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At least 379 records · Page 21Linked to original sources

PubMed2003

Spectral intermode coupling in a model of isotropic turbulence.

We investigate the nonlinear coupling between the so-called explicit modes, identified with wave numbers k such that 0< or =k< or =k(c), and implicit modes, defined such that k(c)< or =k< or =k(max). Here k(c) is an arbitrarily chosen cutoff wave number and k(max) is the ultraviolet cutoff as determined by viscous damping. The stresses arising from the nonlinearity in the Navier-Stokes equations are categorized as "implicit-implicit" (or "Reynolds") and "explicit-implicit" (or "cross"). These arise from dynamic coupling between different regions of wave number space. Their respective effects on momentum, kinetic energy, and energy flux are assessed. The analysis is based on a model system comprising the Navier-Stokes equations and the Edwards-Fokker-Planck energy equation [S. F. Edwards, J. Fluid Mech. 18, 239 (1964)] which is known to retain all the symmetries of homogeneous, isotropic turbulence. The Reynolds stress is found to be responsible for long-range energy transfers. It can be represented by an effective viscosity and is mainly determined by dynamical friction. The cross term is more complicated, involving both diffusive and frictional effects. For long-range coupling it can be expressed as a modification of the effective viscosity, while for short-range coupling it may be modeled on the assumption that implicit scales are slaved to explicit scales. Thus, both the random and coherent aspects of intermode coupling in turbulent flows are relevant in the cross term. The imposition of a continuity requirement on energy transfer leads to a new parametrization that represents the effect of absent modes in a truncated spectral simulation, and takes into account the phase-coupling (coherent) effects, as well as the usual viscositylike (random) effects.

Journal Article↗

PubMed1994

On the efficiency and reversibility of active ligand transport induced by alternating rectangular electric pulses.

The stationary-state kinetic properties of a simplified two-state electro-conformational coupling model (ECC) in the presence of alternating rectangular electric potential pulses are derived analytically. Analytic expressions for the transport flux, the rate of electric energy dissipation, and the efficiency of the transducing system are obtained as a function of the amplitude and frequency of the oscillation. These formulas clarify some fundamental concept of the ECC model and are directly applicable to the interpretation and design of experiments. Based on these formulas, the reversibility and the degree of coupling of the system can be studied quantitatively. It is found that the oscillation-induced free energy transduction is reversible and tight-coupled only when the amplitude of the oscillating electric field is infinitely large. In general, the coupling is not tight when the amplitude of the electric field is finite. Furthermore, depending on the kinetic parameters of the model, there may exist a "critical" electric field amplitude, below which free energy transduction is not reversible. That is, energy may be transduced from the electric to the chemical, but not from the chemical to the electric.

Carrier Proteins↗

PubMed2002

Physiologically based pharmacokinetic (PBPK) models for nasal tissue dosimetry of organic esters: assessing the state-of-knowledge and risk assessment applications with methyl methacrylate and vinyl acetate.

Mathematical models have been developed to describe nasal epithelial tissue dosimetry with two compounds, vinyl acetate (VA) and methyl methacrylate (MMA), that cause toxicity in these tissues These models couple computational fluid dynamics (CFD) calculations that map airflow patterns within the nose with physiologically based pharmacokinetic (PBPK) models that integrate diffusion, metabolism, and tissue interactions of these compounds. Dose metrics estimated in these models for MMA and VA, respectively, were rates of MMA metabolism per volume of tissue and alterations in pH in target tissues associated with VA hydrolysis and metabolism. In this article, four scientists who have contributed significantly to development of these models describe the many similarities and relatively few differences between the MMA and VA models. Some differences arise naturally because of differences in target tissues, in the calculated measures of tissue dose, and in the modes of action for highly extracted vapors (VA) compared with poorly extracted vapors (MMA). A difference in the approach used to estimate metabolic parameters from human tissues provides insights into interindividual extrapolation and identifies opportunities for studies with human nasal tissues to enhance current risk assessments. In general, the differences in model structure for these two esters were essential for describing the biology of the observed responses and in accounting for the different measures of target tissue dose. This article is intended to serve as a guide for understanding issues of optimum model structure and optimal data sources for these nasal tissue dosimetry models. We also hope that it leads to greater international acceptance of these hybrid CFD/PBPK modeling approaches for improving risk assessment for many nasal toxicants. In general, these models predict either equivalent (VA) or lower (MMA) nasal tissue doses in humans compared with tissue doses at equivalent exposure concentrations in rats.

