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At least 289 records · Page 16Linked to original sources

PubMed2002

Hydraulic properties and leachate level analysis of Kimpo metropolitan landfill, Korea.

Hydraulic properties of waste and cover soil from Kimpo Metropolitan Landfill were experimentally measured by laboratory tests. The degree of compaction was changed to identify the effect on hydraulic conductivity, field capacity, and permanent wilting point. Properties were utilized in developing a reliable numerical tool for leachate analysis. HELP, a simulation model for hydrologic evaluation of landfill performance, was adopted for that purpose. For calibration, results from simulation using the parameter values measured by laboratory tests were compared against the field data. The model was applied to predict the leachate level change according to the degree of compaction and cover soil thickness variation. It was found that the increase in the degree of compaction for intermediate cover soil and waste results in the decrease of field capacity and hydraulic conductivity, hence, the increase of leachate level. The effect of cover layer thickness on the leachate level was minor. Based on the findings from laboratory and numerical experiments, a guideline for reclamation practice was recommended.

Calibration↗

PubMed2001

Hydroxyapatite as a filler for dental composite materials: mechanical properties and in vitro bioactivity of composites.

Hydroxyapatite (HAp) powder was treated with gamma-methacryloxypropyltrimethoxy-silane (gamma-MPS) using standard techniques in both non-polar and polar systems. Infrared spectra (DRIFT) and thermogravimetric analysis (TGA) confirmed the presence of gamma-MPS on the surface of the HAp filler particles. Series of experimental composites consisting of bisphenol-a-glycidyl methacrylate (BisGMA) based resin and untreated or treated HAp filler were produced to determine the mechanical properties and in vitro bioactivity. The incorporation of HAp filler into the BisGMA base resin had an enhancing effect on the flexural strength and Young's modulus of the base resin, the latter being increased by a factor of three. The mechanical properties of the filled resin were not affected by the surface treatment of the HAp, but filler loading was found to have a significant effect on Young's modulus. Higher proportions of silane-treated HAp of smaller particle size could be incorporated in the monomer phase giving rise to composites of higher stiffness. Examination of the fracture surfaces showed that the silanized HAp particles maintained better contact with the polymer matrix. In vitro study revealed that the composites incorporating silanized HAp formed a compact and continuous calcium phosphate layer on their surface after 4 weeks immersion in a simulated body fluid (SBF).

Journal Article↗

PubMed2000

Structure of free Thermus flavus 5 S rRNA at 1.3 nm resolution from synchrotron X-ray solution scattering.

The shape of free Thermus flavus 5 S rRNA in solution at 1.3 nm resolution is restored from synchrotron x-ray scattering data using an ab initio simulated annealing algorithm. The free 5 S rRNA is a bent elongated molecule displaying a compact central region and two projecting arms, similar to those of the tRNA. The atomic models of the 5 S rRNA domains A-D-E and B-C in the form of elongated helices can be well accommodated within the shape, yielding a tentative model of the structure of the free 5 S rRNA in solution. Its comparison with the recent protein-RNA map in the ribosome (Svergun, D. I., and Nierhaus, K. H. (2000) J. Biol. Chem. 275, 14432-14439) indicates that the 5 S rRNA becomes essentially more compact upon complex formation with specific ribosomal proteins. A conceivable conformational change involves rotation of the B-C domain toward the A-D-E domain. The model of free 5 S rRNA displays no interactions between domains E and C, but such interactions are possible in the bound molecule.

Algorithms↗

PubMed2002

Phosphorylation-induced conformational changes in a mitogen-activated protein kinase substrate. Implications for tyrosine hydroxylase activation.

