PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “Equilibrium optimization”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 307 records · Page 17Linked to original sources
PubMed1997

Conformational investigation of alpha,beta-dehydropeptides. VIII. N-acetyl-alpha,beta-dehydroamino acid N'-methylamides: conformation and electron density perturbation from infrared and theoretical studies.

The Fourier transform infrared spectra are analyzed in the regions of Vs(N-H), amide I, amide II and Vs(C alpha = C beta) bands for a series of Ac-delta Xaa-NHMe, where delta Xaa = delta Ala, (Z)-delta Abu, (Z)-delta Leu, (Z)-delta Phe and delta Val, to determine the predominant solution conformation of these alpha,beta-dehydropeptide-related molecules and the electron distribution perturbation in their amide bonds. The measurements were performed in dichloromethane (DCM). To confirm and rationalize the assignments, the spectra of the respective series of saturated Ac-Xaa-NHMe, recorded in DCM, and the spectra of these two series of unsaturated and saturated compounds, recorded in acetonitrile, were examined. To help interpret the spectroscopic results, the equilibrium geometrical parameters for some selected amides were used. These were optimized with ab initio methods in the 6-31G** basis set. Each of the dehydroamides studied adopted a C5 structure, which in Ac-delta Ala-NHMe is fully extended and accompanied by the strong C5 hydrogen bond. Interaction with the C alpha = C beta bond lessened the amidic resonance within each of the flanking amide groups. The N-terminal C = O bond was noticeably shorter, both amide bonds were longer than the corresponding bonds in the saturated entities and the N-terminal amide system was distorted. Ac-delta Ala-NHMe constituted an exception. Its C-terminal amide bond was shorter than the standard one and both amide systems were prototypically planar.

Amides↗
PubMed1987

Regulation of nitrogenase activity by oxygen in Azospirillum brasilense and Azospirillum lipoferum.

The nitrogenase activity of the microaerophilic bacteria Azospirillum brasilense and A. lipoferum was completely inhibited by 2.0 kPa of oxygen (approximately 0.02 atm of O2) in equilibrium with the solution. The activity could be partially recovered at optimal oxygen concentrations of 0.2 kPa. In contrast to the NH4+ switch off, no covalent modification of the nitrogenase reductase (Fe protein) was involved, as demonstrated by Western-blotting and 32P-labeling experiments. However, the inhibition of the nitrogenase activity under anaerobic conditions was correlated with covalent modification of the Fe protein. In contrast to the NH4+ switch off, no increase in the cellular glutamine pool and no modification of the glutamine synthetase occurred under anaerobic switch-off conditions. Therefore, a redox signal, independent of the nitrogen control of the cell, may trigger the covalent modification of the nitrogenase reductase of A. brasilense and A. lipoferum.

Amino Acids↗
PubMed2005

[Studies of immunoaffinity chromatography for carbofuran].

The purified anti-carbofuran antibody was conjugated to carbonyl diimidazole (CDI)-activated Sepharose CL-4B to synthesize the immunosorbent for the immunoaffinity chromatographic (IAC) column specific to carbofuran. The conditions of IAC were optimized as follows: pH 7.2 phosphate buffer (PB) was used as equilibrium and adsorbent medium, and methanol-water (60:40, v/v) as eluent. The results showed that the dynamic column capacity was up to 1.58 mg/L bed volume. The efficiency of enrichment of IAC was more than 167 times when the initial concentration of carbofuran in a standard sample solution was lower than 2 microg/L. The spiked river water was cleaned up and enriched by IAC, and carbofuran in eluate was determined by enzyme linked immunosorbent assay (ELISA). The average recovery of carbofuran from river water was 89.8% with the relative standard deviation of 4.8% at the spiked level of 0.1 mg/L. Meanwhile the eluate was determined by high performance liquid chromatography (HPLC), the results from HPLC correlated well with those from ELISA. The IAC method of carbofuran was successfully established.

Antibodies↗
PubMed2006

The frequency of the perfect genotype in a population subject to pleiotropic mutation.

