Proteomic analysis of k-casein micro-heterogeneity

The proteome of bovine milk is dominated by just six gene products that constitute approximately 95% of milk protein. Nonetheless, over 150 protein spots can be readily detected following two-dimensional electrophoresis of whole milk. Many of these represent isoforms of the major gene products produced through extensive posttranslational modification. Peptide mass fingerprinting of in-gel tryptic digests (using matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) in reflectron mode with alpha-cyano-4-hydroxycinnamic acid as the matrix) identified 10 forms of K-casein with isoelectric point (pl) values from 4.47 to 5.81, but could not distinguish between them. MALDI-TOF MS in linear mode, using sinapinic acid as the matrix, revealed a large tryptic peptide (mass > 5990 Da) derived from the C-terminus that contained all the known sites of genetic variance, phosphorylation and glycosylation. Two genetic variants present as singly or doubly phosphorylated forms could be distinguished using mass data alone. Glycoforms containing a single acidic tetrasaccharide were also identified. The differences in electrophoretic mobility of these isoforms were consistent with the addition of the acidic groups. While more extensively glycosylated forms were also observed, substantial loss of N-acetylneuraminic acid from the glycosyl group was evident in the MALDI spectra such that ions corresponding to the intact glycopeptide were not observed and assignment of the glycoforms was not possible. However, by analysing the pl shifts observed on the two-dimensional gels in conjunction with the MS data, the number of N-acetylneuraminic acid residues, and hence the glycoforms present, could be determined.

Analysis of dynamical tunneling experiments with a Bose-Einstein condensate

Dynamical tunneling is a quantum phenomenon where a classically forbidden process occurs that is prohibited not by energy but by another constant of motion. The phenomenon of dynamical tunneling has been recently observed in a sodium Bose-Einstein condensate. We present a detailed analysis of these experiments using numerical solutions of the three-dimensional Gross-Pitaevskii equation and the corresponding Floquet theory. We explore the parameter dependency of the tunneling oscillations and we move the quantum system towards the classical limit in the experimentally accessible regime.

Three-dimensional solitons in coupled atomic-molecular Bose-Einstein condensates

We present a theoretical analysis of three-dimensional (3D) matter-wave solitons and their stability properties in coupled atomic and molecular Bose-Einstein condensates (BECs). The soliton solutions to the mean-field equations are obtained in an approximate analytical form by means of a variational approach. We investigate soliton stability within the parameter space described by the atom-molecule conversion coupling, the atom-atom s-wave scattering, and the bare formation energy of the molecular species. In terms of ordinary optics, this is analogous to the process of sub- or second-harmonic generation in a quadratic nonlinear medium modified by a cubic nonlinearity, together with a phase mismatch term between the fields. While the possibility of formation of multidimensional spatiotemporal solitons in pure quadratic media has been theoretically demonstrated previously, here we extend this prediction to matter-wave interactions in BEC systems where higher-order nonlinear processes due to interparticle collisions are unavoidable and may not be neglected. The stability of the solitons predicted for repulsive atom-atom interactions is investigated by direct numerical simulations of the equations of motion in a full 3D lattice. Our analysis also leads to a possible technique for demonstrating the ground state of the Schrodinger-Newton and related equations that describe Bose-Einstein condensates with nonlocal interparticle forces.

Finite element analysis of fault bend influence on stick-slip instability along an intra-plate fault

Earthquakes have been recognized as resulting from stick-slip frictional instabilities along the faults between deformable rocks. A three-dimensional finite-element code for modeling the nonlinear frictional contact behaviors between deformable bodies with the node-to-point contact element strategy has been developed and applied here to investigate the fault geometry influence on the nucleation and development process of the stick-slip instability along an intra-plate fault through a typical fault bend model, which has a pre-cut fault that is artificially bent by an angle of 5.6degrees at the fault center. The numerical results demonstrate that the geometry of the fault significantly affects nucleation, termination and restart of the stick-slip instability along the intra-plate fault, and all these instability phenomena can be well simulated using the current finite-element algorithm.

