bluuebunny/crossref_metadata_2025_split huggingface dataset:
X-ray instrumentation for protein crystallography with SR (abstract)
Authors: Popov A. N. , Kheiker D. M. , Harutunyan E. G. 
Published: July 2002

The station is intended for x-ray analysis of single crystals, primarily that of proteins with the beam of synchrotron radiation from the superconducting wiggler of a special storage ring E=2.0 GeV, I=0.3 A in the town of Zelenograd (TNK).1 The dimensions of the radiation source are 2.352 σx⋅σz=1.5×0.05 mm2, the brightness for λ=1.5 Å is 1015 photon/(s mm2 mrad.2 0.1% (Δλ/λ)). The station comprises the device forming the monochromatized primary beam (λ=0.5–2.2 Å, Δλ/λ−3∼10−4) that consists of an asymmetric focusing monochromator with triangular-shaped Si or Ge crystal curved as a round cylinder,2 a segmented mirror of total external reflection placed behind the monochromator on a rotating bench consisting of 8 flat glass 200×50×25 mm2 segments that form a surface imitating an elliptical cylinder, three pairs of horizontal and vertical slits, monitor–ionization chamber, four-circle diffractometer with scintillation counter and horizontal main axis placed on the adjustable carriage that can turn about the monochromator axis; position-sensitive proportional chamber with spherical drift space, 512×512 elements of space resolution and time resolution of 106 photons per second that can be vertically shifted and bent around the holder horizontal axis. The monochromator goniometer as well as the crystal bend and the mirror segments are driven by the multiple-turn potientiometers by the computer and CAMAC interface.
The automatic four-circle goniometer device is controlled by stepping drives, the angles being controlled by means of 16 register absolute optoelectronic detectors and the same computer. The data from the position-sensitive detector are read through the increment channel to annex memory of 256 K word (16 registered) capacity in the CAMAC block and then to the computer to be followed by visualization on the coloured display. All the station units are to be manufactured in 1991. The working out and manufacturing of the instrumentation is being fulfilled by the Institute of Crystallography of the USSR Academy of Sciences, the Department of nonfilm chambers of the High Energy Laboratory of the Joint Institute for Nuclear Research (Dubna) and the Special Design Bureau at the Institute of Crystallography.
Photodissociation processes in the CH molecule
Authors: van Dishoeck Ewine F. 
Published: July 2002

The photodissociation processes in the CH molecule have been investigated using ab initio self-consistent-field with configuration-interaction (CI) methods. Potential energy curves of all states which dissociate into the lowest four atomic limits have been calculated, as well as those of several higher-lying states with Rydberg character. Transition dipole moments connecting the excited states with the lowest states have been obtained. Direct photodissociation of CH may occur by absorption into the continua of the B 2∑− and 2 2∑+ states, and cross sections for absorption from the X 2Π v″=0 state into these states are reported. Indirect photodissociation of CH may take place by absorption into bound states, which are subsequently dissociated through interactions with continuum states. The A 2Δ vibrational levels couple with the continuum of the X 2Π state through the nuclear rotational operator. The nuclear rotational coupling elements have been obtained from the CI wave functions, and predissociation rates are presented. The C 2∑+ v′=0 state is shown to be predissociated efficiently by spin-orbit coupling with the B 2∑− state. The 2, 3, and 4 2Π states of CH interact strongly through the radial nuclear kinetic energy operator. The nuclear radial coupling elements between these states have been computed by numerical differentiation of the CI wave functions. The coupled equations for the nuclear wave functions have been solved in a diabatic formulation. The calculated cross section for
absorption into the coupled states is similar to that found recently for absorption into the 2 2Π and 3 2Π states of the OH molecule: it consists of a series of resonances with asymmetric Beutler–Fano profiles superimposed on a strong continuous background. The 3(F)2∑+ state, as well as the higher-lying (Rydberg) states, may interact with the 2Π states through rotational coupling or with the 2 4∑− state through spin-orbit coupling. Due to uncertainties in the coupling elements, the efficiencies with which these states are dissociated are not well determined, but they are probably small for most states. The photodissociation rate of CH by the unattenuated interstellar radiation field has been computed. The total rate is 9.5×10−10 s−1. The 2 2∑+ and coupled 2Π channels are most effective in the photodissociation of interstellar CH.
Coverage dependent desorption kinetics of CO from Rh(111) using time-resolved specular helium scattering
Authors: Peterlinz K. A. , Curtiss T. J. , Sibener S. J. 
Published: July 2002

