bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effects of Solvent and Anharmonicity on Incoherent Inelastic Neutron Scattering Spectra of Proteins
Authors: Kitao Akio , Takeda Masaki
Published: November 2002

We investigated the protein energy landscape using molecular dynamics simulation and normal mode analysis. The dynamical structure factor of a protein, staphylococcal nuclease (SNase), is calculated from the model calculations based on the Jumping-Among-Minima (JAM) model. In this model, the protein dynamics is described in terms of two types of motions: intra- and inter-substate motions. These results are compared in order to investigate the effects of solvent and anharmonicity on protein dynamics. From the comparison of the structure factors, we derive information on the nature of the dynamics in the low frequency region.
Backscattering Spectrometers at the ESS
Authors: Andersen K.H.
Published: November 2002

Calculations are presented for backscattering spectrometers under consideration for the ESS. In particular, novel instrumentation concepts such as pulse-shaping choppers and ballistic guides are considered. Instruments covering energy resolutions from 1 to 10 µeV are presented and their expected performance at the ESS is compared to existing instruments. For µeV energy resolutions, the combination of a coupled moderator and a pulse-shaping chopper is shown to perform well compared to the conventional poisoned-moderator instrument.
Neutron Spin Echo Studies on Poly(Vinyl Alcohol) Gel in a Mixture of Dimethyl Sulfoxide and Water
Authors: Kanaya T. , Takahashi N. , Nishida K. , Kaji K. , Seto H. , Nagao M. , Kawabata Y. , Takeda T.
Published: November 2002

Dynamics of poly(vinyl alcohol) (PVA) gel have been investigated using a neutron spin echo technique. The intermediate scattering function I(Q,t) of the gel shows a very rapid decay and a non-decaying component in time ranges shorter and longer than about 3 ns, respectively, in the Q range of 0.03–0.1 Å−1. This Q range corresponds to the so-called Porod’s region, suggesting that we are seeing the dynamics of cross-linking points of the gel. We therefore analyzed the data assuming that the cross-linking point performs a random motion in a restricted region around its quasi-equilibrium position.
Temperature- and Pressure-dependences of Shape Fluctuations in a Ternary Microemulsion System
Authors: Kawabata Youhei , Seto Hideki , Nagao Michihiro , Takeda Takayoshi
Published: November 2002

Shape fluctuations in a microemulsion system composed of Aerosol-OT (AOT), D2O and deuterated decane were investigated by means of neutron spin echo. In this system, a water-in-oil droplet structure at ambient temperature and pressure decomposes into two-phases, both with increasing temperature and pressure. However, its dynamical behavior was different. The observed effective diffusion constant of the droplet shape fluctuation increased with increasing temperature, while it decreased with increasing pressure. Temperature- and pressure-dependences of a bending modulus of AOT monolayers were estimated, and it was confirmed that AOT monolayers become floppy with increasing temperature and stiff with increasing pressure.
Observation of Concentration Fluctuations in Polymer Gels Performed by Neutron Spin Echo
Authors: Koizumi Satoshi , Monkenbusch Michael , Richter Dieter , Schwahn Dietmar , Farago Bela , Annaka Masahiko
Published: November 2002

We applied these methods of small-angle neutron scattering (SANS) and neutron spin echo (NSE) on a swollen poly (N-isopropyl acrylamide) (NIPA) gel in order to observe the elastic scattering of frozen concentration fluctuations due to crosslinks. We successfully obtained the structure factor for the frozen concentration fluctuations in a q-domain of q > 0.01 A−1 while in a q-domain of q < 0.01 A−1; this attempt failed due to the limited performance of the q-resolution and the Fourier time tF of the current specifications of the NSE spectrometers. This technical hurdle for the spectrometer should be overcome on an intensified neutron source for the next generation, realizing tF of µs-order and the q-resolution down closer to 0.001 A−1.
Interaction between Polymer and Surfactant Mesophases
Authors: Lal Jyotsana
Published: November 2002

The interaction of polymers with flexible surfactant layers may modify strongly the elasticity and fluctuations of the layers. This effect has been studied in two surfactant mesophases. Neutron Spin Echo (NSE) spectroscopy was used to probe the modification of membrane fluctuations first in the case of dilute microemulsion droplets both in the presence and absence of polymer. A second example studied more recently was hydrophobically modified polymers (polysoaps) interacting with fluctuating lamellar bilayers of a nonionic surfactant.
Optimisation of Data Collection and Processing for Efficient Strain Scanning
Authors: Webster P.J. , Kang W.P.
Published: November 2002

A constraint to the academic and industrial exploitation of neutron strain scanning is its cost in relation to that of alternative techniques. Generally, a large proportion of the resource cost is that for beam-time. The efficient utilisation of beam-time can be enhanced by optimising data collection and processing. The selection of three principal related factors — detector range, angular step size and the counting time — determines the data quality and uncertainties in defining the Bragg peak parameters required to determine strain. Theoretical and numerical analysis of computed and experimental data are used to establish a general set of well-founded, semi-empirical but theoretically-based, practical “rules of thumb” to be used when making strain measurements to a specified statistical uncertainty. The “rules” apply mostly to constant wavelength techniques where the angular position and other profile parameters of a single symmetrical Bragg peak are required but have relevance for fixed angle time-of-flight methods.
A Contraction‐based Ratio‐cut Partitioning Algorithm
Authors: Saab Youssef
Published: November 2002

