bluuebunny/crossref_metadata_2025 huggingface dataset:
LOW ENERGY SOLAR AND GALACTIC COSMIC RAYS AT 1 AU
Authors: CASOLINO MARCO
Published: July 2002

In this work we present some of the recent results obtained with the satellite missions NINA-1 and NINA-2 and the experiments on board MIR space station Sileye-1 and 2. The aim is the study of the low energy (10 MeV - 2 GeV) cosmic ray component and different periods of the solar cycle and during Solar Energetic Particle events. Other items of physics include the measurement of the secondary cosmic ray component, produced in the interaction with the upper layers of Earth's atmosphere and the evaluation of the absorbed and equivalent doses inside MIR.
NEUTRINOS AS DARK MATTER CONDIDATES
Authors: MASIERO ANTONIO , PASCOLI SILVIA
Published: July 2002

We review some properties of neutrinos in relation to the dark matter and baryogenesis problems.
From Quantum Affine Groups to the Exact Dynamical Correlation Function of the Heisenberg Model
Authors: Bougourzi A. H. , Couture M. , Kacir M.
Published: July 2002

The exact form factors of the Heisenberg models XXX and XXZ have been recently computed through the quantum affine symmetry of XXZ model in the thermodynamic limit. We use them to derive an exact formula for the contribution of two spinons to the dynamical correlation function of XXX model at zero temperature.
Exact Solutions of Low-Dimensional Reaction-Diffusion Systems
Authors: Cadilhe António M. R. , Glasser M. Lawrence , Privman Vladimir
Published: July 2002

We briefly review some common diffusion-limited reactions with emphasis on results for two-species reactions with anisotropic hopping. Our review also covers single-species reactions. The scope is that of providing reference and general discussion rather than details of methods and results. Recent exact results for a two-species model with anisotropic hopping and with 'sticky' interaction of like particles, obtained by a novel method which allows exact solution of certain single-species and two-species reactions, are discussed.
Atomic Number Scaling of the Nickel-Like Soft X-Ray Lasers
Authors: Daido H. , Ninomiya S. , Imani T. , Okaichi Y. , Takagi M. , Kodama R. , Takabe H. , Kato Y. , Koike F. , Nilsen J. , Murai K.
Published: July 2002

We report the review of the experimental results obtained at the Institute of Laser Engineering, Osaka University, of the soft X-ray lasing in various Ni-like ions whose atomic numbers range from 47(Ag) to 66(Dy). The lasing wavelengths are between 14 nm and 5 nm. X-ray lasing in these materials were obtained when the plasma profiles were properly controlled in time and space by irradiation of curved slab targets with multiple laser pulses. We also describe the original work of the atomic physics calculations which provide the transition energies, transition probabilities and other atomic constants for Ni-like ion species whose atomic numbers range from 36 to 92 calculated with GRASP code (multi-configuration Dirac Fock code) and YODA code (relativistic distorted wave code). Based on these atomic constants, we have calculated the kinetics of the population inversion with a simplified rate equation model in conjunction with a one-dimensional hydrodynamic code to find out the desired pumping conditions. We show a possibility for significant improvement in the pumping efficiency with the use of a picosecond laser irradiating a properly configured preformed plasma. Finally, a simplified estimation of the pumping efficiency is described based on the atomic constants and plasma physics issues.
Classical Trajectory Methods for Polyatomic Molecules
Authors: Sewell Thomas D. , Thompson Donald L.
Published: July 2002

Monte Carlo classical trajectory methods for simulating intramolecular dynamics, including chemical reactions, in large polyatomic molecules are described. Methods for performing calculations corresponding to various kinds of experiments are discussed. Some approaches for formulating potential-energy surfaces are described.
An Interpolating Ansatz for the Ground State of the Spinless Fermion Hamiltonian in D=1 and 2
Authors: Martín-Delgado Miguel A. , Sierra Germán
Published: July 2002

We propose an interpolating ansatz between the strong coupling and weak coupling regimes of a system of spinless interacting fermions in 1D and 2D lattices at half-filling. We address relevant issues such as the existence of Long Range Order, quantum phase transitions and the evaluation of ground state energy. In 1D our method is capable of unveiling the existence of a critical point in the coupling constant at (t/U) c =0.7483 as in fact occurs in the exact solution at a value of 0.5. In our approach this phase transition is described as an example of Bifurcation Phenomena in the variational computation of the ground state energy. In 2D the van Hove singularity plays an essential role in changing the asymptotic behaviour of the system for large values of t/U. In particular, the staggered magnetization for large t/U does not display the Hartree–Fock law [Formula: see text] but instead we find the law [Formula: see text]. Moreover, the system does not exhibit bifurcation phenomena and thus we do not find a critical point separating a CDW state from a fermion "liquid" state.
Current Distributions and the De Haas–Van Alphen Oscillation in a Planar System of Hall Electrons
Authors: Shizuya K.
Published: July 2002