We consider a large population of asexual organisms characterised by a number of quantitative traits that are subject to stabilising selection. Mutation is taken to act pleiotropically, with every mutation generally changing all of the traits under selection. We focus on the equilibrium distribution of the population, where mutation and selection are in balance. It has been previously established that the equilibrium distribution of genotypic effects may be anomalous, as it may contain a singular spike--a Dirac delta function--corresponding to a non-zero proportion of the population having exactly optimal genotypic values. In the present work, we present exact results for the case where three traits are under selection. These results give the equilibrium genetic variance of the population, and the proportion of the population that have the optimal genotype. This is achieved for two different spherically symmetric distributions of mutant effects. Additionally, a simple and robust numerical approach is also presented that allows the treatment of some other mutation distributions, where there are an arbitrary number of selected traits.

Animals↗
PubMed1988

Approach to stationary two-dimensional pattern: influence of focusing time and immobiline/carrier ampholytes concentrations.

Horizontal two-dimensional (2-D) electrophoresis with immobilized pH gradients (IPG) in the first dimension for buffer soluble proteins and for complex proteins solubilized in the presence of Nonidet P-40 (Görg et al., Electrophoresis 1987, 8, 45-51), has been extended to analyze basic proteins of yeast cells focused under non-equilibrium and equilibrium conditions. Transient state isoelectric focusing (IEF) in IPG gels revealed sample smearing and background staining, displaying horizontal streaks in the resultant 2-D patterns. Inclusion of 0.5% carrier ampholytes (CA) to the IPG gel (IPG-CA), resulted in the formation of many sharp protein bands after transient state IEF with resultant distinct spots in the 2-D patterns; however, resolution was poor and the gel contained heavy background staining. With prolonged focusing time, background staining disappeared and there was less difference in the final steady state IEF patterns obtained with IPG and IPG-CA. Reduction of the Immobiline concentration to one third the manufacturer's recommended amount did not improve IEF resolution with respect to streaking and background staining under either transient state or equilibrium conditions. In general, spot intensities were less on 2-D gels using diluted IPG gels than with "standard" IPG gels. Optimization of 2-D electrophoresis with IPGs in the first dimension was strongly related to IEF conditions. The use of IPG gels focused to equilibrium should not only improve inter-gel reproducibility and resolution but also the quality of the final 2-D patterns with respect to background staining and horizontal streaking.

Ampholyte Mixtures↗
PubMed1978

Glucose-6-phosphate dehydrogenase of Anabaena sp. Kinetic and molecular properties.

The kinetic and molecular properties of cyanobacterial glucose-6-phosphate dehydrogenase, partly purified from Anabaena sp. ATCC 27893, show that it undergoes relatively slow, reversible transitions between different aggregation states which differ in catalytic activity. Sucrose gradient centrifugation and polyacrylamide gel electrophoresis reveal three pincipal forms, with approximate molecular weights of 120 000 (M1), 240 000 (M2) and 345 000 (M3). The relative catalytic activities are: M1 less than M2 less than M3. In concentrated solutions of the enzyme, the equilibrium favors the more active, oligomeric forms. Dilution in the absence of effectors shifts the equilibrium in favor of the M1 form, with a marked diminution of catalytic activity. This transition is prevented by a substrate, glucose-6-phosphate, and also by glutamine. The other substrate, nicotinamide adenine dinucleotide phosphate (NADP+), and (in crude cell-free extracts) ribulose-1,5-diphosphate are negative effectors, which tend to maintain the enzyme in the M1 form. The equilibrium state between different forms of the enzyme is also strongly dependent on hydrogen ion concentration. Although the optimal pH for catalytic activity is 7.4, dissociation to the hypoactive M1 form is favored at pH values above 7; a pH of 6.5 is optimal for maintenance of the enzyme in the active state. Reduced nicotamide adenine dinucleotide phosphate (NADPH) and adenosine 5'-triphosphate (ATP), inhibit catalytic activity, but do not significantly affect the equilibrium state. The relevance of these findings to the regulation of enzyme activity in vivo is discussed.

Adenosine Triphosphate↗
PubMed2002

A theoretical assessment of a thermal technique to measure acoustic power radiated by ultrasound transducers.

