Description It is currently possible in an efficient way to calculate the distance between two hard convex objects with a generic shape and to predict their collision [ED4HB]. The first application of such algorithms has been tested on the molecular dynamics of a systems of classical hard ellipsoids of revolution [DeMicheleHE06]. The same methods allows to simulate shaped step interactions[DeMichelSticky06]. The recent introduction of an algorithm for the rotation of objects with a generic inertia tensor completes such approach [vanZonCondMat]. Moreover,following the lines of [BD4HS], it seems to be possible to extend classical Molecular Dynamics simulation to the Brownian Dynamics simulation of interest in the field of colloids and suspensions. A renewed interest for assemblies of hard shaped objects stems from the field of colloidal science; nevertheless,simulations of the dynamics of hard objects [Allen89,Allen93] needs to be revived and theoretical investigations on the dynamics of shaped objects reconsidered. Besides, we believe that there is a potential interest in several cross-disciplinary scientific and technological fields. Such belief stems from an analysis of the current investigations in several fields: * theory of molecular liquids: while hard-spheres are widely understood and form the reference system for many theories of the dynamics and the statics, there no such understanding for shaped objects [GrayGubbinsBook] * granular fluids: simulations of shaped particles are practically limited to hard needles * geo-mechanics: soil rheology employs mostly models and simulations where grains are spherical or, in the most sophisticated cases, ellipsoidal [Ouadfel99,Ouadfel01]. The new rheology introduced by switching from spheres to elongated objects should induce to take account of shape as a must, not as an optional. * powders: same situation than in geo-mechanics [Ouadfel99,Antony04]. * fruit & vegetables: damages due to processing, transportation and handling are studied via simulations of spheres that represent potatoes, tomatoes, apples [LoodtsMSTh]. Damages are predicted looking at the collision points on the spheres; from our experience on ellipsoids, we believe that at least the collision frequency and the magnitude of the impact is deeply influenced even by a little elongation of the objects. Moreover, experiments for the mechanical characterizations require at least a description in terms of an ellipsoidal object [Cherng05]. * colloids and nanoassembly: despite the possibility of controlling the shape of the particles [vanDillen2004], hard spheres remain the main reference system. * lyotropic liquid crystals: several overlap criteria [Allen93,Het99,Blaak99] allow the simulation of specific hard objects and point out the importance of the shape on the appearance of new liquid-crystal phases. No general method to investigate and quantify such effect exists for at least convex objects. * coarse-grained proteins: from experimental data, at least Human Serum Albumin can be modeled as an hard ellipsoid with a repulsive stepwise potential [Sjoberg97]. * go-models [Go83] for folding: rigid sub-sequences of a protein could be modelled by a single shaped unit speeding up the simulations. * computer science, computer graphics, game design, robotics, virtual reality: distance calculations and collision prediction are the core for the realization of virtual environments and robotic manipulations; again, most algorithm are specific and not shape-independent [Ju01,Eberly01]. In conclusion, we believe that it is timely to promote a cross-disciplinary meeting on the subject in order to create an enlarged community sharing the same interests on simulating hard bodies References [RapaBook] D. C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge University Press, Kwiecie/n 2004. [Miller04] S. Miller, S. Luding. Event-driven molecular dynamics in parallel. Journal of Computational Physics, 193:306-316, 2004. [Paul06] G. Paul. A Complexity O(1) Priority Queue for Event Driven Molecular Dynamics Simulations. ArXiv Physics e-prints, physics/0606226 2006. [Allen89] M.P. Allen, D. Frenkel, J. Talbot. Molecular dynamics simulation using hard particles. Comput. Phys. Rep., 9:301-353, 1989. [Allen93] M. P. Allen, G.T. Evans, D. Frenkel, B. M. Mulder. Hard convex body fluids. Adv. Chem. Phys., 86:1-166, 1993. [Dokholyan98] N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, E. I. Shakhnovich. Discrete molecular dynamics studies of the folding of a protein-like model. ArXiv Condensed Matter e-prints, cond-mat/9812291 1998. [DeMicheleHE06] C. De Michele, A. Scala, R. Schilling, F. Sciortino. Molecular correlation functions for uniaxial ellipsoids in the isotropic state. J. Chem. Phys., 124:104509, 2006. [DeMichelSticky06] C. De