Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Equilibrium optimization”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 667 records · Page 37Linked to original sources
PubMed2005

Thermal equilibrium of high- and low-spin forms of cytochrome P450 BM-3: repositioning of the substrate?

We demonstrate that cytochrome P450 BM-3 in complex with N-palmitoylglycine undergoes a spin state change between room temperature, where optimal activity is seen, and low temperatures, where X-ray diffraction characterization has been carried out. On the basis of NMR measurements of the full-length protein, this spin state change is likely to be accompanied by a general structural rearrangement in the enzyme pocket. The substrate remains bound at all temperatures. We propose that the substrate may "slide" from a position directly atop the heme (thus displacing the ligating water) to the more distant position (thus restoring the ligating water) as the temperature is lowered. This proposal is evaluated on the basis of computational modeling of the protein-ligand complex, using a novel induced fit methodology. We thereby generate a structure with the ligand in close contact with the heme, similar in energy to the experimental structure. With this combination of theory and experiment we provide a specific proposal of how ligands may be positioned for chemistry for this enzyme.

Bacterial Proteins↗
PubMed1982

Interpretation of tracer studies on plasma protein turnover: comparison of methods and optimization of techniques.

1. A comparison of several published methods for analysing plasma protein turnover data has been undertaken, with particular reference to rapidly metabolized proteins such as members of the complement series. 2. With the exception of the equilibrium time method, most methods proved adequate for the determination of overall fractional catabolic rates. A further exception is that the renal clearance method becomes invalid when the fractional catabolic rate approaches the renal iodide clearance, but this may be the method of choice for slowly metabolized proteins if accurate urine collections can be ensured. 3. For the measurement of the ratio of extra to intra-vascular protein pool size a clear preference emerged for the method of C. M. E. Matthews (1957, Physics in Medicine and Biology, 2, 36-53). For rapidly metabolized proteins the calculations must be preceded by a correction for the non-protein bound iodide retained in the intra- and extra-vascular spaces. 4. The accurate calculation of fractional catabolic rate in the extravascular pool generally requires more experimental data than are commonly collected as well as an accurate correction for non-protein bound label that remains unexcreted. Only two techniques hold promise of accurate results: Nosslin's rate equations method and a development of Vitek's deconvolution method described herein. Nosslin's integrated rate equations method is particularly affected by systematic errors in renal iodide clearance estimates and should probably not be further used for this purpose.

Blood Chemical Analysis↗
PubMedDate not supplied

[Organs of hearing and equilibrium during ontogenesis of mammals].

The peripheral part of acoustic analyzer was studied during pre- and postnatal development of mammals. The main trends of structural evolution of the outer, middle, and inner ear were followed in representatives of different ecological groups during postnatal development. The use of ecologomorphological approach made it possible to establish that specific structural features of the hearing organ in different mammals are determined by adaptation to specific acoustic properties of the environment. It was shown that morphofunctional adaptations directed at optimization of acoustic sensitivity in different environmental conditions were leading in the hearing organ evolution. Comparative-embryological studies of the peripheral part of acoustic system made it possible to determine the stages of formation of individual structures and establish general patterns of prenatal development of the organs of hearing and equilibrium in different mammals.

Animals↗
PubMed1994

Calculated optimal cooling rates for ram and human sperm cryopreservation fail to conform with empirical observations.

The permeability coefficient to water (Lp) and its associated activation energy (Ea) were measured for ram (8.47 microns/min/atm at 25 degrees C, 1.06 kcal/mol) and human (2.89 microns/min/atm at 30 degrees C, 1.93 kcal/mol) spermatozoa. By use of these figures, predictive water loss curves were calculated, from published equations, for different cooling rates from 100 degrees C/min to 100,000 degrees C/min. The calculated curves show that ram spermatozoa cooled at even the fastest rate would be in osmotic equilibrium by -20 degrees C, and human spermatozoa cooled at rates up to 10,000 degrees C/min would be in equilibrium by -15 degrees C. If the nucleation temperature for spermatozoa is taken to be between -20 degrees C and -30 degrees C, then ram and human spermatozoa cooled at these rates would apparently not exhibit any intracellular freezing. There is a significant discrepancy between these calculated optimal cooling rates and the published empirically derived optimal rates of 50 degrees C/min for ram and 10 degrees C/min for human. The failure of ram and human spermatozoa to conform with the established and previously successful model for prediction of optimal cooling rates suggests that damage sustained at high cooling rates may be unrelated to intracellular ice formation.

