bluuebunny/crossref_metadata_2025 huggingface dataset:
Activation of Ultrafine particles by supersaturation in condensational process
Authors: Kousaka Yasuo , Okuyana Kikuo , Niida Tohru , Hosokawa Takahiro , Mimura Tadaaki
Published: May 2005

The Activation of ultrafine particles as the condensation nuclei, or heterogeneous nucleation of ultrafine particles, has been observed in various supersaturated vapors. Monodisperse NaCl, ZnCl2, Ag and silicon oil particles, 5–15 mm in diameter, are used as the condensation nuclei and water, hexanol, dibutyl phthalate (DBP) and di‐2‐ethyl‐hexyl sebacate (DEHS) are used as teh vapors. The supersaturated atmosphere is formed in the mixing type condensation nucleus counter (CNC) where a room temperature aerosol is mixed with warm air saturated by each vapor and the supersaturation ratio is controlled by changing the temperature of the saturated air. The number ratios of activated particles to total particles are observed at various supersaturation ratios. It is found that the activation of particles depends in a complicated manner on the combination of the substances of particles with condensing vapors, that is, activation in some particle‐vapor systems is explained by the Kelvin effect but not in others.
A Universal Aerosol Sampling Probe for High Efficiency Particle sampling from flowing gas streams
Authors: Liu Professor Benjamin Y. H. , Pui David Y. H.
Published: May 2005

An aerosol sampling inlet has been developed to collect representative samples from the flowing gas stream. The inlet is referred to as the “Universal Aerosol Sampling Probe” because it is capable of efficient sampling over a wide range of free stream velocity without the need to change either the probe tip or sampling flow rate. It is a multi‐nozzle device consisting of one or more outer nozzles to extract a sample isokinetically and decelerate it from the relatively high stream velocity to a relatively low velocity. An inner nozzle is then used to extract a representative particle sample for delivery to the impactor or other particle collectors placed downstream. The approach enables a representative particle sample to be extracted at a fixed flow rate, irrespective of the velocity of the gas stream in which the probe is placed. The theoretical considerations leading to the design of such a universal probe are described. It is followed by the description of an experimental evalution of a prototype device. Good agreement was found between the experimental results and the theoretical prediction.
The Development of a True Biaxial Shear Tester
Authors: Harder Joachim , Schwedes Jörg
Published: May 2005

To investigate the influence of the stress history on the yield limit a shear tester was developed, in which stresses or strains in x‐ and y‐direction can be applied independently of each other. Since there are no shear stresses on the boundary surfaces of the sample these stresses are principal stresses and the Mohr stress circles are known for each state of stress. First results from shear tests with limestone show a significant influence of the different ways of consolidation on the yield limit, i. e. the flow properties of a bulk solid will depend on the stress history. The flow function, however, which is essential for silo design, proves to be invariable of the stress history.
Dual Gas Flow Chromatographic Method for the Determination of Surface area and pore distribution of porous particles
Authors: Yan Ji‐min , Zhang Qi‐yuan
Published: May 2005

A dual gas flow chromatographic method is proposed. In this method, two different gas streams are introduced separately, one as the carrier gas and the other as the gas for creating the adsorption equilibrium. The thermodesorbed absorbate is eluted by a pure carrier gas. The complete curve of adsorption isotherm can be determined easily; therefore, both the specific area and the pore size distribution can be obtained at ordinary pressure. In addition, this method can be easily changed into the continuous flow method given by Nelsen and Eggertsen [1]. The relationship among R (rate) ‐ V (volume) ‐ A (area) ‐ α (ratio) in elution chromatography are investigated, and the volume of desorbed gas can be obtained from Vd = KRAd directly with K = (αV)/(RA). The standardization for peak area is simplified and more convenient for the treatment by a microcomputer. Some results of specific surface area and pore size distribution by this method, and their comparison with those from other methods are given altogether, and the coincidence is good.
Investigations into Coulter Sizing of Biological Particles; Theoretical Background and Instrumental Improvements
Authors: Kachel Volker
Published: May 2005

The electric resistance pulse or electric sens Xing zone method, primarily invented by W. H. Coulter, is well suited for volume measurements of biological cells and other particles.

This review summarizes the methodological investigations at the Max‐Planck‐Institut für Biochemie into the Coulter method, particularly for measuring biological cells.

The distribution of the electric field in Coulter orifices was measured in enlarged model orifices and, additionally, calculated by computer programs. It is shown that the local resistance pulse height depends on the square of the local electrical field‐strength and that the particle path in the orifice influences the measured pulse heights and the orientation and deformation of particles.

A new transducer system is explained which uses hydrodynamic focusing and allows short time kinetic measurements. It is equipped with a calibrator system which serves also as general control unit.
Surface Analysis of Pulverised Fuel Ash by Secondary Ion Mass Spectrometry and X‐ray Photoelectron Spectroscopy
Authors: Allen Geoffrey C. , Warner Anthony G. , Jones Allan R.
Published: May 2005

Samples of pulverised fuel ash (PFA) obtained both from power stations and from laboratory combustion experiments have been examined by SIMS (secondary ion mass spectrometry) and XPS (x‐ray photo‐electron spectroscopy).

