SEARCH · PubMed Health

Results for “Compaction simulator”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,009 records · Page 56Linked to original sources

PubMed1991

Segmental differences in the stability of the trp-repressor peptide backbone.

Exchange lifetimes of amide protons in trp-repressor with and without the corepressor, L-tryptophan, were studied by heteronuclear 2D NMR spectroscopy. The amide proton exchange times revealed pronounced differences in the stability of different regions of the trp-repressor. The dimeric core of the molecule is relatively compact and homogeneous in terms of the measured parameters in both apo- and holorepressors. On the other hand the DNA-binding region appears less stable and more susceptible to the exchange of its backbone protons with the solvent. The NMR findings reported here are consistent with and amplify information on the stability of the trp-repressor obtained by other methods.

Amino Acid Sequence↗

PubMed2005

Computational studies of the cationic aluminium(chloro) hydroxides by quantum chemical ab initio methods.

Cationic aluminium(chloro) hydroxide complexes with two to four aluminium atoms were studied using quantum chemical methods. Complexes were studied in both gas and liquid phase. The liquid environment was modeled by using a conductor-like screening model (COSMO). COSMO calculations were carried out as a single point calculation at the optimized gas phase structures. Water (epsilon = 78.54) was used as the solvent. The minimum energy structures obtained from the gas phase studies were mostly compact cyclic structures. Aluminium preferred to be five-coordinated in oxygen rich clusters. Core oxygen preferred three-fold coordination but in the largest clusters the four-coordinated oxygen was observed. Water reacted dissociatively with hydrogen poor clusters. The COSMO calculations showed that the optimal structures of cationic aluminium(chloro) hydroxides tend to be more open in the liquid than in the gas phase.

Aluminum↗

PubMed2002

Knotting probability of DNA molecules confined in restricted volumes: DNA knotting in phage capsids.

When linear double-stranded DNA is packed inside bacteriophage capsids, it becomes highly compacted. However, the phage is believed to be fully effective only if the DNA is not entangled. Nevertheless, when DNA is extracted from a tailless mutant of the P4 phage, DNA is found to be cyclic and knotted (probability of 0.95). The knot spectrum is very complex, and most of the knots have a large number of crossings. We quantified the frequency and crossing numbers of these knots and concluded that, for the P4 tailless mutant, at least half the knotted molecules are formed while the DNA is still inside the viral capsid rather than during extraction. To analyze the origin of the knots formed inside the capsid, we compared our experimental results to Monte Carlo simulations of random knotting of equilateral polygons in confined volumes. These simulations showed that confinement of closed chains to tightly restricted volumes results in high knotting probabilities and the formation of knots with large crossing numbers. We conclude that the formation of the knots inside the viral capsid is driven mainly by the effects of confinement.

Bacteriophages↗

PubMed2002

Universality classes for self-avoiding walks in a strongly disordered system.

We study the behavior of self-avoiding walks (SAWs) on square and cubic lattices in the presence of strong disorder. We simulate the disorder by assigning random energy epsilon taken from a probability distribution P(epsilon) to each site (or bond) of the lattice. We study the strong disorder limit for an extremely broad range of energies with P(epsilon) is proportional to 1/epsilon. For each configuration of disorder, we find by exact enumeration the optimal SAW of fixed length N and fixed origin that minimizes the sum of the energies of the visited sites (or bonds). We find the fractal dimension of the optimal path to be d(opt)=1.52+/-0.10 in two dimensions (2D) and d(opt)=1.82+/-0.08 in 3D. Our results imply that SAWs in strong disorder with fixed N are much more compact than SAWs in disordered media with a uniform distribution of energies, optimal paths in strong disorder with fixed end-to-end distance R, and SAWs on a percolation cluster. Our results are also consistent with the possibility that SAWs in strong disorder belong to the same universality class as the maximal SAW on a percolation cluster at criticality, for which we calculate the fractal dimension d(max)=1.64+/-0.02 for 2D and d(max)=1.87+/-0.05 for 3D, values very close to the fractal dimensions of the percolation backbone in 2D and 3D.

Journal Article↗

PubMed2006

Preconditioned superprism-based photonic crystal demultiplexers: analysis and design.

