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At least 433 records · Page 24Linked to original sources
PubMed1991

A practical method to integrate some stiff systems.

A compact, absolutely stable numerical method is presented to integrate stiff systems of pseudo-linear, ordinary, first-order differential equations, commonly found in the simulation of biological models. Solutions are stepwise approximated by a complete set of first order rational polynomials. Mass balance is preserved by the approximations. No matrix inversions are required. Besides being stable, the method is also convergent and can be used with deferred approximation to the limit h = 0. Comparisons between this method and the Stoer-Bullirsch algorithm and fourth-order Runge-Kutta method are presented.

Algorithms↗
PubMed1993

Differential stability of beta-sheets and alpha-helices in beta-lactamase: a high temperature molecular dynamics study of unfolding intermediates.

beta-Lactamase, which catalyzes beta-lactam antibiotics, is prototypical of large alpha/beta proteins with a scaffolding formed by strong noncovalent interactions. Experimentally, the enzyme is well characterized, and intermediates that are slightly less compact and having nearly the same content of secondary structure have been identified in the folding pathway. In the present study, high temperature molecular dynamics simulations have been carried out on the native enzyme in solution. Analysis of these results in terms of root mean square fluctuations in cartesian and [phi, psi] space, backbone dihedral angles and secondary structural hydrogen bonds forms the basis for an investigation of the topology of partially unfolded states of beta-lactamase. A differential stability has been observed for alpha-helices and beta-sheets upon thermal denaturation to putative unfolding intermediates. These observations contribute to an understanding of the folding/unfolding processes of beta-lactamases in particular, and other alpha/beta proteins in general.

Enzyme Stability↗
PubMed1987

Comparative morphology, histology and growth of the dental plates of the Devonian dipnoan Chirodipterus.

The dental plates of the Devonian lungfish Chirodipterus australis Miles (Osteichthyes; Dipnoi) are shown to have achieved their characteristic morphology by a growth process different from that assumed for the plates of genera such as Dipterus. Each plate was thickened by the addition of layers of bone that also extended the plate labially, thus providing the base on which and into which dentine grew. Distinctive features of the dentition are: (a) labial increase of the dentine mass by the addition of blister-like denticles of simple enamel-covered dentine, which is initially ingrown by pleromic dentine and subsequently resorbed and replaced by petrodentine; (b) increase in the midline by a similar process that results in the addition of one (or possibly two) new ridges; (c) resorption of the posterior edge of the pterygoid plates and the posterior and posteromedial edges of the prearticular plates, with subsequent development over the resorbed surfaces of several generations of simple regenerative dentine; (d) resorption and redeposition of pleromic dentine and bone in a triangular region posteromedially on the pterygoid plates; (e) the formation of tuberosities that simulate teeth at a short distance in from the labial edge, by four processes: formation of an undulating plate margin, differential growth of petrodentine (hard compact dentine) within the pulp cavity, differential wear of the petrodentine and the adjacent bone plus pleromic dentine, and slightly greater growth of the petrodentine towards the occlusal surface relative to the adjacent bone and dentine; (f) expansion of the large flat surfaces of the plates by gradual replacement of the bone and dentine at the proximal ends of the furrows and also by the development of linkages of petrodentine across the furrows; (g) development of isolated tuberosities on the flat posterolateral parts of the plates. The petrodentine of the ridges, tuberosities and plateaus of the plates is indistinguishable structurally and in its mode of growth from the petrodentine in extant species of dipnoans. Plates similar to those of C. australis have been observed in Stomiahykus, Archaeonectes, Conchodus, Palaedaphus and Sunwapta, as well as several species usually referred to as Dipterus. Sunwapta may be congeneric with C. australis.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗
PubMed2004

Molecular dynamics simulation of the transition from dispersed to solid phase.

Molecular dynamics simulations in two dimensions of particles interacting with finite potentials comparable to k(B)T yield aggregates which cross over from a fractal to a compact crystalline morphology. Growth kinetics and aggregate size distributions evolve from nonequilibrium to equilibrium limits.

