1,721,083 research outputs found
On the establishment of thermal diffusion in binary Lennard-Jones liquids
Full text linkThe establishment of thermal diffusion in an Ar-Kr Lennard-Jones mixture is investigated via dynamical non equilibrium molecular dynamics [G. Ciccotti, G. Jacucci, Phys. Rev. Lett. 35, 789 (1975)]. We observe, in particular, the evolution of the density and temperature fields of the system following the onset of the thermal gradient. In stationary conditions, we also compute the Soret coefficient of the mixture. This study confirms that dynamical non equilibrium molecular dynamics is an effective tool to gather information on transient phenomena, even though the full evolution of the mass and energy fluxes associated to the temperature and density fields requires, in this case, a more substantial numerical effort than the one employed here
Thermotransport coefficients of a classical binary ionic mixture by non-equilibrium molecular dynamics
No full textThe authors present a non-equilibrium molecular dynamics (NEMD) computation of both direct and cross thermotransport coefficients of a strong coupled binary mixture of positive charges in a negative neutralising background (binary ionic mixture) in the special case in which the charge and mass ratios of the mobile species are the same. They use a modified version of the MacGowan-Evans NEMD algorithm. They find that the direct coefficients qualitatively agree with the predictions of the one-fluid approximation. The authors show that the cross properties depend mainly on the relative interaction energy of the two different species in the mixture, while the range of interaction gives a small correction
A correct, reversible Trotter splitting for the evolution operator in molecular dynamics simulations of molecular systems with constraints
No full textFor generating an isobaric–isothermal ensemble in molecular dynamics simulations of atomic systems a correct ensemble distribution can be obtained by the approach of Martyna, Tobias and Klein [J. Chem. Phys. 101, 4177–4189 (1994)]. The constituting equations of the latter approach have been also generalised to molecular systems [M. E. Tuckerman, Statistical Mechanics: Theory and Molecular Simulation, Oxford Graduate Texts (2010)] using the molecular virial instead of the atomic one. An isothermal–isobaric method for systems with holonomic molecular constraints has been also introduced in the past [G. Kalibaeva, M. Ferrario and G. Ciccotti, Mol. Phys. 101 765–778 (2003)] but the factorisation was not worked out completely, resulting in a non-reversible first-order algorithm. Here, we propose the correct factorisation and implement a reversible integrator based on Martyna, Tobias and Klein equations for a system of molecules subjected to holonomic constraints. We add to the algorithm the Suzuki–Yoshida treatment that improves the energy conservation or permits to go to larger time steps. Finally, we test our algorithm by applying it to the dynamics of a Ortotherphenyl model
Computer Simulation in Condensed Matter: From Materials to Chemical Biology. Vol. 2
No full text.The school that was held at the Ettore Majorana Foundation and Center for Scientific Culture (EMFCSC), Erice (Sicily), in July 2005, aimed to provide an up-to-date overview of almost all technical advances of computer simulation in statistical mechanics, giving a fair glimpse of the domains of interesting appli- cations. Full details on the school programme and participants, plus some ad- ditional material, are available at its Web site, http://cscm2005.unimore.it Computer simulation is now a very well established and active field, and its applications are far too numerous and widespread to be covered in a single school lasting less than 2 weeks. Thus, a selection of topics was required, and it was decided to focus on perspectives in the celebration of the 65th birthday of Mike Klein, whose research has significantly pushed forward the frontiers of computer simulation applications in a broad range, from materials science to chemical biology. Prof. M. L. Klein (Dept. Chem., Univ. Pennsylvania, Philadelphia, USA) is internationally recognized as a pioneer in this field; he is the winner of both the prestigious Aneesur Rahman Prize for Computa- tional Physics awarded by the American Physical Society, and its European counterpart, the Berni J. Alder CECAM Prize, given jointly with the Euro- pean Physical Society. The festive session held on July 23rd, 2005, highlighting these achievements, has been a particular focus in this school. In the frame- work of the EMFCSC International School of Solid State Physics Series, the present school was the 34th course of its kind. However, this school can be