bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing irregular surfaces to enclose macromolecular complexes for mesoscale modeling using the discrete surface charge optimization (DISCO) algorithm
Authors: Zhang Qing , Beard Daniel A. , Schlick Tamar 
Published: October 2003

AbstractSalt‐mediated electrostatics interactions play an essential role in biomolecular structures and dynamics. Because macromolecular systems modeled at atomic resolution contain thousands of solute atoms, the electrostatic computations constitute an expensive part of the force and energy calculations. Implicit solvent models are one way to simplify the model and associated calculations, but they are generally used in combination with standard atomic models for the solute. To approximate electrostatics interactions in models on the polymer level (e.g., supercoiled DNA) that are simulated over long times (e.g., milliseconds) using Brownian dynamics, Beard and Schlick have developed the DiSCO (Discrete Surface Charge Optimization) algorithm. DiSCO represents a macromolecular complex by a few hundred discrete charges on a surface enclosing the system modeled by the Debye‐Hückel (screened Coulombic) approximation to the Poisson‐Boltzmann equation, and treats the salt solution as continuum solvation. DiSCO can represent the nucleosome core particle (>12,000 atoms), for example, by 353 discrete surface charges distributed on the surfaces of a large disk for the nucleosome core particle and a slender cylinder for the histone tail; the charges are optimized with respect to the Poisson‐Boltzmann solution for the electric field, yielding a ∼5.5% residual. Because regular surfaces enclosing macromolecules are not sufficiently general and may be suboptimal for certain systems, we develop a general method to construct irregular models tailored to the geometry of macromolecules. We also compare charge optimization based on both the electric field and electrostatic potential refinement. Results indicate that irregular surfaces can lead to a more accurate approximation (lower residuals), and the refinement in terms of the electric field is more robust. We also show that surface smoothing for irregular models is important, that the charge optimization (by the TNPACK minimizer) is efficient and does not depend on the initial assigned values, and that the residual is acceptable when the distance to the model surface is close to, or larger than, the Debye length. We illustrate applications of DiSCO's model‐building procedure to chromatin folding and supercoiled DNA bound to Hin and Fis proteins. DiSCO is generally applicable to other interesting macromolecular systems for which mesoscale models are appropriate, to yield a resolution between the all‐atom representative and the polymer level. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2063–2074, 2003
Ab initio quality properties for macromolecules using the ADMA approach
Authors: Exner Thomas E. , Mezey Paul G. 
Published: October 2003

AbstractWe describe new developments of an earlier linear scaling algorithm for ab initio quality macromolecular property calculations based on the adjustable density matrix assembler (ADMA) approach. In this approach, a large molecule is divided into fuzzy fragments, for which quantum chemical calculations can easily be done using moderate‐size “parent molecules” that contain all the local interactions within a selected distance. If greater accuracy is required, a larger distance is chosen. With the present extension of this approximation, properties of the large molecules, like the electron density, the electrostatic potential, dipole moments, partial charges, and the Hartree–Fock energy are calculated. The accuracy of the method is demonstrated with test cases of medium size by comparing the ADMA results with direct quantum chemical calculations. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1980–1986, 2003
Bond energies for molecules, clusters, and deposit systems
Authors: Jug Karl , Geudtner Gerald 
Published: October 2003

AbstractA new approach is suggested to the assignment of bond energies in molecules and clusters. It uses a shareholder principle for the redistribution of the shifts in atomic energies, which arise in a molecule, on the bonds. The scheme is directly suitable for semiempirical methods, where only one‐ and two‐center terms occur. MSINDO calculations are performed to demonstrate the suitability of the approach for molecules and clusters. As an application the bonding in a deposit system is analyzed for the case of copper on magnesium oxide. It is found that copper atoms do not only bind to the preferred oxygen sites but also substantially to the magnesium sites. The copper‐copper bonds are the strongest and will determine the structure of copper clusters on magnesium oxide surfaces. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2013–2022, 2003
An environmental pseudopotential approach to molecular interactions: Implementation in MOLPRO
Authors: Valderrama E. , Wheatley R. J. 
Published: October 2003

AbstractWe present the implementation into the MOLPRO package of a model for the interaction of a central system with its surrounding environment. The properties of a target system enclosed by a noncovalently bound environment or solvent are modeled as those of a system embedded into the effective pseudopotential arising from the exact electrostatic Coulomb potential and the approximated exchange–repulsion potential. For the latter we use the charge‐density overlap model, which relates the exchange–repulsion interaction energy between two species with the overlap of their ground‐state electron charge densities. The solutions of the modified Hartree–Fock equations for the target system are obtained self‐consistently. This way the exchange–induction effects arising from the converged electron–charge density of the embedded system are implicitly included. Inclusion of the correlation effects is provided by the use of post‐Hartree–Fock and density–functional techniques available in the MOLPRO package. The computational and conceptual advantages provided by this approach are shown in the calculation of the dipole polarizabilities of halide and chalcogenide anions in different environments. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2075–2082, 2003
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA‐LF
Authors: Piquemal Jean‐Philip , Williams‐Hubbard Ben , Fey Natalie , Deeth Robert J. , Gresh Nohad , Giessner‐Prettre Claude 
Published: October 2003

