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PubMed2001

Point-dipole approximation of the exciton coupling model versus type of bonding and of excitons in porphyrin supramolecular structures.

The application of the exciton coupling model to interacting porphyrin chromophores is discussed. Covalently bonded systems and ionic or electrostatically bonded homoassociates require different orientations of the transition dipole moments in order to explain the experimental results: according to the symmetry of the assembly for covalently bonded porphyrins, and assuming isolated chromophores for ionic bonded porphyrins. Further, for covalently bonded systems, an extended exciton coupling has been demonstrated, but the ionic systems are in agreement with non-extended couplings. The relation of these facts to a molecular description of solid-state Wannier-Mott or Frenkel excitons is briefly discussed.

Journal Article↗

PubMed2006

Interpreting DNA vibrational circular dichroism spectra using a coupling model from two-dimensional infrared spectroscopy.

Two-dimensional infrared spectroscopy was recently used to measure the vibrational couplings between carbonyl bonds located on DNA nucleobases (Krummel, A. T.; Mukherjee, P.; Zanni, M. T. J. Phys. Chem. B 2003, 107, 9165 and Krummel, A. T.; Zanni, M. T. J. Phys. Chem. B 2006, 110, 13991). Here, we extend the coupling model derived from these 2D IR experiments to simulate the vibrational absorption and vibrational circular dichroism (VCD) spectra of three double-stranded DNA oligomers: poly(dG)-poly(dC), poly(dG-dC), and dGGCC. Using this model, we determine that the VCD spectrum of A-form poly(dG)-poly(dC) is dominated by interactions between stacked bases, whereas the coupling between base pairs and stacked bases carries equal importance in the VCD spectrum of B-form poly(dG-dC). We also simulate the absorption and VCD spectra of dGGCC, which is a combination of A- and B-form configurations. These simulations give insight into the structural interpretation of VCD and absorption spectroscopies that have long been used to monitor DNA secondary structure and kinetics.

Circular Dichroism↗

PubMed2003

Prediction of beta-turns from amino acid sequences using the residue-coupled model.

We evaluated the prediction of beta-turns from amino acid sequences using the residue-coupled model with an enlarged representative protein data set selected from the Protein Data Bank. Our results show that the probability values derived from a data set comprising 425 protein chains yielded an overall beta-turn prediction accuracy 68.74%, compared with 94.7% reported earlier on a data set of 30 proteins using the same method. However, we noted that the overall beta-turn prediction accuracy using probability values derived from the 30-protein data set reduces to 40.74% when tested on the data set comprising 425 protein chains. In contrast, using probability values derived from the 425 data set used in this analysis, the overall beta-turn prediction accuracy yielded consistent results when tested on either the 30-protein data set (64.62%) used earlier or a more recent representative data set comprising 619 protein chains (64.66%) or on a jackknife data set comprising 476 representative protein chains (63.38%). We therefore recommend the use of probability values derived from the 425 representative protein chains data set reported here, which gives more realistic and consistent predictions of beta-turns from amino acid sequences.

Algorithms↗

PubMed2000

[Coupling model of the substrate premeabling through the cytoplasmic membrane and Monod kinetics].

Based on the analysis of the substrate permeabling through the cytoplasmic membrane, the corresponding simple transport models are proposed. By coupling of the model with the Monod kinetics, it was discovered that form of Monod kinetics doesn't change, but the kinetics parameter affected by the transport processes. This result is fit well with the literature conclusion and experimental data.

Biological Transport↗

PubMed2005

A dynamic coupling model for sum frequency chiral response from liquids composed of molecules with a chiral side chain and an achiral chromophore.

A theoretical formulation for optically active sum frequency generation (OA-SFG) from isotropic chiral solutions was proposed for molecules with a chiral side chain and an intrinsically achiral chromophore. Adapting an electron correlation model first proposed by Höhn and Weigang for linear optical activity, we presented a dynamic coupling model for OA-SFG near the electronic resonance of the achiral chromophore. As a demonstration, we used this model to explain the observed OA-SFG spectra of a series of amino acids near the electronic resonance of the intrinsically achiral carboxyl group. Our model shows that the nonlinear chiroptical response comes about by the through-space correlative electronic interactions between the chiral side chain and the achiral chromophore, and its magnitude is determined by the position and orientation of the bonds that make up the chiral side chain. Using the bond polarizability values in the literature and the conformations of amino acids obtained from calculation, we were able to reproduce the relative OA-SFG strength from a series of amino acids.