We present the analysis and design of a new type of photonic crystal (PC) demultiplexers (i.e., preconditioned demultiplexer), in which the simultaneous existence of the superprism effect and the negative effective index for diffraction results in a compact structure by canceling the second-order spectral phase to avoid beam broadening inside the PC. This approach considerably relaxes the requirements for the large area of the structure and the small divergence of the input beam. As a result, the size of the preconditioned demultiplexers varies as N(2.5) (N being the number of wavelength channels) compared to the N(4) variation in the conventional superprism-based PC demultiplexers. We use a generalized effective index model to analyze, design, and optimize these demultiplexing structures. This approximate model can be used to extract all the basic properties of the PC device simply from the band structure and eliminates the need to go through tedious simulations especially for three-dimensional structures. Our results show that the preconditioned superprism-based PC demultiplexers have 2 orders of magnitude smaller size compared to the conventional ones.

Journal Article↗

PubMed1997

The effect of strain state on the biostability of a poly(etherurethane urea) elastomer.

The effect of deformation state on degradation of a PEUU without added stabilizers was examined in an oxidative environment that simulates the in vivo biodegradation of the polymer. Polymer tubes were stressed uniaxially and biaxially over glass mandrels and treated in 20% hydrogen peroxide/0.1 M cobalt chloride solution for 12 days at 37 degrees C. The amount of degradation was determined from the ATR-FTIR peak height of the amorphous aliphatic ether absorbance at 1110 cm-1. If a uniaxial stress was applied, degradation was inhibited and the amount of surface ether remaining after treatment increased linearly with strain. If the stress was biaxial, the amount of degradation was not reduced unless the strain was greater than 200%. Decreased degradation correlated with the amount of soft-segment orientation. The decreased degradation rate was attributed to compaction of the polyether phase by orientation, which resulted in lower permeability to oxidative agents, particularly oxygen. Macroscopic damage was confined to a thin peeling surface layer if the stress was uniaxial. In comparison, biaxially stressed PEUU ruptured.

Biocompatible Materials↗

PubMed1998

Mechanism and evolution of protein dimerization.

We have investigated the mechanism and the evolutionary pathway of protein dimerization through analysis of experimental structures of dimers. We propose that the evolution of dimers may have multiple pathways, including (1) formation of a functional dimer directly without going through an ancestor monomer, (2) formation of a stable monomer as an intermediate followed by mutations of its surface residues, and (3), a domain swapping mechanism, replacing one segment in a monomer by an equivalent segment from an identical chain in the dimer. Some of the dimers which are governed by a domain swapping mechanism may have evolved at an earlier stage of evolution via the second mechanism. Here, we follow the theory that the kinetic pathway reflects the evolutionary pathway. We analyze the structure-kinetics-evolution relationship for a collection of symmetric homodimers classified into three groups: (1) 14 dimers, which were referred to as domain swapping dimers in the literature; (2) nine 2-state dimers, which have no measurable intermediates in equilibrium denaturation; and (3), eight 3-state dimers, which have stable intermediates in equilibrium denaturation. The analysis consists of the following stages: (i) The dimer is divided into two structural units, which have twofold symmetry. Each unit contains a contiguous segment from one polypeptide chain of the dimer, and its complementary contiguous segment from the other chain. (ii) The division is repeated progressively, with different combinations of the two segments in each unit. (iii) The coefficient of compactness is calculated for the units in all divisions. The coefficients obtained for different cuttings of a dimer form a compactness profile. The profile probes the structural organization of the two chains in a dimer and the stability of the monomeric state. We describe the features of the compactness profiles in each of the three dimer groups. The profiles identify the swapping segments in domain swapping dimers, and can usually predict whether a dimer has domain swapping. The kinetics of dimerization indicates that some dimers which have been assigned in the literature as domain swapping cases, dimerize through the 2-state kinetics, rather than through swapping segments of performed monomers. The compactness profiles indicate a wide spectrum in the kinetics of dimerization: dimers having no intermediate stable monomers; dimers having an intermediate with a stable monomer structure; and dimers having an intermediate with a stable structure in part of the monomer. These correspond to the multiple evolutionary pathways for dimer formation. The evolutionary mechanisms proposed here for dimers are applicable to other oligomers as well.

Biological Evolution↗

PubMed2000

Structure of the human IgE-Fc C epsilon 3-C epsilon 4 reveals conformational flexibility in the antibody effector domains.