The current distribution is studied for a finite-width two-dimensional system of Hall electrons, with a clear distinction drawn between the equilibrium edge current and the Hall current. It is pointed out that both the distribution and direction of the equilibrium edge current change dramatically as the number of electron edge states increases, and that this alternating edge current is another manifestation of the de Haas–van Alphen effect. The Hall-current distribution is substantially different from the edge current distribution, and it is shown numerically that the fast-traveling electrons along the sample edge are not the main carriers of the Hall current.
Two Dimensional Graphite Films on Metals and Their Intercalation
Authors: Gall N. R. , Rut'kov E. V. , Tontegode A. Ya.
Published: July 2002

Two-dimensional graphite films (2DGF) on solids are wonderful objects, real nature-made two-dimensional crystals. Formation on active metal surface of a 2DGF with extremely high adsorption, chemical and catalytic passivity leads to a number of staggering effects. The review is devoted to 2DGF on metals and their nature, structure, modes of formation and physico chemical properties. A nature of absorption bond between 2DGF and metal substrate is discussed in details. A special attention is paid to intercalation of 2DGF — a process when foreign atoms and even molecules (fullerenes C 60 molecules) spontaneously penetrate between graphite film and metal substrate. Modes of intercalation are discussed and a mechanism of it, based on thermal movements of carbon atoms of a graphite layer, proposed earlier, is used for explanation of experimental data. A new, practically important effect-superefficient diffusion of alkaline atoms into transition metal bulk, covered by 2DGF, is reported.
The Saxon–Hutner Theorem, its Converse Theorem and their Applications to Localization and Delocalization Problems in Binary Quasiperiodic Lattices
Authors: Iguchi Kazumoto
Published: July 2002

In this paper we discuss the application of the Saxon–Hutner theorem and its converse theorem in one-dimensional binary disordered lattices to the one-dimensional binary quasiperiodic lattices. We first summarize some basic theorems in one-dimensional periodic lattices. We discuss how the bulk and edge states are treated in the transfer matrix method. Second, we review the Saxon–Hutner theorem and prove the converse theorem, using the so-called Fricke identities. Third, we present an alternative approach for a rigorous proof of the existence of a Cantor-set spectrum in the Fibonacci lattice and in the related binary quasiperiodic lattices by means of the theorems together with their trace map with the invariant I. We obtain that if I > 0, then the spectrum is always a Cantor set, which was first proved for the Fibonacci lattice by Sütö and generalized for other quasiperiodic lattices by Bellissard, Iochum, Scopolla, and Testard. Fourth, we rigorously prove the existence of extended states in the spectrum of a class of binary quasiperiodic lattices first studied by Kolář and Ali. Fifth, we discuss the so-called gap labeling theorem emphasized by Bellissard and the classic argument of Kohn and Thouless for localized states in a one-dimensional disordered lattice in terms of the language of the transfer matrix method.
Exchanges of "Quanta" Among Distinguishable and Indistinguishable Objects
Authors: Bonelli Antonio , Ruffo Stefano
Published: July 2002

Beginning with a physical problem of exchange of n indistinguishable "quanta" of energy in an ensemble of k oscillators we define a new wide class of combinatorial problems, which also contains statistics intermediate between Fermi–Dirac and Bose–Einstein. One such problem is related to the number theoretic problem of computing the partitions of positive integers. After establishing such a connection, we give explicit formulas for the partitions M(n,k) of an integer n into k parts with k ≤ 4. Moreover, we derive a recursion relation for fixed n and varying k which is valid for any k. A formula which relates partitions to the cardinality of the partition set taking order into account is also derived. The leading asymptotic behavior for n large is obtained for any k. A suggestive interpretation of this formulas is proposed in terms of simplicial lattices. Recursive formulas at fixed k and varying n are then written for k ≤ 5 using the concept of factorial triangle, which is amenable for generalizations to larger k's. The problem of distinct partitions is mapped onto the probability problem of ball removal with replacement, for which we give again recursive solution formulas. Finally, the method of generalized Tartaglia triangle allows the derivation of recursive formulas for limited partitions which take order into account. This latter result is related to the problem of finding the number of distinct ways of dividing n indistinguishable objects into k distinguishable groups, for which explicit summations had been previously found.
Effects of Interface Scattering on the Electronic Conductivity of Bimetallic Films
Authors: Dong Z. C. , Sheng L. , Zhang Weiyi , Xing D. Y. , Dong Jinming
Published: July 2002

We have extended our previous study on the electronic transport in metallic films to include the rough interface using the quantum statistical approach. The one-particle Green's function and the in-plane conductivity are calculated by taking into account both the quantum size effects and scattering processes resulting from bulk impurities, rough surfaces, and a rough interface. Our result shows that the conductivity is a sensitive function of interface roughness and decreases rapidly as the roughness increases. It is found that in the thin-film limit and in the lowest-order approximation of the surface and interface scatterings, the total conductivity is given by a sum of conductivities of all the subbands and the scattering rates for each subband due to the impurities, surfaces, and interface are additive.
THE GENERALIZED HÉNON MAPS: EXAMPLES FOR HIGHER-DIMENSIONAL CHAOS
Authors: RICHTER HENDRIK
Published: July 2002

