Showing papers by "National Institute of Standards and Technology published in 2002"

The Protein Data Bank.

Abstract: The Protein Data Bank [PDB; Berman, Westbrook et al. (2000), Nucleic Acids Res. 28, 235–242; http://www.pdb.org/] is the single worldwide archive of primary structural data of biological macromolecules. Many secondary sources of information are derived from PDB data. It is the starting point for studies in structural bioinformatics. This article describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource. The reader should come away with an understanding of the scope of the PDB and what is provided by the resource.

Automatic evaluation of machine translation quality using n-gram co-occurrence statistics

Abstract: Evaluation is recognized as an extremely helpful forcing function in Human Language Technology R&D. Unfortunately, evaluation has not been a very powerful tool in machine translation (MT) research because it requires human judgments and is thus expensive and time-consuming and not easily factored into the MT research agenda. However, at the July 2001 TIDES PI meeting in Philadelphia, IBM described an automatic MT evaluation technique that can provide immediate feedback and guidance in MT research. Their idea, which they call an "evaluation understudy", compares MT output with expert reference translations in terms of the statistics of short sequences of words (word N-grams). The more of these N-grams that a translation shares with the reference translations, the better the translation is judged to be. The idea is elegant in its simplicity. But far more important, IBM showed a strong correlation between these automatically generated scores and human judgments of translation quality. As a result, DARPA commissioned NIST to develop an MT evaluation facility based on the IBM work. This utility is now available from NIST and serves as the primary evaluation measure for TIDES MT research.

Architecture for a large-scale ion-trap quantum computer

Abstract: Among the numerous types of architecture being explored for quantum computers are systems utilizing ion traps, in which quantum bits (qubits) are formed from the electronic states of trapped ions and coupled through the Coulomb interaction. Although the elementary requirements for quantum computation have been demonstrated in this system, there exist theoretical and technical obstacles to scaling up the approach to large numbers of qubits. Therefore, recent efforts have been concentrated on using quantum communication to link a number of small ion-trap quantum systems. Developing the array-based approach, we show how to achieve massively parallel gate operation in a large-scale quantum computer, based on techniques already demonstrated for manipulating small quantum registers. The use of decoherence-free subspaces significantly reduces decoherence during ion transport, and removes the requirement of clock synchronization between the interaction regions.

A Functional Basis for Engineering Design: Reconciling and Evolving Previous Efforts

Abstract: In engineering design, all products and artifacts have some intended reason behind their existence: the product or artifact function. Functional modeling provides an abstract, yet direct, method for understanding and representing an overall product or artifact function. Functional modeling also strategically guides design activities such as problem decomposition, physical modeling, product architecting, concept generation, and team organization. A formal function representation is needed to support functional modeling, and a standardized set of function-related terminology leads to repeatable and meaningful results from such a representation. We refer to this representation as a functional basis; in this paper, we seek to reconcile and integrate two independent research efforts into a significantly evolved functional basis. These efforts include research from the National Institute of Standards and Technology and two US universities, and their industrial partners. The overall approach for integrating the functional representations and the final results are presented. This approach also provides a mechanism for evaluating whether future revisions are needed to the functional basis and, if so, how to proceed. The integration process is discussed relative to differences, similarities, insights into the representations, and product validation. Based on the results, a more versatile and comprehensive design vocabulary emerges. This vocabulary will greatly enhance and expand the frontiers of research in design repositories, product architecture, design synthesis, and general product modeling.

New developments in the Inorganic Crystal Structure Database (ICSD): accessibility in support of materials research and design.

Abstract: The materials community in both science and industry use crystallographic data models on a daily basis to visualize, explain and predict the behavior of chemicals and materials. Access to reliable information on the structure of crystalline materials helps researchers concentrate experimental work in directions that optimize the discovery process. The Inorganic Crystal Structure Database (ICSD) is a comprehensive collection of more than 60 000 crystal structure entries for inorganic materials and is produced cooperatively by Fachinformationszentrum Karlsruhe (FIZ), Germany, and the US National Institute of Standards and Technology (NIST). The ICSD is disseminated in computerized formats with scientific software tools to exploit the content of the database. Features of a new Windows-based graphical user interface for the ICSD are outlined, together with directions for future development in support of materials research and design.

