactions play an important direct role in the function of many membrane proteins. We argue they are key players in membrane structure, modulate membrane proteins in more subtle ways than direct binding, and are important for understanding the mechanism of classes of hydrophobic drugs. By directly comparing membrane proteins from different families in the same, complex lipid mixture, we found a unique lipid environment for every protein. Extending this work, we identified both differences and similarities in the lipid environment of GPCRs, dependent on which family th

APA, Harvard, Vancouver, ISO, and other styles

43

Yang, Peng, Peng Liu, and Junmao Li. "The Regulatory Network of Gastric Cancer Pathogenesis and Its Potential Therapeutic Active Ingredients of Traditional Chinese Medicine Based on Bioinformatics, Molecular Docking, and Molecular Dynamics Simulation." Evidence-Based Complementary and Alternative Medicine 2022 (November 26, 2022): 1–17. http://dx.doi.org/10.1155/2022/5005498.

Full text

Abstract:

Objective. This study aims to investigate the functional gene network in gastric carcinogenesis by using bioinformatics; besides, the diagnostic utility of key genes and potential active ingredients of traditional Chinese medicine (TCM) for treatment in gastric cancer have been explored. Methods. The Cancer Genome Atlas and Gene Expression Omnibus databases have been applied to analyze the differentially expressed genes (DEGs) between gastric cancer and normal gastric tissues. Then, the DEGs underwent Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses using the Metas

APA, Harvard, Vancouver, ISO, and other styles

44

Loftus, Neil, and Husnu S. Narman. "Use of Machine Learning in Interactive Cybersecurity and Network Education." Sensors 23, no. 6 (2023): 2977. http://dx.doi.org/10.3390/s23062977.

Full text

Abstract:

Cybersecurity is a complex subject for students to pursue. Hands-on online learning through labs and simulations can help students become more familiar with the subject at security classes to pursue cybersecurity education. There are several online tools and simulation platforms for cybersecurity education. However, those platforms need more constructive feedback mechanisms, and customizable hands-on exercises for users, or they oversimplify or misrepresent the content. In this paper, we aim to develop a platform for cybersecurity education that can be used either with a user interface or comm

APA, Harvard, Vancouver, ISO, and other styles

45

Brown, Guy J., Godfrey G. S. Collins, David G. Dewhurst, and Ian E. Hughes. "Computer Simulations in Teaching Neuromuscular Pharmacology—Time for a Change from Traditional Methods?" Alternatives to Laboratory Animals 16, no. 2 (1988): 163–74. http://dx.doi.org/10.1177/026119298801600207.

Full text

Abstract:

Two interactive computer programs are described which illustrate different approaches to teaching the pharmacology of neuromuscular transmission. Both programs are based on a simulation of the in vivo sciatic nerve–tibialis anterior muscle preparation of the cat. Program 1 simulates the preparation and allows students to follow a schedule set by the teacher, or design experiments themselves using drugs (including unknowns) and procedures selected from an extensive menu. The sequence of events and the doses used are entirely in the hands of the user and students “learn by discovery”. Program 2

APA, Harvard, Vancouver, ISO, and other styles

46

Chakrabarty, Broto, Varun Naganathan, Kanak Garg, Yash Agarwal, and Nita Parekh. "NAPS update: network analysis of molecular dynamics data and protein–nucleic acid complexes." Nucleic Acids Research 47, W1 (2019): W462—W470. http://dx.doi.org/10.1093/nar/gkz399.

Full text

Abstract:

Abstract Network theory is now a method of choice to gain insights in understanding protein structure, folding and function. In combination with molecular dynamics (MD) simulations, it is an invaluable tool with widespread applications such as analyzing subtle conformational changes and flexibility regions in proteins, dynamic correlation analysis across distant regions for allosteric communications, in drug design to reveal alternative binding pockets for drugs, etc. Updated version of NAPS now facilitates network analysis of the complete repertoire of these biomolecules, i.e., proteins, prot

APA, Harvard, Vancouver, ISO, and other styles

47

Zou, Yu, Zhiwei Liu, Zhiqiang Zhu та Zhenyu Qian. "Structural Influence and Interactive Binding Behavior of Dopamine and Norepinephrine on the Greek-Key-Like Core of α-Synuclein Protofibril Revealed by Molecular Dynamics Simulations". Processes 7, № 11 (2019): 850. http://dx.doi.org/10.3390/pr7110850.

Full text

Abstract:

The pathogenesis of Parkinson’s disease (PD) is closely associated with the aggregation of α-synuclein (αS) protein. Finding the effective inhibitors of αS aggregation has been considered as the primary therapeutic strategy for PD. Recent studies reported that two neurotransmitters, dopamine (DA) and norepinephrine (NE), can effectively inhibit αS aggregation and disrupt the preformed αS fibrils. However, the atomistic details of αS-DA/NE interaction remain unclear. Here, using molecular dynamics simulations, we investigated the binding behavior of DA/NE molecules and their structural influenc

APA, Harvard, Vancouver, ISO, and other styles

48

Byregowda, Bharath Harohalli, Krishnaprasad Baby, Swastika Maity, et al. "Network pharmacology and in silico approaches to uncover multitargeted mechanism of action of Zingiber zerumbet rhizomes for the treatment of idiopathic pulmonary fibrosis." F1000Research 13 (March 22, 2024): 216. http://dx.doi.org/10.12688/f1000research.142513.1.

Full text

Abstract:

Background Idiopathic pulmonary fibrosis (IPF) is a disease with high mortality, and there are only two specific drugs available for therapeutic management with limitations. The study aims to identify comprehensive therapeutic mechanisms of Zingiber zerumbet rhizomes (ZZR) to treat IPF by using network pharmacology followed battery of in silico studies. Methods The protein-protein interaction network was developed using Cytoscape to obtain core disease targets involved in IPF and their interactive molecules of ZZR. Based on the pharmacophore properties of phytomolecules from ZZR, the drug targ

APA, Harvard, Vancouver, ISO, and other styles

49

Pavlov, Evgen, Makoto Taiji, Arturs Scukins, Anton Markesteijn, Sergey Karabasov, and Dmitry Nerukh. "Visualising and controlling the flow in biomolecular systems at and between multiple scales: from atoms to hydrodynamics at different locations in time and space." Faraday Discuss. 169 (2014): 285–302. http://dx.doi.org/10.1039/c3fd00159h.

Full text

Abstract:

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allo

APA, Harvard, Vancouver, ISO, and other styles

50

Park, Chailim, and Heewon Kye. "Efficient Massive Computing for Deformable Volume Data Using Revised Parallel Resampling." Sensors 22, no. 16 (2022): 6276. http://dx.doi.org/10.3390/s22166276.

Full text

Abstract:

In this paper, we propose an improved parallel resampling technique. Parallel resampling is a deformable object generation method based on volume data applied to medical simulations. Existing parallel resampling is not suitable for massive computing, because the number of samplings is high and floating-point precision problems may occur. This study addresses these problems to obtain improved user latency when performing medical simulations. Specifically, instead of interpolating values after volume sampling, the efficiency is improved by performing volume sampling after coordinate interpolatio

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!