The generalized Hénon maps (GHM) are discrete-time systems with given finite dimension, which show chaotic and hyperchaotic behavior for certain parameter values and initial conditions. A study of these maps is given where particularly higher-dimensional cases are considered.
HYPERBOLIC MODELS FOR CHEMOSENSITIVE MOVEMENT
Authors: HILLEN THOMAS
Published: July 2002

Chemosensitive movement describes the active orientation of individuals on chemical signals. In cases of cellular slime molds or flagellated bacteria, chemosensitive movement leads to aggregation and pattern formation. The classical mathematical model to describe chemosensitive movement is the diffusion based Patlak–Keller–Segel model. It suffers from the drawback of infinite propagation speeds. The relevant model parameters (motility and chemosensitivity) are related to population statistics. Hyperbolic models respect finite propagation speeds and the relevant model parameters (turning rate, distribution of new chosen velocities) are based on the individual movement patterns of the species at hand. In this paper hyperbolic models (in 1-D) and a transport model (in n-D) for chemosensitive movement are discussed and compared to the classical model. For the hyperbolic and transport models the following topics are reviewed: parabolic limit (which in some cases leads to the Patlak–Keller–Segel model), local and global existence, asymptotic behavior and moment closure. The moment closure approach leads to models based on Cattaneo's law of heat conduction (telegraph equation).
DIRECT INTERACTION BETWEEN BARYONS AND THE EXTENSION OF THE RELATIVISTIC MEAN FIELD THEORY FOR NUCLEAR MATTER
Authors: ZHANG QI-REN , GREINER WALTER
Published: July 2002

We propose a new version of the relativistic mean field theory for nuclear matter. The theory is based on an effective relativistic Lagrangian, in which, besides interactions via exchange mesons, baryons also interact with each other directly. The direct interaction is introduced to represent the compositeness of the baryon and to simulate the quark-quark interaction between them.
INVERSE PATCHWORK TRANSFORM
Authors: CHARLES P. D. , BROWN C. A. , JOHNSEN W. A.
Published: July 2002

The patchwork method uses triangular patches to estimate surface area as a function of patch size. The patch area can be interpreted as a scale of observation. Using the patchwork method, one can identify crossover scales, or thresholds, which distinguish scales where a surface is best described by Euclidean or fractal geometries. An inverse patchwork transform is proposed by which a set of relative areas and crossover data can be transformed to derive topographical data. The inverse patchwork transform and patchwork method provide mathematical basis functions for conversion between two domains-scales of observation and surface topography, providing a system for synthesizing surface data with desired characteristics. This method can also serve as a tool for aiding in surface design and manufacture.
THE PATCHWORK METHOD AND IMAGE PROCESSING
Authors: CHARLES P. D. , BROWN C. A.
Published: July 2002

The patchwork method uses triangular patches to estimate surface area as a function of patch size. The patch area can be interpreted as a scale of observation. Using the patchwork method, one can identify crossover scales, or thresholds, which distinguish scales where a surface is best described by Euclidean or fractal geometries. A method is proposed for application of the patchwork method to video images of luminance intensity data. By recursively subdividing an image and applying the patchwork method, or by using a moving average and applying the patchwork method to a set of small subimages, the patchwork method can be applied for each pixel in the source image to obtain a new set of pixel intensities. Depending which characteristic is used, crossover values or level of detail at varying scales of observation, the resulting intensities highlight regions of fractal complexity or boundaries between image segments best described by Euclidean or fractal geometries. Often, the resulting image displays interesting properties and is useful in feature recognition, image segmentation, and image enhancement.
FRACTAL PLASTIC SHEAR BANDS
Authors: POLIAKOV ALEXEI N. B. , HERRMANN HANS J. , PODLADCHIKOV YURI YU. , ROUX STÉPHANE
Published: July 2002

We present a numerical study model of shear bands in rocks with a non-associated plastic flow rule. The system drives spontaneously into a state in which the length distribution of shear bands follows a power law and where the spatial organization of the shear bands appears to be fractal. The distribution of local gradients in deviatoric strain rate has different scaling exponents for each moment which we calculate and discuss. Samples of granodiorite from the Pyrenees sheared under high confining pressure are analyzed and their properties compared with the numerical results.
EARLY SIMULTANEOUS INFLUENCE OF MANUFACTURING ACROSS STAGES OF THE PRODUCT DEVELOPMENT PROCESS: IMPACT ON TIME AND COST
Authors: COLLINS PAUL D. , HULL FRANK M.
Published: July 2002

This paper focuses on the concept of ESI (early simultaneous influence) as a cornerstone of concurrent engineering. How much influence downstream functions such as manufacturing engineering should exert in product design decisions is investigated by stage of development. Six stages were defined as: (1) research, (2) product concept, (3) prototype and test, (4) final design, (5) tooling and facilities, and (6) ramp-up to full production. Performance is measured as time compression at the tooling and facilities stage and reduction in manufactured cost. Results from analysis of 74 companies suggest that manufacturing influence has significant effects on performance at the first three stages. Its peak impact is at the third stage, a crossroads of work by up and downstream functions. If the design is new, however, the peak impact of ESI is earlier as indicated by significant interaction effects at the research and product concept stages. We also show that high levels of manufacturing influence at the end stage have a weak negative interaction effect with performance when designs are new. To the extent that high levels of manufacturing influence within their own domain preclude reciprocal influence by upstream functions, this result is consistent with the notion of concurrency as simultaneous influence by multiple functions at all points along the value chain.
Strategies for transitioning 'old economy' firms to e-business
Authors: Pinker Edieal J. , Seidmann Abraham , Foster Reginald C.
Published: July 2002

