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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jinghua Yang; Aykut Dengi; Sarma Vrudhula;

    Systems powered by harvested energy must consume very low power and withstand frequent interruptions in power. Nonvolatile logic (NVL) addresses the latter by saving the system state in flipflops enhanced with spin-transfer torque magnetic tunnel junctions (STT-MTJs) as the nonvolatile storage devices. Manufacturing variations in the STT-MTJs and in CMOS transistors significantly reduce yield, leading to overdesign and high-energy consumption. A detailed analysis of the design tradeoffs in the driver circuitry for performing backup and restore, and a novel method to design the energy optimal driver for a given yield is presented. Next, efficient designs of two nonvolatile flip-flop (NVFF) circuits are presented, in which the backup time is determined on a per-chip basis, resulting in minimizing the energy wastage and satisfying the yield constraint. To achieve a yield of 98%, the conventional approach would have to expend nearly $5\times $ more energy than the minimum required, whereas the proposed tunable approach expends only 26% more energy than the minimum. Also included are the energy consumption of the proposed NVFF designs when used in two larger function blocks. Experimental results were based on a commercial 40-nm process design kit, and HSPICE simulations with foundry supplied statistical models and data.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ IEEE Transactions on...arrow_drop_down
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    IEEE Transactions on Very Large Scale Integration (VLSI) Systems
    Article . 2018 . Peer-reviewed
    License: IEEE Copyright
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ IEEE Transactions on...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      IEEE Transactions on Very Large Scale Integration (VLSI) Systems
      Article . 2018 . Peer-reviewed
      License: IEEE Copyright
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Makhatadze, George; Tzul, Franco; Schweiker, Katrina;

    Ionizable residues play important role in protein structure, stability and function. In globular proteins, majority of ionizable residues are located on the protein surface. We have previously used computational approach to optimized surface charge-charge interactions in several globular proteins: ubiquitin, the activation domain of human procarboxypeptidase A2 (ADA2), the fibronectin typeIII domain (TnfIII), acylphosphatase (ACP), the N-terminal domain of human U1A protein (U1A), Cdc42 GTPase, Fyn SH3 domain, and cold shock protein CspB(1-3). Biophysical studies have shown that all the designed variants have increased thermodynamic stability. Here we have measured experimentally the folding kinetics of the wild-type and designed variants of four proteins: U1A, Ten, ACP and ADA2. We have also performed native topology-based model simulations that correspond to a funneled energy landscape, but explicitly include non-native charge-charge interactions. Analysis of computer simulations provided molecular details for the experimentally observed changes in the folding rates of charge-charge optimized variants.This work was supported by grants from the National Science Foundation MCB-0110396.References:1. Gribenko, A.V., Patel, M.M., Liu, J., McCallum, S.A., Wang, C., and Makhatadze, G.I. (2009) Rational stabilization of enzymes by computational redesign of surface charge-charge interactions, Proc Natl Acad Sci USA 106, 2601-2606.2. Makhatadze, G.I., Loladze, V.V., Gribenko, A.V., and Lopez, M.M. (2004) Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions, J Mol Biol 336, 929-942.3. Schweiker, K.L., Zarrine-Afsar, A., Davidson, A.R., and Makhatadze, G.I. (2007) Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions, Protein Sci 16, 2694-2702.4. Strickler, S.S., Gribenko, A.V., Gribenko, A.V., Keiffer, T.R., Tomlinson, J., Reihle, T., Loladze, V.V., and Makhatadze, G.I. (2006) Protein stability and surface electrostatics: a charged relationship, Biochemistry 45, 2761-2766.

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    Biophysical Journal
    Article
    License: Elsevier Non-Commercial
    Data sources: UnpayWall
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    Biophysical Journal
    Article . 2013 . Peer-reviewed
    License: Elsevier Non-Commercial
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      Biophysical Journal
      Article
      License: Elsevier Non-Commercial
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      Biophysical Journal
      Article . 2013 . Peer-reviewed
      License: Elsevier Non-Commercial
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Xiaofei, Nan; Gang, Fu; Zhengdong, Zhao; Sheng, Liu; +7 Authors

