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At least 433 records · Page 24Linked to original sources
PubMed2005

Pressure-dependent transition in protein dynamics at about revealed by molecular dynamics simulation.

Molecular dynamics simulations of a crystalline protein, Staphylococcal nuclease, over the pressure range 1 bar to 15 kbar reveal a qualitative change in the internal protein motions at approximately 4 kbar. This change involves the existence of two linear regimes in the mean-square displacement for internal protein motion, (P) with a twofold decrease in the slope for P>4 kbar. The major effect of pressure on the dynamics is a loss, with increasing pressure of large amplitude, collective protein modes below 2 THz effective frequency, accompanied by restriction of large-scale solvent translational motion.

Computer Simulation↗
PubMed2005

Parallels between the dynamics at the noise-perturbed onset of chaos in logistic maps and the dynamics of glass formation.

We develop the characterization of the dynamics at the noise-perturbed edge of chaos in logistic maps in terms of the quantities normally used to describe glassy properties in structural glass formers. Following the recognition [Phys. Lett. A 328, 467 (2004)] that the dynamics at this critical attractor exhibits analogies with that observed in thermal systems close to vitrification, we determine the modifications that take place with decreasing noise amplitude in ensemble- and time-averaged correlations and in diffusivity. We corroborate explicitly the occurrence of two-step relaxation, aging with its characteristic scaling property, and subdiffusion and arrest for this system. We also discuss features that appear to be specific to the map.

Journal Article↗
PubMed2006

Dynamics, dynamic soft elasticity, and rheology of smectic-C elastomers.

We present a theory for the low-frequency, long-wavelength dynamics of soft smectic-C elastomers with locked-in smectic layers. Our theory, which goes beyond pure hydrodynamics, predicts a dynamic soft elasticity of these elastomers and allows us to calculate the storage and loss moduli relevant for rheology experiments as well as the mode structure.

Journal Article↗
PubMed2002

Dynamic structure of He-Ne mixtures by molecular dynamics simulation: from hydrodynamic to fast and slow sound modes.

Molecular dynamics (MD) results for the dynamic structure of a He(0.77)Ne(0.23) gas mixture at two densities (15.8 and 36.1 nm(-3)) show a clear crossover from hydrodynamic modes to distinct excitations for the two species. The higher density dispension curve neatly shows high- and low-frequency branches setting on with a rather localized transition. The lower density results agree very well with existing neutron scattering data and, in particular, display hydrodynamic behavior up to k approximately 2 nm(-1), in contrast with the conclusions of previous simulation studies. A smooth transition to fast sound is shown to take place for 2<k/nm(-1)<5, where the present MD data fill the existing gap in the experimental results.

Journal Article↗
PubMed2002

Four-body reaction dynamics: complete correlated fragment measurement of the dissociative photodetachment dynamics of O(-)(8).

The four-body dissociative photodetachment (DPD) dynamics of O-8 were studied using photoelectron photofragment coincidence (PPC) spectroscopy. All four neutral photofragments were measured in coincidence with the photodetached electron, yielding a five-body kinematically complete experiment. Velocity and angular correlations for DPD of O(-)(8) are presented and compared to those for O(-)(6). The DPD dynamics and energetics of O(-)(8).are found to be similar to those of O-4 and O-6 implying that the additional solvating O(2) molecules act essentially as spectators, but exhibit inequivalent kinematic behavior implying asymmetric solvation.

Journal Article↗
PubMed2002

Single-particle and collective dynamics of protein hydration water: a molecular dynamics study.

We present an analysis based on molecular dynamics simulations of water single particle and collective density fluctuations in a protein crystal at 150 and 300 K. For the collective dynamics, the calculations predict the existence of two sound modes. The first one around 35 meV is highly dispersive and the second one around 9 meV is weakly dispersive in the k range studied here (0.5<k<4.2 A(-1)). We provide evidence that the boson peak around 4 meV in the single particle spectra arises from translational motion, is present in the coherent spectra, and is distinct from the two sound modes.