When devising an e-business strategy for legacy firms, be wary of the five myths of e-business development while embracing the five guidelines of managerial responsibility and leadership.
Understanding and overcoming resistance to ethnographic design research
Authors: Gilmore David
Published: July 2002

Have you ever had to convince someone about why an ethnographic approach is the right one to get information about users to drive design on a particular project? If so, you'll find the following article, by David Gilmore of IDEO, to be particularly helpful. David brings a lot of experience to this question: He has been involved in user-centered design for over 21 years, doing ethnographic design research at IDEO since 1997 and previously at Nottingham University and Apple Research Labs among others.One other note: You will notice that there is a new co-editor for the Business column, David Siegel. David has been working closely with me to edit this column for some time, so although this is the first article with him in an "official" role, it is not the first time he has made his mark on the magazine. Please join me in welcoming him. ---
Susan Dray
Back and forth between guarded and modal logics
Authors: Grädel Erich , Hirsch Colin , Otto Martin
Published: July 2002

Guarded fixed-point logic μGF extends the guarded fragment by means of least and greatest fixed points, and thus plays the same role within the domain of guarded logics as the modal μ-calculus plays within the modal domain. We provide a semantic characterization of μGF within an appropriate fragment of second-order logic, in terms of invariance under guarded bisimulation. The corresponding characterization of the modal μ-calculus, due to Janin and Walukiewicz, is lifted from the modal to the guarded domain by means of model theoretic translations. Guarded second-order logic, the fragment of second-order logic which is introduced in the context of our characterization theorem, captures a natural and robust level of expressiveness with several equivalent characterizations. For a wide range of issues in guarded logics it may take up a role similar to that of monadic second-order in relation to modal logics. At the more general methodological level, the translations between the guarded and modal domains make the intuitive analogy between guarded and modal logics available as a tool in the further analysis of the model theory of guarded logics.
The 3D visibility complex
Authors: Durand Frédo , Drettakis George , Puech Claude
Published: July 2002

Visibility problems are central to many computer graphics applications. The most common examples include hidden-part removal for view computation, shadow boundaries, mutual visibility of objects for lighting simulation. In this paper, we present a theoretical study of 3D visibility properties for scenes of smooth convex objects. We work in the space of light rays, or more precisely, ofmaximal free segments. We group segments that "see" the same object; this defines the3D visibility complex. The boundaries of these groups of segments correspond to thevisual eventsof the scene (limits of shadows, disappearance of an object when the viewpoint is moved, etc.). We provide a worst case analysis of the complexity of the visibility complex of 3D scenes, as well as a probabilistic study under a simple assumption for "normal" scenes. We extend the visibility complex to handle temporal visibility. We give an output-sensitive construction algorithm and present applications of our approach.
Wanted:project teams with a blend of is professional orientations
Authors: Klein Gary , Jiang James J. , Tesch Debbie B.
Published: July 2002

Desired qualities include a strong technical orientation, end-user empathy, and organizational awareness.
Safe 'composability' of middleware services
Authors: Venkatasubramanian Nalini
Published: July 2002

Look to composable middleware frameworks to ensure safe middleware interactions for ubiquitous computing applications.
The ever-expanding network of local and federal databases
Authors: Munro Neil
Published: July 2002

Walking the ethical and legal line when it comes to accessing personal information.
Cultural complications of ERP
Authors: Davison Robert
Published: July 2002

Valuable lessons learned from implementation experiences in parts of the world with different cultural heritages.
PAVING THE PATH
Authors: Benson A. A.
Published: July 2002

▪ Abstract  Fortuitous preparation and experiences led to the opportunity to use radioactive carbon dioxides to discern the path of carbon in photosynthesis. The search for the CO2 acceptor led to recognition of the growth stimulatory effect of methanol and its derivatives. With the techniques developed, radiochromatographic exploration led to discovery of major membrane lipids containing phosphorus, sulfur, and arsenic.
ROOTGRAVITROPISM: An Experimental Tool to Investigate Basic Cellular and Molecular Processes Underlying Mechanosensing and Signal Transmission in Plants
Authors: Boonsirichai K. , Guan C. , Chen R. , Masson P. H.
Published: July 2002