Partitioning is a fundamental problem in the design of VLSI circuits. In recent years, ratio‐cut partitioning has received attention due to its tendency to partition circuits into their natural clusters. Node contraction has also been shown to enhance the performance of iterative partitioning algorithms. This paper describes a new simple ratio‐cut partitioning algorithm using node contraction. This new algorithm combines iterative improvement with progressive cluster formation. Under suitably mild assumptions, the new algorithm runs in linear time. It is also shown that the new algorithm compares favorably with previous approaches.
Improving Datapath Testability by Modifying Controller Specification
Authors: Flottes M. L. , Rouzeyre B. , Volpe L.
Published: November 2002

A digital circuit includes two main parts: a controller and a datapath. After connection of these two parts, both are subject to a sharp fall in testability due to the lack of controllability and observability at the interface. In this paper, we propose a method for specifying the control part in order to restore the testability of the datapath to a level close to the initial one, in other words its testability before connection. This testability driven specification affects the next state logic as well as the decoder part of the controller but does not make use of any scan‐based element. Based on the finite automata theory and on results of a testability analysis performed on the datapath, the proposed method entails very little area penalty.
A Synthesizable VHDL Model of the Exact Solution for Three‐dimensional Hyperbolic Positioning System
Authors: Bucher Ralph , Misra D.
Published: November 2002

This paper presents a synthesizable VHDL model of a three‐dimensional hyperbolic positioning system algorithm. The algorithm obtains an exact solution for the three‐dimensional location of a mobile given the locations of four fixed stations (like a global positioning system [GPS] satellite or a base station in a cell) and the signal time of arrival (TOA) from the mobile to each station. The detailed derivation of the steps required in the algorithm is presented. A VHDL model of the algorithm was implemented and simulated using the IEEE numeric_std package. Signals were described by a 32‐bit vector. Simulation results predict location of the mobile is off by 1 m for best case and off by 36 m for worst case. A C + + program using real numbers was used as a benchmark for the accuracy and precision of the VHDL model. The model can be easily synthesized for low power hardware implementation.
Reduction of Power Dissipation in Dynamic BiCMOS Logic Gates by Transistor Reordering
Authors: Hasan S. M. Rezaul , Wahab Yufridin
Published: November 2002

This paper explores the deterministic transistor reordering in low‐voltage dynamic BiCMOS logic gates, for reducing the dynamic power dissipation. The constraints of load driving (discharging) capability and NPN turn‐on delay for MOSFET reordered structures has been carefully considered. Simulations shows significant reduction in the dynamic power dissipation for the transistor reordered BiCMOS structures. The power‐delay product figure‐of‐merit is found to be significantly enhanced without any associated silicon‐area penalty. In order to experimentally verify the reduction in power dissipation, original and reordered structures were fabricated using the MOSIS 2 μm N‐well analog CMOS process which has a P‐base layer for bipolar NPN option. Measured results shows a 20% reduction in the power dissipation for the transistor reordered structure, which is in close agreement with the simulation.
Simultaneous Buffer‐sizing and Wire‐sizing for Clock Trees Based on Lagrangian Relaxation
Authors: Lee Yu-Min , Chen Charlie Chung-Ping , Chang Yao-Wen , Wong D. F.
Published: November 2002

Delay, power, skew, area and sensitivity are the most important concerns in current clock‐tree design. We present in this paper an algorithm for simultaneously optimizing the above objectives by sizing wires and buffers in clock trees. Our algorithm, based on Lagrangian relaxation method, can optimally minimize delay, power and area simultaneously with very low skew and sensitivity. With linear storage overall and linear runtime per iteration, our algorithm is extremely economical, fast and accurate; for example, our algorithm can solve a 6201‐wire‐segment clock‐tree problem using about 1‐minute runtime and 1.3‐MB memory and still achieve pico‐second precision on an IBM RS/6000 workstation.
Performance Driven Global Routing Through Gradual Refinement
Authors: Hu Jiang , Sapatnekar Sachin S.
Published: November 2002

We propose a heuristic for VLSI interconnect global routing that can optimize routing congestion, delay and number of bends, which are often competing objectives. Routing flexibilities under timing constraints are obtained and exploited to reduce congestion subject to timing constraints. The wire routes are determined through gradual refinement according to probabilistic estimation on congestions so that the congestion is minimized while the number of bends on wires is limited. The experiments on both random generated circuits and benchmark circuits confirm the effectiveness of this method.
CMOS Delay and Power Model Equations for Simultaneous Transistor and Interconnect Wire Analysis and Optimization
Authors: Lee Sangho , Greeneich Edwin W.
Published: November 2002