considered as being the third (and perhaps last?) event in a series of comprehensive schools on computer simulation, 10 years after the COMO Euroconference on “Monte Carlo and Molecular Dy- namics of Condensed Matter systems,” and 20 years after the VARENNA Enrico Fermi Summer School on “Molecular Dynamics of Statistical Mechan- ical Systems.” Comparing the topics emphasized upon in these schools, both the progress in achieving pioneering applications to problems of increasing complexity, and the impressive number of new methodological developments are evident. While the focus of the Varenna School was mostly on Molecular Dynamics (MD) and its applications from simple to complex fluids, the Como school included both Monte Carlo (MC) simulations of lattice systems (from quantum problems to the advanced analysis of critical phenomena in classi- cal systems like the simple Ising model), and the density functional theory of electronic structure up to the Car-Parrinello ab initio Molecular Dynamics techniques (CPMD). At the Erice school, a new focus was put on the para- digma of “Multiscale Simulation”, i.e. the idea to combine different methods of simulation on different scales of length and time in a coherent fashion. This method allow us to clarify the properties of complex materials or biosystems where a single technique (like CPMD or MD or MC etc.) due to excessive needs of computer resources is bound to fail. Good examples presented at this school for such multiscale simulation approaches included MD studies of polymers coupled with a solvent, which is described only in a coarse-grained fashion by the lattice Boltzmann technique and hybrid quantum mechanical/molecular mechanics (QM/MM) methods for CPMD simulations of biomolecules, etc. As a second “leitmotif,” emphasis has been put on rapidly emerging novel simulation techniques. Techniques that have been dealt with at this school in- clude the methods of “transition path sampling” (i.e. a Monte Carlo sampling not intending to clarify the properties of a state in the space of thermodynamic variables, but the properties of the dominating paths that lead “in the course of a transition” from one stable state to another), density of state methods (like Wang-Landau sampling and multicanonical Monte Carlo, allowing an elegant assessment of free energy differences and free energy barriers, etc.) and so on. These techniques promise substantial progress with famous “grand challenge problems” like the kinetics of protein folding, as well as with classi- cal ubiquitous problems like the theory of nucleation phenomena. Other sub- jects where significant progress in methodological aspects was made included cluster algorithms for off-lattice systems, evolutionary design in biomedical physics, construction of coarse-grained models describing the self-assembly and properties of lipid layers or of liquid crystals under confinement and/or shear, glass simulations, novel approaches to quantum chemistry, formulation of models to correctly describe the essence of dry friction and lubrication, rare event sampling, quantum Monte Carlo methods, etc. The diversity of this list vividly illustrates the breadth and impact that simulation methods have today. While the most simple MC and MD methods have been invented about 50 years ago (the celebration of the 50th anniversary of the Metropolis algorithm was held in 2003, the 50th anniversary of the Alder-Wainwright spectacular first discovery by MD of the (then unexpected) phase transition in the hard sphere fluid is due in 2007), even the “second generation” of scientists, who started out 30-40 years ago as “simulators” are now already the “old horses” of the field, either close to the end of their scientific career, or, in the best case, near it. Thus, we can clearly observe that the task of developing the computer simulation methodology is further taken over with vigor by the “third generation” of well-established younger scientists who have emerged in the field. Because two of the organizers of the school (KB, GC) do belong to the “old horse” category, it was clearly necessary to get an energetic younger co-organizer involved (MF), and we also felt it was the appropriate time that the most senior experts need not give the main lectures of the school, but rather the younger generation who are now most actively driving forward the frontier of research. Of course, it was crucial to involve the very valuable experience and knowledge of our senior colleagues into the school as well, and we are very glad that so many of them have accepted our invitation to give one-hour seminars providing tutorial introductions to various advanced research topics, which is at the heart of the research interests of