▪ Abstract  The ability of plant organs to use gravity as a guide for growth, named gravitropism, has been recognized for over two centuries. This growth response to the environment contributes significantly to the upward growth of shoots and the downward growth of roots commonly observed throughout the plant kingdom. Root gravitropism has received a great deal of attention because there is a physical separation between the primary site for gravity sensing, located in the root cap, and the site of differential growth response, located in the elongation zones (EZs). Hence, this system allows identification and characterization of different phases of gravitropism, including gravity perception, signal transduction, signal transmission, and curvature response. Recent studies support some aspects of an old model for gravity sensing, which postulates that root-cap columellar amyloplasts constitute the susceptors for gravity perception. Such studies have also allowed the identification of several molecules that appear to function as second messengers in gravity signal transduction and of potential signal transducers. Auxin has been implicated as a probable component of the signal that carries the gravitropic information between the gravity-sensing cap and the gravity-responding EZs. This has allowed the identification and characterization of important molecular processes underlying auxin transport and response in plants. New molecular models can be elaborated to explain how the gravity signal transduction pathway might regulate the polarity of auxin transport in roots. Further studies are required to test these models, as well as to study the molecular mechanisms underlying a poorly characterized phase of gravitropism that is independent of an auxin gradient.
RUBISCO: Structure, Regulatory Interactions, and Possibilities for a Better Enzyme
Authors: Spreitzer Robert J. , Salvucci Michael E.
Published: July 2002

▪ Abstract  Ribulose-1,5-bisphosphate (RuBP) carboxylase/oxygenase (Rubisco) catalyzes the first step in net photosynthetic CO2assimilation and photorespiratory carbon oxidation. The enzyme is notoriously inefficient as a catalyst for the carboxylation of RuBP and is subject to competitive inhibition by O2, inactivation by loss of carbamylation, and dead-end inhibition by RuBP. These inadequacies make Rubisco rate limiting for photosynthesis and an obvious target for increasing agricultural productivity. Resolution of X-ray crystal structures and detailed analysis of divergent, mutant, and hybrid enzymes have increased our insight into the structure/function relationships of Rubisco. The interactions and associations relatively far from the Rubisco active site, including regulatory interactions with Rubisco activase, may present new approaches and strategies for understanding and ultimately improving this complex enzyme.
PHYTOCHROMESCONTROLPHOTOMORPHOGENESIS BYDIFFERENTIALLYREGULATED, INTERACTINGSIGNALINGPATHWAYS INHIGHERPLANTS
Authors: Nagy Ferenc , Schäfer Eberhard
Published: July 2002

▪ Abstract  In this review the kinetic properties of both phytochrome A and B measured by in vivo spectroscopy in Arabidopsis are described. Inactivation of phyA is mediated by destruction and that of phyB by fast dark reversion. Recent observations, describing a complex interaction network of various phytochromes and cryptochromes, are also discussed. The review describes recent analysis of light-dependent nuclear translocation of phytochromes and genetic and molecular dissection of phyA- and phyB-mediated signal transduction. After nuclear transport, both phyA- and phyB-mediated signal transduction probably include the formation of light-dependent transcriptional complexes. Although this hypothesis is quite attractive and probably true for some responses, it cannot account for the complex network of phyA-mediated signaling and the interaction with the circadian clock. In addition, the biological function of phytochromes localized in the cytosol remains to be elucidated.
Error-Prone Repair DNA Polymerases in Prokaryotes and Eukaryotes
Authors: Goodman Myron F.
Published: July 2002

▪ Abstract  DNA repair is crucial to the well-being of all organisms from unicellular life forms to humans. A rich tapestry of mechanistic studies on DNA repair has emerged thanks to the recent discovery of Y-family DNA polymerases. Many Y-family members carry out aberrant DNA synthesis—poor replication accuracy, the favored formation of non-Watson-Crick base pairs, efficient mismatch extension, and most importantly, an ability to replicate through DNA damage. This review is devoted primarily to a discussion of Y-family polymerase members that exhibit error-prone behavior. Roles for these remarkable enzymes occur in widely disparate DNA repair pathways, such as UV-induced mutagenesis, adaptive mutation, avoidance of skin cancer, and induction of somatic cell hypermutation of immunoglobulin genes. Individual polymerases engaged in multiple repair pathways pose challenging questions about their roles in targeting and trafficking. Macromolecular assemblies of replication-repair “factories” could enable a cell to handle the complex logistics governing the rapid migration and exchange of polymerases.
Biological Roles of Proteases in Parasitic Protozoa
Authors: Klemba Michael , Goldberg Daniel E.
Published: July 2002

▪ Abstract  Proteases from a variety of protozoan parasites have been characterized at the molecular and cellular levels, and the many roles that proteases play in these organisms are coming into focus. Central roles have been proposed for proteases in diverse processes such as host cell invasion and egress, encystation, excystation, catabolism of host proteins, differentiation, cell cycle progression, cytoadherence, and both stimulation and evasion of host immune responses. Detailed structural and functional characterization of parasite proteases has led to novel insights into the workings of these fascinating catalytic machines. The possibility of developing selective inhibitors of key proteases of pathogenic parasites into novel chemotherapeutic strategies is being vigorously explored.
V(D)J Recombination: RAG Proteins, Repair Factors, and Regulation
Authors: Gellert Martin
Published: July 2002

