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At least 559 records · Page 31Linked to original sources
PubMed1993

Hydration of proteins. A comparison of experimental residence times of water molecules solvating the bovine pancreatic trypsin inhibitor with theoretical model calculations.

A 1 ns trajectory from a molecular dynamics study of 1.4 ns total length was used for a detailed analysis of the residence times of water molecules located near 227 selected bovine pancreatic trypsin inhibitor (BPTI) atoms. The simulation was performed using the GROMOS force field, with apolar hydrogen atoms treated as united atoms, and the SPC/E water model. The system consisted of 568 BPTI atoms and 2371 water molecules. The theoretical results are in good agreement with experimental data available from nuclear magnetic resonance spectroscopy. The residence times of individual water molecules coming near a given BPTI atom, as obtained from the simulation, vary greatly and range between 10 and 500 ps. The effective residence time, calculated using a correlation function technique from the presence of all individual water molecules visiting the hydration shell of a given BPTI atom, never exceeds 200 ps. The average residence time near backbone and side-chain atoms is approximately 39 ps and 24 ps, respectively. The shortest residence times, on average, are found near charged atoms (19 ps), whereas near non-polar and polar side-chain atoms the residence times are 25 ps and 36 ps, respectively. There is no apparent correlation between the residence times of the hydration water molecules of solvent-accessible residues and their location in different regular or non-regular secondary structures.

Amino Acid Sequence↗
PubMed2001

A theoretical model of intracellular devitrification.

Devitrification of the intracellular solution can cause significant damage during warming of cells cryopreserved by freezing or vitrification. Whereas previous theoretical investigations of devitrification have not considered the effect of cell dehydration on intracellular ice formation, a new model which couples membrane-limited water transport equations, classical nucleation theory, and diffusion-limited crystal growth theory is presented. The model was used to explore the role of cell dehydration in devitrification of human keratinocytes frozen in the presence of glycerol. Numerical simulations demonstrated that water transport during cooling affects subsequent intracellular ice formation during warming, correctly predicting observations that critical warming rate increases with increasing cooling rate. However, for cells with a membrane transport activation energy less than approximately 50 kJ/mol, devitrification was also affected by cell dehydration during warming, leading to a reversal of the relationship between cooling rate and critical warming rate. Thus, for low warming rates (less than 10 degrees C/min for keratinocytes), the size and total volume fraction of intracellular ice crystals forming during warming decreased with decreasing warming rate, and the critical warming rate decreased with increasing cooling rate. The effects of water transport on the kinetics of intracellular nucleation and crystal growth were elucidated by comparison of simulations of cell warming with simulations of devitrification in H(2)O-NaCl-glycerol droplets of constant size and composition. These studies showed that the rate of intracellular nucleation was less sensitive to cell dehydration than was the crystal growth rate. The theoretical methods presented may be of use for the design and optimization of freeze-thaw protocols.

Cryopreservation↗
PubMed2001

Community-based interventions to reduce low income, African American women's risk of sexually transmitted diseases: a randomized controlled trial of three theoretical models.

A community-based sample of disadvantaged African American women (n = 445) was recruited to participate in 1 of 3 theoretically driven experimental interventions based on either the theory of gender and power, social learning theory, or cognitive behavioral theory. Intervention outcomes were compared with a waiting list control condition. From baseline to postintervention, women in the experimental interventions showed differential change on cognitive indices (knowledge and attitudes) and skill acquisition (partner negotiation skills, correct condom application, lubricant selection, and information-provision to social networks) whereas control participants were unchanged. Women in the 3 experimental interventions also completed follow-up assessments for 1 year following the interventions. In all 3 experimental conditions, condom use increased relative to the control group and there were no differences between the experimental interventions. Women who participated in one of the theoretically grounded interventions continued to increase condom use over the following year. Women entering new relationships reported significantly more condom use than did women who remained in ongoing relationships. The findings suggest that intervention models that have proven effective for women who engage in high-risk behavior may be less effective for women in established relationships for whom risk is primarily derived from the extrarelationship behavior of their partners.

Adult↗
PubMed2001

Theoretical Model of Electrode Polarization and AC Electroosmotic Fluid Flow in Planar Electrode Arrays.

