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  • Biochemistry  (23)
  • Theoretical, Physical and Computational Chemistry  (5)
  • Applied demography  (4)
  • 1
    Electronic Resource
    Electronic Resource
    Unveiling the demographic ‘action’ in class-action lawsuits: Two instructional cases (1999)
    Springer
    Population research and policy review 18 (1999), S. 489-503 
    Details
    ISSN: 1573-7829
    Keywords: Applied demography ; Class action ; Law ; Teaching
    Source: Springer Online Journal Archives 1860-2000
    Topics: Sociology
    Notes: Abstract Population turnover, cohort survival, and intercohort transmission of effects are concepts widely applicable beyond the customary domains of demographic analysis. One such application involves a cohort of victims referenced in time and place by a common harm for which legal redress is sought through a class-action lawsuit. Two instructional case studies illustrate applications of demographic reasoning and data to certain generic questions such litigation may pose: How many claimants will remain by some future date? How prevalent will they then be in the population? How feasible will it be to redress the harm years later? These cases illustrate the use of familiar demographic concepts and simple demographic reasoning to draw legally relevant conclusions from available data. Specific instructional applications include: accounting for demographic factors that deplete the original class over time and dilute its surviving members among residents at the referenced place; integrating the use of administrative record, census, and vital statistics data; and devising approximate estimates of turnover within local populations. Training is broadly suited to assignments aimed at applying common-sense demographic reasoning to devise nonstandard solutions to measurement problems.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006381629603
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  • 2
    Electronic Resource
    Electronic Resource
    Applying demographic analysis in affirmative action disputes: An instructional case (1998)
    Springer
    Population research and policy review 17 (1998), S. 457-478 
    Details
    ISSN: 1573-7829
    Keywords: Affirmative action ; Applied demography ; Employment discrimination ; Labor pool ; Minorities
    Source: Springer Online Journal Archives 1860-2000
    Topics: Sociology
    Notes: Abstract This instructional case study illustrates applications of demographic concepts, data, and techniques in evaluating affirmative action goals for equalizing employment opportunity. Courts of law addressing employment discrimination disputes need an accurate picture of each minority group's proportion in a pool of prospective employees. The demographic and socioeconomic factors conditioning those proportions vary from place to place. In the situation examined here, the court originally used an imperfect population standard to set hiring goals. The case traces the multiple failures to account for those conditioning influences and describes the resulting distortions of legal purpose. In analyzing this failure, students gain experience in clarifying issues in dispute, devising measures to fit legal standards, and delineating qualified labor pools. Specific instructional applications include: using census data to document how local population structure and composition determine each minority group's presence in the workforce; and using administrative data to delineate the relevant labor pools for setting affirmative action goals. Training is broadly suited to assignments where applied demographers must delineate the ethnic and racial composition of a pool of workers eligible to be hired or promoted.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1006017911057
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  • 3
    Electronic Resource
    Electronic Resource
    Demographic influences on Latinos' political empowerment: Comparative local illustrations (1998)
    Springer
    Population research and policy review 17 (1998), S. 223-246 
    Details
    ISSN: 1573-7829
    Keywords: Applied demography ; Latinos in the USA ; Local political power ; California
    Source: Springer Online Journal Archives 1860-2000
    Topics: Sociology
    Notes: Abstract How do Latinos gain local political power, given their demographic proportions and characteristics in a community's population? This paper examines the influences of population structure, socioeconomic factors, and residential patterns on the process by which Latinos have translated their numbers into an effective political presence in five California cities. The distinctive routes to empowerment evidenced in these cities reveal the varied possibilities local demographic settings may offer and the sensitivity of different election systems to those settings. Two alternatives are considered: (1) a change from election at large to election by single-member district, or (2) augmentation of Latinos' citywide voting strength in deciding the second- or third-place winner in a multi-member at-large election format. The findings can inform local districting efforts planned around the 2000 census. Their implications extend more broadly to courts applying laws intended to safeguard minority voting rights; and to public policies aimed at balancing interests that unify a community and those that may divide its members.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1005914503677
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  • 4
    Electronic Resource
    Electronic Resource
    Applying demographic analysis to store site selection (1996)
    Springer
    Population research and policy review 15 (1996), S. 479-489 
    Details
    ISSN: 1573-7829
    Keywords: Applied demography ; Consumer ; Location ; Site ; Shopper ; Store
    Source: Springer Online Journal Archives 1860-2000
    Topics: Sociology
    Notes: Abstract This case study illustrates how applied demographic analysis can help structure business decisionmaking. We screened every one of several thousand square miles within metropolitan Southern California to identify the 10 best locations for a large supermarket catering to onestop shoppers. Locations were selected based on potential sales volume (irrespective of nearby competitors), future stability of the resident consumer base, and specific demographic factors likely to enhance sales potential among target shoppers (e.g., dual-earner families). The client placed as much importance on how the results were derived as on our recommendations. As a result, our analytic framework for comparing high-potential locations played a central role in structuring the client's thinking. This framework, together with the empirical analysis, illustrate how applied demographers can operationalize business questions about consumer markets and guide a client toward a more systematic way of reaching decisions.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00125866
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  • 5
    Electronic Resource
    Electronic Resource
    The reaction of n-butyllithium with benzoic acid: is nucleophilic addition competitive with deprotonation?Dedicated to Frederick G. Bordwell for his many and continuing contributions to physical organic chemistry (1997)
    Chichester : Wiley-Blackwell
    Journal of Physical Organic Chemistry 10 (1997), S. 537-541 
    Details
    ISSN: 0894-3230
    Keywords: n-Butyllithium ; benzoic acid ; nucleophilic addition ; deprotonation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Physics
    Notes: ---An evaluation of a branching vs sequential mechanism for the reaction of benzoic acid with n-butyllithium favors the latter. © 1997 John Wiley & Sons, Ltd.
