Replica Algorithm Research Articles

Core Hunter II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search

BackgroundSampling core subsets from genetic resources while maintaining as much as possible the genetic diversity of the original collection is an important but computationally complex task for gene bank managers. The Core Hunter computer program was developed as a tool to generate such subsets based on multiple genetic measures, including both distance measures and allelic diversity indices. At first we investigate the effect of minimum (instead of the default mean) distance measures on the performance of Core Hunter. Secondly, we try to gain more insight into the performance of the original Core Hunter search algorithm through comparison with several other heuristics working with several realistic datasets of varying size and allelic composition. Finally, we propose a new algorithm (Mixed Replica search) for Core Hunter II with the aim of improving the diversity of the constructed core sets and their corresponding generation times.ResultsOur results show that the introduction of minimum distance measures leads to core sets in which all accessions are sufficiently distant from each other, which was not always obtained when optimizing mean distance alone. Comparison of the original Core Hunter algorithm, Replica Exchange Monte Carlo (REMC), with simpler heuristics shows that the simpler algorithms often give very good results but with lower runtimes than REMC. However, the performance of the simpler algorithms is slightly worse than REMC under lower sampling intensities and some heuristics clearly struggle with minimum distance measures. In comparison the new advanced Mixed Replica search algorithm (MixRep), which uses heterogeneous replicas, was able to sample core sets with equal or higher diversity scores than REMC and the simpler heuristics, often using less computation time than REMC.ConclusionThe REMC search algorithm used in the original Core Hunter computer program performs well, sometimes leading to slightly better results than some of the simpler methods, although it doesn’t always give the best results. By switching to the new Mixed Replica algorithm overall results and runtimes can be significantly improved. Finally we recommend including minimum distance measures in the objective function when looking for core sets in which all accessions are sufficiently distant from each other. Core Hunter II is freely available as an open source project at http://www.corehunter.org.

Evaluating the Performance of Equitable Dominating based Content Distribution Network Design

Problem statement: In this study, we considered an efficient and resi lient large file content push problem in a large scale distributed content d elivery networks and investigated the Quality of Service (QoS) requirements for content distribution . We investigated the effect of equitable dominatin g set in SON formation and how it was useful in reduc ing the redundancy? Approach: At first, we constructed an equitable dominating set based semantic overlay network of surrogate servers to form th e logical infrastructure of the CDN by choosing the o ptimal number of surrogate servers. Then we proposed a novel Efficient Fault Resilient Replica Algorithm (EFRRA) to replicate the content from the origin server to the dominant set of surrogate serv ers in an efficient and reliable manner. Results: We assessed the efficiency and resiliency of the propo sed EFRRA algorithm by conducting simulation experiments and compared its performance with traditional content replication algorithms stated in the literature. We extended the simulation experiments to analyze the role of EDSON in maintaining uniform CDN utility of above 0.9. Conclusion: It also observed that equitable dominating set bas ed SON was useful in keeping the average replication time stab le and much more predictable. We also investigated the quality of service requirements for the content dis tribution and evaluated the performance of EDSON based CDN in terms of mean response time, mean CDN utility, latency and hit ratio percentage.

Monte Carlo investigation of phase transitions in the frustrated Heisenberg model on a triangular lattice

The critical properties and phase transitions of the three-dimensional frustrated antiferromagnetic Heisenberg model on a triangular lattice have been investigated using the Monte Carlo method with a replica algorithm. The critical temperature has been determined and the character of the phase transitions has been analyzed using the method of fourth-order Binder cumulants. A second-order phase transition has been found in the three-dimensional frustrated Heisenberg model on a triangular lattice. The static magnetic and chiral critical exponents of the heat capacity α, the susceptibility γ and γk, the magnetization β and βk, the correlation length ν and νk, as well as the Fisher exponents η and ηk, have been calculated in terms of the finite-size scaling theory. It has been demonstrated that the three-dimensional frustrated antiferromagnetic Heisenberg model on a triangular lattice forms a new universality class of the critical behavior.

