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At least 577 records · Page 32Linked to original sources
PubMed1996

Theoretical Modeling of Water Exchange on [Pd(H(2)O)(4)](2+), [Pt(H(2)O)(4)](2+), and trans-[PtCl(2)(H(2)O)(2)].

Density functional theory is applied to modeling the exchange in aqueous solution of H(2)O on [Pd(H(2)O)(4)](2+), [Pt(H(2)O)(4)](2+), and trans-[PtCl(2)(H(2)O)(2)]. Optimized structures for the starting molecules are reported together with trigonal bipyramidal (tbp) systems relevant to an associative mechanism. While a rigorous tbp geometry cannot by symmetry be the actual transition state, it appears that the energy differences between model tbp structures and the actual transition states are small. Ground state geometries calculated via the local density approximation (LDA) for [Pd(H(2)O)(4)](2+) and relativistically corrected LDA for the Pt complexes are in good agreement with available experimental data. Nonlocal gradient corrections to the LDA lead to relatively inferior structures. The computed structures for analogous Pd and Pt species are very similar. The equatorial M-OH(2) bonds of all the LDA-optimized tbp structures are predicted to expand by 0.25-0.30 Å, while the axial bonds change little relative to the planar precursors. This bond stretching in the transition state counteracts the decrease in partial molar volume caused by coordination of the entering water molecule and can explain qualitatively the small and closely similar volumes of activation observed. The relatively higher activation enthalpies of the Pt species can be traced to the relativistic correction of the total energies while the absolute DeltaH() values for exchange on [Pd(H(2)O)(4)](2+) and [Pt(H(2)O)(4)](2+) are reproduced using relativistically corrected LDA energies and a simple Born model for hydration. The validity of the latter is confirmed via some simple atomistic molecular mechanics estimates of the relative hydration enthalpies of [Pd(H(2)O)(4)](2+) and [Pd(H(2)O)(5)](2+). The computed DeltaH() values are 57, 92, and 103 kJ/mol compared to experimental values of 50(2), 90(2), and 100(2) kJ/mol for [Pd(H(2)O)(4)](2+), [Pt(H(2)O)(4)](2+), and trans-[PtCl(2)(H(2)O)(2)], respectively. The calculated activation enthalpy for a hypothetical dissociative water exchange at [Pd(H(2)O)(4)](2+) is 199 kJ/mol. A qualitative analysis of the modeling procedure, the relative hydration enthalpies, and the zero-point and finite temperature corrections yields an estimated uncertainty for the theoretical activation enthalpies of about 15 kJ/mol.

Journal Article↗
PubMedDate not supplied

Wobble base-pairing in codon-anticodon interactions: a theoretical modelling study.

The Crick wobble hypothesis attributes the phenomenon of codon degeneracy to a certain impreciseness of pairing between the third base of the codon and the first base of the anticodon. This theoretical study investigates the pairing properties of some wobble bases, including both, observed and unobserved pairs. Some wobble base-pairs are predicted to follow the Watson-Crick pairs in configuration and pairing facility, while others deviate from this norm. The observed U:V pair is unique in that a pairing configuration may be suggested for it wherein the hydrogen-bonding involves the exocyclic 5-carboxymethoxy group of V. By comparing the theoretical data on the configurations of these pairs with the evidence for their existence/non-existence in nature, some guidelines emerge for differentiating between observed and unobserved base pairs on the basis of the pairing configuration.

Adenine↗
PubMedDate not supplied

[Investigation of helical plant virus ribonucleoprotein structures with the help of tritium planigraphy and theoretical modeling].

The results of the studies of helical plant virus structures by tritium planigraphy (TP) method are discussed. TP method is based on bombardment of macromolecular objects with a stream of tritium atoms, followed by analysis of tritium label distribution along the macromolecule. By combining the TP data with the results of theoretical predictions of the protein structure, it turned out to be possible to propose a model of the coat protein structure in the virions of potato virus X (the type member of potexvirus group) and potato virus A (one of the members of potyvirus group). With the help of TP it also managed to find subtle differences in the coat protein structure between wildtype tobacco mosaic virus (strain U1) and its mutant with two amino acid substitutions in the coat protein and alter host specificity.