Amino Acids↗

PubMed2003

Modeling coupled interactions of carbon, water, and ozone exchange between terrestrial ecosystems and the atmosphere. I: model description.

A new biophysical model (FORFLUX) is presented to study the simultaneous exchange of ozone, carbon dioxide, and water vapor between terrestrial ecosystems and the atmosphere. The model mechanistically couples all major processes controlling ecosystem flows trace gases and water implementing recent concepts in plant eco-physiology, micrometeorology, and soil hydrology. FORFLUX consists of four interconnected modules-a leaf photosynthesis model, a canopy flux model, a soil heat-, water- and CO2- transport model, and a snow pack model. Photosynthesis, water-vapor flux and ozone uptake at the leaf level are computed by the LEAFC3 sub-model. The canopy module scales leaf responses to a stand level by numerical integration of the LEAFC3model over canopy leaf area index (LAI). The integration takes into account (1) radiative transfer inside the canopy, (2) variation of foliage photosynthetic capacity with canopy depth, (3) wind speed attenuation throughout the canopy, and (4) rainfall interception by foliage elements. The soil module uses principles of the diffusion theory to predict temperature and moisture dynamics within the soil column, evaporation, and CO2 efflux from soil. The effect of soil heterogeneity on field-scale fluxes is simulated employing the Bresler-Dagan stochastic concept. The accumulation and melt of snow on the ground is predicted using an explicit energy balance approach. Ozone deposition is modeled as a sum of three fluxes- ozone uptake via plant stomata, deposition to non-transpiring plant surfaces, and ozone flux into the ground. All biophysical interactions are computed hourly while model projections are made at either hourly or daily time step. FORFLUX represents a comprehensive approach to studying ozone deposition and its link to carbon and water cycles in terrestrial ecosystems.

Air Pollution↗

PubMed1996

A cross-coupling model of vertical vergence adaptation.

Vertical disparity vergence aligns the two eyes in response to vertical misalignment (disparity) of the two ocular images. An adaptive response to vertical disparity vergence is demonstrated by the continuation of vertical vergence when one eye is occluded. The adaptive response is quantified by vertical phoria, the eye alignment error during monocular viewing. Vertical phoria can be differentially adapted to vertical disparities of opposite sign located at two positions along the horizontal or vertical head-referenced axes. Vertical phoria aftereffects vary in amplitude as the eyes move from one adapted direction of gaze to another along the adaptation axis. A cross-coupling model was developed to account for the spatial variations of vertical phoria aftereffects. The model is constrained according to both single cell recordings of eye position sensitive neurons, and eye position measurements during and following adaptation. The vertical phoria is computed by scaling the activities of eye position sensitive neurons and converting the scaled activities into a vertical vergence signal. The three components of the model are: neural activities associated with conjugate eye position, cross-coupling weights to scale the activities, and vertical vergence transducers to convert the weighted activities to vertical vergence. The model provides a biologically plausible mechanism for vertical vergence adaptation.

Adaptation, Physiological↗

PubMed1993

The existence of non-axisymmetric bilayer vesicle shapes predicted by the bilayer couple model.

The existence of non-axisymmetric shapes with minimal bending energy is proved by means of a mathematical model. A parametric model is used; the shapes considered have an elliptical top view whilst their front view contour is described using Cassini ovals. Taking into account the bilayer couple model, the minimization of the membrane bending energy is performed at a constant membrane area A, a constant enclosed volume V and a constant difference between the two membrane leaflet areas delta A. It is shown that for certain sets of A, V and delta A the non-axisymmetric shapes calculated with the use of the parametric model have lower energy than the corresponding axisymmetric shapes obtained by the exact solution of the general variational problem. As an exact solution of the general variational problem for non-axisymmetric shapes would yield even lower energy, this indicates the existence of non-axisymmetric shapes with minimal bending energy in a region of the V/delta A phase diagram.

Lipid Bilayers↗

PubMed2004

Dynamics of supercooled and glassy dipropyleneglycol dibenzoate as functions of temperature and aging: Interpretation within the coupling model framework.

Dielectric relaxation measurements of a typical small molecular glassformer, dipropyleneglycol dibenzoate show the presence of two secondary relaxations. Their dynamic properties differ in the equilibrium liquid and glassy states, as well as the changes during structural recovery after rapid quenching the liquid to form a glass. These differences enable us to identify the slower secondary relaxation as the genuine Johari-Goldstein (JG) beta-relaxation, acting as the precursor of the primary alpha-relaxation. Agreement between the JG beta-relaxation time and the independent relaxation time of the coupling model leads to predicted quantitative relations between the JG beta-relaxation and the alpha-relaxation that are supported by the experimental data.