The parameters affecting the temperature rise in an insonified absorber are studied computationally. Finite-element and analytical solutions are obtained for the transient energy equation in a cylindrical absorber. When the ultrasound beam radius is less than the radius of the absorber, the temperature field is seen to be considerably more complex than when the absorber cross section is uniformly heated. Circumstances in which power predictions based upon uniform heating would result in appreciable error are identified. The rise time required to achieve equilibrium is studied as a function of operational parameters, including absorber geometry and thermal properties as well as ultrasound beamwidth and frequency. The rise time is seen to increase approximately as the square of the absorber length, while optimized temperature rise increases linearly with absorber length, demonstrating a tradeoff in ultrasound power determination via equilibrium temperature measurements: longer lengths produce higher sensitivity, but also longer times before measurements can be made. A transient technique that may bypass this tradeoff is suggested.

Calibration↗
PubMed2006

An exploration of electronic structure and nuclear dynamics in tropolone. I. The X 1A1 ground state.

The ground electronic state (X 1A1) of tropolone has been examined theoretically by exploiting extensive sets of basis functions [e.g., 6-311++G(d,p) and aug-cc-pVDZ] in conjunction with the high levels of electron correlation made possible by density functional (DFT/B3LYP), Moller-Plesset perturbation (MP2), and coupled-cluster [CCSD and CCSD(T)] methods. Unconstrained MP2 and CCSD optimization procedures performed with the reference 6-311++G(d,p) basis predict a slightly nonplanar equilibrium structure characterized by a small barrier to skeletal inversion (< or =10 cm(-1) magnitude). Complementary harmonic frequency analyses have shown this nonplanarity to be a computational artifact arising from adversely tuned carbon d-orbital exponents embodied in the standard definitions of several Pople-type basis sets. Correlation-consistent bases such as Dunning's aug-cc-pVDZ are less susceptible to these effects and were employed to confirm that the X 1A1 hypersurface supports a rigorously planar global minimum. The fully optimized geometries and vibrational force fields obtained by applying potent coupled-cluster schemes to the relaxed-equilibrium (Cs) and transition-state (C2v) conformers of tropolone afford a trenchant glimpse of the key features that mediate intramolecular hydron exchange in this model system. By incorporating perturbative triples corrections at the substantial CCSD(T) level of theory, an interoxygen distance of r(O...O)=2.528 A was determined for the minimum-energy configuration, with the accompanying proton-transfer reaction being hindered by a barrier of 2557.0 cm(-1) height. The potential energy landscape in tropolone, as well as the nature of the attendant hydron migration process, is discussed within the framework of the encompassing G4 molecular symmetry group.

Chemistry, Physical↗
PubMed1990

The role of oligomerization in regulation of maize phosphoenolpyruvate carboxylase activity. Influence of Mg-PEP and malate on the oligomeric equilibrium of PEP carboxylase.

A purification procedure which yields a near homogenous preparation of phosphoenolpyruvate (PEP) carboxylase from the leaves of Zea mays is reported. The enzyme had a final specific activity of 33.3 micromoles per minute per milligram protein. Size exclusion high performance liquid chromatography and dynamic laser-light scattering spectroscopy showed that PEP carboxylase exists in an equilibrium of aggregates. Enzyme predominantly in the dimeric configuration is less active (when assayed at sub-optimal Mg-PEP concentrations, less than 0.4 millimolar) than when in its tetrameric arrangement. The difference in activity diminishes and disappears as the concentration of the substrate Mg-PEP increases. The substrate drives the equilibrium toward the tetramer, while malate, an inhibitor of PEP carboxylase, shifts the equilibrium toward the dimer. It thus appears that the quaternary structure (oligomeric state) of maize PEP carboxylase can be regulated by the naturally occurring effector molecules Mg-PEP and malate which in turn can control the enzyme's activity.

Chromatography, High Pressure Liquid↗
PubMed2002

Truffle aroma analysis by headspace solid phase microextraction.

