Institute for Computer Aided Design

Part I derives a new topological formula for the terminalpair reliability of complex networks. The formula generates only non-cancelling terms. The non-cancelling terms in the reliability expression correspond one-to-one with the acyclic subgraphs of the given probabilistic graph. Part II introduces the concept of neutral sequences in acyclic graphs; several of their important properties are established. Based on these results a powerful algorithm for generating the reliability expression is presented. The reliability expression is obtained in symbolic factored form. Examples indicate that the present algorithm is appreciably faster than earlier methods. The properties of cyclic and acyclic graphs established in this paper are significant new results in the theory of digraphs and have further ramifications and wider application than in reliability.

Automotive collision warning systems (CWS) can enhance hazard identification and management. However, false alarms (FAs), which occur as a random activation of the system not corresponding to a threat and not interpretable by the driver, and unnecessary alarms (UAs), which occur in situations judged hazardous by the algorithm but not by the driver, may limit CWS effectiveness. A driving simulator was used to investigate the influence of CWS (accurate, UA, FA, none) and distraction on driver performance during non-critical and critical events. FAs and UAs differentially influenced trust and compliance. FAs diminished trust and compliance, whereas the context associated with UAs fostered trust and compliance during subsequent events. This study suggests current warning descriptions based on signal detection theory need to be expanded to represent how different types of alarms affect drivers.

Using an algebraic condition of vanishing discriminant for multiple roots of fourth-degree polynomials, we derive an analytical expression of a shadow size as a function of a charge in the Reissner-Nordstr\"om (RN) metric [1,2]. We consider shadows for negative tidal charges and charges corresponding to naked singularities $q={\mathcal{Q}}^{2}/{M}^{2}>1$, where $\mathcal{Q}$ and $M$ are black hole charge and mass, respectively, with the derived expression. An introduction of a negative tidal charge $q$ can describe black hole solutions in theories with extra dimensions, so following the approach we consider an opportunity to extend the RN metric to negative ${\mathcal{Q}}^{2}$, while for the standard RN metric ${\mathcal{Q}}^{2}$ is always non-negative. We found that for $q>9/8$, black hole shadows disappear. Significant tidal charges $q=\ensuremath{-}6.4$ (suggested by Bin-Nun [3--5]) are not consistent with observations of a minimal spot size at the Galactic Center observed in mm-band; moreover, these observations demonstrate that a Reissner-Nordstr\"om black hole with a significant charge $q\ensuremath{\approx}1$ provides a better fit of recent observational data for the black hole at the Galactic Center in comparison with the Schwarzschild black hole.

A method for producing half-tone pictures by computer is presented. The basic method, which is very simple, works well in most cases, but does not handle all objects correctly. The extended method, which copes with all cases, is also described. The functions used for calculating the intensity of parts of objects, and the method for handling transparency, are discussed. Examples of pictures produced by this method are included, and the times taken to generate them are tabulated. The extended algorithm compares favourably in speed and storage requirements with other published algorithms.

We present the results for CAPRI Round 50, the fourth joint CASP-CAPRI protein assembly prediction challenge. The Round comprised a total of twelve targets, including six dimers, three trimers, and three higher-order oligomers. Four of these were easy targets, for which good structural templates were available either for the full assembly, or for the main interfaces (of the higher-order oligomers). Eight were difficult targets for which only distantly related templates were found for the individual subunits. Twenty-five CAPRI groups including eight automatic servers submitted ~1250 models per target. Twenty groups including six servers participated in the CAPRI scoring challenge submitted ~190 models per target. The accuracy of the predicted models was evaluated using the classical CAPRI criteria. The prediction performance was measured by a weighted scoring scheme that takes into account the number of models of acceptable quality or higher submitted by each group as part of their five top-ranking models. Compared to the previous CASP-CAPRI challenge, top performing groups submitted such models for a larger fraction (70-75%) of the targets in this Round, but fewer of these models were of high accuracy. Scorer groups achieved stronger performance with more groups submitting correct models for 70-80% of the targets or achieving high accuracy predictions. Servers performed less well in general, except for the MDOCKPP and LZERD servers, who performed on par with human groups. In addition to these results, major advances in methodology are discussed, providing an informative overview of where the prediction of protein assemblies currently stands.

Proteochemometric (PCM) modelling is a computational method to model the bioactivity of multiple ligands against multiple related protein targets simultaneously.