The elemental analysis is at present semi‐quantitative and indicates presence of sulphur mainly as sulphate ion in the outer surface layer (5–10 nm) of some samples. Other elements, notably Mg, Fe, K and Ti appear at higher concentrations, up to ∼ 10% once the outer 10–20 nm surface layers have been removed by ion etching.
Electromagnetic Imaging Using Mutual Inductance Tomography: Potential for process applications
Authors: Peyton Anthony J. , Yu Zhi Zhong , Al‐Zeibak Said , Saunders Neville H. , Borges Antonio Rui
Published: May 2005

An overview of Electro‐Magnetic Tomography (EMT) using mutual inductance measurements is presented. The paper reviews the technique and principle of operation and gives a description of three case studies, which cover some of the generic design considerations and which illustrate the potential variety for inductive EMT systems. Results from the systems are described. These systems are presently experimental and possible future developments and applications are discussed.
Three‐Dimensional Reconstruction of Temperature and Velocity Fields in a Furnace
Authors: Schwarz Alexander
Published: May 2005

In this paper a reconstruction method is presented, which allows the calculation of three‐dimensional temperature and velocity fields in an industrial furnace by measuring the propagation times of sound waves. Transceiver systems working in a coal fired power station and reconstructing two‐dimensional fields are well known. Referring to these real conditions, the idea was to use two measurement planes situated over each other and projecting the fields in the volume between them. Some simulations show that weak inhomogeneous fields can be well reconstructed, whereas in the presence of turbulent flow and noise a reconstruction is critical.
Diameter Distribution of Spherical Primary Grains in the boolean model from small‐angle scattering
Authors: Gille Wilfried
Published: May 2005

A method for determining the size‐distribution density of small spheres which are arranged, without any interaction between them, at random positions in space and form an isotropic twophase system is presented. In the case of higher volume fractions, frequent overlapping between the spheres is a logical consequence. This effect is an essential feature of the model itself and is well considered and observed. Stereological information, which contains all the necessary data about the unknown size distribution, is obtained from the angular intensity distribution (small‐angle scattering experiment) of the particle system concerned. The resulting formula still includes, in a first representation, the volume fractionpas a free parameter. In a second step, a general analytical method for the determination of the volume fractionpfrom the set covariance of the considered random closed set is derived. Therefore, the unknown diameter distribution can be obtained in every detail, starting from the scattering curve of the sample, by way of two independent working steps.
Particle Shapes Produced by Comminution in the Szego Mill
Authors: Trass Olev , Ramesh Koka V. , Papachristodoulou George
Published: May 2005

The shapes of particles produced by comminution in the Szego Mill, a planetary ringroller mill, in different coal grinding operations show that particle shape is dependent on the type of operation, and help explain the breakage mechanisms. Dry grinding produces particles with a low aspect ratio due to interparticle attrition; significant briquetting of fine particles may occur. In slurry grinding flaky particles are produced which are selected for breakage at rates lower than those for granular particles. Similar observations have been made with other materials. Coal‐oil‐water grinding is accompanied by the formation of coal‐oil agglomerates. Their breakage produces uniform particles with a low aspect ratio due to interparticle attrition within the agglomerates.
A Method for Increasing the Sensitivity of Phase Doppler Interferometry to seed particles in liquid spray flows
Authors: Friedman Jacob A. , Renksizbulut Metin
Published: May 2005

A method has been developed to increase the sensitivity of phase Doppler interferometry‐based particle sizing systems to small particles in the presence of a spray containing large and small droplets; an important consideration when using seed particles to track the gas‐phase velocity in multi‐phase flows. The method, applicable to PDPA systems configured to operate in first and higher order refraction mode, involves doping the sprayed liquid with a dye that is strongly absorbing at the incident laser wavelengths. This results in greatly diminished scattered intensity from larger droplets, thus allowing the photomultiplier gain to be set to a level sufficient to easily detect small particles without saturation. Tests conducted indicate that, at a collection angle of 30° and droplet absorptivity of γ = 0.014/μm, the PDPA can accurately size absorbing droplets up to approximately 200 μm. This upper limit can be extended by changing selection angle. Tests performed with an actual spray demonstrated that the method allowed detection of 1 μm to 235 μm droplets; more than four times the instrument's usual range of 50: 1. A data correction scheme to determine the effective probe volume radius for each particle size class has been developed for absorbing particles, as standard correction schemes derived for non‐absorbing droplets excessively weigh distributions toward smaller particles.
Scattering of a First‐Order Gaussian Beam by an infinite cylinder with arbitrary location and arbitrary orientation
Authors: Gouesbet Gérard
Published: May 2005

The theory of scattering of a first‐order Gaussian beam by an infinite cylinder with arbitrary location and arbitrary orientation is presented. A component of the theory is the use of the theory of distributions.
Perimeter Exploration of Linear Chains of Circles
Authors: Surowiec Charles M. , Jones Thomas B.
Published: May 2005