An experimental design has been used to optimize the extraction of volatile compounds from summer truffle aroma (Tuber aestivum) by using headspace solid phase microextraction. The extracted compounds have been analyzed by gas chromatography with a flame ionization detector and by gas chromatography-mass spectrometry (GC-MS). In an attempt to develop an objective method to fully characterize truffle aroma, a fiber of medium polarity (for flavors) was used to avoid discrimination toward very nonpolar and polar volatile compounds. To optimize the extraction conditions, a response surface experimental design was applied considering three factors such as extraction temperature, equilibrium time, and extraction time. From the statistical analysis of the experimental design, it was possible to determine that the most important factor influencing the abundance of aroma compounds was the extraction temperature. Optimal extraction temperature was established at approximately 50 degrees C. By using GC-MS, it was possible to identify 37 compounds, most of them previously described as responsible for truffle aroma.

Ascomycota↗
PubMed2005

Optimizing the driving function for nonequilibrium free-energy calculations in the linear regime: a variational approach.

We consider the issue of optimizing linear-regime nonequilibrium simulations to estimate free-energy differences. In particular, we focus on the problem of finding the best-possible driving function lambda(t) that, for a given thermodynamic path, simulation algorithm, and amount of computational effort, minimizes dissipation. From the fluctuation-dissipation theorem it follows that, in the linear-response regime, the dissipation is controlled by the magnitude and characteristic correlation time of the equilibrium fluctuations in the driving force. As a result, the problem of finding the optimal switching scheme involves the solution of a standard problem in variational calculus: the minimization of a functional with respect to the switching function. In practice, the minimization involves solving the associated Euler-Lagrange equation subject to a set of boundary conditions. As a demonstration we apply the approach to the simple, yet illustrative problem of computing the free-energy difference between two classical harmonic oscillators with very different characteristic frequencies.

Journal Article↗
PubMed1994

Optimal control of antagonistic muscle stiffness during voluntary movements.

This paper presents a study on the control of antagonist muscle stiffness during single-joint arm movements by optimal control theory with a minimal effort criterion. A hierarchical model is developed based on the physiology of the neuromuscular control system and the equilibrium point hypothesis. For point-to-point movements, the model provides predictions on (1) movement trajectory, (2) equilibrium trajectory, (3) muscle control inputs, and (4) antagonist muscle stiffness, as well as other variables. We compared these model predictions to the behavior observed in normal human subjects. The optimal movements capture the major invariant characteristics of voluntary movements, such as a sigmoidal movement trajectory with a bell-shaped velocity profile, an 'N'-shaped equilibrium trajectory, a triphasic burst pattern of muscle control inputs, and a dynamically modulated joint stiffness. The joint stiffness is found to increase in the middle of the movement as a consequence of the triphasic muscle activities. We have also investigated the effects of changes in model parameters on movement control. We found that the movement kinematics and muscle control inputs are strongly influenced by the upper bound of the descending excitation signal that activates motoneuron pools in the spinal cord. Furthermore, a class of movements with scaled velocity profiles can be achieved by tuning the amplitude and duration of this excitation signal. These model predictions agree with a wide body of experimental data obtained from normal human subjects. The results suggest that the control of fast arm movements involves explicit planning for both the equilibrium trajectory and joint stiffness, and that the minimal effort criterion best characterizes the objective of movement planning and control.

Arm↗
PubMed2005

Communities adjust their temperature optima by shifting producer-to-consumer ratio, shown in lichens as models: I. Hypothesis.

An apparent paradox exists in the ecology of Antarctic lichens: their net photosynthetic temperature optimum (around 0 degrees C) lies far below the temperature optima of their constituent algae and fungi (around 20 degrees C). To address this paradox, we consider lichens as microbial communities and propose the "community adaptation" hypothesis, which posits that in each thermal regime there is an equilibrium between photosynthetic primary producers (photobionts), and heterotrophic consumers (mycobiont and parasymbiont fungi). This equilibrium, expressed as the producer/consumer ratio (R(p/c)), maximizes the fitness of the community. As respiration increases with temperature, more rapidly than does photosynthesis, R(p/c )will shift accordingly in warm habitats, resulting in a high-growth temperature optimum for the community (the lichen). This lends lichens an adaptive flexibility that enables them to function optimally at any thermal regime within the tolerance limits of the constituent organisms. The variable equilibrium of producers and consumers may have a similar role in thermal adaptation of more complex communities and ecosystems.

Adaptation, Physiological↗
PubMed1996

Theoretical analysis of the kinetics of DNA hybridization with gel-immobilized oligonucleotides.