Capsid Proteins↗
PubMed1990

Theoretical model of ventricular interdependence: pericardial effects.

One ventricle can influence the filling characteristics of the opposite ventricle directly through the myocardium and indirectly through the pericardium. Based on definitions of compliances and volumes, we developed a theoretical analysis that indicated that the magnitude of interdependence was related to the relative compliances of the left and right ventricular free walls, septum, and pericardium. This analysis was verified in postmortem canine hearts. Balloons were inserted into each ventricle, and left ventricle pressure (delta Pl) and volume (delta Vl) changes caused by increasing right ventricular pressure (delta Pr) and volume (delta Vr) or pericardial pressure (delta Pp) were recorded. For delta Pl/delta Pr, delta Pl/delta Pp, delta Pl/delta Vr, delta Vl/delta Pr, delta Vl/delta Pp, and delta Vl/delta Vr measurements, the standard error of estimates was small and the predicted and measured values were significantly related (P less than 0.05); the values were 0.88 +/- 0.16, 0.87 +/- 0.17, 0.93 +/- 0.05, 0.95 +/- 0.09, 0.96 +/- 0.05, and 0.96 +/- 0.04, respectively. These coupling coefficients (delta Pl/delta Pr, delta Pl/delta Pp, etc.) a direct measurement of interdependence, indicated that pericardial-to-ventricular coupling is greater than ventricular-ventricular coupling (delta Pl/delta Pp greater than delta Pl/delta Pr, 0.91 +/- 0.09 vs. 0.23 +/- 0.09, P less than 0.01; delta Vl/delta Pp greater than delta Vl/delta Pr, -1.04 +/- 0.35 vs. -0.19 +/- 0.05, P less than 0.05). This study, by developing a theoretical analysis and by direct measurements, provides a better understanding of ventricular interdependence and may help to predict effects of cardiac tamponade and constrictive pericarditis on ventricular interdependence.

Blood Pressure↗
PubMedDate not supplied

Testing a theoretical model of exercise behavior for older adults.

BACKGROUND: Although there are many known benefits to exercise, only 10-30% of older adults report regular exercise. Understanding the factors that explain exercise behavior in older adults will help structure interventions that motivate these individuals to initiate and adhere to regular exercise. OBJECTIVE: The purpose of this study was to test the impact of components from two theoretical perspectives that explain exercise behavior, social cognitive theory, and the transtheoretical model. METHODS: This was a descriptive study using a sample of 179 older adults living independently in an East Coast continuing care retirement community (CCRC). A single one-time interview was completed and included: (a) stage of change for exercise, (b) self-efficacy and outcome expectations, (c) health status, (d) fear of falling, and (e) exercise activity. Model testing used structural equation modeling. RESULTS: Testing of the hypothesized model showed that 11 of the 22 paths were statistically significant. Health status and social support influenced self-efficacy and outcome expectations which directly influenced stage of change and exercise. Social support likewise directly influenced stage of change. Together the variables in the model explained 64% of exercise behavior in older adults. There was a poor fit of the hypothesized model to the data with a chi2 of 144.7, degrees of freedom (df) of 23 and a ratio of 6.3. The revised model fit the data better chi2 = 80.5, df = 19, p <.05, chi2/df = 4.2) and there was improved fit when compared to the hypothesized model (chi2 difference of 64.0, df difference of 4, p < or = l. DISCUSSION: The combined testing of the mediating components of the theory of self-efficacy as well as the incorporation of the stage of change to explain exercise behavior in older adults suggests that both of these approaches are useful. Stage of change may be particularly useful to help determine the most appropriate intervention to increase activity and exercise in older adults.

Aged↗
PubMed1992

A theoretical model of LDL-receptor trapping on a spherical cell.