Efficient, generalized delay and power equations are proposed for large scale CMOS circuit analysis and optimization achieved by transistor and interconnect wire minimization. The proposed model equations are used to analyze the entire power‐delay trade‐off with less complexity and faster computation time. New equations can be adopted to perform the optimization of transistor and interconnect wire size concurrently. A single stage CMOS circuit and a clock generation block fabricated in 0.48 um CMOS process are given as experimental examples.
Timing‐Driven‐Testable Convergent Tree Adders
Authors: Huang Johnnie A. , Chen Chien-In Henry
Published: November 2002

Carry lookahead adders have been, over the years, implemented in complex arithmetic units due to their regular structure which leads to efficient VLSI implementation for fast adders. In this paper, timing‐driven testability synthesis is first performed on a tree adder. It is shown that the structure of the tree adder provides for a high fanout with an imbalanced tree structure, which likely contributes to a racing effect and increases the delay of the circuit. The timing optimization is then realized by reducing the maximum fanout of the adder and by balancing the tree circuit. For a 56‐b testable tree adder, the optimization produces a 6.37%increase in speed of the critical path while only contributing a 2.16% area overhead. The full testability of the circuit is achieved in the optimized adder design.
Using Temporal and Functional Information in Crosstalk Aware Static Timing Analysis
Authors: Xiao Tong , Marek-Sadowska Malgorzata
Published: November 2002

Crosstalk‐induced delay in deep sub‐micron digital circuits can be quite significant and difficult to determine because of dependency on neighboring signals. In this paper we study the problem of incorporating temporal and functional information to improve the accuracy of crosstalk aware static timing analysis. We propose an efficient method to compute a signal′s earliest and latest arrival times when timing windows and slew rate ranges are known for its inputs and its coupling neighbors′ inputs. We show that iteratively updating timing windows is necessary when signals on the same path are mutually coupled. The accuracy of static timing analysis can be further improved by our functional correlation analysis. The proposed techniques have been applied in crosstalk aware static timing analysis, which can guide timing‐driven layout synthesis and quick timing verification in deep submicron technologies. Experimental results demonstrate that the proposed methods significantly reduce the pessimism in predicting circuit performance.
A New Characterization Method for Delay and Power Dissipation of Standard Library Cells
Authors: Sulistyo Jos B. , Ha Dong S.
Published: November 2002

A simplified method for characterization of standard library cells based on the linear delay model is presented in this paper. The linear model is chosen as it allows rapid characterization with a modest number of simulations, while achieving acceptable accuracy. All the parameters of cell delays are defined as 50%‐to‐50% delays, as distinguished from 50%‐to‐threshold or threshold‐to‐50% often used in commercial tools. We found that the 50%‐to‐50% definition of delays is more consistent and leads to closed‐form formula. A subset of library cells in a 0.25 μm technology was characterized using the proposed technique. A test circuit was subsequently generated and simulated to determine the accuracy of the proposed characterization method. SPICE simulations on the test circuit show that the timing estimations obtained through the proposed method is accurate to within 5.6%, and the power estimation was accurate to 4.2%, ignoring parasitics on interconnections.
A Comparison of Modern Hyperbolic Methods for Semiconductor Device Simulation: NTK Central Scheme Vs. CLAWPACK
Authors: Gardner Carl L. , Gelb Anne , Hernandez Justin
Published: November 2002

Two modern hyperbolic methods—a second‐order Godunov method in the software package CLAWPACK and the second‐order Nessyahu–Tadmor–Kurganov (NTK) central scheme—are compared for simulating an electron shock wave in the classical hydrodynamic model for semiconductor devices.

The NTK central scheme, which does not employ Riemann problem solutions, is described in detail. Special attention is paid in both methods to handling the source terms in the hydrodynamic model. CLAWPACK incorporates the source terms by a splitting method, while our version of the NTK scheme is unsplit.
Particle‐based Full‐band Approach for Fast Simulation of Charge Transport in Si, GaAs, and InP
Authors: Saraniti Marco , Hu Yibing , Goodnick Stephen M.
Published: November 2002

We discuss the application of the fullband cellular automaton (CA) method for the simulation of charge transport in several semiconductors. Basing the selection of the state after scattering on simple look‐up tables, the approach is physically equivalent to the full band Monte Carlo (MC) approach but is much faster. Furthermore, the structure of the pre‐tabulated transition probabilities naturally allows for an extension of the model to fully anisotropic scattering without additional computational burden. Simulation results of transport of electrons and holes in several materials are discussed, with particular emphasis on the transient response of photo‐generated carriers in InP and GaAs. Finally, a discussion on parallel algorithms is presented, for the implementation of the code on workstation clusters.
Integration of the Density Gradient Model into a General Purpose Device Simulator
Authors: Wettstein Andreas , Penzin Oleg , Lyumkis Eugeny
Published: November 2002

A generalized Density Gradient model has been implemented into the device simulator Dessis [DESSIS 7.0 reference manual (2001). ISE Integrated Systems Engineering AG, Balgriststrasse 102, CH‐8008 Zürich].We describe the multidimensional discretization scheme used and discuss our modifications to the standard Density Gradient model. The evaluation of the model shows good agreement to results obtained by the Schro¨dinger equation.
A Comparison of Resonant Tunneling Based on Schrödinger′s Equation and Quantum Hydrodynamics
Authors: Ben Abdallah Naoufel , Pinaud Olivier , Gardner Carl L. , Ringhofer Christian
Published: November 2002