IEEE standard 802.16: a technical overview of the WirelessMAN/sup TM/ air interface for broadband wireless access

Abstract: The broadband wireless access industry, which provides high-rate network connections to stationary sites, has matured to the point at which it now has a standard for second-generation wireless metropolitan area networks. The IEEE standard 802.16, with its WirelessMAN/sup TM/ air interface, sets the stage for widespread and effective deployments worldwide. This article overviews the technical medium access control and physical layer features of this new standard.

Rabi oscillations in a large Josephson-junction qubit.

Abstract: We have designed and operated a circuit based on a large-area current-biased Josephson junction whose two lowest energy quantum levels are used to implement a solid-state qubit. The circuit allows measurement of the qubit states with a fidelity of 85% while providing sufficient decoupling from external sources of relaxation and decoherence to allow coherent manipulation of the qubit state, as demonstrated by the observation of Rabi oscillations. This qubit circuit is the basis of a scalable quantum computer.

Self-organization of supramolecular helical dendrimers into complex electronic materials

Abstract: The discovery of electrically conducting organic crystals1 and polymers1,2,3,4 has widened the range of potential optoelectronic materials5,6,7,8,9, provided these exhibit sufficiently high charge carrier mobilities6,7,8,9,10 and are easy to make and process. Organic single crystals have high charge carrier mobilities but are usually impractical11, whereas polymers have good processability but low mobilities1,12. Liquid crystals exhibit mobilities approaching those of single crystals and are suitable for applications13,14,15,16,17,18, but demanding fabrication and processing methods limit their use. Here we show that the self-assembly of fluorinated tapered dendrons can drive the formation of supramolecular liquid crystals with promising optoelectronic properties from a wide range of organic materials. We find that attaching conducting organic donor or acceptor groups to the apex of the dendrons leads to supramolecular nanometre-scale columns that contain in their cores π-stacks of donors, acceptors or donor–acceptor complexes exhibiting high charge carrier mobilities. When we use functionalized dendrons and amorphous polymers carrying compatible side groups, these co-assemble so that the polymer is incorporated in the centre of the columns through donor–acceptor interactions and exhibits enhanced charge carrier mobilities. We anticipate that this simple and versatile strategy for producing conductive π-stacks of aromatic groups, surrounded by helical dendrons, will lead to a new class of supramolecular materials suitable for electronic and optoelectronic applications.

A Schrödinger cat superposition state of an atom

Abstract: A "Schrodinger cat"-like state of matter was generated at the single atom level. A trapped 9Be+ ion was laser-cooled to the zero-point energy and then prepared in a superposition of spatially separated coherent harmonic oscillator states. This state was created by application of a sequence of laser pulses, which entangles internal (electronic) and external (motional) states of the ion. The Schrodinger cat superposition was verified by detection of the quantum mechanical interference between the localized wave packets. This mesoscopic system may provide insight into the fuzzy boundary between the classical and quantum worlds by allowing controlled studies of quantum measurement and quantum decoherence.

Nobel Lecture: Bose-Einstein condensation in a dilute gas, the first 70 years and some recent experiments

Abstract: Bose-Einstein condensation, or BEC, has a long and rich history dating from the early 1920s. In this article we will trace briefly over this history and some of the developments in physics that made possible our successful pursuit of BEC in a gas. We will then discuss what was involved in this quest. In this discussion we will go beyond the usual technical description to try and address certain questions that we now hear frequently, but are not covered in our past research papers. These are questions along the lines of: How did you get the idea and decide to pursue it? Did you know it was going to work? How long did it take you and why? We will review some our favorites from among the experiments we have carried out with BEC. There will then be a brief encore on why we are optimistic that BEC can be created with nearly any species of magnetically trappable atom. Throughout this article we will try to explain what makes BEC in a dilute gas so interesting, unique, and experimentally ${\mathrm{challenging}.}^{1}$

Surface modification of Sylgard-184 poly(dimethyl siloxane) networks by ultraviolet and ultraviolet/ozone treatment.

