A statistical mechanics description of complex molecular systems involves the determination of ensembles of conformations that represent their Boltzmann distributions. The observable properties of these systems can be then predicted by calculating averages over such ensembles. In principle, given accurate energy functions and efficient sampling methods, these ensembles can be generated by molec...

We analyse a linear regression problem with nonconvex regularization called smoothly clipped absolute deviation (SCAD) under an overcomplete Gaussian basis for Gaussian random data. We propose an approximate message passing (AMP) algorithm considering nonconvex regularization, namely SCAD-AMP, and analytically show that the stability condition corresponds to the de Almeida–Thouless condition in...

In typical Data Grids large amounts of replicated data are stored all over the globe in different storage systems with access latencies ranging from seconds to hours. The task of a replica management system is not only to keep track of the replicas but also to select those replicas that can be accessed by an application program with a minimal response or transfer time. Most wide-area replicatio...

The replica method is a non-rigorous but widely-accepted technique from statistical physics used in the asymptotic analysis of large, random, nonlinear problems. This paper applies the replica method to non-Gaussian maximum a posteriori (MAP) estimation. It is shown that with random linear measurements and Gaussian noise, the asymptotic behavior of the MAP estimate of an n-dimensional vector “d...

In distributed systems, communication cost is one of the major concerns. Many existing research have been conducted on placement of data to reduce communication cost and improve performance in widely distributed systems. All these research works focus on independent data objects. However, data are correlated due to accesses from clients and the correlation has some impact on date placement. In ...

Data Grids support data-intensive applications in wide area Grid systems. They utilize local storage systems as distributed data stores by replicating datasets. Replication is a commonly used technique in a distributed environment. The motivation of replication is that replication can improve data availability, data access performance, and load balancing. Usually a complete file is copied to ma...

Parallel replica exchange sampling is an extended ensemble technique often used to accelerate the exploration of the conformational ensemble of atomistic molecular simulations of chemical systems. Inter-process communication and coordination requirements have historically discouraged the deployment of replica exchange on distributed and heterogeneous resources. Here we describe the architecture...

Using the replica method, we analyze the mass dependence of the QCD 3 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 QCD 3 partition function and the QCD 4 partition function continued to half-integer topological charge. ...

A small change in the Hamiltonian scaling in Replica Exchange with Solute Tempering (REST) is found to improve its sampling efficiency greatly, especially for the sampling of aqueous protein solutions in which there are large-scale solute conformation changes. Like the original REST (REST1), the new version (which we call REST2) also bypasses the poor scaling with system size of the standard Te...

This paper deals with the replica placement problem on fully homogeneous tree networks known as the Replica Placement optimization problem. The client requests are known beforehand, while the number and location of the servers are to be determined. We investigate the latter problem using the Closest access policy when adding QoS and bandwidth constraints. We propose an optimal algorithm in two ...