The kinetics of the trapping of LDL-receptor complexes by coated pits on the surface of fibroblasts is examined in this paper. We have recently developed a mathematical formalism to extend Keizer's non-linear, non-equilibrium fluctuation-dissipation theory to the kinetics of chemical systems constrained to a spherical surface. Keizer's theory is ideally suited to the study of open biological systems. In the past it has been used to investigate endocytosis on fibroblasts. However, these applications have modeled the cell membrane with an infinite plane. As such, the finite size of the cellular membrane, as well as its precise symmetry, could not be incorporated into the previous studies. Thus in this paper we use our recently developed methodology to reexamine the trapping step in endocytosis on spherical cells. For cell surface processes, the theoretical consideration of a spherical symmetry or an infinite plane, in model calculations, will depend on the experimental or in vivo conditions of the processes of interest. For a spherical symmetry, we find that the finite size of the cell surface does not significantly affect the rate of the trapping step given the empirically determined values for the relevant parametes on fibroblasts. This result supports the approximation used in the previous investigation. However, this and other analyses indicate that the finitie size of the biological surface probably is an important parameter for processes which occur on smaller biological surfaces such as those found on organelles.

Fibroblasts↗
PubMed1994

Actin-crosslinking protein regulation of filament movement in motility assays: a theoretical model.

The interaction of single actin filaments on a myosin-coated coverslip has been modeled by several authors. One model adds a component of "frictional drag" by myosin heads that oppose movement of the actin filaments. We have extended this concept by including the resistive drag from actin crosslinking proteins to understand better the relationship among crosslinking number, actin-myosin force generation, and motility. The validity of this model is supported by agreement with the experimental results from a previous study in which crosslinking proteins were added with myosin molecules under otherwise standard motility assay conditions. The theoretical relationship provides a means to determine many physical parameters that characterize the interaction between a single actin filament and a single actin-crosslinking molecule (various types). In particular, the force constant of a single filamin molecule is calculated as 1.105 pN, approximately 3 times less than a driving myosin head (3.4 pN). Knowledge of this parameter and others derived from this model allows a better understanding of the interaction between myosin and the actin/actin-binding protein cytoskeleton and the role of actin-binding proteins in the regulation and modulation of motility.

Actins↗
PubMed1986

Theoretical models for predicting the effect of bridging group recognition and conjugate substitution on hapten enzyme immunoassay dose-response curves.

Models for predicting the effect of immunological recognition of the bridge group on the dose-response curves obtained with heterogeneous hapten enzyme immunoassays are presented. Appropriate theoretical treatment shows that the greater affinity of antibodies toward the enzyme-labeled species than for the unlabeled hapten analyte results in assays with limited detection capabilities. This problem is compounded when enzyme conjugates possessing multiple haptens are used. In equilibrium type competitive arrangements, the concentrations of binder and labeled hapten may be optimized to some extent to improve assay performance. However, the results presented show that only when assays are performed in a sequential binding mode using carefully controlled timing of reagent incubations can the detection capabilities of the assays be fully maximized for analyte measurements. Unfortunately, it is also shown that such sequential binding approaches render the assays essentially nonselective. The effect of decreasing the affinity of the binder to the enzyme-labeled hapten relative to the unlabeled analyte by using heterologous conjugates in equilibrium arrangements is shown to improve detection capabilities but also at the expense of reduced selectivity. Suggestions for reagent concentrations and conjugate substitution (degree of conjugation), which provide optimized dose-response curves at a given ED50 value, are also presented as are proposals for using different binders which do not exhibit bridging group recognition.

Antibody Affinity↗
PubMed1987

Theoretical modelling of protein synthesis.

This article provides an overview of the use of mathematical and computer modelling in furthering the understanding of protein synthesis. In particular, we discuss issues such as the nature of the rate limiting step(s), error rates, tRNA-codon adaptation, codon bias, attenuation control, and problems of selection and error corrections, focussing on their theoretical treatment.