the speakers. In this way, it was possible to produce an exciting event on the forefront of research on computer simulation in condensed matter, in a very stimulating and interactive atmosphere, with plenty of fruitful discussions. It is with great pleasure that we end this preface with several acknowl- edgments. This school, of which the lecture notes are collected here, could not have taken place without the generous support of the European Commu- nity under the Marie Curie Conference and Training Courses, Contract No. MSCF-CT-2003-503840. We are grateful to the coordinators of this program, Michel Mareschal and Berend Smit, for their help in securing this support. We also wish to thank the CECAM secretaries, Emmanuelle Crespeau and Emilie Bernard. We thank the Ettore Majorana Foundation and Centre for Scientific Cul- ture in Erice, Sicily, for providing their excellent facilities to hold this school, and also Giorgio Benedek, Director of the International School of Solid State Physics, for the opportunity to hold our school as its 34th course: for his enthu- siastic support during the school, and for his personal scientific participation. We are particularly grateful to him for providing the beautiful facilities of Erice. MF thanks Davide Calanca, INFM-S3, Modena, for his valuable help in setting up the Web site of the school. We thank the director of the physics department of the University of Rome “La Sapienza”, Guido Martinelli, and the Administrative Secretary of the De- partment, Mrs. Maria Vittoria Marchet and her assistant, Mrs. Maria Proi- etto, for helping us in the difficult duty of managing all the financial matters. Mrs. Fernanda Lupinacci deserves grateful appreciation for her devoted and untiring presence and skillful help in overcoming all practical difficulties re- lated to the organizational needs, and for providing a hospitable atmosphere to all the participants. We are very grateful to Daan Frenkel, Mike Klein, and Peter Nielaba for their very valuable input when setting up the scientific program of the school, to all the lecturers, for their willingness to engage in the endeavor, and to all the participants, for their engagement and enthusiasm. May 2006 Mauro Ferrario Giovanni Ciccotti Kurt Binde
Computer Simulation in Condensed Matter: From Materials to Chemical Biology. Vol. 1
No full textThe school that was held at the Ettore Majorana Foundation and Center for Scientific Culture (EMFCSC), Erice (Sicily), in July 2005, aimed to provide an up-to-date overview of almost all technical advances of computer simulation in statistical mechanics, giving a fair glimpse of the domains of interesting appli- cations. Full details on the school programme and participants, plus some ad- ditional material, are available at its Web site, http://cscm2005.unimore.itComputer simulation is now a very well established and active field, and its applications are far too numerous and widespread to be covered in a single school lasting less than 2 weeks. Thus, a selection of topics was required, and it was decided to focus on perspectives in the celebration of the 65th birthday of Mike Klein, whose research has significantly pushed forward the frontiers of computer simulation applications in a broad range, from materials science to chemical biology. Prof. M. L. Klein (Dept. Chem., Univ. Pennsylvania, Philadelphia, USA) is internationally recognized as a pioneer in this field; he is the winner of both the prestigious Aneesur Rahman Prize for Computa- tional Physics awarded by the American Physical Society, and its European counterpart, the Berni J. Alder CECAM Prize, given jointly with the Euro- pean Physical Society. The festive session held on July 23rd, 2005, highlighting these achievements, has been a particular focus in this school. In the frame- work of the EMFCSC International School of Solid State Physics Series, the present school was the 34th course of its kind.However, this school can be considered as being the third (and perhaps last?) event in a series of comprehensive schools on computer simulation, 10 years after the COMO Euroconference on “Monte Carlo and Molecular Dy- namics of Condensed Matter systems,” and 20 years after the VARENNA Enrico Fermi Summer School on “Molecular Dynamics of Statistical Mechan- ical Systems.” Comparing the topics emphasized upon in these schools, both the progress in achieving pioneering applications to problems of increasing complexity, and the impressive number of new methodological developments are evident. While the focus of the Varenna School was mostly on Molecular Dynamics (MD) and its applications from simple to complex fluids, the Como school included both Monte Carlo (MC) simulations of lattice systems (from