    AbstractBackgroundIt is commonly believed that including domain knowledge in a prediction model is desirable. However, representing and incorporating domain information in the learning process is, in general, a challenging problem. In this research, we consider domain information encoded by discrete or categorical attributes. A discrete or categorical attribute provides a natural partition of the problem domain, and hence divides the original problem into several non-overlapping sub-problems. In this sense, the domain information is useful if the partition simplifies the learning task. The goal of this research is to develop an algorithm to identify discrete or categorical attributes that maximally simplify the learning task.ResultsWe consider restructuring a supervised learning problem via a partition of the problem space using a discrete or categorical attribute. A naive approach exhaustively searches all the possible restructured problems. It is computationally prohibitive when the number of discrete or categorical attributes is large. We propose a metric to rank attributes according to their potential to reduce the uncertainty of a classification task. It is quantified as a conditional entropy achieved using a set of optimal classifiers, each of which is built for a sub-problem defined by the attribute under consideration. To avoid high computational cost, we approximate the solution by the expected minimum conditional entropy with respect to random projections. This approach is tested on three artificial data sets, three cheminformatics data sets, and two leukemia gene expression data sets. Empirical results demonstrate that our method is capable of selecting a proper discrete or categorical attribute to simplify the problem, i.e., the performance of the classifier built for the restructured problem always beats that of the original problem.ConclusionsThe proposed conditional entropy based metric is effective in identifying good partitions of a classification problem, hence enhancing the prediction performance.

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    Europe PubMed Central
    Article . 2011
    Data sources: PubMed Central
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    BMC Bioinformatics
    Article
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    Data sources: UnpayWall
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    BMC Bioinformatics
    Article . 2011 . Peer-reviewed
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Europe PubMed Centra...arrow_drop_down
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      Europe PubMed Central
      Article . 2011
      Data sources: PubMed Central
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      BMC Bioinformatics
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      BMC Bioinformatics
      Article . 2011 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: H. Goelzer; H. Goelzer; H. Goelzer; S. Nowicki; +49 Authors

    Abstract. The Greenland ice sheet is one of the largest contributors to global meansea-level rise today and is expected to continue to lose mass as the Arcticcontinues to warm. The two predominant mass loss mechanisms are increasedsurface meltwater run-off and mass loss associated with the retreat ofmarine-terminating outlet glaciers. In this paper we use a large ensemble ofGreenland ice sheet models forced by output from a representative subset ofthe Coupled Model Intercomparison Project (CMIP5) global climate models to project ice sheet changes and sea-level risecontributions over the 21st century. The simulations are part of theIce Sheet Model Intercomparison Project for CMIP6 (ISMIP6). We estimate thesea-level contribution together with uncertainties due to future climateforcing, ice sheet model formulations and ocean forcing for the twogreenhouse gas concentration scenarios RCP8.5 and RCP2.6. The resultsindicate that the Greenland ice sheet will continue to lose mass in bothscenarios until 2100, with contributions of 90±50 and 32±17 mm to sea-level rise for RCP8.5 and RCP2.6, respectively. The largestmass loss is expected from the south-west of Greenland, which is governed bysurface mass balance changes, continuing what is already observed today.Because the contributions are calculated against an unforced controlexperiment, these numbers do not include any committed mass loss, i.e. massloss that would occur over the coming century if the climate forcingremained constant. Under RCP8.5 forcing, ice sheet model uncertaintyexplains an ensemble spread of 40 mm, while climate model uncertainty andocean forcing uncertainty account for a spread of 36 and 19 mm,respectively. Apart from those formally derived uncertainty ranges, thelargest gap in our knowledge is about the physical understanding andimplementation of the calving process, i.e. the interaction of the ice sheetwith the ocean. info:eu-repo/semantics/published

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    CORE (RIOXX-UK Aggregator)
    Article . 2020
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    The Cryosphere (TC)
    Other literature type . Article . 2020 . Peer-reviewed
    License: CC BY
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    St Andrews Research Repository
    Article . 2020 . Peer-reviewed
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    The Cryosphere
    Article . 2020
    Data sources: NARCIS
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    DI-fusion
    Article . 2020 . Peer-reviewed
    Data sources: DI-fusion
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    The Cryosphere (TC)
    Article . 2020
    Data sources: JAIRO
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    https://doi.org/10.5194/tc-201...
    Preprint . 2020
    License: CC BY
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    The Cryosphere; The Cryosphere (TC)
    Article . Preprint . 2020
    License: CC BY
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    Hal-Diderot
    Article . 2020
    Data sources: Hal-Diderot
    https://doi.org/10.5194/egusph...
    Other literature type . 2020
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      The Cryosphere (TC)
      Other literature type . Article . 2020 . Peer-reviewed
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      St Andrews Research Repository
      Article . 2020 . Peer-reviewed
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      The Cryosphere
      Article . 2020
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      DI-fusion
      Article . 2020 . Peer-reviewed
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      The Cryosphere (TC)
      Article . 2020
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      https://doi.org/10.5194/tc-201...
      Preprint . 2020
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      The Cryosphere; The Cryosphere (TC)
      Article . Preprint . 2020
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      Hal-Diderot
      Article . 2020
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      https://doi.org/10.5194/egusph...
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    Authors: Kortemeyer, G.; Bauer, W.; Haglin, K.; Murray, J.; +1 Authors