Perimeter data, obtained from structured walks performed upon straight chains of circles and displayed in Richardson plots, reveal two distinct classes of discontinuities: textural and structural. Textural discontinuities contain information about the surface features of the profile, while structural discontinuities reveal the profile's overall shape. The origins of both types of discontinuities have easy explanations. The highly predictable behavior of the structural discontinuities serves as the basis of a newly proposed method of analysis for perimeter data. The number of structural discontinuities is equal to N, the number of circles in the chain; furthermore, the value of the step size \documentclass{article}\pagestyle{empty}\begin{document}$ \underline {\lambda} $\end{document} * associated with the first structural discontinuity is inversely related to N. These properties seem is be retained when the circles slightly intersect and also when the circles vary in diameter. Analysis of the structural discontinuities may provide a new method suitable for automated examination of chain‐like agglomerate particles.
Particle Velocity Measurements in Dense Fluidized Beds
Authors: Dencs BÉLa
Published: May 2005

The average local velocity of the upward of particles motion was determined in a dense fluidized bed by the means of a fibre optical probe. The probe consists of two independent light gates. The particles passing in front of the light gates reflect the light, generating sign sequences that are analysed by computer. From the average time difference of the sign sequences and from the distance of the light gates, the average local velocity can be calculated. The average local velocity of the particles along the height and diameter of the fluidized bed and also as a function of the fluidization air velocity was examined. It was concluded that the average local velocity is closely correlated with the local porosity of the dense fluidized bed and depends mainly on the fluidization air velocity. Using a fibre optical probe, the optimum range of the fluidization air velocity can be determined.
The Measurement of Particles Suspended in a stirred vessel using microphotography and digital image analysis
Authors: Kramer Timothy A. , Clark Mark M.
Published: May 2005

A novel technique to determine the size of particles suspended in a stirred vessel is investigated. The method uses microphotography to obtain a still image of the particles in situ. The equivalent circular diameter of the particles is obtained from the photographs using digital image analysis. The particles used for the test were certified particle size standards of a very small tolerance in diameter deviation. The size comparison was determined as a percent error between the measured particle diameter (equivalent circular diameter) and the diameter established by the particle manufacturer. To determine the limiting ranges of particle size and concentrations, spherical particles in a size range of approximately 1 to 10.0 μm (microns) in diameter were employed in the test. Concentrations varied from 0.00005% to 0.1% (mass basis). For each particle size, an aqueous solution of the particles was prepared at the desired concentration and placed in a stirred vessel. Photographs of the solutions were made at 25.5x, 40x, 60x and 80x magnification. For all sizes of particles, the entire range of concentration was examined.

The results indicate a minimum size resolution of approximately 3μm, in a corresponding concentration range of 0.0001% to 0.05%. Similar limits on concentration were found for the larger diameter particles, although a true upper limit for the largest particle sizes was not established. The functional concentration range appears to shift towards higher mass concentrations with increasing particle size. For 2.92 μm diameter particles, the error in size measurement was found to be below 10% for a concentration range of 0.0005% to 0.05%. Additionally, a relationship between turbidity and the error was seen at low particle concentration levels where decreasing levels of turbidity generated increasing levels of error.
Generalized Lorenz‐Mie Theory for Non‐Spherical Particles with applications to phase‐Doppler anemometry
Authors: Doicu Adrian , Ebert Fritz , Schabel Samuel
Published: May 2005

The Scattering of focused laser beams by arbitrarily shaped dielectric bodies is investigated theoretically. The beam description is based on Davis third‐order beam approximation for the field components. The scattering problem can be solved on a spherical basis by the extended boundary condition method or by the so‐called modified version of the extended boundary condition method. For spheroidal particles with small eccentricities, a perturbation technique for the internal subproblem of the extended boundary condition method is described. This procedure is applied to analyse the influence of the particle shape and orientation on the response of a phase‐Doppler system.
On the Optical Diagnosis and Sizing of Spherical Coated and Multilayered Particles with phase‐Doppler anemometry
Authors: Onofri Fabrice , Blondel Damien , Gréhan Gérard , Gouesbet Gérard
Published: May 2005

After having recalled basic theoretical results concerning the extension of generalized Lorenz‐Mie theory to the case of multilayered spheres, results connected with phase‐Doppler anemometry are considered, showing the influence of Gaussian beam intensity profiles on the light scattering properties of these particles. Particular emphasis is placed on the case of water‐coated carbon core particles, for which the possibility of obtaining simultaneous size measurements of the core and outer diameters is discussed. The sensitivity of the technique to particles with a refractive index profile is also considered, showing that this technique is more sensitive to changes in the average refractive index of the particles than to refractive index profiles, such as produced by high pressure and temperature stresses, at least for the studied geometry.
Basic Studies of Electrohydrodynamic Atomization Process using phase Doppler measurement technique
Authors: Naqwi Amir A. , Hartman Ruppert P. A. , Marijnissen Jan C. M.
Published: May 2005