Computer Simulation↗
PubMed2005

Universal dynamic exponent at the liquid-gas transition from molecular dynamics.

The liquid-gas system is expected to exhibit distinct dynamic behavior in the fluid's critical region (model H). We present molecular dynamics simulations of a Lennard-Jones fluid model starting from specially designed, near-equilibrium, initial conditions. By following the fluid's relaxation towards equilibrium, we calculate the requisite transport coefficients in the critical region. The results yield the scaling behavior of the thermal diffusion coefficient D(T) approximately xi(-1.023+/-0.018) (xi is the correlation length) and a nonconventional divergent heat conductivity, all of which are in accord with mode-coupling and renormalization group predictions, as well as some experimental data.

Journal Article↗
PubMed2000

Quasi-dynamical electron diffraction - a kinematic type of expression for the dynamical diffracted-beam amplitudes

It is shown that to a good approximation the dynamical diffracted electron-beam amplitudes may be expressed in a form that is identical to that of the kinematic theory of electron diffraction. The validity of this approximate form of the dynamical electron diffraction is illustrated for thin films of GaAs and Au crystals, and its implications in electron crystallography for structural determination and refinement are discussed.

Journal Article↗
PubMed2003

Dynamics of Ca2+-saturated calmodulin D129N mutant studied by multiple molecular dynamics simulations.

Fifteen independent 1-nsec MD simulations of fully solvated Ca(2+) saturated calmodulin (CaM) mutant D129N were performed from different initial conditions to provide a sufficient statistical basis to gauge the significance of observed dynamical properties. In all MD simulations the four Ca(2+) ions remained in their binding sites, and retained a single water ligand as observed in the crystal structure. The coordination of Ca(2+) ions in EF-hands I, II, and III was sevenfold. In EF-hand IV, which was perturbed by the mutation of a highly conserved Asp129, an anomalous eightfold Ca(2+) coordination was observed. The Ca(2+) binding loop in EF-hand II was observed to dynamically sample conformations related to the Ca(2+)-free form. Repeated MD simulations implicate two well-defined conformations of Ca(2+) binding loop II, whereas similar effect was not observed for loops I, III, and IV. In 8 out of 15 MD simulations Ca(2+) binding loop II adopted an alternative conformation in which the Thr62 >C=O group was displaced from the Ca(2+) coordination by a water molecule, resulting in the Ca(2+) ion ligated by two water molecules. The alternative conformation of the Ca(2+) binding loop II appears related to the "closed" state involved in conformational exchange previously detected by NMR in the N-terminal domain fragment of CaM and the C-terminal domain fragment of the mutant E140Q. MD simulations suggest that conformations involved in microsecond exchange exist partially preformed on the nanosecond time scale.

Asparagine↗
PubMed1980

Synthesis, pharmacological, conformational, and dynamic studies of the potent hormone antagonists [1-penicillamine, 4-threonine]-oxytocin and [1-penicillamine, 2-phenylalanine, 4-threonine]-oxytocin. Conformational and dynamic considerations in the design of antagonists.

The solid phase synthesis of [1-penicillamine, 4-threonine]-oxytocin and [1-penicillamine, 2-phenylalanine, 4-threonine]-oxytocin is reported. The two compounds have no in vitro milk ejecting activity and no in vivo or in vitro oxytocic activity, but both are potent antagonists in these three assay systems. In the in vitro oxytocic assay, [1-penicillamine, 4-threonine]- and [1-penicillamine, 2-phenylalanine, 4-threonine]-oxytocin have pA2 values of 7.55 +/- 0.04 and 7.67 +/- 0.02, respectively, and both inhibit the uterine contractile response to oxytocin in nonpregnant and pregnant rats. [1-Penicillamine, 2-phenylalanine, 4-threonine]-oxytocin has a weak antipressor activity and at high doses, consistently caused a weak and transient fall in blood pressure in the rat. Carbon-13 nuclear magnetic resonance chemical shift parameters and spin-lattice relaxation times (T1) indicate that these two new oxytocin antagonists have very similar conformation and dynamic properties to oxytocin inhibitors which have previously been examined. These results are discussed in terms of conformational and dynamic models of oxytocin antagonism at the uterus. It is suggested that conformational restrictions at the 2- and 4-positions of penicillamine-1 analogues of oxytocin are important to antagonist activity and potency.