Journal Article↗

PubMed2006

Building on the WLF/free volume framework: utilization of the coupling model in the relaxation dynamics of the gelatin/cosolute system.

The onset of softening in the glass transition dispersion of the gelatin/cosolute system at 78% solids was examined using the stress relaxation modulus and dynamic oscillatory data on shear. Measurements were made between 5 and -70 degrees C, and isothermal runs were reduced to a master curve covering 21 orders of magnitude in the time domain. The sharpness with which the mechanical properties of our system changed with temperature was reflected in the shift factor a(T) used to pinpoint the glass transition temperature (T(g)). The prevalent analytical framework traditionally employed to follow the transition from the rubbery to glasslike consistency in biomaterials is that of the free volume theory in conjunction with the WLF equation. Increasingly, the combined WLF/free volume approach is challenged by the coupling model, which is able to provide additional insights into the physics of intermolecular interactions in synthetic materials at the vicinity of T(g). The model in the form of the Kohlrausch-Williams-Watts function described well the spectral shape of the local segmental motions of gelatin/cosolute at T(g). The analysis provided the intermolecular interaction constant and apparent relaxation time, parameters which depend on chemical structure. Results appear to be encouraging for further explorations of the dynamics of densely packed biomaterials at the glass transition region.

Animals↗

PubMed1990

Excitation-contraction coupling model to estimate the recirculating fraction of activator calcium in intact cardiac muscle.

Potentiated contractions were evoked with rapid pace pause maneuver in 14 length-clamped ferret papillary muscles paced 12 times/min at 25 degrees C. At 1.25 mM [Ca2+]o the average steady-state force was 2.94 +/- 1.08 g/mm2 and the potentiated contraction averaged 10.96 +/- 1.61 g/mm2. At 5.0 mM [Ca2+]o the steady-state force increased to 6.18 +/- 1.23 g/mm2 and the potentiated contraction averaged 12.08 +/- 1.15 g/mm2. Under the conditions of these experiments the potentiated contraction obtained at 5.0 mM [Ca2+]o is equal to the maximum twitch tension (Fmax) these muscles can generate. We have previously shown that Fmax is an equivalent of maximal calcium activated force. Since there is a beat to beat nearly exponential decay of the evoked potentiation, the fraction (= fraction x) of the potentiation that is not dissipated with each beat is nearly constant. Using an excitation-contraction coupling model we have previously found that x reflects a measure of the recirculating fraction of activator calcium. Because the tension-calcium relationship is better characterized by a sigmoidal curve, we have now incorporated the Hill equation in the model. To account for the inverse relationship between [Ca2+]i and the magnitude of the slow inward current, a term for negative feedback (h) was also included. We have determined the quantity (x-h) because x and h could not be determined separately. The quantity (x-h) was denoted as x'. The average values of x' at 1.25 and 5.0 mM [Ca2+]o were significantly different (p less than 0.0001), approximately 20% at the lower [Ca2+]o and about 50% at the higher [Ca2+]o.(ABSTRACT TRUNCATED AT 250 WORDS)

Acetylcholine↗

PubMed2001

Model coupling intraparticle diffusion/sorption, nonlinear sorption, and biodegradation processes.

Diffusion, sorption and biodegradation are key processes impacting the efficiency of natural attenuation. While each process has been studied individually, limited information exists on the kinetic coupling of these processes. In this paper, a model is presented that couples nonlinear and nonequilibrium sorption (intraparticle diffusion) with biodegradation kinetics. Initially, these processes are studied independently (i.e., intraparticle diffusion, nonlinear sorption and biodegradation), with appropriate parameters determined from these independent studies. Then, the coupled processes are studied, with an initial data set used to determine biodegradation constants that were subsequently used to successfully predict the behavior of a second data set. The validated model is then used to conduct a sensitivity analysis, which reveals conditions where biodegradation becomes desorption rate-limited. If the chemical is not pre-equilibrated with the soil prior to the onset of biodegradation, then fast sorption will reduce aqueous concentrations and thus biodegradation rates. Another sensitivity analysis demonstrates the importance of including nonlinear sorption in a coupled diffusion/sorption and biodegradation model. While predictions based on linear sorption isotherms agree well with solution concentrations, for the conditions evaluated this approach overestimates the percentage of contaminant biodegraded by as much as 50%. This research demonstrates that nonlinear sorption should be coupled with diffusion/sorption and biodegradation models in order to accurately predict bioremediation and natural attenuation processes. To our knowledge this study is unique in studying nonlinear sorption coupled with intraparticle diffusion and biodegradation kinetics with natural media.