Codon↗
PubMedDate not supplied

Theoretical models for the mechanisms of benign paroxysmal positional vertigo.

Benign paroxysmal positional vertigo (BPPV) is a common vestibular disorder resulting from a malfunction of the semicircular canal. Prior studies attempting to elucidate the mechanics of BPPV have focused on clinical and laboratory findings, and have discussed theoretical aspects only in qualitative terms. The goal of this study is to create a mathematical description of BPPV mechanics based on biophysical principles, in order to improve the physiopathological understanding of the most common varieties of the disorder, canalithiasis and cupulolithiasis. First, the abnormal stimulus being applied to the vestibular system during BPPV episodes is estimated by an analysis of the vestibulo-ocular reflex (VOR) response of clinical BPPV patients. The magnitude and time course of the head motion stimulus that would, in a normal test subject, produce a VOR response similar to that observed during BPPV nystagmus are inferred from eye motion data using an inverse transfer function approach. Next, physicomathematical models to describe the mechanics of the abnormal stimulations of the crista are created: the cupulolithiasis model is based on the principle that dense particulate matter becomes attached to the cupula of affected patients and effectively changes the specific gravity of the cupula; the canalithiasis model is based on the hydrodynamic effects from a cluster of particles falling within the canal endolymph. The stimuli predicted by these two models are compared to the stimuli estimated from physiological and clinical studies. The model predictions are found to be consistent with the empirical evidence for a reasonable set of model parameters. The cupulolithiasis model predicts a value of 0.69 micro g as the mass of particles contributing to the disorder. The canalithiasis model predicts a value of 0.087 micro g. These results support and expand our understanding of the mechanisms underlying the production of the cupulolithiasis and canalithiasis varieties of vertigo in humans. On the basis of these models, several predictions that can help the clinician improve the evaluation of BPPV patients are discussed.

Calcinosis↗
PubMedDate not supplied

A theoretical model for smoking prevention studies in preteen children.

The age of the onset of smoking is on a continual decline, with the prime age of tobacco use initiation being 12-14 years. A weakness of the limited research conducted on smoking prevention programs designed for preteen children (ages 10-12) is a well-defined theoretical basis. A theoretical perspective is needed in order to make a meaningful transition from empirical analysis to application of knowledge. Bandura's Social Cognitive Theory (1977, 1986), the Theory of Reasoned Action (Ajzen & Fishbein, 1980), and other literature linking various concepts to smoking behaviors in preteens were used to develop a model that may be useful for smoking prevention studies in preteen children.

Adolescent↗
PubMed2000

Ventricular energetics in Fontan circulation: evaluation with a theoretical model.

BACKGROUND: Both pulmonary and systemic circulation must be maintained by a single pump in Fontan circulation. This unique property of Fontan circulation may be related to decreased exercise tolerance or increased instantaneous postoperative mortality rate, often observed in patients with this circulation. To better understand Fontan physiology, the present study theoretically investigated cardiac performance of Fontan circulation by using ventricular-vascular coupling framework analysis. METHODS: End-systolic volume elastance (Ees), as a chamber contractile property, and effective arterial elastance (Ea), a lumped measure of ventricular afterload, were estimated both in normal left ventricular systemic circulation and in Fontan circulation. RESULTS: End-systolic volume elastance was decreased and Ea was increased in Fontan circulation. Both ventricular external stroke work (SW) and mechanical efficiency (EFF) under Fontan circulation were lower compared with those under normal circulation. Furthermore, the Ees-Ea relationship in Fontan circulation predicted limited cardiac reserve in terms of SW and EFF. Such cardiac performance in Fontan circulation stemmed from increased impedance due to the additional connection of the pulmonary vascular bed to the systemic vasculature and from the lack of a compensatory increase in contractility for increased afterload. CONCLUSIONS: Thus, it was inferred that Fontan circulation had intrinsic disadvantages and this may explain, in part, abnormal functional status and decline in survival following this procedure.

