Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “dynamics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 451 records · Page 25Linked to original sources
PubMed2006

Sensitive high-resolution white-light Schlieren technique with a large dynamic range for the investigation of ablation dynamics.

We developed a modified Hoffman contrast technique with a 12 ns pulsed incoherent extended white-light source that enables an easily interpretable visualization of ablation plumes with high resolution, a large dynamic range, and color information. By comparison, a conventional dark-field setup with a slitlike laser light source provides large sensitivity but a small dynamic range, and it is difficult to interpret the filtered images.

Algorithms↗
PubMed2005

Backbone dynamics of a symmetric calmodulin dimer in complex with the calmodulin-binding domain of the basic-helix-loop-helix transcription factor SEF2-1/E2-2: a highly dynamic complex.

Calmodulin (CaM) interacts specifically as a dimer with some dimeric basic-Helix-Loop-Helix (bHLH) transcription factors via a novel high affinity binding mode. Here we report a study of the backbone dynamics by (15)N-spin relaxation on the CaM dimer in complex with a dimeric peptide that mimics the CaM binding region of the bHLH transcription factor SEF2-1. The relaxation data were measured at multiple magnetic fields, and analyzed in a model-free manner using in-house written software designed to detect nanosecond internal motion. Besides picosecond motions, all residues also experience internal motion with an effective correlation time of approximately 2.5 ns with squared order parameter (S(2)) of approximately 0.75. Hydrodynamic calculations suggest that this can be attributed to motions of the N- and C-terminal domains of the CaM dimer in the complex. Moreover, residues with significant exchange broadening are found. They are clustered in the CaM:SEF2-1mp binding interface, the CaM:CaM dimer interface, and in the flexible helix connecting the CaM N- and C-terminal domains, and have similar exchange times (approximately 50 micros), suggesting a cooperative mechanism probably caused by protein:protein interactions. The dynamic features presented here support the conclusion that the conformationally heterogeneous bHLH mimicking peptide trapped inside the CaM dimer exchanges between different binding sites on both nanosecond and microsecond timescales. Nature has thus found a way to specifically recognize a relatively ill-fitting target. This novel mode of target-specific binding, which neither belongs to lock-and-key nor induced-fit binding, is characterized by dimerization and continuous exchange between multiple flexible binding alternatives.

Binding Sites↗
PubMed2005

Conformational dynamics of RNA-peptide binding: a molecular dynamics simulation study.

Molecular dynamics simulations of the binding of the heterochiral tripeptide KkN to the transactivation responsive (TAR) RNA of HIV-1 is presented, using an all-atom force field with explicit water. To obtain starting structures for the TAR-KkN complex, semirigid docking calculations were performed that employ an NMR structure of free TAR RNA. The molecular dynamics simulations show that the starting structures in which KkN binds to the major groove of TAR (as it is the case for the Tat-TAR complex of HIV-1) are unstable. On the other hand, the minor-groove starting structures are found to lead to several binding modes, which are stabilized by a complex interplay of stacking, hydrogen bonding, and electrostatic interactions. Although the ligand does not occupy the binding position of Tat protein, it is shown to hinder the interhelical motion of free TAR RNA. The latter is presumably necessary to achieve the conformational change of TAR RNA to bind Tat protein. Considering the time evolution of the trajectories, the binding process is found to be ligand-induced and cooperative. That is, the conformational rearrangement only occurs in the presence of the ligand and the concerted motion of the ligand and a large part of the RNA binding site is necessary to achieve the final low-energy binding state.

Binding Sites↗
PubMed2006

Conformational and dynamical properties of disaccharides in water: a molecular dynamics study.

Explicit-solvent molecular dynamics simulations (50 ns, 300 K) of the eight reducing glucose disaccharides (kojibiose, sophorose, nigerose, laminarabiose, maltose, cellobiose, isomaltose, and gentiobiose) have been carried out using the GROMOS 45A4 force field (including a recently reoptimized carbohydrate parameter set), to investigate and compare their conformational preferences, intramolecular hydrogen-bonding patterns, torsional dynamics, and configurational entropies. The calculated average values of the glycosidic torsional angles agree well with available experimental data, providing validation for the force field and simulation methodology employed in this study. These simulations show in particular that: 1) (1-->6)-linked disaccharides are characterized by an increased flexibility, the absence of any persistent intramolecular hydrogen bond and a significantly higher configurational entropy (compared to the other disaccharides); 2) cellobiose presents a highly persistent interresidue hydrogen bond and a significantly lower configurational entropy (compared to the other disaccharides); 3) persistent hydrogen bonds are observed for all disaccharides (except (1-->6)-linked) and typically involve a hydrogen donor in the reducing residue and an acceptor in the nonreducing one; 4) the probability distributions associated with the glycosidic dihedral angles and psi are essentially unimodal for all disaccharides, and full rotation around these angles occurs at most once or twice for (never for psi) on the 50-ns timescale; and 5) the timescales associated with torsional transitions (except around and psi) range from approximately 30 ps (rotation of hydroxyl groups) to the nanosecond range (rotation of the lactol and hydroxymethyl groups, and around the omega-glycosidic dihedral angle in (1-->6)-linked disaccharides).