▪ Abstract  V(D)J recombination is the specialized DNA rearrangement used by cells of the immune system to assemble immunoglobulin and T-cell receptor genes from the preexisting gene segments. Because there is a large choice of segments to join, this process accounts for much of the diversity of the immune response. Recombination is initiated by the lymphoid-specific RAG1 and RAG2 proteins, which cooperate to make double-strand breaks at specific recognition sequences (recombination signal sequences, RSSs). The neighboring coding DNA is converted to a hairpin during breakage. Broken ends are then processed and joined with the help of several factors also involved in repair of radiation-damaged DNA, including the DNA-dependent protein kinase (DNA-PK) and the Ku, Artemis, DNA ligase IV, and Xrcc4 proteins, and possibly histone H2AX and the Mre11/Rad50/Nbs1 complex. There may be other factors not yet known. V(D)J recombination is strongly regulated by limiting access to RSS sites within chromatin, so that particular sites are available only in certain cell types and developmental stages. The roles of enhancers, histone acetylation, and chromatin remodeling factors in controlling accessibility are discussed. The RAG proteins are also capable of transposing RSS-ended fragments into new DNA sites. This transposition helps to explain the mechanism of RAG action and supports earlier proposals that V(D)J recombination evolved from an ancient mobile DNA element.
Biochemistry of Na,K-ATPase
Authors: Kaplan Jack H.
Published: July 2002

▪ Abstract  The Na,K-ATPase or sodium pump carries out the coupled extrusion and uptake of Na and K ions across the plasma membranes of cells of most higher eukaryotes. It is a member of the P-type ATPase superfamily. This heterodimeric integral membrane protein is composed of a 100-kDa α-subunit with ten transmembrane segments and a heavily glycosylated β subunit of about 55 kDa, which is a type II membrane protein. Current ideas on how the protein achieves active transport are based on a fusion of results of transport physiology, protein chemistry, and heterologous expression of mutant proteins. Recently acquired high resolution structural information provides an important new avenue for a more complete understanding of this protein. In this review, the current status of knowledge of Na,K-ATPase is discussed, and areas where there is still considerable uncertainty are highlighted.
Lipoprotein Receptors in the Nervous System
Authors: Herz Joachim , Bock Hans H.
Published: July 2002

▪ Abstract  The low-density–lipoprotein (LDL) receptor family is an evolutionarily ancient gene family of structurally closely related cell-surface receptors. Members of the family are involved in the cellular uptake of extracellular ligands and regulate diverse biological processes including lipid and vitamin metabolism and cell-surface protease activity. Some members of the family also participate in cellular signaling and regulate the development and functional maintenance of the nervous system. Here we review the roles of this family of multifunctional receptors in the nervous system and focus on recent advances toward the understanding of the mechanisms by which lipoprotein receptors and their ligands transmit and modulate signals in the brain.
DNA Replication in Eukaryotic Cells
Authors: Bell Stephen P. , Dutta Anindya
Published: July 2002

▪ Abstract  The maintenance of the eukaryotic genome requires precisely coordinated replication of the entire genome each time a cell divides. To achieve this coordination, eukaryotic cells use an ordered series of steps to form several key protein assemblies at origins of replication. Recent studies have identified many of the protein components of these complexes and the time during the cell cycle they assemble at the origin. Interestingly, despite distinct differences in origin structure, the identity and order of assembly of eukaryotic replication factors is highly conserved across all species. This review describes our current understanding of these events and how they are coordinated with cell cycle progression. We focus on bringing together the results from different organisms to provide a coherent model of the events of initiation. We emphasize recent progress in determining the function of the different replication factors once they have been assembled at the origin.
Active Site Tightness and Substrate Fit in DNA Replication
Authors: Kool Eric T.
Published: July 2002

▪ Abstract  Various physicochemical factors influence DNA replication fidelity. Since it is now known that Watson-Crick hydrogen bonds are not necessary for efficient and selective replication of a base pair by DNA polymerase enzymes, a number of alternative physical factors have been examined to explain the efficiency of these enzymes. Among these factors are minor groove hydrogen bonding, base stacking, solvation, and steric effects. We discuss the concept of active site tightness in DNA polymerases, and consider how it might influence steric (size and shape) effects of nucleotide selection in synthesis of a base pair. A high level of active site tightness is expected to lead to higher fidelity relative to proteins with looser active sites. We review the current data on what parts and dimensions of active sites are most affected by size and shape, based on data with modified nucleotides that have been examined as polymerase substrates. We also discuss recent data on nucleotide analogs displaying higher fidelity than the natural ones. The published data are discussed with a view toward testing this sterically based hypothesis and unifying existing observations into a narrowly defined range of effects.
Nuclear Actin and Actin-Related Proteins in Chromatin Remodeling
Authors: Olave Ivan A. , Reck-Peterson Samara L. , Crabtree Gerald R.
Published: July 2002