quantum problems to the advanced analysis of critical phenomena in classi- cal systems like the simple Ising model), and the density functional theory of electronic structure up to the Car-Parrinello ab initio Molecular Dynamics techniques (CPMD). At the Erice school, a new focus was put on the para- digma of “Multiscale Simulation”, i.e. the idea to combine different methods of simulation on different scales of length and time in a coherent fashion. This method allow us to clarify the properties of complex materials or biosystems where a single technique (like CPMD or MD or MC etc.) due to excessive needs of computer resources is bound to fail. Good examples presented at this school for such multiscale simulation approaches included MD studies of polymers coupled with a solvent, which is described only in a coarse-grained fashion by the lattice Boltzmann technique and hybrid quantum mechanical/molecular mechanics (QM/MM) methods for CPMD simulations of biomolecules, etc.As a second “leitmotif,” emphasis has been put on rapidly emerging novel simulation techniques. Techniques that have been dealt with at this school in- clude the methods of “transition path sampling” (i.e. a Monte Carlo sampling not intending to clarify the properties of a state in the space of thermodynamic variables, but the properties of the dominating paths that lead “in the course of a transition” from one stable state to another), density of state methods (like Wang-Landau sampling and multicanonical Monte Carlo, allowing an elegant assessment of free energy differences and free energy barriers, etc.) and so on. These techniques promise substantial progress with famous “grand challenge problems” like the kinetics of protein folding, as well as with classi- cal ubiquitous problems like the theory of nucleation phenomena. Other sub- jects where significant progress in methodological aspects was made included cluster algorithms for off-lattice systems, evolutionary design in biomedical physics, construction of coarse-grained models describing the self-assembly and properties of lipid layers or of liquid crystals under confinement and/or shear, glass simulations, novel approaches to quantum chemistry, formulation of models to correctly describe the essence of dry friction and lubrication, rare event sampling, quantum Monte Carlo methods, etc. The diversity of this list vividly illustrates the breadth and impact that simulation methods have today.While the most simple MC and MD methods have been invented about 50 years ago (the celebration of the 50th anniversary of the Metropolis algorithm was held in 2003, the 50th anniversary of the Alder-Wainwright spectacular first discovery by MD of the (then unexpected) phase transition in the hard sphere fluid is due in 2007), even the “second generation” of scientists, who started out 30-40 years ago as “simulators” are now already the “old horses” of the field, either close to the end of their scientific career, or, in the best case, near it. Thus, we can clearly observe that the task of developing the computer simulation methodology is further taken over with vigor by the “third generation” of well-established younger scientists who have emerged in the field. Because two of the organizers of the school (KB, GC) do belong to the “old horse” category, it was clearly necessary to get an energetic younger co-organizer involved (MF), and we also felt it was the appropriate time that the most senior experts need not give the main lectures of the school, but rather the younger generation who are now most actively driving forward the frontier of research. Of course, it was crucial to involve the very valuable experience and knowledge of our senior colleagues into the school as well, and we are very glad that so many of them have accepted our invitation to give one-hour seminars providing tutorial introductions to various advanced research topics, which is at the heart of the research interests of the speakers. In this way, it was possible to produce an exciting event on the forefront of research on computer simulation in condensed matter, in a very stimulating and interactive atmosphere, with plenty of fruitful discussions.It is with great pleasure that we end this preface with several acknowl- edgments. This school, of which the lecture notes are collected here, could not have taken place without the generous support of the European Commu- nity under the Marie Curie Conference and Training Courses, Contract No. MSCF-CT-2003-503840. We are grateful to the coordinators of this program, Michel Mareschal and Berend Smit, for their help in securing this support. We also wish to thank the CECAM secretaries, Emmanuelle Crespeau and Emilie Bernard.We thank the Ettore