Journal Article↗
PubMed1982

Studies in cutaneous aging: I. The elastic fiber network.

We studied by light and electron microscopy the elastic fibers in he sun exposed and sun protected skin of normal and psoriatic individuals of different ages in order to separate the changes of actinic damage from those of chronological aging. The sun exposed skin showed 2 types of elastic fiber abnormalities-one related to actinic damage and the other to chronological aging. The sun protected buttock skin showed only the latter. From ages 30 to 70, a minority of the elastic fibers exhibited abnormalities that appeared to represent a process of fiber disintegration. After age 70, the majority of elastic fibers showed these abnormalities. These abnormalities were present without accompanying inflammatory cells. Also, there was morphological evidence of continuing synthesis of elastic fibers during the lifetime of these subjects, except that from ages 50-93, the fibers appeared to be loosely, rather than compactly, assembled. Incubation of dermal slices from buttock skin of young adults with porcine pancreatic elastase and bovine chymotrypsin produced elastic fiber degradation that closely simulated the changes that were observed in aged sun protected skin. We propose that one of the features of cutaneous aging is a slow, spontaneous, progressive degradative process inherent in the elastic fiber that can be enzymatically accelerated from decades to hours by elastase and chymotrypsin.

Adolescent↗
PubMedDate not supplied

Rabbit tissue model (RTM) harvesting technique.

A method for creating a tissue model using a female rabbit for laparoscopic simulation exercises is described. The specimen is called a Rabbit Tissue Model (RTM). Dissection techniques are described for transforming the rabbit carcass into a small, compact unit that can be used for multiple training sessions. Preservation is accomplished by using saline and refrigeration. Only the animal trunk is used, with the rest of the animal carcass being discarded. Practice exercises are provided for using the preserved organs. Basic surgical skills, such as dissection, suturing, and knot tying, can be practiced on this model. In addition, the RTM can be used with any pelvic trainer that permits placement of larger practice specimens within its confines.

Animals↗
PubMed2004

[Effect of soil tillage on phosphorus loss from slope land: an experimental study].

Intensive soil erosion and nutrient loss from slope land not only resulted in the serious degradation of soil quality, but also threatened the water environment of the lower area. In this paper, a simulated rainfall experiment with loessial soil was conducted to study the characteristics of the loss of different phosphorus forms under the conditions of tillage and compaction (no-tillage). The results showed that in comparing with compaction, tillage increased the loss of dissolved P(DP), sediment extractable P(SEP) and sediment total P(STP) by 10 times due to the increase of runoff and sediment amount. The forms of the lost P were mainly sediment-combined P, and the ratios of DP/BAP and BAP/TP in the lost runoff were 12% and 2.6% under compaction, and 15% and 2.4% under tillage, respectively. The application of no-tillage or mulch-keeping fallow in Summer was effective to decrease soil and nutrient loss from slope land, which would be effective and significant both to soil degradation prevention and water environment protection in the lower area of Loess Plateau.

Conservation of Natural Resources↗
PubMed2002

The energy landscape of unsolvated peptides: helix formation and cold denaturation in Ac-A4G7A4 + H+.

Ion mobility measurements and molecular dynamics simulations were performed for unsolvated A4G7A4 + H+ and Ac-A4G7A4 + H+ (Ac = acetyl, A = alanine, G = glycine) peptides. As expected, A4G7A4 + H+ adopts a globular conformation (a compact, random-looking, three-dimensional structure) over the entire temperature range examined (100-410 K). Ac-A4G7A4 + H+ on the other hand is designed to have a flat energy landscape with a marginally stable helical state. This peptide shows at least four different conformations at low temperatures (<230 K). The two conformations with the largest cross sections are attributed to - and partial -helices, while the one with the smallest cross section is globular. The other main conformation may be partially helical. Ac-A4G7A4 + H+ becomes predominantly globular at intermediate temperatures and then becomes more helical as the temperature is raised further. This unexpected behavior may be due to the helix having a higher vibrational entropy than the globular state, as predicted by some recent calculations (Ma, B.; Tsai, C.-J.; Nussinov, R. Biophys. J. 2000, 79, 2739-2753).