Mitogen-activated protein (MAP) kinase-mediated phosphorylation of specific residues in tyrosine hydroxylase leads to an increase in enzyme activity. However, the mechanism whereby phosphorylation affects enzyme turnover is not well understood. We used a combination of fluorescence resonance energy transfer (FRET) measurements and molecular dynamics simulations to explore the conformational free energy landscape of a 10-residue MAP kinase substrate found near the N terminus of the enzyme. This region is believed to be part of an autoregulatory sequence that overlies the active site of the enzyme. FRET was used to measure the effect of phosphorylation on the ensemble of peptide conformations, and molecular dynamics simulations generated free energy profiles for both the unphosphorylated and phosphorylated peptides. We demonstrate how FRET transfer efficiencies can be calculated from molecular dynamics simulations. For both the unphosphorylated and phosphorylated peptides, the calculated FRET efficiencies are in excellent agreement with the experimentally determined values. Moreover, the FRET measurements and molecular simulations suggest that phosphorylation causes the peptide backbone to change direction and fold into a compact structure relative to the unphosphorylated state. These results are consistent with a model of enzyme activation where phosphorylation of the MAP kinase substrate causes the N-terminal region to adopt a compact structure away from the active site. The methods we employ provide a general framework for analyzing the accessible conformational states of peptides and small molecules. Therefore, they are expected to be applicable to a variety of different systems.

Animals↗

PubMed2005

Kertész line in the three-dimensional compact U(1) lattice Higgs model.

The three-dimensional lattice Higgs model with compact U(1) gauge symmetry and unit charge is investigated by means of Monte Carlo simulations. The full model with fluctuating Higgs amplitude is simulated, and both energy as well as topological observables are measured. The data show a Higgs and a confined phase separated by a well-defined phase boundary, which is argued to be caused by proliferating vortices. For fixed gauge coupling, the phase boundary consists of a line of first-order phase transitions at small Higgs self-coupling, ending at a critical point. The phase boundary then continues as a Kertész line across which thermodynamic quantities are non-singular. Symmetry arguments are given to support these findings.

Journal Article↗

PubMed1990

In vitro comparison of the cytotoxicity of twelve endodontic materials using a new technique.

An in vitro method for the cytotoxicity testing of endodontic materials is described which aims to simulate the clinical situation. Materials can be tested in the presence or absence of a compacted layer of dentine chips mimicking the periapical dentine plug. A total of twelve materials were tested. In the absence of dentine, Kloroperka, Biocalex, Diaket and Endomethasone were slightly cytotoxic; AH26 with and without silver, Sealapex, Tubliseal and Kerr's pulp canal sealer were moderately cytotoxic, while Forfenan, Spad and Kri paste were strongly cytotoxic. In the presence of dentine the cytotoxicity of these materials was considerably reduced, with the exception of Endomethasone, Forfenan, Spad and Kri paste. The method provides a satisfactory alternative to implantation testing and is an inexpensive and reproducible test system in which dentine can be incorporated.

Administration, Topical↗

PubMed2003

Design and assessment of microlenslet-array relay optics.

Recent progress in micro-optics fabrication and optical modeling software opens the opportunity to investigate how microlenslet-array-based compact relay systems can be designed and assessed. We present various optical configurations that include an appropriate baffle computation to eliminate ghost images, followed by an analysis of image quality. The investigation shows the existing trade-off between compactness of the system and a tiling effect observed in the corresponding image, an effect we refer to as lensletization. To yield meaningful optical modeling results, we provide insight into ray-tracing optimization while ensuring a sufficient signal-to-noise ratio. The results show that, given no discernable lensletization, the most compact configuration to image gray-scale images is the 5f-based system. Finally, simulations of the imaging of gray scale and color bitmaps through microlenslet arrays are demonstrated for the first time to our knowledge.

Journal Article↗

PubMed2003

Neural network training with global optimization techniques.

This paper presents an approach of using Simulated Annealing and Tabu Search for the simultaneous optimization of neural network architectures and weights. The problem considered is the odor recognition in an artificial nose. Both methods have produced networks with high classification performance and low complexity. Generalization has been improved by using the backpropagation algorithm for fine tuning. The combination of simple and traditional search methods has shown to be very suitable for generating compact and efficient networks.

Algorithms↗

PubMed2002

Large clusters in supercritical percolation.