Amino Acid Sequence↗
PubMedDate not supplied

An in vitro biomechanical comparison of a limited-contact dynamic compression plate fixation with a dynamic compression plate fixation of osteotomized equine third metacarpal bones.

OBJECTIVES: To compare the monotonic biomechanical properties and fatigue life of a broad, limited contact, dynamic compression plate (LC-DCP) fixation with a broad, dynamic compression plate (DCP) fixation to repair osteotomized equine 3rd metacarpal (MC3) bones. STUDY DESIGN: In vitro biomechanical testing of paired cadaveric equine MC3 with a mid-diaphyseal osteotomy, stabilized by 1 of 2 methods for fracture fixation. ANIMAL POPULATION: Twelve pairs of adult equine cadaveric MC3 bones. METHODS: Twelve pairs of equine MC3 were divided into 3 test groups (4 pairs each) for (1) 4-point bending single cycle to failure testing, (2) 4-point bending cyclic fatigue testing, and (3) torsional single cycle to failure testing. An LC-DCP (8-hole, 4.5 mm) was applied to the dorsal surface of 1 randomly selected bone from each pair. One DCP (8-hole, 4.5 mm broad) was applied dorsally to the contralateral bone from each pair. All plates and screws were applied using standard AO/ASIF techniques to MC3 bones that had mid-diaphyseal osteotomies. Mean test variable values for each method were compared using a paired t-test within each group. Significance was set at P<.05. RESULTS: The mean 4-point bending yield load, yield bending moment, composite rigidity, failure load, and failure bending moment of LC-DCP fixation were significantly greater (P<.01) than those of broad DCP fixation. Mean cycles to failure for 4-point bending was significantly (P<.001) greater for broad DCP fixation compared with broad LC-DCP fixation. Mean yield load, mean composite rigidity, and mean failure load in torsion was significantly (P<.02) greater for broad LC-DCP fixation compared with broad DCP fixation. CONCLUSION: Broad LC-DCP offers increased stability in static overload testing, however, it offers significantly less stability in cyclic fatigue testing. CLINICAL RELEVANCE: The clinical relevance of the cyclic fatigue data supports the conclusion that the broad DCP fixation is biomechanically superior to the broad LC-DCP fixation in osteotomized equine MC3 bones despite the results of the static overload testing.

Animals↗
PubMedDate not supplied

An in vitro biomechanical comparison of a prototype equine metacarpal dynamic compression plate fixation with double dynamic compression plate fixation of osteotomized equine third metacarpal bones.

OBJECTIVES: To compare the monotonic biomechanical properties of a prototype equine third metacarpal dynamic compression plate (EM-DCP) fixation with a double broad dynamic compression plate (DCP) fixation to repair osteotomized equine third metacarpal (MC3) bones. STUDY DESIGN: In vitro biomechanical testing of paired cadaveric equine MC3 with a mid-diaphyseal osteotomy, stabilized by 1 of 2 methods for fracture fixation. POPULATION: Twelve pairs of adult equine cadaveric MC3 bones. METHODS: Twelve pairs of equine MC3 were divided into 3 test groups (4 pairs each) for (1) 4-point bending single cycle to failure testing, (2) 4-point bending cyclic fatigue testing, and (3) torsional testing. The EM-DCP (10-hole, 4.5 mm) was applied to the dorsal surface of one randomly selected bone from each pair. Two DCPs, 1 dorsally (10-hole, 4.5 mm broad) and 1 laterally (9-hole, 4.5 mm broad) were applied to the contralateral bone from each pair. All plates and screws were applied using standard AO/ASIF techniques to MC3 bones that had mid-diaphyseal osteotomies. Mean test variable values for each method were compared using a paired t-test within each group. Significance was set at P<.05. RESULTS: Mean 4-point bending yield load, yield bending moment, bending composite rigidity, failure load and failure bending moment of the EM-DCP fixation were significantly greater (P<.0001) than those of the double broad DCP fixation. Mean cycles to failure in 4-point bending of the EM-DCP fixation was significantly greater (P<.0008) than that of the double broad DCP fixation. Mean yield load, composite rigidity, and failure load in torsion of the EM-DCP fixation were significantly greater (P<.0035) than that of the double broad DCP fixation. CONCLUSION: The EM-DCP provides increased stability in both static overload testing and cyclic fatigue testing. CLINICAL RELEVANCE: Results of this in vitro study support the conclusion that the prototype EM-DCP fixation is biomechanically superior to the double broad DCP fixation for the stabilization of osteotomized equine MC3.