Linearized measurements of the coverage dependent desorption rates of CO from Rh(111) were made with a novel three molecular beam apparatus. To measure these isothermal and essentialy isosteric rates we introduce a new kinetic response amplifier, namely time-resolved specular helium scattering, which makes use of the large attenuation cross section that CO has for specular helium scattering. The measurements are made by using one intense and continuous CO beam to establish a specific adsorbate coverage while another low intensity and chopped CO beam is used to weakly modulate the adsorbate density around the selected steady state. The transient helium reflectivity waveforms we measure during the modulated CO scattering contain the desired kinetic information, and are typically one to almost two orders of magnitude more sensitive to the desorption kinetics than are the signals arising from direct detection of desorbing CO. Desorption rates are reported for 0≤θCO≤0.22 and 440 K ≤TS≤555 K.
He diffraction measurements revealed that the CO overlayer was disordered for all conditions for which kinetics were measured, and that the sticking coefficient varied with coverage as S0(1−3θ). At least a second order expansion of the chemical potential in terms of CO coverage was needed to explain these rates. The experimentally determined desorption rates can be fit equally well by placing the coverage dependence in either the pre-exponential factor or in the activation energy: k(θ,TS) =1.33×1014 exp[0.344θ+48.8θ2 −(32.3 kcal/mol)/(kbTS)]s−1, k(θ,TS) =1.33×1014 exp[−(32.3−1.62θ −38.3θ2 kcal/mol)/(kbTS)] s−1. The measured He diffraction data, sticking coefficient, specular He scattering attenuation vs CO coverage, and increase in CO desorption rate with increasing coverage imply nearest-neighbor repulsive interactions. The use of time-resolved specular He scattering for studying coverage dependent reactions is also discussed.
Chemistry in strong laser fields: An example from methyl iodide photodissociation
Authors: Hammerich Audrey Dell , Kosloff Ronnie , Ratner Mark A. 
Published: July 2002

Time-dependent quantum-mechanical theories and simulations provide a clear and intuitive description of molecular processes. Due to ensuing simplification of the theory and the generally employed numerical algorithms, the vast majority of these treatments are based upon perturbation theory. Especially in light of the current level of experimental sophistication, with experiments being realized which are influenced by the spectral, temporal, and spatial shape of the laser pulse, it is important to move beyond treatments limited to weak fields or idealized δ-function wave forms. Various methods to examine the results of high-field simulations are presented. All of the techniques are shown to have the familiar linear response form in the weak-field limit. In a time-dependent framework the difference between the linear and nonlinear response expressions can be seen from expectation values over stationary versus nonstationary states. The high-field photodissociation of methyl iodide illustrates this approach. Methyl iodide represents a physical system well suited for examining the effects of such exciting laser-field characteristics as strength, linewidth, and frequency upon the photodissociation dynamics. Its dissociation occurs upon coupled repulsive excited electronic potential-energy surfaces which have recently been revised to fit the most current experimental data. The effect of the surface intersection has previously been typically studied by examining the branching and the internal state distributions of the products in the two channels as a function of excitation frequency only.
The collinear photodissociation dynamics is examined using a numerically exact time-dependent quantum-mechanical method. The equations of motion for the amplitudes upon the ground and two coupled excited electronic surfaces, explicitly incorporating the laser field, are integrated by a scheme which employs a low-order polynomial approximation to the evolution operator. The effects of the three field characteristics upon the branching ratio and internal state distributions of the products and the spectroscopy of the process are delineated. The course of the photodissociation dynamics is shown to be affected by these characteristics. The results demonstrate the causal connections between the pulse shape and the resulting photoprocesses. Practical manifestations of strong fields (power broadening, sub-threshold absorption, higher harmonic generation, emission shaping of the ground state, temporal development) are stressed.
Molecular dynamics of water in oriented DPPC multilayers studied by quasielastic neutron scattering and deuterium-nuclear magnetic resonance relaxation
Authors: König S. , Sackmann E. , Richter D. , Zorn R. , Carlile C. , Bayerl T. M. 
Published: July 2002