Smooth quantum hydrodynamic (QHD) model simulations of the current–voltage curve of a resonant tunneling diode at 300K are compared with that predicted by the mixed‐state Schrödinger equation approach. Although the resonant peak for the QHD simulation occurs at 0.15V instead of the Schrödinger equation value of 0.2V, there is good qualitative agreement between the current–voltage curves for the two models, including the predicted peak current values.
Fresh Water Fish Habitat Science and Management in India
Authors: Ghosh S. K. , Ponniah A. G.
Published: November 2002

India is a land of diverse topography, climate and natural resource. There are 12 major rivers and 48 lesser rivers with a total catchment area of 277.6 million hectares. The fresh water resources of the country which are varied harbor 587 species of finfish and account for 9.3 percent of global inland fish production. India's natural capital of fish habitat resource has been eroded as reflected in loss of bio-diversity and reduced fish landings. Studies on the ecology, environment and fisheries of five major river systems in addition to reservoirs and flood plain lake fisheries have been conducted with greater focus on water quality and less on physical habitat parameters.

The Central Water Commission is responsible for development of all freshwater bodies whereas, the National River Conservation Directorate is responsible for river conservation. River conservation programs cover major rivers in 10 States of the country, the ‘Ganga Action Plan’ being the most important. These projects target improvement in water quality and not fish habitat improvement. Lack of concern for fish habitat is reflected in the planning of Farakka barrage on the river Ganga (The Ganges) and its impact on ‘Hilsa’ run. Environmental laws have not achieved desired objectives for lack of enforcement mechanisms. Fishery scientists and resource users are not involved in the river conservation program.

The fresh water habitat management situation in India evokes both concern and hope. Concern arises out of the missing elements in the existing fish habitat research, planning and management of resource. The hope for the future is our increasing awareness of the need for better resource management and environmental conservation. India has a responsibility to conserve these natural assets for future generations. Potential steps are outlined.
Fish Habitat Science and Management in Finnish Freshwaters
Authors: Jurvelius Juha , Auvinen Heikki
Published: November 2002

The area of Finnish inland waters is 33,500 km2. Forty fish species, eleven of them indigenous, have been encountered in the area. The annual catch from inland fisheries is around 40,000 metric tons. The largest changes in fish habitats in Finnish inland waters have been caused by hydropower construction and timber-floating in rivers, and eutrophication and water level regulation in lakes. River-spawning fish species have lost their spawning habitats or access to spawning sites. In many lakes, eutrophication together with selective gill-net fishing has shifted the fish assemblages towards dominance by cyprinids and other small-sized plankton feeders. Acid precipitation has affected fish stocks in ca. 1% of the 56,000 lakes. Acidification has decreased during the past decade. The management and use of water resources is regulated by the Water Act. To meet the requirements of the Act, e.g., in water construction works the use of the best available techniques (BAT) is required. Enhancement of fish habitats and natural reproduction is gaining importance in fisheries management instead of or together with stocking of young fish. Timber-floating has ceased in streams and rivers, and rehabilitation programs for fishery purposes have been carried out. Habitat-hydraulic models have been used to guide rehabilitation programs in rivers to meet the needs of juvenile salmonids. In lakes, eutrophication from point sources have been reduced. Reduction of non-point loads is now in the focus. Modelling of interactions in fish community, fishing and stocking has given promising results in fisheries management. Water level regulation practices that take into account the survival of fish eggs and larvae are considered in large reservoirs and lakes. In the future, the dynamics of ecosystems should be given more emphasis to mitigate the combined effects of anthropogenic influences on fish habitats and communities.
Science for freshwater fish habitat management in Canada: Current status and future prospects
Authors: Minns Charles K.
Published: November 2002

Canada's diverse freshwaters support a rich biodiversity of more than 200 species. Canada has strong legislation capable of conserving and protecting freshwaters habitats. Fish are a key driver and indicator for restoration and conservation efforts. Many of Canada's freshwater species in Canada are thought to be at risk.

Apart species such as brook trout, lake trout, walleye, and yellow perch, the ecology and habitat requirements of most freshwater species are poorly known. Studies have mainly been descriptive and comparative but experimental, ecosystem-scale integration, and modelling activities are increasing. While science related to fish and their habitats is growing, little is focused on the links between the production and dynamics of fish populations and communities, and the supply and distribution of habitats at various scales.

Habitat management is still mainly reactive, assessing development at the site-level with considerable uncertainty about the mitigation and compensation actions approved to offset habitat losses and modifications. Communication between science and management is improving. Canada has invested much energy on cumulative impact assessment but effective methods for tracking cumulative change and the interaction of multiple stresses have not emerged. Nonetheless there is a broad consensus on the need to take an ecosystem-based approach to sustainable use of Canada's natural renewable resources, including freshwaters and their fish. Management needs to shift to a more proactive approach supported by better deployment of available science and scientific methods. Science should emphasize quantitative whole ecosystem studies of fish and habitat especially the development of models and experimental manipulations.