Air Movements↗

PubMed1991

Effect of tertiary amine on the carbodiimide-mediated peptide synthesis.

The effect of tertiary amine (DIEA) on reaction rate and product purity of a carbodiimide/HOBt-mediated peptide synthesis was studied. It was found that very rapid activation can be achieved using carbodiimide/HOBt in non-polar solvents, such as DCM. Although the HOBt is poorly soluble in DCM, the activation proceeds within 2 min, probably forming the HOBt-ester. By such a preactivation followed by a coupling in the presence of DIEA the rate of coupling is comparable with other rapid methods using BOP or TBTU, and no racemization was found in a model coupling (less than 0.1%). For comparison, syntheses of neurotensin by means of different coupling reagents (BOP, TBTU, OPfp-esters) and the DIEA-catalyzed coupling after carbodiimide/HOBt-activation under comparable conditions have shown that these procedures are of the same value in view of coupling efficiency and product purity.

Amines↗

PubMed2000

Connectivity of marine populations: open or closed?

Most marine populations are thought to be well connected via long-distance dispersal of larval stages. Eulerian and Lagrangian flow models, coupled with linear mortality estimates, were used to examine this assumption. The findings show that when simple advection models are used, larval exchange rates may be overestimated; such simplistic models fail to account for a decrease of up to nine orders of magnitude in larval concentrations resulting from diffusion and mortality. The alternative process of larval retention near local populations is shown to exist and may be of great importance in the maintenance of marine population structure and management of coastal marine resources.

Animals↗

PubMed1967

The regulatory process in the de-repression of enzyme synthesis. Alkaline phosphatase of Bacillus subtilis.

1. The kinetics of de-repression of alkaline phosphatase in Bacillus subtilis were studied after the removal of P(i). Enzyme activity appeared about 10min. after removal of P(i), whereas ;enzyme-forming potential' appeared after 6min. 2. Protein synthesis is not impaired for at least 20min. on removal of P(i), but RNA synthesis is considerably diminished. 3. Adding chloramphenicol to cells without P(i), just at the time they start to make enzyme-forming potential, does not affect the differential rate of enzyme synthesis compared with total protein. Enzyme-forming potential accumulates to about normal levels in the presence of chloramphenicol, even though peptide-bond formation is inhibited by more than 95%. 4. Similar experiments performed with actinomycin C show more complex effects. Actinomycin initially prevents RNA synthesis and also the synthesis of enzyme-forming potential. After some minutes RNA synthesis resumes at a low rate, to be followed 4min. later by enzyme synthesis. Enzyme-forming potential can accumulate in the presence of actinomycin after the resumption of RNA synthesis. Protein synthesis, initially inhibited by actinomycin as a consequence of the effect on RNA synthesis, is later directly inhibited by actinomycin. 5. Adding actinomycin to de-repressed cells already making enzyme stops enzyme synthesis within 4-5min. Enzyme synthesis resumes, as before, 4min. after the resumption of RNA synthesis. 6. Adding P(i) together with actinomycin to de-repressed cells synthesizing enzyme does not result in a lower yield of enzyme compared with actinomycin alone. 7. Actinomycin is less effective an inhibitor of RNA and protein synthesis in P(i)-starved cells if P(i) is also added. 8. These results are discussed in view of the three main models for the regulation of enzyme induction: regulation at the level of transcription only, at translation only, or a coupled model in which transcription requires concomitant translation. It is concluded that the present evidence most powerfully supports the model of transcriptional regulation.

Alkaline Phosphatase↗

PubMed1992

Mössbauer study of the native, reduced and substrate-reacted Desulfovibrio gigas aldehyde oxido-reductase.

