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PubMed2006

Transition metal quinone-thiosemicarbazone complexes 3: Spectroscopic characterizations of spin-mixed iron (III) of naphthoquinone-thiosemicarbazones.

An interesting series of iron (III) complexes with naphthoquinone-thiosemicarbazones are synthesized and physico-chemically characterized by elemental analysis, UV-vis, IR, EPR and magnetic susceptibility measurements. They possess a cationic octahedral [FeL2]+ species and a tetrahedral [FeCl4]- anion and exhibit unusual spin-mixed states involving high-spin and low-spin ferric centers as revealed from magnetic behavior with significant amount of exchange interactions mediated by intermolecular associations. The magnetic susceptibility data is fitted with S1=5/2 and S2=1/2 Heisengberg's exchange coupled model; H=-2JS1S2 and the magnetic exchange interactions are found to be of the order of -13.6 cm-1 indicating the moderate coupling between two paramagnetic centers present in different chemical and structural environment. The presence of spin-paired iron (III) cation having dxz2dxz2dxz1 ground state is revealed from the EPR spectra with three prominent peaks while the high-spin tetrahedral iron (III) anion exhibits characteristics g=4 signal whose intensity increases with lowering the temperature suggesting its influence on the magnetic properties of the complex molecule. FTIR measurements indicate tridentate ONS donor systems involving quinone/hydroxyl oxygen, imine/hydrazinic nitrogen and thione/thiol sulfur atoms as binding sites for naphthoquinone-thiosemicarbazones.

Electron Spin Resonance Spectroscopy↗

PubMed2005

Prediction of collective diffusion coefficient of bovine serum albumin in aqueous electrolyte solution with hard-core two-Yukawa potential.

A new method to predict concentration dependence of collective diffusion coefficient of bovine serum albumin (BSA) in aqueous electrolyte solution is developed based on the generalized Stokes-Einstein equation which relates the diffusion coefficient to the osmotic pressure. The concentration dependence of osmotic pressure is evaluated using the solution of the mean spherical approximation for the two-Yukawa model fluid. The two empirical correlations of sedimentation coefficient are tested in this work. One is for a disordered suspension of hard spheres, and another is for an ordered suspension of hard spheres. The concentration dependence of the collective diffusion coefficient of BSA under different solution conditions, such as pH and ionic strength is predicted. From the comparison between the predicted and experimental values we found that the sedimentation coefficient for the disordered suspension of hard spheres is more suitable for the prediction of the collective diffusion coefficients of charged BSA in aqueous electrolyte solution. The theoretical predictions from the hard-core two-Yukawa model coupled with the sedimentation coefficient for a suspension of hard spheres are in good agreement with available experimental data, while the hard sphere model is unable to describe the behavior of diffusion due to its neglect of the double-layer repulsive charge-charge interaction between BSA molecules.

Algorithms↗

PubMed2003

Rapid agonist-evoked coupling of type II Ins(1,4,5)P3 receptor with human transient receptor potential (hTRPC1) channels in human platelets.

Depletion of intracellular Ca2+ stores results in the activation of SMCE (store-mediated Ca2+ entry) in many cells. The mechanism of activation of SMCE is poorly understood. In human platelets, a secretion-like coupling model may be involved. This proposes that store depletion results in trafficking of portions of the endoplasmic reticulum to the plasma membrane, enabling coupling between proteins in the two membranes. In support of this, we have shown that, in human platelets, agonist-evoked Ca2+ store depletion results in de novo and reversible coupling of the Ins P3RII [type II inositol (1,4,5)trisphosphate receptor] with the putative Ca2+ entry channel hTRPC1 [human canonical transient receptor potential 1 (protein); Rosado, Brownlow and Sage (2002) J. Biol. Chem. 277, 42157-42163]. A crucial test of the hypothesis that this coupling activates SMCE is that it should occur rapidly enough to account for agonist-evoked Ca2+ entry. In the present study, we have used quenched- and stopped-flow approaches to determine the latencies of thrombin-evoked coupling of Ins P3RII with hTRPC1 and of thrombin-evoked bivalent cation entry using Mn2+ quenching of fura 2 fluorescence. Thrombin-evoked Mn2+ entry was detected with a latency of 0.81+/-0.07 s (S.E.M., n =7) or 1.36+/-0.09 s (S.E.M., n =7) at a concentration of 1.0 or 0.1 unit/ml respectively. Coupling between Ins P3RII and hTRPC1, assessed at 100 ms intervals, was first detected with a latency of 0.9 or 1.4 s after stimulation with thrombin at a concentration of 1.0 or 0.1 unit/ml respectively. These results support the hypothesis that de novo coupling of Ins P3RII with hTRPC1 could activate SMCE in human platelets.