Previously formulated monotonicity criteria for explicit two-level difference schemes designed for hyperbolic equations (S.K. Godunov’s, A. Harten’s (TVD schemes), characteristic criteria) are extended to multileveled, including implicit, stencils. The characteristic monotonicity criterion is used to develop a universal algorithm for constructing high-order accurate nonlinear monotone schemes (for an arbitrary form of the desired solution) based on their analysis in the space of grid functions. Several new fourth-to-third-order accurate monotone difference schemes on a compact three-level stencil and nonexpanding (three-point) stencils are proposed for an extended system, which ensures their monotonicity for both the desired function and its derivatives. The difference schemes are tested using the characteristic monotonicity criterion and are extended to systems of hyperbolic equations.

<div class="htmlview paragraph">This paper presents an overview of the Iowa Driving Simulator (IDS), including its implementation and experimental applications. The Center for Computer-Aided Design (CCAD) at The University of Iowa began developing the IDS in 1990 with primary funding from the state of Iowa and the Advanced Research Projects Agency (ARPA). The simulator utilizes a recently developed real-time multibody dynamics formulation to create high fidelity, operator-in-the-loop vehicle simulations, a large six-degree-of-freedom hexapod motion base, wide field-of-view textured graphics with directional audio sources, and several interchangeable, instrumented cabs to provide realistic cueing feedback to the driver.</div> <div class="htmlview paragraph">Human factors issues currently being investigated by IDS researchers include experimental studies for the design and use of automated highway systems, usage of raised pavement markers for lane edge-line delineation, IVHS collision warning and roadway departure warning systems, advanced traveler information systems, performance assessment of challenged drivers, verification of driver performance in virtual environments, and more general issues of simulator fidelity and perceived realism. Two applications of the IDS are detailed: a study of Automated Highway Systems (AHS) and vehicle virtual prototyping on a virtual proving ground.</div>

Recent experiments have utilizied high-power subpicosecond laser pulses to effect the ultrafast heating of a condensed material to temperatures far above the critical temperature. Using optical diagnostics it was established that a complicated density profile with sharp gradients, differing substantially from an ordinary rarefaction wave, forms in the expanding heated matter. The present letter is devoted to the analysis of the expansion of matter under the conditions of the experiments reported by D. von der Linde, K. Sokolowski-Tinten, and J. Bialkowski, Appl. Surf. Science 109/110, 1 (1996); K. Sokolowski-Tinten, J. Bialkowski, A. Cavalleri et al., Proc. Soc. Photo-Opt. Instum. Eng. 3343, 46 (1998); and, K. Sokolowski-Tinten, J. Bialkowski, A. Cavalleri et al., Phys. Rev. Lett. 81, 224 (1998). It is shown that if the unloading adiabat passes through the two-phase region, a thin liquid shell filled with low-density two-phase matter forms in the expanding material. The shell moves with a constant velocity. The velocity in the two-phase material is a linear function of the coordinate (flow with uniform deformation), and the density is independent of the coordinate and decreases with time as t −1.

The dynamics of the melting of a surface nanolayer and the formation of thermal and shock waves in metals irradiated by femtosecond laser pulses has been investigated both experimentally and theoretically. A new experimental-computational method has been implemented to determine the parameters of laser-induced shock waves in metallic films. Data on the strength properties of the condensed phase in aluminum films at an extremely high strain rate ( $$ \dot V $$ /V ∼ 109 s−1)under the action of a laser-induced shock wave have been obtained.

An equation of state is a fundamental characteristic of a substance. It is necessary in numerous studies and practically important problems of high energy density physics. In this review, we consider the modern requirements to equations of state, theoretical and experimental methods used to study the thermodynamic properties of a substance, different aspects of constructing wide-range equations of state, and examples of application of wide-range equations of state in simulation of high-energy processes.

Energy evaluation using fast Fourier transforms (FFTs) enables sampling billions of putative complex structures and hence revolutionized rigid protein-protein docking. However, in current methods, efficient acceleration is achieved only in either the translational or the rotational subspace. Developing an efficient and accurate docking method that expands FFT-based sampling to five rotational coordinates is an extensively studied but still unsolved problem. The algorithm presented here retains the accuracy of earlier methods but yields at least 10-fold speedup. The improvement is due to two innovations. First, the search space is treated as the product manifold [Formula: see text], where [Formula: see text] is the rotation group representing the space of the rotating ligand, and [Formula: see text] is the space spanned by the two Euler angles that define the orientation of the vector from the center of the fixed receptor toward the center of the ligand. This representation enables the use of efficient FFT methods developed for [Formula: see text] Second, we select the centers of highly populated clusters of docked structures, rather than the lowest energy conformations, as predictions of the complex, and hence there is no need for very high accuracy in energy evaluation. Therefore, it is sufficient to use a limited number of spherical basis functions in the Fourier space, which increases the efficiency of sampling while retaining the accuracy of docking results. A major advantage of the method is that, in contrast to classical approaches, increasing the number of correlation function terms is computationally inexpensive, which enables using complex energy functions for scoring.