The Desulfovibrio gigas aldehyde-oxido-reductase contains molybdenum and iron-sulfur clusters. Mössbauer spectroscopy was used to characterize the iron-sulfur clusters. Spectra of the enzyme in its oxidized, partially reduced and benzaldehyde-reacted states were recorded at different temperatures and applied magnetic fields. All the iron atoms in D. gigas aldehyde oxido-reductase are organized as [2Fe-2S] clusters. In the oxidized enzyme, the clusters are diamagnetic and exhibit a single quadrupole doublet with parameters (delta EQ = 0.62 +/- 0.02 mm/s and delta = 0.27 +/- 0.01 mm/s) typical for the [2Fe-2S]2+ state. Mössbauer spectra of the reduced clusters also show the characteristics of a [2Fe-2S]1+ cluster and can be explained by a spin-coupling model proposed for the [2Fe-2S] cluster where a high-spin ferrous ion (S = 2) is antiferromagnetically coupled to a high-spin ferric ion (S = 5/2) to form a S = 1/2 system. Two ferrous sites with different delta EQ values (3.42 mm/s and 2.93 mm/s at 85 K) are observed for the reduced enzyme, indicating the presence of two types of [2Fe-2S] clusters in the D. gigas enzyme. Taking this observation together with the re-evaluated value of iron content (3.5 +/- 0.1 Fe/molecule), it is concluded that, similar to other Mo-hydroxylases, the D. gigas aldehyde oxido-reductase also contains two spectroscopically distinguishable [2Fe-2S] clusters.

Aldehyde Oxidoreductases↗

PubMed2006

High-order excitations in state-universal and state-specific multireference coupled cluster theories: model systems.

For the first time high-order excitations (n>2) have been studied in three multireference couple cluster (MRCC) theories built on the wave operator formalism: (1) the state-universal (SU) method of Jeziorski and Monkhorst (JM) (2) the state-specific Brillouin-Wigner (BW) coupled cluster method, and (3) the state-specific MRCC approach of Mukherjee (Mk). For the H4, P4, BeH(2), and H8 models, multireference coupled cluster wave functions, with complete excitations ranging from doubles to hextuples, have been computed with a new arbitrary-order string-based code. Comparison is then made to corresponding single-reference coupled cluster and full configuration interaction (FCI) results. For the ground states the BW and Mk methods are found, in general, to provide more accurate results than the SU approach at all levels of truncation of the cluster operator. The inclusion of connected triple excitations reduces the nonparallelism error in singles and doubles MRCC energies by a factor of 2-10. In the BeH(2) and H8 models, the inclusion of all quadruple excitations yields absolute energies within 1 kcal mol(-1) of the FCI limit. While the MRCC methods are very effective in multireference regions of the potential energy surfaces, they are outperformed by single-reference CC when one electronic configuration dominates.

Journal Article↗

PubMed1999

Identification of electrically stimulated quadriceps muscles in paraplegic subjects.

This work establishes a method for the noninvasive in vivo identification of parametric models of electrically stimulated muscle in paralyzed individuals, when significant inertial loads and/or load transitions are present. The method used differs from earlier work, in that both the pulse width and stimulus period (interpulse interval) modulation are considered. A Hill-type time series model, in which the output is the product of two factors (activation and torque-angle) is used. In this coupled model, the activation dynamics depend upon velocity. Sequential nonlinear least squares methods are used in the parameter identification. The ability of the model, using identified time-varying parameters, to accurately predict muscle torque outputs is evaluated, along with the variability of the identified parameters. This technique can be used to determine muscle parameter models for biomechanical computer simulations, and for real-time adaptive control and monitoring of muscle response variations such as fatigue.

Algorithms↗

PubMed2002

A statistical method for predicting automobile driving posture.

A new model for predicting automobile driving posture is presented. The model, based on data from a study of 68 men and women in 18 vehicle package and seat conditions, is designed for use in posturing the human figure models that are increasingly used for vehicle interior design. The model uses a series of independent regression models, coupled with data-guided inverse kinematics, to fit a whole-body linkage. An important characteristic of the new model is that it places greatest importance on prediction accuracy for the body locations that are most important for vehicle interior design: eye location and hip location. The model predictions were compared with the driving postures of 120 men and women in five vehicles. Errors in mean eye location predictions in the vehicles were typically less than 10 mm. Prediction errors were largely independent of anthropometric variables and vehicle layout. Although the average posture of a group of people can be predicted accurately, individuals' postures cannot be predicted precisely because of interindividual posture variance that is unrelated to key anthropometric variables. The posture prediction models developed in this research can be applied to posturing computer-rendered human models to improve the accuracy of ergonomic assessments of vehicle interiors.

Adult↗

PubMed2004

A mathematical model of the dynamics of odontogenic cyst growth.