Strong frequency-dependent fluid flow has been observed near the surface of microelectrode arrays. Modeling this phenomenon has proven to be difficult, with existing theories unable to account for the qualitative trend observed in the frequency spectra of this flow. Using recent electrode polarization results, a more comprehensive model of the double layer on the electrode surface is used to obtain good theoretical agreement with experimental data. Copyright 2001 Academic Press.

Journal Article↗
PubMed2000

Theoretical models for the oxygen radical mechanism of water oxidation and of the water oxidizing complex of photosystem II.

Hybrid density functional theory is used to study reasonably realistic models of the oxygen-evolving manganese complex in photosystem II. Since there is not yet any X-ray structure of the complex, other types of experimental and theoretical information are used to construct the model complexes. In these complexes, three manganese centers are predicted to be closely coupled by mu-oxo bonds in a triangular orientation. Using these models, the previously suggested oxygen radical mechanism for O2 formation is reinvestigated. It is found that the oxygen radical in the S3 state now appears in a bridging position between two manganese atoms. It is still suggested that only one manganese atom is redox-active. Instead, a number of surprisingly large trans-effects are found, which motivate the existence and define the function of the other manganese atoms in the Mn4 cluster. Calcium has a strong chelating effect which helps in the creation of the necessary oxygen radical. In the present model the chemistry preceding the actual O-O bond formation occurs in an incomplete cube with a missing corner and with two manganese and one calcium in three of the corners. The external water providing the second oxygen of O2 enters in the missing corner of the cube. The present findings are in most cases in good agreement with experimental results as given in particular by EXAFS.

Electron Transport↗
PubMed1994

Significance of viable skin layers in percutaneous permeation and its implication in mathematical models: theoretical consideration based on parameters for betamethasone 17-valerate.

The role of viable skin layers (viable epidermis and dermis) is examined by the three-layer model using parameter values for betamethasone 17-valerate. The mathematical three-layer diffusion model indicates that the lag time and half-life after vehicle removal in epidermis and split-thickness skin are longer than those in stratum corneum without viable layers, even if drug flux at steady-state is minimally altered. The theoretical values of the lag time and half-life predicted for epidermis and split-thickness-skin samples are compatible with the values observed in another in vitro study. The results predicted by the three-layer model indicate that the simplified model (single-layer or compartment model), which regards the whole skin as one diffusion layer or one compartment, may be warranted because all three skin layers have the same half-life after vehicle removal. The parameters used in the simplified model are estimated from some of the following values directly obtainable in the experiment: flux from skin and amount in the whole skin at steady-state, lag time, and drug concentration or amount maintained to be unchanged in the donor site. However, the simplified model often cannot resolve some discrepancy between the data and model (e.g., the ratio of the half-life to lag time) even if the data may be explained by the three-layer model.

Betamethasone Valerate↗
PubMed2003

A theoretical model of nitric oxide transport in arterioles: frequency- vs. amplitude-dependent control of cGMP formation.

Nitric oxide (NO) plays many important physiological roles, including the regulation of vascular smooth muscle tone. In response to hemodynamic or agonist stimuli, endothelial cells produce NO, which can diffuse to smooth muscle where it activates soluble guanylate cyclase (sGC), leading to cGMP formation and smooth muscle relaxation. The close proximity of red blood cells suggests, however, that a significant amount of NO released will be scavenged by blood, and thus the issue of bioavailability of endothelium-derived NO to smooth muscle has been investigated experimentally and theoretically. We formulated a mathematical model for NO transport in an arteriole to test the hypothesis that transient, burst-like NO production can facilitate efficient NO delivery to smooth muscle and reduce NO scavenging by blood. The model simulations predict that 1) the endothelium can maintain a physiologically significant amount of NO in smooth muscle despite the presence of NO scavengers such as hemoglobin and myoglobin; 2) under certain conditions, transient NO release presents a more efficient way for activating sGC and it can increase cGMP formation severalfold; and 3) frequency-rather than amplitude-dependent control of cGMP formation is possible. This suggests that it is the frequency of NO bursts and perhaps the frequency of Ca(2+) oscillations in endothelial cells that may limit cGMP formation and regulate vascular tone. The proposed hypothesis suggests a new functional role for Ca(2+) oscillations in endothelial cells. Further experimentation is needed to test whether and under what conditions in silico predictions occur in vivo.

