Relevant bibliographies by topics / Molecular simulation

Academic literature on the topic 'Molecular simulation'

Author: Grafiati
Published: 4 June 2021
Last updated: 7 July 2024

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

Select a source type:

Contents

Consult the lists of relevant articles, books, theses, conference reports, and other scholarly sources on the topic 'Molecular simulation.'

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.

Journal articles on the topic "Molecular simulation"

1

Okumura, Hisashi, Satoru G. Itoh, and Yuko Okamoto. "1P585 Explicit Symplectic Molecular Dynamics Simulation for Rigid-Body Molecules in the Canonical Ensemble(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S293. http://dx.doi.org/10.2142/biophys.46.s293_1.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Osborne, I. S. "Molecular simulation." Science 349, no. 6254 (September 17, 2015): 1297–98. http://dx.doi.org/10.1126/science.349.6254.1297-e.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Potoff, Jeffrey, and Ioannis Economou. "Molecular simulation." Fluid Phase Equilibria 498 (October 2019): 160. http://dx.doi.org/10.1016/j.fluid.2019.05.027.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Liu, Zhimin, Zhigang Xu, Dan Wang, Yuming Yang, Yunli Duan, Liping Ma, Tao Lin, and Hongcheng Liu. "A Review on Molecularly Imprinted Polymers Preparation by Computational Simulation-Aided Methods." Polymers 13, no. 16 (August 10, 2021): 2657. http://dx.doi.org/10.3390/polym13162657.

Full text
Abstract:
Molecularly imprinted polymers (MIPs) are obtained by initiating the polymerization of functional monomers surrounding a template molecule in the presence of crosslinkers and porogens. The best adsorption performance can be achieved by optimizing the polymerization conditions, but this process is time consuming and labor-intensive. Theoretical calculation based on calculation simulations and intermolecular forces is an effective method to solve this problem because it is convenient, versatile, environmentally friendly, and inexpensive. In this article, computational simulation modeling methods are introduced, and the theoretical optimization methods of various molecular simulation calculation software for preparing molecularly imprinted polymers are proposed. The progress in research on and application of molecularly imprinted polymers prepared by computational simulations and computational software in the past two decades are reviewed. Computer molecular simulation methods, including molecular mechanics, molecular dynamics and quantum mechanics, are universally applicable for the MIP-based materials. Furthermore, the new role of computational simulation in the future development of molecular imprinting technology is explored.
APA, Harvard, Vancouver, ISO, and other styles
5

Katkar, Ashwini, and Vinitkumar Jayaprakash Dongre. "Assessing Molecular Throughput and Efficiency through Simulation in Diffusion-Based Molecular Communication." Indian Journal Of Science And Technology 17, no. 6 (February 12, 2024): 524–32. http://dx.doi.org/10.17485/ijst/v17i6.2814.

Full text
Abstract:
Objectives: This study investigates the correlation of critical factors influencing throughput and efficiency in diffusion-based molecular communication systems. Method: The study presents a simulation model for 3-D diffusion-based molecular communication, incorporating essential parameters such as molecule size, transmission rate, diffusion rate, and transmitter-receiver distance. Findings: Through comprehensive simulations, the study reveals the effects of different parameters on throughput and efficiency in diffusion-based molecular communication. It highlights the critical trade-offs associated with system design and optimization. The study reveals the key factors influencing the transmission capabilities, the receiver congestion, and the overall efficiency of the communication system. Novelty: In this study, we give a study overview of the latest work of performance metrics in the field of molecular communication. A novel algorithm is proposed to find the throughput and efficiency of molecular communication. The proposed framework analyzes the intricate relationship between system parameters and performance metrics, emphasizing the potential for system optimization. Our simulation work demonstrates how the model parameters influence the performance of the molecular communication system, providing insights for enhancing the system's performance in applications such as targeted drug delivery in the future. Keywords: Molecular Communication, Diffusion, Transmission Rate, Throughput, Efficiency
APA, Harvard, Vancouver, ISO, and other styles
6

Chen, Xueye. "Molecular dynamics simulation of nanofluidics." Reviews in Chemical Engineering 34, no. 6 (November 27, 2018): 875–85. http://dx.doi.org/10.1515/revce-2016-0060.

Full text
Abstract:
Abstract This review reports the progress on the recent development of molecular dynamics simulation of nanofluidics. Molecular dynamics simulations of nanofluidics in nanochannel structure, surface roughness of nanochannel, carbon nanotubes, electrically charged, thermal transport in nanochannels and gases in nanochannels are illustrated and discussed. This paper will provide an expedient and valuable reference to designers who intend to research molecular dynamics simulation of nanofluidic devices.
APA, Harvard, Vancouver, ISO, and other styles
7

Rakkapao, Natthida. "Molecular Dynamics Simulation of Gas Transport in Polyisoprene Matrix." Advanced Materials Research 844 (November 2013): 209–13. http://dx.doi.org/10.4028/www.scientific.net/amr.844.209.