Majorana Foundation and Centre for Scientific Cul- ture in Erice, Sicily, for providing their excellent facilities to hold this school, and also Giorgio Benedek, Director of the International School of Solid State Physics, for the opportunity to hold our school as its 34th course: for his enthu- siastic support during the school, and for his personal scientific participation. We are particularly grateful to him for providing the beautiful facilities of Erice.MF thanks Davide Calanca, INFM-S3, Modena, for his valuable help in setting up the Web site of the school.We thank the director of the physics department of the University of Rome “La Sapienza”, Guido Martinelli, and the Administrative Secretary of the De- partment, Mrs. Maria Vittoria Marchet and her assistant, Mrs. Maria Proi- etto, for helping us in the difficult duty of managing all the financial matters. Mrs. Fernanda Lupinacci deserves grateful appreciation for her devoted and untiring presence and skillful help in overcoming all practical difficulties re- lated to the organizational needs, and for providing a hospitable atmosphere to all the participants.We are very grateful to Daan Frenkel, Mike Klein, and Peter Nielaba for their very valuable input when setting up the scientific program of the school, to all the lecturers, for their willingness to engage in the endeavor, and to all the participants, for their engagement and enthusiasm.May 2006Mauro Ferrario Giovanni Ciccotti Kurt Binde
Constant pressure-constant temperature molecular dynamics: a correct constrained NPT ensemble using the molecular virial
No full textIn the present work we introduce a simple, Nose-Hoover style isothermal-isobaric molecular dynamics method for systems with holonomic molecular constraints and the molecular representation of the virial. We prove, using the non-Hamiltonian dynamics approach, recently developed by Tuckerman et al. [1999, Europhys. Lett., 45, 149], that the phase space distribution, generated by our equations, samples the desired ensemble under all circumstances. We also write down the explicit reversible integrator for our equations. This integrator has been implemented in the last version of the DLProtein program
Equilibrium and Rate Constants, and Reaction Mechanism of the HF Dissociation in the HF(H2O)(7) Cluster by ab Initio Rare Event Simulations
No full textWe perform restrained hybrid Monte Carlo (MC) simulations to compute the equilibrium constant of the dissociation reaction of HF in HF(H2O)(7). We find that the I-IF is a stronger acid in the cluster than in the bulk, and its acidity is higher at lower T. The latter phenomenon has a vibrational entropic origin, resulting from a counterintuitive balance of intra- and intermolecular terms. We find also a temperature dependence of the reactions mechanism. At low T (<= 225 K) the dissociation reaction follows a concerted path, with the H atoms belonging to the relevant hydrogen bond chain moving synchronously. At higher T (300 K), the first two hydrogen atoms move together, forming an intermediate metastable state having the structure of an eigen ion (H9O4+), and then the third hydrogen migrates completing the reaction. We also compute the dissociation rate constant, k(RP). At very low T (<= 75 K) k(RP) depends strongly on the temperature, whereas it gets almost constant at higher T degrees(s). With respect to the bulk, the HF dissociation in the HF(H2O)(7) is about 1 order of magnitude faster. This is due to a lower free energy barrier for the dissociation in the cluster
Mechanical Constraints in Molecular Dynamics Simulation
No full textAdvances in computational power and algorithm development have stimulated molecular dynamics research on diverse large and complicated physical systems. Part of this progress relies on algorithms that are able to account for widely separated time scales or activated processes that would otherwise degrade computational efficiency. This chapter describes how holonomic constraints can be used to overcome such difficulties. The constrained dynamical equations, the statistical mechanics that follows from these equations, and the algorithms needed to simulate the dynamics are presented. Examples related to rare event sampling and adiabatic dynamics are given to illustrate the methods
Theory and methods for rare events
No full textThis paper reviews the transition path theory (TPT) for activated events and summarizes a
set of methods and algorithms to compute all relevant quantities of this theory: free energy, rate and
mechanism of the event. We provide a set of examples to illustrate the applicability of the methods to
problems in chemistry, biophysics and material science
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