Dominating Set Theory based Semantic Overlay Networks for Efficient and Resilient Content Distribution

Recently overlay networks have emerged as an efficient and flexible method for content distribution. An overlay network is a network running on top of another network, usually the Internet. This network is formed by a subset of underlying physical nodes. The connections between the overlay nodes are provided by overlay links, each of which is usually composed of one or more physical link. These networks are employed in many settings to provide logical communication infrastructure over an existing communication networks. The main objective of the overlay network is to reduce routing path lengths, stretched by the overlay routing process. In the existing solutions developed, a kind of fixed infrastructure in the form of excessive message exchange is necessary to guarantee good overlay properties. The scope of our effort is to construct an overlay network based on Dominating Set Theory to optimize the number of nodes for large data transfer. Fast Replica algorithm is applied to reduce the content transfer time for replicating the content within the semantic network. A dynamic parallel access scheme is introduced to download a file from different peers in parallel from the Semantic Overlay Network (SON), where the end users can access the members of the SON at the same time, fetching different portions of that file from different peers and reassembling them locally. That is, the load is dynamically shared among all the peers. To eliminate the need for retransmission requests from the end users, an enhanced digital fountain with Tornado codes is applied. Decoding algorithm at the receiver will reconstruct the original content. In this no feedback mechanisms are needed to ensure reliable delivery. This paper analyzes the performance of sequential unicast, multiple unicast and fast replica with tornado content distribution strategies in terms of content replication time and delivery ratio. This paper also analyzes the impact of dominating set theory for the construction of semantic overlay networks.

Simulation studies of the fidelity of biomolecular structure ensemble recreation

We examine the ability of Bayesian methods to recreate structural ensembles for partially folded molecules from averaged data. Specifically we test the ability of various algorithms to recreate different transition state ensembles for folding proteins using a multiple replica simulation algorithm using input from "gold standard" reference ensembles that were first generated with a Go-like Hamiltonian having nonpairwise additive terms. A set of low resolution data, which function as the "experimental" phi values, were first constructed from this reference ensemble. The resulting phi values were then treated as one would treat laboratory experimental data and were used as input in the replica reconstruction algorithm. The resulting ensembles of structures obtained by the replica algorithm were compared to the gold standard reference ensemble, from which those "data" were, in fact, obtained. It is found that for a unimodal transition state ensemble with a low barrier, the multiple replica algorithm does recreate the reference ensemble fairly successfully when no experimental error is assumed. The Kolmogorov-Smirnov test as well as principal component analysis show that the overlap of the recovered and reference ensembles is significantly enhanced when multiple replicas are used. Reduction of the multiple replica ensembles by clustering successfully yields subensembles with close similarity to the reference ensembles. On the other hand, for a high barrier transition state with two distinct transition state ensembles, the single replica algorithm only samples a few structures of one of the reference ensemble basins. This is due to the fact that the phi values are intrinsically ensemble averaged quantities. The replica algorithm with multiple copies does sample both reference ensemble basins. In contrast to the single replica case, the multiple replicas are constrained to reproduce the average phi values, but allow fluctuations in phi for each individual copy. These fluctuations facilitate a more faithful sampling of the reference ensemble basins. Finally, we test how robustly the reconstruction algorithm can function by introducing errors in phi comparable in magnitude to those suggested by some authors. In this circumstance we observe that the chances of ensemble recovery with the replica algorithm are poor using a single replica, but are improved when multiple copies are used. A multimodal transition state ensemble, however, turns out to be more sensitive to large errors in phi (if appropriately gauged) and attempts at successful recreation of the reference ensemble with simple replica algorithms can fall short.

Parallel replica dynamics with a heterogeneous distribution of barriers: Application to n-hexadecane pyrolysis

Parallel replica dynamics simulation methods appropriate for the simulation of chemical reactions in molecular systems with many conformational degrees of freedom have been developed and applied to study the microsecond-scale pyrolysis of n-hexadecane in the temperature range of 2100-2500 K. The algorithm uses a transition detection scheme that is based on molecular topology, rather than energetic basins. This algorithm allows efficient parallelization of small systems even when using more processors than particles (in contrast to more traditional parallelization algorithms), and even when there are frequent conformational transitions (in contrast to previous implementations of the parallel replica algorithm). The parallel efficiency for pyrolysis initiation reactions was over 90% on 61 processors for this 50-atom system. The parallel replica dynamics technique results in reaction probabilities that are statistically indistinguishable from those obtained from direct molecular dynamics, under conditions where both are feasible, but allows simulations at temperatures as much as 1000 K lower than direct molecular dynamics simulations. The rate of initiation displayed Arrhenius behavior over the entire temperature range, with an activation energy and frequency factor of E(a) = 79.7 kcal/mol and log A/s(-1) = 14.8, respectively, in reasonable agreement with experiment and empirical kinetic models. Several interesting unimolecular reaction mechanisms were observed in simulations of the chain propagation reactions above 2000 K, which are not included in most coarse-grained kinetic models. More studies are needed in order to determine whether these mechanisms are experimentally relevant, or specific to the potential energy surface used.