IgE antibodies mediate antiparasitic immune responses and the inflammatory reactions of allergy and asthma. We have solved the crystal structure of the human IgE-Fc Cepsilon3-Cepsilon4 domains to 2.3 A resolution. The structure reveals a large rearrangement of the N-terminal Cepsilon3 domains when compared to related IgG-Fc structures and to the IgE-Fc bound to its high-affinity receptor, FcepsilonRI. The IgE-Fc adopts a more compact, closed configuration that places the two Cepsilon3 domains in close proximity, decreases the size of the interdomain cavity, and obscures part of the FcepsilonRI binding site. IgE-Fc conformational flexibility may be required for interactions with two distinct IgE receptors, and the structure suggests strategies for the design of therapeutic compounds for the treatment of IgE-mediated diseases.

Antibody Specificity↗

PubMed1995

Solution structure of the human pp60c-src SH2 domain complexed with a phosphorylated tyrosine pentapeptide.

Human pp60c-src is a cellular nonreceptor tyrosine kinase that participates in cytosolic signal transduction and has been implicated in the development of malignant tumors in the human breast and colon. Signal transduction is mediated by highly specific interactions between the SH2 domain and receptor phosphorylated tyrosine binding motifs. To elucidate the molecular conformation and interactions in solution, a family of highly resolved nuclear magnetic resonance (NMR) structures was determined for the src SH2 domain complexed with a high-affinity phosphorylated pentapeptide, acetyl-p YEEIE-OH. The 23 structures, generated with a distance geometry (DG) and a dynamical simulated annealing (SA) procedure, satisfied 2072 experimental restraints derived from a variety of multifrequency/multidimensional and isotope-filtered NMR data. Superimposition of residues 143-245 upon the mean coordinate set yielded an atomic rmsd of 0.58 +/- 0.09 A for the N, C alpha, C' atoms and 1.04 +/- 0.08 for all the non-hydrogen atoms. Residues in the ordered secondary structure regions superimpose to 0.29 +/- 0.04 A for the N, C alpha, C' and 0.73 +/- 0.08 A for all the non-hydrogen atoms. The angular order parameter calculated for the phi, psi angles was > 0.9 for 81 of the 106 protein residues. The main protein conformational features are three antiparallel beta-strands that traverse a compact core with an alpha-helix on each side of the core near the N- and C-termini. The observed intermolecular nuclear Overhauser effects (NOE) from the pY, +1E, and +3I residues positioned the ligand in an extended conformation across the SH2 domain surface with the pY and +3I side chains inserted into the protein binding pockets. In general, the protein conformation is consistent with previously reported structures of different SH2 domain complexes determined by X-ray crystallography. However, inter- or intramolecular interactions involving the guanidinium side chains of the solvated R alpha A2 or the buried R beta B5 were not observed at pH = 5.5 or 7.0. If such interactions exist in solution, the absence of any confirming data probably arises from rapid exchange with solvent and/or undetermined dynamic components. Thus, the unrestrained R alpha A2 side chain did not show an amino-aromatic interaction or a hydrogen bond to the -1 carbonyl oxygen as observed in the crystal structures. This result is consistent with the solution structure of a different SH2 domain complex. A more detailed comparison between the crystal structure and the NMR-derived solution structures of the same src SH2 domain complex is presented.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗

PubMed2001

Helix unfolding in unsolvated peptides.

The conformations of unsolvated Ac-K(AGG)(5)+H(+) and Ac-(AGG)(5)K+H(+) peptides (Ac = acetyl, A = alanine, G = glycine, and K = lysine) have been examined by ion mobility measurements over a wide temperature range (150-410 K). The Ac-K(AGG)(5)+H(+) peptide remains a globule (a compact, roughly spherical structure) over the entire temperature range, while both an alpha-helix and a globule are found for Ac-(AGG)(5)K+H(+) at low temperature. As the temperature is raised the alpha-helix unfolds. Rate constants for loss of the helix (on a millisecond time scale) have been determined as a function of temperature and yield an Arrhenius activation energy and preexponential factor of 38.2 +/- 1.0 kJ mol(-1) and 6.5 +/- 3.7 x 10(9) s(-1), respectively. The alpha-helix apparently does not unfold directly into the globule, but first converts into a long-lived intermediate which survives to a significantly higher temperature before converting. According to molecular dynamics simulations, there is a partially untwisted helical conformation that has both a low energy and a well-defined geometry. This special structure lies between the helix and globule and may be the long-lived intermediate.