Abstract: We report on the surface modification of Sylgard-184 poly(dimethyl siloxane) (PDMS) networks by ultraviolet (UV) radiation and ultraviolet/ozone (UVO) treatment. The effects of the UV light wavelength and ambient conditions on the surface properties of Sylgard-184 are probed using a battery of experimental probes, including static contact angle measurements, Fourier transform infrared spectroscopy, near-edge X-ray absorption fine structure, and X-ray reflectivity. Our results reveal that when exposed to UV, the PDMS macromolecules in the surface region of Sylgard-184 undergo chain scission, involving both the main chain backbone and the side groups. The radicals formed during this process recombine and form a network whose wetting properties are similar to those of a UV-modified model PDMS. In contrast to the UV radiation, the UVO treatment causes very significant changes in the surface and near-surface structure of Sylgard-184. Specifically, the molecular oxygen and ozone created during the UVO process interact with the UV-modified specimen. As a result of these interactions, the surface of the sample contains a large number of hydrophilic (mainly -OH) groups. In addition, the material density within the first approximately 5 nm reaches about 50% of that of pure silica. A major conclusion that can be drawn from the results and analysis described in this work is that the presence of the silica fillers in Sylgard-184 does not alter the surface properties of the UVO- and UV-modified Sylgard-184.

New developments in the Inorganic Crystal Structure Database (ICSD): accessibility in support of materials research and design

Abstract: The materials community in both science and industry use crystallographic data models on a daily basis to visualize, explain and predict the behavior of chemicals and materials. Access to reliable information on the structure of crystalline materials helps researchers concentrate experimental work in directions that optimize the discovery process. The Inorganic Crystal Structure Database (ICSD) is a comprehensive collection of more than 60 000 crystal structure entries for inorganic materials and is produced cooperatively by Fachinformationszentrum Karlsruhe (FIZ), Germany, and the US National Institute of Standards and Technology (NIST). The ICSD is disseminated in computerized formats with scientific software tools to exploit the content of the database. Features of a new Windows-based graphical user interface for the ICSD are outlined, together with directions for future development in support of materials research and design.

Anatomy of spin-transfer torque

Abstract: Spin-transfer torques occur in magnetic heterostructures because the transverse component of a spin current that flows from a nonmagnet into a ferromagnet is absorbed at the interface. We demonstrate this fact explicitly using free-electron models and first-principles electronic structure calculations for real material interfaces. Three distinct processes contribute to the absorption: (1) spin-dependent reflection and transmission, (2) rotation of reflected and transmitted spins, and (3) spatial precession of spins in the ferromagnet. When summed over all Fermi surface electrons, these processes reduce the transverse component of the transmitted and reflected spin currents to nearly zero for most systems of interest. Therefore, to a good approximation, the torque on the magnetization is proportional to the transverse piece of the incoming spin current.

SP 800-30. Risk Management Guide for Information Technology Systems

Abstract: Risk management is the process of identifying risk, assessing risk, and taking steps to reduce risk to an acceptable level. Organizations use risk assessment, the first step in the risk management methodology, to determine the extent of the potential threat, vulnerabilities, and the risk associated with an information technology (IT) system. The output of this process helps to identify appropriate controls for reducing or eliminating risk during the risk mitigation process, the second step of risk management, which involves prioritizing, evaluating, and implementing the appropriate risk-reducing controls recommended from the risk assessment process. This guide provides a foundation for the development of an effective risk management program, containing both the definitions and the practical guidance necessary for assessing and mitigating risks identified within IT systems throughout their system development life cycle (SDLC). The ultimate goal is to help organizations to better manage IT-related mission risks.Organizations may choose to expand or abbreviate the comprehensive processes and steps suggested in this guide and tailor them to their site environment in managing IT-related mission risks. In addition, this guide provides information on the selection of cost-effective security controls. These controls can be used to mitigate risk for the better protection of mission-critical information and the IT systems that process, store, and carry this information.The third step in the process is continual evaluation and assessment. In most organizations, IT systems will continually be expanded and updated, their components changed, and their software applications replaced or updated with newer versions. In addition, personnel changes will occur and security policies are likely to change over time. These changes mean that new risks will surface and risks previously mitigated may again become a concern. Thus, the risk management process is ongoing and evolving.

