A new, evidence-based, theory for knowledge reuse in security risk analysis

Security risk analysis (SRA) is a key activity in software engineering but requires heavy manual effort. Community knowledge in the form of security patterns or security catalogs can be used to support the identification of threats and security controls. However, no evidence-based theory exists about the effectiveness of security catalogs when used for security risk analysis. We adopt a grounded theory approach to propose a conceptual, revised and refined theory of SRA knowledge reuse. The theory refinement is backed by evidence gathered from conducting interviews with experts (20) and controlled experiments with both experts (15) and novice analysts (18). We conclude the paper by providing insights into the use of catalogs and managerial implications

Prediction of the Translocation Kinetics of a Protein from Its Mechanical Properties

AbstractProteins are actively unfolded to pass through narrow channels in macromolecular complexes that catalyze protein translocation and degradation. Catalyzed unfolding shares many features that characterize the mechanical unfolding of proteins using the atomic force microscope (AFM). However, simulations of unfolding induced by the AFM and when a protein is translocated through a pore suggest that each process occurs by distinct pathways. The link, if any, between each type of unfolding, therefore, is not known. We show that the mechanical unfolding energy landscape of a protein, obtained using an atomistic molecular model, can be used to predict both the relative mechanical strength of proteins when unfolded using the AFM and when unfolded by translocation into a pore. We thus link the two processes and show that the import rate through a pore not only depends on the location of the initiation tag but also on the mechanical properties of the protein when averaged over all the possible geometries that are relevant for a given translocation initiation site

Protein mechanics probed using simple molecular models

Background: Single-molecule experimental techniques such as optical tweezers or atomic force microscopy are a direct probe of the mechanical unfolding/folding of individual proteins. They are also a means to investigate free energy landscapes. Protein force spectroscopy alone provides limited information; theoretical models relate measurements to thermodynamic and kinetic properties of the protein, but do not reveal atomic level information. By building a molecular model of the protein and probing its properties through numerical simulation, one can gauge the response to an external force for individual interatomic interactions and determine structures along the unfolding pathway. In combination, single-molecule force probes and molecular simulations contribute to uncover the rich behavior of proteins when subjected to mechanical force. Scope of review: We focus on how simplified protein models have been instrumental in showing how general properties of the free energy landscape of a protein relate to its response to mechanical perturbations. We discuss the role of simple protein models to explore the complexity of free energy landscapes and highlight important conceptual issues that more chemically accurate models with all-atom representations of proteins and solvent cannot easily address. Major conclusions: Native-centric, coarse-grained models, despite simplifications in chemical detail compared to all-atom models, can reproduce and interpret experimental results. They also highlight instances where the theoretical framework used to interpret single-molecule data is too simple. However, these simple models are not able to reproduce experimental findings where non-native contacts are involved. General significance: Mechanical forces are ubiquitous in the cell and it is increasingly clear that the way a protein responds to mechanical perturbation is important

O(^3P) +CO_2 Collisions at Hyperthermal Energies: Dynamics of Nonreactive Scattering, Oxygen Isotope Exchange, and Oxygen-Atom Abstraction

The dynamics of O(^3P) + CO_2 collisions at hyperthermal energies were investigated experimentally and theoretically. Crossed-molecular-beams experiments at Ecoll = 98.8 kcal mol^(–1) were performed with isotopically labeled ^(12)C^(18)O_2 to distinguish products of nonreactive scattering from those of reactive scattering. The following product channels were observed: elastic and inelastic scattering (^(16)O(^3P) + ^(12)C^(18)O^2), isotope exchange (^(18)O + ^(16)O^(12)C^(18)O), and oxygen-atom abstraction (^(18)O^(16)O + ^(12)C^(18)O). Stationary points on the two lowest triplet potential energy surfaces of the O(^3P) + CO_2 system were characterized at the CCSD(T)/aug-cc-pVTZ level of theory and by means of W4 theory, which represents an approximation to the relativistic basis set limit, full-configuration-interaction (FCI) energy. The calculations predict a planar CO_3(C_(2v),^3A″) intermediate that lies 16.3 kcal mol^(–1) (W4 FCI excluding zero point energy) above reactants and is approached by a C_(2v) transition state with energy 24.08 kcal mol^(–1). Quasi-classical trajectory (QCT) calculations with collision energies in the range 23–150 kcal mol^(–1) were performed at the B3LYP/6-311G(d) and BMK/6-311G(d) levels. Both reactive channels observed in the experiment were predicted by these calculations. In the isotope exchange reaction, the experimental center-of-mass (c.m.) angular distribution, T(θ_(c.m.)), of the ^(16)O^(12)C^(18)O products peaked along the initial CO_2 direction (backward relative to the direction of the reagent O atoms), with a smaller isotropic component. The product translational energy distribution, P(E_T), had a relatively low average of E_T = 35 kcal mol^(–1), indicating that the ^(16)O^(12)C^(18)O products were formed with substantial internal energy. The QCT calculations give c.m. P(E_T) and T(θ_(c.m.)) distributions and a relative product yield that agree qualitatively with the experimental results, and the trajectories indicate that exchange occurs through a short-lived CO_3^* intermediate. A low yield for the abstraction reaction was seen in both the experiment and the theory. Experimentally, a fast and weak ^(16)O^(18)O product signal from an abstraction reaction was observed, which could only be detected in the forward direction. A small number of QCT trajectories leading to abstraction were observed to occur primarily via a transient CO_3 intermediate, albeit only at high collision energies (149 kcal mol^(–1)). The oxygen isotope exchange mechanism for CO_2 in collisions with ground state O atoms is a newly discovered pathway through which oxygen isotopes may be cycled in the upper atmosphere, where O(^3P) atoms with hyperthermal translational energies can be generated by photodissociation of O_3 and O_2

