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Results for “Equilibrium optimization”

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PubMed2004

Femtomole mixer for microsecond kinetic studies of protein folding.

We have developed a microfluidic mixer for studying protein folding and other reactions with a mixing time of 8 mus and sample consumption of femtomoles. This device enables us to access conformational changes under conditions far from equilibrium and at previously inaccessible time scales. In this paper, we discuss the design and optimization of the mixer using modeling of convective diffusion phenomena and a characterization of the mixer performance using microparticle image velocimetry, dye quenching, and Forster resonance energy-transfer (FRET) measurements of single-stranded DNA. We also demonstrate the feasibility of measuring fast protein folding kinetics using FRET with acyl-CoA binding protein.

Acyl Coenzyme A↗

PubMed2006

Influence of methanol on the dynamics of the retention and release of cyprodinil by an agricultural soil.

The influence of methanol on the adsorption of the fungicide cyprodinil by a crop soil was studied by equilibrium measurements and by determining the retention-release dynamics in a continuous stirred flow tank reactor (CSTR). Equilibrium measurements showed the effective coefficient of partition of cyprodinil between soil and solution, K(dc), decreases linearly as the concentration of methanol in the solution increases until a percentage of 20% is reached. In CSTR experiments, the retention of cyprodinil was found to be almost reversible; up to a 95% of the fungicide was desorbed. The retention-release dynamics showed biphasic behavior and was partially controlled by diffusion. This behavior was reproduced by a model of diffusion into micropores identifying the soil particles as spheres and taking into account both intraparticle nonlinear adsorption and nonlinear adsorption at external surfaces. In all cases, the sorption kinetics was not the limiting step. The main effect of methanol in the retention-release dynamics ended up being based on the changes produced in the adsorption equilibrium. Methanol also increased the effective diffusion coefficient and decreased the mass transfer coefficient. The optimized Freundlich's isotherm coefficients for <5% methanol were lower than those obtained from the batch experiments.

Adsorption↗

PubMed2005

The combined simulation approach of atomistic and continuum models for the thermodynamics of lysozyme crystals.

We have studied the thermodynamic properties of hen egg white lysozyme crystals using a novel simulation method combining atomistic Monte Carlo simulation to calculate van der Waals interactions and the boundary element method to solve the Poisson-Boltzmann equation for the electrostatic interactions. For computational simplicity, we treat the protein as a rigid body, using the crystallographic coordinates of all non-hydrogen atoms of the protein to describe the detailed shape. NVT Monte Carlo simulations are carried out for tetragonal and orthorhombic crystals to obtain the van der Waals energy, incorporating an implicit solvation effect. For crystal phases, an optimally linearized Poisson-Boltzmann equation is used to include the effect of the Donnan equilibrium of the salt ions. The Helmholtz energy is obtained from expanded ensemble Monte Carlo simulations. By using the force field parameters that had previously been tuned for the solution properties, reasonable agreement with experiment is found for the crystallization energy of the tetragonal form. The prediction of the entropy is also reasonable with a slight underestimation suggesting the release of a few water molecules per protein during the crystallization. However, the predictions of the properties of the orthorhombic crystal are poor, probably due to differences in the solvation structure as indicated by experiments, and also as a result of the approximate force field used.

Algorithms↗

PubMed2006

Variational reduced-density-matrix theory applied to the potential energy surfaces of carbon monoxide in the presence of electric fields.

The variational optimization of the energy with respect to the two-electron reduced-density matrix (2-RDM), constrained by N-representability conditions, can determine the shape of molecular potential energy surfaces with useful accuracy. In this paper, we apply the 2-RDM method with a first-order optimization algorithm [Mazziotti, D. A. Phys. Rev. Lett. 2004, 93, 213001] to investigating the potential energy surfaces of carbon monoxide in the presence and absence of an electric field. Two beneficial characteristics of the 2-RDM method for computing potential energy surfaces include the following: (i) its ability to capture multireference effects without specifying any reference wave function or density matrix and (ii) its guarantee of a global energy minimum in the variational optimization. The 2-RDM method produces electronic ground-state energies with similar accuracy at equilibrium and nonequilibrium geometries in both the presence and the absence of the electric field. Computed dipole moments are similar in accuracy to the values from the computationally expensive configuration interaction with single, double, triple, and quadruple excitations. These surfaces have important applications in quantum molecular control theory.

Carbon Monoxide↗

PubMed2006

Geometries and magnetisms of the Zr(n) (n=2-8) clusters: the density functional investigations.

