Recommended gas transport properties of argon at low density using ab initio potential

The most important transport properties of argon have been calculated using classical kinetic theory expressions in conjunction with high-quality ab initio potential energy values computed by Patkowski and Szalewicz. Dilute gas transport properties have been calculated for the viscosity, thermal conductivity, self-diffusion coefficient and thermal diffusion factor from 83 to 10,000 K. Comparisons between experimental transport property data and values presently calculated indicate that the present theoretical predictions may be employed as recommended values for this set of transport properties over a wide temperature range.     

A comparative analysis of the structure of the myoglobin, cytochrome b5, and alpha-chymotrypsin hydrophobic nuclei

The myoglobin, cytochrome b5 and alpha-chymotrypsin hydrophobic nucleus sizes were calculated as well as sizes of theoretical spherical nucleus, radii that are equal to the lengths of phenylalanine and tryptophan lateral groups. All calculated values of sizes lie in the (0.99-1.65) nm3 interval. The quantitative estimation of analyzed proteins nucleus heterogeneous composition has been shown.     

CD spectrum and conformational distribution of cyclotuftsin in solution

CD spectra for low-energy conformations of the tuftsin cycloanalogue, , were calculated. A theoretical spectrum obtained as the weighted average of calculated spectra for individual peptide backbone conformers is qualitatively consistent with an experimental CD spectrum in aqueous solution. The conformational distribution allows one to achieve agreement between calculated and experimental values of structural parameters of the cyclotuftsin molecule investigated by NMR spectroscopy.

CD spectrum calculation Theoretical conformational analysis Tuftsin cycloanalog Peptide conformation     

Surface viscosity measurements from large bilayer vesicle tether formation. II. Experiments.

A mechanical experiment has been developed that measures an upper bound for the viscosity of a lipid bilayer membrane. In this experiment, strands of membrane (tethers) are formed from phospholipid vesicles attached to micropipettes by subjecting the vesicles to fluid drag. The rate of tether formation is measured as a function of the velocity of the suspending fluid. The surface viscosity can be calculated from this data using a theoretical relationship derived in a companion paper. Because of the multilamellar character of the vesicles, these values provide an upper bound for the viscosity of a single bilayer. The smallest values obtained in these measurements fell in the range 5.0-13.0 x 10(-6) dyn s/cm. These values are in relatively good agreement with the values calculated from lateral and rotational mobility measurements.     

Plasma equilibrium in a double-dipole magnetic confinement system with a separatrix

Results are presented from theoretical studies of plasma equilibrium consistent with the convective stability of ideal interchange modes in axisymmetric configurations with an outward-decreasing field that may have a separatrix limiting the plasma volume. A two-dimensional numerical code is developed to solve the Grad-Shafranov equation with a convectively stable pressure distribution at an arbitrary value of β. The problem is solved for an actual geometry of the magnetic field produced by thin current rings. Configurations of a double-dipole confinement system are calculated for the parameters measured in experiments carried out in the Magnetor device, as well as for higher β values. A configuration of a model mirror system with a divertor is also calculated. The code allows one to optimize confinement systems operating at high β values at which equilibrium still can exist.     

类比法研究木材径向导热系数

根据木材的细胞结构,应用类比推理方法,推导木材的径向导热系数的数学表达式,从中得出木材径向导热系数仅是木材孔隙率函数的结论．孔隙率越大,导热系数越小,并应用该表达式计算20种木材的径向导热系数,理论值的最大误差不超过14％,平均误差在5％以内。     

Short order nanohole arrays in metals for highly sensitive probing of local indices of refraction as the basis for a highly multiplexed biosensor technology

A small array of subwavelength apertures patterned in a gold film on glass was characterized for use as a biosensor. It is widely believed that such arrays allow the resonance of photons with surface plasmons in the metallic film. Surface plasmon methods (and other evanescent wave methods) are extremely well suited for the measure of real time biospecific interactions. An extremely high sensitivity of 88,000%/refractive index unit was measured on an array with theoretical active area of .09 microm2. The formation of a biological monolayer was monitored. Both sensitivity and resolution were determined through measurement. The measured resolution, for a sensor with an active area of less than 1.5 microm2, is 9.4 x 10(-8) refractive index units which leads to a calculated sensitivity of 3.45E6%/refractive index unit. These values far exceed theoretical and calculated values of other grating coupled surface plasmon resonance (SPR) detectors and prism based SPR detectors. Because the active sensing area can be quite small (.025 microm2) single molecule studies are possible as well as massive multiplexing on a single chip format.     

