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Characterization of Pathogens in Clinical Specimens via Suppression of Host Background for Efficient Second Generation Sequencing Analyses

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

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TYPE Conference YEAR 2012
OSTI

Optimized pulses for the control of uncertain qubits

Physical Review A - Atomic, Molecular, and Optical Physics

Carroll, Malcolm; Witzel, Wayne W.

The construction of high-fidelity control fields that are robust to control, system, and/or surrounding environment uncertainties is a crucial objective for quantum information processing. Using the two-state Landau-Zener model for illustrative simulations of a controlled qubit, we generate optimal controls for π/2 and π pulses and investigate their inherent robustness to uncertainty in the magnitude of the drift Hamiltonian. Next, we construct a quantum-control protocol to improve system-drift robustness by combining environment-decoupling pulse criteria and optimal control theory for unitary operations. By perturbatively expanding the unitary time-evolution operator for an open quantum system, previous analysis of environment-decoupling control pulses has calculated explicit control-field criteria to suppress environment-induced errors up to (but not including) third order from π/2 and π pulses. We systematically integrate this criteria with optimal control theory, incorporating an estimate of the uncertain parameter to produce improvements in gate fidelity and robustness, demonstrated via a numerical example based on double quantum dot qubits. For the qubit model used in this work, postfacto analysis of the resulting controls suggests that realistic control-field fluctuations and noise may contribute just as significantly to gate errors as system and environment fluctuations.

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TYPE Journal Article YEAR 2012
OSTIDOI

Copy of Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

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TYPE Presentation YEAR 2012
OSTI

Automated Molecular Biology Platform Enabling Rapid & Efficient SGS Analysis of Pathogens in Clinical Samples

Branda, Steven B.; Jebrail, Mais J.; Van De Vreugde, James L.; Langevin, Stanley A.; Bent, Zachary B.; Curtis, Deanna J.; Lane, Pamela L.; Carson, Bryan C.; La Bauve, Elisa L.; Patel, Kamlesh P.; Ricken, James B.; Schoeniger, Joseph S.; Solberg, Owen D.; Williams, Kelly P.; Misra, Milind; Powell, Amy J.; Pattengale, Nicholas D.; May, Elebeoba E.; Lane, Todd L.; Lindner, Duane L.; Young, Malin M.; VanderNoot, Victoria A.; Thaitrong, Numrin T.; Bartsch, Michael B.; Renzi, Ronald F.; Tran-Gyamfi, Mary B.; Meagher, Robert M.

Abstract not provided.

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TYPE Conference YEAR 2012
OSTI

Cooperative application/OS DRAM fault recovery

Hoemmen, Mark F.; Ferreira, Kurt; Heroux, Michael A.; Brightwell, Ronald B.

Exascale systems will present considerable fault-tolerance challenges to applications and system software. These systems are expected to suffer several hard and soft errors per day. Unfortunately, many fault-tolerance methods in use, such as rollback recovery, are unsuitable for many expected errors, for example DRAM failures. As a result, applications will need to address these resilience challenges to more effectively utilize future systems. In this paper, we describe work on a cross-layer application/OS framework to handle uncorrected memory errors. We illustrate the use of this framework through its integration with a new fault-tolerant iterative solver within the Trilinos library, and present initial convergence results.

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TYPE SAND Report YEAR 2012
DOIOSTI

Evaluating operating system vulnerability to memory errors

Ferreira, Kurt; Pedretti, Kevin T.T.; Brightwell, Ronald B.

Reliability is of great concern to the scalability of extreme-scale systems. Of particular concern are soft errors in main memory, which are a leading cause of failures on current systems and are predicted to be the leading cause on future systems. While great effort has gone into designing algorithms and applications that can continue to make progress in the presence of these errors without restarting, the most critical software running on a node, the operating system (OS), is currently left relatively unprotected. OS resiliency is of particular importance because, though this software typically represents a small footprint of a compute node's physical memory, recent studies show more memory errors in this region of memory than the remainder of the system. In this paper, we investigate the soft error vulnerability of two operating systems used in current and future high-performance computing systems: Kitten, the lightweight kernel developed at Sandia National Laboratories, and CLE, a high-performance Linux-based operating system developed by Cray. For each of these platforms, we outline major structures and subsystems that are vulnerable to soft errors and describe methods that could be used to reconstruct damaged state. Our results show the Kitten lightweight operating system may be an easier target to harden against memory errors due to its smaller memory footprint, largely deterministic state, and simpler system structure.