Michele, G. Gabrielli, P. Tartaglia, F. Sciortino. Dynamics in the presence of attractive patchy interactions. J. Phys. Chem. B, 110:8064, 2006. [CiccottiDIA] G. Ciccotti, G. Kalibaeva. Simulation of a diatomic liquid using hard spheres model. Journal of Statistical Physics, 115:701-714, 2004. [delaPenaCondMat] L.H. de la Pena, R. van Zon, J. Schofield, S.B. Opps. Discontinuous molecular dynamics for semi-flexible and rigid bodies. ArXiv Condensed Matter e-prints, cond-mat/0607527, 2006. [vanZonCondMat] R. van Zon, J. Schofield. Numerical implementation of the exact dynamics of free rigid bodies. ArXiv Condensed Matter e-prints, cond-mat/0607529, 2006. [CiccottiSDE] Ciccotti G., G. Kalibaeva. Deterministic and stochastic algorithms for mechanical systems under constraints. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 362:1583-1594, 2004. [BD4HS] A. Scala, C. De Michele, Th. Voigtmann. Event-driven brownian dynamics for hard spheres. ArXiv Condensed Matter e-prints, 2006. [Tao05] Y.-G. Tao, W. K. den Otter, W. J. Briels. Kayaking and Wagging of Rods in Shear Flow. Physical Review Letters, 95(23):237802, 2005. [Ouadfel99] H. Ouadfel, L. Rothenburg. An algorithm for detecting inter-ellipsoid contacts. Computers and Geotechnics, 24:245-263, 1999. [Ouadfel01] H. A Ouadfel, L. Rothenburg. `stress-force-fabric` relationship for assemblies of ellipsoids. Mechanics of Materials, 33:201-221, 2001. [Antony04] S.J. Antony, R.O. Momoh, M.R. Kuhn. Micromechanical modelling of oval particulates subjected to bi-axial compression. Computational Materials Science, 29:494498, 2004. [Het99] Mengtao Het, Paul Siders. Monte carlo calculation of orientationally anisotropic pair distributions and energy transfer in a model monolayer. J. Phys. Chem., 94:7280-7288, 1999. [Blaak99] R. Blaak, D. Frenkel, B. M. Mulder. Do cylinders exhibit a cubatic phase? Journal of Chemical Physics, 100:11652-11659, 1999. [LoodtsMSTh] J. Loodts. The discrete element method for the simulation of granular flows. Praca magisterska, Agricultural Engineering, Katholieke Universiteit Leuven, Belgium, 2001. [Eberly01] D. H. Eberly. 3D Game Engine Design. Academic Press, 2001. [Ju01] M. Ju, J. Liu, S. Shiang, Y. Chien, K. Hwang, W. Lee. A novel collision detection method based on enclosed ellipsoid. Proceedings of 2001 IEEE Conference on Robotics and Automation, pag.21-26, 2001.
Simulation of Hard Bodies
antonio scala
2007
Abstract
Description It is currently possible in an efficient way to calculate the distance between two hard convex objects with a generic shape and to predict their collision [ED4HB]. The first application of such algorithms has been tested on the molecular dynamics of a systems of classical hard ellipsoids of revolution [DeMicheleHE06]. The same methods allows to simulate shaped step interactions[DeMichelSticky06]. The recent introduction of an algorithm for the rotation of objects with a generic inertia tensor completes such approach [vanZonCondMat]. Moreover,following the lines of [BD4HS], it seems to be possible to extend classical Molecular Dynamics simulation to the Brownian Dynamics simulation of interest in the field of colloids and suspensions. A renewed interest for assemblies of hard shaped objects stems from the field of colloidal science; nevertheless,simulations of the dynamics of hard objects [Allen89,Allen93] needs to be revived and theoretical investigations on the dynamics of shaped objects reconsidered. Besides, we believe that there is a potential interest in several cross-disciplinary scientific and technological fields. Such belief stems from an analysis of the current investigations in several fields: * theory of molecular liquids: while hard-spheres are widely understood and form the reference system for many theories of the dynamics and the statics, there no such understanding for shaped objects [GrayGubbinsBook] * granular fluids: simulations of shaped particles are practically limited to hard needles * geo-mechanics: soil rheology employs mostly models and simulations where grains are spherical or, in the most sophisticated cases, ellipsoidal [Ouadfel99,Ouadfel01]. The new rheology introduced by switching from spheres to elongated objects should induce to take account of shape as a must, not as an optional. * powders: same situation than in geo-mechanics [Ouadfel99,Antony04]. * fruit & vegetables: damages due to processing, transportation and handling are studied via simulations of spheres that represent potatoes, tomatoes, apples [LoodtsMSTh]. Damages are predicted looking at the collision points on the spheres; from our experience on ellipsoids, we believe that at least the collision frequency and the magnitude of the impact is deeply influenced even by a little elongation of the objects. Moreover, experiments for the mechanical characterizations require