A planar phase Doppler system is used to measure submicron droplets generated by an electrospray. Measured drop dia‐meters are correlated with the liquid properties and the condition for transition of the spray from the single‐jet mode to the multi‐jet mode is introduced. In another set of measurements using a standard phase Doppler system, combined size and velocity data are employed to deduce the drag force on the drops. In a situation where the drag force is balanced primarily by the electric force, the phase Doppler measurements allow to estimate the power‐law relationship between the charge on a drop and its diameter and hence, many provide insights into the underlying atomization mechanisms.
Dual‐Mode Phase‐Doppler Anemometer
Authors: Tropea Cameron , Xu Tian‐Hua , Onofri Fabrice , Géhan Gérad , Haugen Per , Stieglmeier Manfred
Published: May 2005

The accurate measurement of mass flux is identified as being essential for the successful use of phase‐Doppler anemometry (PDA) in many applications, in particular with sprays. Thus measured sizes of individual droplets and the cross‐sectional area to which the flux measurement is referenced must be reliable. This paper investigates sources of measurement error in each of these quantities and provides means to eliminates or minimize these errors. A new PDA configuration, termed dual–mode PDA, is introduced as an implementation of these suggestions. Example measurements illustrate the advantages of the system over conventional arrangements.
Deformation of liquid droplets during collisions with hot walls: Experimental and Numerical Results
Authors: Karl Alexander , Anders Klaus , Rieber Martin , Frohn Arnold
Published: May 2005

Measurements of droplet deformation during wall impingement were performed for ethanol droplets and water droplets with diameters ranging from 100 to 200 μm. The wall temperature is well above the Leidenfrost temperature of the droplet liquid. With monodisperse droplet streams and a special illumination technique, slow motion images of the phenomena can be obtained. Measurements with high temporal resolution below 1 μs are possible using a standard video camera. The experimental results are compared with numerical results, which were obtained by solving the three‐dimensional Navier‐Stokes equations for incompressible fluids including surface tension effects. The fluids are treated with the volume‐of‐fluid method and the free surface is modeled according to the continuum‐surface‐force model. Numerical and experimental results show good agreement.
Holographic Investigations of a Diesel Jet injected into a high‐pressure test chamber
Authors: Schaller Johannes K. , Stojanoff Christo G.
Published: May 2005

A Diesel spray injected into a high‐pressure test chamber was investigated with two different holographic techniques. The usual off‐axis recording geometry was used to investigate the very early beginning of the injection. Double pulsing of the recording laser facilitated velocity measurements. By using two different reference angles for the two recording the two images can be separated upon reconstruction of the holograms. Thus superior image quality could be achieved. Processes leading to jet formation could be identified: the spray tip is periodically axially decelerated and radially accelerated. Consequently, liquid moves at the tip off axis. The spray consists of fast central region surrounded by a slower outer jet region. The outer jet region exhibits periodic droplet concentration fluctuations which are interpreted as a result of the periodic processes at the spray tip. Some high concentration regions in the outer jet region were investigated using a dark‐field holographic technique. This technique permits single droplet velocity measurements and local droplet concentration determination at extremely high droplet concentrations. The most important result of these investigations is that no correlation between the local droplet concentration and the droplet velocity could be found.
Production of Fine Particles from Melts of Metals or Highly Viscous Fluids by ultrasonic standing wave atomization
Authors: Andersen Olaf , Hansmann Stephan , Bauckhage Klaus
Published: May 2005

Ultrasonic standing wave atomization (USWA) is a new process capable of atomizing both high surface energy liquids and highly viscous liquids. Atomization is achieved through acoustic forces acting upon a liquid jet which is guided into the central pressure node of a standing wave field. Spherical metal powders with minimum mass median diameters of less than 15 μm have been produced from metal melts with surface tensions of about 0.5 N/m. Organic liquids with viscosities between 1 and 10 Pas have been atomized, yielding mass median diameters from 20 to 330 μm. The influence of different operating parameters on the mass median diameter of metal melts and highly viscous liquids was evaluated. Parameters which were varied were ambient gas pressure, vibration amplitude of the transducers, mass flow rate, density of liquid, viscosity of the liquid, surface tension and the outlet diameter. The powders and sprays were analyzed with laser diffraction particle sizers. The physical background of the atomization process is discussed and an equation for the prediction of the mass median diameter is derived.
Influence of Refractive Index on Particle Size Analysis using the turbidimetric spectrum method
Authors: Wang Nai‐ning , Wei Jin‐ming , Hong Chang‐yi , Zhang Hong‐wu
Published: May 2005

The light scattering technique is now widely used in particle sizing, and includes the turbidimetric spectrum method. Although it has been reported that the light scattering technique, especially the turbidimetric method, is sensitive to refractive index, quantitative studies are rare. In this work, the effects of refractive index on the turbidimetric spectrum method were comprehensively investigated and detailed results are presented.
Calculation of the Stokes and Aerodynamic Equivalent Diameters of a short reinforcing fiber
Authors: Henn Arthur R.
Published: May 2005

A concern about all reinforcing fibers is the extent to which they are respirable. The degree of respirability of a particle is frequently estimated in terms of its aerodynamic equivalent diameter being less than a certain value (typically 3.5 to 7 μ). However, the aerodynamic equivalent diameter, like the Stokes diameter, is only defined exactly for spheres, which is far from the shape of acicular fibers. Thus, it is useful to be able to calculate, based on actual fiber diameter and aspect ratio, the effective Stokes and aerodynamic equivalent diameters of various fibers. The present paper derives simple expression for relating the two effective diameters to actual fiber dimensions.

