Biological water: Femtosecond dynamics of macromolecular hydration

The unique features of a macromolecule and water as a solvent make the issue of solvation unconventional, with questions about the static versus dynamic nature of hydration and the, physics of orientational and translational diffusion at the boundary. For proteins, the hydration shell that covers the surface is critical to the stability of its structure and function. Dynamically speaking, the residence time of water at the surface is a signature of its mobility and binding. With femtosecond time resolution it is possible to unravel the shortest residence times which are key for the description of the hydration layer, static or dynamic. In this article we review these issues guided by experimental studies, from this laboratory, of polar hydration dynamics at the surfaces of two proteins (Subtilisin Carlsberg (SC) and Monellin). The natural probe tryptophan amino acid was used for the interrogation of the dynamics, and for direct comparison we also studied the behavior in bulk water - a complete hydration in 1 ps. We develop a theoretical description of solvation and relate the theory to the experimental observations. In this - theoretical approach, we consider the dynamical equilibrium in the hydration shell, defining the rate processes for breaking and making the transient hydrogen bonds, and the effective friction in the layer which is defined by the translational and orientational motions of water molecules. The relationship between the residence time of water molecules and the observed slow component in solvation dynamics is a direct one. For the two proteins studied, we observed a "bimodal decay" for the hydration correlation function, with two primary relaxation times: ultrafast, typically 1 ps or less, and longer, typically 15-40 ps, and both are related to the residence time at the protein surface, depending on the binding energies. We end by making extensions to studies of the denatured state of the protein, random coils, and the biomimetic micelles, and conclude with our thoughts on the relevance of the dynamics of native structures to their functions.

Discovery of Application Workloads from Network File Traces

An understanding of application I/O access patterns is useful in several situations. First, gaining insight into what applications are doing with their data at a semantic level helps in designing efficient storage systems. Second, it helps create benchmarks that mimic realistic application behavior closely. Third, it enables autonomic systems as the information obtained can be used to adapt the system in a closed loop.All these use cases require the ability to extract the application-level semantics of I/O operations. Methods such as modifying application code to associate I/O operations with semantic tags are intrusive. It is well known that network file system traces are an important source of information that can be obtained non-intrusively and analyzed either online or offline. These traces are a sequence of primitive file system operations and their parameters. Simple counting, statistical analysis or deterministic search techniques are inadequate for discovering application-level semantics in the general case, because of the inherent variation and noise in realistic traces.In this paper, we describe a trace analysis methodology based on Profile Hidden Markov Models. We show that the methodology has powerful discriminatory capabilities that enable it to recognize applications based on the patterns in the traces, and to mark out regions in a long trace that encapsulate sets of primitive operations that represent higher-level application actions. It is robust enough that it can work around discrepancies between training and target traces such as in length and interleaving with other operations. We demonstrate the feasibility of recognizing patterns based on a small sampling of the trace, enabling faster trace analysis. Preliminary experiments show that the method is capable of learning accurate profile models on live traces in an online setting. We present a detailed evaluation of this methodology in a UNIX environment using NFS traces of selected commonly used applications such as compilations as well as on industrial strength benchmarks such as TPC-C and Postmark, and discuss its capabilities and limitations in the context of the use cases mentioned above.

In-situ measurements of concentration and temperature during transient solidification of aqueous solution of ammonium chloride using laser interferometry

The variation in temperature and concentration plays a crucial role in predicting the final microstructure during solidification of a binary alloy. Most of the experimental techniques used to measure concentration and temperature are intrusive in nature and affect the flow field. In this paper, the main focus is laid on in-situ, non-intrusive, transient measurement of concentration and temperature during the solidification of a binary mixture of aqueous ammonium chloride solution (a metal-analog system) in a top cooled cavity using laser based Mach-Zehnder Interferometric technique. It was found from the interferogram, that the angular deviation of fringe pattern and the total number of fringes exhibit significant sensitivity to refractive index and hence are functions of the local temperature and concentration of the NH4Cl solution inside the cavity. Using the fringe characteristics, calibration curves were established for the range of temperature and concentration levels expected during the solidification process. In the actual solidification experiment, two hypoeutectic solutions (5% and 15% NH4Cl) were chosen. The calibration curves were used to determine the temperature and concentration of the solution inside the cavity during solidification of 5% and 15% NH4Cl solution at different instants of time. The measurement was carried out at a fixed point in the cavity, and the concentration variation with time was recorded as the solid-liquid interface approached the measurement point. The measurement exhibited distinct zones of concentration distribution caused by solute rejection and Rayleigh Benard convection. Further studies involving flow visualization with laser scattering confirmed the Rayleigh Benard convection. Computational modeling was also performed, which corroborated the experimental findings. (C) 2011 Elsevier Ltd. All rights reserved.

Implications of program phase behavior on timing analysis

Knowledge about program worst case execution time (WCET) is essential in validating real-time systems and helps in effective scheduling. One popular approach used in industry is to measure execution time of program components on the target architecture and combine them using static analysis of the program. Measurements need to be taken in the least intrusive way in order to avoid affecting accuracy of estimated WCET. Several programs exhibit phase behavior, wherein program dynamic execution is observed to be composed of phases. Each phase being distinct from the other, exhibits homogeneous behavior with respect to cycles per instruction (CPI), data cache misses etc. In this paper, we show that phase behavior has important implications on timing analysis. We make use of the homogeneity of a phase to reduce instrumentation overhead at the same time ensuring that accuracy of WCET is not largely affected. We propose a model for estimating WCET using static worst case instruction counts of individual phases and a function of measured average CPI. We describe a WCET analyzer built on this model which targets two different architectures. The WCET analyzer is observed to give safe estimates for most benchmarks considered in this paper. The tightness of the WCET estimates are observed to be improved for most benchmarks compared to Chronos, a well known static WCET analyzer.