Random packings of frictionless particles.

Abstract: We conduct numerical simulations of random packings of frictionless particles at T = 0. The packing fraction where the pressure becomes nonzero is the same as the jamming threshold, where the static shear modulus becomes nonzero. The distribution of threshold packing fractions narrows, and its peak approaches random close packing as the system size increases. For packing fractions within the peak, there is no self-averaging, leading to exponential decay of the interparticle force distribution.

Rapid microfluidic mixing.

Abstract: A preformed T-microchannel imprinted in polycarbonate was postmodified with a pulsed UV excimer laser (KrF, 248 nm) to create a series of slanted wells at the junction. The presence of the wells leads to a high degree of lateral transport within the channel and rapid mixing of two confluent streams undergoing electroosmotic flow. Several mixer designs were fabricated and investigated. All designs were relatively successful at low flow rates (0.06 cm/s, ≥75% mixing), but had varying degrees of success at high flow rates (0.81 cm/s, 45−80% mixing). For example, one design operating at high flow rates was able to split an incoming fluorescent stream into two streams of varying concentrations depending on the number of slanted wells present. The final mixer design was able to overcome stream splitting at high flow rates, and it was shown that the two incoming streams were 80% mixed within 443 μm of the T-junction for a flow rate of 0.81 cm/s. Without the presence of the mixer and at the same high flow rate, a...

Imaging Quasiparticle Interference in Bi2Sr2CaCu2O8+δ

Abstract: Scanning tunneling spectroscopy of the high-Tc superconductor Bi2Sr2CaCu2O8+delta reveals weak, incommensurate, spatial modulations in the tunneling conductance. Images of these energy-dependent modulations are Fourier analyzed to yield the dispersion of their wavevectors. Comparison of the dispersions with photoemission spectroscopy data indicates that quasiparticle interference, due to elastic scattering between characteristic regions of momentum-space, provides a consistent explanation for the conductance modulations, without appeal to another order parameter. These results refocus attention on quasiparticle scattering processes as potential explanations for other incommensurate phenomena in the cuprates. The momentum-resolved tunneling spectroscopy demonstrated here also provides a new technique with which to study quasiparticles in correlated materials.

Atom-molecule coherence in a Bose-Einstein condensate.

Abstract: Recent advances in the precise control of ultracold atomic systems have led to the realisation of Bose–Einstein condensates (BECs) and degenerate Fermi gases. An important challenge is to extend this level of control to more complicated molecular systems. One route for producing ultracold molecules is to form them from the atoms in a BEC. For example, a two-photon stimulated Raman transition in a 87Rb BEC has been used to produce 87Rb2 molecules in a single rotational-vibrational state1, and ultracold molecules have also been formed2 through photoassociation of a sodium BEC. Although the coherence properties of such systems have not hitherto been probed, the prospect of creating a superposition of atomic and molecular condensates has initiated much theoretical work3,4,5,6,7. Here we make use of a time-varying magnetic field near a Feshbach resonance8,9,10,11,12 to produce coherent coupling between atoms and molecules in a 85Rb BEC. A mixture of atomic and molecular states is created and probed by sudden changes in the magnetic field, which lead to oscillations in the number of atoms that remain in the condensate. The oscillation frequency, measured over a large range of magnetic fields, is in excellent agreement with the theoretical molecular binding energy, indicating that we have created a quantum superposition of atoms and diatomic molecules—two chemically different species.

