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The major emphasis of this paper is on analytical techniques for predicting the performance of various collection fusion scenarios. Knowledge of analytical models of information retrieval system performance, both with single processors and with multiple processors, increases our understanding of the parameters (e.g., number of documents, ranking algorithms, stemming algorithms, stop word lists, etc.) affecting system behavior. While there is a growing literature on the implementation of distributed information retrieval systems and digital libraries, little research has focused on analytic models of performance. We analytically describe the performance for single and multiple processors, both when different processors have the same parameter values and when they have different values. The use of different ranking algorithms and parameter values at different sites is examined. [ABSTRACT FROM AUTHOR]

Addresses the role and place of accommodating women in the Church of God in Christ (COGIC). Assumption of accommodationist roles by women; Viewing of liberation within the confines of an accommodationist's stance; Purpose of women in the COGIC; Basis of analysis on empirical information and firsthand knowledge by author.

The strongest critics of plea bargaining argue that the practice should be abolished because it coerces defendants to give up their right to trial and because it results in irrational sentences for criminal defendants, Neither charge is applicable to a system of plea negotiations that meets four basic criteria: (1) the defendant always has the alternative of an jury trial at which both verdict and sentence are determined solely on the merits: (2) the defendant is represented through, out negotiations by competent counsel; (3) both defense and prosecution have equal access to relevant evidence; and (4) both possess sufficient resources to take a ease to trial. The most fruitful direction of reform is to seek to achieve these conditions rather than attempt to eliminate plea bargaining. [ABSTRACT FROM AUTHOR]

An analysis of a quasi-experiment is made to discuss about plea bargains, concession giving and their effects on the criminal justice process. A quasi-experimental research situation was provided unintentionally by the prosecuting attorney of Hampton County. It is stated that the conventional wisdom surrounding plea bargaining is grounded in the general proposition that the guilty pleas are secured primarily through granting concessions to defendants. The experience in the county has tended to confirm the importance of concessions in securing pleas. Related to it, the lower proportion of guilty pleas that are obtained in drug sale cases after the prosecution has stopped making charge concessions is tabulated for analysis. The county's experience with a limited attempt to stop plea bargaining illustrates that plea bargaining is difficult to eliminate because it reduces the uncertainties and risks inherent in a trial for all court participants, including the defendant. In conclusion, the author questions how any fundamental shift away from bargain justice could occur without an even more fundamental change in the incentive structures of participants.

Examines the system for achieving toxic dump site cleanup in New York. Use of alternative dispute resolution by the state to lower transaction costs in toxic dump site cleanup concerns; Motivations and incentives that influence the behavior of individuals involved in resolutions; Political factors associated with variation across cases.

A method is presented for reducing a curvilinear response to a set of numbers which describe the curve. An analysis of such numbers including reconstruction of the curves is presented. A numerical example is used to illustrate the entire procedure. [ABSTRACT FROM AUTHOR]

This article reports that clusters are groups of individual items that have been placed together or are treated as a unit, usually because of the similarity between the items that are placed into a cluster. This article suggests that, in some circumstances, retrieving from clusters provides better performance than does retrieval without clustering. However, in other circumstances, the reverse may be true and clustering may result in performance inferior to that obtained without clustering. Future retrieval system designers will need to address whether circumstances exist where clustering improves performance sufficiently and equally importantly, whether the system they are proposing will use clusters in such a way that they increase query processing speed and throughput. While studying the clustering hypothesis leads one to directly study the effects of clustering on performance or the distribution of relevant documents across clusters, one can also study the performance of clustering by examining the p and b values of clusters.

Presents lists of statistical bibliography in the United States from 1965 to 1966. 'International Bibliography of Income and Wealth'; 'Analysis and Projection of Demand and Production; 'Review of the International Statistical Institute'.

We present a procedure for enhanced sampling of molecular dynamics simulations through informed stochastic resetting. Many phenomena, such as protein folding and crystal nucleation, occur over time scales inaccessible in standard simulations. We recently showed that stochastic resetting can accelerate molecular simulations that exhibit broad transition time distributions. However, standard stochastic resetting does not exploit any information about the reaction progress. For a model system and chignolin in explicit water, we demonstrate that an informed resetting protocol leads to greater accelerations than standard stochastic resetting in molecular dynamics and Metadynamics simulations. This is achieved by resetting only when a certain condition is met, e.g., when the distance from the target along the reaction coordinate is larger than some threshold. We use these accelerated simulations to infer important kinetic observables such as the unbiased mean first-passage time and direct transit time. For the latter, Metadynamics with informed resetting leads to speedups of 2-3 orders of magnitude over unbiased simulations with relative errors of only ∼35-70%. Our work significantly extends the applicability of stochastic resetting for enhanced sampling of molecular simulations.

