The simulation of diffusional association (SDA) Brownian dynamics software package has been widely used in the study of biomacromolecular association. Initially developed to calculate bimolecular protein–protein association rate constants, it has since been extended to study electron transfer rates, to predict the structures of biomacromolecular complexes, to investigate the adsorption of proteins to inorganic surfaces, and to simulate the dynamics of large systems containing many biomacromolecular solutes, allowing the study of concentration‐dependent effects. These extensions have led to a number of divergent versions of the software. In this article, we report the development of the latest version of the software (SDA 7). This release was developed to consolidate the existing codes into a single framework, while improving the parallelization of the code to better exploit modern multicore shared memory computer architectures. It is built using a modular object‐oriented programming scheme, to allow for easy maintenance and extension of the software, and includes new features, such as adding flexible solute representations. We discuss a number of application examples, which describe some of the methods available in the release, and provide benchmarking data to demonstrate the parallel performance. © 2015 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

Newly synthesized polypeptides undergo various cotranslational maturation steps, including N-terminal enzymatic processing, chaperone-assisted folding and membrane targeting, but the spatial and temporal coordination of these steps is unclear. We show that Escherichia coli methionine aminopeptidase (MAP) associates with ribosomes through a charged loop that is crucial for nascent-chain processing and cell viability. MAP competes with peptide deformylase (PDF), the first enzyme to act on nascent chains, for binding sites at the ribosomal tunnel exit. PDF has extremely fast association and dissociation kinetics, which allows it to frequently sample ribosomes and ensure the processing of nascent chains after their emergence. Premature recruitment of the chaperone trigger factor, or polypeptide folding, negatively affect processing efficiency. Thus, the fast ribosome association kinetics of PDF and MAP are crucial for the temporal separation of nascent-chain processing from later maturation events, including chaperone recruitment and folding.

Recent research has recognized that many people simultaneously hold positive and negative attitudes about important political issues. This paper reviews the concept of attitudinal ambivalence and introduces a survey measure of ambivalence adapted from the experimental literature. An analysis of two statewide telephone surveys of Florida voters reveals that (1) a number of voters have ambivalent attitudes about abortion rights; (2) the amount of ambivalence varies according to the circumstances (elective versus traumatic) under which an abortion is obtained; (3) ambivalence about elective abortions is essentially unrelated to ambivalence about traumatic abortions; (4) voters who support abortion rightsare more ambivalent about elective abortions than about traumatic abortions, whereas the pattern is reversed for abortion rights opponents; and (5) extreme views in support of or opposition to abortion rights can sometimes mitigate the amount of ambivalence felt by voters.

Elections are sometimes seen as legitimizing institutions, promoting system-level support among citizens by allowing them to have input into the political process. However, prior research has found that this is less true among supporters of losing candidates, who often exhibit lower levels of political trust and satisfaction with democracy. We analyze NES survey data from 1964 to 2004, as well as surveys from Florida and the nation following the controversial presidential election of 2000, and find that (1) losers exhibit lower levels of political trust, satisfaction with democracy, confidence that government is responsive to citizens, and in early 2001 were less inclined to extend legitimacy to the newly elected president; (2) losers also are more likely to endorse “rationalizations” as explanations of the election outcome, to be less satisfied with the choice of candidates offered in the election, and to perceive the electoral process as unfair; and (3) voter interpretations of the election mediate the relationships between winning/losing on the one hand, and trust, responsiveness, and satisfaction with democracy on the other. These findings suggest that the so-called legitimizing function of elections is far from a universal phenomenon.

Recent research has recognized that many people simultaneously hold positive and negative attitudes about important political issues. In this article, we review the concept of attitudinal ambivalence and propose a survey-based measure of ambivalence adapted from the experimental literature. Extending our earlier work on abortion, analysis of a statewide telephone survey of Florida residents reveals that (1) many people have ambivalent attitudes about issues related to gay and lesbian rights; (2) the amount of ambivalence varies according to the specific rights in question (military service, gay marriage and adoption, membership in youth organizations such as Boy Scouts, and others); (3) ambivalence on gay rights is to some extent a function of conflict among citizens’ underlying core values; and (4) under certain circumstances, ambivalence appears to mediate the relationship between a person’s issue preferences with regard to gay rights and his or her evaluation of political leaders and institutions.