Showing papers by "Rensselaer Polytechnic Institute published in 2013"

Overlapping community detection in networks: The state-of-the-art and comparative study

Abstract: This article reviews the state-of-the-art in overlapping community detection algorithms, quality measures, and benchmarks. A thorough comparison of different algorithms (a total of fourteen) is provided. In addition to community-level evaluation, we propose a framework for evaluating algorithms' ability to detect overlapping nodes, which helps to assess overdetection and underdetection. After considering community-level detection performance measured by normalized mutual information, the Omega index, and node-level detection performance measured by F-score, we reached the following conclusions. For low overlapping density networks, SLPA, OSLOM, Game, and COPRA offer better performance than the other tested algorithms. For networks with high overlapping density and high overlapping diversity, both SLPA and Game provide relatively stable performance. However, test results also suggest that the detection in such networks is still not yet fully resolved. A common feature observed by various algorithms in real-world networks is the relatively small fraction of overlapping nodes (typically less than 30p), each of which belongs to only 2 or 3 communities.

Is Corporate Social Responsibility (CSR) Associated with Tax Avoidance? Evidence from Irresponsible CSR Activities

Abstract: We examine the empirical association between corporate social responsibility (CSR) and tax avoidance. Our findings suggest that firms with excessive irresponsible CSR activities have a higher likelihood of engaging in tax-sheltering activities and greater discretionary/permanent book-tax differences. Moreover, at the onset of FASB Interpretation No. 48, these firms have more uncertain tax positions; also, these firms' initial tax positions are likely supported by weaker facts and circumstances as indicated by their larger post-FIN 48 settlements with tax authorities and their higher likelihood of a net decrease in the overall level of uncertain tax positions after FIN 48. Collectively, these results suggest that firms with excessive irresponsible CSR activities are more aggressive in avoiding taxes, lending credence to the idea that corporate culture affects tax avoidance. Data Availability: Data are available from public sources identified in the study.

Modular optimization of multi-gene pathways for fatty acids production in E. coli

Abstract: Microbial fatty acid-derived fuels have emerged as promising alternatives to petroleum-based transportation fuels. Here we report a modular engineering approach that systematically removed metabolic pathway bottlenecks and led to significant titre improvements in a multi-gene fatty acid metabolic pathway. On the basis of central pathway architecture, E. coli fatty acid biosynthesis was re-cast into three modules: the upstream acetyl coenzyme A formation module; the intermediary acetyl-CoA activation module; and the downstream fatty acid synthase module. Combinatorial optimization of transcriptional levels of these three modules led to the identification of conditions that balance the supply of acetyl-CoA and consumption of malonyl-CoA/ACP. Refining protein translation efficiency by customizing ribosome binding sites for both the upstream acetyl coenzyme A formation and fatty acid synthase modules enabled further production improvement. Fed-batch cultivation of the engineered strain resulted in a final fatty acid production of 8.6 g l(-1). The modular engineering strategies demonstrate a generalized approach to engineering cell factories for valuable metabolites production.

Stanford University Unstructured (SU 2 ): An open-source integrated computational environment for multi-physics simulation and design

Abstract: This paper describes the history, objectives, structure, and current capabilities of the Stanford University Unstructured (SU 2 ) tool suite. This computational analysis and design software collection is being developed to solve complex, multi-physics analysis and optimization tasks using arbitrary unstructured meshes, and it has been designed so that it is easily extensible for the solution of Partial Differential Equation-based (PDE) problems not directly envisioned by the authors. At its core, SU 2 is an open-source collection of C++ software tools to discretize and solve problems described by PDEs and is able to solve PDE-constrained optimization problems, including optimal shape design. Although the toolset has been designed with Computational Fluid Dynamics (CFD) and aerodynamic shape optimization in mind, it has also been extended to treat other sets of governing equations including potential flow, electrodynamics, chemically reacting flows, and several others. In our experience, capabilities for computational analysis and optimization have improved considerably over the past two decades. However, the ability to integrate the resulting software packages into coupled multi-physics analysis and design optimization solvers has remained a challenge: the variety of approaches chosen for the independent components of the overall problem (flow solvers, adjoint solvers, optimizers, shape parameterization, shape deformation, mesh adaption, mesh deformation, etc) make it difficult to (a) expand the range of applicability to situations not originally envisioned, and (b) to reduce the overall burden of creating integrated applications. By leveraging well-established object-oriented software architectures (using C++) and by enabling a common interface for all the necessary components, SU 2 is able to remove these barriers for both the beginner and the seasoned analyst. In this paper we attempt to describe our efforts to develop SU 2 as an integrated platform. In some senses, the paper can also be used as a software reference manual for those who might be interested in modifying it to suit their own needs. We carefully describe the C++ framework and object hierarchy, the sets of equations that can be currently modeled by SU 2 , the available choices for numerical discretization, and conclude with a set of relevant validation and verification test cases that are included with the SU 2 distribution. We intend for SU 2 to remain open source and to serve as a starting point for new capabilities not included in SU 2 today, that will hopefully be contributed by users in both academic and industrial environments.