Calculated results are compared with experimental data for glass fiber and three fractions of phosphate fiber [1], which is a short, reinforcing inorganic fiber. Agreement is seen to be good. Phosphate fiber was fractionated using a sedimentation technique described in the paper. The resulting fractions were characterized by semi‐manual measurements of micrographic dimensions and compared with results obtained from particle size instruments based on sedimentation principles. Based on these results, a large weight fraction of phosphate fiber is predicted not to be respirable.
The design, synthesis, and crystallization of an alpha‐helical peptide
Authors: Eisenberg David , Wilcox William , Eshita Steven M. , Pryciak Peter M. , Ho Siew Peng , Degrado William F.
Published: May 2005

Twelve‐ and sixteen‐residue peptides have been designed to form tetrameric alphahelical bundles. Both peptides are capable of folding into amphiphilic alpha‐helices, with leucyl residues along one face and glutamyl and lysyl residues along the opposite face. Four such amphiphilic alpha‐helices are capable of forming a noncovalently bonded tetramer. Neighboring helices run in antiparallel directions in the design, so that the complex has 222 symmetry. In the designed tetramer, the leucyl side chains interdigitate in the center in a hydrophobic interaction, and charged side chains are exposed to the solvent. The designed 12‐mer(ALPHA‐1) has been synthesized, and it forms helical aggregates in aqueous solution as judged by circular dichroic spectroscopy. It has also been crystallized and characterized by x‐ray diffraction. The crystal symmetry is compatible with (but does not prove) the design. The design can be extended to a four‐alpha‐helical bundle formed from a single polypeptide by adding three peptide linkers.
Peptide and ester synthesis in organic solvents catalyzed by seryl proteases linked to alumina
Authors: Pugnière M. , Skalli A. , Coletti‐Previero M.‐A. , Previero A.
Published: May 2005

Trypsin and α‐chymotrypsin were immobilized to alumina‐phosphocolamine complex, activated by glutaraldehyde. The immobilized enzymes show a great stability toward organic solvents miscible or immiscible with water. In the presence of a low concentration of water, the immobilized enzymes catalyzed transesterification reactions as well as peptide synthesis. The synthesized peptides were stable toward the immobilized enzymes.
Isolation and characterization of native human renin derived from Chinese hamster ovary cells
Authors: Poorman Roger A. , Palermo Daniel P. , Post Leonard E. , Murakami Kazuo , Kinner John H. , Smith Clark W. , Reardon Ilene , Heinrikson Robert L.
Published: May 2005

Transfection of Chinese hamster ovary (CHO) cells with a plasmid containing the cDNA for human preprorenin has provided cell lines that secrete 15 mg of native prorenin per liter of culture medium. Tryptic activation of the prorenin occurs by selective cleavage of the Arg66‐Leu67 bond (numbering as in preprorenin). The renin product, purified in a single step and in high yield by affinity chromatography, is fully stable for as long as 8 months when stored in solution at 4°C and pH 6.5. Purity of the renin was judged to be greater than 95% by gel electrophoresis, compositional and N‐terminal sequence analyses, and specific enzyme activity. An important aspect of the present work is the development of a direct assay for renin which permits accurate and reproducible evaluation of enzyme units and kinetic parameters. Application of methods described herein, combined with appropriate scale‐up fermentation capabilities, provides the means for generating gram quantities of human renin and its zymogen.
An algorithm for determining the conformation of polypeptide segments in proteins by systematic search
Authors: Moult J. , James M. N. G.
Published: May 2005

The feasibility of determining the conformation of segments of polypeptide chain up to six residues in length in globular proteins by means of systematic search through the possibles conformations has been investigated. Trial conformations are generated by using representative sets of ϕ, ψ, and χ angels that have been derived from an examination of the distributions of these angles in refined protein structures. A set of filters based on simple rules that protein structures obey is used to reduce the number of conformations to a manageable total. The most important filters are the maintenance of chain integrity and the avoidance of tooshort van der Waals contacts with the rest of the protein and with other portions of the segment under construction. The procedure is intended to be used with approximate models so that allowance is made throughout for errors in the rest of the structure. All possible main chains are first constructed and then all possible side‐chain conformations are built onto each of these. The electrostatic energy, including a solvent screening term, and the exposed hyrophobic area are evaluated for each accepted conformation. The method has been tested on two segments of chain in the trypsin like enzyme from Streptomyces griseus. It is found that there is a wide spread of energies among the accepted conformations, and the lowest energy ones have satisfactorily small root mean square deviations from the X‐ray structure.
The restoration of electron micrographs blurred by drift and rotation
Authors: Carragher Bridget , Bluemke David A. , Potel Michael J. , Josephs Robert
Published: May 2005