Carbohydrate Sequence↗
PubMedDate not supplied

Phosphorus desorption dynamics in soil and the link to a dynamic concept of bioavailability.

Soils under intensive livestock farming and heavily fertilized with animal manure may have elevated soil phosphorus (P) contents. We determined P desorption kinetics in batch experiments using soils from a pot experiment where grass was cropped on a P-rich noncalcareous sandy soil without P addition, to lower the soil P content. A diffusion model was used to describe P desorption kinetics from a spherical aggregate. The model was calibrated with data from the batch experiments. Simulation results show that in the pot experiment, P desorption from the solid phase of the inner layers was initially far from equilibrium with the rest of the aggregate, but desorption came closer to equilibrium as the soil P content decreased further. A simple tool is presented, referred to as the dynamic bioavailability index (DBI), to determine whether kinetics of P desorption limits plant uptake. This tool is the dimensionless ratio of the modeled maximal diffusive flux from soil aggregates to solution and the plant uptake rate measured in the pot experiment. The DBI was initially much larger than one; the maximal possible P desorption rate exceeded the uptake rate, so uptake was not limited by desorption. The DBI stabilized at a value somewhat larger than one after a while, due to soil transport limitations. This decrease coincided with a large decrease of the P content in the grass to a value (far) below what is considered as optimal; the supply rate of P from soil to the root cannot meet the demand needed for optimal P uptake. The DBI could be seen as a promising onset to a new dynamic approach of bioavailability.

Adsorption↗
PubMed1999

Cervical myelopathy due to dynamic compression by the laminectomy membrane: dynamic MR imaging study.

Dynamic magnetic resonance (MR) imaging is useful in assessing delayed neurologic deterioration after multilevel cervical laminectomy. The authors report a case of a 75-year-old woman who deteriorated 24 years after a C4-C7 laminectomy. When the extension MR demonstrated marked spinal cord compression attributable to a laminectomy membrane, the patient had an anterior diskectomy and fusion performed, after which she demonstrated significant neurologic improvement. In this and other cases, the dynamic MR may be a useful tool in discerning the etiology of the delayed neurologic changes occurring in postoperative patients.

Aged↗
PubMed1999

On the convergence of the conformational coordinates basis set obtained by the essential dynamics analysis of proteins' molecular dynamics simulations.

In this article we present a quantitative evaluation of the convergence of the conformational coordinates of proteins, obtained by the Essential Dynamics method. Using a detailed analysis of long molecular dynamics trajectories in combination with a statistical assessment of the significance of the measured convergence, we obtained that simulations of a few hundreds of picoseconds are in general sufficient to provide a stable and statistically reliable definition of the essential and near constraints subspaces, at least within the nanoseconds time range. Proteins 1999;36:419-424.

Algorithms↗
PubMed2000

Enzyme activity and dynamics: xylanase activity in the absence of fast anharmonic dynamics.

The activity and dynamics of a simple, single subunit enzyme, the xylanase from Thermotoga maritima strain Fj SS3B.1 have been measured under similar conditions, from -70 to +10 degrees C. The internal motions of the enzyme, as evidenced by neutron scattering, undergo a sharp transition within this temperature range; they show no evidence for picosecond-timescale anharmonic behaviour (e.g. local diffusive motions or jumps between alternative conformations) at temperatures below -50 degrees C, whereas these motions are strongly activated at higher temperatures. The activity follows Arrhenius behaviour over the whole of the temperature range investigated, -70 to +10 degrees C. The results indicate that a temperature range exists over which the enzyme rate-limiting step is independent of fast anharmonic dynamics.

Enzyme Activation↗
PubMed2000

Dynamics of proteins predicted by molecular dynamics simulations and analytical approaches: application to alpha-amylase inhibitor.