Volatile, Isotope, and Organic Analysis of Martian Fines with the Mars Curiosity Rover

Abstract: Samples from the Rocknest aeolian deposit were heated to ~835°C under helium flow and evolved gases analyzed by Curiosity's Sample Analysis at Mars instrument suite. H2O, SO2, CO2, and O2 were the major gases released. Water abundance (1.5 to 3 weight percent) and release temperature suggest that H2O is bound within an amorphous component of the sample. Decomposition of fine-grained Fe or Mg carbonate is the likely source of much of the evolved CO2. Evolved O2 is coincident with the release of Cl, suggesting that oxygen is produced from thermal decomposition of an oxychloride compound. Elevated δD values are consistent with recent atmospheric exchange. Carbon isotopes indicate multiple carbon sources in the fines. Several simple organic compounds were detected, but they are not definitively martian in origin.

Efficiency droop in light‐emitting diodes: Challenges and countermeasures

Abstract: Efficiency droop, i.e. the loss of efficiency at high operating current, afflicts nitride-based light-emitting diodes (LEDs). The droop phenomenon is currently the subject of intense research, as it retards the advancement of solid-state lighting which is just starting to supplant fluorescent as well as incandescent lighting. Although the technical community does not yet have consented to a single cause of droop, this article provides a summary of the present state of droop research, reviews currently discussed droop mechanisms, and presents a recently developed theoretical model for the efficiency droop. In the theoretical model, carrier leakage out of the active region caused by the asymmetry of the pn junction, specifically the disparity between electron and hole concentrations and mobilities, is discussed in detail. The model is in agreement with the droop's key behaviors not only for GaInN LEDs but also for AlGaInP LEDs.

Payments for ecosystem services and the fatal attraction of win-win solutions

Abstract: In this commentary we critically discuss the suitability of payments for ecosystem services and the most important challenges they face. While such instruments can play a role in improving environmental governance, we argue that over-reliance on payments as win-win solutions might lead to ineffective outcomes, similar to earlier experience with integrated conservation and development projects. Our objective is to raise awareness, particularly among policy makers and practitioners, about the limitations of such instruments and to encourage a dialogue about the policy contexts in which they might be appropriate.

Optogenetic protein clustering and signaling activation in mammalian cells

Abstract: We report an optogenetic method based on Arabidopsis thaliana cryptochrome 2 for rapid and reversible protein oligomerization in response to blue light. We demonstrated its utility by photoactivating the β-catenin pathway, achieving a transcriptional response higher than that obtained with the natural ligand Wnt3a. We also demonstrated the modularity of this approach by photoactivating RhoA with high spatiotemporal resolution, thereby suggesting a previously unknown mode of activation for this Rho GTPase.

Cosolvent Effects on Protein Stability

Abstract: Proteins are marginally stable, and the folding/unfolding equilibrium of proteins in aqueous solution can easily be altered by the addition of small organic molecules known as cosolvents. Cosolvents that shift the equilibrium toward the unfolded ensemble are termed denaturants, whereas those that favor the folded ensemble are known as protecting osmolytes. Urea is a widely used denaturant in protein folding studies, and the molecular mechanism of its action has been vigorously debated in the literature. Here we review recent experimental as well as computational studies that show an emerging consensus in this problem. Urea has been shown to denature proteins through a direct mechanism, by interacting favorably with the peptide backbone as well as the amino acid side chains. In contrast, the molecular mechanism by which the naturally occurring protecting osmolyte trimethylamine N-oxide (TMAO) stabilizes proteins is not clear. Recent studies have established the strong interaction of TMAO with water. Detailed molecular simulations, when used with force fields that incorporate these interactions, can provide insight into this problem. We present the development of a model for TMAO that is consistent with experimental observations and that provides physical insight into the role of cosolvent-cosolvent interaction in determining its preferential interaction with proteins.