The geometries, stabilities, and electronic and magnetic properties of small-sized Zr(n) (n=2-8) clusters with different spin configurations were systematically investigated by using density functional approach. Emphasis is placed on studies that focus on the total energies, equilibrium geometries, growth-pattern behaviors, fragmentation energies, and magnetic characteristics of zirconium clusters. The optimized geometries show that the large-sized low-lying Zr(n) (n=5-8) clusters become three-dimensional structures. Particularly, the relative stabilities of Zr(n) clusters in terms of the calculated fragmentation energies and second-order difference of energies are discussed, exhibiting that the magic numbers of stabilities are n=2, 5, and 7 and that the pentagonal bipyramidal D(5h) Zr(7) geometry is the most stable isomer and a nonmagnetic ground state. Furthermore, the investigated magnetic moments confirm that the atomic averaged magnetic moments of the Zr(n) (n not equal to 2) display an odd-even oscillation features and the tetrahedron C(s) Zr(4) structure has the biggest atomic averaged magnetic moment of 1.5 mu(B)/at. In addition, the calculated highest occupied molecular orbital-lowest unoccupied molecular orbital gaps indicate that the Zr(n) (n=2 and 7) clusters have dramatically enhanced chemical stabilities.

Journal Article↗

PubMed2005

Thermodynamics of magnetohydrodynamic flows with axial symmetry.

We present strategies based upon optimization principles in the case of the axisymmetric equations of magnetohydrodynamics (MHD). We derive the equilibrium state by using a minimum energy principle under the constraints of the MHD axisymmetric equations. We also propose a numerical algorithm based on a maximum energy dissipation principle to compute in a consistent way the nonlinearly dynamically stable equilibrium states. Then, we develop the statistical mechanics of such flows and recover the same equilibrium states giving a justification of the minimum energy principle. We find that fluctuations obey a Gaussian shape and we make the link between the conservation of the Casimirs on the coarse-grained scale and the process of energy dissipation. We contrast these results with those of two-dimensional hydrodynamical turbulence where the equilibrium state maximizes a H function at fixed energy and circulation and where the fluctuations are nonuniversal.

Journal Article↗

PubMed1991

The design of a panel study under an alternating Poisson process assumption.

We discuss the design of a panel study for the estimation of the average durations in the two states of an alternating Poisson process. Two types of designs are examined. The first fixes the number of follow-up waves but permits the total length of follow-up to vary, and the second varies the number of follow-up waves with fixed length. Simple expressions for nearly optimal designs are presented, and we compare these with designs allowing for continuous observation. Both equilibrium and nonequilibrium cases are examined. An example is given using morbidity data to illustrate how these results can be applied.

Follow-Up Studies↗

PubMedDate not supplied

Haemodiafiltration.

Using haemodiafiltration--a combination of haemodialysis and haemofiltration--an increased clearance rate for middle and small molecules can be obtained compared to the single technique alone. Low molecular weight substances are removed mainly by diffusion, and middle molecules predominantly by convection. Using currently available equipment the duration of therapy can thus be reduced by at least one-third, compared with haemodialysis, without deterioration in the patient's general condition. The withdrawal of large volumes of fluid is markedly better tolerated by the patient than with other short-time blood purification procedures. With the aid of haemodiafiltration both molecular groups can be diminished independently of each other according to individual demand, thereby leading to optimization of dialysis therapy.

Acid-Base Equilibrium↗

PubMed2006

Computational determination of aqueous pKa values of protonated benzimidazoles (Part 2).

Our aim is to develop an effective computational procedure for predicting the aqueous acid equilibrium constants of protonated benzimidazoles at 298.15 K. The experimental determination of these values, apart from been laborious, is a challenge because of the low water solubility of these compounds. Using a variety of descriptors, quantitative structure-property relationships (QSPR) are explored between the experimental aqueous pKa values of a group of fifteen benzimidazoles and descriptors calculated at the B3LYP/6-31+G(d,p) level of theory. Solvent effects are taken into account with the PCM solvation model through both single-point energy calculations (PCM(sp)), and in the geometry optimizations and frequency calculations (PCM(opt)). Descriptors considered are the Gibbs free-energy change of the acid equilibrium in water, the charges on the acidic hydrogen, and on the basic nitrogen, several orbital energies of the protonated and neutral species, and the volume of the solvent cavity. Multiple linear regressions are used to correlate descriptors to the experimental pKa values. Several QSPR equations reproduce the experimental data more accurately, and show stronger correlations than previously attempted methodologies. The predictive capabilities of the QSPR methodologies are tested with four compounds that were not included in the set of benzimidazoles initially investigated. In addition, a correlation between experimental pKa values in water and in a 50% ethanol-water solution is used to estimate aqueous pKa values.

Benzimidazoles↗

PubMed2003

Linear two-step gradient counter-current chromatography analysis based on a recursive solution of an equilibrium stage model.