Microbial rhodopsins (MRs) are a diverse and abundant family of photoactive membrane proteins that serve as model systems for biophysical techniques. Optogenetics utilizes genetic engineering to insert specialized proteins into specific neurons or brain regions, allowing for manipulation of their activity through light and enabling the mapping and control of specific brain areas in living organisms. The obstacle of optogenetics lies in the fact that light has a limited ability to penetrate biological tissues, particularly blue light in the visible spectrum. Despite this challenge, most optogenetic systems rely on blue light due to the scarcity of red-shifted opsins. Finding additional red-shifted rhodopsins would represent a major breakthrough in overcoming the challenge of limited light penetration in optogenetics. However, determining the wavelength absorption maxima for rhodopsins based on their protein sequence is a significant hurdle. Current experimental methods are time-consuming, while computational methods lack accuracy. The paper introduces a new computational approach called RhoMax that utilizes structure-based geometric deep learning to predict the absorption wavelength of rhodopsins solely based on their sequences. The method takes advantage of AlphaFold2 for accurate modeling of rhodopsin structures. Once trained on a balanced train set, RhoMax rapidly and precisely predicted the maximum absorption wavelength of more than half of the sequences in our test set with an accuracy of 0.03 eV. By leveraging computational methods for absorption maxima determination, we can drastically reduce the time needed for designing new red-shifted microbial rhodopsins, thereby facilitating advances in the field of optogenetics.

The light-oxygen-voltage (LOV) domains of phototropins emerged as essential constituents of light-sensitive proteins, helping initiate blue light-triggered responses. Moreover, these domains have been identified across all kingdoms of life. LOV domains utilize flavin nucleotides as co-factors and undergo structural rearrangements upon exposure to blue light, which activates an effector domain that executes the final output of the photoreaction. LOV domains are versatile photoreceptors that play critical roles in cellular signaling and environmental adaptation; additionally, they can noninvasively sense and control intracellular processes with high spatiotemporal precision, making them ideal candidates for use in optogenetics, where a light signal is linked to a cellular process through a photoreceptor. The ongoing development of LOV-based optogenetic tools, driven by advances in structural biology, spectroscopy, computational methods, and synthetic biology, has the potential to revolutionize the study of biological systems and enable the development of novel therapeutic strategies., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.

Photoisomerization of azobenzenes from their stable E isomer to the metastable Z state is the basis of numerous applications of these molecules. However, this reaction typically requires ultraviolet light, which limits applicability. In this study, we introduce disequilibration by sensitization under confinement (DESC), a supramolecular approach to induce the E -to- Z isomerization by using light of a desired color, including red. DESC relies on a combination of a macrocyclic host and a photosensitizer, which act together to selectively bind and sensitize E -azobenzenes for isomerization. The Z isomer lacks strong affinity for and is expelled from the host, which can then convert additional E- azobenzenes to the Z state. In this way, the host-photosensitizer complex converts photon energy into chemical energy in the form of out-of-equilibrium photostationary states, including ones that cannot be accessed through direct photoexcitation.

Many simulation methods concerning solvated molecules are based on the assumption that the solvated species and the solvent can be characterized by some representative structures of the solute and some embedding potential corresponding to this structure. While the averaging of the solvent configurations to obtain an embedding potential has been studied in great detail, this hinges on a single solute structure representation. This assumption is re-examined and generalized for conformationally flexible solutes and tested on 4 nonrigid systems. In this generalized approach, the solute is characterized by a set of representative structures and the corresponding embedding potentials. The representative structures are identified by means of subdividing the statistical ensemble, which in this work is generated by a constant-temperature molecular dynamics simulation. The embedding potential defined in the Frozen-Density Embedding Theory is used to characterize the average effect of the solvent in each subensemble. The numerical examples concern the vertical excitation energies of protonated retinal Schiff bases in protein environments. It is comprehensively shown that subensemble averaging leads to huge computational savings compared with explicit averaging of the excitation energies in the whole ensemble while introducing only minor errors in the case of the systems examined.