Abundance and Isotopic Composition of Gases in the Martian Atmosphere from the Curiosity Rover

Abstract: Volume mixing and isotope ratios secured with repeated atmospheric measurements taken with the Sample Analysis at Mars instrument suite on the Curiosity rover are: carbon dioxide (CO2), 0.960(±0.007); argon-40 (40Ar), 0.0193(±0.0001); nitrogen (N2), 0.0189(±0.0003); oxygen, 1.45(±0.09) × 10−3; carbon monoxide, < 1.0 × 10−3; and 40Ar/36Ar, 1.9(±0.3) × 103. The 40Ar/N2 ratio is 1.7 times greater and the 40Ar/36Ar ratio 1.6 times lower than values reported by the Viking Lander mass spectrometer in 1976, whereas other values are generally consistent with Viking and remote sensing observations. The 40Ar/36Ar ratio is consistent with martian meteoritic values, which provides additional strong support for a martian origin of these rocks. The isotopic signature δ13C from CO2 of ~45 per mil is independently measured with two instruments. This heavy isotope enrichment in carbon supports the hypothesis of substantial atmospheric loss.

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

Abstract: The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.

Evidence for perchlorates and the origin of chlorinated hydrocarbons detected by SAM at the Rocknest aeolian deposit in Gale Crater

Abstract: [1] A single scoop of the Rocknest aeolian deposit was sieved (<150 μm), and four separate sample portions, each with a mass of ~50mg, were delivered to individual cups inside the Sample Analysis at Mars (SAM) instrument by the Mars Science Laboratory rover’ ss ample acquisition system. The samples were analyzed separately by the SAM pyrolysis evolved gas and gas chromatograph mass spectrometer analysis modes. Several chlorinated hydrocarbons including chloromethane, dichloromethane, trichloromethane, a chloromethylpropene, and chlorobenzene were identified by SAM above background levels with abundances of ~0.01 to 2.3nmol. The evolution of the chloromethanes observed during pyrolysis is coincident with the increase in O2 released from the Rocknest sample and the decomposition of a product of N-methyl-N-(tert-butyldimethylsilyl)-trifluoroacetamide (MTBSTFA), a chemical whose vapors were released from a derivatization cup inside SAM. The best candidate for the oxychlorine compounds in Rocknest is a hydrated calcium perchlorate (Ca(ClO4)2·nH2O), based on the temperature release of O2 that correlates with the release of the chlorinated hydrocarbons measured by SAM, although other chlorine-bearing phases are being considered. Laboratory analog experiments suggest that the reaction of Martian chlorine from perchlorate decomposition with terrestrial organic carbon from MTBSTFA during pyrolysis can explain the presence of three chloromethanes and a chloromethylpropene detected by SAM. Chlorobenzene may be attributed to reactionsofMartian chlorine released during pyrolysiswith terrestrial benzene or toluene derived from 2,6-diphenylphenylene oxide (Tenax) on the SAM hydrocarbon trap. At this time we do not have definitive evidence to support a nonterrestrial carbon source for these chlorinated hydrocarbons, nor do we exclude the possibility that future SAM analyses will reveal the presence of organic compounds native to the Martian regolith.

Curiosity at Gale Crater, Mars: Characterization and Analysis of the Rocknest Sand Shadow

Abstract: The Rocknest aeolian deposit is similar to aeolian features analyzed by the Mars Exploration Rovers (MERs) Spirit and Opportunity. The fraction of sand <150 micrometers in size contains ~55% crystalline material consistent with a basaltic heritage and ~45% x-ray amorphous material. The amorphous component of Rocknest is iron-rich and silicon-poor and is the host of the volatiles (water, oxygen, sulfur dioxide, carbon dioxide, and chlorine) detected by the Sample Analysis at Mars instrument and of the fine-grained nanophase oxide component first described from basaltic soils analyzed by MERs. The similarity between soils and aeolian materials analyzed at Gusev Crater, Meridiani Planum, and Gale Crater implies locally sourced, globally similar basaltic materials or globally and regionally sourced basaltic components deposited locally at all three locations.

Improved measurement of electron antineutrino disappearance at Daya Bay

Abstract: With 2.5× the previously reported exposure, the Daya Bay experiment has improved the measurement of the neutrino mixing parameter sin^2 2θ_(13) = 0.089 ± 0.010(stat) ± 0.005(syst). Reactor anti-neutrinos were produced by six 2.9 GW_(th) commercial power reactors, and measured by six 20-ton target-mass detectors of identical design. A total of 234,217 anti-neutrino candidates were detected in 127 days of exposure. An anti-neutrino rate of 0.944±0.007(stat)±0.003(syst) was measured by three detectors at a flux-weighted average distance of 1648 m from the reactors, relative to two detectors at 470 m and one detector at 576 m. Detector design and depth underground limited the background to 5 ± 0.3% (far detectors) and 2 ± 0.2% (near detectors) of the candidate signals. The improved precision confirms the initial measurement of reactor anti-neutrino disappearance, and continues to be the most precise measurement of θ_(13).