Alanine↗

PubMed2001

Molecular dynamics simulations on the mycotoxin fumonisin B1.

The solution conformational properties of the mycotoxin fumonisin B(1) have been studied using molecular dynamics methodology. Fumonisins have been shown to inhibit sphinganine (sphingosine) N-acyltransferase (ceramide synthase) and show a wide range of toxic effects in many animals. This study of the solution properties of fumonisin B(1) attempts to add to the structural models necessary for the understanding of the binding and activity properties. The computational method uses a box with periodic boundaries, filled with explicit TIP3P water molecules, the substrate fumonisin B(1), and selected counterions for charge neutrality. The starting structure of fumonisin B(1) is added to the box by excluding water molecules. The explicit image method using 12-A cutoffs is applied to the system and molecular dynamics are carried out on different starting conformations at 300 K in 100-picosecond (ps) steps. Examination of the resulting equilibrated conformations suggests that the structure is relatively extended and that previous computational studies in vacuo, showing a compact folded structure, may not be consistent with the solution structure.

Acyltransferases↗

PubMed2005

Proteins and polymers.

Proteins, chain molecules of amino acids, behave in ways which are similar to each other yet quite distinct from standard compact polymers. We demonstrate that the Flory theorem, derived for polymer melts, holds for compact protein native state structures and is not incompatible with the existence of structured building blocks such as alpha helices and beta strands. We present a discussion on how the notion of the thickness of a polymer chain, besides being useful in describing a chain molecule in the continuum limit, plays a vital role in interpolating between conventional polymer physics and the phase of matter associated with protein structures.

Algorithms↗

PubMed2000

Structure of a conserved domain common to the transcription factors TFIIS, elongin A, and CRSP70.

TFIIS is a transcription elongation factor that consists of three domains. We have previously solved the structures of domains II and III, which stimulate arrested polymerase II elongation complexes in order to resume transcription. Domain I is conserved in evolution from yeast to human species and is homologous to the transcription factors elongin A and CRSP70. Domain I also interacts with the transcriptionally active RNA polymerase II holoenzyme and therefore, may have a function unrelated to the previously described transcription elongation activity of TFIIS. We have solved the structure of domain I of yeast TFIIS using NMR spectroscopy. Domain I is a compact four-helix bundle that is structurally independent of domains II and III of the TFIIS. Using the yeast structure as a template, we have modeled the homologous domains from elongin A and CRSP70 and identified a conserved positively charged patch on the surface of all three proteins, which may be involved in conserved functional interactions with the transcriptional machinery.

Amino Acid Sequence↗

PubMed1991

Salt dependent changes in structure and dynamics of circular single stranded DNA of filamentous phages of Escherichia coli.

We have analyzed the static and dynamic behaviour of the circular single stranded DNA of the filamentous Escherichia coli phages F1 and M13mp8 in solution as a function of salt concentration using static and dynamic light scattering and sedimentation analysis in the analytical ultracentrifuge. We show by static light scattering that native and denatured single stranded DNA behave like a randomly coiled macromolecule at all salt concentrations used. The size of the native single stranded DNA is governed by the formation of secondary structures. While the radius of gyration decreases with increasing salt concentration the translational diffusion of the center-of-mass of native single stranded DNA and the sedimentation coefficient increase with increasing salt concentration in a biphasic manner. Below 100 mM monovalent cation concentration there is a strong dependence of the hydrodynamic parameters upon salt which is reduced approx. 3-fold at higher salt concentrations. We attribute the compaction of single stranded DNA by salt to electrostatic shielding and, in case of native single stranded DNA, secondary structure formation. Internal motions of the native single stranded DNA are observable at all salt concentrations and can be interpreted with a model of segmental diffusion of the elements of the polymer chain. The observed segmental diffusion coefficient of the native single stranded polynucleotide increases with increasing salt under the conditions investigated.

Coliphages↗

PubMed1996

Virtual reality volumetric display techniques for three-dimensional medical ultrasound.