A theoretical evaluation of growth yields of yeasts

Growth yields of Saccharomyces cerevisiae and Candida utilis in carbon-limited chemostat cultures were evaluated. The yields on ethanol and acetate were much lower in S. cerevisiae, in line with earlier reports that site I phosphorylation is absent in this yeast. However, during aerobic growth on glucose both organisms had the same cell yield. This can be attributed to two factors: --S. cerevisiae had a lower protein content than C. utilis; --uptake of glucose by C. utilis requires energy whereas in S. cerevisiae it occurs via facilitated diffusion. Theoretical calculations showed that, as a result of these two factors, the ATP requirement for biomass formation in C. utilis is 35% higher than in S. cerevisiae (theoretical YATP values of 20.8 and 28.1, respectively). The experimental YATP for anaerobic growth of S. cerevisiae on glucose was 16 g biomass.mol ATP-1. In vivo P/O-ratios can be calculated for aerobic growth on ethanol and acetate, provided that the gap between the theoretical and experimental ATP requirements as observed for growth on glucose is taken into account. This was done in two ways: --via the assumption that the gap is independent of the growth substrate (i.e. a fixed amount of ATP bridges the difference between the theoretical and experimental values). --alternatively, on the assumption that the difference is a fraction of the total ATP expenditure, that is dependent on the substrate. Calculations of P/O-ratios for growth of both yeasts on glucose, ethanol, and acetate made clear that only by assuming a fixed difference between theoretical and experimental ATP requirements, the P/O-ratios are more or less independent of the growth substrate. These P/O-ratios are approximately 30% lower than the calculated mechanistic values.     

Theoretical versus Practical Energy: A Plea for More Transparency in the Energy Calculation of Different Rechargeable Battery Systems

Electrochemical energy storage at a large scale poses one of the main technological challenges of this century. The scientific community in academia and industry worldwide intensively is exploring various alternative rechargeable battery concepts beside state‐of‐the‐art lithium ion batteries (LIBs), for example, all‐solid‐state batteries, lithium/sulfur batteries, magnesium/sulfur batteries or dual‐ion batteries that could outperform LIBs in different aspects. Often, these concepts also promise very high theoretical energies per mass or volume. However, as theoretical values exclude numerous relevant parameters, they do not translate directly into practically achievable energy values: The gaps between practical capacities and voltages compared to the theoretical values differ for each system. In order to provide high transparency and to illustrate which cell components are most important in the limitation of the practical energy values, in this study, the specific energies and energy densities are calculated in six subsequent steps—from the theoretical energy values of the active materials alone to the practical energy values in an 18650 cylindrical cell. By providing a tool to calculate the energy values of six different battery technologies with different assumptions made evident, this study aims for more transparency and reliability in the comparison of different cell chemistries.     

The Influence of pH on Phosphatidylethanolamine Monolayer at the Air/Aqueous Solution Interface

The dependence of the interfacial tension of a phosphatidylethanolamine (PE) monolayer on the pH of the aqueous solution has been studied. A theoretical equation is derived to describe this dependence. A simple model of the influence of pH on the phosphatidylethanolamine monolayer at the air/hydrophobic chains of PE is presented. The contributions of additive phosphatidylethanolamine forms (both interfacial tension values and molecular area values) depend on pH. The interfacial tension values and the molecular area values for PEH⁺ and PEOH^? forms of phosphatidylethanolamine were calculated. The assumed model was verified experimentally. The experimental results agreed with those derived from the theoretical equation in a whole range of pH values.     

Measuring the effects of heat wave episodes on the human body’s thermal balance

During the peak of an extensive heat wave episode on 23–25 July 2007, simultaneous thermophysiological measurements were made in two non-acclimated healthy adults of different sex in a suburban area of Greater Athens, Greece. Based on experimental measurements of mean skin temperature and metabolic heat production, heat fluxes to and from the human body were calculated, and the biometeorological index heat load (HL) produced was determined according to the heat balance equation. Comparing experimental values with those derived from theoretical estimates revealed a great heat stress for both individuals, especially the male, while theoretical values underestimated heat stress. The study also revealed that thermophysiological factors, such as mean skin temperature and metabolic heat production, play an important role in determining heat fluxes patterns in the heat balance equation. The theoretical values of mean skin temperature as derived from an empirical equation may not be appropriate to describe the changes that take place in a non-acclimated individual. Furthermore, the changes in metabolic heat production were significant even for standard activity.     