Full text
Abstract:
Molecular Dynamics (MD) simulation was employed to study the diffusivity of biogas in a PI matrix with the aim to verify simulations as a useful tool to predict PI membrane properties for biogas treatment. The simulation model of PI numerical was reliable and accurate in predicting both the material properties and the diffusivity of gases in PI matrix. The diffusion coefficients (D) of the major components in biogas, namely CH4, CO2, H2O, O2, and N2, were computed by simulating trajectories of each gas in PI matrix at 300 K. The simulations gave DCO2 that was 6 times larger than DCH4, and this agrees well with permeabilities reported in the literature. This suggests that PI membranes could be used to treat biogas by separating CO2 and CH4. However, the diffusivities of N2, H2O, and CH4 are closely similar, so PI membranes are not capable of separating these. The potential application of PI membrane to CO2/CH4 separation seems worth further exploration.
APA, Harvard, Vancouver, ISO, and other styles
8

MAHAJAN, DHIRAJ K., and SUMIT BASU. "ON THE SIMULATION OF UNIAXIAL, COMPRESSIVE BEHAVIOR OF AMORPHOUS, GLASSY POLYMERS WITH MOLECULAR DYNAMICS." International Journal of Applied Mechanics 02, no. 03 (September 2010): 515–41. http://dx.doi.org/10.1142/s1758825110000639.

Full text
Abstract:
Molecular dynamics (MD) simulations offer an interesting route to simulating deformation and fracture behavior of amorphous glassy polymers. However, MD simulations are performed at extremely high rates and on very small samples (though periodic boundary conditions are routinely used) containing at most hundreds of chains which are much shorter than in real life. In this work, we try to assess the extent to which MD simulations produce physically realistic stress–strain responses and identify aspects of the simulation procedure that can be controlled closely in order to avoid numerical artifacts. We show that, when an appropriate protocol for sample generation and simulation of deformation is followed, in spite of the obvious constraints imposed by the simulation technique, MD simulations have the capability to generate realistic stress–strain curves and reproduce many experimental trends pertaining to them.
APA, Harvard, Vancouver, ISO, and other styles
9

SHINTO, Hiroyuki. "Molecular Dynamics Simulation." Journal of the Japan Society of Colour Material 86, no. 10 (2013): 380–85. http://dx.doi.org/10.4011/shikizai.86.380.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Frenkel, Daan, Berend Smit, Jan Tobochnik, Susan R. McKay, and Wolfgang Christian. "Understanding Molecular Simulation." Computers in Physics 11, no. 4 (1997): 351. http://dx.doi.org/10.1063/1.4822570.

Full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Dissertations / Theses on the topic "Molecular simulation"

1

Cai, Qiong. "Hybrid molecular dynamics simulation." Thesis, University of Edinburgh, 2007. http://hdl.handle.net/1842/10849.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Bekker, Hendrik. "Molecular dynamics simulation methods revised." [Groningen] : [Groningen] : Rijksuniversiteit Groningen ; [University Library Groningen] [Host], 1996. http://irs.ub.rug.nl/ppn/14860532X.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Do, Hainam. "Molecular simulation of simple fluids." Thesis, University of Nottingham, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546280.

Full text
Abstract:
Free energy is the criterion of stability and is essential for determining phase equilibrium properties, for example. However, calculation of free energies for complex systems, such as fluids by computer simulation, is extremely difficult. In this thesis, we show how the partition function of fluids can be calculated directly from simulations; this allows us to obtain the absolute Helmholtz free energy (F) via F- -k8TInQ. Our method radically simplifies the process of calculating absolute free energies of continuous systems. As the method has been developed in the past few months, we have not yet applied it to the study of phase equilibria. This task will be part of our future work. In the rest of the thesis, we have focused on the application of more established simulation techniques to the urgent problem of finding environmentally friendly refrigerant fluids. Methane and fluoromethanes are possible candidates. However, they are flammable. 1-1-1-2-tetrafluoroethane, on the other hand, has for a long time been used in domestic refrigeration and automobile air-conditioning systems. However, it will be banned in Europe from 2011, due to concerns about its global warming impact. Carbon dioxide has received much attention as a fluid that can be used in combination with other refrigerants to minimise flammability and toxicity, and has a very low global warming potential. Thus, it could be mixed with those refrigerants to form new environmentally friendly refrigerant mixtures. Unfortunately, little information on the thermophysical properties of these mixtures is available. We simulate the thermophysical properties of these important industrial refrigerants and their mixtures with carbon dioxide using both empirical and in-house firstprinciples potentials. Simulations also provide a microscopic-level understanding of the structure of liquids, which is not accessible via experiment. Our high-quality ab initio force fields have reproduced the thermophysical properties for carbon dioxide, methane, fluorinated methanes, and mixtures of carbon dioxide and methane and carbon dioxide and fluorinated methanes. Multi-body effects play a crucial role in determining the thermophysical properties of fluids and inclusion of a three-body effect substantially improves the prediction of the phase-coexistence properties. Our studies should be of relevance to a broad range of mixtures of fluoroalkanes and carbon dioxide. Our efforts in making the first-principle force fields for carbon dioxide and fluorinated methanes pave the way for larger fluorinated hydrocarbons to come in the future.
APA, Harvard, Vancouver, ISO, and other styles
4