Mapping joint ROM on a cube using electromagnetic trackers

This paper presents a unified framework using the unit cube for measurement, representation and usage of the range of motion (ROM) of body joints with multiple degrees of freedom (d.o.f) to be used for digital human models (DHM). Traditional goniometry needs skill and kn owledge; it is intrusive and has limited applicability for multi-d.o.f. joints. Measurements using motion capture systems often involve complicated mathematics which itself need validation. In this paper we use change of orientation as the measure of rotation; this definition does not require the identification of any fixed axis of rotation. A two-d.o.f. joint ROM can be represented as a Gaussian map. Spherical polygon representation of ROM, though popular, remains inaccurate, vulnerable due to singularities on parametric sphere and difficult to use for point classification. The unit cube representation overcomes these difficulties. In the work presented here, electromagnetic trackers have been effectively used for measuring the relative orientation of a body segment of interest with respect to another body segment. The orientation is then mapped on a surface gridded cube. As the body segment is moved, the grid cells visited are identified and visualized. Using the visual display as a feedback, the subject is instructed to cover as many grid cells as he can. In this way we get a connected patch of contiguous grid cells. The boundary of this patch represents the active ROM of the concerned joint. The tracker data is converted into the motion of a direction aligned with the axis of the segment and a rotation about this axis later on. The direction identifies the grid cells on the cube and rotation about the axis is represented as a range and visualized using color codes. Thus the present methodology provides a simple, intuitive and accura te determination and representation of up to 3 d.o.f. joints. Basic results are presented for the shoulder. The measurement scheme to be used for wrist and neck, and approach for estimation of the statistical distribution of ROM for a given population are also discussed.

COMPARISON AND CROSS-VALIDATION OF OPTICAL TECHNIQUES IN DIFFERENT SWIRL SPRAY REGIMES

This paper deals with an experimental study of pressure-swirl hydraulic injector nozzles using non-intrusive optical techniques. Experiments were conducted to study atomization characteristics using two nozzles with different orifice diameters, 0.3 mm and 0.5 mm, and injection pressures, 0.3-3.5 Mpa, which correspond to Reynolds number (Re-p) = 7,000-45,000, depending on nozzle utilized. Three laser diagnostic techniques were utilized: Shadowgraph, PIV (Particle Image Velocimetry), and PDPA (Phase Doppler Particle Anemometry). Measurements made in the spray in both axial and radial directions indicate that velocity, average droplet diameter profiles, and spray dynamics are highly dependent on the nozzle characteristics and injection pressure. Limitations of these techniques in the different flow regimes, related to the primary and secondary breakups as well as coalescence, are provided. Results indicate that all three techniques provide similar results throughout the different regimes. Shadowgraph and PDPA were possible in the secondary atomization and coalescence regimes while PIV measurements could be made only at the end of secondary atomization and coalescence.

THE EFFECTS OF SURFACTANT ON SIMPLEX NOZZLE SPRAY BEHAVIOR AND ITS COMPARISON TO LIQUID FUELS

Pressure-swirl nozzles (simplex nozzles) are used in various field applications such as aero-engines, power generation, spray painting and agricultural irrigation. For this particular nozzle, research in the past decade has dealt with the development of numerical models for predicting droplet distribution profiles. Although these results have been valuable, the experimental results have been contradictory, therefore fundamental understanding of the influence of properties in nozzle is important. This paper experimentally investigates the effect of surfactants on breakup and coalescence. Since most of the fuels and biofuels have low surface tension compared to water, a comparative analysis between a surfactant solution and a liquid fuel is imperative. For this experimental study, a simplex nozzle characterized as flow number 0.4 will be utilized. The injection pressures will range from 0.3 - 4Mpa while altering the surface tension from 72 to 28mN/m. By applying Phase Doppler Particle Anemometry (PDPA) which is a non-intrusive laser diagnostic technique, the differences in spray characteristics due to spray surface tension can be highlighted. The average droplet diameter decreases for a low surface tension fluid in the axial direction in comparison to pure water. The average velocity of droplets is surprisingly lower in the same spray zone. Measurements made in the radial direction show no significant changes, but at the locations close to the nozzle, water droplets have larger diameter and velocity. The results indicate the breakup and coalescence regimes have been altered when surface tension is lowered. A decrease in surface tension alters the breakup length while increasing the spray angle. Moreover, higher injection pressure shortens the breakup length and decrease in overall diameter of the droplets. By performing this experimental study the fundamentals of spray dynamics, such as spray formation, liquid breakup length, and droplet breakup regimes can be observed as a function of surface tension and how a surrogate fuel compares with a real fuel for experimental purposes. This knowledge potentially will lead to designing a better atomizer or new biofuels.

A Full Body Steerable Wind Display for a Locomotion Interface

This paper presents the Treadport Active Wind Tunnel (TPAWT)-a full-body immersive virtual environment for the Treadport locomotion interface designed for generating wind on a user from any frontal direction at speeds up to 20 kph. The goal is to simulate the experience of realistic wind while walking in an outdoor virtual environment. A recirculating-type wind tunnel was created around the pre-existing Treadport installation by adding a large fan, ducting, and enclosure walls. Two sheets of air in a non-intrusive design flow along the side screens of the back-projection CAVE-like visual display, where they impinge and mix at the front screen to redirect towards the user in a full-body cross-section. By varying the flow conditions of the air sheets, the direction and speed of wind at the user are controlled. Design challenges to fit the wind tunnel in the pre-existing facility, and to manage turbulence to achieve stable and steerable flow, were overcome. The controller performance for wind speed and direction is demonstrated experimentally.