We have investigated the restoration of electron micrographs exhibiting blurring due to drift and rotation. Blurring due to drift arises in micrographs taken of a specimen which is moving relative to the image plane. A related problem is that of rotational blurring which arises in micrographs of thin sections of helical particles viewed in cross section. The twist of the particle within the finite thickness of the section causes the image to appear rotationally blurred about the helical axis.

Restoration algorithms were evaluated by applying them to the restoration of blurred model images degraded by additive Gaussian noise. Model images were also used to investigate how an incorrect estimate of the point spread function function describing the blur would effect the restoration. Images were, if necessary, geometrically transformed to a space in which the point spread function of the blur can be considered as linear and space invariant as, under these conditions, the restoration algorithms are greatly simplified. In the case of the rotationally blurred images this procedur was accomplished by transforming the image to polar coordinates.

The restoration techniques were successfully applied to blurred micrographs of bacteriophage T4 and crystals of catalase. The quality of the restoration was judged by comparisons of the restored images to undegraded images. Application to micrographs of rotationally blurred cross sections of helical macrofibers of sickle hemoglobin resulted in a reduction in the amount of rotational blurring.
Preliminary x‐ray diffraction analysis of HhaII endonuclease‐DNA cocrystals
Authors: Chandrasegaran Srinivasan , Smith Hamilton O. , Amzel Mario L. , Ysern Xavier
Published: May 2005

HhaII restriction endonuclease purified from an overproducing recombinant E. coli clone has been cocrystallized with a heptanucleotide duplex, d‐GGAGTCC:GGACTCC. The cocrystals are monoclonic and belong to the space group C2. The unit cell dimensions are a = 199.0±1.0 Å, b = 100.0±0.5 Å, c = 80.3±0.4 Å, and β = 101.0±1.0°. There appear to be two dimers per asymmetric unit and the crystals diffract to 4‐Å resolution.
Predicting antibody hypervariable loop conformations II: Minimization and molecular dynamics studies of MCPC603 from many randomly generated loop conformations
Authors: Fine R. M. , Wang H. , Shenkin P. S. , Yarmush D. L. , Levinthal C.
Published: May 2005

We describe a method for predicting the conformations of loops in proteins and its application to four of the complementarity determining regions [CDRs] in the crystallographically determined structure of MCPC603. The method is based on the generation of a large number of randomly generated conformations for the backbone of the loop being studied, followed by either minimization or molecular dynamics followed by minimization starting from these random structures. The details of the algorithm for the generation of the loops are presented in the first paper in this series (Shenkin etal.[submitted]). The results of minimization and molecular dynamics applied to these loops is presented here. For the two shortest CDRs studied (H1 and L2, which are five and seven amino acids long), minimizations and dynamics simulations which ignore interactions of the loop amino acids beyond the carbon ture closely. This suggests that these loops fold independently of sequence variation. For the third CDR (L3, which is nine amino acids), those portions of the CDR near its base which are hydrogen bonded to framework are well replicated by our procedures, but the top of the loop shows singificant conformational variability. This variability persists when side chain interactions for the MCPC603 sequence are included. For a fourth CDR (H3, which is 11 amino acids long), new low‐energy backbone conformations are found; however, only those which are close to the crystal are compatible with the sequence when side chain interactions are taken into account. Results from minimuzation and dynamics on single CDRs with all other CDRs removed are presented. These allow us to explore the extent to which individual CDR conformations are determined by interactions with framework only.
Estimation of uncertainties in X‐ray refinement results by use of perturbed structures
Authors: Kuriyan John , Karplus Martin , Petsko Gregory A.
Published: May 2005

The uncertainties in the refined parameters for a 1.5‐Å X‐ray structure of carbon‐monoxy (FeII) myoglobin are estimated by combining energy minimization with least‐squares refinement against the X‐ray data. The energy minimization, done without reference to the X‐ray data, provide perturbed structures which are used to restart conventional X‐ray refinement. The resulting refined structures have the same, or better, R‐factor and stereochemical parameters as the original X‐ray structure, but deviate from it by 0.13 Å rms for the backbone atoms and 0.31 Å rms for the sidechain atoms. Atoms interacting with a disordered sidechain, Arg 45 CD3, are observed to have larger positional uncertainties. The uncertainty in the B‐factors, within the isotropic harmonic motion approximation, is estimated to be 15%. The resulting X‐ray structures are more consistent with the energy parameters used in simulations.
Subunit assembly and metabolic stability of E. coli RNA polymerase
Authors: Ishihama Akira , Fujita Nobuyuki , Glass Robert E.
Published: May 2005

Immunological cross‐reaction was employed for identification of proteolytic fragments of E. coli RNA polymerase genered both in vitro and in vivo. Several species of partially denatured but assembled RNA polymerase were isolated, which were composed of fragments of the two large subunits, β and β′, and the two small and intact subunits, α and σ. Comparison of the rate and pathway of proteolytic cleavage in vitro of unassembled subunits, subassemblies, and intact enzymes indicated that the susceptibility of RNA polymerase subunits to proteolytic degradation was dependent on the assembly state.