    Transport models have successfully described many aspects of intermediate energy heavy-ion collision dynamics. As the energies increase in these models to the ultrarelativistic regime, Lorentz covariance and causality are not strictly respected. The standard argument is that such effects are not important to final results; but they have not been seriously considered at high energies. We point out how and why these happen, how serious of a problem they may be and suggest ways of reducing or eliminating the undesirable effects. RevTeX, 23 pages, 9 (uuencoded) figures; to appear in Phys. Rev C

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    Physical Review C
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    Physical Review C
    Article . 1995 . Peer-reviewed
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    Article . 1995
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      Physical Review C
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      Physical Review C
      Article . 1995 . Peer-reviewed
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    Authors: Morgann Berg; Jason M. Kephart; Amit Munshi; Walajabad S. Sampath; +2 Authors

    Post-deposition CdCl$_2$ treatment of polycrystalline CdTe is known to increase photovoltaic efficiency. However, the precise chemical, structural, and electronic changes that underpin this improvement are still debated. In this study, spectroscopic photoemission electron microscopy was used to spatially map the vacuum level and ionization energy of CdTe films, enabling the identification of electronic structure variations between grains and grain boundaries. In vacuo preparation and inert transfer of oxide-free CdTe surfaces isolated the separate effects of CdCl$_2$ treatment and ambient oxygen exposure. Qualitatively, grain boundaries displayed lower work function and downward band bending relative to grain interiors, but only after air exposure of CdCl$_2$-treated CdTe. Analysis of numerous space charge regions at grain boundaries (GBs) showed an average depletion width of 290 nm and an average band bending magnitude of 70 meV, corresponding to a GB trap density of 10$^{11}$ cm$^{-2}$ and a net carrier density of 10$^{15}$ cm$^{-3}$. These results suggest that both CdCl$_2$ treatment and oxygen exposure may be independently tuned to enhance CdTe photovoltaic performance by engineering the interface and bulk electronic structure.

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    ACS Applied Materials & Interfaces
    Article . 2018 . Peer-reviewed
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    Article . 2018
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      ACS Applied Materials & Interfaces
      Article . 2018 . Peer-reviewed
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    Authors: Bryan S. McLean; Robert P. Guralnick;

    AbstractShifts in reproductive timing are among the most commonly documented responses of organisms to global climate change. However, our knowledge of these responses is biased towards taxa that are easily observable and abundant in existing biodiversity data sets. Mammals are common subjects in reproductive biology, but mammalian phenology and its drivers in the wild remain poorly understood because many species are small, secretive, or too labor‐intensive to monitor. We took an informatics‐based approach to reconstructing breeding phenology in the widespread North American deer mouse (Peromyscus maniculatus) using individual‐level reproductive observations from digitized museum specimens and field censuses spanning >100 yr and >45 degrees of latitude. We reconstructed female phenology in different regions and tested the importance of three environmental variables (photoperiod, temperature, precipitation) as breeding cues. Photoperiod and temperature were strong positive and negative breeding cues, respectively, whereas precipitation was not a significant predictor of breeding phenology. However, phenologies and the use of environmental cues varied substantially among regions, and we found evidence that these cueing repertoires are tuned to ecosystem‐specific limiting conditions. Our results reiterate the importance of ecological context in optimizing reproduction and demonstrate how harmonization across biodiversity data resources allows new insight into phenology and its drivers in wild mammals.

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    Ecology
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    Ecology
    Article . 2021 . Peer-reviewed
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    Ecology
    Article . 2020
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      Ecology
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      Ecology
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      Article . 2020
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    Authors: Ganhui Lan; Sean X. Sun;

    AbstractMyosin-VI is a dimeric isoform of unconventional myosins. Single molecule experiments indicate that myosin-VI and myosin-V are processive molecular motors, but travel toward opposite ends of filamentous actin. Structural studies show several differences between myosin-V and VI, including a significant difference in the light-chain domain connecting the motor domains. Combining the measured kinetics of myosin-VI with the elasticity of the light chains, and the helical structure of F-actin, we compare and contrast the motility of myosin-VI with myosin-V. We show that the elastic properties of the light-chain domain control the stepping behavior of these motors. Simple models incorporating the motor elastic energy can quantitatively capture most of the observed data. Implications of our result for other processive motors are discussed.