Animals↗
PubMed2002

The minimum energy hypothesis: a unified model of fixation resolution.

OBJECTIVE: To present a new theoretical construct, the Minimum Energy Hypothesis, which explains structural changes observed in the spine concomitant to spinal joint fixation resolution in initial investigations. DESIGN: Theoretical analysis. HYPOTHESIS: A unified theory of manipulative effectiveness is proposed that integrates the fixation and sensory tonus models of manipulation. The theory is based on the fact that the spine will assume a position of minimum internal energy when mechanical equilibrium is achieved. By using a simple mathematical model, it is shown that the fixation model and the sensory tonus models are 2 different aspects of the same theoretical construct. The Minimum Energy Hypothesis predicts that the spine will seek an optimal minimum energy configuration if the constraints preventing it from doing so are removed. Constraints are hypothesized to be joint fixations caused by inflammation in and about the spine and its sequella, muscle spasm, fibroadipose and scar tissue, and ultimately, degeneration. It is further hypothesized that the use of a computerized mechanical manipulative device may resolve such fixations, an example of which is radiographically demonstrable cervical hypolordosis. CONCLUSION: A unified theory of manipulative effectiveness based on the concept of minimum energy to attain mechanical equilibrium is brought forward to explain the results of initial investigations.

Biomechanical Phenomena↗
PubMed1999

Self-consistent estimation of inter-residue protein contact energies based on an equilibrium mixture approximation of residues.

Pairwise contact energies for 20 types of residues are estimated self-consistently from the actual observed frequencies of contacts with regression coefficients that are obtained by comparing "input" and predicted values with the Bethe approximation for the equilibrium mixtures of residues interacting. This is premised on the fact that correlations between the "input" and the predicted values are sufficiently high although the regression coefficients themselves can depend to some extent on protein structures as well as interaction strengths. Residue coordination numbers are optimized to obtain the best correlation between "input" and predicted values for the partition energies. The contact energies self-consistently estimated this way indicate that the partition energies predicted with the Bethe approximation should be reduced by a factor of about 0.3 and the intrinsic pairwise energies by a factor of about 0.6. The observed distribution of contacts can be approximated with a small relative error of only about 0.08 as an equilibrium mixture of residues, if many proteins were employed to collect more than 20,000 contacts. Including repulsive packing interactions and secondary structure interactions further reduces the relative errors. These new contact energies are demonstrated by threading to have improved their ability to discriminate native structures from other non-native folds.

Computer Simulation↗
PubMedDate not supplied

[The evolutionarily optimal rates of body development. The age of onset of sexual maturity and species-specific longevity as the parameters optimized during evolution].

Dynamics of biological community of the "resource--consumer" type considering age structure of consumer population is described by a system of differential equations with special derivatives. On the basis of such a model, a competition model for non-crossing populations with different individual development rates is elaborated. It is shown that only a population with development rates maximizing the Malthusian function (reaching zero value at the equilibrium state of the system) is able to survive under competition for food resources. Equilibrium density of the resources is provided being minimal. Thus maximum energy influx into the population is gained. Search algorithm of evolutionary values of puberty, age and maximal longevity of individuals belonging to the consumer population is proposed. Analytic dependence of maximal longevity on environmental factors and some other parameters are found. Aging is considered to be mechanism leading to death while individual approaches evolutionary optimal longevity.

Animals↗
PubMed2000

Predicting long-term response to selection.

