Cascaded walks in protein sequence space: use of artificial sequences in remote homology detection between natural proteins

Over the past two decades, many ingenious efforts have been made in protein remote homology detection. Because homologous proteins often diversify extensively in sequence, it is challenging to demonstrate such relatedness through entirely sequence-driven searches. Here, we describe a computational method for the generation of `protein-like' sequences that serves to bridge gaps in protein sequence space. Sequence profile information, as embodied in a position-specific scoring matrix of multiply aligned sequences of bona fide family members, serves as the starting point in this algorithm. The observed amino acid propensity and the selection of a random number dictate the selection of a residue for each position in the sequence. In a systematic manner, and by applying a `roulette-wheel' selection approach at each position, we generate parent family-like sequences and thus facilitate an enlargement of sequence space around the family. When generated for a large number of families, we demonstrate that they expand the utility of natural intermediately related sequences in linking distant proteins. In 91% of the assessed examples, inclusion of designed sequences improved fold coverage by 5-10% over searches made in their absence. Furthermore, with several examples from proteins adopting folds such as TIM, globin, lipocalin and others, we demonstrate that the success of including designed sequences in a database positively sensitized methods such as PSI-BLAST and Cascade PSI-BLAST and is a promising opportunity for enormously improved remote homology recognition using sequence information alone.

Space-time correlations of fluctuating velocities in turbulent shear flows

Space-time correlations or Eulerian two-point two-time correlations of fluctuating velocities are analytically and numerically investigated in turbulent shear flows. An elliptic model for the space-time correlations in the inertial range is developed from the similarity assumptions on the isocorrelation contours: they share a uniform preference direction and a constant aspect ratio. The similarity assumptions are justified using the Kolmogorov similarity hypotheses and verified using the direct numerical simulation DNS of turbulent channel flows. The model relates the space-time correlations to the space correlations via the convection and sweeping characteristic velocities. The analytical expressions for the convection and sweeping velocities are derived from the Navier-Stokes equations for homogeneous turbulent shear flows, where the convection velocity is represented by the mean velocity and the sweeping velocity is the sum of the random sweeping velocity and the shearinduced velocity. This suggests that unlike Taylor’s model where the convection velocity is dominating and Kraichnan and Tennekes’ model where the random sweeping velocity is dominating, the decorrelation time scales of the space-time correlations in turbulent shear flows are determined by the convection velocity, the random sweeping velocity, and the shear-induced velocity. This model predicts a universal form of the spacetime correlations with the two characteristic velocities. The DNS of turbulent channel flows supports the prediction: the correlation functions exhibit a fair good collapse, when plotted against the normalized space and time separations defined by the elliptic model.

Performance analysis of bit error rate for free space optical communication with tip-tilt compensation based on gamma-gamma distribution

In this paper, the gamma-gamma probability distribution is used to model turbulent channels. The bit error rate (BER) performance of free space optical (FSO) communication systems employing on-off keying (OOK) or subcarrier binary phase-shift keying (BPSK) modulation format is derived. A tip-tilt adaptive optics system is also incorporated with a FSO system using the above modulation formats. The tip-tilt compensation can alleviate effects of atmospheric turbulence and thereby improve the BER performance. The improvement is different for different turbulence strengths and modulation formats. In addition, the BER performance of communication systems employing subcarrier BPSK modulation is much better than that of compatible systems employing OOK modulation with or without tip-tilt compensation.