Ultrasound imaging offers a safe, inexpensive method for obtaining medical data. It is also desirable in that data can be acquired at real-time rates and the necessary hardware can be compact and portable. The work presented here documents our attempts at providing interactive 3-D visualization of ultrasound data. We have found two volume rendering visualization packages to be quite useful and have extended one to perform stereographic volume visualization. Using a relatively inexpensive pair of commercial stereo glasses, we believe we have found a combination of tools that offers a viable system for enhancing 3-D ultrasound visualization.

Computer Simulation↗

PubMed2006

Azobenzene as conformational switch in model peptides.

The photoinduced isomerization of azobenzene between the extended (trans) and compact (cis) conformations is reversibly triggered by light of two differing wavelengths. The resulting changes in molecular geometry have been extensively utilized to photoswitch transformations in chemical species reversibly for applications in optoelectronic devises as well as to photocontrol conformational states in (bio)polymers. The high isomerization yield, remarkable photostability and ultrafast kinetics (few ps) of azobenzene are well suited for the design of small, defined model systems that allow detailed folding studies to be carried out both experimentally and theoretically on the same molecules. In our and other laboratories such systems were recently obtained with cyclic peptides of defined conformational preferences as well as with alpha-helical and beta-hairpin peptides. These should, by comparison of simulation and experiment, permit an assessment and improvement of the theoretical description on the one hand and a detailed interpretation of the ultrafast conformational dynamics on the other. The phototriggered changes in conformational states lead to concurrent changes in biophysical properties that can be exploited in the photocontrol of biochemical and biological events, as exemplarily discussed with redox-active cyclic bis-cysteinyl peptides and receptor ligands.

Azo Compounds↗

PubMed1998

Coupled B-snake grids and constrained thin-plate splines for analysis of 2-D tissue deformations from tagged MRI.

Magnetic resonance imaging (MRI) is unique in its ability to noninvasively and selectively alter tissue magnetization and create tagged patterns within a deforming body such as the heart muscle. The resulting patterns define a time-varying curvilinear coordinate system on the tissue, which we track with coupled B-snake grids. B-spline bases provide local control of shape, compact representation, and parametric continuity. Efficient spline warps are proposed which warp an area in the plane such that two embedded snake grids obtained from two tagged frames are brought into registration, interpolating a dense displacement vector field. The reconstructed vector field adheres to the known displacement information at the intersections, forces corresponding snakes to be warped into one another, and for all other points in the plane, where no information is available, a C1 continuous vector field is interpolated. The implementation proposed in this paper improves on our previous variational-based implementation and generalizes warp methods to include biologically relevant contiguous open curves, in addition to standard landmark points. The methods are validated with a cardiac motion simulator, in addition to in-vivo tagging data sets.

Computer Simulation↗

PubMed1998

Influence of Llamas, Horses, and Hikers on Soil Erosion from Established Recreation Trails in Western Montana, USA

/ Various types of recreational traffic impact hiking trails uniquely and cause different levels of trail degradation; however, trail head restrictions are applied similarly across all types of packstock. The purpose of this study was to assess the relative physical impact of hikers, llamas, and horses on recreational trails. Horse, llama, and hiker traffic were applied to 56 separate plots on an existing trail at Lubrecht Experimental Forest in western Montana. The traffic was applied to plots at intensities of 250 and 1000 passes along with a no-traffic control under both prewetted and dry trail conditions. Soil erosion potential was assessed by sediment yield and runoff (using a Meeuwig type rainfall simulator), changes in soil bulk density, and changes in soil surface roughness. Soil moisture, slope, and rainfall intensity were recorded as independent variables in order to evaluate the extent that they were held constant by the experimental design. Horse traffic consistently made more sediment available for erosion from trails than llama, hiker, or no traffic when analyzed across wet and dry trail plots and high and low intensity traffic plots. Although total runoff was not significantly affected by trail user, wet trail traffic caused significantly greater runoff than dry trail traffic. Llama traffic caused a significant increase in sediment yield compared to the control, but caused erosion yields not significantly different than hiker traffic. Trail traffic did not increase soil compaction on wet trails. Traffic applied to dry trail plots generally resulted in a significant decrease in soil bulk density compared to the control. Decreased soil bulk density was negatively correlated with increased sediment yield and appeared to result in increased trail roughness for horse traffic compared to hiker or llama traffic. Differences described here between llama and horse traffic indicate that trail managers may want to consider managing packstock llamas independent of horses.KEY WORDS: Recreational impacts; Sediment yield; Trail degradation

Journal Article↗