Foulger, Stephen Hans. "Molecular simulation of liquid crystalline." Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/11246.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Boothroyd, Simon. "Phase equilibria from molecular simulation." Thesis, Lancaster University, 2018. http://eprints.lancs.ac.uk/126751/.

Full text
Abstract:
Phase equilibria are at the heart of many properties of substances, such as their solubility, manufacturability, and stability. They are of significant industrial and commercial interest, perhaps most importantly to the pharmaceutical industry where drug stability and solubility are two of the largest challenges of drug development. The focus of this thesis then was to develop a molecular level understanding of phase equilibria, and produce tools and models to predict phase stability. An emphasis was given to exploring solid-solid and solid-liquid equilibria and stability. Specifically, the work presented here aimed to elucidate what drives the formation of multicomponent crystals, improve available models for exploring phase equilibria phenomena and explore solubility prediction from first principles as a potentially more powerful alternative to correlation based methods. These three fundamental areas were explored by employing molecular simulation in combination with the machinery of statistical mechanics, utilising advanced sampling methods and free energy calculations. This approach has led to the development of a foundation for understanding multicomponent crystal formation in terms of molecular affinities and packing, the characterisation of a set of soft coarse-grained potentials for use in phase equilibria studies, which overcome the main limitations of the most widely used potential, and finally, the development of a novel method for solubility prediction from first principles. Here, this novel method was successfully applied to an ionic (aqueous sodium chloride) and small molecular (urea in methanol and aqueous urea) system. In the future, these results are expected to lead to a set of guidelines for predicting (and perhaps prohibiting) multicomponent crystal formation, the development of a higher class of coarse-grained transferable force field with utility in studying phase equilibria, and powerful approach for predicting solubility of even large, flexible molecules (such as pharmaceuticals).
APA, Harvard, Vancouver, ISO, and other styles
6

Durandurdu, Murat. "Molecular Statics Simulation in Aluminum." Thesis, Virginia Tech, 1999. http://hdl.handle.net/10919/33528.

Full text
Abstract:
Effects of dislocation emission from a mode I crack and of pinning distances on the behavior of the crack and on fracture toughness in aluminum were studied by using the Molecular Statics Technique with atomic interactions described in terms of the Embedded Atom Method.

It was found that aluminum is a ductile material in which the cracks generate dislocations, blunting the cracks. The blunting and the dislocation shielding reduce the local stress intensity factor. Also, twinning, which has not been observed experimentally in Aluminum due to the high stacking fault, was obtained in the simulation. Probably, the low temperature facilitates twin formation.

The applied stress intensity factor required to propagate the crack tip increases at first, and then becomes constant as the maximum distance that the first dislocation can travel away from the crack tip increases. These effects can be attributed to dislocation shielding and crack blunting. The maximum distance of the emitted dislocations from the crack tip is the equilibrium distance for the largest simulation performed (400,000 atoms) while for the smaller simulations the dislocations are hindered by the fixed boundary condition of the model. On the other hand, the total local stress intensity factor at the crack tip and the local stress intensity factor along the slip plane remain basically constant as the maximum distance of the emitted dislocations from the crack tip increases. For distances larger than , these local stress intensity factors start to increase slightly.
Master of Science

APA, Harvard, Vancouver, ISO, and other styles
7

Burgos, Marmol Jose Javier. "Molecular simulation of polymer nanocomposites." Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/molecular-simulation-of-polymer-nanocomposites(56a195bb-81ed-4eb8-81d7-b3357d7f2316).html.

