Jaegil Kim, Thomas Keyes, John E. Straub · The Journal of Chemical Physics · 2010
We present a powerful replica exchange method, particularly suited to first-order phase transitions associated with the backbending in the statistical temperature, by merging an optimally designed generalized ensemble sampling with replica exchanges. The key ingredients of our method are parametrized effective sampling weights, smoothly joining ordered and disordered phases with a succession of unimodal energy distributions by transforming unstable or metastable energy states of canonical ensembles into stable ones. The inverse mapping between the sampling weight and the effective temperature provides a systematic way to design the effective sampling weights and determine a dynamic range of relevant parameters. Illustrative simulations on Potts spins with varying system size and simulation conditions demonstrate a comprehensive sampling for phase-coexistent states with a dramatic acceleration of tunneling transitions. A significant improvement over the power-law slowing down of mean tunneling times with increasing system size is obtained, and the underlying mechanism for accelerated tunneling is discussed.
Cited by 94Open access
Young Hyun Kim (8648472), Bock-Young Jung (9530239), Sang-Sun Han (2617066) et al. · Figshare · 2020
<p>(a) Filled with light-body impression materials and seated together with the stone models, (b) 50 N of pressure was applied for 5 minutes using static load equipment, (c) the pressure was removed from the stone models after polymerization, (d) cylinder-shaped molds were filled with putty, (e) the specimen was created, (f) the specimen was sectioned buccolingually and mesiodistally at the midline.</p>
Cited by 0Open access
Satoru Itoh, Hisashi Okumura · arXiv (Cornell University) · 2012
We propose a new method for molecular dynamics and Monte Carlo simulations, which is referred to as the replica-permutation method (RPM), to realize more efficient sampling than the replica-exchange method (REM).In RPM not only exchanges between two replicas but also permutations among more than two replicas are performed. Furthermore, instead of the Metropolis algorithm, the Suwa-Todo algorithm is employed for replica-permutation trials to minimize its rejection ratio. We applied RPM to particles in a double-well potential energy, Met-enkephalin in vacuum, and a C-peptide analog of ribonuclease A in explicit water. For a comparison purposes, replica-exchange molecular dynamics simulations were also performed. As a result, RPM sampled not only the temperature space but also the conformational space more efficiently than REM for all systems. From our simulations of C-peptide, we obtained the α-helix structure with salt-bridges between Gly2 and Arg10 which is known in experiments. Calculating its free-energy landscape, the folding pathway was revealed from an extended structure to the α-helix structure with the salt-bridges. We found that the folding pathway consists of the two steps: The first step is the "salt-bridge formation step", and the second step is the "α-helix formation step".
Cited by 1Open access
Gernot Akemann, D. Dalmazi, P.H. Damgaard et al. · Brunel University Research Archive (BURA) (Brunel University London) · 2000
Using the replica method, we analyze the mass dependence of the QCD3 partition function in a parameter range where the leading contribution is from the zero momentum Goldstone fields. Three complementary approaches are considered in this article. First, we derive exact relations between the QCD3 partition function and the QCD4 partition function continued to half-integer topological charge. The replica limit of these formulas results in exact relations between the corresponding microscopic spectral densities of QCD3 and QCD4. Replica calculations, which are exact for QCD4 at half-integer topological charge, thus result in exact expressions for the microscopic spectral density of the QCD3 Dirac operator. Second, we derive Virasoro constraints for the QCD3 partition function. They uniquely determine the small-mass expansion of the partition function and the corresponding sum rules for inverse Dirac eigenvalues. Due to de Wit-'t Hooft poles, the replica limit only reproduces the small mass expansion of the resolvent up to a finite number of terms. Third, the large mass expansion of the resolvent is obtained from the replica limit of a loop expansion of the QCD3 partition function. Because of Duistermaat-Heckman localization exact results are obtained for the microscopic spectral density in this way.
Cited by 0Open access
E. Kanzieper · Nuclear Physics B · 2001
Cited by 9Open access
P.H. Damgaard · Research at the University of Copenhagen (University of Copenhagen) · 2001
Theoretical High-Energy Physics
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Kanzieper, E. · arXiv (Cornell University) · 1999
Recent developments [Kamenev and Mezard, cond-mat/9901110, cond-mat/9903001; Yurkevich and Lerner, cond-mat/9903025; Zirnbauer, cond-mat/9903338] have revived a discussion about applicability of the replica approach to description of spectral fluctuations in the context of random matrix theory and beyond. The present paper, concentrating on invariant non-Gaussian random matrix ensembles with orthogonal, unitary and symplectic symmetries, aims to demonstrate that both the bosonic and the fermionic replicas are capable of reproducing nonperturbative fluctuation formulas for spectral correlation functions in entire energy scale, including the self-correlation of energy levels, provided no sigma-model mapping is used.