If current trends of fish habitat loss are maintained in Canada, further declines in the quality and diversity of freshwater fish resources are certain despite our apparent natural wealth. Modest investments in securing the future of its freshwater fishery resources based on scientific advice may yet begin movement toward an ecologically sustainable future.
Spatial Characterization of Water Quality in Seven Eastern Kentucky Reservoirs Using Multivariate Analyses
Authors: Davis Stephen E. , Reeder Brian C.
Published: November 2002

We conducted water quality surveys along seven eastern Kentucky reservoirs three times during the 1994 growing season in order to understand the spatial variability within and between impoundments from a common geological setting. Sixteen parameters were measured at sites along the reservoirs representing each zone (riverine, transition, or lacustrine), and eight of these parameters displayed a statistically significant site/zone effect. Most of these were particle-associated parameters (total Fe, NH4+, total suspended solids, and total phosphorus) that decreased significantly down-reservoir. Water transparency increased significantly down-reservoir, in accordance with this pattern. Temperature and dissolved oxygen also showed a significant spatial effect, as temperature was highest towards the riverine end and dissolved oxygen was highest at the lacustrine end. Six parameters showed significant variability among these reservoirs, including ammonium and chlorophyll a. The remaining four (conductivity, sulfate, alkalinity and pH) displayed similar patterns across reservoirs apparently as a result of local geologic attributes. Another goal of this work was to use a multivariate statistical approach to aid in understanding the relationships between water quality parameters in this region and to group zones within a reservoir according to their similarities in water quality. Principal Components Analysis reduced sixteen parameters to five principal components that accounted for 74 percent of the total variability in water quality. Two of these principal components contained all of the particle-associated and local-geologic parameters, and accounted for 42% of the total variability. Cluster analyses showed that the water quality signatures of two reservoirs were quite different from the rest. Interestingly, these represented the most pristine and most disturbed watersheds of all seven systems. Our findings are relevant to the management of these and other similar reservoir systems.
Organochlorine contamination in the fish of the River Ganges, India
Authors: Kumari Anupma , Sinha R. K. , Gopal Krishna
Published: November 2002

Concentrations of persistent organochlorine residues were measured in economically important fish of the River Ganges from different locations in Bihar. The contamination pattern of organochlorines in fishes from several locations was Dichlorodiphenyltrichloroethanes (DDTs) >Hexachlorocyclohexanes (HCHs) >aldrin>endosulfan. The average wet weight concentrations in the muscles of fishes was; DDTs, 13.6 to 1665.9 ng g-1; HCHs, 115.8 to 1206.8 ng g-1; aldrin, 3.1 to 86.1 ng g-1; and endosulfan 2.9 to 74.5 ng g-1. The study indicates that organochlorine contaminants are still entering the Ganges river system, and suggests that the human population that consumes contaminated fish from the river may be at risk from those contaminants.
ElectRelease – electrically disbonding epoxy adhesive
Authors: Haydon Donald
Published: November 2002

ElectRelease was originally developed to temporarily bond monitoring instruments to supersonic fighter aircraft permitting subsequent disbonding without surface damage or marking. ElectRelease is an electrically disbonding epoxy adhesive. Article describes the development of the adhesive and its properties and applications.
Rapid manufacturing advances at Loughborough
Authors: Rooks Brian
Published: November 2002

An outline of the current activities in the Rapid Manufacturing (RM) Group at Loughborough University, one of the new Innovation Research Centres funded by the Engineering and Physical Science Research Council (EPSRC). A description is given of the facilities available for research and some of the projects underway – laminated tools for die casting, laser fusion of functionally‐graded materials, and design for RM. Another activity is the industrial Consortium that helps its members in the application of RM technologies. Three Consortium projects are described: deep slot tooling production using copper plated rapid prototype (RP) produced electrodes, cost reduction through RP‐produced patterns for investment casting, and production of thin walled investment cast components with RP‐built low thermal conductivity tooling.
VDAS: a virtual design and assembly system in a virtual reality environment
Authors: Ji Ping , Choi Albert C.K. , Tu Lizhong
Published: November 2002

The paper presents a virtual design and assembly system (VDAS) developed in a virtual reality (VR) environment. The VDAS is a VR‐based engineering application which allows engineers to design, modify and assemble mechanical products. As a prototype, this system has a knowledge‐based library of standard mechanical fastening parts, so a great deal of work is reduced during the product modeling stage. Besides, product models can be directly inserted or modified with a friendly user interface in the immersive VR environment. In order to reach the target of virtual design and integrate VR and computer aided design, the system adopts the variational design approach, so a product model has not only the geometric information, but also variation information and even assembly match information. Finally, the VDAS has the function of assembly planning, and several interactive manipulations, such as part modification, assembly plan verification and modification, have been realized.
The automated filling of bonded joints – Part 1 two dimensional joints
Authors: Young Ken , Pearson Ian , Bull R.
Published: November 2002