Full text
Abstract:
Polymer nanocomposites (PNCs) are hybrid materials incorporating organic or inorganic nanoparticles (NPs) with at least one dimension in the submicron scale. Over the last two decades, these materials have drawn a remarkable attention due to their central role in industrial formulations and technological applications, extending from food packaging to smart coatings. Incorporating nanoparticles (NPs) to a polymer matrix can significantly alter the conformation and the mobility of the polymer chains in their proximity. Moreover, understanding the delicate balance between the enthalpic and entropic interactions is crucial to control and predict the ability of NPs to diffuse and disperse in the polymer matrix. The impact of these interactions on the structure and the dynamics of polymer chains and NPs is fully revealed in how a number of macroscopic properties changes, justifying the high interest on these materials for industrial applications. In this thesis, the impact on the structure, dynamics, viscosity and thermal conductivity of a number of microscopic properties is investigated by performing Molecular Dynamics (MD) simulations. Specifically, the PNC is represented by a coarse-grained model of a melt of linear homopolymer chains containing spherical NPs. Throughout this work, a number of parameters are modified in order to unveil possible patterns in the PNC’s performance. To this end, this work focuses on the consequences of modifying the NP size dispersity, NP-polymer chain relative size, and chains’ degree of stiffness. Four theoretical models describing the diffusivity of NPs, three of which include nano-scale corrections, have been averaged to study the dependence of dilute NPs’ diffusivity on the NP polydispersity index. By comparing these models to the simulation results at different degrees of polydispersity, it is possible to obtain a more complete picture of their validity as compared to the monodisperse case. Regarding the diffusion of polymer chains, simulation results were in good agreement with the experimental results previously obtained by Composto and coworkers (Soft Matter 2012, 8, 6512), which relate the chains’ diffusivity to the average interparticle distance. As far as the transport properties are concerned, they show a weaker dependence on the polydispersity index. By contrast, results on viscosity and thermal conducitivity show that they are conditioned by the polymer-NP specific interfacial area and the inverse average mass, respectively. These results are in good agreement with previous experimental results. A deeper examination of this intriguing deviation from viscosity predictions in traditional composites, reveals a non-trivial combination of thickening and thinning effects contributing to the final viscosity of the PNC. This thesis also address the influence of the chains’ stiffness on the dynamical and viscous behaviour. An isotropic-to-nematic phase transition is observed, regardless of the NP-monomer interactions, below which a monotonic increase of both properties is observed, whereas orientationally ordered systems dramatically modify them, resulting into a steep increase or a smooth decrease depending on the direction in which they are measured.
APA, Harvard, Vancouver, ISO, and other styles
8

Freitas, Rodrigo Moura 1989. "Molecular simulation = methods and applications = Simulações moleculares : métodos e aplicações." [s.n.], 2013. http://repositorio.unicamp.br/jspui/handle/REPOSIP/278440.

Full text
Abstract:
Orientador: Maurice de Koning
Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Física Gleb Wataghin
Made available in DSpace on 2018-08-23T00:50:21Z (GMT). No. of bitstreams: 1 Freitas_RodrigoMoura_M.pdf: 11496259 bytes, checksum: 41c29f22d80da01064cf7a3b9681b05f (MD5) Previous issue date: 2013
Resumo: Devido aos avanços conceptuais e técnicos feitos em física computacional e ciência dos materiais computacional nos estamos aptos a resolver problemas que eram inacessíveis a alguns anos atrás. Nessa dissertação estudamos a evolução de alguma destas técnicas, apresentando a teoria e técnicas de simulação computacional para estudar transições de fase de primeira ordem com ênfase nas técnicas mais avançadas de calculo de energia livre (Reversible Scaling) e métodos de simulação de eventos raros (Forward Flux Sampling) usando a técnica de simulação atomística da Dinâmica Molecular. A evolução e melhora da e ciência destas técnicas e apresentada junto com aplicações a sistemas simples que permitem solução exata e também ao caso mais complexo da transição de fase Martenstica. Também apresentamos a aplicação de métodos numéricos no estudo do modelo de Pauling para o gelo. Nos desenvolvemos e implementamos um novo algoritmo para a criação e ciente de estruturas de gelo desordenadas. Este algoritmo de geração de cristais de gelo nos permitiu criar células de gelo Ih de tamanhos que não eram possíveis antes. Usando este algoritmo abordamos o problema de efeitos de tamanho finito não estudados anteriormente
Abstract: Due to the conceptual and technical advances being made in computational physics and computational materials science we have been able to tackle problems that were inaccessible a few years ago. In this dissertation we study the evolution of some of these techniques, presenting the theory and simulation methods to study _rst order phase transitions with emphasis on state-of-the-art free-energy calculation (Reversible Scaling) and rare event (Forward Flux Sampling) methods using the atomistic simulation technique of Molecular Dynamics. The evolution and efficiency improvement of these techniques is presented together with applications to simple systems that allow exact solution as well as the more the complex case of Martensitic phase transitions. We also present the application of numerical methods to study Pauling\'s model of ice. We have developed and implemented a new algorithm for efficient generation of disordered ice structures. This ice generator algorithm allows us to create ice Ih cells of sizes not reported before. Using this algorithm we address finite size effects not studied before
Mestrado
Física
Mestre em Física
APA, Harvard, Vancouver, ISO, and other styles
9

Vaitheeswaran, Subramanian. "Computer Simulations of Partially Confined Water." Fogler Library, University of Maine, 2004. http://www.library.umaine.edu/theses/pdf/VaitheeswaranS2004.pdf.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Ernst, Matthew Brian. "Molecular dynamics simulation of DNA lesions." Online access for everyone, 2005. http://www.dissertations.wsu.edu/Thesis/Fall2005/m%5Fernst%5F121305.pdf.

