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Статті в журналах з теми "Atomic-level detailed simulations"
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Chrobak, Artur, Grzegorz Ziółkowski, Dariusz Chrobak, and Grażyna Chełkowska. "From Atomic Level to Large-Scale Monte Carlo Magnetic Simulations." Materials 13, no. 17 (August 21, 2020): 3696. http://dx.doi.org/10.3390/ma13173696.
Повний текст джерелаАнотація:
This paper refers to Monte Carlo magnetic simulations for large-scale systems. We propose scaling rules to facilitate analysis of mesoscopic objects using a relatively small amount of system nodes. In our model, each node represents a volume defined by an enlargement factor. As a consequence of this approach, the parameters describing magnetic interactions on the atomic level should also be re-scaled, taking into account the detailed thermodynamic balance as well as energetic equivalence between the real and re-scaled systems. Accuracy and efficiency of the model have been depicted through analysis of the size effects of magnetic moment configuration for various characteristic objects. As shown, the proposed scaling rules, applied to the disorder-based cluster Monte Carlo algorithm, can be considered suitable tools for designing new magnetic materials and a way to include low-level or first principle calculations in finite element Monte Carlo magnetic simulations.
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Bal, Kristof M., and Erik C. Neyts. "Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations." Chemical Science 7, no. 8 (2016): 5280–86. http://dx.doi.org/10.1039/c6sc00498a.
Повний текст джерела
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Bottaro, Sandro, and Kresten Lindorff-Larsen. "Biophysical experiments and biomolecular simulations: A perfect match?" Science 361, no. 6400 (July 26, 2018): 355–60. http://dx.doi.org/10.1126/science.aat4010.
Повний текст джерелаАнотація:
A fundamental challenge in biological research is achieving an atomic-level description and mechanistic understanding of the function of biomolecules. Techniques for biomolecular simulations have undergone substantial developments, and their accuracy and scope have expanded considerably. Progress has been made through an increasingly tight integration of experiments and simulations, with experiments being used to refine simulations and simulations used to interpret experiments. Here we review the underpinnings of this progress, including methods for more efficient conformational sampling, accuracy of the physical models used, and theoretical approaches to integrate experiments and simulations. These developments are enabling detailed studies of complex biomolecular assemblies.
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Mulholland, Adrian J. "Computational enzymology: modelling the mechanisms of biological catalysts." Biochemical Society Transactions 36, no. 1 (January 22, 2008): 22–26. http://dx.doi.org/10.1042/bst0360022.
Повний текст джерелаАнотація:
Simulations and modelling [e.g. with combined QM/MM (quantum mechanics/molecular mechanics) methods] are increasingly important in investigations of enzyme-catalysed reaction mechanisms. Calculations offer the potential of uniquely detailed, atomic-level insight into the fundamental processes of biological catalysis. Highly accurate methods promise quantitative comparison with experiments, and reliable predictions of mechanisms, revolutionizing enzymology.
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Ding, Jun, Mark Asta, and Robert O. Ritchie. "On the question of fractal packing structure in metallic glasses." Proceedings of the National Academy of Sciences 114, no. 32 (July 25, 2017): 8458–63. http://dx.doi.org/10.1073/pnas.1705723114.
Повний текст джерелаАнотація:
This work addresses the long-standing debate over fractal models of packing structure in metallic glasses (MGs). Through detailed fractal and percolation analyses of MG structures, derived from simulations spanning a range of compositions and quenching rates, we conclude that there is no fractal atomic-level structure associated with the packing of all atoms or solute-centered clusters. The results are in contradiction with conclusions derived from previous studies based on analyses of shifts in radial distribution function and structure factor peaks associated with volume changes induced by pressure and compositional variations. The interpretation of such shifts is shown to be challenged by the heterogeneous nature of MG structure and deformation at the atomic scale. Moreover, our analysis in the present work illustrates clearly the percolation theory applied to MGs, for example, the percolation threshold and characteristics of percolation clusters formed by subsets of atoms, which can have important consequences for structure–property relationships in these amorphous materials.
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Comitani, Federico, Claudio Melis, and Carla Molteni. "Elucidating ligand binding and channel gating mechanisms in pentameric ligand-gated ion channels by atomistic simulations." Biochemical Society Transactions 43, no. 2 (April 1, 2015): 151–56. http://dx.doi.org/10.1042/bst20140259.