Animals↗
PubMed1985

A qualitative dynamic analysis of reiterant speech production: phase portraits, kinematics, and dynamic modeling.

The departure point of the present paper is our effort to characterize and understand the spatiotemporal structure of articulatory patterns in speech. To do so, we removed segmental variation as much as possible while retaining the spoken act's stress and prosodic structure. Subjects produced two sentences from the "rainbow passage" using reiterant speech in which normal syllables were replaced by /ba/ or /ma/. This task was performed at two self-selected rates, conversational and fast. Infrared LEDs were placed on the jaw and lips and monitored using a modified SELSPOT optical tracking system. As expected, when pauses marking major syntactic boundaries were removed, a high degree of rhythmicity within rate was observed, characterized by well-defined periodicities and small coefficients of variation. When articulatory gestures were examined geometrically on the phase plane, the trajectories revealed a scaling relation between a gesture's peak velocity and displacement. Further quantitative analysis of articulator movement as a function of stress and speaking rate was indicative of a language-modulated dynamical system with linear stiffness and equilibrium (or rest) position as key control parameters. Preliminary modeling was consonant with this dynamical perspective which, importantly, does not require that time per se be a controlled variable.

Female↗
PubMed2004

Global nature of dynamic protein-chromatin interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins.

Genome structure and gene expression depend on a multitude of chromatin-binding proteins. The binding properties of these proteins to native chromatin in intact cells are largely unknown. Here, we describe an approach based on combined in vivo photobleaching microscopy and kinetic modeling to analyze globally the dynamics of binding of chromatin-associated proteins in living cells. We have quantitatively determined basic biophysical properties, such as off rate constants, residence time, and bound fraction, of a wide range of chromatin proteins of diverse functions in vivo. We demonstrate that most chromatin proteins have a high turnover on chromatin with a residence time on the order of seconds, that the major fraction of each protein is bound to chromatin at steady state, and that transient binding is a common property of chromatin-associated proteins. Our results indicate that chromatin-binding proteins find their binding sites by three-dimensional scanning of the genome space and our data are consistent with a model in which chromatin-associated proteins form dynamic interaction networks in vivo. We suggest that these properties are crucial for generating high plasticity in genome expression.

Animals↗
PubMed1992

Focal liver disease: comparison of dynamic contrast-enhanced CT and T2-weighted fat-suppressed, FLASH, and dynamic gadolinium-enhanced MR imaging at 1.5 T.

Dynamic contrast medium-enhanced computed tomography (CT), T2-weighted fat-suppressed spin-echo (T2FS) magnetic resonance (MR) imaging, and breath-hold T1-weighted fast low-angle shot (FLASH) MR imaging before and after dynamic gadopentetate dimeglumine injection were compared in 73 patients with clinically suspected liver disease. Observer confidence for presence of focal lesions was determined by using receiver operating characteristic analysis. For all MR images, hepatic lesion-liver signal-to-noise ratios were evaluated qualitatively. and resolution and presence of artifacts were evaluated qualitatively. Lesion detection was greatest with T2FS (n = 272) and enhanced FLASH (n = 244) and was statistically greater with both of these than with CT (n = 220) and FLASH (n = 219) (P less than .03). Correct lesion characterization was greatest with enhanced FLASH (n = 236) (P less than .01), followed by CT (n = 199), FLASH (n = 164), and T2FS (n = 144). Enhanced FLASH was particularly successful in characterization of 5-mm- to 1.5-cm-diameter lesions as cystic or solid.