AbstractTo account for the distortion of the coordination sphere that takes place in complexes containing open‐shell metal cations such as Cu(II), we implemented, in sum of interactions between fragments ab initio computed (SIBFA) molecular mechanics, an additional contribution to take into account the ligand field splitting of the metal d orbitals. This term, based on the angular overlap model, has been parameterized for Cu(II) coordinated to oxygen and nitrogen ligands. The comparison of the results obtained from density functional theory computations on the one hand and SIBFA or SIBFA‐LF on the other shows that SIBFA‐LF gives geometric arrangements similar to those obtained from quantum mechanical computations. Moreover, the geometric improvement takes place without downgrading the energetic agreement obtained from SIBFA. The systems considered are Cu(II) interacting with six water molecules, four ammonia or four imidazoles, and four water plus two formate anions. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1963–1970, 2003
Theoretical study of the internal elimination reactions of xanthate precursors
Authors: Claes L. , François J.‐P. , Deleuze M. S. 
Published: October 2003

AbstractThe gas‐phase internal elimination (Ei) reaction of ethyl xanthate (CH3‐CH2‐S‐CS‐O‐CH3) has been investigated by means of Hartree–Fock, second‐order Møller–Plesset, and density functional theory (DFT) using the Becke three‐parameter Lee–Yang–Parr (B3LYP) functional and the modified Perdew–Wang one‐parameter model for kinetics (MPW1K). Considerable differences between the ground‐ and transition‐state geometries and the calculated activation energies are observed from one approach to the other, which justifies first a careful calibration of the methods against the results of benchmark CCSD(T) calculations. Compared with these, DFT calculations along with the MPW1K functional are found to be an appropriate choice for describing the Ei reaction of xanthate precursors. The precursor conformation and the transition states involved in the internal conversion of xanthate precursors of cyano derivatives of ethylene, and of cis‐ and trans‐stilbene, are then characterized in detail by means of this functional. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2023–2031, 2003
A dynamic mean field theory for dissipative interacting many‐electron systems: Markovian formalism and its implementation
Authors: Yokojima Satoshi , Chen Guanhua , Xu Ruixue , Yan Yijing 
Published: October 2003

AbstractTo demonstrate its applicability for realistic open systems, we apply the dynamic mean field quantum dissipative theory to simulate the photo‐induced excitation and nonradiative decay of an embedded butadiene molecule. The Markovian approximation is adopted to further reduce the computational time, and the resulting Markovian formulation assumes a variation of Lindblad's semigroup form, which is shown to be numerically stable. In the calculation, all 22 valence electrons in the butadiene molecule are taken as the system and treated explicitly while the nuclei of the molecules are taken as the immediate bath of the system. It is observed that (1) various excitations decay differently, which leads to different peak widths in the absorption spectra; and (2) the temperature dependences of nonradiative decay rates are distinct for various excitations, which can be explained by the different electron‐phonon couplings. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 2083–2092, 2003
Social development: the intellectual heritage
Authors: Midgley James 
Published: October 2003

AbstractBecause social development is primarily concerned with practical matters, little attention has been paid to the ideas, concepts and theories that inform social development interventions. Most publications on social development make little reference to theoretical issues, and most practitioners are unaware of the conceptual derivation of their activities. However, although seldom recognized or acknowledged, social development practice has, in a subtle and indirect way, been informed and shaped by a variety of intellectual ideas that, in turn, reveal a commitment to different normative perspectives. This paper traces the contribution these perspectives have made to social development over the years. By documenting this intellectual heritage, it hopes to promote a greater awareness of theoretical issues and, at the same time, to foster social development's conceptualization. Copyright © 2003 John Wiley & Sons, Ltd.
The practice of design: developing the Chars Livelihoods Programme in Bangladesh
Authors: Brocklesby Mary Ann , Hobley Mary 
Published: October 2003