▪ Abstract  The existence and function of actin in the nucleus has been hotly debated for forty years. Recently, β-actin was found to be a component of mammalian SWI/SNF-like BAF chromatin remodeling complexes and still more recently other SWI/SNF-related chromatin remodeling complexes in yeast, flies, and man. Although the function of actin in these chromatin remodeling complexes is only starting to be explored, the fact that actin is one of the most regulated proteins in the cell suggests that control of nuclear actin may be a critical regulatory point in the control of chromatin remodeling. Actin rapidly shuttles between the nucleus and the cytoplasm offering additional sites and modes of regulation. In addition, actin-related proteins (Arps) are also components of these chromatin remodeling complexes and have been implicated in transcriptional control in yeast. The observation that the BAF chromatin remodeling complex in which actin was originally identified, is also a human tumor suppressor complex necessary for the actions of the retinoblastoma protein indicates that the study of nuclear actin is likely to contribute to understanding cell growth control.
Biomechanical Dynamics of the Heart with MRI
Authors: Axel Leon
Published: July 2002

▪ Abstract  Magnetic resonance imaging (MRI) provides a noninvasive way to evaluate the biomechanical dynamics of the heart. MRI can provide spatially registered tomographic images of the heart in different phases of the cardiac cycle, which can be used to assess global cardiac function and regional endocardial surface motion. In addition, MRI can provide detailed information on the patterns of motion within the heart wall, permitting calculation of the evolution of regional strain and related motion variables within the wall. These show consistent patterns of spatial and temporal variation in normal subjects, which are affected by alterations of function due to disease. Although still an evolving technique, MRI shows promise as a new method for research and clinical evaluation of cardiac dynamics.
DNA Microarray Technology: Devices, Systems, and Applications
Authors: Heller Michael J.
Published: July 2002

▪ Abstract  In this review, recent advances in DNA microarray technology and their applications are examined. The many varieties of DNA microarray or DNA chip devices and systems are described along with their methods for fabrication and their use. This includes both high-density microarrays for high-throughput screening applications and lower-density microarrays for various diagnostic applications. The methods for microarray fabrication that are reviewed include various inkjet and microjet deposition or spotting technologies and processes, in situ or on-chip photolithographic oligonucleotide synthesis processes, and electronic DNA probe addressing processes. The DNA microarray hybridization applications reviewed include the important areas of gene expression analysis and genotyping for point mutations, single nucleotide polymorphisms (SNPs), and short tandem repeats (STRs). In addition to the many molecular biological and genomic research uses, this review covers applications of microarray devices and systems for pharmacogenomic research and drug discovery, infectious and genetic disease and cancer diagnostics, and forensic and genetic identification purposes. Additionally, microarray technology being developed and applied to new areas of proteomic and cellular analysis are reviewed.
Conformational Regulation of Integrin Structure and Function
Authors: Shimaoka Motomu , Takagi Junichi , Springer Timothy A.
Published: July 2002

▪ Abstract  Integrins are a structurally elaborate family of heterodimers that mediate divalent cation-dependent cell adhesion in a wide range of biological contexts. The inserted (I) domain binds ligand in the subset of integrins in which it is present. Its structure has been determined in two alternative conformations, termed open and closed. In striking similarity to signaling G proteins, rearrangement of a Mg2+-binding site is linked to large conformational movements in distant backbone regions. Mutations have been used to stabilize either the closed or open structures. These show that the snapshots of the open conformation seen only in the presence of a ligand or a ligand mimetic represent a high-affinity, ligand-binding conformation, whereas those of the closed conformation correspond to a low-affinity conformation. The C-terminal α-helix moves 10 Å down the side of the domain in the open conformation. Locking in the conformation of the preceding loop is sufficient to increase affinity for ligand 9000-fold. This C-terminal “bell-rope” provides a mechanism for linkage to conformational movements in other domains. The transition from the closed to open conformation has been implicated in fast (<1 s) regulation of integrin affinity in response to activation signals from inside the cell. Recent integrin structures and functional studies reveal interactions between β-propeller, I, and I-like domains in the headpiece, and a critical role for integrin EGF domains in the stalk region. These studies suggest that the headpiece of the integrin faces down toward the membrane in the inactive conformation and extends upward in a “switchblade”-like opening motion upon activation. These long-range structural rearrangements of the entire integrin molecule involving multiple interdomain contacts appear closely linked to conformational changes in the I domain, which result in increased affinity and competence for ligand binding.
Phase-Field Models for Microstructure Evolution
Authors: Chen Long-Qing
Published: July 2002

▪ Abstract  The phase-field method has recently emerged as a powerful computational approach to modeling and predicting mesoscale morphological and microstructure evolution in materials. It describes a microstructure using a set of conserved and nonconserved field variables that are continuous across the interfacial regions. The temporal and spatial evolution of the field variables is governed by the Cahn-Hilliard nonlinear diffusion equation and the Allen-Cahn relaxation equation. With the fundamental thermodynamic and kinetic information as the input, the phase-field method is able to predict the evolution of arbitrary morphologies and complex microstructures without explicitly tracking the positions of interfaces. This paper briefly reviews the recent advances in developing phase-field models for various materials processes including solidification, solid-state structural phase transformations, grain growth and coarsening, domain evolution in thin films, pattern formation on surfaces, dislocation microstructures, crack propagation, and electromigration.
Extending the Time Scale in Atomistic Simulation of Materials
Authors: Voter Arthur F. , Montalenti Francesco , Germann Timothy C.
Published: July 2002