The statistical behavior of the size of large finite clusters in supercritical percolation on a finite lattice is investigated (below the critical dimension of the space d(c)=6). For this purpose, an approximate system of ordinary differential equations for a number of finite clusters is obtained. The correlation between the critical exponents zeta that determine the cluster decay law (ln n(s) approximately -s(zeta)) and the surface of clusters is shown. It is found that for clusters without self-intersections having a maximal surface zeta=1. For clusters with a small number of self-intersections zeta=1-eta. Here eta is a function depending on the ratio of the surface area of a cluster to its size, which tends to zero, when the surface tends to a maximum. For compact clusters with a minimum or near-minimum surface area, the first correction to the cluster decay law above percolation threshold (ln n(s) approximately -s((d-1)/d)) has been found on the basis of the drop model and the derived system of equations. The predictions are tested numerically on two- and three-dimensional lattices by Monte Carlo simulations. The results of the work allow one to conclude that above the percolation threshold majority of large clusters are compact and that the cluster surface is the main factor affecting its behavior in supercritical percolation.

Journal Article↗

PubMedDate not supplied

Flexural and creep properties of human jaw compact bone for FEA studies.

The aim of this work was to improve the constitutive model of the human mandible and dentition system by taking into account the non-linear material properties of the structural boney matrix that forms the human jaw bone or mandible. Due to the specific structure of the jaw bone the time dependence of the mechanical properties also forms an important stage of the quantification process. The lack of specific experimental data of this type of material prevents the implementation of these properties into finite element simulations which results in poor quality modelling. Here an attempt was made to determine elastic and viscoelastic mechanical characteristics of the compact bone tissue forming the mandible. The elastic properties of compact bone were determined experimentally from 3 point bending tests and the viscoelastic properties were evaluated from creep tests in compression. A particular human jaw from this complex study was used to reconstruct a geometric model for further numerical experiments.

Aged↗

PubMed2004

Design and simulation of a high-resolution stationary SPECT system for small animals.

Exciting new SPECT systems can be created by combining pinhole imaging with compact high-resolution gamma cameras. These new systems are able to solve the problem of the limited sensitivity-resolution trade-off that hampers contemporary small animal SPECT. The design presented here (U-SPECT-III) uses a set of detectors placed in a polygonal configuration and a cylindrical collimator that contains 135 pinholes arranged in nine rings. Each ring contains 15 gold pinhole apertures that focus on the centre of the cylinder. A non-overlapping projection is acquired via each pinhole. Consequently, when a mouse brain is placed in the central field-of-view, each voxel in the cerebrum can be observed via 130 to 135 different pinholes simultaneously. A method for high-resolution scintillation detection is described that eliminates the depth-of-interaction problem encountered with pinhole cameras, and is expected to provide intrinsic detector resolutions better than 150 microm. By means of simulations U-SPECT-III is compared to a simulated dual pinhole SPECT (DP-SPECT) system with a pixelated array consisting of 2.0 x 2.0 mm NaI crystals. Analytic calculations indicate that the proposed U-SPECT-III system yields an almost four times higher linear and about sixty times higher volumetric system resolution than DP-SPECT, when the systems are compared at matching system sensitivity. In addition, it should be possible to achieve a 15 up to 30 times higher sensitivity with U-SPECT-III when the systems are compared at equal resolution. Simulated images of a digital mouse-brain phantom show much more detail with U-SPECT-III than with DP-SPECT. In a resolution phantom, 0.3 mm diameter cold rods are clearly visible with U-SPECT-III, whereas with DP-SPECT the smallest visible rods are about 0.6-0.8 mm. Furthermore, with U-SPECT-III, the image deformations outside the central plane of reconstruction that hamper conventional pinhole SPECT are strongly suppressed. Simulation results indicate that future pinhole SPECT systems are likely to bring about significant improvements in radio-molecular imaging of small animals.

Animals↗

PubMed1999

Simulation of the packing of idealized transmembrane alpha-helix bundles.