Blood Platelets↗

PubMed2003

A mathematical model of phytoremediation for petroleum-contaminated soil: model development.

We present a simple model for root length density that combines the generally accepted spatial (exponential decrease with depth) and temporal (sinusoidal) variability of root length. Parameters in this model for root length density can be determined from assumed or measured information regarding the annual biomass turnover, maximum standing biomass, and maximum depth of root penetration. The root length density model, coupled with information regarding the average root lifespan, gives specific root growth and senescence functions that are the forcing functions for the phytoremediation model. We present a screening level mathematical model for phytoremediation that accounts for the growth and senescence of roots in the system. This is an important factor for recalcitrant, immobile compounds found in weathered crude oil contaminated soils. The phytoremediation model is based on variable volume compartments that have individual first-order degradation rate constants; as the roots move through the soil, the soil cycles through the rhizosphere zone, decaying root zone and bulk soil zone. Thus, although the oil is immobile, as the roots penetrate through the soil the oil is brought into contact with the rhizosphere.

Algorithms↗

PubMed2004

Direct current electrical conduction block of peripheral nerve.

Electrical currents can be used to produce a block of action potential conduction in whole nerves. This block has a rapid onset and reversal. The mechanism of electrical nerve conduction block has not been conclusively determined, and inconsistencies appear in the literature regarding whether the block is produced by membrane hyperpolarization, depolarization, or through some other means. We have used simulations in a nerve membrane model, coupled with in vivo experiments, to identify the mechanism and principles of electrical conduction block. A nerve simulation package (Neuron) was used to model direct current (dc) block in squid, frog, and mammalian neuron models. A frog sciatic nerve/gastrocnemius preparation was used to examine nerve conduction block in vivo. Both simulations and experiments confirm that depolarization block requires less current than hyperpolarization block. Dynamic simulations suggest that block can occur under both the real physical electrode as well as adjacent virtual electrode sites. A hypothesis is presented which formulates the likely types of dc block and the possible block current requirements. The results indicate that electrical currents generally produce a conduction block due to depolarization of the nerve membrane, resulting in an inactivation of the sodium channels.

Action Potentials↗

PubMed2006

Phase-model analysis of coupled neuronal oscillators with multiple connections.

Synchronization of the coupled neuronal oscillators with multiple connections of different coupling nature is analyzed using the phase-model reduction method. Each coupling connection contributes to the dynamic behavior of the system in a complex nonlinear fashion. In the phase-model scheme, the contribution of the individual connections can be separated in terms of the effective coupling functions associated with each connection and a linear superposition of them provides the total effective coupling of the coupled system. The case of multiple connections with various conduction time delays is also examined, which is shown to be capable of promoting synchronization over an ensemble of spatially distributed neuronal oscillators in an efficient way.

Hippocampus↗

PubMed2003

Anticipating the response of excitable systems driven by random forcing.

We study the regime of anticipated synchronization in unidirectionally coupled model neurons subject to a common external aperiodic forcing that makes their behavior unpredictable. We show numerically and by analog hardware electronic circuits that, under appropriate coupling conditions, the pulses fired by the slave neuron anticipate (i.e., predict) the pulses fired by the master neuron. This anticipated synchronization occurs even when the common external forcing is white noise.