Optimal guidance of low-thrust interplanetary space vehicles

The low-thrust guidance problem is defined as the minimum terminal variance (MTV) control of a space vehicle subjected to random perturbations of its trajectory. To accomplish this control task, only bounded thrust level and thrust angle deviations are allowed, and these must be calculated based solely on the information gained from noisy, partial observations of the state. In order to establish the validity of various approximations, the problem is first investigated under the idealized conditions of perfect state information and negligible dynamic errors. To check each approximate model, an algorithm is developed to facilitate the computation of the open loop trajectories for the nonlinear bang-bang system. Using the results of this phase in conjunction with the Ornstein-Uhlenbeck process as a model for the random inputs to the system, the MTV guidance problem is reformulated as a stochastic, bang-bang, optimal control problem. Since a complete analytic solution seems to be unattainable, asymptotic solutions are developed by numerical methods. However, it is shown analytically that a Kalman filter in cascade with an appropriate nonlinear MTV controller is an optimal configuration. The resulting system is simulated using the Monte Carlo technique and is compared to other guidance schemes of current interest.

Unsteady ejectors: The effect of driver jet mark-space ratio

mark Unsteady ejectors can be driven by a wide range of driver jets. These vary from pulse detonation engines, which typically have a long gap between each slug of fluid exiting the detonation tube (mark-space ratios in the range 0.1-0.2) to the exit of a pulsejet where the mean mass flow rate leads to a much shorter gap between slugs (mark-space ratios in the range 2-3). The aim of this paper is to investigate the effect of mark-space ratio on the thrust augmentation of an unsteady ejector. Experimental testing was undertaken using a driver jet with a sinusoidal exit velocity profile. The mean value, amplitude and frequency of the velocity profile could be changed allowing the length to diameter ratio of the fluid slugs L/D and the mark-space ratio (the ratio of slug length to the spacing between slugs) L/S to be varied. The setup allowed L/S of the jet to vary from 0.8 to 2.3, while the L/D ratio of the slugs could take any values between 3.5 and 7.5. This paper shows that as the mark-space ratio of the driver jet is increased the thrust augmentation drops. Across the range of mark-space ratios tested, there is shown to be a drop in thrust augmentation of 0.1. The physical cause of this reduction in thrust augmentation is shown to be a decrease in the percentage time over which the ejector entrains ambient fluid. This is the direct result ofthe space between consecutive slugs in the driver jet decreasing. The one dimensional model reported in Heffer et al. [1] is extended to include the effect of varying L/S and is shown to accurately capture the experimentally measured behavior ofthe ejector. Copyright © 2010 by the American Institute of Aeronautics and Astronautics, Inc.

Outage probability of the gaussian MIMO free-space optical channel with PPM

Atmospheric effects can significantly degrade the reliability of free-space optical communications. One such effect is scintillation, caused by atmospheric turbulence, refers to random fluctuations in the irradiance and phase of the received laser beam. In this paper we inv stigate the use of multiple lasers and multiple apertures to mitigate scintillation. Since the scintillation process is slow, we adopt a block fading channel model and study the outage probability under the assumptions of orthogonal pulse-position modulation and non-ideal photodetection. Assuming perfect receiver channel state information (CSI), we derive the signal-to-noise ratio (SNR) exponents for the cases when the scintillation is lognormal, exponential and gammagamma distributed, which cover a wide range of atmospheric turbulence conditions. Furthermore, when CSI is also available at the transmitter, we illustrate very large gains in SNR are possible (in some cases larger than 15 dB) by adapting the transmitted power. Under a long-term power constraint, we outline fundamental design criteria via a simple expression that relates the required number of lasers and apertures for a given code rate and number of codeword blocks to completely remove system outages. Copyright © 2009 IEEE.

Growth of Space Ordered on GaAs（100） Vicinal 1.3μm InAs Quantum Dots Substrates by MOCVD

Space ordered 1.3μm self-assembled InAs QDs are grown on GaAs（100） vicinal substrates by MOCVD. Photoluminescence measurements show that the dots on vicinal substrates have a much higher PL intensity and a narrower FWHM than those of dots on exact substrates, which indicates better material quality. To obtain 1.3μm emissions of InAs QDs, the role of the so called InGaAs strain cap layer （SCL） and the strain buffer layer （SBL） in the strain relaxation process in quantum dots is studied. While the use of SBL results only in a small change of emission wavelength,SCL can extend the QD＇s emission over 1.3μm due to the effective strain reducing effect of SCL.

