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At least 757 records · Page 42Linked to original sources
PubMed1999

A theoretical model successfully identifies features of hepatitis B virus capsid assembly.

The capsids of most spherical viruses are icosahedral, an arrangement of multiples of 60 subunits. Though it is a salient point in the life cycle of any virus, the physical chemistry of virus capsid assembly is poorly understood. We have developed general models of capsid assembly that describe the process in terms of a cascade of low order association reactions. The models predict sigmoidal assembly kinetics, where intermediates approach a low steady state concentration for the greater part of the reaction. Features of the overall reaction can be identified on the basis of the concentration dependence of assembly. In simulations, and on the basis of our understanding of the models, we find that nucleus size and the order of subsequent "elongation" reactions are reflected in the concentration dependence of the extent of the reaction and the rate of the fast phase, respectively. The reaction kinetics deduced for our models of virus assembly can be related to the assembly of any "spherical" polymer. Using light scattering and size exclusion chromatography, we observed polymerization of assembly domain dimers of hepatitis B virus (HBV) capsid protein. Empty capsids assemble at a rate that is a function of protein concentration and ionic strength. The kinetics of capsid formation were sigmoidal, where the rate of the fast phase had second-power concentration dependence. The extent of assembly had third-power concentration dependence. Simulations based on the models recapitulated the concentration dependences observed for HBV capsid assembly. These results strongly suggest that in vitro HBV assembly is nucleated by a trimer of dimers and proceeds by the addition of individual dimeric subunits. On the basis of this mechanism, we suggest that HBV capsid assembly could be an important target for antiviral therapeutics.

Capsid↗
PubMed1999

Theoretical Model Studies of the Iron Dimer Complex of MMO and RNR.

Hybrid DFT calculations are used to study the structures and chemistry of the diiron complex of MMO and RNR. The chemical model used is larger than the ones used previously and contains the full first ligand sphere. New types of structures are suggested for the intermediates observed in the reactions of these enzymes. To obtain the very short Fe-Fe distances recently measured by EXAFS, it is suggested that both compound Q of MMO and compound X of RNR have two bridging carboxylates like the reduced diferrous complex but unlike the diferric complex. Antiferromagnetic coupling is shown to have significant effects on the electronic structure of the complexes and is also important for achieving the short Fe-Fe distance. The new model is also used to study the activation of methane, and a pure hydrogen abstraction transition state is located where a hydrogen of methane is abstracted by a bridging &mgr;-oxo ligand. The combination of the methyl radical with the bridging &mgr;-OH ligand formed occurs without a barrier and is extremely exothermic. This reaction should therefore be very fast. A symmetric transition state for the activation of O(2) is also proposed leading from a suggested compound P to compound Q. In this process, one of the carboxylate bridges of the reduced complex has to move away from O(2) toward one of the irons. These results are discussed in relation to recent experiments.

Journal Article↗
PubMed2005

A theoretical model for indirect dissociative electron attachment.

In this paper, we describe a computational model that allows us to avoid having to perform a very large number of tedious calculations on electronically metastable anions when studying indirect DEA processes. By indirect, we mean that the electron attaches to an orbital in one region of the molecule but a bond is subsequently broken in another region. For such events, one must describe the coupling between two diabatic anion states, corresponding to the occupation of orbitals in the two regions of the molecule, to achieve a correct description. We introduce a simple 2 x 2 matrix model as well as physically reasonable and computationally efficient approximations to the diabatic states in regions where they are metastable. We show this model to be highly effective when applied to several indirect DEA processes that we studied earlier with brute-force methods. The main advantage of using this model is that one can avoid having to carry out a large number of calculations on metastable anion states; only one or two such calculations are required.

Journal Article↗
PubMed2006

A study of cysteamine ionization in solution by Raman spectroscopy and theoretical modeling.

Different cysteamine (H2N-CH2-CH2-SH) ionization forms have been studied by polarized Raman spectroscopy in solutions prepared with H2O and D2O and by DFT calculations at the B3LYP/6-31++G(d,p) level. To account for solvation effects, we employed the integral equation formalism polarizable continuum model (IEFPCM) option and explicit water molecules. Calculated relative energies and Raman spectra revealed that gauche rotamers around the C-C bond are the most stable conformers in solution. The experimental pKa values and Raman spectra of various ionization forms were best predicted by using a model with three explicit water molecules and the IEFPCM option. In general, the use of IEFPCM tends to lower the calculated frequencies for a few bands, but in some cases (S-H stretching mode) this effect is expressed very strongly. Potential energy distribution (PED) analysis of gauche conformers of various cysteamine ionization forms provided the possibility of discriminating spectroscopically methylene groups adjacent to sulfur, (CH2)S, and nitrogen, (CH2)N, sites. In general, stretching and scissoring modes as well as wagging and twisting vibrations of the (CH2)N group were found to be at higher frequencies. The influence of ionization of SH and NH2 groups on the vibrational spectrum is discussed, and Raman markers for further amine group ionization studies are suggested.

Cysteamine↗
PubMed2004

Theoretical model for photochemical or thermally activated immobilization of macromolecules.