    Additional Material: 2 Ill.
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Free energy perturbation calculations on models of active sites: Applications to adenosine deaminase inhibitors (1990)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 11 (1990), S. 994-1002 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute -9.8 kcal/mol to the free energy of binding, with a 108-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is -11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO-2 group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540110811
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  • 7
    Electronic Resource
    Electronic Resource
    Comparison of ab initio, semiempirical, and molecular mechanics calculations for the conformational analysis of ring systems (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 525-532 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C5 — C8 cyclic alkanes were chosen since these structures present a finite set of conformations and transition-state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2-dideoxyribose to determine the effect of heteroatoms on the results for the 5-membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5-membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1-center energies of the semiempirical calculations. The 2-center bonding and nonbonding energies followed reasonable trends for the conformers. The core-repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for H—H interactions partly explains the propensity of the 5-membered rings to optimize to near planarity (decreasing 1,2-diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130413
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  • 8
    Electronic Resource
    Electronic Resource
    AMBERCUBE MD, parallelization of Amber's molecular dynamics module for distributed-memory hypercube computers (1993)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 312-329 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fully functional parallel version of the molecular dynamics (MD) module of AMBER3a has been implemented. Procedures parallelized include the calculation of the long-range nonbonded Coulomb and Lennard-Jones interactions, generation of the pairlist, intramolecular bond, angle, dihedral, 1-4 nonbonded interaction terms, coordinate restraints, and the SHAKE bond constraint algorithm. As far as we can determine, this is the first published description where a distributed-memory MIMD parallel implementation of the SHAKE algorithm has been designed to treat not only hydrogen-containing bonds but also all heavy-atom bonds, and where “shaken” crosslinks are supported as well. We discuss the subtasking and partitioning of an MD time-step, load balancing the nonbonded evaluations, describe in algorithmic detail how parallelization of SHAKE was accomplished, and present speedup, efficiency, and benchmarking results achieved when this hypercube adaptation of the MD module AMBER was applied to several variant molecular systems. Results are presented for speedup and efficiency obtained on the nCUBE machine, using up to 128 processors, as well as benchmarks for performance comparisons with the CRAY YMP and FPS522 vector machines. © 1993 John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540140307
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  • 9
    Electronic Resource
    Electronic Resource
    Free energy perturbation calculations on parallel computers: Demonstrations of scalable linear speedup (1994)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 15 (1994), S. 351-373 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A coarse-grain parallel implementation of the free energy perturbation (FEP) module of the AMBER molecular dynamics program is described and then demonstrated using five different molecular systems. The difference in the free energy of (aqueous) solvation is calculated for two monovalent cations ΔΔGaq(Li+ Δ Cs+), and for the zero-sum ethane-to-ethane′ perturbation ΔΔGaq(CH3—methyl—X → X—methyl—CH3), where X is a ghost methyl. The difference in binding free energy for a docked HIV-1 protease inhibitor into its ethylene mimetic is examined by mutating its fifth peptide bond, ΔG(CO—NH → CH=CH). A potassium ion (K+) is driven outward from the center of mass of ionophore salinomycin (SAL-) in a potential of mean force calculation ΔGMeOH(SAL- · K+) carried out in methanol solvent. Parallel speedup obtained is linearly proportional to the number of parallel processors applied. Finally, the difference in free energy of solvation of phenol versus benzene, ΔΔGoct(phenol → benzene), is determined in water-saturated octanol and then expressed in terms of relative partition coefficients, Δ log(Po/w). Because no interprocessor communication is required, this approach is scalable and applicable in general for any parallel architecture or network of machines. FEP calculations run on the nCUBE/2 using 50 or 100 parallel processors were completed in clock times equivalent to or twice as fast as a Cray Y-MP. The difficulty of ensuring adequate system equilibrium when agradual configurational reorientation follows the mutation of the Hamiltonian is discussed and analyzed. The results of a successful protocol for overcoming this equilibration problem are presented. The types of molecular perturbations for which this method is expected to perform most efficiently are described. © 1994 by John Wiley & Sons, Inc.
    Additional Material: 11 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540150310
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  • 10
    Electronic Resource
    Electronic Resource
    Free energy perturbation calculations involving potential function changes (1992)
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 13 (1992), S. 362-370 
    Details
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The solvation free energies of thymine and adenine were calculated using free energy methods to examine the effect of applying Lennard-Jones 6-12 and 10-12 perturbations to the hydrogen-bonding groups. The calculations were performed using a new free energy algorithm developed for the AMBER 4.0 program package that allows an interaction described by a Lennard-Jones 6-12 potential to be changed into one described by a hydrogen bond 10-12 potential. The algorithm applied allows this change to occur smoothly without the generation of more extrema on the potential surface. Results using this algorithm have been compared with those determined using the standard AMBER 3.0 Revision A program package, which provides for 6-12 to 6-12 parameter perturbations only. We have also developed a procedure to perform pyrimidine to purine nucleoside mutations to calculate the relative free energies of solvation directly. The theoretical results are compared to experimental energies derived from solvation and vaporization data taken from the literature. The free energies calculated using the new algorithm show good agreement with the derived experimental values. This is also true for the calculations that employ the 6-12 function only, but with 6-12 parameters modified to reflect the correct hydrogen-bonding interactions. However, perturbation of the “standard” 6-12 parameters without changing the functional form proves to be less effective in determining solvation free energies correctly, and demonstrates the importance of accurate hydrogen bond descriptions in free energy simulations.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/jcc.540130309
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