Lande's equation for predicting the response of trait means to a shift in optimal trait values is tested using a stochastic simulation model. The simulated population is finite, and each individual has a finite number of loci. Therefore, selection may cause allele frequencies and distributions to change over time. Since the equation assumes constant genetic parameters, the degree to which such allelic changes affect predictions can be examined. Predictions are based only on information available at generation zero of directional selection. The quality of the predictions depends on the nature of allelic distributions in the original population. If allelic effects are approximately normally distributed, as assumed in Lande's Gaussian approximation to the continuum-of-alleles model, the predictions are very accurate, despite small changes in the G matrix. If allelic effects have a leptokurtic distribution, as is likely in Turelli's 'house-of-cards' approximation, the equation underestimates the rate of response and correlated response, and overestimates the time required for the trait means to reach their equilibrium values. Models with biallelic loci have limits as to the amount of trait divergence possible, since only two allelic values are available at each of a finite set of loci. If the new optimal trait values lie within these limits, predictions are good, if not, singularity in the G matrix results in suboptimal equilibria, despite the presence of genetic variance for each individual trait.

Gene Frequency↗
PubMed2003

Evaluation of a high temperature immobilised enzyme reactor for production of non-reducing oligosaccharides.

There is interest in the production of non-reducing carbohydrates due to their potential application in various industrial fields, particularly the food industry. In this paper, we describe the development of an immobilised cell bioprocess for the synthesis of non-reducing maltodextrins at high temperatures. The trehalosyl-dextrins-forming enzyme (TDFE) isolated from the thermoacidophilic archaeon Sulfolobus solfataricus (strain MT4), was recently expressed at high yields in Escherichia coli (strain Rb-791). Here, we evaluate different matrices, such as polyacrylamide gel, crude egg white, chitosan and calcium alginate for their effectiveness in immobilising whole recombinant E. coli cells subjected to prior thermal permeabilisation. Calcium-alginate based gels formed a solid biocatalyst with a good activity yield and the best enzymatic stability at the operating temperature (75 degrees C). Therefore, these beads were used to pack a glass column reactor to perform the bioconversion of interest. Optimal operating parameters were defined in relation to the substrate stream flow-rate and the substrate-to-biocatalyst ratio. The production of trehalosylmaltotetraose from maltohexaose reached equilibrium with a constant of about 2.6 at 75 degrees C. The bioreactor was exploited for production of trehalosylmaltodextrins from a commercial mixture of maltodextrins, achieving a productivity of 106.5 mg ml(-1) h(-1) (g biocatalyst)(-1) with ~40% conversion when using a 30% (w/v) solution.

Bioreactors↗
PubMed1990

Effect of lipid composition on the transfer of sterols mediated by non-specific lipid transfer protein (sterol carrier protein2).

The rate of non-specific lipid transfer protein (nsLTP)-mediated exchange is independent of structure for dissimilar sterols: cholesterol, lanosterol, sitosterol and vitamin D-3. Conversely, the nsLTP-mediated exchange of cholesterol is markedly affected by the phospholipid composition of the donor liposome. Negatively charged phosphatidylglycerols strikingly increase cholesterol exchange in the presence of nsLTP while not altering the exchange in the absence of nsLTP. The presence of unsaturated acyl chains in the phospholipid enhances exchange. Sphingomyelin drastically decreases cholesterol exchange, as does di-O-alkylphosphatidylcholine. Decreased exchange produced by these substitutions can be reversed by addition of phosphatidylcholine. The presence of an acyl group and a negative charge in the phospholipid are critical for the nsLTP-mediated transfer of cholesterol. In addition to these studies on composition of the donor membrane, the charge on the membrane also appears critical. Maximal exchange rates accompany optimization of potential interaction of negatively charged surface and the basic nsLTP. The nsLTP also mediates an approximately equal rate of exchange of cholesterol and phosphatidylcholine. However, approaching equilibrium, only half of the phospholipid can be exchanged while there is exchange of about 90% of cholesterol. Thus, it appears that only the phospholipid in an outer membrane layer may be available whereas cholesterol is fully available. Therefore, in contrast to a 'carrier' model we suggest that nsLTP facilitates exchange by binding to the membranes, and binding is highly dependent upon lipid composition. Once bound, the protein functions as a bridge between membranes, thus, facilitating exchange.