AbstractThis article examines development programme design, using the Chars Livelihoods Programme in Bangladesh as a case study. Central to the Programme was the need to address the deep structural barriers preventing the exercise of voice by the extreme poor. By describing how this issue was tackled in the design process, the article explores the room for manoeuvre to engage in processes of social development relating to extreme poverty by focusing on ‘citizen participation’, ‘voice’ and ‘responsiveness’. It argues that within the confines of a conventional, bureaucratic planning process, opportunities to be innovative may be limited. However, to refuse the challenge, is to disregard the role design plays in opening up spaces for future action. It concludes by arguing that design is an inherently politicised process, which involves choices about whose voice is heard, whose power is respected and whose is disputed. This issue cannot be ignored by initiatives that seek to eliminate extreme poverty through citizenship participation in development. Copyright © 2003 John Wiley & Sons, Ltd.
Social development as knowledge building: research as a sphere of policy influence
Authors: Fisher Eleanor , Holland Jeremy D. 
Published: October 2003

AbstractThe value of using social development knowledge as a tool for building development policy was promoted by the British bilateral donor in the late 1990s. This article takes the case of a capacity building initiative that sought to build social development knowledge as a resource for policy formulation in ‘southern’ countries. Situating knowledge as a development resource presents difficulties for intervention processes that have historically developed to provide access to economic and social assets. This article highlights some of the problems involved in trying to build social development capacity and questions the suitability of this style of intervention. Inappropriate and short‐term support for knowledge capacity building carries the danger that the traditional separation between the academic and practice spheres will be reinforced, making the process of democratising social knowledge more difficult. Copyright © 2003 John Wiley & Sons, Ltd.
Organizational meta‐scripts as a source of high reliability: the case of an army armored brigade
Authors: Zohar Dov , Luria Gil 
Published: October 2003

AbstractMany high‐reliability organizations must deal with the problem of requisite cognitive variety in operators of interactively complex technological systems. The present study describes an organizational script strategy dealing with this problem, based on development of shared meta‐scripts sustained by continuous learning. Analysis of mission briefing and debriefing protocols in an armored brigade indicated that most task‐related interactions were based on script language (i.e., verbs and action phrases signifying particular meta‐scripts and relevant contingencies). These protocols suggest that script‐trained operators construe complex missions as interchangeable combinations of 15 meta‐scripts, reducing cognitive demands or requisite variety to manageable proportions. An ongoing learning process, maintained via repeated script‐based feedback during debriefings, further reduces cognitive demands by increasing available variety in operators. Implications for performance reliability in ordinary organizations are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Organizational climate as a moderator of safety knowledge–safety performance relationships
Authors: Smith‐Crowe Kristin , Burke Michael J. , Landis Ronald S. 
Published: October 2003

AbstractUsing training history data and supervisory ratings of 133 hazardous waste workers' safety performance collected within two organizations in the U.S. nuclear waste industry, this study examined organizational climate for the transfer of safety training as a moderator of relationships between safety knowledge and safety performance. The trend in the results was consistent with the hypothesis that these relationships would be stronger in the less restrictive (more supportive) organizational climate. The implications of these findings for promoting safe work behaviors through the creation of a positive and strategically focused organizational climate for the transfer of safety training are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Latent errors and adverse organizational consequences: a conceptualization
Authors: Ramanujam Rangaraj , Goodman Paul S. 
Published: October 2003

AbstractWe develop the concept of latent errors—uncorrected deviations from procedures and policies that have no direct adverse consequences—and examine the complex relationships between organizational antecedents, latent errors, and adverse consequences. Latent errors, with varying levels of frequency, are present in all organizations whereas extreme adverse outcomes are rare. Thus, all organizations become potential objects of study in research on errors. Latent errors enable the design of ex ante studies of errors that avoid sampling on the dependent variable. The basic elements of our framework focus on two critical linkages. First is the role of antecedent factors such as incentives and goals in contributing to the presence of latent errors. Second, we explore how positive and negative feedback systems and external triggers link an acceleration of latent errors with adverse organizational outcomes. We also discuss how variations in context (e.g., whether work activities are co‐located or distributed) may affect these factors. Implications for research on high‐reliability organizations are discussed. Copyright © 2003 John Wiley & Sons, Ltd.
Structuring for high reliability: HR practices and mindful processes in reliability‐seeking organizations
Authors: Vogus Timothy J. , Welbourne Theresa M. 
Published: October 2003

AbstractThis paper theoretically and empirically connects the literature on high‐reliability organizations (HROs) to a broader set of organizations, which we call reliability‐seeking organizations. Unlike HROs, which operate high‐hazard technologies, reliability‐seeking organizations operate in high‐hazard environments. Reliability‐seeking organizations are tightly coupled to their unpredictable and complex environments in such a manner that although the human mortality rate is low, the risk of small failures amplifying into organizational mortality is high. To cope with these environments, reliability‐seeking organizations organize to remain open and flexible to emerging information and achieve the reliability demanded by their environments—intensity of innovation. These organizations utilize skilled temporary employees, positive employee relations, and an emphasis on training to innovate, and, in turn, generate greater financial performance. We test these hypotheses using a sample of 184 initial public offering (IPO) software firms that conducted their IPO between 1993 and 1996 and our results are consistent with our theorizing. Firms that utilized these human resource practices innovated more frequently and firms with more innovations had higher stock prices over time. Our findings combine to suggest a theoretical model of structural antecedents of a different type of reliability—intensity of innovation Copyright © 2003 John Wiley & Sons, Ltd.
Developmental anomalies in skeletal remains from the Great Moravia and Middle Ages cemeteries at Devín (Slovakia)
Authors: Masnicová S. , Beňuš R. 
Published: October 2003