The dynamics of water between highly oriented multilayers of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) has been studied in two time domains at different hydration levels. Incoherent quasielastic neutron scattering (QENS) and deuterium-nuclear magnetic resonance (NMR) longitudinal (T1) relaxation were employed to investigate both the high-frequency motions of water (10−9–10−11 s time scale) and their anisotropy, while 2H-NMR transverse (T2) relaxation was used for obtaining information on low frequency dynamical processes (microsecond time scale). Our results show that high frequency dynamics (picosecond-time scale) at low hydration (three to four water molecules per lipid) can be understood solely as a uniaxial rotation of the water molecules tightly bound to DPPC head groups with a correlation time τrot≊62 ps at 55 °C and a rotational radius of 1±0.1 Å, but with no detectable translational degrees of freedom. The 2H-NMR T1 data (nanosecond-time scale) can be explained satisfactorily on the basis of fast rotations with the correlation time above and a slower reorientation of the rotational axis (correlation time τ1≊6 ns).
Both QENS and 2H-NMR T1 measurements provide an apparent activation energy of Ea=32±1.0 kJ/mol for this process. Increasing the hydration level of the multilayers leaves the rotational motion essentially unchanged, but enables additional translational motion which can be considered as a jump diffusion process (diffusion coefficient D=16±1×10−10 m2/s at 44 °C and a mean residence time of τ0=2.0±0.5 ps) of nonbound water. It is interesting to note that this diffusion is completely isotropic on the characteristic length scale of this QENS experiment (≤10 Å). Temperature variation shows that the phase state of the lipids has no significant effect on the high frequency dynamics of the water molecules. Measurements of the 2H-NMR quadrupolar splitting of water (D2O) at temperatures around the phase transition temperature Tm of the oriented DPPC multilayers clearly show a coexistence of the crystalline Lβ′ phase and of the fluid Lα phase over a range of up to 4 °C at both sides of Tm. The intermediate Pβ′ (‘‘ripple’’) phase is suppressed as we worked at hydration levels below saturation. In the coexistence range, exchange of water takes place between crystalline and fluid lipid domains due to water diffusion. This exchange causes a pronounced minimum of the 2H-NMR transverse relaxation time T2 at Tm since this low frequency process satisfies approximately a critical damping condition for a two-site chemical exchange process.
Molecular dynamics simulations of liquid, interface, and ionic solvation of polarizable carbon tetrachloride
Authors: Chang Tsun-Mei , Peterson Kirk A. , Dang Liem X. 
Published: July 2002

In this study, we construct a nonadditive polarizable model potential to describe the intermolecular interactions between carbon tetrachloride, CCl4, based on classical molecular dynamics techniques. The potential parameters are refined to accurately describe the experimental thermodynamic and structural properties of liquid CCl4 at 298 K. We then carried out additional liquid CCl4 simulations at temperatures in the range of 250–323 K to examine the temperature dependence of the thermodynamic properties. The computed liquid densities and the enthalpies of vaporization are in excellent agreement with experimental values. The structures of liquid CCl4 can be analyzed by examining the radial distribution functions and angular distribution functions. It is found that the liquid CCl4 forms an interlocking structure and that a local orientational correlation is observed between neighboring CCl4 molecules. We also investigate the CCl4 liquid/vapor interface using this potential model. The density profile shows that the interface is not sharp at a microscopic level and has a thickness of roughly 5 Å at 273 K. The results of angular distribution function calculations suggest that CCl4 molecules do not have a preferred orientation at the interface. The calculated surface tension is 31±2 dyn/cm, in good agreement with the experimental value of 28 dyn/cm. This model potential is also used to examine the interactions between Cs+ and small (CCl4)n (n=1–6) clusters. A tetrahedral configuration is found for the minimum structure of the Cs+(CCl4)4 cluster.
It is noticed that the polarization energy is the dominant component of the total interaction of these ionic clusters, indicating the importance of including explicitly the polarization in the ionic interactions. In the study of Cs+ solvation in liquid CCl4, we observe a well-defined solvation shell around the Cs+ with a coordination number of six CCl4 molecules. It is also found that Cs+ induces a strong local orientational order in liquid CCl4. Accurate ab initio electronic structure calculations were also carried out on the CCl4 dimer and the Cs+(CCl4) cluster to compare to the results from the molecular dynamics simulations.
Polar solvation dynamics of polyatomic solutes: Simulation studies in acetonitrile and methanol
Authors: Kumar P. V. , Maroncelli M. 
Published: July 2002

This paper describes results of simulations of solvation dynamics of a variety of solutes in two reference solvents, acetonitrile and methanol. Part of these studies involve attempts to realistically model the solvation dynamics observed experimentally with the fluorescence probe coumarin 153 (C153). After showing that linear response simulations afford a reliable route to the dynamics of interest, experimental and simulation results for C153 are compared. Agreement between the observed and calculated dynamics is found to be satisfactory in the case of acetonitrile but poor in the case of methanol. The latter failure is traced to a lack of realism in the dielectric properties of the methanol model employed. A number of further simulations are then reported for solvation of a number of atomic, diatomic, and benzenelike solutes which are used to elucidate what features of the solute are important for determining the time dependence of the solvation response. As far as large polyatomic solutes like C153 are concerned, the solute attribute of foremost importance is shown to be the ‘‘effective moment’’ of its charge distribution (actually the difference between the S1 and S0 charge distributions). This effective moment, determined from consideration of continuum electrostatics, provides a simple measure of how rapidly the solute’s electric field varies spatially in the important regions of the solvent. Simulations of fictitious excitations in a benzene solute show that this single quantity is able to correlate the dynamics observed in widely different solutes.
Also explored is the effect of solute motion on its solvation dynamics. While of minor relevance for large solutes like C153, in small solutes of the size of benzene, solute motion can dramatically enhance the rate of solvation. A model based on independent solvent dynamics and solute rotational motion is able to account for the bulk of the observed effects. Finally, the influence of solute polarizability on solvation dynamics is considered. Simulations of diatomic molecules with a classical polarizability show that the rate of solvation decreases roughly in proportion to the polarizability of the solute. This dynamical effect can be understood in terms of the change that polarizability produces on the solvation force constant. These simulations indicate that the magnitude of the effect should be relatively small (10%–25%) in real systems, at least in the linear response limit.
Relevance Theory And Pragmatic Impairment
Authors: Leinonen Eeva , Kerbel Debra 
Published: July 2002