The covalent immobilization of macromolecules on surfaces and within 3-dimensional networks is quantitatively described using a model based on Poisson statistics. This model determines the immobilized density or layer thickness as a function of molecular weight of the macromolecule or radiant exposure prior to and following the surface deposition of the macromolecule. Measurements of immobilized layer thickness provide first-order rate constants for decomposition of the surface-bound linker molecules and an estimate of the surface-bound linker density. The model predicts the relative density of immunocomplexed antibodies as a function of the irradiation time used to immobilize antigens. By providing the average number of bonds to the immobilized molecule, the model enables studies of the effect of multiple bonds on the activity of biomolecules. Experimental data by the authors and from the literature validate the model.

Journal Article↗
PubMed1998

A Broader Theoretical Model for Feedback in Ambulatory Care.

Ask faculty if they provide feedback and they will likely reply "Sure, it's important, I do it all the time". Ask medical students if they receive feedback and they may say, "We hardly ever get it". Ask most residents if they receive feedback and you get "Rarely, but it's not that helpful anyway". How is it that these perceptions are so strikingly different? Can they be talking about the same thing? If we wish to improve the educational value of feedback, we must understand these differences. One useful clue is provided by the adage "do as I say, not as I do". This saying suggests that there are two types of feedback: that which we can measure against a standard and describe (traditional feedback), and that which comes from being immersed in real situations (situated feedback). This dichotomy is a useful construct from which to understand feedback.

Journal Article↗
PubMed1997

HIV risk reduction for incarcerated women: a comparison of brief interventions based on two theoretical models.

Although female inmates are seropositive at rates that exceed those of male inmates, few studies, have evaluated HIV risk reduction interventions for incarcerated women. This demonstration project compared an intervention based on social cognitive theory against a comparison condition based on the theory of gender and power. Incarcerated women (N = 90) were assessed at baseline, postintervention, and again 6 months later. Both interventions produced increased self efficacy, self-esteem, Attitudes Toward Prevention Scale scores, AIDS knowledge, communication skill, and condom application skills that maintained through the 6-month follow-up period. Participants in the intervention based on social cognitive theory showed greater improvement in condom application skills, and women in the program based on the theory of gender and power evidenced greater commitment to change. The results suggests brief interventions in prison settings are feasible and beneficial. However, it is not yet known whether the changes will generalize into the natural environment after the women's release into the community.

Acquired Immunodeficiency Syndrome↗
PubMed1985

Effects of anxiety on analogical reasoning: a test of three theoretical models.

Three mediational theories of anxiety and performance, namely, cue utilization theory (Easterbrook, 1959), attentional theory (Mandler & Sarason, 1952; Wine, 1971), and working memory capacity theory (M. W. Eysenck, 1979), were compared for their efficacy in explaining anxiety-induced performance decrements on a task of analogical reasoning. One hundred two subjects who varied in their trait and state anxiety levels completed 100 geometric analogies under either relaxed (reassurance, non-time-limited) or stressed (ego-threat, time-limited) conditions. Response time and error rate data for nine levels of task complexity (1-, 2-, and 3-element analogies with zero, one, or two transformations per element) were analyzed by means of multivariate analysis of variance. Results in the relaxed condition supported attentional theory in that the more anxious subjects were both slower and less accurate than were the less anxious subjects. In the stressed condition, none of the three anxiety-performance theories was supported. More anxious subjects were faster but made more errors than did less anxious subjects. Thus in the stressed condition, performance differences suggested differences in speed-accuracy trade-off strategies rather than differences in processing abilities. The limitations of attentional theory and the need to study the effects of anxiety and time stress on information processing are discussed.

Achievement↗
PubMed1996

Work-related stress and blood pressure: current theoretical models and considerations from a behavioral medicine perspective.

There is extensive evidence that the prevalence of human hypertension is related to psychosocial factors, possibly including chronic exposure to stress. A tripartite model, consistent with the literature on stress and health, may help to define this relationship better. Its 3 components are environmental stressors, individual factors affecting the perception of stress, and the individual's physiological susceptibility. To date, researchers have looked at individual parts of this model, but rarely at all 3. Some models of work stress (e.g., the job strain, effort-reward, and person-environment fit models) focus on work-related stressors alone or in conjunction with individual characteristics. Other models (e.g., the defense-defeat, John Henryism, and reactivity models) focus on individual differences in response, with little attention paid to the nature of the stressors. The authors suggest that it is timely to integrate these approaches and to look for physiological mechanisms.

Adaptation, Psychological↗
PubMed2006

Workplace harassment from the victim's perspective: a theoretical model and meta-analysis.

Although workplace harassment affects the lives of many employees, until recently it has been relatively ignored in the organizational psychology literature. First, the authors introduced an attribution- and reciprocity-based model that explains the link between harassment and its potential causes and consequences. The authors then conducted a meta-analysis to examine the potential antecedents and consequences of workplace harassment. As shown by the meta-analysis, both environmental and individual difference factors potentially contributed to harassment and harassment was negatively related to the well-being of both individual employees and their employing organizations. Furthermore, harassment contributed to the variance in many outcomes, even after controlling for 2 of the most commonly studied occupational stressors, role ambiguity and role conflict.

Aggression↗