Biological Transport↗
PubMed1989

Analytic solution of a dynamic pool model incorporating constant marginal cost and discount rates.

A simple dynamic pool model is extended to describe the economics of a single-species fishery by incorporating constant marginal cost and discount rates. Assuming that the population has already come to equilibrium under an initial fishing mortality rate and that any change in that rate is to be sustained indefinitely, the model can be solved analytically to yield the optimal fishing mortality rate. When this rate is expressed as a proportion of the natural mortality rate, the solution takes the form of a third-degree polynomial whose coefficients are simple functions of four other parameters. The solution exhibits positive conservation effects as long as all four parameters are sufficiently high. These conservation effects may be great enough to warrant closing the fishery when the marginal cost rate exceeds a well-defined limit.

Animals↗
PubMed2000

Kinetic and computational study of dissociative substitution and phosphine exchange at tetrahedrally distorted cis-Pt(SiMePh2)2(PMe2Ph)2.

The substitution kinetics of Me2PhP in cis-Pt(SiMePh2)2(PMe2Ph)2 (1) by the chelating ligand bis(diphenylphosphino)ethane has been followed at 25.0 degrees C in dichloromethane by stopped-flow spectrophotometry. Addition of the leaving ligand causes mass-law retardation compatible with a dissociative process via a three-coordinate transition state or intermediate. Exchange of Me2PhP in 1 has been studied by variable-temperature magnetization transfer 1H NMR in toluene-d8, giving kex326 = 1.76 +/- 0.12 s-1, delta H++ = 117.8 +/- 2.1 kJ mol-1, and delta S++ = 120 +/- 7 J K-1 mol-1. An exchange rate constant independent of the concentrations of free phosphine, a strongly positive delta S++, and nearly equal exchange and ligand dissociation rate constants also support a dissociative process. Density functional theory (DFT) calculations for a dissociative process give an estimate for the Pt-P bond energy of 98 kJ mol-1 for R = R' = Me, which is in reasonable agreement with the experimental activation energy given the differences between the substituents used in the calculation and those employed experimentally. DFT calculations on cis-Pt(PR3)2(SiR'3)2 (R = H, CH3; R' = H, CH3) are consistent with the experimental molecular structure and show that methyl substituents on the Si donors are sufficient to induce the observed tetrahedral twist. The optimized Si-Pt-Si angle in cis-Pt(SiH3)2(PH3)2 is not significantly altered by changing the P-Pt-P angle from its equilibrium value of 104 degrees to 80 degrees or 120 degrees. The origin of the tetrahedral twist is therefore not steric but electronic. The Si-Pt-Si angle is consistently less than 90 degrees, but the Si-Si distance is still too long to support an incipient reductive elimination reaction with its attendant Si-Si bonding interaction. Instead, it appears that four tertiary ligands introduce a steric strain which can be decreased by a twist of two of the ligands out of the plane; this twist is only possible when two strong sigma donors are cis to each other, causing a change in the metal's hybridization.

Journal Article↗
PubMed2005

A calculation of the rovibronic energies and spectrum of the B1A1 electronic state of SiH2.

The B1A1 electronic state of silylene (SiH2) is the second excited singlet state of the molecule and, like the analogous c state of methylene (CH2), it is quasilinear with symmetry 1sigmag+ at linearity. This state dissociates to Si(1D) + H2(1sigmag+). At equilibrium, the B state of SiH2 has an energy that we calculate to be 0.71 eV above that of the dissociation products. However, there is a barrier to dissociation that allows quasibound rovibrational levels to occur, and some have been observed recently [Y. Muramoto et al., J. Chem. Phys. 122, 154302 (2005)]. Starting with our analytical ab initio potential-energy surface, we adjusted it in a fitting to the experimental term values in order to determine the optimum potential-energy function in the bound region. This potential has a C2v equilibrium structure with a SiH bond length of 1.459 angstroms and a bond angle of 165.4 degrees; the barrier to linearity is only 129 cm(-1). Using the optimized potential-energy surface we calculate B-state term values, and using our calculated y and z dipole moment surfaces, we simulate the rotation-vibration spectrum of the state in order to assist in the detection of the matrix isolation spectrum.