Action Potentials↗

PubMed1996

A Kinetic Study of Copper Ion Extraction by Kelex 100 at a Heptane-Water Interface

A study of the kinetics of Cu2+ extraction by 7-(4-ethyl-1-methyloctyl)8-hydroxyquinoline (Kelex 100) has been undertaken in a static transfer cell, where the total concentration of the Cu2+-Kelex 100 complex in the organic phase is monitored in situ as the reaction proceeds using attenuated total internal reflectance spectroscopy. The temporal characteristics of the extraction of Cu2+ from water into heptane could be accounted for using a simple one-dimensional diffusion model coupled with a reaction-limited interaction between Cu2+ and Kelex 100. Rate constants for the reaction of Kelex 100 and Cu2+ at a model interface were obtained from stopped flow experiments using a neutral micelle (C12E8) system. These rate constants were used to model the reaction between Cu2+ and Kelex 100 at the heptane-water interface.

Journal Article↗

PubMed2004

Monitoring forest carbon sequestration with remote sensing and carbon cycle modeling.

Sources and sinks of carbon associated with forests depend strongly on the management regime and spatial patterns in potential productivity. Satellite remote sensing can provide spatially explicit information on land cover, standage class, and harvesting. Carbon-cycle process models coupled to regional climate databases can provide information on potential rates of production and related rates of decomposition. The integration of remote sensing and modeling thus produces spatially explicit information on carbon storage and flux. This integrated approach was employed to compare carbon flux for the period 1992-1997 over two 165-km2 areas in western Oregon. The Coast Range study area was predominately private land managed for timber production, whereas the West Cascades study area was predominantly public land that was less productive but experienced little harvesting in the 1990s. In the Coast Range area, 17% of the land base was harvested between 1991 and 2000. Much of the area was in relatively young, productive-age classes that simulations indicate are a carbon sink. Mean annual harvest removals from the Coast Range were greater than mean annual net ecosystem production. On the West Cascades study area, a relatively small proportion (< 1%) of the land was harvested and the area as a whole was accumulating carbon. The spatially and temporally explicit nature of this approach permits identification of mechanisms underlying land base carbon flux.

Carbon↗

PubMed2002

Ca(2+)-induced movement of tropomyosin in skeletal muscle thin filaments observed by multi-site FRET.

To obtain information on Ca(2+)-induced tropomyosin (Tm) movement in Ca(2+)-regulated muscle thin filaments, frequency-domain fluorescence energy transfer data were collected between 5-(2-iodoacetyl-amino-ethyl-amino)naphthalene-1-sulfonic acid at Cys-190 of Tm and phalloidin-tetramethylrhodamine B isothiocyanate bound to F-actin. Two models were used to fit the experimental data: an atomic coordinate (AC) model coupled with a search algorithm that varies the position and orientation of Tm on F-actin, and a double Gaussian distance distribution (DD) model. The AC model showed that little or no change in transfer efficiency is to be expected between different sites on F-actin and Tm if Ca(2+) causes azimuthal movement of Tm of the magnitude suggested by structural data (C. Xu, R. Craig, L. Tobacman, R. Horowitz, and W. Lehman. 1999. Biophys. J. 77:985-992). However, Ca(2+) produced a small but significant change in our phase/modulation versus frequency data, showing that changes in lifetime decay can be detected even when a change of the steady-state transfer efficiency is very small. A change in Tm azimuthal position of 17 on the actin filament obtained with the AC model indicates that solution data are in reasonable agreement with EM image reconstruction data. In addition, the data indicate that Tm also appears to rotate about its axis, resulting in a rolling motion over the F-actin surface. The DD model showed that the distance from one of the two chains of Tm to F-actin was mainly affected, further verifying that Ca(2+) causes Tm to roll over the F-actin surface. The width of the distance distributions indicated that the position of Tm in absence and in presence of Ca(2+) is well defined with appreciable local flexibility.

Adenosine Triphosphatases↗

PubMed1982

Photoselection and circular dichroism in the purple membrane.