Theoretical investigation of convective instability in inclined and fluid-saturated three-dimensional fault zones.

The convective instability of pore-fluid flow in inclined and fluid-saturated three-dimensional fault zones has been theoretically investigated in this paper. Due to the consideration of the inclined three-dimensional fault zone with any values of the inclined angle, it is impossible to use the conventional linear stability analysis method for deriving the critical condition (i.e., the critical Rayleigh number) which can be used to investigate the convective instability of the pore-fluid flow in an inclined three-dimensional fault zone system. To overcome this mathematical difficulty, a combination of the variable separation method and the integration elimination method has been used to derive the characteristic equation, which depends on the Rayleigh number and the inclined angle of the inclined three-dimensional fault zone. Using this characteristic equation, the critical Rayleigh number of the system can be numerically found as a function of the inclined angle of the three-dimensional fault zone. For a vertically oriented three-dimensional fault zone system, the critical Rayleigh number of the system can be explicitly derived from the characteristic equation. Comparison of the resulting critical Rayleigh number of the system with that previously derived in a vertically oriented three-dimensional fault zone has demonstrated that the characteristic equation of the Rayleigh number is correct and useful for investigating the convective instability of pore-fluid flow in the inclined three-dimensional fault zone system. The related numerical results from this investigation have indicated that: (1) the convective pore-fluid flow may take place in the inclined three-dimensional fault zone; (2) if the height of the fault zone is used as the characteristic length of the system, a decrease in the inclined angle of the inclined fault zone stabilizes the three-dimensional fundamental convective flow in the inclined three-dimensional fault zone system; (3) if the thickness of the stratum is used as the characteristic length of the system, a decrease in the inclined angle of the inclined fault zone destabilizes the three-dimensional fundamental convective flow in the inclined three-dimensional fault zone system; and that (4) the shape of the inclined three-dimensional fault zone may affect the convective instability of pore-fluid flow in the system. (C) 2004 Published by Elsevier B.V.

Capillary phenomena in the framework of the two-dimensional density functional theory

We present results of application of the density functional theory (DFT) to adsorption and desorption in finite and infinite cylindrical pores accounting for the density distribution in radial and axial directions. Capillary condensation via formation of bridges is considered using canonical and grand canonical versions of the 2D DFT. The potential barrier of nucleation is determined as a function of the bulk pressure and the pore diameter. In the framework of the conventional assumptions on intermolecular interactions both 1D and 2D DFT versions lead to the same results and confirm the classical scenario of condensation and evaporation: the condensation occurs at the vapor-like spinodal point, and the evaporation corresponds to the equilibrium transition pressure. The analysis of experimental data on argon and nitrogen adsorption on MCM-41 samples seems to not completely corroborate this scenario, with adsorption branch being better described by the equilibrium pressure - diameter dependence. This points to the necessity of the further development of basic representations on the hysteresis phenomena.

Strength analysis of steel-concrete composite beams in combined bending and shear

Despite experimental evidences, the contributions of the concrete slab and composite action to the vertical shear strength of simply supported steel-concrete composite beams are not considered in current design codes, which lead to conservative designs. In this paper, the finite element method is used to investigate the flexural and shear strengths of simply supported composite beams under combined bending and shear. A three-dimensional finite element model has been developed to account for geometric and material nonlinear behavior of composite beams, and verified by experimental results. The verified finite element model is than employed to quantify the contributions of the concrete slab and composite action to the moment and shear capacities of composite beams. The effect of the degree of shear connection on the vertical shear strength of deep composite beams loaded in shear is studied. Design models for vertical shear strength including contributions from the concrete slab and composite action and for the ultimate moment-shear interaction ate proposed for the design of simply supported composite beams in combined bending and shear. The proposed design models provide a consistent and economical design procedure for simply supported composite beams.

