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By using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20-residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (gamma). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the(More)
The accelerated molecular dynamics (aMD) method has recently been shown to enhance the sampling of biomolecules in molecular dynamics (MD) simulations, often by several orders of magnitude. Here, we describe an implementation of the aMD method for the OpenMM application layer that takes full advantage of graphics processing units (GPUs) computing. The aMD(More)
OBJECTIVE The purpose of this study was to reiterate the predominance of CT in evaluating ventriculoperitoneal shunt malfunction in terms of cost-effectiveness, reduction of radiation exposure, and turnaround time as the measurement parameters. MATERIALS AND METHODS This retrospective study included patients 18 years and older with a history of(More)
Discrete-space Markov models are a convenient way of describing the kinetics of biomolecules. The most common strategies used to validate these models employ statistics from simulation data, such as the eigenvalue spectrum of the inferred rate matrix, which are often associated with large uncertainties. Here, we propose a Bayesian approach, which makes it(More)
SUMMARY Markov state models (MSMs) for the study of biomolecule folding simulations have emerged as a powerful tool for computational study of folding dynamics. MSMExplorer is a visualization application purpose-built to visualize these MSMs with an aim to increase the efficacy and reach of MSM science. AVAILABILITY MSMExplorer is available for download(More)
When accounting for structural fluctuations or measurement errors, a single rigid structure may not be sufficient to represent a protein. One approach to solve this problem is to represent the possible conformations as a discrete set of observed conformations, an ensemble. In this work, we follow a different richer approach, and introduce a framework for(More)
Clustering is a typical approach to study conformation space where close conformations are grouped into the same state. It not only provides a concise representation of the free energy landscape but also is a necessary preprocessing step for building many other more complicated representations such as Markov State Model. However, since the conformation(More)
Convergence of Internet Protocol based networks is a necessary requirement today. One important aspect of convergence is seamless integration of wired- wireless network. Internetworking of wired-wireless network is important from Quality of Service (QoS) perspective. Providing a wired network support to an overloaded wireless network for load sharing,(More)
In this paper we have considered a Wireless Mesh Network (WMN) with multiple internet gateways (IGW) and wired network support for maximizing the delivery in the WMN access network. We have considered the WMN in IEEE 802.11s framework that nodes can transit from one IGW region to the other seamlessly based on the Quality of Service (QOS) requirements. Then(More)
With the recent advancements in distributed computing, it is now possible to simulate molecular dynamics of large systems over unprecedented time scales. However, due to the sheer size of the generated trajectories, it is no longer possible to reliably extract relevant chemical and biological information from a simulation through visual inspection alone a(More)