The implementation of gradients in continuously operated chromatographic counter-current processes has recently attracted considerable interest as a method to improve the performance of this effective separation method. If liquid mobile phases are applied it is advantageous to set the solvent strength in the desorbent stream higher than that in the feed stream. As a consequence. the components to be separated are more retained in the adsorption zones and more easily eluted in the desorption zones. Due to the additional degrees of freedom the design and the optimization of such a two-step gradient counter-current process is difficult. In this paper a steady state equilibrium stage model is used to simulate the process under linear conditions. A simple solution of the underlying model equations is presented capable to describe efficiently the unit for large stage numbers typically encountered in chromatographic columns. Due to the rapidity of the algorithm developed a broad range of operating conditions can be evaluated systematically for different types of gradients. The impact of (a) the functional dependence of the adsorption equilibrium constants on the solvent composition, (b) the number of equilibrium stages and (c) the specification of purity requirements is illustrated and discussed based on results of parametric calculations. The results achieved emphasize the potential of two-step gradient counter-current chromatography.

Countercurrent Distribution↗

PubMedDate not supplied

[Correlation of acid-base equilibrium and glycolysis during muscle activity].

Interdependence between acid-base equilibrium of blood and accumulation of lactate depending on the intensity of exertion during swimming and individual reaction to the exertion has been analyzed when examining high-qualification sportsmen. Prognostication and optimization criteria of acidosis prophylaxis are suggested.

Acid-Base Equilibrium↗

PubMed2004

Self-enforcing climate-change treaties.

In the absence of world government, an effective treaty to control the emissions of greenhouse gases should be self-enforcing. A self-enforcing treaty has the property that, if a country expects other countries to abide by the treaty, it will be in the self-interest of that country to abide by the treaty too. (A difficulty with the Kyoto Protocol is that it does not appear to lay the groundwork for a self-enforcing treaty). A self-enforcing treaty can be modeled as a Nash equilibrium of a suitably defined dynamic game among a large number of sovereign countries of diverse sizes and economic capabilities. We study such a game and characterize its equilibria (typically there are many) and the global-Pareto-optimal solutions. We identify one of the equilibria, which we call "business as usual," with the current situation. The multiplicity of equilibria provides an opportunity to move from the inefficient business-as-usual equilibrium to one or more equilibria that are Pareto-superior. Using a calibrated model with 184 countries, we give numerical illustrations of business-as-usual and global-Pareto-optimal trajectories and estimate the potential welfare gains from a self-enforcing treaty.

Journal Article↗

PubMed1982

Exchange between inorganic phosphate and adenosine triphosphate in (Na+,K+)-ATPase.

(Na+,K+)-ATPase is able to catalyze a continuous ATP in equilibrium Pi exchange in the presence of Na+ and in the absence of a transmembrane ionic gradient. At pH 7.6 the Na+ concentration required for half-maximal activity is 85 mM and at pH 5.1 it is 340 mM. In the presence of optimal Na+ concentration, the rate of exchange is maximal at pH 6.0 and varies with ADP and Pi concentration in the assay medium. ATP in equilibrium Pi exchange is inhibited by K+ and by ouabain.

Adenosine Diphosphate↗

PubMed2000

Apparent and true enantioselectivity in enantioseparations.

The separation factor of two compounds in chromatography is the ratio of their equilibrium constants or retention factors. This parameter is universally employed to investigate their resolution and to optimize the experimental conditions of their analysis. In enantioseparations, the situation is more complex because there is a mixed retention mechanism. The retention factor is the sum of two contributions, one enantioselective, the other nonselective. Although both contribute to retention, the latter being identical for the two enantiomers and does not contribute to their separation. We show how these two contributions can be measured and how it becomes necessary to distinguish between the apparent, alpha(app), and the true, alpha(true), separation factors. The existence of nonselective sites is responsible for alpha(app) being less than alpha(true). Depending on the difference between these two factors, the more effective approach to improve a separation is either to increase the enantioselectivity or to reduce the nonselective interactions. Practical applications to separations of different beta-blockers on cellobiohydrolase are discussed. The apparent enantioselectivity of alprenolol is larger and increases faster with increasing pH than that of the more hydrophobic propranolol, in spite of the importance of hydrophobic interactions in the enantioselective mechanism. These two unexpected properties are discussed and explained.

Adrenergic beta-Antagonists↗

PubMed1982

Spreading and staining of human metaphase chromosomes on aminoalkylsilane-treated glass slides.