AbstractThis paper summarizes aspects of relevance theory that are useful for exploring impairment of pragmatic comprehension in children. It explores data from three children with pragmatic language diffi culties within this framework. Relevance theory is seen to provide a means of explaining why, in a given context, a particular utterance is problematic. It thus enables one to move on from mere description of problematic behaviours towards their explanation. The theory provides a clearer delineation between the explicit and the implicit, and hence between semantics and pragmatics. This enables one to place certain difficulties more firmly within semantics and others within pragmatics. Relevance, and its maximization in communication, are squarely placed within human cognition, which suggests a close connection between pragmatic and cognitive (dis)functioning. Relevance theory thus emerges as a powerful tool in the exploration and understanding of pragmatic language difficulties in children and offers therapeutically valuable insight into the nature of interactions involving individuals with such impairments.
Fast probabilistic analysis of sequence function using scoring
matrices
Authors: Wu Thomas D. , Nevill-Manning Craig G. , Brutlag Douglas L. 
Published: July 2002

Abstract
*To whom correspondence should be addressed.
3Present address: Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA. E-mail: twu@gene.com.
Motivation: We present techniques for increasing the speed of sequence analysis using scoring matrices. Our techniques are based on calculating, for a given scoring matrix, the quantile function, which assigns a probability, or p, value to each segmental score. Our techniques also permit the user to specify a p threshold to indicate the desired trade-off between sensitivity and speed for a particular sequence analysis. The resulting increase in speed should allow scoring matrices to be used more widely in large-scale sequencing and annotation projects.
Results: We develop three techniques for increasing the speed of sequence analysis: probability filtering, lookahead scoring, and permuted lookahead scoring. In probability filtering, we compute the score threshold that corresponds to the user-specified p threshold. We use the score threshold to limit the number of segments that are retained in the search process. In lookahead scoring, we test intermediate scores to determine whether they will possibly exceed the score threshold. In permuted lookahead scoring, we score each segment in a particular order designed to maximize the likelihood of early termination. Our two lookahead scoring techniques reduce substantially the number of residues that must be examined. The fraction of residues examined ranges from 62 to 6%, depending on the p threshold chosen by the user. These techniques permit sequence analysis with scoring matrices at speeds that are several times faster than existing programs. On a database of 12 177 alignment blocks, our techniques permit sequence analysis at a speed of 225 residues/s for a p threshold of 10−6, and 541 residues/s for a p threshold of 10−20.
In order to compute the quantile function, we may use either an independence assumption or a Markov assumption. We measure the effect of first- and second-order Markov assumptions and find that they tend to raise the p value of segments, when compared with the independence assumption, by average ratios of 1.30 and 1.69, respectively. We also compare our technique with the empirical 99.5th percentile scores compiled in the BLOCKSPLUS database, and find that they correspond on average to a p value of 1.5 × 10−5.
Availability: The techniques described above are implemented in a software package called EMATRIX. This package is available from the authors for free academic use or for licensed commercial use. The EMATRIX set of programs is also available on the Internet at http://motif.stanford.edu/ematrix.
Binary analysis and optimization-based normalization of gene
expression data
Authors: Shmulevich Ilya , Zhang Wei 
Published: July 2002

Abstract
Motivation: Most approaches to gene expression analysis use real-valued expression data, produced by high-throughput screening technologies, such as microarrays. Often, some measure of similarity must be computed in order to extract meaningful information from the observed data. The choice of this similarity measure frequently has a profound effect on the results of the analysis, yet no standards exist to guide the researcher.
Results: To address this issue, we propose to analyse gene expression data entirely in the binary domain. The natural measure of similarity becomes the Hamming distance and reflects the notion of similarity used by biologists. We also develop a novel data-dependent optimization-based method, based on Genetic Algorithms (GAs), for normalizing gene expression data. This is a necessary step before quantizing gene expression data into the binary domain and generally, for comparing data between different arrays. We then present an algorithm for binarizing gene expression data and illustrate the use of the above methods on two different sets of data. Using Multidimensional Scaling, we show that a reasonable degree of separation between different tumor types in each data set can be achieved by working solely in the binary domain. The binary approach offers several advantages, such as noise resilience and computational efficiency, making it a viable approach to extracting meaningful biological information from gene expression data.
Contact: is@ieee.org