Journal Article↗
PubMed2000

A new demographic function maximized by life-history evolution.

A goal of life-history theory has been to understand what combination of demographic traits is maximized by natural selection. In practice, researchers usually choose either density-independent population growth rate, lambda, or lifetime reproductive success, R0 (expected number of offspring produced in a lifetime). Others have shown that the maxima of density-independent lambda and R0 are evolutionarily stable strategies under specific density-dependent conditions: population regulation by equal density dependence among all age classes for lambda and by density dependence on a single age class for R0. Here I extend these connections between density-independent optimization models and density-dependent invasion function models in two ways. First, I derive a new demographic function for which a maximum corresponds to attainability of the equilibrium strategy or stability of the mean rather than stability of the variance of the strategy distribution. Second, I show explicitly a continuous range of cases with maxima between those for the lambda and R0. Graphical and biological interpretations are given for an example model. Finally, exceptions to a putative life-history generality (from lambda and R0 models), that high early-life mortality selects for high iteroparity, are shown.

Biological Evolution↗
PubMed2002

Experimental and biphasic FEM determinations of the material properties and hydraulic permeability of the meniscus in tension.

Tensile tests and biphasic finite element modeling were used to determine a set of transversely isotropic properties for the meniscus, including the hydraulic permeability coefficients and solid matrix properties. Stress-relaxation tests were conducted on planar samples of canine meniscus samples of different orientations, and the solid matrix properties were determined from equilibrium data. A 3-D linear biphasic and tranversely isotropic finite element model was developed to model the stress-relaxation behavior of the samples in tension, and optimization was used to determine the permeability coefficients, k1 and k2, governing fluid flow parallel and perpendicular to the collagen fibers, respectively. The collagen fibrillar orientation was observed to have an effect on the Young's moduli (E1=67.8 MPa, E2=11.1 MPa) and Poisson's ratios (v12=2.13, v21 =1.50, v23=1.02). However, a significant effect of anisotropy on permeability was not detected (k1 =0.09x10(-16) m4/Ns, k2=0.10x10(-16) m4/Ns). The low permeability values determined in this study provide insight into the extent of fluid pressurization in the meniscus and will impact modeling predictions of load support in the meniscus.

Animals↗
PubMed1980

Secondary structure in denatured DNA is responsible for its reaction with antinative DNA antibodies of systemic lupus erythematosus sera.

Experiments were designed to determine the basis for the strong competitive reaction of denatured DNA with systemic lupus erythematosus (SLE) antinative DNA antibodies. Secondary structure in denatured DNA was reflected in hyperchromicity upon heating and in multiphase kinetics of its digestion by S1 nuclease. Partial digestion by S1 nuclease completely eliminated the ability of denatured DNA to react with antidenatured DNA antibodies, but not its ability to react with SLE sera. S1 nuclease-resistant cores were isolated from extensively digested denatured DNA. These cores had secondary structure, including some stable fold-back helical regions. The cores, from 20 to several hundred base pairs in size, competed with native DNA for binding by SLE sera. Other experiments measured reactions of denatured DNA under conditions that affected its secondary structure content. Its competitive activity decreased as temperature was increased from 0 degrees to 37 degrees C, whereas the activity of native DNA was not altered in this temperature range. With DNA pieces of 90-110 base pairs, native fragments were much more effective than the denatured fragments, in which stable helical structure is less likely to occur than in high molecular weight denatured DNA. Competitive assays with mononucleotides, oligonucleotides, homopolymers, and RNA-DNA hybrids also indicated that two strands of polydeoxyribonucleotide were required for optimal reactions with these SLE serum antibodies. The antibodies can measure stable helical regions in denatured DNA; they may also stabilize short helical regions that occur in an equilibrium of conformational forms.