Alanine↗
PubMed1994

Lattice model simulations of polypeptide chain folding.

Simulated annealing methods are applied to simple cubic lattice C alpha models of eight small monomeric globular proteins and their transition from a random chain to a low energy compact state is examined. The lowest energy structures are compared to their crystal forms using coordinate distance deviations, dRMS and RMS, and by distance contact maps. Analysis of the transition region indicates that, for this model, collapse begins with a rapid decline in radius of gyration followed continuously by chain repackings that lead to progressively lower values of chain energy. Chain repackings represent a highly cooperative interplay between the formation of local and non-local interactions. The components of this transition are characterized by rapid relaxation of shorter chain segments to form local contacts and slower relaxations of longer chain segments to form non-local contacts. Final structures obtained with this procedure contain many of the gross topologies of their native structures.

Computer Simulation↗
PubMed2003

Computational simulation of the statistical properties of unfolded proteins.

A simple Monte Carlo method was used to generate ensembles of simulated polypeptide conformations that are restricted only by steric repulsion. The models used for these simulations were based on the sequences of four real proteins, ranging in size from 26 to 268 amino acid residues, and included all non-hydrogen atoms. Two sets of calculations were performed, one that included only intra-residue steric repulsion terms and those between adjacent residues, and one that included repulsion terms between all possible atom pairs, so as to explicitly account for the excluded volume effect. Excluded volume was found to increase the average radius of gyration of the chains by 20-40%, with the expansion factor increasing with chain length. Contrary to recent suggestions, however, the excluded volume effect did not greatly restrict the distribution of dihedral angles or favor native-like topologies. The average dimensions of the ensembles calculated with excluded volume were consistent with those measured experimentally for unfolded proteins of similar sizes under denaturing conditions, without introducing any adjustable scaling factor. The simulations also reproduced experimentally determined effective concentrations for the formation of disulfide bonds in reduced and unfolded proteins. The statistically generated ensembles included significant numbers of conformations that were nearly as compact as the corresponding native proteins, as well as many that were as accessible to solvent as a fully extended chain. On the other hand, conformations with as much buried surface area as the native proteins were very rare, as were highly extended conformations. These results suggest that the overall properties of unfolded proteins can be usefully described by a random coil model and that an unfolded polypeptide can undergo significant collapse while losing only a relatively small fraction of its conformational entropy.

Biophysical Phenomena↗
PubMed2005

Embryo development and survival in beef cattle administered ergotamine tartrate to simulate fescue toxicosis.

Two experiments were performed to determine whether administration of ergotamine tartrate altered embryo development (Exp. 1) and uterine competency to establish pregnancy (Exp. 2) in beef cattle. Animals were fed daily either 0 (CON) or 40 mug/kg body weight of ergotamine tartrate (ERGOT). Following a 30-d period on respective diets, animals in Exp. 1 were artificial inseminated at estrus (d = 0) and single embryo recoveries performed on day 7; whereas, animals in Exp. 2 received two frozen-thawed embryos on day 7. As an indicator of ergotamine effects, prolactin was decreased throughout both experiments in ERGOT compared to CON animals (p<0.05). Furthermore, rectal temperature (RT) tended to increase during both experiments in ERGOT compared to CON (p= 0.06). In Exp. 1, embryo recovery (p=0.08) and the percentage of transferable embryos (p=0.09) tended to be greater for CON than for ERGOT. Percentage of embryos that developed to compacted morula or greater was increased for CON compared to ERGOT heifers (p<0.05). In Exp. 2, pregnancy rates of transferred embryos did not differ between treatment groups. Thus, administration of ERGOT to simulate fescue toxicosis altered developmental potential of embryos, but does not appear to affect uterine competency to establish pregnancy.

