Crossover from fractal to compact growth from simulations of two-phase flow with finite viscosity ratio in two-dimensional porous media.
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Journal Article↗
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Crossover from fractal to compact flow from simulations of two-phase flow with finite viscosity ratio in two-dimensional porous media.
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Journal Article↗
[Studies on packing of powder. IV. The use of digital computer for simulation of powder compaction on two-dimensional model (author's transl)].
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Chemical Phenomena↗
[Studies on packing of powder. VII. The use of digital computer for simulation of powder compaction on two-dimensional model (author's transl)].
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Computers↗
Comments on 'compact bone: numerical simulation of mechanical characteristics'.
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Algorithms↗
Microscopic two-dimensional lattice model of dimer granular compaction with friction.
We study by Monte Carlo simulation the compaction dynamics of hard dimers in two dimensions under the action of gravity, subjected to vertical and horizontal shaking, considering also the case in which a friction force acts for horizontal displacements of the dimers. These forces are modeled by introducing effective probabilities for all kinds of moves of the particles. We analyze the dynamics for different values of the time tau during which the shaking is applied to the system and for different intensities of the forces. It turns out that the density evolution in time follows a stretched exponential behavior if tau is not very large, while a power law tail develops for larger values of tau. Moreover, in the absence of friction, a critical value tau(*) exists, which signals the crossover between two different regimes: for tau tau(*) it reaches logarithmically a maximal saturation value. Such behavior smears out when a finite friction force is present. In this situation the dynamics is slower and lower asymptotic densities are attained. In particular, for significant friction forces, the final density decreases linearly with the friction coefficient. We also compare the frictionless single tap dynamics to the sequential tapping dynamics, observing in the latter case an inverse logarithmic behavior of the density evolution, as found in the experiments.
Journal Article↗
Correlation between changes in nuclear magnetic resonance order parameters and conformational entropy: molecular dynamics simulations of native and denatured staphylococcal nuclease.
Recent work has suggested that changes in NMR order parameters may quantitatively reflect changes in the conformational entropy of a protein ensemble. The extent of the mathematical relationship between local entropy changes as seen by NMR order parameters and the full protein entropy change is a complex issue. As a step towards a fuller understanding of this problem, molecular dynamics calculations of both native and denatured staphylococcal nuclease were performed. The N-H bond vector motion, in both explicit and implicit solvent, was analyzed to estimate local and global entropy changes. The calculated N-H bond vector order parameters from simulation agreed on average with experimental values for both native and denatured structures. However, the inverted-U profile of order parameters versus residue number observed experimentally for denatured nuclease was only partially reproduced by simulation of compact denatured structures. Comparisons made across the full set of simulations revealed a correlation between the N-H order parameter-based conformational entropy change and the total quasiharmonic-based conformational entropy change between the native and denatured structures. The calculations showed that about 25% of the total entropy change was reflected by changes in simulated S2 values. This result suggests that NMR-derived order parameters may be used to provide a reasonable estimate of the total conformational entropy change on protein folding.
Magnetic Resonance Spectroscopy↗
Bone-like apatite layer formation on hydroxyapatite prepared by spark plasma sintering (SPS).
Hydroxyapatite (HA) compacts with high density and superior mechanical properties were fabricated by spark plasma sintering (SPS) using spray-dried HA powders as feedstock. The formation of bone-like apatite layer on SPS consolidated HA compacts were investigated by soaking the HA compacts in simulated body fluid (SBF) for various periods (maximum of 28 days). The structural changes in HA post-SBF were analyzed with scanning electron microscopy, grazing incidence X-ray diffraction and X-ray photoelectron spectroscopy. It was found that a layer consisting microcrystalline carbonate-containing hydroxyapatite was formed on the surface of HA compacts after soaking for 24h. The formation mechanism of apatite on the surface of HA compacts after soaking in SBF was attributed to the ion exchange between HA compacts and the SBF solution. The increase in ionic concentration of calcium and phosphorus as well as the increase in pH after SBF immersion resulted in an increase in ionic activity product of apatite in the solution, and provided a specific surface with a low interface energy that is conducive to the nucleation of apatite on the surface of HA compacts.
Apatites↗
Molecular dynamics simulation of interaction of histone-like protein of mycobacterium tuberculosis (Hlpmt) and histone of clostridium pasteurianum (DBHclopa) with 35 based paired GC rich U-bend DNA.
Three dimensional structure of the first ninety two residues of histone like protein from Mycobacterium tuberculosis (Hlpmt) and histone of Clostridium pasteurianum (DBHclopa) are obtained here, on the basis of amino acid sequences of the two proteins, making use of secondary structure prediction programs, sequence search and HOMOLOGY based modeling tools available on Internet. The proteins were docked to a 35 base paired GC rich U bend DNA (U35DNA). Structures of proteins Hlpmt and DBHclopa; U35DNA; and complexes: Hlpmt-U35DNA and DBHclopa-U35DNA were optimized by molecular mechanics (MM) and simulated for 260 pico seconds (ps) in vacuum by molecular dynamics (MD) technique using AMBER 4.0 package with Cornell et al force field. The proteins, when simulated alone, showed compaction. DBHclopa showed larger compaction compared with Hlpmt. U35DNA when simulated alone straightened out and assumed a B-form. In the complexes, Hlpmt showed same order of compaction as in absence of DNA, while DBHclopa showed reduced compaction. In the presence of Hlpmt two ends of helicoidal axis of U35DNA came closer, but slightly out of plane, indicative of its role in overwinding and packaging double stranded DNA. DBHclopa did not give rise to DNA overwinding. The results show architectural role of Hlpmt and DBHclopa in DNA packaging and its sequence dependence.