The properties of aminoalkylsilane-treated glass slides for the preparation of metaphase spreads and their staining quality have been studied and compared with those of slides which had only been cleaned in ethanol/ether. The parameters investigated were: (1) the average area of metaphases from cultures of blood from both healthy donors and haematology patients; (2) the influence of the positively charged 'coating' on the quality of quinacrine- and Giemsa-banding patterns; (3) non-specific background staining for these banding methods; (4) the number of metaphases as compared to the number of interphase cell nuclei per area of preparation; and (5) the Feulgen-staining intensities of chromosomes and chicken erythrocyte nuclei. The quality of metaphase preparations and the differential staining of chromosomes is better on aminoalkysilane-treated glass slides than that of preparations on routinely cleaned normal microscope slides. In the preparations on aminoalkylsilane-treated slides, the distribution of the cells over the glass surface is more homogeneous; and no influence could be detected on the relative frequency of metaphases as compared to the number of non-divided cell nuclei; the average area per metaphase is increased by about 10% and consequently the number of overlapping chromosomes is decreased. Preparations on aminoalkylsilane-treated glass, after Q-, G- and DAPI-banding procedures, always showed less binding of the staining compounds to the glass slide (a cleaner background) than those on routinely cleaned microscope glass slides. The Feulgen-pararosaniline staining intensities of human metaphase chromosomes and chicken erythrocyte nuclei are the same on aminoalkylsilane-treated slides and on routinely cleaned glass slides. Furthermore, the reproducibility and constancy of quinacrine banding was improved by development of an equilibrium staining method which does not require a washing procedure. The medium, containing 0.002% quinacrine, allows optimal staining results to be obtained for microphotography purposes within 30 min of staining (for visual inspection at least 90 min is required) and is used as the embedding medium. In combination with aminoalkylsilane-treated glass slides, this procedure leads to a clean background and reproducible banding patterns of excellent quality, the results being better and more constant than those of methods described before.

Azure Stains↗

PubMed1985

Action of phospholipase A2 on bilayers. Effect of fatty acid and lysophospholipid additives on the kinetic parameters.

Action of pig pancreatic phospholipase A2 on the ternary codispersions of diacylphosphatidylcholine, 1-acyllysophosphatidylcholine and fatty acids is examined. The binding and kinetic constants are found to be the same under a variety of conditions. These parameters and the catalytic turnover number change with the phase-transition temperature of the ternary codispersions, and optimal binding, kinetic and catalytic constants are seen in the phase-transition range where an equilibrium exists between laterally separated phases. The effect of changing the structure of any of the three components is also via a change in the phase-transition temperature of their ternary codispersions. These observations suggest that the binding of pig pancreatic phospholipase A2 to the defect sites on the substrate interface determines the substrate concentration dependence of the initial rate of hydrolysis, and the catalytic turnover by the bound enzyme also depends upon the phase state of the bilayer. An additive-induced stabilization of the defects in the substrate bilayer is postulated to account for the enhanced binding of the enzyme to the bilayer.

Animals↗

PubMed1990

Carbohydrate-enzyme conjugates for competitive EIA.

Enzyme glycoconjugates prepared from oligosaccharides or polysaccharides are efficient and durable reagents for direct, competitive enzyme immunoassays based on solid phase antibody. This assay format facilitates simple measurement of association constants and relative inhibitory power of oligosaccharides, while also providing a sensitive quantitative assay of bacterial polysaccharide antigens. Enzyme-saccharide conjugates were prepared by established glycoconjugate methodologies, and protocols for their optimal use were established by investigating the effects of solid phase antibody concentration on the kinetic equilibrium of binding for different antigen-enzyme conjugate concentrations, in the presence and absence of inhibitor. Four discrete monoclonal antibody-carbohydrate antigen systems were studied and it is demonstrated for each, that the relative inhibitory power of oligosaccharides may be readily measured in a convenient assay format, and that association constants can be extrapolated from the same assay data.

Alkaline Phosphatase↗

PubMed2004

Development of a nanoparticle-based surface-modified fluorescence assay for the detection of prion proteins.

A nanoparticle-based immunoassay for the detection of recombinant bovine prion protein (PrP) was developed as a step in the development of screening tools for the prevention of the spread of transmissible spongiform encephalopathies. The assay is based on the competitive binding between PrP and a peptide-fluorophore to a nanoparticle-labeled antibody which is specific for a conserved prion sequence. The fluorophore, when bound to the antibody, is subject to surfaced-modified fluorescence, enabling detection of changes in the concentration of bound fluorophore in the presence of prion protein. Important factors considered during the development of the assay were ease of use, robustness, and detection level. The effects of pH and nanoparticle conjugation chemistry on surface-modified fluorescence observed in the assay were explored. Effects of concentrations of antibody and fluorophore on reproducibility and detection limits were examined. At present, the detection limits of the system are approximately equal to the antibody-peptide fluorophore equilibrium dissociation constant, which is near one nanomolar concentration. Improved assay performance could be obtained by optimization of the nanoparticle surface resonance effects. The simplicity of the assay and ease of use may make the type of assay described in this report attractive for screening purposes in the food industry.

Feasibility Studies↗