Animals↗
PubMed1997

Molecular dynamics simulations of Leu-enkephalin in water and DMSO.

The structure of Leu-enkephalin (L-Enk) and Met-enkephalin (M-Enk) have frequently been studied, in particular by nuclear magnetic resonance spectroscopy. After more than 20 years of research, it was concluded that enkephalins have no preferred structure in aqueous solution, but that they may have in other solvents. We have performed molecular dynamics simulations of zwitterionic L-Enk in water, and zwitterionic as well as neutral L-Enk dimethyl sulfoxide (DMSO). In water the peptide is very flexible, although there seems to be a preference for compact conformations. In DMSO, the peptide forms a clear salt bridge in the zwitterionic form, but has no preferred conformation in the neutral form. This difference in conformation may provide an explanation for measurements in DMSO in which multiple conformations were found to exist. In this paper we introduce a new formulation for a dihedral angle autocorrelation function, and apply it to study side-chain dynamics in L-Enk. We find that the side-chain dynamics of the large Tyr and Phe residues cannot be adequately sampled in 2.0-ns simulations, while this does seem to be possible for the smaller Leu side chain.

Dimethyl Sulfoxide↗
PubMed2006

Dynamics of Asp23-Lys28 salt-bridge formation in Abeta10-35 monomers.

In the amyloid fibrils formed from long fragments of the amyloid beta-protein (Abeta-protein), the monomers are arranged in parallel and lie perpendicular to the fibril axis. The structure of the monomers satisfies the amyloid self-organization principle; namely, the low free energy state of the monomer maximizes the number of intra- and interpeptide contacts and salt bridges. The formation of the intramolecular salt bridge between Asp(D)23 and Lys(K)28 ensures that unpaired charges are not buried in the low-dielectric interior. We have investigated, using all-atom molecular dynamics simulations in explicit water, whether the D23-K28 interaction forms spontaneously in the isolated Abeta10-35 monomer. To validate the simulation protocol, we show, using five independent trajectories spanning a total of 100 ns, that the pKa values of the titratable groups are in good agreement with experimental measurements. The computed free energy disconnectvity graph shows that broadly the ensemble of compact random coil conformations can be clustered into four basins that are separated by free energy barriers ranging from 0.3 to 2.7 kcal/mol. There is significant residual structure in the conformation of the peptide in each of the basins. Due to the desolvation penalty, the structural motif with a stable turn involving the residues VGSN and a preformed D23-K28 contact is a minor component of the simulated structures. The extent of solvation of the peptides in the four basins varies greatly, which underscores the dynamical fluctuations in the monomer. Our results suggest that the early event in the oligomerization process must be the expulsion of discrete water molecules that facilitates the formation of interpeptide-interaction-driven stable structures with an intramolecular D23-K28 salt bridge and an intact VGSN turn.

Amyloid beta-Peptides↗
PubMedDate not supplied

[Influence of cartilage cap modelling on FEM simulation of femoral head stress].

The present study reports on the finite element analysis (FEA) of the femoral head in a process of preparation for a program for the realistic simulation of correctional osteotomies of the proximal femur. While the material properties have been studied extensively, only few publications consider the influence of the cartilage layer geometry on FE stimulation of the hip joint. Various models of the femoral head with and without the cartilage layer are generated and analysed. On looking at the maximum surface stresses, we found a strong influence of the cartilage layer and the subchondral osseous layer on the magnitude of the von Mises equivalent stress. The model with an anatomically realistic cartilage layer and compact bone shows stresses of between 4 and 5.5 MPa, depending on the position of the joint, while the model with a concentric cartilage layer has a maximum von Mises stress of 0.8 MPa. Only on simulation of a "realistic" cartilage layer, with a maximum thickness at the "pole" and minimum thickness at the "equator" do the changes in stress distribution--determined by changes in the position of the femoral head--become visible. Owing to major artefacts and the inability to create a realistic cartilage layer, voxel-based models of the femur are not suitable for the simulation of the femoral head surface.