Adsorption↗

PubMed2004

Inspiratory flow in the nose: a model coupling flow and vasoerectile tissue distensibility.

We have developed a discrete multisegmental model describing the coupling between inspiratory flow and nasal wall distensibility. This model is composed of 14 individualized compliant elements, each with its own relationship between cross-sectional area and transmural pressure. Conceptually, this model is based on flow limitation induced by the narrowing of duct due to collapsing pressure. For a given inspiratory pressure and for a given compliance distribution, this model predicts the area profile and inspiratory flow. Acoustic rhinometry and posterior rhinomanometry were used to determine the initial geometric area and mechanical characteristics of each element. The proposed model, used under steady-state conditions, is able to simulate the pressure-flow relationship observed in vivo under normal conditions (4 subjects) and under pathological conditions (4 vasomotor rhinitis and 3 valve syndrome subjects). Our results suggest that nasal wall compliance is an essential parameter to understand the nasal inspiratory flow limitation phenomenon and the associated increase of resistance that is well known to physiologists. By predicting the functional pressure-flow relationship, this model could be a useful tool for the clinician to evaluate the potential effects of treatments.

Adult↗

PubMed2000

Disjoining potential and spreading of thin liquid layers in the diffuse-interface model coupled to hydrodynamics

The hydrodynamic phase field model is applied to the problem of film spreading on a solid surface. The disjoining potential, responsible for modification of the fluid properties near a three-phase contact line, is computed from the solvability conditions of the density field equation with appropriate boundary conditions imposed on the solid support. The equations describing the motion of a spreading film are derived in the lubrication approximation (in the limit of small contact angles). In the case of quasiequilibrium spreading, it is shown that the correct sharp-interface limit is obtained, and sample solutions are obtained by numerical integration. It is further shown that evaporation or condensation may strongly affect the dynamics near the contact line, and that it is necessary to account for kinetic retardation of the interphase transport to build up a consistent theory.

Journal Article↗

PubMed1998

Electromechanical coupling model of gating the large mechanosensitive ion channel (MscL) of Escherichia coli by mechanical force.

We have developed a theoretical electromechanical coupling (EMC) model of gating of the large-conductance mechanosensitive ion channel (MscL). The model presents the first attempt to explain the pressure-dependent transitions between the closed and open channel conformations on a molecular level by assuming 1) a homohexameric structural model of the channel, 2) electrostatic interactions between various domains of the homohexamer, 3) structural flexibility of the N-terminal portion of the monomer, and 4) mechanically and electrostatically induced displacement of the N-terminal domain relative to other structural domains of the protein. In the EMC model, 12 membrane-spanning alpha-helices (six each of the M1 and M2 transmembrane domains of the MscL monomer), are envisaged to line the channel pore with a diameter of 40 A, whereas the N- and C-termini are oriented toward each other inside the pore when the channel is closed. The model proposes that stretching the membrane bilayer by mechanical force causes the monomers to be pulled away from and slightly tilted toward each other. This relative movement of alpha-helices could serve as a trigger to initiate a "swing-like" motion of the N-terminus around the glycine residue G14 that may act as a pivot. The analysis of the attractive and repulsive coulomb forces between all domains of the channel homohexamer suggested that an inclination angle of approximately 3.0 degrees - 4.1 degrees between the oppositely oriented channel monomers should suffice for the N-terminus to turn away from other domains causing the channel to open. According to the EMC model the minimal free energy change, deltaG, that could initiate the opening of the channel was 2 kT. Also, the model predicted that the negative pressure required for channel open probability, Po = 0.5, should be between 50 and 80 mmHg. These values were in a good agreement with the experimentally estimated pressures of 60-70 mmHg obtained with the MscL reconstituted in liposomes. Furthermore, consistent with a notion that the N-terminus may present a mechanosensitive structural element providing a mechanism to open the MscL by mechanical force, the model provides a simple explanation for the variations in pressure sensitivity observed with several MscL mutants having either deletions or substitutions in N- or C-terminus, or site-directed mutations in the S2-S3 loop.

Amino Acid Sequence↗

PubMed2005

A numerical coupling model to analyze the blood flow, temperature, and oxygen transport in human breast tumor under laser irradiation.