AbstractDevelopmental anomalies were scored and prevalences were computed for two skeletal collections from Devín (southwestern Slovakia). The first sample Devín‐Hrad (DH) is dated to the Middle Ages (11th–12thcentury) and includes 217 skeletons. The second collection Devín‐Za kostolom (FR) includes 112 burials and is dated to the Great Moravian period (9thcentury). In both samples, the evidence of spina bifida occulta occurred most frequently of all the defects examined (24% in DH, 23% in FR). Sacralization (8% in DH, 7% in FR) was more common than lumbarization (2% in DH, 0% in FR), and spondylolysis (7% in DH, 4% in FR) was relatively frequent in both samples. The other developmental defects occurred in only one or a few individuals and represented sporadic occurrences. Copyright © 2003 John Wiley & Sons, Ltd.
University of San Diego palynological investigation of the Dos Cabezas giants
Authors: Geyer P. S. , Larson T. S. , Stroik L. 
Published: October 2003

AbstractBeginning in 1999, coprolite soil samples were collected from the skeletal remains of Moche giants excavated at the archaeological site of Dos Cabezas, northern Peru. In 2000, a pilot palynological study was undertaken to ascertain if pollen was recoverable from them. The results of this study encouraged us to form a student team to continue the laboratory research. It was also decided to sample as many of the excavated skeletal remains from the giants' tombs as possible.Following the 2001 field season a palynological study was performed on the three individuals (one adult giant and two children) recovered from Tomb 3 in 1999. Pollen was extracted and analysed. The combined results of this archaeobotanical study are significant and in one instance have led us into insights into the possible causes of death of these three contemporaneous internments. This report represents only the preliminary results of this ongoing research. Copyright © 2003 John Wiley & Sons, Ltd.
The incidence of diffuse idiopathic skeletal hyperostosis and social status correlations in Lithuanian skeletal materials
Authors: Jankauskas R. 
Published: October 2003

AbstractNumerous indications in literature argue that diffuse idiopathic skeletal hyperostosis (DISH) is aetiologically linked with obesity and late onset (type II) diabetes. Thus its incidence should differ in socially stratified societies where individuals have different access to food resources. The incidence of DISH was evaluated in a skeletal sample of 458 adult individuals from the Iron Age, Mediaeval, and Early Modern periods. Social status was defined either by grave inventory (Iron Age) or burial location (within a church, or urban or rural cemeteries). Diagnostic criteria for DISH were right side anterior longitudinal spinal ligament or extra‐spinal ligament (enthesis) ossification. No differences between chronological groups were found. The incidence of DISH had definite age affinity: it increased with age: from 0.00% in 20–30 year olds to 30.23% in the 50+ year old group (p<0.001). It was also closely associated with sex: male/female ratio was 6.9 (p<0.01). Social status was slightly but significantly related with DISH: incidence among high social status individuals was 27.14%, average or urban was 11.86%, poor or rural was 7.14% (p<0.001). Our results confirm that DISH is associated with the male sex and advanced age and support the hypothesis that the incidence of DISH is related to life style, possibly as a result of different nutritional patterns. Copyright © 2003 John Wiley & Sons, Ltd.
Luigi Boccherini and the Barocco cello: an 18th century striking case of occupational disease
Authors: Ciranni R. , Fornaciari G. 
Published: October 2003

AbstractThe aim of this paper is to elaborate an ergonomic model based on the study of acquired muscle‐skeletal lesions related to Boccherini's intensive activity as Barocco cellist. The body of the famous musician was submitted to external examination, macroscopic analysis and radiographic study. Palaeopathological studies of the skeleton showed a considerable number of changes such as severe rhizoarthritis of the right thumb, heavy epicondylitis of the left elbow, loss of physiological cervical and lumbar spine lordosis and high thoracic left scoliosis with maximum on T3‐T4. A case of tibiae valgae was diagnosed at the level of the legs. The acquired muscle‐skeletal lesions found seemed to be correlated to Boccherini's cello activity. Direct observation of a present‐day cellist allowed us to better understand how repetitive strain injuries were responsible for the situation which appears in the ergonomic model described. Copyright © 2003 John Wiley & Sons, Ltd.