Cartilage, Articular↗
PubMed2005

Memory effects in vibrated granular systems: response properties in the generalized random sequential adsorption model.

We investigate, by numerical simulation, the dynamical response of a granular system to an abrupt change in shaking intensity within the framework of the reversible random sequential adsorption models. We analyse the two-dimensional lattice model in which, in addition to the adsorption-desorption process, there is diffusion of the adsorbed particles on the surface. Our model reproduces qualitatively the densification kinetics and the memory effects of vibrated granular materials. An interpretation of the simulation results is provided by the analysis of the insertion probability function. The importance of the diffusional relaxation is discussed. We conclude that a complex time-evolution of the density could be explained as a consequence of the variation of the diffusion rate during the compaction. We study the nonequilibrium time-dependent density-density autocorrelation function and show that the model displays out-of-equilibrium dynamical effects such as aging.

Adsorption↗
PubMed1994

Cyclic fatigue and fracture in pyrolytic carbon-coated graphite mechanical heart-valve prostheses: role of small cracks in life prediction.

A fracture-mechanics based study has performed to characterize the fracture toughness and rates of cyclic fatigue-crack growth of incipient flaws in prosthetic heart-valve components made of pyrolytic carbon-coated graphite. Such data are required to predict the safe structural lifetime of mechanical heart-valve prostheses using damage-tolerant analysis. Unlike previous studies where fatigue-crack propagation data were obtained using through-thickness, long cracks (approximately 2-20 mm long), growing in conventional (e.g., compact-tension) samples, experiments were performed on physically small cracks (approximately 100-600 microns long), initiated on the surface of the pyrolytic-carbon coating to simulate reality. Small-crack toughness results were found to agree closely with those measured conventionally with long cracks. However, similar to well-known observations in metal fatigue, it was found that based on the usual computations of the applied (far-field) driving force in terms of the maximum stress intensity, Kmax, small fatigue cracks grew at rates that exceeded those of long cracks at the same applied stress intensity, and displayed a negative dependency on Kmax; moreover, they grew at applied stress intensities less than the fatigue threshold value, below which long cracks are presumed dormant. To resolve this apparent discrepancy, it is shown that long and small crack results can be normalized, provided growth rates are characterized in terms of the total (near-tip) stress intensity (incorporating, for example, the effect of residual stress); with this achieved, in principle, either form of data can be used for life prediction of implant devices. Inspection of the long and small crack results reveals extensive scatter inherent in both forms of growth-rate data for the pyrolytic-carbon material.

Graphite↗
PubMed1997

Structural comparisons of muscle and nonmuscle actins give insights into the evolution of their functional differences.

Actin is a highly conserved protein although many isoforms exist. In vertebrates and insects the different actin isoforms can be grouped by their amino acid sequence and tissue-specific gene expression into muscle and nonmuscle actins, suggesting that the different actins may have a functional significance. We ask here whether atomic models for G- and F-actins may help to explain this functional diversity. Using a molecular graphics program we have mapped the few amino acids that differ between isoactins. A small number of residues specific for muscle actins are buried in internal positions and some present a remarkable organization. Within the molecule, the replacements observed between muscle and nonmuscle actins are often accompanied by compensatory changes. The others are dispersed on the protein surface, except for a cluster located at the N-terminus which protrudes outward. Only a few of these residues specific for muscle actins are present in known ligand binding sites except the N-terminus, which has a sequence specific for each isoactin and is directly implicated in the binding to myosin. When we simulated the replacements of side chains of residues specific for muscle actins to those specific for nonmuscle actins, the N-terminus appears to be less compact and more flexible in nonmuscle actins. This would represent the first conformational grounds for proposing that muscle and nonmuscle actins may be functionally distinguishable. The rest of the molecule is very similar or identical in all the actins, except for a possible higher internal flexibility in muscle actins. We propose that muscle actin genes have evolved from genes of nonmuscle actins by substitutions leading to some conformational changes in the protruding N-terminus and the internal dynamics of the main body of the protein.

Actins↗