Full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Books on the topic "Molecular simulation"

1

Schlick, Tamar. Molecular Modeling and Simulation. New York, NY: Springer New York, 2002. http://dx.doi.org/10.1007/978-0-387-22464-0.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Haile, J. M. Molecular dynamics simulation: Elementary methods. New York: Wiley, 1992.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
3

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

Find full text
APA, Harvard, Vancouver, ISO, and other styles
4

D, Nicholson, ed. Molecular simulation of adsorption phenomena. Boca Raton: Taylor & Francis, 2005.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
5

Maginn, Edward J., and Jeffrey Errington, eds. Foundations of Molecular Modeling and Simulation. Singapore: Springer Singapore, 2021. http://dx.doi.org/10.1007/978-981-33-6639-8.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Raabe, Gabriele. Molecular Simulation Studies on Thermophysical Properties. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-3545-6.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Hou, Dongshuai. Molecular Simulation on Cement-Based Materials. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-13-8711-1.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Snurr, Randall Q., Claire S. Adjiman, and David A. Kofke, eds. Foundations of Molecular Modeling and Simulation. Singapore: Springer Singapore, 2016. http://dx.doi.org/10.1007/978-981-10-1128-3.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

National Institute of Standards and Technology (U.S.), ed. Molecular dynamics simulation of tethered chains. Gaithersburg, MD: U.S. Dept. of Commerce, Technology Administration, National Institute of Standards and Technology, 1998.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
10

The art of molecular dynamics simulation. Cambridge: Cambridge University Press, 1995.

Find full text
APA, Harvard, Vancouver, ISO, and other styles
More sources

Book chapters on the topic "Molecular simulation"

1

Heinecke, Alexander, Wolfgang Eckhardt, Martin Horsch, and Hans-Joachim Bungartz. "Molecular Dynamics Simulation." In Supercomputing for Molecular Dynamics Simulations, 11–29. Cham: Springer International Publishing, 2015. http://dx.doi.org/10.1007/978-3-319-17148-7_2.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

Feig, Michael. "Molecular Simulation Methods." In ACS Symposium Series, 155–78. Washington, DC: American Chemical Society, 2010. http://dx.doi.org/10.1021/bk-2010-1052.ch008.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Li, Zhigang. "Molecular dynamics simulation." In Nanofluidics, 45–78. Boca Raton : Taylor & Francis, a CRC title, part of the Taylor &: CRC Press, 2018. http://dx.doi.org/10.1201/b22007-3.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Priya, Prerna, Minu Kesheri, Rajeshwar P. Sinha, and Swarna Kanchan. "Molecular Dynamics Simulations for Biological Systems." In Pharmaceutical Sciences, 1044–71. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-1762-7.ch040.

Full text
Abstract:
Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.
APA, Harvard, Vancouver, ISO, and other styles
5

Priya, Prerna, Minu Kesheri, Rajeshwar P. Sinha, and Swarna Kanchan. "Molecular Dynamics Simulations for Biological Systems." In Advances in Bioinformatics and Biomedical Engineering, 286–313. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-4666-8811-7.ch014.

Full text
Abstract:
Molecular dynamics simulation is an important tool to capture the dynamicity of biological molecule and the atomistic insights. These insights are helpful to explore biological functions. Molecular dynamics simulation from femto seconds to milli seconds scale give a large ensemble of conformations that can reveal many biological mysteries. The main focus of the chapter is to throw light on theories, requirement of molecular dynamics for biological studies and application of molecular dynamics simulations. Molecular dynamics simulations are widely used to study protein-protein interaction, protein-ligand docking, effects of mutation on interactions, protein folding and flexibility of the biological molecules. This chapter also deals with various methods/algorithms of protein tertiary structure prediction, their strengths and weaknesses.
APA, Harvard, Vancouver, ISO, and other styles
6

Swope, William C., Jed W. Pitera, and Robert S. Germain. "Molecular Simulation and Systems Biology." In Systems Biology, 67–102. Oxford University PressNew York, NY, 2006. http://dx.doi.org/10.1093/oso/9780195300802.003.0003.

Full text
Abstract:
Abstract Although we receive a relatively static view of molecular structure from spectroscopic tools such as x-ray crystallography and nuclear magnetic resonance (NMR), the reality is that molecules are in constant motion at biological temperatures. Intermolecular motions, such as the binding or unbinding of an antibody–antigen complex, have an important role in biological processes. In addition, biomolecules are always flexing, bending, and stretching in ways that affect their function. For example, many proteins display allosteric behavior in which the binding of a ligand to some site on the protein causes the protein to change its shape. This can result in the active site of an enzyme becoming operational. The folding and unfolding of a protein are more extreme examples of intramolecular motions that have a profound impact on biological function. One way to understand the motions of biological molecules is by using a computer to simulate those motions explicitly. The computational techniques used to model intra- and intermolecular motions are known as molecular simulations. Molecular simulations are a set of computational methods that allow the modeling of the motions of molecules. Molecular motions are coupled to the environment—other biomolecules, cofactors, counterions, and water. A typical molecular simulation involves simulating the motions of all of the atoms of a protein or nucleic acid along with all of the surrounding water molecules.
APA, Harvard, Vancouver, ISO, and other styles
7

Chen, Gang. "Molecular Dynamics Simulation." In Nanoscale Energy Transport And Conversion, 452–504. Oxford University PressNew York, NY, 2005. http://dx.doi.org/10.1093/oso/9780195159424.003.0010.