OBJECTIVE: To formulate a mathematical model of odontogenic cyst growth and establish the dynamics of cyst enlargement and role of osmotic pressure forces throughout its growth. STUDY DESIGN: The model assumed a spherical cyst with a semipermeable lining of living cells and a core consisting of degraded cellular material, including generic osmotic material, fed by the continuous death of epithelial cells in the lining. The lining cells were assumed to have both elastic and viscous properties, reflecting the action of physical stresses by the surrounding cyst capsule, composed of fibroblasts and collagen fibers. The model couples the cyst radius and osmotic pressure differences resulting in a system of 2 nonlinear ordinary differential equations. RESULTS: The model predicts that in all parameter regimens the long-time behavior of the cyst is the same and that linear radial expansion results. CONCLUSION: In the early and intermediate stages of cystic growth, osmotic pressure differences play an important role; however, in very large cysts, this role becomes negligible, and cell birth in the lining dominates growth.

Algorithms↗

PubMed2004

A new model of sensorimotor coupling in the development of speech.

We present a computational model that learns a coupling between motor parameters and their sensory consequences in vocal production during a babbling phase. Based on the coupling, preferred motor parameters and prototypically perceived sounds develop concurrently. Exposure to an ambient language modifies perception to coincide with the sounds from the language. The model develops motor mirror neurons that are active when an external sound is perceived. An extension to visual mirror neurons for oral gestures is suggested.

Artificial Intelligence↗

PubMedDate not supplied

Morphology of cell-substratum adhesion. Influence of receptor heterogeneity and nonspecific forces.

Many cell types modulate growth, differentiation, and motility through changes in cell substrate adhesion, including regulation of focal contact formation. Clustering of cell surface adhesion receptors is an essential early step in the development of focal contacts, and thus may influence cell physiology. In this paper, we present a theoretical framework to examine how cell surface chemistry affects receptor clustering. Our one-dimensional tape-peeling model couples the equations of mechanical equilibrium for a cell membrane with kinetic receptor-ligand binding relations. We considered two distinct model scenarios: Adhesion mediated by multiple receptor-ligand interactions of different length and specific binding of a single receptor type occurs in the presence of van der Waals attraction and nonspecific repulsion. In each case, nonuniform (wave-like) membrane morphologies are observed in certain parameter ranges that support the clustering of adhesion receptors. The formation of these morphologies is described in terms of a balance of membrane stresses; when cell-surface potential as a function of separation distance is symmetric between two potential energy minima, nonuniform morphologies are obtained. Increases in the chemical binding energy between receptor and ligand (e.g., increases in ligand density) or decreases in the membrane rigidity result in smaller wavelengths for nonuniform interfaces. Additionally, we show wave-like geometries appear only when the mechanical compliance of receptor-ligand bonds is within an intermediate range, and examine how the mobility of "repellers"--glycocalyx molecules that exert a nonspecific repulsive force--influences membrane morphology. We find fully mobile repellers always redistribute to prevent nonuniform morphologies.

Animals↗

PubMed2006

Functionally relevant electric-field induced perturbations of the prosthetic group of yeast ferrocytochrome c mutants obtained from a vibronic analysis of low-temperature absorption spectra.

We have measured the low temperature (T = 20 K) absorption spectra of the N52A, N52V, N52I, Y67F, and N52AY67F mutants of ferrous Saccharomyces cerevisiae (baker's yeast) cytochrome c. All the bands in the Q0- and Q(v)-band region are split, and the intensity distributions among the split bands are highly asymmetric. The spectra were analyzed by a decomposition into Voigtian profiles. The spectral parameters thus obtained were further analyzed in terms of the vibronic coupling model of Schweitzer-Stenner and Bigman (Schweitzer-Stenner, R.; Bigman, D. J. Phys. Chem. B 2001, 7064-7073) to identify parameters related to electronic and vibronic perturbations of the heme macrocycle. We report that the electronic perturbation is of B(1g) symmetry and reflects the heterogeneity of the electric field at the heme, that is, the difference between the gradients along the perpendicular N-Fe-N axis of the heme core. We found that all the investigated mutations substantially increase this electronic perturbation, so that the spectral properties become similar to those of horse heart cytochrome c. Moreover, the electronic perturbation was found to correlate nonlinearly with the enthalpy changes associated with the reduction of the heme iron. Group theoretical arguments are invoked to propose a simple model which explains how a perturbation of the obtained symmetry can stabilize the reduced state of the heme iron. Finally, vibronic coupling parameters obtained from the analysis of the Q(v)-band region suggest that the investigated mutations decrease the nonplanar deformations of the heme group. This finding was reproduced by a normal mode structural decomposition (NSD) analysis of the N52V and N52VY67F heme conformations obtained from a 1 ns molecular dynamics simulation. We argue that the reduced nonplanarity contributes to the stabilization of the reduced state.