A parameter has been identified that can be used to calculate a joint's bond‐line thicknesses. This was successfully represented by a fourth order polynomial expression and has been used to predict the volume of adhesive required to precisely fill structural joints of unknown bond‐line thickness. This technology was further used to automatically control adhesive injection into pre‐assembled vehicle structural joints for use in an automated production environment. This has great advantage over adhesive application prior to joint assembly as the adhesive remains in the joint rather than contaminating the adherend surface and the bond‐line remains filled. This will be of benefit to the automotive industry. The method is adaptable and can be re‐programmed to cope with a number of applications.
Assuring quality service in higher education: registration and advising attitudes in a private university in Lebanon
Authors: Abouchedid Kamal , Nasser Ramzi
Published: November 2002

The first encounter of students at universities is the administrative office, which leaves a lasting imprint for their entire experience in higher education. With the exponential growth of higher education in the Middle East, private universities face hardened competition in the overall retention of students. Registrar and academic advising offices are vital components to the university as well as the front end to the universities’ service quality. This study attempts to measure student attitudes of registration and academic advising across different faculties to assure positive quality service complementing that of the academic. Keeping in mind that many developing universities in the Middle East and other nations have not yet utilized automated services to meet student needs, the present study provides recommendations in the inroads en route to the development of touch‐tone and Web‐banner automated registration for a positive assessment of service quality.
The design of metadata for the Digital Museum Initiative in Taiwan
Authors: Chen Chao‐chen , Chen Hsueh‐hua , Chen Kuang‐hua , Hsiang Jieh
Published: November 2002

Metadata plays a crucial role in a digital library/museum environment. However, the development of metadata is not an easy task. Its formulation starts with analysing the attributes of collections as well as understanding the user information needs and information seeking behaviour. The issue of interoperability also needs to be considered in terms of both semantics and syntax. This paper discusses issues related to the development of metadata in Taiwan. It describes the development process of a Chinese metadata system, Metadata Interchange for Chinese Information (MICI), and an XML/metadata management system, Metalogy. Both were developed under the Digital Museum Initiative sponsored by the National Science Council of Taiwan.
Usage of information resources by computer engineering students: a case study of Nanyang Technological University, Singapore
Authors: Majid Shaheen , Tee Tan Ai
Published: November 2002

This study investigates the information needs and information seeking behaviour of computer engineering undergraduate students at Nanyang Technological University (NTU), Singapore. The purpose was to investigate the types of information sources used by the students, their preferred information formats, the importance of and reasons for using certain information sources and the use of various electronic information sources. A questionnaire was distributed to 200 randomly selected students and 102 completed questionnaires were returned. The study found that printed materials were the most preferred information format among the students. The top five most preferred information sources, in the order of importance, were books, lecturers, the Internet, friends and manuals. Unexpectedly, the use of databases and electronic journals was quite low among the computer engineering students. The study recommends a promotional campaign for introducing electronic information sources to the library users.
Aiming at quality and coverage combined: blending physical and virtual union catalogues
Authors: Gatenby Janifer
Published: November 2002

This article discusses the deficiencies of search engines and the importance of metadata before examining three models of metadata retrieval: distributed; distributed data with a centralised index; and centralised union catalogue. In listing the advantages and disadvantages of the distributed model, the Z39.50 protocol is used as an example. The OAI harvest protocol is the example of the second model. Virtual union catalogues are compared with a real one. A pan‐European model is discussed as a way to combine the best of all three models, with EUCAT as its base.
Partly folded states of members of the lysozyme/lactalbumin superfamily: A comparative study by circular dichroism spectroscopy and limited proteolysis
Authors: Polverino de Laureto Patrizia , Frare Erica , Gottardo Rossella , van Dael Herman , Fontana Angelo
Published: November 2002

The partly folded states of protein members of the lysozyme (LYS)/α‐lactalbumin (LA) superfamily have been analyzed by circular dichroism (CD) measurements and limited proteolysis experiments. Hen, horse, dog, and pigeon LYSs and bovine LA were used in the present study. These are related proteins of 123‐ to 129‐amino‐acid residues with similar three‐dimensional structures but low similarity in amino acid sequences. Moreover, notable differences among them reside in their calcium‐binding properties and capability to adopt partly folded states or molten globules in acid solution (A‐state) or on depletion of calcium at neutral pH (apo‐state). Far‐ and near‐UV CD measurements revealed that although the structures of hen and dog LYS are rather stable in acid at pH 2.0 or at neutral pH in the absence of calcium, conformational transitions to various extents occur with all other LYS/LA proteins herewith investigated. The most significant perturbation of tertiary structure in acid was observed with bovine LA and LYS from horse milk and pigeon egg‐white. Pepsin and proteinase K were used as proteolytic probes, because these proteases show broad substrate specificity, and therefore, their sites of proteolysis are dictated not by the specific amino acid sequence of the protein substrate but by its overall structure and dynamics. Although hen LYS at pH 2.0 was fully resistant to proteolysis by pepsin, the other members of the LYS/LA superfamily were cleaved at different rates at few sites of the polypeptide chain and thus producing rather large protein fragments. The apo‐form of bovine LA, horse LYS, and pigeon LYS were attacked by proteinase K at pH 8.3, whereas dog and hen LYSs were resistant to proteolysis when reacted under identical experimental conditions. Briefly, it has been found that the proteolysis data correlate well with the extent of conformational transitions inferred from CD spectra and with existing structural informations regarding the proteins herewith investigated, mainly derived from NMR and hydrogen exchange measurements. The sites of initial proteolytic cleavages in the LYS variants occur at the level of the β‐subdomain (approximately chain region 34–57), in analogy to those observed with bovine LA. Proteolysis data are in agreement with the current view that the molten globule of the LYS/LA proteins is characterized by a structured α‐domain and a largely disrupted β‐subdomain. Our results underscore the utility of the limited proteolysis approach for analyzing structure and dynamics of proteins, even if adopting an ensemble of dynamic states as in the molten globule.
The interaction of β2‐glycoprotein I domain V with chaperonin GroEL: The similarity with the domain V and membrane interaction
Authors: Gozu Masayo , Hoshino Masaru , Higurashi Takashi , Kato Hisao , Goto Yuji
Published: November 2002