Protein Docking by the Underestimation of Free Energy Funnels in the Space of Encounter Complexes

Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic global minimization of funnel-shaped energy functions in the space of rigid body motions (SE(3)) while accounting for flexibility of the interface side chains. The method, called semi-definite programming-based underestimation (SDU), employs a general quadratic function to underestimate a set of local energy minima and uses the resulting underestimator to bias further sampling. While SDU effectively minimizes functions with funnel-shaped basins, its application to docking in the rotational and translational space SE(3) is not straightforward due to the geometry of that space. We introduce a strategy that uses separate independent variables for side-chain optimization, center-to-center distance of the two proteins, and five angular descriptors of the relative orientations of the molecules. The removal of the center-to-center distance turns out to vastly improve the efficiency of the search, because the five-dimensional space now exhibits a well-behaved energy surface suitable for underestimation. This algorithm explores the free energy surface spanned by encounter complexes that correspond to local free energy minima and shows similarity to the model of macromolecular association that proceeds through a series of collisions. Results for standard protein docking benchmarks establish that in this space the free energy landscape is a funnel in a reasonably broad neighborhood of the native state and that the SDU strategy can generate docking predictions with less than 5 � ligand interface Ca root-mean-square deviation while achieving an approximately 20-fold efficiency gain compared to Monte Carlo methods.

Towards Improving the Utilisation of University Teaching Space

There is a perception that teaching space in universities is a rather scarce resource. However, some studies have revealed that in many institutions it is actually chronically under-used. Often, rooms are occupied only half the time, and even when in use they are often only half full. This is usually measured by the ‘utilization’ which is defined as the percentage of available ‘seat-hours’ that are employed. Within real institutions, studies have shown that this utilization can often take values as low as 20–40%. One consequence of such a low level of utilization is that space managers are under pressure to make more efficient use of the available teaching space. However, better management is hampered because there does not appear to be a good understanding within space management (near-term planning) of why this happens. This is accompanied, within space planning (long-term planning) by a lack of experise on how best to accommodate the expected low utilizations. This motivates our two main goals: (i) To understand the factors that drive down utilizations, (ii) To set up methods to provide better space planning. Here, we provide quantitative evidence that constraints arising from timetabling and location requirements easily have the potential to explain the low utilizations seen in reality. Furthermore, on considering the decision question ‘Can this given set of courses all be allocated in the available teaching space?’ we find that the answer depends on the associated utilization in a way that exhibits threshold behaviour: There is a sharp division between regions in which the answer is ‘almost always yes’ and those of ‘almost always no’. Through analysis and understanding of the space of potential solutions, our work suggests that better use of space within universities will come about through an understanding of the effects of timetabling constraints and when it is statistically likely that it will be possible for a set of courses to be allocated to a particular space. The results presented here provide a firm foundation for university managers to take decisions on how space should be managed and planned for more effectively. Our multi-criteria approach and new methodology together provide new insight into the interaction between the course timetabling problem and the crucial issue of space planning.

The notion of space in the artistic language of Alfredo Jaar

Conceptual art and communicator role has influenced the work of Chilean architect Alfredo Jaar, which has been proposed report, with other codes [verbal and nonverbal], global events influencing contemporary society. His early training as an architect has driven innovation in the design of artistic space , using the message to convey to the viewer the reason for his work for more than three decades, highlights the artistic composition with various material resources whose purpose lies in conceptualizing various topics relevant in considering the role of artistic communication. Jaar’s style is the sum of his own life experience in relation to the contradictions of the world today, which is exposed and from the perspective of postmodernism from the exploitation of the notion of space as an open stage for visual and expressiveness beyond national borders, societies and cultures of the world.