The transient dichroic ratio D = delta A parallel/delta A perpendicular has been measured in the visible absorption region of bacteriorhodopsin in purple membrane by a flash photolysis method. D is found to be wavelength independent throughout the visible absorption band, and reaches a maximum value of 2.75 +/- 0.15 on reduction of the excitation intensity. This value is close to that expected for a single nondegenerate transition dipole moment and is incompatible with the strong exciton coupling model used to explain circular dichroism (CD) spectrum of purple membrane. A time-dependent analysis of the exciton interaction and consideration of the coupling strength suggests an explanation of these observations. It is concluded that excitation interaction between retinals in purple membrane is of the weak or very weak type defined by Förster.

Bacteriorhodopsins↗

PubMed2006

Calculation of the vibronic structure of the photodetachment spectra of CCCl- and CCBr-.

The vibronic structure of the closely spaced and strongly coupled X 2Sigma+ and A 2Pi states in the photodetachment spectra of CCCl- and CCBr- has been calculated by considering Sigma-Pi vibronic coupling together with spin-orbit coupling. The stretching modes are treated within the so-called linear-vibronic-coupling model. The vibronic and spin-orbit parameters have been determined by accurate ab initio electronic-structure calculations. While the nonrelativistic vibronic-coupling parameters are of approximately equal strength in CCCl and CCBr, the vibronic-coupling parameters of spin-orbit origin are found to be larger in the latter. The calculated photodetachment spectra of both systems are shown to exhibit a complicated vibronic structure due to strong Sigma-Pi vibronic coupling. The spectral envelopes of the calculated photodetachment spectra exhibit a double-hump reminiscent of strongly coupled Exe Jahn-Teller systems.

Journal Article↗

PubMedDate not supplied

Emergence of oscillations in a model of weakly coupled two Bonhoeffer-van der Pol equations.

Bifurcations of periodic solutions in a model of weakly coupled two Bonhoeffer-van der Pol equations are studied. The model realizes a half-center model with reciprocal inhibition, a typical model used in the field of neural motor control to account for the generation of alternating rhythmic bursts observed in motoneurons and spinal neural networks. Several oscillatory solutions such as in-phase, anti-phase as well as out-of-phase solutions emerge from the model's equilibrium as one of the parameters of the model changes. Among the variety of bifurcations exhibited by the model, we analyze Hopf bifurcations, by which several periodic solutions emerge, and illustrate generation mechanisms of alternating oscillations in the model.

Models, Neurological↗

PubMed2000

Radiobiological modeling and clinical trials.

PURPOSE: Standard clinical trial designs can lead to restrictive conclusions: the "best recommended treatments" based on trial results, although generally applicable to patient populations, do not necessarily apply to individual patients. In theory, radiobiological modeling, coupled with reliable predictive assays, can be used to rationalize the selection of patients for particular schedules in trials. MATERIALS AND METHODS: Linear-quadratic modeling of radiotherapy can be used to simulate a clinical trial. This is achieved by random sampling techniques where the key radiobiological parameters (alpha, beta, T(pot) and clonogen number) are selected from known or expected ranges. Clinical trial design in radiotherapy may be improved by formal radiobiological assessment designed to estimate the likely changes in tumor cure probability (TCP) and the likely normal tissue biologically effective dose (BED). Modeling may also be used to rationalize the allocation of patients to a test or standard schedule or for individual optimization of a treatment schedule. Such approaches depend on there being reliable predictive assays of the radiobiological parameters in individual patients. The influence of variations in predictive assay accuracy on the improved outcomes are assessed. RESULTS: Clinical trials, which have been preceded by modeling simulation, offer potentially substantial improvements in the results of cancer treatment by radiotherapy. These exceed the usual gains found in standard clinical trials. CONCLUSION: Future preclinical trial design should include modeling assessments that indicate how best to structure the trial.

Cell Division↗

PubMed1992

Effect of copper(II) chloride on suppression of racemization in peptide synthesis by the mixed anhydride and related methods.