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    Biophysical Journal
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    Europe PubMed Central
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    Biophysical Journal
    Article . 2006 . Peer-reviewed
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      Biophysical Journal
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      Europe PubMed Central
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      Biophysical Journal
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    Authors: Gaurav Sharma; Parales, Rebecca; Singer, Mitchell;

    Figure S5. Maximum likelihood phylogeny for the CheB protein involved in the energy taxis cluster in C. coralloides. The top homologs of the CheB protein (Cc_4975) involved in the energy taxis in C. coralloides were used to generate this represented ML phylogenetic tree with organism names in the outermost ring. The taxonomy lineage at the phylum level is represented in the inner ring where myxobacterial homologs are in blue text, non-Myxococcales Deltaproteobacteria in green text and other taxa in red text. Bootstrap values are provided corresponding to the tree nodes as blue circles with sizes ranging from one (BS value 1) to 15 (BS value 100). (PDF 52 kb)

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    Authors: Sapin, Emmanuel; Carr, Daniel; Jong, Kenneth De; Amarda Shehu;

    Comparison of ensemble of low-cost off â on paths across H-Ras WT and variants. Column 1 lists the different H-Ras sequences investigated. The two different values used in the query of the map are listed in column 2. Columns 3â 5 show summary statistics, such as mean and standard deviation, are reported for path cost, highest energy over structures in a path, and the number of edges in a path. (PDF 17 kb)

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    Research . 2016
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    Research . 2016
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    Authors: Jinghua Yang; Aykut Dengi; Sarma Vrudhula;

    Systems powered by harvested energy must consume very low power and withstand frequent interruptions in power. Nonvolatile logic (NVL) addresses the latter by saving the system state in flipflops enhanced with spin-transfer torque magnetic tunnel junctions (STT-MTJs) as the nonvolatile storage devices. Manufacturing variations in the STT-MTJs and in CMOS transistors significantly reduce yield, leading to overdesign and high-energy consumption. A detailed analysis of the design tradeoffs in the driver circuitry for performing backup and restore, and a novel method to design the energy optimal driver for a given yield is presented. Next, efficient designs of two nonvolatile flip-flop (NVFF) circuits are presented, in which the backup time is determined on a per-chip basis, resulting in minimizing the energy wastage and satisfying the yield constraint. To achieve a yield of 98%, the conventional approach would have to expend nearly $5\times $ more energy than the minimum required, whereas the proposed tunable approach expends only 26% more energy than the minimum. Also included are the energy consumption of the proposed NVFF designs when used in two larger function blocks. Experimental results were based on a commercial 40-nm process design kit, and HSPICE simulations with foundry supplied statistical models and data.

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    IEEE Transactions on Very Large Scale Integration (VLSI) Systems
    Article . 2018 . Peer-reviewed
    License: IEEE Copyright
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      IEEE Transactions on Very Large Scale Integration (VLSI) Systems
      Article . 2018 . Peer-reviewed
      License: IEEE Copyright
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    Authors: Makhatadze, George; Tzul, Franco; Schweiker, Katrina;

    Ionizable residues play important role in protein structure, stability and function. In globular proteins, majority of ionizable residues are located on the protein surface. We have previously used computational approach to optimized surface charge-charge interactions in several globular proteins: ubiquitin, the activation domain of human procarboxypeptidase A2 (ADA2), the fibronectin typeIII domain (TnfIII), acylphosphatase (ACP), the N-terminal domain of human U1A protein (U1A), Cdc42 GTPase, Fyn SH3 domain, and cold shock protein CspB(1-3). Biophysical studies have shown that all the designed variants have increased thermodynamic stability. Here we have measured experimentally the folding kinetics of the wild-type and designed variants of four proteins: U1A, Ten, ACP and ADA2. We have also performed native topology-based model simulations that correspond to a funneled energy landscape, but explicitly include non-native charge-charge interactions. Analysis of computer simulations provided molecular details for the experimentally observed changes in the folding rates of charge-charge optimized variants.This work was supported by grants from the National Science Foundation MCB-0110396.References:1. Gribenko, A.V., Patel, M.M., Liu, J., McCallum, S.A., Wang, C., and Makhatadze, G.I. (2009) Rational stabilization of enzymes by computational redesign of surface charge-charge interactions, Proc Natl Acad Sci USA 106, 2601-2606.2. Makhatadze, G.I., Loladze, V.V., Gribenko, A.V., and Lopez, M.M. (2004) Mechanism of thermostabilization in a designed cold shock protein with optimized surface electrostatic interactions, J Mol Biol 336, 929-942.3. Schweiker, K.L., Zarrine-Afsar, A., Davidson, A.R., and Makhatadze, G.I. (2007) Computational design of the Fyn SH3 domain with increased stability through optimization of surface charge charge interactions, Protein Sci 16, 2694-2702.4. Strickler, S.S., Gribenko, A.V., Gribenko, A.V., Keiffer, T.R., Tomlinson, J., Reihle, T., Loladze, V.V., and Makhatadze, G.I. (2006) Protein stability and surface electrostatics: a charged relationship, Biochemistry 45, 2761-2766.

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    Biophysical Journal
    Article
    License: Elsevier Non-Commercial
    Data sources: UnpayWall
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    Biophysical Journal
    Article . 2013 . Peer-reviewed
    License: Elsevier Non-Commercial
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