Full text
Abstract:
Abstract So far most of our discussion of energy storage and energy transport has been built on the reciprocal space: the dispersion relations between wavevectors and frequencies. We discarded the history of the motion of individual particles (electrons and atoms) and focused on their collective modal behavior. However, the approximate trajectory of individual particles can be traced if the computational power is sufficient, and from the calculated trajectory of all the particles we can evaluate the desired macroscopic properties or examine the microscopic processes in real space. When the particles are individual molecules or atoms, the approach is typically called molecular dynamics simulation. In classical molecular dynamics, the equations of motion for each individual atom in the system are established on the basis of an empirical interatomic force (or potential) and Newton’s second law. These equations for all the atoms in the system are coupled through the interatomic potential and solved numerically. A quantum molecular dynamics simulation solves the coupled time-dependent Schrodinger equations for all the particles in the system. Exact direct numerical solution of the Schrodinger equations for a system comprising a large number of particles is impractical, and so various approximations have been used. For example, Car and Parrinello (1985) combined the classical atomistic simulation for atomic ions with the density function theory for electrons. Both classical and quantum molecular dynamic simulations require extensive computation but are becoming increasingly useful as computers become faster. The simulation results are usually analyzed on the basis of statistical mechanics principles. In this chapter, we focus on classical molecular dynamic simulations, since quantum molecular dynamics is still limited to a small number of atoms. Molecular dynamic simulation methods have been used as a basic tool in a wide range of fields. A single chapter will not be able to cover even a small number of potential applications.
APA, Harvard, Vancouver, ISO, and other styles
8

"Molecular Simulation." In Encyclopedia of Molecular Pharmacology, 993. Cham: Springer International Publishing, 2021. http://dx.doi.org/10.1007/978-3-030-57401-7_300339.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

"Molecular Dynamics Simulation Calculations." In Molecular Dynamics Simulations for Beginners: Key Topics in Materials Science and Engineering, 7–55. ASM International, 2023. http://dx.doi.org/10.31399/asm.tb.mdsbktmse.t56070007.

Full text
Abstract:
Abstract The appendix contains detailed simulation examples through which readers learn how to format and analyze problems using the LAMMPS molecular dynamics simulator. By means of simulation, readers will determine the thermal expansion coefficient of copper, generate stress-strain plots for aluminum at different temperatures, calculate the surface energy of copper for different crystal orientations, investigate diffusion effects in BCC iron, estimate the sliding friction between graphene layers, compare the stacking fault energy of silver and aluminum, and analyze the properties and behaviors of liquids and gases. All examples employ a systematic problem-solving approach and include necessary input code.
APA, Harvard, Vancouver, ISO, and other styles
10

Frenkel, Daan, and Berend Smit. "Molecular Dynamics Simulations." In Understanding Molecular Simulation, 63–107. Elsevier, 2002. http://dx.doi.org/10.1016/b978-012267351-1/50006-7.

Full text
APA, Harvard, Vancouver, ISO, and other styles

Conference papers on the topic "Molecular simulation"

1

Tagaya, Yoichi, Yasunaga Mitsuya, Susumu Ogata, Hedong Zhang, and Kenji Fukuzawa. "A Simulation Method for Spreading Dynamics of Molecularly Thin Lubricant Films on Magnetic Disks Using Bead-Spring Model." In World Tribology Congress III. ASMEDC, 2005. http://dx.doi.org/10.1115/wtc2005-64393.

Full text
Abstract:
An effective simulation technique for describing the spreading properties of molecularly thin lubricant films on magnetic disks has been developed. We propose a molecular precipitation method that can simulate initial molecule arrangement of the films dip-coated onto the disks. Reptation and Rouse models as the model of the molecular motion, and molecular insertion and molecular precipitation methods as the method for putting molecules in initial positions were compared. From the results of the spreading profiles and diffusion coefficients, it has been revealed that the molecular precipitation method combined with the Rouse model is effective in simulating the spreading of the lubricant films.
APA, Harvard, Vancouver, ISO, and other styles
2

Blakeney, Andrew J., Lawrence Ferreira, and Nicholas M. Reynolds. "Molecular simulation of photoresists I: basic techniques for molecular simulation." In SPIE's 1995 Symposium on Microlithography, edited by Robert D. Allen. SPIE, 1995. http://dx.doi.org/10.1117/12.210387.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

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.