To clarify the mechanism of interaction between chaperonin GroEL and substrate proteins, we studied the conformational changes; of the fifth domain of human β2‐glycoprotein I upon binding to GroEL. The fifth domain has a large flexible loop, containing several hydrophobic residues surrounded by positively charged residues, which has been proposed to be responsible for the binding of β2‐glycoprotein I to negatively charged phospholipid membranes. The reduction by dithiothreitol of the three intramolecular disulfide bonds of the fifth domain was accelerated in the presence of stoichiometric amounts of GroEL, indicating that the fifth domain was destabilized upon interaction with GroEL. To clarify the GroEL‐induced destabilization at the atomic level, we performed H/2H exchange of amide protons using heteronuclear NMR spectroscopy. The presence of GroEL promoted the H/2H exchange of most of the protected amide protons, suggesting that, although the flexible loop of the fifth domain is likely to be responsible for the initiation of binding to GroEL, the interaction with GroEL destabilizes the overall conformation of the fifth domain.
Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2
Authors: Nauli Sehat , Kuhlman Brian , Le Trong Isolde , Stenkamp Ronald E. , Teller David , Baker David
Published: November 2002

We recently described two protein G variants (NuG1 and NuG2) with redesigned first hairpins that were almost twice as stable, folded 100‐fold faster, and had a switched folding mechanism relative to the wild‐type protein. To test the structural accuracy of our design algorithm and to provide insights to the dramatic changes in the kinetics and thermodynamics of folding, we have now determined the crystal structures of NuG1 and NuG2 to 1.8 Å and 1.85 Å, respectively. We find that they adopt hairpin structures that are closer to the computational models than to wild‐type protein G; the RMSD of the NuG1 hairpin to the design model and the wild‐type structure are 1.7 Å and 5.1 Å, respectively. The crystallographic B factor in the redesigned first hairpin of NuG1 is systematically higher than the second hairpin, suggesting that the redesigned region is somewhat less rigid. A second round of structure‐based design yielded new variants of NuG1 and NuG2, which are further stabilized by 0.5 kcal/mole and 0.9 kcal/mole.
Metal ions and phosphate binding in the H‐N‐H motif: Crystal structures of the nuclease domain of ColE7/Im7 in complex with a phosphate ion and different divalent metal ions
Authors: Sui Meng‐Jiun , Tsai Li‐Chu , Hsia Kuo‐Chiang , Doudeva Lyudmila G. , Ku Wen‐Yen , Han Gye Won , Yuan Hanna S.
Published: November 2002

H‐N‐H is a motif found in the nuclease domain of a subfamily of bacteria toxins, including colicin E7, that are capable of cleaving DNA nonspecifically. This H‐N‐H motif has also been identified in a subfamily of homing endonucleases, which cleave DNA site specifically. To better understand the role of metal ions in the H‐N‐H motif during DNA hydrolysis, we crystallized the nuclease domain of colicin E7 (nuclease‐ColE7) in complex with its inhibitor Im7 in two different crystal forms, and we resolved the structures of EDTA‐treated, Zn2+‐bound and Mn2+‐bound complexes in the presence of phosphate ions at resolutions of 2.6 Å to 2.0 Å. This study offers the first determination of the structure of a metal‐free and substrate‐free enzyme in the H‐N‐H family. The H‐N‐H motif contains two antiparallel β‐strands linked to a C‐terminal α‐helix, with a divalent metal ion located in the center. Here we show that the metal‐binding sites in the center of the H‐N‐H motif, for the EDTA‐treated and Mg2+‐soaked complex crystals, were occupied by water molecules, indicating that an alkaline earth metal ion does not reside in the same position as a transition metal ion in the H‐N‐H motif. However, a Zn2+ or Mn2+ ions were observed in the center of the H‐N‐H motif in cases of Zn2+ or Mn2+‐soaked crystals, as confirmed in anomalous difference maps. A phosphate ion was found to bridge between the divalent transition metal ion and His545. Based on these structures and structural comparisons with other nucleases, we suggest a functional role for the divalent transition metal ion in the H‐N‐H motif in stabilizing the phosphoanion in the transition state during hydrolysis.
Quantitative chimeric analysis of six specificity determinants that differentiate Escherichia coli aspartate from tyrosine aminotransferase
Authors: Shaffer Wendy A. , Luong Tinh N. , Rothman Steven C. , Kirsch Jack F.
Published: November 2002