Protease inhibitors (PIs) are highly effective drugs against the human immunodeficiency virus (HIV), yet long-term therapeutic use is limited by emergence of HIV type 1 (HIV-1) protease substitutions that confer cross-resistance to multiple protease inhibitor drugs. Atazanavir is a highly potent HIV protease inhibitor with a distinct resistance profile that includes effectiveness against most HIV-1 isolates resistant to one or two PIs. The signature resistance substitution for atazanavir is I50L, and it is frequently (53%) accompanied by a compensatory A71V substitution that helps restore viability and increases atazanavir resistance levels. We measured the binding affinities of wild-type (WT) and I50L/A71V HIV-1 proteases to atazanavir and other currently approved PIs (ritonavir, lopinavir, saquinavir, nelfinavir, indinavir, and amprenavir) by isothermal titration calorimetry. Remarkably, we find that all of the PIs have 2- to 10-fold increased affinities for I50L/A71V protease, except for atazanavir. The results are also manifested by thermal stability measures of affinity for WT and I50L/A71V proteases. Additional biophysical and enzyme kinetics experiments show I50L/A71V protease is a stable enzyme with catalytic activity that is slightly reduced (34%) relative to the WT. Computational modeling reveals that the unique resistance phenotype of I50L/A71V protease likely originates from bulky tert-butyl groups at P2 and P2' (specific to atazanavir) that sterically clash with methyl groups on residue L50. The results of this study provide a molecular understanding of the novel hypersusceptibility of atazanavir-resistant I50L/A71V-containing clinical isolates to other currently approved PIs.

Abstract. Leaf size influences many aspects of tree function such as rates of transpiration and photosynthesis and, consequently, often varies in a predictable way in response to environmental gradients. The recent development of pan-Amazonian databases based on permanent botanical plots has now made it possible to assess trends in leaf size across environmental gradients in Amazonia. Previous plot-based studies have shown that the community structure of Amazonian trees breaks down into at least two major ecological gradients corresponding with variations in soil fertility (decreasing from southwest to northeast) and length of the dry season (increasing from northwest to south and east). Here we describe the geographic distribution of leaf size categories based on 121 plots distributed across eight South American countries. We find that the Amazon forest is predominantly populated by tree species and individuals in the mesophyll size class (20.25–182.25 cm2). The geographic distribution of species and individuals with large leaves (>20.25 cm2) is complex but is generally characterized by a higher proportion of such trees in the northwest of the region. Spatially corrected regressions reveal weak correlations between the proportion of large-leaved species and metrics of water availability. We also find a significant negative relationship between leaf size and wood density.

need for known ligand orientations in terms of the different metrics when compared to current FEP approaches with significant computational savings while additionally offering quantitative estimates of individual atomic contributions to binding free energies. These results further validate the SILCS methodology as an accurate, computationally efficient tool to support lead optimization and drug discovery.

A discrete mathematical model of hydrobiology of coastal zone is constructed and analyzed. The model takes into account the transport and transformation of polluting biogenic elements in water basins. The propagation and transformation of biogenic elements is affected by such physical factors as three-dimensional motion of water taking into account the advective transport and microturbulent diffusion, spatially inhomogeneous distribution of temperature, salinity, and oxygen. Biogenic pollutants typically arrive into the water basin with river flow, which depends on the weather and climate of the geographic region, or with drainage of insufficiently purified domestic and industrial waste or other kinds of anthropogenic impact. Biogenic pollutants can also appear due to secondary pollution processes, such as stirring up and transport of bed silt, shore abrasion, etc. Stoichiometric relations between biogenic nutrients for phytoplankton algae that can be used to determine the limiting nutrient for each species are obtained. Observation models describing the consumption, accumulation of nutrients, and growth of phytoplankton are considered. A three-dimensional mathematical model of transformation of forms of phosphorus, nitrogen, and silicon in the plankton dynamics problem in coastal systems is constructed and analyzed. This model takes into account the convective and diffusive transport, absorption, and release of nutrients by phytoplankton as well as transformation cycles of phosphorus, nitrogen, and silicon forms. Numerical methods for solving the problem that are based on high-order weighted finite difference schemes and take into account the degree of fill of the computation domain control cells are developed. These methods are implemented on a multiprocessing system. They make it possible to improve the accuracy of the numerical solution and decrease the computation time by several fold. Based on the numerical implementation, dangerous phenomena in coastal systems related to the propagation of pollutants, including oil spill, eutrophication, and algae bloom, which causes suffocation phenomena in water basins, are reconstructed.