Adenoma↗
PubMed1997

Ventilation abnormalities in obstructive airways disorder: detection with pulmonary dynamic densitometry by means of spiral CT versus dynamic Xe-133 SPECT.

PURPOSE: To evaluate pulmonary dynamic densitometry (PDD) by means of spiral computed tomography (CT) for detection of ventilation abnormalities in obstructive airways disorders compared with dynamic xenon-133 single photon emission CT. MATERIALS AND METHODS: Eight-second spiral CT was performed during two to three respiratory cycles in six healthy volunteers, 19 patients with airways disorder, and six patients with restrictive lung disease. The data sets were reconstructed as 36 1-second temporally overlapping images at 0.2-second intervals, and regional PDD curves were displayed. Regional ventilation was assessed by means of Xe-133 clearance time. RESULTS: Normal lungs showed smooth, sinusoidal PDD curves with maximal amplitude in lung attenuation change (MALAC) of 54.9 HU +/- 24.5, whereas lungs with obstructive airways disorders with prolonged Xe-133 clearance showed significantly diminished MALAC (31.6 HU +/- 20.1, P < .0001), accompanied by irregularity, asynchronous phase, and deterioration of normal ventral-to-dorsal gradients in MALAC and lung attenuation. Lungs with restrictive diseases without prolonged Xe-133 clearance did not show statistically significant reduction in MALAC. In a total of 251 lung regions, regional MALAC correlated inversely with Xe-133 clearance time (r = -.842). CONCLUSION: PDD by means of spiral CT is acceptable for the detection of ventilation abnormalities in obstructive airways disorder.

Adult↗
PubMedDate not supplied

A review of the concept of circulatory bioassist focused on the "new" demand dynamic cardiomyoplasty: the renewal of dynamic cardiomyoplasty?

After the initial enthusiasm, the dynamic cardiomyoplasty lost its reputation owing to the poor long-term results, caused by the muscular degeneration subsequent to chronic continuous electrical stimulation of the latissimus dorsi. An activity-rest stimulation protocol that avoids full transformation of the skeletal muscle, maintaining muscular properties over time, has been successfully tried. This "demand" stimulation protocol showed in humans good results improving NYHA class, ejection fraction value, and survival. The discussion about the capability of this and a unique kind of cardiocirculatory bioassist is due to be reopened. In fact, heart transplant, percutaneous circulatory-supporting device, multisites stimulation therapy, and total artificial heart have some drawbacks, one of which is the economic cost. In developing countries the more economic demand dynamic cardiomyoplasty may still play a role.

Cardiomyopathy, Dilated↗
PubMed2004

Dynamics of the IRE RNA hairpin loop probed by 2-aminopurine fluorescence and stochastic dynamics simulations.

The iron responsive element (IRE) RNA hairpin loop contains six phylogenetically conserved nucleotides, which constitute part of the sequence-specific binding site of the IRE-binding protein. The NMR structure of the loop has been solved, showing that 3 of the 6 nt are poorly constrained. Here, two purine nucleotides in the IRE loop are individually replaced with the fluorescent purine analog 2-aminopurine (2AP). Steady-state and time-resolved fluorescence methods are used to describe the structure and dynamics of 2AP in the IRE loop. The data indicate that 2AP at the position of the adenosine in the loop moves between stacked and unstacked positions, whereas 2AP at the adjacent guanosine is predominantly solvent exposed. Stochastic dynamics simulations are used to provide a physical description of how those nucleotides might move.

2-Aminopurine↗