Full text
Abstract:
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.
APA, Harvard, Vancouver, ISO, and other styles
4

Mareschal, Michel, Andrei Popruga, Joaquín Marro, Pedro L. Garrido, and Pablo I. Hurtado. "Molecular ordering at an interface by molecular dynamics." In MODELING AND SIMULATION OF NEW MATERIALS: Proceedings of Modeling and Simulation of New Materials: Tenth Granada Lectures. AIP, 2009. http://dx.doi.org/10.1063/1.3082272.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Pottathuparambil, Robin, and Ron Sass. "FPGA-based three-body molecular dynamics simulator." In Simulation (HPCS). IEEE, 2010. http://dx.doi.org/10.1109/hpcs.2010.5547066.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

HARTKE, BERND. "SIMULATION OF MOLECULAR MACHINES." In 25th Solvay Conference on Chemistry. WORLD SCIENTIFIC, 2021. http://dx.doi.org/10.1142/9789811228216_0032.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Takagi, Shu, Gota Kikugawa, and Yoichiro Matsumoto. "Molecular Dynamics Simulation of Nanobubbles." In ASME/JSME 2003 4th Joint Fluids Summer Engineering Conference. ASMEDC, 2003. http://dx.doi.org/10.1115/fedsm2003-45675.

Full text
Abstract:
Some results have been reported recently related to the bubble formation with Molecular Dynamics (MD) simulation method. Some of them conduct the MD simulations of the bubble nucleation including impurity molecules with L-J potential [1,2]. In the present study, we investigate the stability of the nanometer size bubble in water, using molecular dynamics (MD) simulation method. MD simulation of an aqueous surfactant system: water liquid and alcohols below the liquid saturation density is carried out to investigate the stability of “nanobubbles” and the structure of the gas-liquid interface. To analyze the effect of surfactant structure, volume, and polarization on the stability of bubble nuclei, we use water by SPC/E model as the solvent molecules and 1-propanol, 1-pentanol, 1-heptanol as the surfactant molecules. Fig.1 shows the numerical result of instantaneous behavior of nanobubbles under the presence of surfactant in water. The calculation system is the cubic cell which has a side length of 25.057[Å], and a three-dimensional periodic boundary condition is applied. To include the intramolecular motion, AMBER force field [3] is adopted as a potential function. The momentum equations are integrated by velocity-Verlet argorithm [4]. Further, the time integration is extended to the Multi Time Scale algorithm by r-RESPA method [5]. As the surfactant molecules, to evaluate the influence of the hydrophobic effect of surfactants on the stability of bubble nuclei, we adopt 1-propanol (C3H7OH), 1-pentanol (C5H11OH), and 1-heptanol (C7H15OH), and to investigate the influence of the polarization of hydrophilic groups (-OH), “pseudo” 1-pentanol of which charge is cancelled away is also calculated. As a result, it was found that from the MD simulation at the condition that the bubble nuclei could not exist stably in pure water, a stable bubble is formed in aqueous surfactant system and hydroxyl groups of surfactants tend to point to the liquid phase at the gas-liquid interface. It is also shown that the longer hydrophobic chains the surfactants have, the more stably the bubble nuclei can exist.
APA, Harvard, Vancouver, ISO, and other styles
8

Ning, Zuo-Yun, Chang-Ming Nie, Xiao-Long Li, Fang-Shuai Zhang, Wen-Bo Lan, and Sha Gao. "Molecular Imprinted Polymers of Sulfisoxazole by Molecular Simulation." In 2015 International Conference on Energy, Environmental & Sustainable Ecosystem Development (EESED 2015). WORLD SCIENTIFIC, 2015. http://dx.doi.org/10.1142/9789814723008_0063.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Darbandi, Masoud, Rasoul Khaledi-Alidusti, Majid Abbaspour, Hossein Reza Abbasi, and Gerry Schneider. "Study of Cut-Off Radius and Temperature Effects on Water Molecular Behavior Using Molecular Dynamics Method." In ASME 2011 9th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2011. http://dx.doi.org/10.1115/icnmm2011-58216.

Full text
Abstract:
Water molecules are one of the important molecules in nanofluidics. Its structure and its behavior can change with Temperature and cut-off distance parameters. In this study temperature and cut-off distance effects on the nano-scale water molecules behavior are investigated by molecular dynamics simulations. Many water molecular models have been developed in order to help discover the structure of water molecules. In this study, the flexible three centered (TIP3P-C) water potential is used to model the inter- and intramolecular interactions of the water molecules. In this simulation, we have been studied 512 water molecules with periodic boundary conditions and in a simulation box with 25 angstrom dimensions, which gives water density about 0.99 g/cm3. To examine of accuracy of TIP3P-C model, Radial distribution function of remarkable water model has been compared with experimental data. In this paper, to study temperature effect on water behavior, mentioned system with 300, 450 and 600 K have been considered and compared. The results have showed that with decreasing temperature, the tetrahedrality of the distribution of the water molecules around the central water molecule is enhanced, and the hydrogen bonds become more linear. It is found that as the temperature rises, kinetic energy rises too, and it makes that the average number of hydrogen bonds per water molecule decrease. In addition to temperature effects, cut-off radius parameter effects have been considered too, and four different cut-off radiuses 7.5, 9.0, 10.5, and 12.0 angstrom have been studied.
APA, Harvard, Vancouver, ISO, and other styles
10