Arterioles↗
PubMed2005

Graph theoretic modeling of large-scale semantic networks.

During the past several years, social network analysis methods have been used to model many complex real-world phenomena, including social networks, transportation networks, and the Internet. Graph theoretic methods, based on an elegant representation of entities and relationships, have been used in computational biology to study biological networks; however they have not yet been adopted widely by the greater informatics community. The graphs produced are generally large, sparse, and complex, and share common global topological properties. In this review of research (1998-2005) on large-scale semantic networks, we used a tailored search strategy to identify articles involving both a graph theoretic perspective and semantic information. Thirty-one relevant articles were retrieved. The majority (28, 90.3%) involved an investigation of a real-world network. These included corpora, thesauri, dictionaries, large computer programs, biological neuronal networks, word association networks, and files on the Internet. Twenty-two of the 28 (78.6%) involved a graph comprised of words or phrases. Fifteen of the 28 (53.6%) mentioned evidence of small-world characteristics in the network investigated. Eleven (39.3%) reported a scale-free topology, which tends to have a similar appearance when examined at varying scales. The results of this review indicate that networks generated from natural language have topological properties common to other natural phenomena. It has not yet been determined whether artificial human-curated terminology systems in biomedicine share these properties. Large network analysis methods have potential application in a variety of areas of informatics, such as in development of controlled vocabularies and for characterizing a given domain.

Algorithms↗
PubMedDate not supplied

[Theoretical model of radiation-induced cancer].

A model of the dose dependence of the incidence of radiation-induced malignant tumors is proposed to provide a reliable estimation of the carcinogenic risk from low-level radiation. The model describes three main routs (cellular, tissue and system ones) by which radiation influences carcinogenesis. In terms of the two-stage theory of carcinogenesis, the first route deals with the initiating effect of radiation, and the second and third routs, with its promotion action. The proposed model gives a satisfactory combined description of the leukaemogenic effect of gamma-rays and neutrons. A theoretical explanation is presented of the differences in the pattern of the dose dependences of the yield of similar forms of the induced cancer exhibited by radiosensitive and radioresistant animal strains.

Animals↗
PubMed1981

Quantitative cell fusion: derivation and application of theoretical models.

Cell fusion experiments were made on ten cell lines representing seven mammalian species, using inactivated Sendai virus. The extent of fusion was determined microscopically and tabulated as frequencies of cell with different numbers of nuclei. Expected distributions were derived theoretically under certain assumptions concerning the fusion process. A random model was assumed according to which the tendency to fuse depends only on the cell size, expressed as the number of nuclei present in the cell. Three distributions were derived, which were referred to as the simple, additive, and multiplicative models. The additive model pertained to fusions made in cell suspensions and the multiplicative one mainly to fusions in fibroblast monolayers.

Cell Fusion↗
PubMed1985

A theoretical model for the binding of cis-Pt(NH3)2(+2) to DNA.

The binding of cis-Pt(NH3)2B1B2 to the bases B1 and B2, i.e., guanine (G), cytosine (C), adenine (A), and thymine (T), of DNA is studied theoretically. The components of the binding are analyzed and a model structure is proposed for the intrastrand binding to the dB1pdB2 sequence of a kinked double helical DNA. Quantum mechanical calculations of the ligand binding energy indicates that cis-Pt(NH3)2(+2) (cis-PDA) binds to N7(G), N3(C), O2(C), O6(G), N3(A), N7(A), O4(T) and O2(T) in order of decreasing binding energy. Conformational analysis provides structures of kinked DNA in which adjacent bases chelate to cis-PDA. Only bending toward the major groove allows the construction of acceptable square planar complexes. Examples are presented for kinks of -70 degrees and -40 degrees at the receptor site to orient the base pairs for ligand binding to B1 and B2 to form a nearly square planar complex. The energies for complex formation of cis-PDA to the various intra-strand base sites in double stranded DNA are estimated. At least 32 kcal/mole separates the energetically favorable dGpdG.cis-PDA chelate from the dCpdG.cis-PDA chelate. All other possible chelate structures are much higher in energy which correlates with their lack of observation in competition with the preferred dGpdG chelate. The second most favorable ligand energy occurs with N3(C). A novel binding site involving dC(N3)pdG(N7) is examined. Denaturation can result in an anti----syn rotation of C about its glycosidic bond to place N3(C) in the major groove for intrastrand binding in duplex DNA. This novel intrastrand dCpdG complex and the most favored dGpdG structure are illustrated with stereographic projections.