Phylogenetic and physical analysis of the 5'' leader RNA sequences of avian retroviruses.

A study of the secondary structures of the 5'-leader RNA sequences of avian leukosis/sarcoma viruses was conducted using phylogenetic sequence alignment, theoretical structures calculated from base-pairing interactions involving the calculated minimal delta G values, and RNaseT1 sensitivity. The results suggest that all of the avian retroviral RNA leaders may be able to adopt similar conformations. Open reading frames in the leader RNAs may be positioned to facilitate viral activities such as translation and packaging of the genomic RNA into virus particles.     

Revisiting the Thermodynamic Theory of Optimal ATP Stoichiometries by Analysis of Various ATP-Producing Metabolic Pathways

The stoichiometry of ATP-producing metabolic pathways had been analysed theoretically by several authors by using evolutionary arguments and optimality principles. Waddell et al. (Biochem Educ 27:12–13, 1999) analysed (lactate-producing) glycolysis and used linear irreversible thermodynamics. The result was that half of the free-energy difference should be converted into free-energy of ATP and the remaining half should be used to drive the pathway. The calculated stoichiometry is in agreement with the observed yield of two moles of ATP per mole of glucose. Using the same approach, we here analyse eight other metabolic pathways. Although the deviation is not very large, the calculated values do not fit as nicely as for glycolysis as leading to lactate. For example, for O₂ respiration, the theoretical ATP yield equals 27.9. The real value varies among organisms between 26 and 38. For mixed-acid fermentation in Escherichia coli, the theoretical and experimental values are 2.24 and 2, respectively. For arginine degradation in M. pneumoniae, the calculated value is 2.43 mol of ATP, while in vivo only one mole is produced. During evolution, some pathways may not have reached their optimal ATP net production because energy yield is not their only function. Moreover, it should be acknowledged that the approach by linear irreversible thermodynamics is a rough approximation.     

Surface roughness parameters as predictors of anchorage strength in bone: a critical analysis

The surface roughness of a bone implant was defined parametrically. The values of the parameters defining the surface were varied. Some traditionally used surface roughness parameters were calculated. By means of a theoretical model the bone-implant interfacial shear strength was estimated. No simple correlation between the values of the surface roughness parameters and the estimated interfacial shear strength was found. It was concluded that the value of the traditional surface roughness parameters as predictors of interfacial shear strength is limited. If however a change of the surface topography of an implant is restricted to scale a positive correlation was found between the theoretical interfacial shear strength and some surface roughness parameters. It is suggested that the bone-implant interfacial shear strength in the general case be estimated by means of strength analyses based upon a study of the size, shape and density of the individual elements constituting the rough surface.     

Cinemicrographic analysis of the movement of flagellated bacteria. I. The ratio of the propulsive velocity to the frequency of bodily rotation.

On the basis of the hydrodynamic model that the propulsion of flagellated bacteria in a fluid is a consequence of the propagation of helical waves along the length of flagella or flagellar bundles, it is predicted that propulsion must be accompanied by a rotation of bacterial body about the direction of translation (Chwang and Wu, 1971), and that propulsive velocity u is directly proportional to the frequency of bodily rotation fB, the proportional constant being a complicated function of various parameters describing the sizes and shapes of body and flagella. In this study we have measured not only u but also fB by cinemicrography or sometimes by dual cinemicrography, using a mono- trichously flagellated Pseudomonas strain and a multitrichously flagellated Salmonella strain, and calculated the ratio u/fB. Though the values of u/fB thus determined for a number of bacteria of each strain scattered in a wide range, average values of u/fB were likely to be independent of u, in support of the theoretical prediction. Moreover, in Pseudomonas as well as in Salmonella, it was found that the experimental values of u/fB were in semiquantitative agreement with theoretical values expected from the hydrodynamic model for appropriate values of the geometrical parameters. Taking into account these results, it was concluded that the validity of this model has been supported experimentally.     