Повний текст джерелаАнотація:
Pentameric ligand-gated ion channels (pLGICs) are important biomolecules that mediate fast synaptic transmission. Their malfunctions are linked to serious neuronal disorders and they are major pharmaceutical targets; in invertebrates, they are involved in insecticide resistance. The complexity of pLGICs and the limited crystallographic information available prevent a detailed understanding of how they function. State-of-the-art computational techniques are therefore crucial to build an accurate picture at the atomic level of the mechanisms which drive the activation of pLGICs, complementing the available experimental data. We have used a series of simulation methods, including homology modelling, ligand–protein docking, density functional theory, molecular dynamics and metadynamics, a powerful scheme for accelerating rare events, with the guidance of mutagenesis electrophysiology experiments, to explore ligand-binding mechanisms, the effects of mutations and the potential role of a proline molecular switch for the gating of the ion channels. Results for the insect RDL receptor, the GABAC receptor, the 5-HT3 receptor and the nicotinic acetylcholine receptor will be reviewed.
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Artyukhov, Vasilii I., Yuanyue Liu, and Boris I. Yakobson. "Equilibrium at the edge and atomistic mechanisms of graphene growth." Proceedings of the National Academy of Sciences 109, no. 38 (September 4, 2012): 15136–40. http://dx.doi.org/10.1073/pnas.1207519109.
Повний текст джерелаАнотація:
The morphology of graphene is crucial for its applications, yet an adequate theory of its growth is lacking: It is either simplified to a phenomenological-continuum level or is overly detailed in atomistic simulations, which are often intractable. Here we put forward a comprehensive picture dubbed nanoreactor, which draws from ideas of step-flow crystal growth augmented by detailed first-principles calculations. As the carbon atoms migrate from the feedstock to catalyst to final graphene lattice, they go through a sequence of states whose energy levels can be computed and arranged into a step-by-step map. Analysis begins with the structure and energies of arbitrary edges to yield equilibrium island shapes. Then, it elucidates how the atoms dock at the edges and how they avoid forming defects. The sequence of atomic row assembly determines the kinetic anisotropy of growth, and consequently, graphene island morphology, explaining a number of experimental facts and suggesting how the growth product can further be improved. Finally, this analysis adds a useful perspective on the synthesis of carbon nanotubes and its essential distinction from graphene.
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Herasari, Dian, Rukman Hertadi, Fida M. Warganegara, and Akhmaloka Akhmaloka. "Stability and Mobility of Lid Lipmnk in Acetonitrile by Molecular Dynamics Simulations Approach." Biosciences, Biotechnology Research Asia 15, no. 2 (June 6, 2018): 295–99. http://dx.doi.org/10.13005/bbra/2632.
Повний текст джерелаАнотація:
Manuk lipase (lipMNK) from the thermophilic bacterium Geobacillus sp is a double lid lipase containing short and long lid segments. A few studies demonstrated that catalytic action of lipase involved the movement of lid segments from closed to open conformation upon the substrate binding. One factor that affects conformational dynamics of the lid segments is solvent polarity. The presence of acetonitrile in certain concentration has showed to enhance lipase activity. In this study, the effect of acetonitrile to the stability and activity of lipMNK was studied at the atomic level by molecular dynamics (MD) simulation. MD was carried out by NPT ensemble at 358 K for 100 nano seconds in various ratio of acetonitrile:water solvent mixtures. The results showed that the conformation of lipMNK was stable up to 70%. However, the effect of lid movement was significantly observed since the concentration at 20% acetonitrile. Detailed molecular analysis at this acetonitrile concentration revealed that the two lids moved in different modes upon opening and closing movement. In the opening movement, the two lids appeared to move in almost simultaneously, while during the closing movement, it was observed sequentially, started by short segment followed by long segment lid.
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Cayrel, Roger, and Matthias Steffen. "Effects of Photospheric Temperature Inhomogeneities on Lithium abundance Determinations (2D)." Symposium - International Astronomical Union 198 (2000): 437–47. http://dx.doi.org/10.1017/s0074180900167026.
Повний текст джерелаАнотація:
Based on detailed 2D radiation hydrodynamics (RHD) simulations, we have investigated the effects of photospheric temperature inhomogeneities induced by convection on spectroscopic determinations of the lithium abundance. Computations have been performed both for the solar case and for a metal-poor dwarf. NLTE effects are taken into account, using a five-level atomic model for Li I. Comparisons are presented with traditional 1D models having the same effective temperature and gravity. The net result is that, while LTE results differ dramatically between 1D and 2D models, especially in the metal-poor case, this does not remain true when NLTE effects are included: 1D/2D differences in the inferred NLTE Li abundance are always well below 0.1 dex. The present computations still assume LTE in the continuum. New computations removing this assumption are planned for the near future.