Using this method, degradation in vivo was found for some, but not all, of the amber fragments of β subunit in merodiploid cells carrying both wild‐type and mutant rpoB genes. Although the RNA polymerase is a metabolically stable component in exponentially growing cells of E. coli, degradation of the full‐sized subunits was found in two cases, i.e., several temperature‐sensitive E. coli mutants with a defect in the assembly of RNA polymerase and the stationary‐phase cells of a wild‐type E. coli. The in vivo degradation of RNA polymerase was indicated to be initiated by alteration of the enzyme structure.
Continuous compact protein domains
Authors: Zehfus Micheal H.
Published: May 2005

The coefficient of compactness was recently introduced and used to locate domains in lysozyme and ribonuclease (Zehfus and Rose: Bio‐chemistry 25:5759–5765, 1986). Nineteen additional proteins now have been analyzed by using this measure. Complete listings of compact units and plots showing their hierarchic organization are presented for all twenty‐one proteins. Large compact units correspond well to protein domains; however, many smaller compact structures of equal or better compactness are also found. Since small compact units could represent subdomains or protein‐folding intermediates, their structural composition is further examined.
Prediction of secondary structure by evolutionary comparison: Application to the α subunit of tryptophan synthase
Authors: Crawford Irving P. , Niermann Thomas , Kirschner Kasper
Published: May 2005

The amino acid sequences of the α subunits of tryptophan synthase form ten different microorganisms were alingned by standard procedures. The α helics, β strands and turns of each sequence were predicted separately by two standard prediction algorithms and averaged at homologous sequence positions. Additional evidence for conserved secondary structure was derived form profiles of average hydropathy and chain flexibility values, leading to a joint prediction. There is good agreement between (1) predicted β strands, maximal hydropathy and minimal flexibility, and (2) predicted loops, great chain flexibility, and protein segments that accept insertions of various lengths in individual sequences. The α subunit is predicted to have eight repeated β‐loop‐α‐loop motifs with an extra N‐terminal α helix and an intercalated segment of highly conserved residues. This pattern suggests that the teritiary structure of the α subunit is an eightfold α/β barrel. The distribution of conserved amino acid residues and publilshed data on limited proteolysis, chemical modification, and mutagenesis are consistent with the α/β barrel structure. Both the active site of the α subunit and the combining site for the β2 subunit are at the end of the barrel formed by the carboxyl‐termini of the β strands.
Prediction of the three‐dimensional structure of human growth hormone
Authors: Cohen F.E. , Kuntz I.D.
Published: May 2005

In recent years, the protein‐folding problem has attracted the attention of molecular biologists. Efforts have focused on developing heuristic and energy‐based algorithms to predict the three‐dimensional structure of a protein from its amino acid sequence. We have applied a series of heuristic algorithms to the sequence of human growth hormone. A family of five structures which are generically right‐handed fourfold α‐helical bundles are found from an investigaion of ∼108 structures. A plausible receptor binding site is suggested. Independent crystallographic analysis confirms some aspects of these predictions. These methods only deal with the “core” structure, and conformations of many residues are not defined. Further work is required to identify a unique set of coordinates and to clarify the topological alternatives available to α‐helical proteins.
Determination of three‐dimensional protein structures from nuclear magnetic resonance data using fragments of known structures
Authors: Krauli Per J. , Jones T. Alwyn
Published: May 2005

A method to build a three‐dimensional protein model from nuclear magnetic resonance (NMR) data using fragments from a data base of crystallographically determined protein structures is presented. The interproton distances derived from the nuclear Overhauser effect (NOE) data are compared to the precalculated distances in the known protein structures. An efficient search algorithm is used, which arranges the distancs in matrices akin to a Cα diagonal distance plot, and compares the NOE distance matrices for short sequential zones of the protein to the data base matrices. After cluster analysis of the fragments found in this way, the structure is built by aligning fragments in overlapping zones. The sequentially long‐range NOEs cannot be used in the initial fragments search but are vital to discriminate between several possible combinations of different groups of fragments. The method has been tested on one simulated NOE data set derived from a crystal structure and one experimental NMR data set. The method produces models that have good local structure, but may contain larger global errors. These models can be used as the starting point for further refinement, e.g., by restrained molecular dynamics or interactive graphics.
Association of calmodulin and smooth muscle myosin light chain kinase: Application of a lable selection technique with trace acetylated calmodulin
Authors: Jackson Arthur E. , Carraway Kermit L. , Payne M. Elizabeth , Means Anthony R. , Puett David , Brew Keith
Published: May 2005