The aim of this study is to investigate the variation of the blood perfusion rate and distribution of oxygen partial pressure (PO2) in human tumors by a coupling numerical model when laser irradiation is used as an adjuvant method in the treatment of cancer. A two-dimensional finite element (FE) thermal model of a human breast with a tumor was developed. The blood circulation inside the breast was modeled using one-dimensional non-linear equations of pulsatile fluid flow. The distribution of PO2 inside the capillaries, tumor vessels, and surrounding tissue was obtained by the Krogh analysis model. Finally, the variations of the average tumor temperature, blood perfusion, and PO2 during laser heating were computed by coupling the blood circulation, FE thermal, and oxygen transport models.

Breast Neoplasms↗

PubMed2001

An examination of the secretion-like coupling model for the activation of the Ca2+ release-activated Ca2+ current I(CRAC) in RBL-1 cells.

One popular model for the activation of store-operated Ca2+ influx is the secretion-like coupling mechanism, in which peripheral endoplasmic reticulum moves to the plasma membrane upon store depletion thereby enabling inositol 1,4,5-trisphosphate (InsP3) receptors on the stores to bind to, and thus activate, store-operated Ca2+ channels. This movement is regulated by the underlying cytoskeleton. We have examined the validity of this mechanism for the activation of I(CRAC), the most widely distributed and best characterised store-operated Ca2+ current, in a model system, the RBL-1 rat basophilic cell line. Stabilisation of the peripheral cytoskeleton, disassembly of actin microfilaments and disaggregation of microtubules all consistently failed to alter the rate or extent of activation of I(CRAC). Rhodamine-phalloidin labelling was used wherever possible, and revealed that the cytoskeleton had been significantly modified by drug treatment. Interference with the cytoskeleton also failed to affect the intracellular calcium signal that occurred when external calcium was re-admitted to cells in which the calcium stores had been previously depleted by exposure to thapsigargin/ionomycin in calcium-free external solution. Application of positive pressure through the patch pipette separated the plasma membrane from underlying structures (cell ballooning). However, I(CRAC) was unaffected irrespective of whether cell ballooning occurred before or after depletion of stores. Pre-treatment with the membrane-permeable InsP3 receptor antagonist 2-APB blocked the activation of I(CRAC). However, intracellular dialysis with 2-APB failed to prevent I(CRAC) from activating, even at higher concentrations than those used extracellularly to achieve full block. Local application of 2-APB, once I(CRAC) had been activated, resulted in a rapid loss of the current at a rate similar to that seen with the rapid channel blocker La3+. Studies with the more conventional InsP3 receptor antagonist heparin revealed that occupation of the intracellular InsP3-sensitive receptors was not necessary for the activation or maintenance of I(CRAC). Similarly, the InsP3 receptor inhibitor caffeine failed to alter the rate or extent of activation of I(CRAC). Exposure to Li+, which reduces InsP3 levels by interfering with inositol monophosphatase, also failed to alter I(CRAC). Caffeine and Li+ did not affect the size of the intracellular Ca2+ signal that arose when external Ca2+ was re-admitted to cells which had been pre-exposed to thapsigargin/ionomycin in Ca2+-free external solution. Our findings demonstrate that the cytoskeleton does not seem to regulate calcium influx and that functional InsP3 receptors are not required for activation of I(CRAC). If the secretion-like coupling model indeed accounts for the activation of I(CRAC) in RBL-1 cells, then it needs to be revised significantly. Possible modifications to the model are discussed.

Animals↗

PubMed2001

Film rupture in the diffuse interface model coupled to hydrodynamics.

The process of dewetting of a thin liquid film is usually described using a long-wave approximation yielding a single evolution equation for the film thickness. This equation incorporates an additional pressure term-the disjoining pressure-accounting for the molecular forces. Recently a disjoining pressure was derived coupling hydrodynamics to the diffuse interface model [L. M. Pismen and Y. Pomeau, Phys. Rev. E 62, 2480 (2000)]. Using the resulting evolution equation as a generic example for the evolution of unstable thin films, we examine the thickness ranges for linear instability and metastability for flat films, the families of stationary periodic and localized solutions, and their linear stability. The results are compared to simulations of the nonlinear time evolution. From this we conclude that, within the linearly unstable thickness range, there exists a well defined subrange where finite perturbations are crucial for the time evolution and the resulting structures. In the remainder of the linearly unstable thickness range the resulting structures are controlled by the fastest flat film mode assumed up to now for the entire linearly unstable thickness range. Finally, the implications for other forms of disjoining pressure in dewetting and for spinodal decomposition are discussed.

Journal Article↗