at least a description in terms of an ellipsoidal object [Cherng05]. * colloids and nanoassembly: despite the possibility of controlling the shape of the particles [vanDillen2004], hard spheres remain the main reference system. * lyotropic liquid crystals: several overlap criteria [Allen93,Het99,Blaak99] allow the simulation of specific hard objects and point out the importance of the shape on the appearance of new liquid-crystal phases. No general method to investigate and quantify such effect exists for at least convex objects. * coarse-grained proteins: from experimental data, at least Human Serum Albumin can be modeled as an hard ellipsoid with a repulsive stepwise potential [Sjoberg97]. * go-models [Go83] for folding: rigid sub-sequences of a protein could be modelled by a single shaped unit speeding up the simulations. * computer science, computer graphics, game design, robotics, virtual reality: distance calculations and collision prediction are the core for the realization of virtual environments and robotic manipulations; again, most algorithm are specific and not shape-independent [Ju01,Eberly01]. In conclusion, we believe that it is timely to promote a cross-disciplinary meeting on the subject in order to create an enlarged community sharing the same interests on simulating hard bodies References [RapaBook] D. C. Rapaport. The Art of Molecular Dynamics Simulation. Cambridge University Press, Kwiecie/n 2004. [Miller04] S. Miller, S. Luding. Event-driven molecular dynamics in parallel. Journal of Computational Physics, 193:306-316, 2004. [Paul06] G. Paul. A Complexity O(1) Priority Queue for Event Driven Molecular Dynamics Simulations. ArXiv Physics e-prints, physics/0606226 2006. [Allen89] M.P. Allen, D. Frenkel, J. Talbot. Molecular dynamics simulation using hard particles. Comput. Phys. Rep., 9:301-353, 1989. [Allen93] M. P. Allen, G.T. Evans, D. Frenkel, B. M. Mulder. Hard convex body fluids. Adv. Chem. Phys., 86:1-166, 1993. [Dokholyan98] N. V. Dokholyan, S. V. Buldyrev, H. E. Stanley, E. I. Shakhnovich. Discrete molecular dynamics studies of the folding of a protein-like model. ArXiv Condensed Matter e-prints, cond-mat/9812291 1998. [DeMicheleHE06] C. De Michele, A. Scala, R. Schilling, F. Sciortino. Molecular correlation functions for uniaxial ellipsoids in the isotropic state. J. Chem. Phys., 124:104509, 2006. [DeMichelSticky06] C. De Michele, G. Gabrielli, P. Tartaglia, F. Sciortino. Dynamics in the presence of attractive patchy interactions. J. Phys. Chem. B, 110:8064, 2006. [CiccottiDIA] G. Ciccotti, G. Kalibaeva. Simulation of a diatomic liquid using hard spheres model. Journal of Statistical Physics, 115:701-714, 2004. [delaPenaCondMat] L.H. de la Pena, R. van Zon, J. Schofield, S.B. Opps. Discontinuous molecular dynamics for semi-flexible and rigid bodies. ArXiv Condensed Matter e-prints, cond-mat/0607527, 2006. [vanZonCondMat] R. van Zon, J. Schofield. Numerical implementation of the exact dynamics of free rigid bodies. ArXiv Condensed Matter e-prints, cond-mat/0607529, 2006. [CiccottiSDE] Ciccotti G., G. Kalibaeva. Deterministic and stochastic algorithms for mechanical systems under constraints. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, 362:1583-1594, 2004. [BD4HS] A. Scala, C. De Michele, Th. Voigtmann. Event-driven brownian dynamics for hard spheres. ArXiv Condensed Matter e-prints, 2006. [Tao05] Y.-G. Tao, W. K. den Otter, W. J. Briels. Kayaking and Wagging of Rods in Shear Flow. Physical Review Letters, 95(23):237802, 2005. [Ouadfel99] H. Ouadfel, L. Rothenburg. An algorithm for detecting inter-ellipsoid contacts. Computers and Geotechnics, 24:245-263, 1999. [Ouadfel01] H. A Ouadfel, L. Rothenburg. `stress-force-fabric` relationship for assemblies of ellipsoids. Mechanics of Materials, 33:201-221, 2001. [Antony04] S.J. Antony, R.O. Momoh, M.R. Kuhn. Micromechanical modelling of oval particulates subjected to bi-axial compression. Computational Materials Science, 29:494498, 2004. [Het99] Mengtao Het, Paul Siders. Monte carlo calculation of orientationally anisotropic pair distributions and energy transfer in a model monolayer. J. Phys. Chem., 94:7280-7288, 1999. [Blaak99] R. Blaak, D. Frenkel, B. M. Mulder. Do cylinders exhibit a cubatic phase? Journal of Chemical Physics, 100:11652-11659, 1999. [LoodtsMSTh] J. Loodts. The discrete element method for the simulation of granular flows. Praca magisterska, Agricultural Engineering, Katholieke Universiteit Leuven, Belgium, 2001. [Eberly01] D. H. Eberly. 3D Game Engine Design. Academic Press, 2001. [Ju01] M. Ju, J. Liu, S. Shiang, Y. Chien, K. Hwang, W. Lee. A novel collision detection method based on enclosed ellipsoid. Proceedings of 2001 IEEE Conference on Robotics and Automation, pag.21-26, 2001.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