Thermal Degradation and Flammability Properties of Poly(propylene)/Carbon Nanotube Composites

Abstract: Nanocomposites based on poly(propylene) and multi-wall carbon nanotubes (up to 2 vol.-%) were melt blended, yielding a good dispersion of nanotubes without using any organic treatment or additional additives. Carbon nanotubes are found to significantly enhance the thermal stability of poly(propylene) in nitrogen at high temperatures. Specifically, the nanotube additive greatly reduced the heat release rate of poly(propylene). They are found to be at least as effective a flame-retardant as clay/poly(propylene) nanocomposites.

Molecular dynamics simulation of a polymer melt with a nanoscopic particle

Abstract: We perform molecular dynamics simulations of a bead−spring polymer melt surrounding a nanoscopic particle. We explore the effect of the polymer/nanoparticle interactions, surface-to-volume ratio, and boundary conditions on both the structure and dynamics of the polymer melt. We find that the chains near the nanoparticle surface are elongated and flattened and that this effect is independent of the interaction for the range of interactions we study. We show that the glass transition temperature Tg of the melt can be shifted to either higher or lower temperatures by tuning the interactions between polymer and nanoparticle. A gradual change of the polymer dynamics approaching the nanoparticle surface causes the change in the glass transition. The magnitude of the shift is exaggerated by increasing fraction of surface monomers in the system. These behaviors support a “many-layer”-based interpretation of the dynamics. Our findings appear applicable to systems in which surface interactions dominate, including b...

Identification and characterization of a human DNA glycosylase for repair of modified bases in oxidatively damaged DNA.

Abstract: 8-oxoguanine (8-oxoG), ring-opened purines (formamidopyrimidines or Fapys), and other oxidized DNA base lesions generated by reactive oxygen species are often mutagenic and toxic, and have been implicated in the etiology of many diseases, including cancer, and in aging. Repair of these lesions in all organisms occurs primarily via the DNA base excision repair pathway, initiated with their excision by DNA glycosylase/AP lyases, which are of two classes. One class utilizes an internal Lys residue as the active site nucleophile, and includes Escherichia coli Nth and both known mammalian DNA glycosylase/AP lyases, namely, OGG1 and NTH1. E. coli MutM and its paralog Nei, which comprise the second class, use N-terminal Pro as the active site. Here, we report the presence of two human orthologs of E. coli mutM nei genes in the human genome database, and characterize one of their products. Based on the substrate preference, we have named it NEH1 (Nei homolog). The 44-kDa, wild-type recombinant NEH1, purified to homogeneity from E. coli, excises Fapys from damaged DNA, and oxidized pyrimidines and 8-oxoG from oligodeoxynucleotides. Inactivation of the enzyme because of either deletion of N-terminal Pro or Histag fusion at the N terminus supports the role of N-terminal Pro as its active site. The tissue-specific levels of NEH1 and OGG1 mRNAs are distinct, and S phase-specific increase in NEH1 at both RNA and protein levels suggests that NEH1 is involved in replication-associated repair of oxidized bases.

Parallel calculation of electron multiple scattering using Lanczos algorithms

Abstract: Real space multiple scattering calculations of the electronic density of states and x-ray spectra in solids typically scale as the cube of the system and basis set size, and hence are highly demanding computationally. For example, such x-ray absorption near edge structure (XANES) calculations typically require clusters of order ${N}_{R}$ atoms and s, p, and d states for convergence, with ${N}_{R}$ between about ${10}^{2}--{10}^{3};$ for this case about ${10}^{2}$ inversions of ${9N}_{R}\ifmmode\times\else\texttimes\fi{}{9N}_{R}$ matrices are needed, one for each energy point. We discuss here two ways to speed up these calculations: (1) message passing interface (MPI) parallel processing and (2) fast, Lanczos multiple scattering algorithms. Together these algorithms can reduce computation times typically by two orders of magnitude. These are both implemented in a generalization of the ab initio self-consistent FEFF8 code, which thus makes practical XANES calculations in complex systems with of order ${10}^{3}$ atoms. The Lanczos algorithm also yields a natural crossover between full and finite-order multiple scattering with increasing energy, thus differentiating the extended and near-edge regimes.