Cited by 0Open access
Ralf R. Müller · Lecture notes series, Institute For Mathematical Sciences · 2009
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LOOTENS, E, VAN DEN BROECK, Christian · Document Server@UHasselt (UHasselt) · 2007
Using the replica method, we derive quantitative information about the clustering into 2 subgroups of data lying on the surface of an N-dimensional hypersphere. Various clustering algorithms are considered, including the one corresponding to competitive learning.
Cited by 0
Watanabe Ken · International Linear Collider · 2010
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Matteo Campellone, Giorgio Parisi, M. A. Virasoro · Journal of Statistical Physics · 2009
Cited by 12Open access
L. Borgonovo, G. Saint-Martin, O.A. Bernaola et al. · Radiation Measurements · 1997
Cited by 4
Rui Ding, Ziyu Li, Jie Yin · 2020
When the Hadoop distributed file system (HDFS) makes load balancing decisions, the rack-aware strategy of HDFS does not take into account the differences of various node servers comprehensively, which leads to the imbalance of cluster load. According to this defect, we proposed an improved copy placement strategy based on SVM (Support Vector Machine). We took the load of each node server, disk I/O and CPU performance of each node in the cluster into comprehensive consideration, used SVM to classify the nodes according to the characteristic value and finally selected the nodes suitable for placing the copies from the better class of nodes. Experimental results show that our method can effectively improve the load balancing performance of HDFS compared with the original replica storage.
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Giorgio Parisi · arXiv (Cornell University) · 1998
In this talk we review our theoretical understanding of spin glasses paying a particular attention to the basic physical ideas. We introduce the replica method and we describe its probabilistic consequences (we stress the recently discovered importance of stochastic stability). We show that the replica method is not restricted to systems with quenched disorder. We present the consequences on the dynamics of the system when it slows approaches equilibrium are presented: they are confirmed by large scale simulations, while we are still awaiting for a direct experimental verification.
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U. Schulte, Meinhart H. Zenk · Physiologia Plantarum · 1977
Abstract A replica plating method is described for plant cells growing in Petri dishes. The method involved a uniform application of plant cells ( Morinda citrifolia L.) by spraying cells evenly on agar plates containing 60% conditioned medium. Subsequently the cells were allowed to grow through a nylon net. The net was removed from the master plate and placed upside down on replica plates. Cells from colonies adhering to the threads of the net were thus transferred to the replica plate and yielded colonies that, after a growth period of about 10–20 days, corresponded in position to the colonies on the master plate. An 80% transfer of colonies from the master plate to the copy plate was possible.
Cited by 12
Alex Kamenev, Marc Mézard · Journal of Physics A Mathematical and General · 1999
We compute the correlation functions of the eigenvalues in the Gaussian unitary ensemble using the fermionic replica method. We show that non--trivial saddle points, which break replica symmetry, must be included in the calculation in order to reproduce correctly the exact results for the correlation functions at large distance.
Cited by 83Open access
Giorgio Parisi · Journal de Physique I · 1993
In this note I will present some analytic studies of the properties of charge density waves near the depinning point. Computations using the replica method are done in a simplified model
Cited by 3Open access
N. K. Porsani, V. Trombini, Patrícia Aparecida Ana et al. · Cerâmica · 2019
Abstract Biomaterials, such as tricalcium phosphate, can have different resorption rates in the organism that depend on their physicochemical properties, where the surface condition, such as morphology, size of particles and porosity, is important. In this work, we studied the coating of natural Luffa cylindrica matrix with β-tricalcium phosphate, using the dip replica forming method, in order to adjust the surface conditions to meet the demand of bone resorption. The materials were characterized in terms of specific surface area, particle shape, imaging in electronic scanning microscope, and zeta potential in water media. The suspensions used for coating of the matrices were produced with distilled water and sodium silicate as dispersant and carboxymethyl cellulose as a binder element. Rheological measurements were performed on rotational rheometer and viscometer. The products generated with 2.5 wt% of sodium silicate and 0.75 wt% of carboxymethyl cellulose, after sintering, had pore sizes consistent with high rates of reabsorption and porosity that suggest a future use as a biomaterial.
Cited by 3Open access
Hiqmet Kamberaj, Arjan van der Vaart · The Journal of Chemical Physics · 2009
We introduce a new way to perform swaps between replicas in replica exchange molecular dynamics simulations. The method is based on a generalized canonical probability distribution function and flattens the potential of mean force along the temperature coordinate, such that a random walk in temperature space is achieved. Application to a Gō model of protein A showed that the method is more efficient than conventional replica exchange. The method results in a constant probability distribution of the replicas over the thermostats, yields a minimum round-trip time between extremum temperatures, and leads to faster ergodic convergence.
Cited by 16
Giorgio Parisi · Springer Link (Chiba Institute of Technology) · 1993
\nIn this note I will present some analytic studies of the properties of charge density waves near the depinning point. Computations using the replica method are done in a simplified model.\n
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