Amino Acid Sequence↗
Compaction of anisotropic granular materials: experiments and simulations.
We present both experimental and numerical investigations of compaction in granular materials composed of rods. As a function of the particles size and with respect to the container diameter, we have observed large variations of the asymptotic packing volume fraction. The relevant parameter is the ratio between the rod length l and the tube diameter D . Even the compaction dynamics remains unchanged for various particle lengths, and a transition between 3d and 2d ordering for grain orientations is observed for l/D=1 . A toy model for the compaction of needles on a lattice is also proposed. This toy model gives a complementary view of our experimental results and leads to behaviors similar to experimental ones.
Journal Article↗
Predicting the tolerance of proteins to random amino acid substitution.
We have recently proposed a thermodynamic model that predicts the tolerance of proteins to random amino acid substitutions. Here we test this model against extensive simulations with compact lattice proteins, and find that the overall performance of the model is very good. We also derive an approximate analytic expression for the fraction of mutant proteins that fold stably to the native structure, Pf(m), as a function of the number of amino acid substitutions m, and present several methods to estimate the asymptotic behavior of Pf(m) for large m. We test the accuracy of all approximations against our simulation results, and find good overall agreement between the approximations and the simulation measurements.
Amino Acid Sequence↗
Dopaminergic neuronal survival and the effects of bFGF in explant, three dimensional and monolayer cultures of embryonic rat ventral mesencephalon.
Embryonic substantia nigra cells when transplanted into the striatum can reverse many of the defects of Parkinson's disease. The efficacy of such grafts is compromised by the poor survival of grafted dopaminergic neurones; typically, 3-10% survive transplantation. We used three tissue culture models to identify stages in the procedure for the preparation and insertion of grafts which might be responsible for this cell death and to identify environments in which survival is optimised. (1) The ventral mesencephalon was dissected from the donor brain, then placed immediately into culture contained in a collagen gel. (2) The dissected tissue fragments were enzymatically dissociated, then the cells placed into monolayer culture. (3) Enzymatically dissociated tissue was packed into 0.5-mm-diameter porous tubes, to simulate the compaction of cells into a graft deposit in the host brain. Dissociation of the tissue by itself caused the death of approximately 30% of dopaminergic neurones, as judged by the difference in cell counts between the intact embryonic day 14 (E14) mesencephalon, and cells dissociated then packed into tubes. Of the dissociated neurones approximately 60% died during the first 24 h and 87% during the first 3 days in monolayer culture, while only 7% of dopaminergic neurones in three-dimensional cultures and 11% of neurones in explant cultures died over the first 3 days. Embryonic dopaminergic neurones are clearly very vulnerable to adverse conditions during the first days after their removal from the donor brain. The excellent survival of neurones in three-dimensional and explant cultures indicates that close association with other cells, which may provide greatly improved access to trophic factors, can enable the cells to survive this period of vulnerability. In contrast to its effects in monolayer cultures, bFGF had no effect on dopaminergic neuronal survival in either explant or three-dimensional cultures.
Animals↗
An on-line algorithm for creating self-organizing fuzzy neural networks.
This paper presents a new on-line algorithm for creating a self-organizing fuzzy neural network (SOFNN) from sample patterns to implement a singleton or Takagi-Sugeno (TS) type fuzzy model. The SOFNN is based on ellipsoidal basis function (EBF) neurons consisting of a center vector and a width vector. New methods of the structure learning and the parameter learning, based on new adding and pruning techniques and a recursive on-line learning algorithm, are proposed and developed. A proof of the convergence of both the estimation error and the linear network parameters is also given in the paper. The proposed methods are very simple and effective and generate a fuzzy neural model with a high accuracy and compact structure. Simulation work shows that the SOFNN has the capability of self-organization to determine the structure and parameters of the network automatically.
Algorithms↗
On the significance of the vector potential squared.
We consider the gauge potential A and argue that the minimum value of the volume integral of A2 (in Euclidean space) may have physical meaning, particularly in connection with the existence of topological structures. A lattice simulation comparing compact and noncompact "photodynamics" shows a jump in this quantity at the phase transition, supporting this idea.
Journal Article↗
Quantitative trait loci for root-penetration ability and root thickness in rice: comparison of genetic backgrounds.