A new method of DNA sequencing by hybridization using a microchip containing a set of immobilized oligonucleotides is being developed. A theoretical analysis is presented of the kinetics of DNA hybridization with deoxynucleotide molecules chemically tethered in a polyacrylamide gel layer. The analysis has shown that long-term evolution of the spatial distribution and of the amount of DNA bound in a hybridization cell is governed by "retarded diffusion," i.e., diffusion of the DNA interrupted by repeated association and dissociation with immobile oligonucleotide molecules. Retarded diffusion determines the characteristic time of establishing a final equilibrium state in a cell, i.e., the state with the maximum quantity and a uniform distribution of bound DNA. In the case of cells with the most stable, perfect duplexes, the characteristic time of retarded diffusion (which is proportional to the equilibrium binding constant and to the concentration of binding sites) can be longer than the duration of the real hybridization procedure. This conclusion is indirectly confirmed by the observation of nonuniform fluorescence of labeled DNA in perfect-match hybridization cells (brighter at the edges). For optimal discrimination of perfect duplexes from duplexes with mismatches the hybridization process should be brought to equilibrium under low-temperature nonsaturation conditions for all cells. The kinetic differences between perfect and nonperfect duplexes in the gel allow further improvement in the discrimination through additional washing at low temperature after hybridization.

DNA↗
PubMed2000

Optimal sex ratios in structured populations.

In this paper, we develop a general method to determine evolutionary equilibrium sex ratios and to check evolutionary stability, continuous stability and invadability in exact genetic models with or without dominance. This method is then applied to three kinds of models for structured populations: the first one concerns Hamilton's LMC model, except that only a fraction beta of female offspring mate with male offspring born in the same colonies, while a fraction 1-beta mate with male offspring chosen at random within the whole population; in the second model, it is assumed that partial dispersal of inseminated females occurs after mating; in the third model, partial dispersal of male and female offspring occurs before mating. In the first model, the effect of population regulation is studied while, in the other models, two kinds of dispersal are considered: proportional and uniform.

Animals↗
PubMed1998

Hydration and conformational equilibria of simple hydrophobic and amphiphilic solutes.

We consider whether the continuum model of hydration optimized to reproduce vacuum-to-water transfer free energies simultaneously describes the hydration free energy contributions to conformational equilibria of the same solutes in water. To this end, transfer and conformational free energies of idealized hydrophobic and amphiphilic solutes in water are calculated from explicit water simulations and compared to continuum model predictions. As benchmark hydrophobic solutes, we examine the hydration of linear alkanes from methane through hexane. Amphiphilic solutes were created by adding a charge of +/-1e to a terminal methyl group of butane. We find that phenomenological continuum parameters fit to transfer free energies are significantly different from those fit to conformational free energies of our model solutes. This difference is attributed to continuum model parameters that depend on solute conformation in water, and leads to effective values for the free energy/surface area coefficient and Born radii that best describe conformational equilibrium. In light of these results, we believe that continuum models of hydration optimized to fit transfer free energies do not accurately capture the balance between hydrophobic and electrostatic contributions that determines the solute conformational state in aqueous solution.

Alkanes↗
PubMed1983

Efficiency of energy conversion in model biological pumps. Optimization by linear nonequilibrium thermodynamic relations.

Experimental investigations showed linear relations between flows and forces in some biological energy converters operating far from equilibrium. This observation cannot be understood on the basis of conventional nonequilibrium thermodynamics. Therefore, the efficiencies of a linear and a nonlinear mode of operation of an energy converter (a hypothetical redox-driven H+ pump) were compared. This comparison revealed that at physiological values of the forces and degrees of coupling (1) the force ratio permitting optimal efficiency was much higher in the linear than in the nonlinear mode and (2) the linear mode of operation was at least 10(6)-times more efficient that the nonlinear one. These observations suggest that the experimentally observed linear relations between flows and forces, particularly in the case of oxidative phosphorylation, may be due to a feedback regulation maintaining linear thermodynamic relations far from equilibrium. This regulation may have come about as the consequence of an evolutionary drive towards higher efficiency.

Energy Metabolism↗