Abstract Fundamental physical phenomena in metals irradiated by ultrashort laser pulses with absorbed fluences higher than few tens of mJ/cm 2 are investigated. For those fluences, laser‐produced electron distribution function relaxes to equilibrium Fermi distribution with electron temperature T e within a short time of 10‐100 fs. Because the electron subsystem has T e highly exceeding much the ion subsystem temperature T i the well‐known twotemperature hydrodynamic model (2T‐HD) is used to evaluate heat propagation associated with hot conductive electron diffusion and electron‐ion energy exchange. The model coefficients of electron heat conductivity κ ( ϱ , T e , T i ) and electron‐ion coupling parameter α ( ϱ , T e ) together with 2T equation of state E ( ϱ , T e , T i ) and P ( ϱ , T e , T i ) are calculated. Modeling with 2T‐HD code shows transition of electron heat wave from supersonic to subsonic regime of prop‐agation. At the moment of transition the heat wave emits a compression wave moving into the bulk of met al. Nonlinear evolution of the compression wave after its separation from the subsonic heat wave till spallation of rear‐side layer of a film is traced in both 2T‐HD modeling and molecular dynamics (MD) simulation. For fluences above some threshold the nucleation of voids in frontal surface layer is initiated by strong tensile wave following the compression wave. If the absorbed fluence is ∼30 % above the ablation threshold than void nucleation develops quickly to heavily foam the molten met al. Long‐term evolution of the metal foam including foam breaking and freezing is simulated. It is shown that surface nano‐structures observed in experiments are produced by very fast cooling of surface molten layer followed by recrystallization of supercooled liquid in disintegrating foam having complex geometry. Characteristic lengths of such surface nanostructures, including frozen pikes and bubbles, are of the order of thickness of molten layer formed right after laser irradiation. (© 2013 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Adult NZB mice (greater than 15 wk old) have very few bone marrow cells that can give rise to sIg+ clonable B cells during liquid culture. This deficiency corresponds to extremely low numbers of cells with cytoplasmic but not surface mu chains of IgM and reduced numbers of cells bearing a high molecular weight B-lineage antigen. Depletion of Thy-1-bearing cells and appropriate mixing experiments did not provide evidence either that suppressor cells are responsible for this phenomenon or that accessory cells are defective in NZB mice. Nor did it seem that B cells were being produced in extramedullary sites. B cell precursors were detectable in very young NZB mice, exceeded control values at 4-5 wk of age, and then declined rapidly. In contrast, these persisted for greater than 1 yr in normal BALB/c, DBA/2, and CBA/H mice. It appears possible that intermediate stages in B-lineage differentiation become prematurely exhausted through an accelerated aging process in NZB mice. These chronological changes have implications for understanding the sequence of events that lead to B lymphocyte formation and the processes that normally regulate it.

Using the experimental graphene layer spacing of the stage 1 model as a constraint, the effective atomic charge of lithium, in lithium-intercalated graphite (LIG) was determined. In order to confirm that lithium in LIG exists in a partially ionic state, quantum mechanical calculations were also carried out for several lithium-carbon systems. Using a fixed the graphene layer spacing and structures for hexagonal graphite, stage 3, stage 2, and stage 1 models, were obtained. The more lithium is intercalated into the graphite, the wider the layer spacing becomes. The distortion of structures due to lithium intercalation was not observed until the stage 1 model was formed. In stage 1 and stage 2 models, the graphene layers shifted from ABAB to AAAA stacking as lithium was intercalated to the hexagonal graphite. However, the stage 3 model showed a shift of layers from ABABAB to AB'AAB''A stacking, where B' and B'' represent the graphene layers which have shifted slightly from B. Only the graphene layers that have the intercalated lithium layers between them shifted to AA stacking. © 2001 The Electrochemical Society. All rights reserved.

Abstract We combine theoretical and experimental methods to study the processes induced by fast laser heating of metal foils. These processes reveal themselves through motion of frontal (irradiated) and rear‐side foil boundaries. The irradiated targets are 0.3‐2 micron thick aluminum foils deposited on much thicker (150 microns) glass plate. The instant boundary positions is measured by pump‐probe technique having ∼40‐150 fs time and ∼1 nm spatial resolutions. Ultrashort laser pulse transforms a frontal surface layer with thickness d T into two‐temperature ( T e ≫ T i ) warm dense matter state. Its quantitative characteristics including its thickness are defined by poorly known coefficients of electron‐ion energy exchange α and electron heat conductivity κ . Fast laser heating rises pressure in the d T ‐layer and therefore produce acoustic waves. Propagation and reflection from the frontal and rear boundaries of these waves causes the displacement Δ x ( t ) of boundary positions. Pressure wave profiles, and hence functions Δ x ( t ), depend on thickness d T . This is why the experimental detection of Δ x ( t ) opens a way to accurate evaluation of the coefficients α and κ (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)