Extracting Structural Information of a Heteropolymer from Force-Extension Curves

We present a theory for the reverse analysis on the sequence information of a single H/P two-letter random hetero-polymer (RHP) from its force-extension(f-z) curves during quasi static stretching. Upon stretching of a self-assembled RHP, it undergoes several structural transitions. The typical elastic response of a hetero-polymeric globule is a set of overlapping saw-tooth patterns. With consideration of the height and the position of the overlapping saw-tooth shape, we analyze the possibility of extracting the binding energies of the internal domains and the corresponding block sizes of the contributing conformations.Comment: 5 figures 7 page

First Order Bipolaronic Transition at Finite Temperature in the Holstein Model

We investigate the Holstein model by using the dynamical mean-field theory combined with the exact diagonalization method. Below a critical temperature Tcr, a coexistence of the polaronic and the bipolaronic solutions is found for the same value of the electron-phonon coupling $ in the range gc1(T)<g<gc2(T). In the coexistence region, the system shows a first order phase transition from the bipolaronic to the polaronic states as T decreases at T=Tp(<Tcr), where the double occupancy and the lattice fluctuation together with the anharmonicity of the effective ion potential change discontinuously without any symmetry breaking. The obtained bipolaronic transition seems to be consistent with the rattling transition in the beta-pyrochlore oxide KOs2O6.Comment: 5 pages, 5 figures, J. Phys. Soc. Jpn. 79 (2010) 09370

Mechanical response of random heteropolymers

We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical random sequences. This transition is sharp in the limit of infinitely long chain molecules. But for chain lengths relevant to biological macromolecules, partially unfolded conformations prevail over an intermediate range of stress. These necklace-like structures, comprised of alternating compact and extended subunits, are stabilized by quenched variations in the composition of finite chain segments. The most stable arrangements of these subunits are largely determined by preferential extension of segments rich in solvophilic monomers. This predicted significance of necklace structures explains recent observations in protein stretching experiments. We examine the statistical features of select sequences that give rise to mechanical strength and may thus have guided the evolution of proteins that carry out mechanical functions in living cells.Comment: 10 pages, 6 figure

Vaping industry-funded academic scholarships

While the benefits versus the risks of increased e-cigarette use among adults remains unsettled, the fact that 21% of high school students in 2018 have used e-cigarettes in the last month is concerning to almost all policymakers and clinicians. A recent e-cigarette marketing technique involves the promotion of scholarships for students. Given the novelty of these promotions, we undertook an analysis to understand how widespread this practice is in the USA, along with characteristics of such scholarships

Nonadiabatic Superconductivity and Vertex Corrections in Uncorrelated Systems

We investigate the issue of the nonadiabatic superconductivity in uncorrelated systems. A local approximation is employed coherently with the weak dependence on the involved momenta. Our results show that nonadiabatic vertex corrections are never negligible, but lead to a strong suppression of $T_c$ with respect to the conventional theory. This feature is understood in terms of the momentum-frequency dependence of the vertex function. In contrast to strongly correlated systems, where the small ${\bf q}$-selection probes the positive part of vertex function, vertex corrections in uncorrelated systems are essentially negative resulting in an effective reduction of the superconducting pairing. Our analysis shows that vertex corrections in nonadiabatic regime can be never disregarded independently of the degree of electronic correlation in the system.Comment: 4 pages, 3 eps fig

HW-SW Emulation Framework for Temperature-Aware Design in MPSoCs

New tendencies envisage Multi-Processor Systems-On-Chip (MPSoCs) as a promising solution for the consumer electronics market. MPSoCs are complex to design, as they must execute multiple applications (games, video), while meeting additional design constraints (energy consumption, time-to-market). Moreover, the rise of temperature in the die for MPSoCs can seriously affect their final performance and reliability. In this paper, we present a new hardware-software emulation framework that allows designers a complete exploration of the thermal behavior of final MPSoC designs early in the design flow. The proposed framework uses FPGA emulation as the key element to model the hardware components of the considered MPSoC platform at multi-megahertz speeds. It automatically extracts detailed system statistics that are used as input to our software thermal library running in a host computer. This library calculates at run-time the temperature of on-chip components, based on the collected statistics from the emulated system and the final floorplan of the MPSoC. This enables fast testing of various thermal management techniques. Our results show speed-ups of three orders of magnitude compared to cycle-accurate MPSoC simulator