Modeling of adsorption and nucleation in infinite cylindrical pores by two-dimensional density functional theory

In this paper, we present an analysis of argon adsorption in cylindrical pores having amorphous silica structure by means of a nonlocal density functional theory (NLDFT). In the modeling, we account for the radial and longitudinal density distributions, which allow us to consider the interface between the liquidlike and vaporlike fluids separated by a hemispherical meniscus in the canonical ensemble. The Helmholtz free energy of the meniscus was determined as a function of pore diameter. The canonical NLDFT simulations show the details of density rearrangement at the vaporlike and liquidlike spinodal points. The limits of stability of the smallest bridge and the smallest bubble were also determined with the canonical NLDFT. The energy of nucleation as a function of the bulk pressure and the pore diameter was determined with the grand canonical NLDFT using an additional external potential field. It was shown that the experimentally observed reversibility of argon adsorption isotherms at its boiling point up to the pore diameter of 4 nm is possible if the potential barrier of 22kT is overcome due to density fluctuations.

Analytical solutions of linear finite- and small-strain one-dimensional consolidation

Analytical solutions are presented for linear finite-strain one-dimensional consolidation of initially unconsolidated soil layers with surcharge loading for both one- and two-way drainage. These solutions complement earlier solutions for initially unconsolidated soil layers without surcharge and initially normally consolidated soil layers with surcharge. Small-strain solutions for the consolidation of initially unconsolidated soil layers with surcharge loading are also presented, and the relationship between the earlier solutions for initially unconsolidated soil without surcharge and the corresponding small-strain solutions, which was not addressed in the earlier work, is clarified. The new solutions for initially unconsolidated soil with surcharge loading can be applied to the analysis of low stress consolidation tests and to the partial validation of numerical solutions of non-linear finite-strain consolidation. They also clarify a formerly perplexing aspect of finite-strain solution charts first noted in numerical solutions. Copyright (C) 2004 John Wiley Sons, Ltd.

Using two dimensional sectional distributions to infer three dimensional volumetric distributions - Validation using tomography

The critical process parameter for mineral separation is the degree of mineral liberation achieved by comminution. The degree of liberation provides an upper limit of efficiency for any physical separation process. The standard approach to measuring mineral liberation uses mineralogical analysis based two-dimensional sections of particles which may be acquired using a scanning electron microscope and back-scatter electron analysis or from an analysis of an image acquired using an optical microscope. Over the last 100 years, mathematical techniques have been developed to use this two dimensional information to infer three-dimensional information about the particles. For mineral processing, a particle that contains more than one mineral (a composite particle) may appear to be liberated (contain only one mineral) when analysed using only its revealed particle section. The mathematical techniques used to interpret three-dimensional information belong, to a branch of mathematics called stereology. However methods to obtain the full mineral liberation distribution of particles from particle sections are relatively new. To verify these adjustment methods, we require an experimental method which can accurately measure both sectional and three dimensional properties. Micro Cone Beam Tomography provides such a method for suitable particles and hence, provides a way to validate methods used to convert two-dimensional measurements to three dimensional estimates. For this study ore particles from a well-characterised sample were subjected to conventional mineralogical analysis (using particle sections) to estimate three-dimensional properties of the particles. A subset of these particles was analysed using a micro-cone beam tomograph. This paper presents a comparison of the three-dimensional properties predicted from measured two-dimensional sections with the measured three-dimensional properties.

Dimensional change behavior of caribbean pine using an environmental scanning electron microscope

Moisture transport and dimensional change during wood drying or wetting processes were analyzed based on pictures from an environmental scanning electron microscope (ESEM). This provides quantitative relationships between dimensional changes of total area, cell wall, and lumen, and moisture content for earlywood and latewood. Earlywood and latewood behave similarly but show some quantitative differences. The overall outcome for sections containing both kinds of wood seems to be dominated by the latewood behavior. The observed strain behavior of wood during drying is anisotropic in ways that are inconsistent with explanations solely related to microfibril orientation or earlywood/latewood interactions and more likely may be influenced by ray tracheids.