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Pujol-Navarro, Neret, Karina Kubiak-Ossowska, Valerie Ferro, and Paul Mulheran. "Simulating Peptide Monolayer Formation: GnRH-I on Silica." International Journal of Molecular Sciences 22, no. 11 (May 24, 2021): 5523. http://dx.doi.org/10.3390/ijms22115523.
Повний текст джерелаАнотація:
Molecular dynamics (MD) simulations can provide a detailed view of molecule behaviour at an atomic level, which can be useful when attempting to interpret experiments or design new systems. The decapeptide gonadotrophin-releasing hormone I (GnRH-I) is known to control fertility in mammals for both sexes. It was previously shown that inoculation with silica nanoparticles (SiNPs) coated with GnRH-I makes an effective anti-fertility vaccine due to how the peptide adsorbs to the nanoparticle and is presented to the immune system. In this paper, we develop and employ a protocol to simulate the development of a GnRH-I peptide adlayer by allowing peptides to diffuse and adsorb in a staged series of trajectories. The peptides start the simulation in an immobile state in solution above the model silica surface, and are then released sequentially. This facile approach allows the adlayer to develop in a natural manner and appears to be quite versatile. We find that the GnRH-I adlayer tends to be sparse, with electrostatics dominating the interactions. The peptides are collapsed to the surface and are seemingly free to interact with additional solutes, supporting the interpretations of the GNRH-I/SiNP vaccine system.
Дисертації з теми "Atomic-level detailed simulations"
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Ghatage, Dhairyashil. "Multiscale modeling and simulation of boundary-driven singular flows." Thesis, 2018. https://etd.iisc.ac.in/handle/2005/5391.
Повний текст джерелаЧастини книг з теми "Atomic-level detailed simulations"
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Munteanu, Daniela, and Jean-Luc Autran. "Interactions between Terrestrial Cosmic-Ray Neutrons and III–V Compound Semiconductors." In Modeling and Simulation in Engineering - Selected Problems. IntechOpen, 2020. http://dx.doi.org/10.5772/intechopen.92774.
Повний текст джерелаАнотація:
This work explores by numerical simulation the impact of high-energy atmospheric neutrons and their interactions with III–V binary compound semiconductors. The efforts have focused on eight III–V semiconductors: GaAs, AlAs, InP, InAs, GaSb, InSb, GaN, and GaP. For each material, extensive Geant4 numerical simulations have been performed considering a bulk target exposed to a neutron source emulating the atmospheric neutron spectrum at terrestrial level. Results emphasize in detail the reaction rates per type of reaction (elastic, inelastic, nonelastic) and offer a classification of all the neutron-induced secondary products as a function of their atomic number, kinetic energy, initial stopping power, and range. Implications for single-event effects (SEEs) are analyzed and discussed, notably in terms of energy and charge deposited in the bulk material and in the first nanometers of particle range with respect to the critical charge for modern complementary metal oxide semiconductor (CMOS) technologies.
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Ray, Sujay. "Adaptive Simulated Annealing Algorithm to Solve Bio-Molecular Optimization." In Handbook of Research on Natural Computing for Optimization Problems, 475–89. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0058-2.ch020.
Повний текст джерелаАнотація:
Energy minimization is a paramount zone in the field of computational and structural biology for protein modeling. It helps in mending distorted geometries in the folded functional protein by moving its atoms to release internal constraints. It attempts to hold back to zero value for the net atomic force on every atom. But to overcome certain disadvantages in energy minimization, Simulated Annealing (SA) can be helpful. SA is a molecular dynamics technique, where temperature is gradually reduced during the simulation. It provides the best configuration of bio-molecules in shorter time. With the advancement in computational knowledge, one essential but less sensitive variant of SA: Adaptive Simulated Annealing (ASA) algorithm is beneficial, because it automatically adjusts the temperature scheme and abrupt opting of step. Therefore it benefits to prepare stable protein models and further to investigate protein-protein interactions. Thus, a residue-level study can be analyzed in details for the benefit of the entire biota.
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Tossell, John A., and David J. Vaughan. "The Future." In Theoretical Geochemistry. Oxford University Press, 1992. http://dx.doi.org/10.1093/oso/9780195044034.003.0011.
