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Simulating Normalized Constants: From Importance Sampling to Bridge Sampling to Path Sampling
 Statistical Science, 13, 163–185. COMPARISON OF METHODS FOR COMPUTING BAYES FACTORS 435
, 1998
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Cited by 145 (4 self)
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MessagePassing MultiCell Molecular Dynamics on the Connection Machine 5
 Parallel Computing
, 1993
"... We present a new scalable algorithm for shortrange molecular dynamics simulations on distributed memory MIMD multicomputer based on a messagepassing multicell approach. We have implemented the algorithm on the Connection Machine 5 (CM5) and demonstrate that mesoscale molecular dynamics with mor ..."
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Cited by 26 (4 self)
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We present a new scalable algorithm for shortrange molecular dynamics simulations on distributed memory MIMD multicomputer based on a messagepassing multicell approach. We have implemented the algorithm on the Connection Machine 5 (CM5) and demonstrate that mesoscale molecular dynamics with more than 10 8 particles is now possible on massively parallel MIMD computers. Typical runs show single particle updatetimes of 0:15¯s in 2 dimensions (2D) and approximately 1¯s in 3 dimensions (3D) on a 1024 node CM5 without vector units, corresponding to more than 1.8 GFlops overall performance. We also present a scaling equation which agrees well with actually observed timings. To appear in Parallel Computing (1993) Present address: Department of Mathematics, University of Oregon, Eugene, OR 97403. y To whom correspondence should be addressed. 1 Introduction The molecular dynamics (MD) method [1, 2, 3] has been known for several decades and has been used successfully in atomistic...
Molecular Dynamics Simulations Of Polymer Systems
"... A brief general introduction into Molecular Dynamics methods for polymers is given. For the statics and dynamics of an isolated chain, a simple microcanonical algorithm is severely hampered by ergodicity problems due to mode conservation. Coupling the system to a Langevin heat bath solves this probl ..."
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Cited by 1 (0 self)
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A brief general introduction into Molecular Dynamics methods for polymers is given. For the statics and dynamics of an isolated chain, a simple microcanonical algorithm is severely hampered by ergodicity problems due to mode conservation. Coupling the system to a Langevin heat bath solves this problem, but also screens hydrodynamic interactions for a chain in a bath of solvent molecules. Rouse scaling laws should hold whenever longrange interactions and entanglements are not important; this is important for controlling the relevant time scales as well as for checking the correctness of simulation algorithms. As an application, a single chain in a bath of solvent particles is discussed. In this system, the longrange nature of the hydrodynamic interaction induces pronounced finite size effects, which are analyzed using Ewald summation methods. Furthermore, simulations on the dynamics of entangled melts are considered. Starting from the reptation picture, we discuss the difficulties t...
NORMALIZING CONSTANTS
"... Abstract. Computing (ratios of) normalizing constants of probability models is a fundamental computational problem for many statistical and scientific studies. Monte Carlo simulation is an effective technique, especially with complex and highdimensional models. This paper aims to bring to the atten ..."
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Abstract. Computing (ratios of) normalizing constants of probability models is a fundamental computational problem for many statistical and scientific studies. Monte Carlo simulation is an effective technique, especially with complex and highdimensional models. This paper aims to bring to the attention of general statistical audiences of some effective methods originating from theoretical physics and at the same time to explore these methods from a more statistical perspective, through establishing theoretical connections and illustrating their uses with statistical problems. We show that the acceptance ratio method and thermodynamic integration are natural generalizations of importance sampling, which is most familiar to statistical audiences. The former generalizes importance sampling through the use of a single “bridge ” density and is thus a case of bridge sampling in the sense of Meng and Wong. Thermodynamic integration, which is also known in the numerical analysis literature as Ogata’s method for highdimensional integration, corresponds to the use of infinitely many and continuously connected bridges (and thus a “path”). Our path sampling formulation offers more flexibility and thus potential efficiency to thermodynamic integration, and the search of optimal paths turns out to have close connections with the Jeffreys prior density and the Rao and Hellinger distances between two densities. We provide an informative theoretical example as well as two empirical examples (involving 17 to 70dimensional integrations) to illustrate the potential and implementation of path sampling. We also discuss some open problems.
Journal of Statistical Physics, Vol. 82. Nos. 5/6, 1996 TwoDimensional Gas of Disks: Thermal Conductivity
, 1995
"... The phenomenon of heat conduction in a twodimensional gas of N hard disks is studied in the hydrostatic regime by means of nonequilibrium molecular dynamics (N ranging from 100 to 8000). For systems with N>~I500 the temperature and density profiles observed are in excellent agreement with the conti ..."
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The phenomenon of heat conduction in a twodimensional gas of N hard disks is studied in the hydrostatic regime by means of nonequilibrium molecular dynamics (N ranging from 100 to 8000). For systems with N>~I500 the temperature and density profiles observed are in excellent agreement with the continuous theory, but the conductivity k differs from the one derived from Enskog's theory in a systematic way. This difference seems to slowly decrease with increasing density.
Transport Properties of Anisotropic Polar Fluids: 2. Dipolar Interaction
, 906
"... Number of figures: 12 ..."
References [1] B. J. Alder, in Molecular Dynamics Simulation of Statisticalmechanical
"... The molasses tail in dense hard core fluids is investigated by extensive eventdriven molecular dynamics simulation through the orientational autocorrelation functions. Near the fluidsolid phase transition, there exist three regimes in the relaxation of the pair orientational autocorrelation functi ..."
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The molasses tail in dense hard core fluids is investigated by extensive eventdriven molecular dynamics simulation through the orientational autocorrelation functions. Near the fluidsolid phase transition, there exist three regimes in the relaxation of the pair orientational autocorrelation function, namely the kinetic, molasses (stretched exponential), and diffusional power decay. The density dependence of both the molasses and diffusional power regimes are evalutated and the latter compares with theoretical predictions in three dimensions. The largest cluster at the freezing density of only a few sphere diameter in size persist for only 30 picoseconds ( ∼ 2.8×10 −11 [s]). The most striking observation through the bond orientatinal order parameter is
Computational Mechanical Modeling of the Behavior of Carbon Nanotubes
"... Abstract: This paper presents a computational method for the mechanical simulation of carbon nanotubes, whose complexity is linear on the number of atoms. The regularity of a graphene lattice at its energy ground permits the definition of a tiling scheme that is applied to the surface of nanometric ..."
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Abstract: This paper presents a computational method for the mechanical simulation of carbon nanotubes, whose complexity is linear on the number of atoms. The regularity of a graphene lattice at its energy ground permits the definition of a tiling scheme that is applied to the surface of nanometric carbon pipes. The scheme employs elementary Yshaped cells and proposes a coherent combination of a discrete approach with a continuous elastic beam reference for the numerical simulation of complex structures. In the molecular region, the employed potential is obtained from the local harmonic approximation and leads to an explicit formulation of the acting forces, therefore permitting the dynamical prediction of large deformations as bending and torsion. The study includes a numerical consistency check based on the conservation of the global energy of the molecular system. As a conclusion, future developments and possible applications of the proposed scheme are presented.