Analysis of transient eddy currents in MRI using a cylindrical FDTD method

Most magnetic resonance imaging (MRI) spatial encoding techniques employ low-frequency pulsed magnetic field gradients that undesirably induce multiexponentially decaying eddy currents in nearby conducting structures of the MRI system. The eddy currents degrade the switching performance of the gradient system, distort the MRI image, and introduce thermal loads in the cryostat vessel and superconducting MRI components. Heating of superconducting magnets due to induced eddy currents is particularly problematic as it offsets the superconducting operating point, which can cause a system quench. A numerical characterization of transient eddy current effects is vital for their compensation/control and further advancement of the MRI technology as a whole. However, transient eddy current calculations are particularly computationally intensive. In large-scale problems, such as gradient switching in MRI, conventional finite-element method (FEM)-based routines impose very large computational loads during generation/solving of the system equations. Therefore, other computational alternatives need to be explored. This paper outlines a three-dimensional finite-difference time-domain (FDTD) method in cylindrical coordinates for the modeling of low-frequency transient eddy currents in MRI, as an extension to the recently proposed time-harmonic scheme. The weakly coupled Maxwell's equations are adapted to the low-frequency regime by downscaling the speed of light constant, which permits the use of larger FDTD time steps while maintaining the validity of the Courant-Friedrich-Levy stability condition. The principal hypothesis of this work is that the modified FDTD routine can be employed to analyze pulsed-gradient-induced, transient eddy currents in superconducting MRI system models. The hypothesis is supported through a verification of the numerical scheme on a canonical problem and by analyzing undesired temporal eddy current effects such as the B-0-shift caused by actively shielded symmetric/asymmetric transverse x-gradient head and unshielded z-gradient whole-body coils operating in proximity to a superconducting MRI magnet.

Comparative proteomic analysis to study molecular events during gonad development in mice

Sex determination represents a critical bifurcation in the road of embryonic development. It is based on a finely regulated network of gene activity, as well as protein-protein interactions and activation or silencing of signaling pathways. Despite the identification of a number of critical genes, many aspects of the molecular cascade that drives the differentiation of the embryonic gonad into either a testis or an ovary remain poorly understood. To identify new proteins involved in this cascade, we employed two-dimensional gel electrophoresis and mass spectrometry to compare the protein expression profiles of fetal mouse testes and ovaries. Three proteins, hnRPA1, TRA1, and HSC71, were found to be expressed in a male-specific manner and this expression was confirmed by real-time reverse transcriptase polymerase chain reaction (RT-PCR) and in situ hybridization. Moreover, HSC71 was found to be hyperphosphorylated in male compared to female gonads, emphasizing the advantage of the proteomic approach in allowing the detection of posttranslational modifications.

Leading coordinate analysis of reaction pathways in proton chain transfer: Application to a two-proton transfer model for the green fluorescent protein

The ‘leading coordinate’ approach to computing an approximate reaction pathway, with subsequent determination of the true minimum energy profile, is applied to a two-proton chain transfer model based on the chromophore and its surrounding moieties within the green fluorescent protein (GFP). Using an ab initio quantum chemical method, a number of different relaxed energy profiles are found for several plausible guesses at leading coordinates. The results obtained for different trial leading coordinates are rationalized through the calculation of a two-dimensional relaxed potential energy surface (PES) for the system. Analysis of the 2-D relaxed PES reveals that two of the trial pathways are entirely spurious, while two others contain useful information and can be used to furnish starting points for successful saddle-point searches. Implications for selection of trial leading coordinates in this class of proton chain transfer reactions are discussed, and a simple diagnostic function is proposed for revealing whether or not a relaxed pathway based on a trial leading coordinate is likely to furnish useful information.

NMR of conotoxins: structural features and an analysis of chemical shifts of post-translationally modified amino acids

Conotoxins are small conformationally constrained peptides found in the venom of marine snails of the genus Conus. They are usually cysteine rich and frequently contain a high degree of post-translational modifications such as C-terminal amidation, hydroxylation, carboxylation, bromination, epimerisation and glycosylation. Here we review the role of NMR in determining the three-dimensional structures of conotoxins and also provide a compilation and analysis of H-1 and C-13 chemical shifts of post-translationally modified amino acids and compare them with data from common amino acids. This analysis provides a reference source for chemical shifts of post-translationally modified amino acids. Copyright (C) 2006 John Wiley & Sons, Ltd.