Cold Temperature↗

PubMed2002

Mechanisms of long-distance dispersal of seeds by wind.

Long-distance dispersal (LDD) is central to species expansion following climate change, re-colonization of disturbed areas and control of pests. The current paradigm is that the frequency and spatial extent of LDD events are extremely difficult to predict. Here we show that mechanistic models coupling seed release and aerodynamics with turbulent transport processes provide accurate probabilistic descriptions of LDD of seeds by wind. The proposed model reliably predicts the vertical distribution of dispersed seeds of five tree species observed along a 45-m high tower in an eastern US deciduous forest. Simulations show that uplifting above the forest canopy is necessary and sufficient for LDD, hence, they provide the means to define LDD quantitatively rather than arbitrarily. Seed uplifting probability thus sets an upper bound on the probability of long-distance colonization. Uplifted yellow poplar seeds are on average lighter than seeds at the forest floor, but also include the heaviest seeds. Because uplifting probabilities are appreciable (as much as 1 5%), and tree seed crops are commonly massive, some LDD events will establish individuals that can critically affect plant dynamics on large scales.

Computer Simulation↗

PubMed2002

Discrete nonlinear model with substrate feedback.

We consider a prototypical model in which a nonlinear field (continuum or discrete) evolves on a flexible substrate which feeds back to the evolution of the main field. We identify the underlying physics and potential applications of such a model and examine its simplest one-dimensional Hamiltonian form, which turns out to be a modified Frenkel-Kontorova model coupled to an extra linear equation. We find static kink solutions and study their stability, and then examine moving kinks (the continuum limit of the model is studied too). We observe how the substrate effectively renormalizes properties of the kinks. In particular, a nontrivial finding is that branches of stable and unstable kink solutions may be extended beyond a critical point at which an effective intersite coupling vanishes; passing this critical point does not destabilize the kink. Kink-antikink collisions are also studied, demonstrating alternation between merger and transmission cases.

Journal Article↗

PubMed2004

The origin of vibrational mode couplings in various secondary structural motifs of polypeptides.

Electrostatic (through-space) and covalent (through-bond) contributions to couplings involving the C[double bond]O and C[bond]N vibrational stretching modes of the amide group in the alpha-helix and the parallel and antiparallel beta-sheet structures of alanine polypeptides are analyzed. Coupling constants computed at the density functional theory level are compared with the transition dipole coupling model and the complete electrostatic interaction between transition densities. We find that the transition densities of C[double bond]O modes are localized, and the electrostatic mechanism then holds. In contrast, the C[bond]N mode transition densities are delocalized, and covalent contributions to the coupling are significant.

Models, Molecular↗

PubMed2004

Store-operated channels: diversity and activation mechanisms.

This perspective addresses two questions: How many store-operated channels (SOCs) are there, and how many mechanisms can account for SOC activation by depleted stores? Accumulating evidence suggests that the SOC family is not limited to the calcium-selective SOC that is responsible for ICRAC (Ca2+-SOC), but includes poorly selective cation SOCs (cat-SOCs) that may satisfy physiological needs in diverse excitable and nonexcitable cells. A growing number of studies in different cell types support the idea that all the members of SOC family (Ca2+-SOC and cat-SOC) may be activated by depletion of the stores through the same mechanism, which is mediated by calcium influx factor (CIF) and calcium-independent phospholipase A2 (iPLA2). A conformational coupling model is also discussed. To account for the most recent findings, we propose that two distinct classes of calcium-conducting channels may exist in plasma membrane, which respond to different signals: SOCs, which are activated by depletion of calcium stores through the CIF-iPLA2 mechanism [no inositol triphosphate (IP3) needed]; and IP3 receptor-operated channels (IP3ROCs), which are activated by IP3 receptor through a direct coupling mechanism (no store depletion is needed). This model, with two separate mechanisms linked to different channels, may resolve many conflicting findings and interpretations and may give a new perspective on the diversity of calcium influx pathways.

Animals↗