Creating Shared Public Space in the Contested City: The Role of Urban Design

This paper examines relevant characteristics of the ‘contested city’ and the concept of ‘public space’ in that problematic context. It offers an appraisal of the historical and contemporary role of urban design in shaping social space and interrogates the feasibility of using urban design to facilitate more integrated cityscapes. It presents detailed case studies of two ‘contested cities’, Nicosia and Belfast, based on content analysis of policy and planning documents, extensive site analyses in both places, interviews and seminar discussions with policy makers, planners, community and civic leaders. The paper comprises four dimensions—conceptual, descriptive, analytical and prescriptive—and in its final section identifies core values and relevant policies for the potential achievement of shared space in contested cities.

Architecture in Cinema: A Relation of Representation Based on Space

Architecture, whether in the foreground or background, is an intrinsic part of any film, and cinema holds a position as a transformative reference in contemporary architecture. This book addresses the role of architecture in cinema, and through a focus on the use of space, it presents a critical overview of the relation between the two. Through framing, flattening and editing, cinematic space, as the representation of architectural space, focuses on its certain qualities, while eliminating others. Thus, cinema emphasizes individual aspects of space that may be overlooked when the whole context is considered. Space 'acts' in the foreground rather than simply filling the background in the films of Peter Greenaway and Wim Wenders, which are used to analyze two significant cinematic approaches to space, space as form and space as symbol. The detailed analysis of Greenaway's The Belly of an Architect and Wenders' Der Himmel über Berlin (Wings of Desire) offers an innovative and original perspective on space to those interested in both fields of architecture and film studies.

Re-imaging the Periphery: The Reproduction of Space in Cairo

This chapter examines Cairo’s path towards reassembling a modern spatial order in one of its oldest quarters, Bulaq Abul Ela, and the implications of this on the spatial experience of its inhabitants. The ambitions of space reproduction in Cairo are revealed during the attempt to engender a debate as to how this vision affected Bulaq’s riverfront zone as its periphery; how it was spatialised and to what extent the planners’ conception of urban space actually responded to the people’s needs when creating a new spatial reality. It uncovers the peripheral/central position that residents assume with regards to their living spaces to reveal new meanings, images, stories and places to replace the increasingly undesirable authentic fabric of Bulaq.

Reliability Assessment of 3-D Space Frame Structures Applying Stochastic Finite Element Analysis

Throughout design development of satellite structure, stress engineer is usually challenged with randomness in applied loads and material properties. To overcome such problem, a risk-based design is applied which estimates satellite structure probability of failure under static and thermal loads. Determining probability of failure can help to update initially applied factors of safety that were used during structure preliminary design phase. These factors of safety are related to the satellite mission objective. Sensitivity-based analysis is to be implemented in the context of finite element analysis (probabilistic finite element method or stochastic finite element method (SFEM)) to determine the probability of failure for satellite structure or one of its components.

Bringing down the walls: Is the notion of ‘promoting shared space’ commensurate with effective transformation of contested places in Belfast?

This article is a reflexive and critical examination of recent empirical research on effective practice in the management and ‘transformation’ of contested urban space at sectarian interfaces in Belfast. By considering the development of interfaces, the areas around them and policy responses to their persistence, the reality of contested space in the context of ‘peace building’ is apparent; with implications for local government as central to the statutory response. Belfast has developed an inbuilt absence of connectivity; where freedom of movement is particularly restricted and separation of contested space is the policy default position. Empirical research findings focus attention on the significance of social and economic regeneration and fall into three specific areas that reflect both long-term concerns within neighbourhoods and the need for adequate policy responses and action ‘on the ground’. Drawing on Elden and Sassen we reconfigure the analytical framework by which interfaces are defined, with implications for policy and practice in post-conflict Belfast. Past and current policy for peace-building in Northern Ireland, and transforming the most contested space, at interfaces in Belfast, is deliberately ambiguous and offers little substance having failed to advance from funding-led linguistic compliance to a sustainable peace-building methodology.