The aim of this study is to investigate if the packing motifs of native transmembrane helices can be produced by simulations with simple potentials and to develop a method for the rapid generation of initial candidate models for integral membrane proteins composed of bundles of transmembrane helices. Constituent residues are mapped along the helix axis in order to maintain the amino acid sequence-dependent properties of the helix. Helix packing is optimized according to a semi-empirical potential mainly composed of four components: a bilayer potential, a crossing angle potential, a helix dipole potential and a helix-helix distance potential. A Monte Carlo simulated annealing protocol is employed to optimize the helix bundle system. Necessary parameters are derived from theoretical studies and statistical analysis of experimentally determined protein structures. Preliminary testing of the method has been conducted with idealized seven Ala(20) helix bundles. The structures generated show a high degree of compactness. It was observed that both bacteriorhodopsin-like and delta-endotoxin-like structures are generated in seven-helix bundle simulations, within which the composition varies dependent upon the cooling rate. The simulation method has also been employed to explore the packing of N = 4 and N = 12 transmembrane helix bundles. The results suggest that seven and 12 transmembrane helix bundles resembling those observed experimentally (e.g., bacteriorhodopsin, rhodopsin and cytochrome c oxidase subunit I) may be generated by simulations using simple potentials.

Bacteriorhodopsins↗

PubMed2004

A reactive force field simulation of liquid-liquid phase transitions in phosphorus.

A force field model of phosphorus has been developed based on density functional (DF) computations and experimental results, covering low energy forms of local tetrahedral symmetry and more compact (simple cubic) structures that arise with increasing pressure. Rules tailored to DF data for the addition, deletion, and exchange of covalent bonds allow the system to adapt the bonding configuration to the thermodynamic state. Monte Carlo simulations in the N-P-T ensemble show that the molecular (P(4)) liquid phase, stable at low pressure P and relatively low temperature T, transforms to a polymeric (gel) state on increasing either P or T. These phase changes are observed in recent experiments at similar thermodynamic conditions, as shown by the close agreement of computed and measured structure factors in the molecular and polymer phases. The polymeric phase obtained by increasing pressure has a dominant simple cubic character, while the polymer obtained by raising T at moderate pressure is tetrahedral. Comparison with DF results suggests that the latter is a semiconductor, while the cubic form is metallic. The simulations show that the T-induced polymerization is due to the entropy of the configuration of covalent bonds, as in the polymerization transition in sulfur. The transition observed with increasing P is the continuation at high T of the black P to arsenic (A17) structure observed in the solid state, and also corresponds to a semiconductor to metal transition.

Journal Article↗

PubMed2006

Chemical surface modification of high-strength porous Ti compacts by spark plasma sintering.

The biological properties of a titanium (Ti) implant depend on its surface oxide film. The aims of the present study were to increase the specific surface oxide area on Ti using a porous structure and to study the relationship between the amount of apatite coating in simulated body fluid (SBF) and the actual surface area on titanium powders. Ti powders of 110 microm average diameter were sintered by spark plasma sintering. The sintered compacts had a porosity of 28%, a compressive elastic modulus of 7.9 GPa and an ultimate strength of 112 MPa. The compressive strength of the compacts was increased to 588 MPa by subsequent annealing in a vacuum furnace at 1000 degrees C for 24 h. The sintered compacts were treated with aqueous NaOH solution and subsequently heated at 600 degrees C. The pretreated compacts showed apatite crystal precipitation in SBF. The amounts of precipitates through the compacts were compared with those of the Ti plate substrates subjected to the same chemical pretreatment. It was confirmed that the amounts of precipitates through the compacts were more than one hundred times higher than those on the Ti plates. It was concluded that the metal porous compacts developed may be used as functional materials for immobilizing functional proteins and/or drugs, because the precipitated apatite can adsorbed these substances.

Apatites↗

PubMed2025

RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.