Liu, Chao, Liming Wan, Xinming Zhang, and Danling Zeng. "Investigation of Fractional Characteristic of Molecular Motion by Molecular Dynamics Simulation." In ASME 2004 International Mechanical Engineering Congress and Exposition. ASMEDC, 2004. http://dx.doi.org/10.1115/imece2004-62334.

Full text
Abstract:
Molecular dynamics simulation (MDS) is adopted to investigate the characteristic of fractional motion of molecules in liquid phase, vapor phase and liquid-vapor interface in the paper. Based on the theory of mean free path and Shannon sampling theorem, the way to determine a universal criterion of time step of simulation is presented. It is shown that there exists difference in the regular pattern of molecular motion in the state of liquid and vapor phase. The fractional features are different for different matter states. Under the condition of same temperature, the characteristic fractional number of molecular motion in liquid state is greater than one in vapor state. It is shown that the fractional dimension numbers in the X, Y and Z direction of the liquid-vapor interface are different. This proves that the liquid-vapor interface has anisotropic character.
APA, Harvard, Vancouver, ISO, and other styles

Reports on the topic "Molecular simulation"

1

THOMPSON, AIDAN P. Molecular Simulation of Reacting Systems. Office of Scientific and Technical Information (OSTI), March 2002. http://dx.doi.org/10.2172/793349.

Full text
APA, Harvard, Vancouver, ISO, and other styles
2

THOMPSON, AIDAN P. Molecular Dynamics Simulation of Polymer Dissolution. Office of Scientific and Technical Information (OSTI), February 2003. http://dx.doi.org/10.2172/808631.

Full text
APA, Harvard, Vancouver, ISO, and other styles
3

Kelley, C. T. Simulation of Devices with Molecular Potentials. Fort Belvoir, VA: Defense Technical Information Center, December 2013. http://dx.doi.org/10.21236/ada602991.

Full text
APA, Harvard, Vancouver, ISO, and other styles
4

Mountain, Raymond D., and Joseph Hubbard. Molecular dynamics simulation of tethered chains. Gaithersburg, MD: National Institute of Standards and Technology, 1998. http://dx.doi.org/10.6028/nist.ir.6150.

Full text
APA, Harvard, Vancouver, ISO, and other styles
5

Micci, Michael M. Molecular Dynamics Simulation of Supercritical Spray Phenomena. Fort Belvoir, VA: Defense Technical Information Center, September 2008. http://dx.doi.org/10.21236/ada492151.

Full text
APA, Harvard, Vancouver, ISO, and other styles
6

Gu, Wei, and B. P. Schoenborn. Molecular dynamics simulation of hydration in myoglobin. Office of Scientific and Technical Information (OSTI), September 1995. http://dx.doi.org/10.2172/104441.

Full text
APA, Harvard, Vancouver, ISO, and other styles
7

Moyers, Aidan, Stephen Bierschenk, Michael Becker, and Desiderio Kovar. Molecular dynamics simulation of yttria particle impacts. Office of Scientific and Technical Information (OSTI), February 2023. http://dx.doi.org/10.2172/1923628.

Full text
APA, Harvard, Vancouver, ISO, and other styles
8

Rzhetsky, Andrey, and Dimitris Anastassiou. COMPUTATIONAL ANALYSIS AND SIMULATION OF BACTERIAL MOLECULAR NETWORKS. Office of Scientific and Technical Information (OSTI), December 2009. http://dx.doi.org/10.2172/968434.

Full text
APA, Harvard, Vancouver, ISO, and other styles
9

Athanassios Z. Panagiotopoulos. MOLECULAR SIMULATION OF PHASE EQUILIBRIA FOR COMPLEX FLUIDS. Office of Scientific and Technical Information (OSTI), September 2009. http://dx.doi.org/10.2172/963731.

Full text
APA, Harvard, Vancouver, ISO, and other styles
10

Moyers, Aidan, Derek Davies, Michael Becker, and Desiderio Kovar. Molecular dynamics simulation of yttria (Y2O3) nanoparticle impacts. Office of Scientific and Technical Information (OSTI), February 2022. http://dx.doi.org/10.2172/1846111.

Full text
APA, Harvard, Vancouver, ISO, and other styles
You might also be interested in the extended bibliographies on the topic 'Molecular simulation' for particular source types:
Journal articles Dissertations / Theses Books
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!

To the bibliography