Drought is the major abiotic stress limiting rice (Oryza sativa) production and yield stability in rainfed lowland and upland ecosystems. Root systems play an important role in drought resistance. Incorporation of root selection criteria in drought resistance improvement is difficult due to lack of reliable and efficient screening techniques. Using a wax-petrolatum layer system simulated to compacted soil layers, root traits were evaluated in a doubled haploid (DH) population derived from the cross between 'IR64' and 'Azucena'. Twelve putative QTLs (quantitative trait loci) were detected by interval mapping comprising four QTLs for root-penetration ability, four QTLs for root thickness, two QTLs for penetrated root number, and two QTLs for total root number. These QTLs individually explained 8.4% to 16.4% of the phenotypic variation. No QTL was detected for maximum penetrated root length by interval mapping. One QTL located between RG104 and RG348 was found to influence both root-penetration ability and root thickness. QTLs for root-penetration ability and root thickness were compared across two populations, 'IR64'-'Azucena' and 'CO39'-'Moroberekan', and different testing conditions. The identified consistent QTLs could be used for marker-assisted selection for deep and thick roots with high root-penetration ability in rice.
Oryza↗
Influence of ambient moisture on the compaction behavior of microcrystalline cellulose powder undergoing uni-axial compression and roller-compaction: a comparative study using near-infrared spectroscopy.
This study evaluates the effect of variation in the ambient moisture on the compaction behavior of microcrystalline cellulose (MCC) powder. The study was conducted by comparing the physico-mechanical properties of, and the near infrared (NIR) spectra collected on, compacts prepared by roller compaction with those collected on simulated ribbons, that is, compacts prepared under uni-axial compression. Relative density, moisture content, tensile strength (TS), and Young modulus were used as key sample attributes for comparison. Samples prepared at constant roller compactor settings and feed mass showed constant density and a decrease in TS with increasing moisture content. Compacts prepared under uni-axial compression at constant pressure and compact mass showed the opposite effect, that is, density increased while TS remained almost constant with increasing moisture content. This suggests difference in the influence of moisture on the material under roller compaction, in which the roll gap (i.e., thickness and therefore density) remains almost constant, vs. under uni-axial compression, in which the thickness is free to change in response to the applied pressure. Key sample attributes were also related to the NIR spectra using multivariate data analysis by the partial least squares projection to latent structures (PLS). Good agreement was observed between the measured and the NIR-PLS predicted values for all key attributes for both, the roller compacted samples as well as the simulated ribbons.
Cellulose↗
Temporal variations in cell migration and traction during fibroblast-mediated gel compaction.
Current models used in our laboratory to assess the migration and traction of a population of cells within biopolymer gels are extended to investigate temporal changes in these parameters during compaction of mechanically constrained gels. The random cell migration coefficient, micro (t) is calculated using a windowing technique by regressing the mean-squared displacement of cells tracked at high magnification in three dimensions with a generalized least squares algorithm for a subset of experimental time intervals, and then shifting the window interval-by-interval until all time points are analyzed. The cell traction parameter, tau(0)(t), is determined by optimizing the solution of our anisotropic biphasic theory to tissue equivalent compaction. The windowing technique captured simulated sinusoidal and step changes in cell migration superposed on a persistent random walk in simulated cell movement. The optimization software captured simulated time dependence of compaction on cell spreading. Employment of these techniques on experimental data using rat dermal fibroblasts (RDFs) and human foreskin fibroblasts (HFFs) demonstrated that these cells exhibit different migration-traction relationships. Rat dermal fibroblast migration was negatively correlated to traction, suggesting migration was not the driving force for compaction with these cells, whereas human foreskin fibroblast migration was positively correlated to traction.
Algorithms↗
The compactEASIE is a feasible training model for endoscopic novices: a prospective randomised trial.
BACKGROUND: The objective benefit of a training using the compact Erlangen Active Simulator for Interventional Endoscopy-simulator was demonstrated in two prospective educational trials (New York, France). The present study analysed whether endoscopic novices are able to reach a comparable level of endoscopic skills as in the above-described projects. METHODS: Twenty-seven endoscopic novices (medical students, first year residents) were enrolled in this prospective, randomised trial. The compact Erlangen Active Simulator for Interventional Endoscopy-simulator with an upper GI-organ package and blood perfusion system was used as a training tool. Basic evaluation of endoscopic skills was performed after a practical and theoretical course in diagnostic upper GI endoscopy followed by a stratified randomisation according to the rating in endoscopic skills into intensive (n=14) and control group (n=13). The intensive group was trained 12 times every second week over 7 months in 4 endoscopic disciplines (manual skills, injection therapy, haemoclip, band ligation) by skilled endoscopist (three trainees/simulator). Assessment was performed (single steps/overall) using an analogue scale from 1 to 10 (1=worst, 10=optimal performance) by expert tutors. The control group was not trained. Blinded final evaluation of all participants was performed in January 2003. RESULTS: We observed in all techniques applied a significant improvement of endoscopic skills and of the performance time in the intensive group compared to the control group (p<0.001). The comparison with the previous projects showed that the intensively trained novices achieved comparable levels of performance to the GI fellows in the New York and France Project (at least 80% of the median score in three out of four techniques). CONCLUSION: Endoscopic novices acquired notable skills in interventional endoscopy in the simulator by an intensive, periodical training using the compactEASIE.
Clinical Competence↗