Multiphysics simulations: Challenges and opportunities

Abstract: We consider multiphysics applications from algorithmic and architectural perspectives, where “algorithmic” includes both mathematical analysis and computational complexity, and “architectural” includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities.

Effect of micro- and nanoscale topography on the adhesion of bacterial cells to solid surfaces.

Abstract: Attachment and biofilm formation by bacterial pathogens on surfaces in natural, industrial, and hospital settings lead to infections and illnesses and even death. Minimizing bacterial attachment to surfaces using controlled topography could reduce the spreading of pathogens and, thus, the incidence of illnesses and subsequent human and financial losses. In this context, the attachment of key microorganisms, including Escherichia coli, Listeria innocua, and Pseudomonas fluorescens, to silica and alumina surfaces with micron and nanoscale topography was investigated. The results suggest that orientation of the attached cells occurs preferentially such as to maximize their contact area with the surface. Moreover, the bacterial cells exhibited different morphologies, including different number and size of cellular appendages, depending on the topographical details of the surface to which they attached. This suggests that bacteria may utilize different mechanisms of attachment in response to surface topography. These results are important for the design of novel microbe-repellant materials.

High-resolution reversible folding of hyperstable RNA tetraloops using molecular dynamics simulations

Abstract: We report the de novo folding of three hyperstable RNA tetraloops to 1–3 A rmsd from their experimentally determined structures using molecular dynamics simulations initialized in the unfolded state. RNA tetraloops with loop sequences UUCG, GCAA, or CUUG are hyperstable because of the formation of noncanonical loop-stabilizing interactions, and they are all faithfully reproduced to angstrom-level accuracy in replica exchange molecular dynamics simulations, including explicit solvent and ion molecules. This accuracy is accomplished using unique RNA parameters, in which biases that favor rigid, highly stacked conformations are corrected to accurately capture the inherent flexibility of ssRNA loops, accurate base stacking energetics, and purine syn-anti interconversions. In a departure from traditional quantum chemistrycentric approaches to force field optimization, our parameters are calibrated directly from thermodynamic and kinetic measurements of intra- and internucleotide structural transitions. The ability to recapitulate the signature noncanonical interactions of the three most abundant hyperstable stem loop motifs represents a significant milestone to the accurate prediction of RNA tertiary structure using unbiased all-atom molecular dynamics simulations.

Isotope ratios of H, C, and O in CO2 and H2O of the martian atmosphere.

Abstract: Stable isotope ratios of H, C, and O are powerful indicators of a wide variety of planetary geophysical processes, and for Mars they reveal the record of loss of its atmosphere and subsequent interactions with its surface such as carbonate formation. We report in situ measurements of the isotopic ratios of D/H and 18O/16O in water and 13C/12C, 18O/16O, 17O/16O, and 13C18O/12C16O in carbon dioxide, made in the martian atmosphere at Gale Crater from the Curiosity rover using the Sample Analysis at Mars (SAM)’s tunable laser spectrometer (TLS). Comparison between our measurements in the modern atmosphere and those of martian meteorites such as ALH 84001 implies that the martian reservoirs of CO2 and H2O were largely established ~4 billion years ago, but that atmospheric loss or surface interaction may be still ongoing.

Soil Diversity and Hydration as Observed by ChemCam at Gale Crater, Mars

Abstract: The ChemCam instrument, which provides insight into martian soil chemistry at the submillimeter scale, identified two principal soil types along the Curiosity rover traverse: a fine-grained mafic type and a locally derived, coarse-grained felsic type. The mafic soil component is representative of widespread martian soils and is similar in composition to the martian dust. It possesses a ubiquitous hydrogen signature in ChemCam spectra, corresponding to the hydration of the amorphous phases found in the soil by the CheMin instrument. This hydration likely accounts for an important fraction of the global hydration of the surface seen by previous orbital measurements. ChemCam analyses did not reveal any significant exchange of water vapor between the regolith and the atmosphere. These observations provide constraints on the nature of the amorphous phases and their hydration.