Повний текст джерелаАнотація:
In this final chapter, an attempt is made to provide an overview of the capabilities of quantum-mechanical methods at the present time, and to highlight the needs for future development and possible future applications of these methods, particularly in areas related to mineral structures, energetics, and spectroscopy. There is also a brief account of some new areas of application, specific directions for future research, and possible developments in the perception and use of quantum-mechanical approaches. The book ends with an epilog on the overall role of “theoretical geochemistry” in the earth and environmental sciences. The local structural characteristics of minerals such as Mg2SiO4, which contain only main-group elements, are reasonably well reproduced by ab initio Hartree-Fock-Roothaan (SCF) cluster calculations at the mediumbasis- set level. Calculations incorporating configuration interaction will inevitably follow and probably lead to somewhat better agreement with experiment. The most pressing needs in this area of study are for the development of systematic procedures for cluster selection and embedding, for a greater understanding of the results at a qualitative level, and for more widespread efficient application of the quantum-chemical results currently available. In the last area, substantial progress has already been made by Lasaga and Gibbs (1987), Sanders et al. (1984), Tsuneyuki et al. (1988), and others, who have used ab initio calculations to generate theoretical force fields which can then be used in molecular-dynamics simulations. If the characteristics of the resultant force fields can be understood at a first-principles level, then it may be possible to understand details of the simulated structures at the same level. Unfortunately, as regards a greater qualitative understanding of the quantum-mechanical calculations, little progress has been made. Rather old qualitative theories describe some aspects of bond-angle variation (Tossell, 1986), but no general model to interpret variations in bond lengths has been developed within either chemistry or geochemistry beyond the model of additive atomic (Slater) or ionic (Shannon and Prewitt) radii. Indeed, global theories of bond-length variations within an ab initio framework seem to be nonexistent. Nonetheless, quantum-chemical studies have shown the presence of intriguing systematics in bond lengths (Gibbs et al., 1987), which had been already noted empirically.
Тези доповідей конференцій з теми "Atomic-level detailed simulations"
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Tsalikis, Dimitrios, Chunggi Baig, Vlasis Mavrantzas, Eleftherios Amanatides, and Dimitrios Mataras. "Hierarchical simulation of microcrystalline PECVD silicon film growth and structure." In 13th International Conference on Plasma Surface Engineering September 10 - 14, 2012, in Garmisch-Partenkirchen, Germany. Linköping University Electronic Press, 2013. http://dx.doi.org/10.3384/wcc2.22-25.
Повний текст джерелаАнотація:
We have designed and implemented a hierarchical simulation methodology capable of addressing the growth rate and microstructural features of thin silicon films deposited through PECVD (Plasma Enhanced Chemical Vapor Deposition). Our main objective is to elucidate the microscopic mechanisms as well as the interplay between atomic level and macroscopic design parameters associated with the development of nano- or micro-scale crystalline regions in the grown film. The ultimate goal is to use multi-scale modeling as a design tool for tackling the issue of local crystallization and its dependence on operating variables. At the heart of our simulation approach is a very efficient, large-scale kinetic Monte Carlo (kMC) algorithm which allows generating samples of representative Si films based on a validated chemistry model. In a second step, the generated film is subjected to an atomistic simulation study which restores the molecular details lost or ignored in the kMC model. The atomistic simulations are computationally very demanding; they are, however, an important ingredient of our work: we use it to back-map the coarse grained model employed in the kMC simulations to an all-atom model which is further relaxed through detailed NPT molecular dynamics (MD) or Monte Carlo simulations. This tunes local structure thus also important morphological details associated with the presence of crystalline and amorphous regions (and the intervening interfacial domains) in the grown film.The kMC algorithm is based on a carefully chosen set of reacting or active radicals (species) in the gas phase impinging the film and a detailed set of surface reactions. Inputs for species fluxes are taken from a well-tuned plasma fluid model that includes a detailed gas phase chemistry reaction scheme. The growth mechanism consists of various surface kinetic events including radical-surface and adsorbed radical-radical interactions, radical-surface diffusion, and surface dissociation reactions. The very fast surface diffusion is decoupled from the rest of the kMC events and is treated deterministically in our work. For a three-dimensional Si(001)-(2x1):H crystalline lattice, our kMC algorithm allows us to simulate film growth over several seconds, resulting in thickness on the order of tens of nanometers. In the following pages we provide more details about the implementation of our kMC algorithm along with validation results.