▪ Abstract  Obtaining a good atomistic description of diffusion dynamics in materials has been a daunting task owing to the time-scale limitations of the molecular dynamics method. We discuss promising new methods, derived from transition state theory, for accelerating molecular dynamics simulations of these infrequent-event processes. These methods, hyperdynamics, parallel replica dynamics, temperature-accelerated dynamics, and on-the-fly kinetic Monte Carlo, can reach simulation times several orders of magnitude longer than direct molecular dynamics while retaining full atomistic detail. Most applications so far have involved surface diffusion and growth, but it is clear that these methods can address a wide range of materials problems.
Learning and Memory Functions of the Basal Ganglia
Authors: Packard Mark G. , Knowlton Barbara J.
Published: July 2002

▪ Abstract  Although the mammalian basal ganglia have long been implicated in motor behavior, it is generally recognized that the behavioral functions of this subcortical group of structures are not exclusively motoric in nature. Extensive evidence now indicates a role for the basal ganglia, in particular the dorsal striatum, in learning and memory. One prominent hypothesis is that this brain region mediates a form of learning in which stimulus-response (S-R) associations or habits are incrementally acquired. Support for this hypothesis is provided by numerous neurobehavioral studies in different mammalian species, including rats, monkeys, and humans. In rats and monkeys, localized brain lesion and pharmacological approaches have been used to examine the role of the basal ganglia in S-R learning. In humans, study of patients with neurodegenerative diseases that compromise the basal ganglia, as well as research using brain neuroimaging techniques, also provide evidence of a role for the basal ganglia in habit learning. Several of these studies have dissociated the role of the basal ganglia in S-R learning from those of a cognitive or declarative medial temporal lobe memory system that includes the hippocampus as a primary component. Evidence suggests that during learning, basal ganglia and medial temporal lobe memory systems are activated simultaneously and that in some learning situations competitive interference exists between these two systems.
QUANTUMMECHANICALMETHODS FORENZYMEKINETICS
Authors: Gao Jiali , Truhlar Donald G.
Published: July 2002

▪ Abstract  This review discusses methods for the incorporation of quantum mechanical effects into enzyme kinetics simulations in which the enzyme is an explicit part of the model. We emphasize three aspects: (a) use of quantum mechanical electronic structure methods such as molecular orbital theory and density functional theory, usually in conjunction with molecular mechanics; (b) treating vibrational motions quantum mechanically, either in an instantaneous harmonic approximation, or by path integrals, or by a three-dimensional wave function coupled to classical nuclear motion; (c) incorporation of multidimensional tunneling approximations into reaction rate calculations.
STUDIES OF POLYMER SURFACES BY SUM FREQUENCY GENERATION VIBRATIONAL SPECTROSCOPY
Authors: Chen Zhan , Shen Y. R. , Somorjai Gabor A.
Published: July 2002

▪ Abstract  Recently, sum frequency generation (SFG) vibrational spectroscopy has been developed into a powerful technique to study surfaces of polymer materials. This review summarizes the significant achievements in understanding surface molecular chemical structures of polymer materials obtained by SFG. It reviews in situ detection at the molecular level of surface structures of some common polymers in air, surface segregation of small end groups, polymer surface restructuring in water, and step-wise changed polymer blend surfaces. Studies of surface glass transition and surface structures modified by rubbing, plasma deposition, UV light irradiation, oxygen ion and radical irradiation, and wet etching are also discussed. SFG probing of polymer surfaces provides valuable insights into the relations between polymer surface structures and surface properties, which will assist in the design of polymer materials with desired surface properties.
ELECTRONIC STRUCTURE AND CATALYSIS ON METAL SURFACES
Authors: Greeley Jeff , Nørskov Jens K. , Mavrikakis Manos
Published: July 2002

▪ Abstract  The powerful computational resources available to scientists today, together with recent improvements in electronic structure calculation algorithms, are providing important new tools for researchers in the fields of surface science and catalysis. In this review, we discuss first principles calculations that are now capable of providing qualitative and, in many cases, quantitative insights into surface chemistry. The calculations can aid in the establishment of chemisorption trends across the transition metals, in the characterization of reaction pathways on individual metals, and in the design of novel catalysts. First principles studies provide an excellent fundamental complement to experimental investigations of the above phenomena and can often allow the elucidation of important mechanistic details that would be difficult, if not impossible, to determine from experiments alone.
Mathematics in Sociology
Authors: Edling Christofer R.
Published: July 2002

▪ Abstract  Since mathematical sociology was firmly established in the 1960s, it has grown tremendously. Today it has an impressive scope and deals with topical problems of social structure and social change. A distinctive feature of today's use of mathematics in sociology is the movement toward a synthesis between process, structure, and action. In combination with an increased attention to social mechanisms and the problems of causality and temporality, this synthesis can add to its relevance for sociology in general. The article presents recent advances and major sociological research streams in contemporary sociology that involve the application of mathematics, logic, and computer modeling.