Antibody Specificity↗
PubMed1991

Purification and functional characterization of membranes derived from the rough endoplasmic reticulum of Saccharomyces cerevisiae.

Isolation and biochemical analysis of the components involved in protein translocation into the rough endoplasmic reticulum (ER) requires starting material highly enriched in membranes derived from this organelle. We have chosen to study the yeast Saccharomyces cerevisiae in order to profit from the ease of genetic manipulation. To date, however, no efficient scheme has been devised that allows the purification of functional rough ER-derived membranes from yeast, largely because proteins have yet to be identified that are rough ER-specific. In the experiments described here, we expressed the human rough ER marker ribophorin I to facilitate the analysis of subcellular fractionation. We found that the endoplasmic reticulum of yeast could be separated into two distinct domains by fractionation on continuous sucrose gradients. This procedure revealed a bimodal distribution of ER markers. The yeast homologue of the heavy chain-binding protein, BiP (encoded by the KAR2 gene), and the product of the SEC62 gene were present in two fractions having equilibrium densities of 1.146 and 1.192 g/ml, respectively. In contrast, our analysis showed that preprotein translocation activity and retention of the rough ER-specific protein ribophorin I were specific only to the membrane fraction with an equilibrium density of 1.192 g/ml. To prepare fractions highly enriched in translocation competent rough ER-derived membranes for analysis, we developed a density shift fractionation scheme that optimizes the purity of membranes containing human ribophorin I. Membranes obtained by this method were found to possess the majority of the appropriate functional markers, including ATP-independent preprotein binding, ribosome binding, and post-translational translocation. Mitochondria, the major contaminant of the 1.192 g/ml fraction, were significantly depleted in density-shifted membrane populations.

Cell Fractionation↗
PubMed1986

Isolation and characterization of a 1,4-beta-D-glucan glucohydrolase from the yeast, Torulopsis wickerhamii.

1,4-beta-D-Glucan glucohydrolase (exo-1,4-beta-D-glucosidase) (EC 3.2.1.74) was isolated from growth supernatants of Torulopsis wickerhamii and was subjected to hydrodynamic, optical (CD), and kinetic analysis after purification to homogeneity by ammonium sulfate precipitation, size exclusion chromatography, ion exchange chromatography, and isopycnic banding centrifugation in cesium chloride. The last step was found to separate the enzyme from strongly associating, high molecular weight polysaccharide. Enzyme homogeneity was established by isoelectric focusing, sodium dodecyl sulfate-gel electrophoresis, and analytical high performance size exclusion chromatography using dual detection. The native exo-1,4-beta-D-glucosidase was found to be a dimer of 151,000 +/- 21,100 daltons by high performance size exclusion chromatography and 143,600 +/- 1,800 daltons by sedimentation equilibrium. The enzyme has a 12% linked carbohydrate content (mostly mannose) and no essential metal ions. Hydrolysis of p-nitrophenyl-beta-D-glucopyranoside was found to be optimal at pH 4.25 and 50 degrees C. The enzyme was found to produce beta-D-glucose from cellodextrins (indicating retention of anomeric configuration during hydrolysis) and demonstrated depolymerization from the non-reducing polymer terminus. The enzyme followed competitive type inhibition with p-nitrophenyl-beta-D-glucopyranoside as substrate and demonstrated high values of Ki for D-glucose and D-cellobiose inhibition (190 and 230 mM, respectively). The exo-1,4-beta-D-glucosidase was found to hydrolyze cellotetraose more rapidly than D-cellobiose and aryl-beta-D-glycosides more rapidly than all other substrates. Low levels of activity were found for the polymeric substrates beta-glucan (yeast cell walls), Avicel, and Walseth cellulose. Although this enzyme demonstrates broad disaccharide substrate specificity, a characteristic common to beta-D-glucosidases from many sources, the ability to hydrolyze higher cellodextrins more rapidly than cellobiose renders this enzyme the first exo-1,4-beta-D-glucosidase purified from yeast.

Amino Acids↗