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Wan, Kaidi, Zhihua Wang, Luc Vervisch, Jun Xia, Yingzu Liu, Yong He, and Kefa Cen. "Large-Eddy Simulation of Alkali Metal Reacting Dynamics in a Preheated Pulverized-Coal Jet Flame Using Tabulated Chemistry." In ASME 2017 Power Conference Joint With ICOPE-17 collocated with the ASME 2017 11th International Conference on Energy Sustainability, the ASME 2017 15th International Conference on Fuel Cell Science, Engineering and Technology, and the ASME 2017 Nuclear Forum. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/power-icope2017-3212.
Повний текст джерелаАнотація:
This paper proposed an approach to modeling alkali metal reacting dynamics in turbulent pulverized-coal combustion (PCC) using tabulated sodium chemistry. With tabulation, detailed sodium chemistry can be incorporated in large-eddy simulation (LES), but the expenses of solving stiff Arrhenius equations can be avoided. The sodium release rate from a pulverized-coal particle is assumed to be proportional to the pyrolysis rate, as a simplification. The chemical forms of released sodium is assumed to be atomic sodium Na, because atomic sodium is predicted to be the favoured species in a flame environment. A detailed sodium chemistry mechanism including 5 sodium species, i.e., Na, NaO, NaO2, NaOH and Na2O2H2, and 24 elementary reactions is tabulated. The sodium chemistry table contains four coordinates, i.e., the equivalence ratio, the mass fraction of the sodium element, the gas-phase temperature, and the progress variable. Apart from the reactions of sodium species, hydrocarbon volatile combustion has been modeled by a partially stirred reactor concept. Since the magnitude of sodium species is very small, i.e., at the ppm level, and the reactions of sodium species are slower than volatile combustion, one-way coupling is used for the interaction between the sodium reactions and volatile combustion, i.e., the former having no influence on the latter. A verification study has been performed to compare the predictions on sodium species evolutions in zero-dimensional simulations using the chemistry table against directly using the detailed sodium mechanism under various initial conditions, and their agreement is always good. The PCC-LES solver used in the present study is validated on a pulverized-coal jet flame ignited by a preheated gas flow. Good agreements between the experimental measurements and the LES results have been achieved on gas temperature, coal burnout and lift-off height. Finally, the sodium chemistry table is incorporated into the LES solver to model sodium reacting dynamics in turbulent pulverized-coal combustion. Properties of Loy Yang brown coal, for which sodium data are available, are used. Characteristics of the reacting dynamics of the 5 sodium species in a pulverized-coal jet flame are then obtained. The results show that Na and NaOH are the two major sodium species in the pulverized-coal jet flame. Na, the atomic sodium, has a high concentration in fuel-rich regions; while the highest NaOH concentration is found in regions close to the stoichiometric condition. It should be pointed out that the proposed chemistry tabulation approach can be extended to modeling potassium reacting dynamics in turbulent multiphase biomass combustion. (CSPE)
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Dini, Daniele. "Between Continuum and Atomistic Contact Mechanics: Could We Bridge the Gap?" In ASME/STLE 2007 International Joint Tribology Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/ijtc2007-44446.
Повний текст джерелаАнотація:
Recently various attempts have been made to compare continuum contact mechanics to atomistic simulations. The general conclusion of these studies is that continuum mechanics is not adequate to study nanoscopic interactions. Although the use of continuum mechanics at the nanometre scale has a number of limitations, some of the results obtained at atomic level using atomistic simulations can be explained at the continuum level by modelling the interacting surfaces as idealised rough contacts. This will be explicitly proven in this paper. The interfacial contact pressure distribution is found for a sphere pressed onto an elastically similar half-space whose surface is populated by a uniform array of spherical asperities (here representing individual atoms). Details of the load suffered by asperities in the contact disk, together with the effects of the roughness on the overall tangential compliance and the frictional energy losses, are found using a recently proposed technique [1]. Results obtained at continuum level are then generalised and compared to those reported in the literature at atomic level. It is shown that the use of the rough contact idealisation described here is capable of reconciling continuum mechanics and atomistic simulations by capturing some of the features that cannot be captured by the means of conventional Hertzian theory.
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Gobinath, N., and J. Cecil. "Investigation of a Framework for Collaborative Activities Across Heterogeneous Engineering Domains." In ASME 2005 International Mechanical Engineering Congress and Exposition. ASMEDC, 2005. http://dx.doi.org/10.1115/imece2005-82105.