Base Sequence↗
PubMed1997

Correspondence between theoretical models and dual energy x-ray absorptiometry measurements of femoral cross-sectional growth during adolescence.

We have developed an analytical model of long bone cross-sectional ontogeny in which appositional growth of the diaphysis is primarily driven by mechanical stimuli associated with increasing body mass during growth and development. In this study, our goal was to compare theoretical predictions of femoral diaphyseal structure from this model with measurements of femoral bone mineral and geometry by dual energy x-ray absorptiometry. Measurements of mid-diaphyseal femoral geometry and structure were made previously in 101 Caucasian adolescents and young adults 9-26 years of age. The data on measured bone mineral content and calculated section modulus were compared with the results of our analytical model of cross-sectional development of the human femur over the same age range. Both bone mineral content and section modulus showed good correspondence with experimental measurements when the relationships with age and body mass were examined. Strong linear relationships were evident for both parameters when examined as a function of body mass.

Absorptiometry, Photon↗
PubMed1981

Kinetics of hog pancreas alpha-amylase; theoretical model of the dual-site enzyme.

The model of the multiple attack mechanism has been proposed for the enzyme consisting of two hypothetical subunits or domains identical in structure and function. The theoretical coefficients of multiple attack: effectiveness and average number of unitary movements, have been computed for such a dual-site model of pancreatic alpha-amylase. Those coefficients affect the values of maximum velocity and Michaelis constant, respectively. Two possible manners of the subunit coupling were considered: symmetric and sequential. The dual-site model with a symmetric type of coupling appeared to be kinetically indistinguishable from the single-site model.

Amylases↗
PubMed1994

A theoretical model to predict contrast sensitivity with bifocal intraocular lenses.

Bifocal intraocular lenses (BIOLs) cause a reduction in image contrast. However, the clinically measurable reduction is much lower than that predicted by experimental results. We therefore compared monofocal IOLs, the True Vista BIOL, and the diffractive BIOL. We measured the modulation transfer function (MTF) of all IOLs in a model eye. Clinically, we determined the contrast sensitivity (CS). For a comparison of the results, the MTF was converted into the theoretical CS of the eye using the age-corrected values of retinal CS. The calculated CS of the BIOLs was similar to the values measured clinically. However, the calculated CS of monofocal IOLs was considerably higher than the clinical values. This difference should be due to the MTF of the normal eye; the MTF of monofocal IOLs was considerably higher than that of the normal eye, whereas the MTF of the BIOLs was lower. Thus, the MTF of the normal eye becomes the limiting factor of this system. The proposed model takes into account the retinal CS and the MTF of the normal eye. Using the MTF of an IOL, the clinical CS can be calculated, and the clinical performance of new IOL designs may be predicted before clinical trials commence.

Adult↗
PubMed2006

Theoretical modeling of postionization fragmentation of rare-gas trimer cations.

The dynamics of ionic rare-gas trimers (Ar(3) (+), Kr(3) (+), and Xe(3) (+)) produced by a sudden ionization of neutral precursors is investigated theoretically with a hybrid classical-quantum method for solving the equations of motion governed by a Hamiltonian obtained from a previously tested diatomics-in-molecules model. Initial conditions are selected with Monte Carlo sampling. Two possibilities for generating the initial electronic state are considered: diabatic (local) and adiabatic (delocalized). The dynamics generally leads to fragmentation, producing either monomer ions or dimer ions in a relatively short time; however, a large number of long-lived metastable trimer ions are also seen in some cases. We have analyzed the dynamics with respect to the fraction of monomer ions produced, the distribution of the kinetic energy of the products, and the distribution of fragmentation times of the trimers. Initial diabatic ionization is associated with much faster fragmentation than adiabatic ionization. Spin-orbit coupling plays an important role in the fragmentation dynamics.

Journal Article↗
PubMed1990

[Urodynamic consequences of urethral stenosis. Hydrodynamic study with a theoretical model].