The six mutations, referred to as the Hex mutations, that together have been shown to convert Escherichia coli aspartate aminotransferase (AATase) specificity to be substantially like that of E. coli tyrosine aminotransferase (TATase) are dissected into two groups, (T109S/N297S) and (V39L/K41Y/T47I/N69L). The letters on the left and right of the numbers designate AATase and TATase residues, respectively. The T109S/N297S pair has been investigated previously. The latter group, the “Grease” set, is now placed in the AATase framework, and the retroGrease set (L39V/Y41K/I47T/L69N) is substituted into TATase. The Grease mutations in the AATase framework were found primarily to lower KMs for both aromatic and dicarboxylic substrates. In contrast, retroGrease TATase exhibits lowered kcats for both substrates. The six retroHex mutations, combining retroGrease and S109T/S297N, were found to invert the substrate specificity of TATase, creating an enzyme with a nearly ninefold preference (kcat/KM) for aspartate over phenylalanine. The retroHex mutations perturb the electrostatic environment of the pyridoxal phosphate cofactor, as evidenced by a spectrophotometric titration of the internal aldimine, which uniquely shows two pKas, 6.1 and 9.1. RetroHex was also found to have impaired dimer stability, with a KD for dimer dissociation of 350 nM compared with the wild type KD of 4 nM. Context dependence and additivity analyses demonstrate the importance of interactions of the Grease residues with the surrounding protein framework in both the AATase and TATase contexts, and with residues 109 and 297 in particular. Context dependence and cooperativity are particularly evident in the effects of mutations on kcat/KM(Asp). Effects on kcat/KM(Phe) are more nearly additive and context independent.
Side‐chain conformational entropy at protein–protein interfaces
Authors: Cole Christian , Warwicker Jim
Published: November 2002

Protein–protein interactions are the key to many biological processes. How proteins selectively and correctly associate with their required protein partner(s) is still unclear. Previous studies of this “protein‐docking problem” have found that shape complementarity is a major determinant of interaction, but the detailed balance of energy contributions to association remains unclear. This study estimates side‐chain conformational entropy (per unit solvent accessible area) for various protein surface regions, using a self‐consistent mean field calculation of rotamer probabilities. Interfacial surface regions were less flexible than the rest of the protein surface for calculations with monomers extracted from homodimer datasets in 21 of 25 cases, and in 8 of 9 for the large protomer from heterodimer datasets. In surface patch analysis, based on side‐chain conformational entropy, 68% of true interfaces were ranked top for the homodimer set and 66% for the large protomer/heterodimer set. The results indicate that addition of a side‐chain entropic term could significantly improve empirical calculations of protein–protein association.
Mechanically unfolding proteins: The effect of unfolding history and the supramolecular scaffold
Authors: Zinober Rebecca C. , Brockwell David J. , Beddard Godfrey S. , Blake Anthony W. , Olmsted Peter D. , Radford Sheena E. , Smith D. Alastair
Published: November 2002

The mechanical resistance of a folded domain in a polyprotein of five mutant I27 domains (C47S, C63S I27)5is shown to depend on the unfolding history of the protein. This observation can be understood on the basis of competition between two effects, that of the changing number of domains attempting to unfold, and the progressive increase in the compliance of the polyprotein as domains unfold. We present Monte Carlo simulations that show the effect and experimental data that verify these observations. The results are confirmed using an analytical model based on transition state theory. The model and simulations also predict that the mechanical resistance of a domain depends on the stiffness of the surrounding scaffold that holds the domain in vivo, and on the length of the unfolded domain. Together, these additional factors that influence the mechanical resistance of proteins have important consequences for our understanding of natural proteins that have evolved to withstand force.
Prediction of novel archaeal enzymes from sequence‐derived features
Authors: Jensen Lars Juhl , Skovgaard Marie , Brunak Søren
Published: November 2002

The completely sequenced archaeal genomes potentially encode, among their many functionally uncharacterized genes, novel enzymes of biotechnological interest. We have developed a prediction method for detection and classification of enzymes from sequence alone (available at http://www.cbs.dtu.dk/services/ArchaeaFun/). The method does not make use of sequence similarity; rather, it relies on predicted protein features like cotranslational and posttranslational modifications, secondary structure, and simple physical/chemical properties.
Synthesis and Structural Characterization of Polymeric Silver(I) Butyl Xanthate
Authors: Xuhong Jiang , Weiguang Zhang , Yun Zhong , Suelein Wang
Published: November 2002

Polymeric silver(I) butyl xanthate, [Ag(Bu-XA)]n, was synthesized and crystallographically characterized. The polymer shows chair conformation of eight-membered ring units and a novel mode of coordination, with a structural arrangement different from that in silver dialkyldithiocarbamate and dialkyldithiophosphates. The polymeric structure of the new complex is formed by corrugated planes.