In segment couplings by the mixed anhydride method using isobutyloxycarbonyl chloride, the use of copper(II) chloride as an additive suppressed racemization completely in the same manner as in the carbodiimide method reported previously. This was confirmed by employing a number of couplings between Z-dipeptides and amino acid esters. The racemization-suppressing effect of other compounds were also evaluated by employing one of these model couplings to be at best only limitedly effective. Copper(II) chloride was effective also in the related method using EEDQ. Thus, in the couplings where a low level of racemization was observed without an additive, the addition of copper(II) chloride eliminated racemization even at ambient temperature where EEDQ is usually used. The effectiveness of copper(II) chloride was confirmed also in the BOP-Cl method. In the presence of HOBt racemization was reduced to a low but still detectable level, while it was suppressed completely by the addition of copper(II) chloride.

Carbon Dioxide↗

PubMed2001

Adsorption of arsenite and arsenate within activated alumina grains: equilibrium and kinetics.

Equilibrium and kinetic adsorption of tri-valent (arsenite) and penta-valent (arsenate) arsenic to activated alumina is elucidated. The properties of activated alumina, including porosity, specific surface area, and skeleton density were first measured. A batch reactor with temperature control was employed to determine both adsorption capacity and adsorption kinetics for arsenite and arsenate to activated-alumina grains. The Freundlich and Langmuir isotherm equations were then used to describe the partitioning behavior for the system at different pH. A pore diffusion model, coupled with the observed Freundlich or Langmuir isotherm equations, was used to interpret an observed experimental adsorption kinetic curve for arsenite at one specific condition. The model was found to fit with the experimental data fairly well, and pore diffusion coefficients can be extracted. The model, incorporated with the interpreted pore diffusion coefficient, was then employed to predict the experimental data for arsenite and arsenate at various conditions, including different initial arsenic concentrations, grain sizes of activated alumina, and system pHs. The model predictions were found to describe the experimental data fairly well, even though the tested conditions substantially differed from one another. The agreement among the models and experimental data indicated that the adsorption and diffusion of arsenate and arsenite can be simulated by the proposed model.

Adsorption↗

PubMedDate not supplied

A hybrid model framework for the optimization of preparative chromatographic processes.

An optimization framework based on the use of hybrid models is presented for preparative chromatographic processes. The first step in the hybrid model strategy involves the experimental determination of the parameters of the physical model, which consists of the full general rate model coupled with the kinetic form of the steric mass action isotherm. These parameters are then used to carry out a set of simulations with the physical model to obtain data on the functional relationship between various objective functions and decision variables. The resulting data is then used to estimate the parameters for neural-network-based empirical models. These empirical models are developed in order to enable the exploration of a wide variety of different design scenarios without any additional computational requirements. The resulting empirical models are then used with a sequential quadratic programming optimization algorithm to maximize the objective function, production rate times yield (in the presence of solubility and purity constraints), for binary and tertiary model protein systems. The use of hybrid empirical models to represent complex preparative chromatographic systems significantly reduces the computational time required for simulation and optimization. In addition, it allows both multivariable optimization and rapid exploration of different scenarios for optimal design.

Algorithms↗

PubMed2003

Tagged particle motion in a dense liquid: feedback effects from the collective dynamics.

The nature of the tagged particle motion in the strongly correlated state of a dense liquid is studied with the self-consistent mode-coupling model. The tagged particle time correlation function psi(s)(q,t) is computed by taking into account the nonlinear feedback effects on its dynamics from the coupling with density fluctuations. We consider the two cases where (a) the short-time dynamics is diffusive resembling colloidal system and (b) the short-time dynamics is Newtonian as in an atomic system. The non-Gaussian parameter alpha(2)(t) is evaluated using the fourth- and second-order spatial moments of the van Hove self-correlation function G(s)(r,t). We observe a two-peaked structure of alpha(2)(t) for both (a) and (b) types of dynamics. We also compare other characteristic aspects of tagged particle dynamics such as the mean square displacement, non-Gaussian nature of G(s)(r,t), and fraction of mobile particles. A qualitative comparison is drawn between the theoretical results with the experimental and computer simulation results on colloids.

Journal Article↗