Повний текст джерелаАнотація:
This paper describes the functions underlying the creation of a collaborative framework to support robust information exchange across heterogeneous engineering domains. The application context relates to nano manipulation of particles such as proteins; the initial findings relating to distributed accomplishment of target activities in this identified context will be elaborated in this paper. In the scenario being considered, the potential project partners who possess skills and resources related to nano tube design, synthesis, manipulation plan, and simulation are identified from a service directory to form a Virtual Enterprise, with which the final target physical manipulation is formulated. In the proposed framework, the user specifications are used by various planning activities and a detailed top level plan is generated, which is represented by <NTDS, NTSS, MPS, SS>, where NTDS (Nano Tube Design Specification) is a representation of the design attributes of a carbon nano tube, NTSS (Nano Tube Synthesis Specification) is a representation that describes the synthesis of nano tube depending upon the design specification, MPS (Manipulation Plan Specification) is a representation which allows to formulate a nano manipulation plan according to user specification, and SS (Simulation Specification) is a representation that allows to generate various test cases to evaluate the nanomanipulator and the associated manipulation plan. The proposed framework is composed of an enterprise level Planning Manager (which generates a detailed top level plan from the user specification), a Design Coordinator (that identifies and evaluates the candidate design companies to find a potential design that can be used for a target nano manipulation tasks), a Synthesis/Manufacturing Coordinator (which focuses on identifying candidate partners and resources capable of manufacturing a specified nano manipulator). In the modeled context, this manipulator is a Nano tube attached to the tip of Atomic Force Microscope (AFM) probe; a Manipulation Plan Coordinator focuses on identifying candidate manipulation plan generators, and a Simulation coordinator deals with identifying candidate simulation tool vendors who provide services to evaluate nano tube and nano manipulation plan. The framework is proposed with scalability in mind so that new modules can be support a ‘plug and play’ type of integration in depending on the customer requirements.
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Cha, Pil-Ryung, Jun Song, T. Kyle Vanderlick, and David J. Srolovitz. "Molecular Dynamics Simulation of Single Asperity Contact." In ASME/STLE 2004 International Joint Tribology Conference. ASMEDC, 2004. http://dx.doi.org/10.1115/trib2004-64335.
Повний текст джерелаАнотація:
Many state-of-art microelectronic, photonic and MEMS devices are based upon or created using small-scale contacts. These include, for example, high frequency, microscale electromechanical switches and nanopatterning of organic optoelectronic materials by contact adhesion, cold welding, and lift-off. The initial stages of contact occur between asperities of micro- and/or nano-scopic dimensions. As a consequence, understanding the processes that occur at the atomic level when two rough surfaces are bought into contact is fundamentally important for a wide range of problems including adhesion, contact formation, contact resistance, materials hardness, friction, wear, and fracture. The centrality of single asperities in the fundamental micromechanical response of contact between two rough surfaces has long been recognized. A wide range of experiments has shown that the conductance of small contacts changes abruptly as a function of contact size. In some cases, the conductance through individual asperities increases in a stepwise manner as the two surfaces are pressed into contact. These jumps conductance appear to be correlated with jumps in the force. The observed force-displacement relation appears to be poorly described by JKR theory during loading, while JKR provides a reasonable description of the behavior in unloading. In this presentation (see Acta Materialia 52, 3983 (2004) for more details), we report the results of molecular dynamics simulations of single asperity contact during multiple cycles of loading and unloading at room temperature. We focus on the mechanisms by which contact deformation occurs and the relationship between contact conductance (and contact area) and the deformation. These simulations account for adhesion, elastic deformation, dislocation generation and migration, the formation of other types of defects and morphology evolution. In order to study the elastic and plastic deformation of the asperities on a rough surface, we set up a model system, as shown in Fig. 1. For simplificity, we consider a single deformable asperity on a deformable substrate that interacts with a flat, rigid plate. We calculate the conductance of the contact during loading and unloading through the modified Sharvin model [12]. To our knowledge, this study represents the first dynamic, atomistic simulation of the elastic and plastic deformation behavior of a single asperity and the corresponding evolution of the contact area and contact conductance. The present simulation results reproduce a large body of existing nano-contact experimental results, including the stepwise variation of contact area and conductance with displacement and the hysteresis in the contact radius and contact resistance versus force curves.