An urethral model was designed to assess the hydrodynamic consequences of stenosis of the bulbar urethra. This model was based on the geometric and hydrodynamic analysis of micturing urethrograms in a patient whose maximum flow rate was 24 ml/s for a bladder pressure of 40 cm of water. It corresponds to the conditions of flow observed wit maximum bladder pressure and flow rate. During this short period, the shape of the urethra is regarded as stable. Calculation took account of the characteristics of a turbulent flow of urine, of the head loss due to friction of the urine on the walls and of the head loss caused by the geometrical changes of the urethra from the neck of the bladder to the meatus. In these conditions, applying Bernouilli's equation allowed plotting of bladder pressure for various levels of urethral resistance. If there is no stenosis, the theoretical maximum flow rate of the model with a bladder pressure of 40 to 80 cm of water should be 19 to 26 ml/s. Calculation showed that a sudden reduction of the diameter to less than 2.5 mm occurring in a segment of the urethra with a diameter of 4 mm accounts for a flox rate lower than 15 ml/s, except when bladder pressure can exceed 100 cm of water. The decrease in the maximum flow rate caused by urethral stenosis is all the greater as bladder pressure remains low or normal, with other causes of head loss or with associated upstream dilatation. Lastly, progressive narrowing leads to a smaller head loss and will therefore be better tolerated than sudden narrowing to the same caliber. Inversely, a long stenosis will be less well tolerated as the head loss due to friction in a long and narrow passage is increased. The diameter of a stenosis accounting for a maximum flow rate of less than 15 ml/s cannot be determined in the absolute. Analyzing the hydrodynamic consequences of stenosis also requires knowing the associated urodynamic and geometric parameters.

Adult↗
PubMedDate not supplied

Theoretical model for myocardial functional characterization: application to a group of patients evaluated before and after surgical revascularization.

BACKGROUND: The functional improvements resulting from coronary revascularization (CABG) in patients with depressed ventricular function may be described by the use of a model combining global or local quantification of myocardial perfusion, viability, and contraction. An illustration of this model, with data provided by conventional radionuclide studies as they are performed routinely in many centers, is presented and the limitations of this approach for predicting the results of CABG are discussed. METHODS AND RESULTS: The model is based on three independent variables, which can be approximated in this preliminary study by parameters derived from standard stress and redistribution/reinjection thallium-201 single-photon emission computed tomography (SPECT) acquisitions with quantification of the tracer uptake defects and from a planar gated blood pool left ventricular ejection fraction (LVEF) measurement: Perfusion is assumed to correspond to 100-stress defect (in percentage), viability is 100-redistribution/reinjection defect, and contraction is 100(LVEF/70), assuming that a normal 70% LVEF corresponds to 100% contraction. In a group of 30 patients prospectively evaluated with this protocol and included in the study on the basis of a pre-CABG LVEF <40%, a significant improvement in LVEF was demonstrated (28.2% +/- 8.5% before CABG vs 35.8% +/- 7.3% after CABG), which is accompanied by a significant decrease of the stress thallium defects (34.8% +/- 13.8% vs 25.6% +/- 10.6%), whereas the average (but not the individual) redistribution/reinjection defects remain almost stable (27.7% +/- 10.9% vs 25.7% +/- 10.1%). As reported in the three-dimensional model, pre-CABG and post-CABG representative points clearly demonstrate the functional improvements for the main variables, but there is a large spectrum of responses to revascularization. It appears that the border between reversible and nonreversible thallium defects does not match the limit between ischemic myocardium (with no contraction alteration and therefore without contraction improvement potential) and hibernating myocardium, which is able to recover mechanical function and therefore is responsible for the improvement of global LVEF. CONCLUSIONS: Thallium SPECT is far from ideal for use as an independent characterization of perfusion and viability because hibernating myocardium may be present in both the fixed and reversible parts of thallium defects. Prediction of functional recovery is conditioned by an accurate identification of viable but underperfused and noncontracting myocardium. In the future, with the use of adequate study protocols that are able to measure viability without interference of perfusion and perfusion independent of viability, the proposed model may be able to characterize regional function as a cluster of representative points for each territory and to delineate areas of the theoretical volume corresponding to a potentially recoverable situation.

Adult↗