RNA G-quadruplexes (rG4s) are emerging as vital structural elements involved in processes like gene regulation, translation, and genome stability. Found in untranslated regions of messenger RNAs (mRNAs), they influence translation efficiency and mRNA localization. Additionally, rG4s of long noncoding RNAs and telomeric RNA play roles in RNA processing and cellular aging. Despite their significance, the atomic-level folding mechanisms of rG4s remain poorly understood due to their complexity. We studied the folding of the r(GGGA)3GGG and r(GGGUUA)3GGG (TERRA) sequences into parallel-stranded rG4 using all-atom enhanced-sampling molecular dynamics simulations, applying well-tempered metadynamics coupled with solute tempering. The obtained folding pathways suggest that RNA initially adopts a compacted coil-like ensemble characterized by dynamic guanine stacking and pairing. The three-quartet rG4 gradually forms from this compacted coil ensemble via diverse routes involving strand rearrangements and guanine incorporations. While the folding mechanism is multipathway, various two-quartet rG4 structures appear to be a common transitory ensemble along most routes. Thus, the process seems more complex than previously predicted, as G-hairpins or G-triplexes do not act as distinct intermediates, even though some are occasionally sampled. We also discuss the challenges of applying enhanced sampling methodologies to such a multidimensional free-energy surface and address the force-field limitations.

G-Quadruplexes↗

PubMed2004

Multiple probes reveal a native-like intermediate during low-temperature refolding of ubiquitin.

We investigate the refolding of ubiquitin Phe45Trp/Ile61Ala (Ub(*)I61A) in a low-temperature, high-viscosity buffer, where folding is slowed so that apparent two-state and three-state mechanisms are readily distinguishable. Ub(*)I61A forms a compact ensemble rapidly (as judged from stopped-flow, small-angle X-ray scattering) with a secondary structure signature similar to that of the native state (as judged from stopped-flow circular dichroism from 215 nm to 250 nm), but the fluorescence signature still resembles the guanidinium-denatured state. The compact ensemble forms over a range of solvent and temperature conditions. The native fluorescence signature, which requires the tryptophan residue to be packed tightly, is acquired at least 500 times more slowly. Molecular dynamics simulations at 495 K show no contraction of the backbone in ethylene glycol buffer compared to pure aqueous buffer, and no significant effect on the local backbone structure of the unfolded protein. Only at higher simulation temperature does a backbone contraction appear. Thus, it appears unlikely that the aqueous ethylene glycol buffer fundamentally changes the folding mechanism of ubiquitin. We suggest that ubiquitin forms a compact ensemble with native-like secondary structure, but without tight packing, long before the native state.

Circular Dichroism↗

PubMed1999

Fatigue-crack propagation in Nitinol, a shape-memory and superelastic endovascular stent material.

Improving the design and performance of medical stents for implantation in the human body is of current interest. This paper describes a study of fatigue-crack propagation behavior in the superelastic alloy Nitinol. Specifically, the objective of this work was to study the effect of environment on cyclic crack-growth resistance in an approximately 50Ni-50Ti (atom %) alloy and to provide the necessary data for the safe life prediction of Nitinol endovascular stents. The material selected for this study was heat treated such that it was superelastic at human body temperature; this was confirmed with monotonic uniaxial tensile tests. Characterization of fatigue-crack growth rates was performed at 37 degrees C on disk-shaped compact-tension samples in environments of air, aerated deionized water, and aerated Hank's solution (a simulated body fluid). The effect of cyclic loading on the uniaxial constitutive behavior was investigated at a strain range of 6.4%, and results indicate that the magnitude of available superelastic strain ( approximately 5.0%) is maintained even after cyclic softening. However, despite the persistence of nucleating the stress-induced martensitic phase after cycling with a maximum strain slightly below the plastic yield point, Nitinol was found to have the lowest fatigue-crack growth resistance of the principal metallic alloys currently used for implant applications.

Alloys↗

PubMedDate not supplied

Crystal structure of chicken liver basic fatty acid-binding protein at 2.7 A resolution.

The three-dimensional structure of chicken liver basic fatty acid-binding protein has been determined at 2.7 A resolution by X-ray crystallography. Phases were calculated using the multiple isomorphous replacement procedure and a preliminary model was built. This model, with an initial R-factor of 0.57, was then improved by a cycle of refinement by simulated annealing which brought the R factor down to 0.32. The protein is structured as a compact 10-stranded-beta-barrel which encapsulates a residual electron density that can be interpreted as a fatty acid molecule. The NH2-terminus portion of the molecule contains two short alpha-helices. The structure of this liver protein appears very similar to that of the Escherichia coli derived rat intestinal FABP recently determined by X-ray diffraction methods.

Animals↗