Modeling and measurements of solid-liquid and vapor-liquid equilibria of polyols and carbohydrates in aqueous solution

The solubilities of five saccharides in water have been measured at various temperatures. This includes the monosaccharides xylose and galactose, and the disaccharides maltose monohydrate, cellobiose and trehalose dihydrate. A method that uses interaction energies and interaction parameters calculated with molecular mechanics methods has shown to give good predictions of the phase behavior of a variety of mixtures, including glycols and small saccharides in aqueous solution. The method is completely predictive, as the strength of the molecular interactions is determined with a theoretical method in the absence of any phase equilibrium data. For calculating solubilities, experimental values for the melting points and the heats of fusion of the compounds under study are, however, necessary. The solubilities of the five saccharides listed above, raffinose and meso-erythritol in water were calculated with this method. The calculated solubilities are in reasonably good agreement with experiment, and in the case of meso-erythritol, which is a polyalcohol (polyol), and galactose, the agreement between prediction and experiment is excellent. Also the vapor pressures of water over several polyols and saccharides in aqueous solution have been predicted with this method, giving results in excellent agreement with the experimental values.     

Analysis of single gene multitrait effects in livestock by the use of Gibbs sampling

The paper presents a method of multivariate data analysis described by a model which involves fixed effects, additive polygenic individual effects and the effects of a major gene. To find the estimates of model parameters, the maximization of likelihood function method is applied. The maximum of likelihood function is computed by the use of the Gibbs sampling approach. In this approach, following the conditional posterior distributions, values of all unknown parameters are generated. On the basis of the obtained samples the marginal posterior densities as well as the estimates of fixed effects, gene frequency, genotypic values, major gene, polygenic and error (co)variances are calculated. A numerical example, supplemented to theoretical considerations, deals with data simulated according to the considered model.     

Laurel forests in Tenerife, Canary Islands

The efficiency of the conductive system in about 40-year-old Laurus azorica trees growing in a laurel forest was evaluated by comparing main stems and leaves (petioles) on the basis of theoretical sap flow values (1) calculated from vessel anatomy (taking vessels as ideal capillaries), (2) derived from measured dye velocity and (3) data taken from direct sap flow measurements. It was found that actual sap flow rate per wood area increases in stems from the pith towards the cambium. The outermost part of the stem is the most important part of the tree for conducting water. Maximum actually measured transpiration (sap flow rate) for the stand was practically identical to the theoretical rate calculated based on petiole anatomy, but it was about 45 times lower than that calculated based on stem anatomy. This illustrates the safety features of stem wood, which due to its high vessel density, is capable of transporting all the water required even when only a small area of its vessels is working. In the petioles, xylem is more efficiently used, but almost all vessels must work in order to supply water to leaves and any disturbance may cause leaf loss.     

High-throughput solubility assay for purified recombinant protein immunogens

A high-throughput assay is described for analysis of the solubility of purified recombinant proteins. The assay is based on affinity purification of proteins in the presence of chaotropic agents followed by a dilution and incubation step to investigate the solubility in the absence of high concentrations of such agents. The assay can be performed in a 96-well format, which makes it well suited for high-throughput applications. For 125 recombinant proteins expressed as part of an antibody-based proteomics effort, experimental solubility data were compared to calculated hydrophobicity values based on the amino acid sequence of each protein. This comparison showed only weak correlation between the theoretical and experimental values, which emphasizes the importance of experimental assays to determine the solubility of recombinant proteins.     

Determination of the Ks values during the growth of Alcaligenes eutrophus on phenol, 2,4-dichlorophenoxyacetic acid and fructose

The determination of the K_S values presented here is based on the estimation of the stationary substrate concentrations in continuous cultivation experiments. The separation of biomass from the suspension was performed by an ultrafiltration step which succeeded within one second. The decay of substrate concentration during sampling was calculated to amount to less than 6% of the stationary substrate concentration at relevant growth rates. The K_S values derived from these reduced substrate concentrations deviated by only 10% from the theoretical values at a biomass concentration of about 1 g/1. Thus relevant kinetic parameters can be calculated from the data obtained by this procedure. Values of 11, 59 and 14 μM were obtained with 2,4-dichlorophenoxyacetic acid (2,4-D), phenol and fructose, respectively. Similar K_S values were derived with 2,4-D and fructose by using a respirationbased determination for reasons of comparison. With phenol this value was only 7 μM which is as cribed to a physiological background.