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TYPE SAND Report YEAR 2012
DOIOSTI

Computational aspects of many-body potentials

MRS Bulletin

Plimpton, Steven J.; Thompson, Aidan P.

We discuss the relative complexity and computational cost of several popular many-body empirical potentials, developed by the materials science community over the past 30 years. The inclusion of more detailed many-body effects has come at a computational cost, but the cost still scales linearly with the number of atoms modeled. This is enabling very large molecular dynamics simulations with unprecedented atomic-scale fidelity to physical and chemical phenomena. The cost and scalability of the potentials, run in serial and parallel, are benchmarked in the LAMMPS molecular dynamics code. Several recent large calculations performed with these potentials are highlighted to illustrate what is now possible on current supercomputers. We conclude with a brief mention of high-performance computing architecture trends and the research issues they raise for continued potential development and use. © 2012 Materials Research Society.

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TYPE Journal Article YEAR 2012
DOIOSTIScopus

The QCAD framework for quantum device modeling

Computational Electronics (IWCE), 2012 15th International Workshop on

Gao, Xujiao G.; Nielsen, Erik N.; Muller, Richard P.; Young, Ralph W.; Salinger, Andrew G.; Carroll, Malcolm

We present the Quantum Computer Aided Design (QCAD) simulator that targets modeling quantum devices, particularly Si double quantum dots (DQDs) developed for quantum computing. The simulator core includes Poisson, Schrodinger, and Configuration Interaction solvers which can be run individually or combined self-consistently. The simulator is built upon Sandia-developed Trilinos and Albany components, and is interfaced with the Dakota optimization tool. It is being developed for seamless integration, high flexibility and throughput, and is intended to be open source. The QCAD tool has been used to simulate a large number of fabricated silicon DQDs and has provided fast feedback for design comparison and optimization.

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TYPE Journal Article YEAR 2012
OSTIDOI

MiniGhost : a miniapp for exploring boundary exchange strategies using stencil computations in scientific parallel computing

Barrett, Richard F.; Vaughan, Courtenay T.; Heroux, Michael A.

A broad range of scientific computation involves the use of difference stencils. In a parallel computing environment, this computation is typically implemented by decomposing the spacial domain, inducing a 'halo exchange' of process-owned boundary data. This approach adheres to the Bulk Synchronous Parallel (BSP) model. Because commonly available architectures provide strong inter-node bandwidth relative to latency costs, many codes 'bulk up' these messages by aggregating data into a message as a means of reducing the number of messages. A renewed focus on non-traditional architectures and architecture features provides new opportunities for exploring alternatives to this programming approach. In this report we describe miniGhost, a 'miniapp' designed for exploration of the capabilities of current as well as emerging and future architectures within the context of these sorts of applications. MiniGhost joins the suite of miniapps developed as part of the Mantevo project.

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TYPE SAND Report YEAR 2012
DOIOSTI

Simple intrinsic defects in GaAs : numerical supplement

Schultz, Peter A.

This Report presents numerical tables summarizing properties of intrinsic defects in gallium arsenide, GaAs, as computed by density functional theory. This Report serves as a numerical supplement to the results published in: P.A. Schultz and O.A. von Lilienfeld, 'Simple intrinsic defects in GaAs', Modelling Simul. Mater. Sci Eng., Vol. 17, 084007 (2009), and intended for use as reference tables for a defect physics package in device models. The numerical results for density functional theory calculations of properties of simple intrinsic defects in gallium arsenide are presented.

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TYPE SAND Report YEAR 2012
DOIOSTI

First principles predictions of intrinsic defects in aluminum arsenide, AlAs : numerical supplement

Schultz, Peter A.

This Report presents numerical tables summarizing properties of intrinsic defects in aluminum arsenide, AlAs, as computed by density functional theory. This Report serves as a numerical supplement to the results published in: P.A. Schultz, 'First principles predictions of intrinsic defects in Aluminum Arsenide, AlAs', Materials Research Society Symposia Proceedings 1370 (2011; SAND2011-2436C), and intended for use as reference tables for a defect physics package in device models.

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TYPE SAND Report YEAR 2012
DOIOSTI
Results 7201–7300 of 9,998
Results 7201–7300 of 9,998