Multiscale simulations have been established as a powerful tool to calculate and predict excitation energies in complex systems such as photoreceptor proteins. In these simulations the chromophore is typically treated using quantum mechanical (QM) methods while the protein and surrounding environment are described by a classical molecular mechanics (MM) force field. The electrostatic interactions between these regions are often treated using electrostatic embedding where the point charges in the MM region polarize the QM region. A more sophisticated treatment accounts also for the polarization of the MM region. In this work, the effect of such a polarizable embedding on excitation energies was benchmarked and compared to electrostatic embedding. This was done for two different proteins, the lipid membrane-embedded jumping spider rhodopsin and the soluble cyanobacteriochrome Slr1393g3. It was found that the polarizable embedding scheme produces absorption maxima closer to experimental values. The polarizable embedding scheme was also benchmarked against expanded QM regions and found to be in qualitative agreement. Treating individual residues as polarizable recovered between 50% and 71% of the QM improvement in the excitation energies, depending on the system. A detailed analysis of each amino acid residue in the chromophore binding pocket revealed that aromatic residues result in the largest change in excitation energy compared to the electrostatic embedding. Furthermore, the computational efficiency of polarizable embedding allowed it to go beyond the binding pocket and describe a larger portion of the environment, further improving the results., Competing Interests: The authors declare no conflict of interest., (2023 THE BIOPHYSICAL SOCIETY OF JAPAN.)

Proteorhodopsin (PR) is a photoactive proton pump found in marine bacteria. There are two phenotypes of PR exhibiting an environmental adaptation to the ocean's depth which tunes their maximum absorption: blue-absorbing proteorhodopsin (BPR) and green-absorbing proteorhodopsin (GPR). This blue/green color-shift is controlled by a glutamine to leucine substitution at position 105 which accounts for a 20 nm shift. Typically, spectral tuning in rhodopsins is rationalized by the external point charge model but the Q105L mutation is charge neutral. To study this tuning mechanism, we employed the hybrid QM/MM method with sampling from molecular dynamics. Our results reveal that the positive partial charge of glutamine near the C 14 -C 15 bond of retinal shortens the effective conjugation length of the chromophore compared to the leucine residue. The derived mechanism can be applied to explain the color regulation in other retinal proteins and can serve as a guideline for rational design of spectral shifts., (© 2022 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Bistable rhodopsins have two stable forms that can be interconverted by light. Due to their ability to act as photoswitches, these proteins are considered as ideal candidates for applications such as optogenetics. In this work, we analyze a recently crystalized bistable rhodopsin, namely the jumping spider rhodopsin-1 (JSR1). This rhodopsin exhibits identical absorption maxima for the parent and the photoproduct form, which impedes its broad application. We performed hybrid QM/MM simulations to study three isomers of the retinal chromophore: the 9- cis , 11- cis and all- trans configurations. The main aim was to gain insight into the specific interactions of each isomer and their impact on the absorption maximum in JSR1. The absorption spectra were computed using sampled snapshots from QM/MM molecular dynamics trajectories and compared to their experimental counterparts. The chromophore-protein interactions were analyzed by visualizing the electrostatic potential of the protein and projecting it onto the chromophore. It was found that the distance between a nearby tyrosine (Y126) residue plays a larger role in the predicted absorption maximum than the primary counterion (E194). Geometric differences between the isomers were also noted, including a structural change in the polyene chain of the chromophore, as well as changes in the nearby hydrogen bonding network.

Gas-phase reactions between pyruvic acid (PA) and HO 2 radicals were examined using ab initio quantum chemistry and transition state theory. The rate coefficients were determined over a temperature range of 200-400 K including tunneling contributions. Six potential reaction pathways were identified. The two hydrogen abstraction reactions yielding the H 2 O 2 product were found to have high barriers. The HO 2 radical was also found to have a catalytic effect on the intramolecular hydrogen transfer reactions occurring by three distinct routes. These hydrogen-shift reactions are very interesting mechanistically although they are highly endothermic. The only reaction that contributes significantly to the consumption of PA is a multistep pathway involving a peroxy-radical intermediate, PA + HO 2 → CH 3 COOH + OH + CO 2 . This exothermic process has potential atmospheric relevance because it produces an OH radical as a product. Atmospheric models currently have difficulty predicting accurate OH concentrations for certain atmospheric conditions, such as environments free of NOx and the nocturnal boundary layer. Reactions of this sort, although not necessary with PA, may account for a portion of this deficit. The present study helps settle the issue of the relative roles of reaction and photolysis in consumption of PA in the troposphere.