Heat Transfer in Microchannels—2012 Status and Research Needs

Abstract: Heat transfer and fluid flow in microchannels have been topics of intense research in the past decade. A critical review of the current state of research is presented with a focus on the future research needs. After providing a brief introduction, the paper addresses six topics related to transport phenomena in microchannels: single-phase gas flow, enhancement in single-phase liquid flow and flow boiling, flow boiling instability, condensation, electronics cooling, and microscale heat exchangers. After reviewing the current status, future research directions are suggested. Concerning gas phase convective heat transfer in microchannels, the antagonist role played by the slip velocity and the temperature jump that appear at the wall are now clearly understood and quantified. It has also been demonstrated that the shear work due to the slipping fluid increases the effect of viscous heating on heat transfer. On the other hand, very few experiments support the theoretical models and a significant effort should be made in this direction, especially for measurement of temperature fields within the gas in microchannels, implementing promising recent techniques such as molecular tagging thermometry (MTT). The single-phase liquid flow in microchannels has been established to behave similar to the macroscale flows. The current need is in the area of further enhancing the performance. Progress on implementation of flow boiling in microchannels is facing challenges due to its lower heat transfer coefficients and critical heat flux (CHF) limits. An immediate need for breakthrough research related to these two areas is identified. Discussion about passive and active methods to suppress flow boiling instabilities is presented. Future research focus on instability research is suggested on developing active closed loop feedback control methods, extending current models to better predict and enable superior control of flow instabilities. Innovative high-speed visualization and measurement techniques have led to microchannel condensation now being studied as a unique process with its own governing influences. Further work is required to develop widely applicable flow regime maps that can address many fluid types and geometries. With this, condensation heat transfer models can progress from primarily annular flow based models with some adjustments using dimensionless parameters to those that can directly account for transport in intermittent and other flows, and the varying influences of tube shape, surface tension and fluid property differences over much larger ranges than currently possible. Electronics cooling continues to be the main driver for improving thermal transport processes in microchannels, while efforts are warranted to develop high performance heat exchangers with microscale passages. Specific areas related to enhancement, novel configurations, nanostructures and practical implementation are expected to be the research focus in the coming years.

LDPC-in-SSD: making advanced error correction codes work effectively in solid state drives

Abstract: Conventional error correction codes (ECCs), such as the commonly used BCH code, have become increasingly inadequate for solid state drives (SSDs) as the capacity of NAND flash memory continues to increase and its reliability continues to degrade. It is highly desirable to deploy a much more powerful ECC, such as low-density parity-check (LDPC) code, to significantly improve the reliability of SSDs. Although LDPC code has had its success in commercial hard disk drives, to fully exploit its error correction capability in SSDs demands unconventional fine-grained flash memory sensing, leading to an increased memory read latency. To address this important but largely unexplored issue, this paper presents three techniques to mitigate the LDPC-induced response time delay so that SSDs can benefit its strong error correction capability to the full extent. We quantitatively evaluate these techniques by carrying out trace-based SSD simulations with runtime characterization of NAND flash memory reliability and LDPC code decoding. Our study based on intensive experiments shows that these techniques used in an integrated way in SSDs can reduce the worst-case system read response time delay from over 100% down to below 20%. With our proposed techniques, a strong ECC alternative can be used in NAND flash memory to retain its reliability to respond the continuous cost reduction, and its relatively small increase of response time delay is acceptable to mainstream application users, considering a huge gain in SSD capacity, its reliability, and the price reduction.

Bonding-induced thermal conductance enhancement at inorganic heterointerfaces using nanomolecular monolayers

Abstract: Manipulating interfacial thermal transport is important for many technologies including nanoelectronics, solid-state lighting, energy generation and nanocomposites. Here, we demonstrate the use of a strongly bonding organic nanomolecular monolayer (NML) at model metal/dielectric interfaces to obtain up to a fourfold increase in the interfacial thermal conductance, to values as high as 430 MW m(-2) K(-1) in the copper-silica system. We also show that the approach of using an NML can be implemented to tune the interfacial thermal conductance in other materials systems. Molecular dynamics simulations indicate that the remarkable enhancement we observe is due to strong NML-dielectric and NML-metal bonds that facilitate efficient heat transfer through the NML. Our results underscore the importance of interfacial bond strength as a means to describe and control interfacial thermal transport in a variety of materials systems.

In-network outlier detection in wireless sensor networks

Abstract: To address the problem of unsupervised outlier detection in wireless sensor networks, we develop an approach that (1) is flexible with respect to the outlier definition, (2) computes the result in-network to reduce both bandwidth and energy consumption, (3) uses only single-hop communication, thus permitting very simple node failure detection and message reliability assurance mechanisms (e.g., carrier-sense), and (4) seamlessly accommodates dynamic updates to data. We examine performance by simulation, using real sensor data streams. Our results demonstrate that our approach is accurate and imposes reasonable communication and power consumption demands.