Blood Circulation↗
PubMed1999

A theoretical model of the competition between hydrolase and carboxylesterase in protection against organophosphorus poisoning.

A system of coupled non-linear differential equations describing interactions between organophosphorus compounds (OPs), OP hydrolase, acetylcholinesterase (AChE), and carboxylesterase (CaE) in a single compartment was derived incorporating irreversible combination of OP with AChE, hydrolytic breakdown of OP, and irreversible combination of OP with CaE. The equations were then uncoupled, providing non-linear differential equations on AChE, CaE and OP concentrations. One steady state solution of the AChE equation provided theoretical expressions for the amounts of OP hydrolyzed, bound with CaE, and bound with AChE. Assuming that the LD50 of an OP reflects the dose that depletes AChE to a 'minimal essential' level and that a single compartment model is applicable in vivo, the steady state solution becomes an equation predicting the LD50 from rate constants, initial enzyme levels, and the allowable AChE depletion. Normalization by initial AChE concentration produced a dimensionless relationship describing an 'OP toxicity surface' that clearly demonstrates regions where hydrolysis and CaE offer protection against OP poisoning. The surface can be used to theoretically predict an LD50 given only kinetic rate constants and effective whole-body AChE and CaE levels. Predictions of LD50s of seven OPs in rats were compared with published data. The relationship was found to adequately predict published LD50s spanning 5 orders of magnitude. The OP toxicity surface relationship provides a conceptual tool for use in OP toxicity research but should be particularly useful in predicting the relative protective effects of catalytic and stoichiometric scavenger mechanisms for an OP.

Acetylcholinesterase↗
PubMed1999

Theoretical model for layer rotations in smectic-A* liquid crystals subject to asymmetric electric fields.

Recently, observations of the rotation of smectic layers under certain experimental conditions have been reported in the literature. In this work, the mechanism of such rotations in chiral smectic-A* liquid crystals under the action of asymmetric, periodic electric fields is studied theoretically. The general conditions for layer rotations have been established using symmetry arguments, and a generalized dynamical theory of the chiral smectic-A* phase, coupling layer rotations and the electroclinic effect, has been developed. The theory is applied in the specific case when an asymmetric sawtooth electric field is applied over the system, and the dependence of the average angular velocity of the smectic layers on the relevant material constants of the liquid crystal and experimental control parameters is calculated. By rewriting the final equations into dimensionless form, it is demonstrated that the system exhibits a universal behavior, reducing the number of independent material constants and control parameters considerably.

Journal Article↗
PubMed1997

A Theoretical Model of Flotation Deinking Efficiency

The associated probabilities of each microprocess occurring in flotation deinking are employed in the development of a kinetic or population balance-type model of the overall flotation process. The overall model contains two kinetic constants: The first, k 1 , governs the overall probability of a free ink particle successfully being intercepted by and adhering to an air bubble; the second, k 2 , is a measure of the probability that a particle/bubble aggregate pair will become unstable and split to yield a "new" free ink particle. The solution to the kinetic model is presented in terms of k 1 and k 2 , which are themselves functions of system parameters such as bubble and particle physical properties (e.g., diameter, density) and fluid properties (e.g., viscosity, surface tension). From this solution, a definition of theoretical flotation efficiency is presented, as well as definitions of other system performance parameters, and selected predictions are displayed.

Journal Article↗
PubMed2007

Theoretical modelling of radiolytic damage of free DNA bases and within DNA macromolecule.

The base damages in living cell are the most frequent product of deleterious effect of ionizing radiation. Experimental yields of modified bases determined in free bases and in the double stranded DNA show significant differences in the yields of stable products of radiolytic attack. An attempt to explain these differences is made with the help of theoretical calculations. The relative probabilities of reactions of the most important radiolytic product, OH(*) radical, with individual nucleobases, nucleosides and short DNA oligomers are calculated and compared to available experimental yields of base damages.

Computer Simulation↗