Elastic properties of model random three-dimensional open-cell solids

Abstract: Most cellular solids are random materials, while practically all theoretical structure-property relations are for periodic models. To generate theoretical results for random models the finite element method (FEM) was used to study the elastic properties of open-cell solids. We have computed the density (rho) and microstructure dependence of the Young's modulus (E) and Poisson's ratio (nu) for four different isotropic random models. The models were based on Voronoi tessellations, level-cut Gaussian random fields, and nearest neighbour node-bond rules. These models were chosen to broadly represent the structure of foamed solids and other (non-foamed) cellular materials. At low densities, the Young's modulus can be described by the relation E proportional to rho (n). The exponent n and constant of proportionality depend on microstructure. We find 1.3 < n < 3, indicating a more complex dependence than indicated by periodic cell theories, which predict n = 1 or 2. The observed variance in the exponent was found to be consistent with experimental data. At low densities we found that nu approximate to 0.25 for three of the four models studied. In contrast, the Voronoi tessellation, which is a common model of foams, became approximately incompressible (nu approximate to 0.5), This behaviour is not commonly observed experimentally. Our studies showed the result was robust to polydispersity and that a relatively large number (15%) of the bonds must be broken to significantly reduce the low-density Poission's ratio to nu approximate to 0.33. (C) 2001 Elsevier Science Ltd. All rights reserved.

Computation of linear elastic properties from microtomographic images: Methodology and agreement between theory and experiment

Abstract: Elastic property‐porosity relationships are derived directly from microtomographic images. This is illustrated for a suite of four samples of Fontainebleau sandstone with porosities ranging from 7.5% to 22%. A finite‐element method is used to derive the elastic properties of digitized images. By estimating and minimizing several sources of numerical error, very accurate predictions of properties are derived in excellent agreement with experimental measurements over a wide range of the porosity. We consider the elastic properties of the digitized images under dry, water‐saturated, and oil‐saturated conditions. The observed change in the elastic properties due to fluid substitution is in excellent agreement with the exact Gassmann's equations. This shows both the accuracy and the feasibility of combining microtomographic images with elastic calculations to accurately predict petrophysical properties of individual rock morphologies. We compare the numerical predictions to various empirical, effective medium ...

Role of protein-water hydrogen bond dynamics in the protein dynamical transition.

Abstract: The role of water in protein dynamics has been investigated using molecular dynamics simulations of crystals and a dehydrated powder. On the 100 ps time scale, the anharmonic and diffusive motions involved in the protein structural relaxation are correlated with the protein-water hydrogen bond dynamics. The complete structural relaxation of the protein requires relaxation of the hydrogen bond network via solvent translational displacement. Inhibiting the solvent translational mobility, and therefore the protein-water hydrogen bond dynamics, has an effect on the protein relaxation similar to dehydration.

Generation of spatially coherent light at extreme ultraviolet wavelengths.

Abstract: We present spatial coherence measurements of extreme ultraviolet (EUV) light generated through the process of high-harmonic up-conversion of a femtosecond laser. With a phase-matched hollow-fiber geometry, the generated beam was found to exhibit essentially full spatial coherence. The coherence of this laser-like EUV source was shown by recording Gabor holograms of small objects. This work demonstrates the capability to perform EUV holography with a tabletop experimental setup. Such an EUV source, with low divergence and high spatial coherence, can be used for experiments involving high-precision metrology, inspection of optical components for EUV lithography, and microscopy and holography with nanometer resolution. Furthermore, the short time duration of the EUV radiation (a few femtoseconds) will enable EUV microscopy and holography to be performed with ultrahigh time resolution.

Experimental determination of the motional quantum state of a trapped atom

Abstract: We reconstruct the density matrices and Wigner functions for various quantum states of motion of a harmonically bound ${}^{9}{\mathrm{Be}}^{+}$ ion. We apply coherent displacements of different amplitudes and phases to the input state and measure the number state populations. Using novel reconstruction schemes we independently determine both the density matrix in the number state basis and the Wigner function. These reconstructions are sensitive indicators of decoherence in the system.