A method is described for rapidly surveying the effects of modifying individual amino acid residues of a protein on its ability to interact specifically with another macromolecule. The procedure has been used to examine the individual roles of the seven lysyl residues of calmodulin in its ability to bind to smooth muscle myosin light chain kinase; previous studies by Jackson et al. (J. Biol. Chem. 261:1226–12232, 1986) have suggested that certain lysines may be located close to the interaction site. Trace [3H]‐acetylated calmodulin, consisting predominantly of molecules acetylated at single sites together with unmodified protein, was incubated in excess (five‐ to 20‐fold) with smooth muscle MLC kinase to allow the modified and unmodified molecules to compete for binding to the enzyme. Subsequently, the calmodulin‐enzyme complex was separated from unbound calmodulin, and the level of acetylation of each of the seven lysines of the bound fraction of calmodulin was determined and compared to that of each corresponding group of the starting preparation. Significant changes were found at only two of the lysines, 21 and 75, where the extent of acetylation in the bound fraction was three‐ and fivefold lower, respectively, than that in the original preparation. These results were reproducible in three separate selection experiments employing both chicken and turkey gizzard MLC kinase. It is concluded that acetylation of calmodulin at either lysine 21 or 75 markedly reduces its affinity for MLC kinase, but acetylation at any of the other lysines (13, 30, 77, 94, or 148) has only minor effects. This finding supports the proposal that the face of the central helix containing lysine 75 is involved in interaction with MLC kinase and suggests also that additional contact near Ca2‐binding site 1 occurs.
Identification of structural motifs from protein coordinate data: Secondary structure and first‐level supersecondary structure*
Authors: Richards Frederic M. , Kundrot Craig E.
Published: May 2005

A computer program is described that produces a description of the secondary structure and supersecondary structure of a polypeptide chain using the list of alpha carbon coordinates as input. Restricting the term “secondary structure” to the conformation of contiguous segments of the chain, the program determines the initial and final residues in helices, extended strands, sharp turns, and omega loops. This is accomplished through the use of difference distance matrices. The distances in idealized models of the segments are compared with the actual structure, and the differences are evaluated for agreement within preset limits. The program assigns 90–95% of the residues in most proteins to at least one type of secondary element

In a second step the now‐defined helices and strands are idealized as straight line segments, and the axial directions and locations are compiled from the input Cα coordinate list. These data are used to check for moderate curvature in strands and helices, and the secondary structure list is corrected where necessary. The geometric relations between these line segments are then calculated and output as the first level of supersecondary structure. A maximum of six parameters are required for a complete description of the relations between each pair. Frequently a less complete description will suffice, for example just the interaxial separation and angle. Both the secondary structure and one aspect of the supersecondary structure can be displayed in a character matrix analogous to the distance matrix format. This allows a quite accurate two‐dimensional display of the three‐dimensional structure, and several examples are presented

A procedure for searching for arbitrary substructures in proteins using distance matrices is also described. A search for the DNA binding helix‐turnhelix motif in the Protein Data Bank serves as an example

A further abstraction of the above data can be made in the form of a metamatrix where each diagonal element represents an entire secondary segment rather than a single atom, and the off‐diagonal elements contain all the parameters describing their interrelations. Such matrices can be used in a straightforward search for higher levels of supersecondary structure or used in toto as a representation of the entire tertiary structure of the polypeptide chain.
Differences in crystal properties and ligand affinities of an antifluorescyl fab (4‐4‐20) in two solvent systems
Authors: Gibson A. L. , Herron J. N. , He X.‐M. , Patrick V. A. , Mason M. L. , Lin J.‐N. , Kranz D. M. , Voss E. W. , Edmundson A. B.
Published: May 2005

An antigen‐binding fragment (Fab) from a murine monoclonal antibody (4‐4‐20) with high affinity for fluorescein was cocrystallized with ligand in polyethylene glycol (PEG) and 2‐methl‐2,4‐pentanediol (MPD) in forms suitable for X‐ray analyses. In MPD the affinity of the intact antibody for fluorescein was 300 times lower than the value (3.4 × 1010 M−1) obtained in aqueous buffers. This decreased affinity was manifested by the partial release of bound fluorescein when MPD was added to solutions of liganded Feb during crystallization trials, In PEG, the ligand remained firmly bound to the protein. The liganded Feb crystallized in the monoclinic space group P21 in PEG, with a = 58.6, b = 97.2, c = 44.5 Å and β = 95.2°. In MPD the space group was triclinic P1, with a = 58.3, b = 43.4, c = 42.3 Å, α = 83.9°, β = 87.6°, and γ = 84.5°. X‐ray diffraction data were collected for both forms to 2.5‐Å resolution. Surprisingly, the triclinic form of the liganed antifluorescyl Feb had the same space group, closely similar cell dimensions, and practically the same orientation in the unit cell as an unliganded Fab (BV04‐01) with activity against single‐stranded DNA.