The dynamics of alpha-amylase inhibitors has been investigated using molecular dynamics (MD) simulations and two analytical approaches, the Gaussian network model (GNM) and anisotropic network model (ANM). MD simulations use a full atomic approach with empirical force fields, while the analytical approaches are based on a coarse-grained single-site-per-residue model with a single-parameter harmonic potential between sufficiently close (r </= 7 A) residue pairs. The major difference between the GNM and the ANM is that no directional preferences can be obtained in the GNM, all residue fluctuations being theoretically isotropic, while ANM does incorporate directional preferences. The dominant modes of motions are identified by (i) the singular value decomposition (SVD) of the MD trajectory matrices, and (ii) the similarity transformation of the Kirchhoff matrices of inter-residue contacts in the GNM or ANM. The mean-square fluctuations of individual residues and the cross-correlations between domain movements retain the same characteristics, in all approaches-although the dispersion of modes and detailed amplitudes of motion obtained in the ANM conform more closely with MD results. The major weakness of the analytical approaches appears, on the other hand, to be their inadequacy to account for the anharmonic motions or multimeric transitions driven by the slowest collective mode observed in MD. Such motions usually suffer, however, from MD sampling inefficiencies, and multiple independent runs should be tested before making conclusions about their validity and detailed mechanisms. Overall this study invites attention to (i) the robustness of the average properties (mean-square fluctuations, cross-correlations) controlled by the low frequency motions, which are invariably reproduced in all approaches, and (ii) the utility and efficiency of the ANM, the computational time cost of which is of the order of "minutes" (real time), as opposed to "days" for MD simulations. Proteins 2000;40:512-524.

Computer Simulation↗
PubMed2000

Bacterial dynamics in first year sea ice and underlying seawater of Saroma-ko Lagoon (Sea of Okhotsk, Japan) and resolute passage (High Canadian Arctic): inhibitory effects of ice algae on bacterial dynamics.

The seasonal development of bacterial abundance in first year bottom ice and underlying seawater were studied at Saroma-ko Lagoon in Hokkaido, Japan, and at Resolute Passage in the High Canadian Arctic during the algal bloom in spring 1992. The aim of this study was to evaluate whether the high algal concentrations reached during the bloom of ice algae have inhibitory effects on bacterial dynamics. Bacterial abundance (measured as total cell count and colony-forming units CFU) increased with the increase of the algal biomass up to 500 micrograms Chla.L-1 in both locations. Culturable fraction (measured as the percentage of CFU counts versus the total cell counts) was between 7% and 22% at Saroma-ko, and approximately 0.08% at Resolute Passage. When algal biomass exceeded 500 micrograms of Chla.L-1, both bacterial abundance and culturable fraction decreased significantly. There was a maximum threshold of algal biomass (between 500 and 800 micrograms of Chla.L-1) after which bacterial dynamics become negatively coupled to the algal biomass. These results suggest that bactericidal and/or bacteriostatic compounds from these extremely high algal concentrations could explain the decrease in bacterial abundance and culturability in bottom ice observed after the ice algae bloom.

Arctic Regions↗
PubMed2001

Pro-inflammatory--anti-inflammatory cytokine dynamics mediated by cytokine-receptor dynamics in monocytes.

Many of the major human diseases, both infectious (septic shock syndromes) and idiopathic (for example, rheumatoid arthritis), are driven by the production of the pro-inflammatory cytokines interleukin-1 (IL-1) and tumour necrosis factor-alpha (TNF-alpha) produced by monocytes and macrophages. These key pro-inflammatory cytokines can, in turn, stimulate the production of additional cytokines which, in totality, generate tissue pathology. A major deactivator of activated, cytokine-producing monocytes and macrophages is the anti-inflammatory cytokine interleukin-10 (IL-10). It is known that the interactions between these three cytokines are pivotal in terms of health and pathology, but almost nothing is known of the dynamics of these interactions. In this study we have modelled the autocrine interactions of TNF-alpha, IL-1 and IL-10 with monocytes. The model constructed is a six-dimensional, continuous-time dynamical system, with free IL-1 and IL- 10 concentrations in the cell's vicinity, and the proportions of bound and free IL-1 and IL-10 cell-surface receptors, which transduce the cell's response to stimulation, as the state variables. The monocyte is assumed to be initially in a quiescent state, and it is stimulated to produce IL-1 by an external stimulus (e.g. exposure to TNF-alpha or lipopolysaccharide, LPS). This in turn invokes an autocrine IL-1 response, and also induces the production of the anti-inflammatory cytokine IL-10, which acts to downregulate IL-1 production. These responses are mediated by specific cell-surface receptors, the concentrations of which may also be subject to stimulated upregulation. We analyse a reduced, four-dimensional version of the model, and explore its asymptotic states. We find a variety of possible outcomes: runaway IL-1 production, multiple stable equilibria, stable limit cycles, and, exceptionally, quasi-periodic behaviour. These behaviours depend crucially on the form of the cell's response functions. The possible biological implications of these phenomena are discussed.

Arthritis, Rheumatoid↗
PubMed2001

Detection of the dynamics of odour emissions from pig farms using dynamic olfactometry and an electronic odour sensor.

The dynamics of odour emissions from a pig house was investigated by olfactometry and using an electronic odour sensor. In addition, several suggested influencing factors on the odour emission were measured to get insight into the reasons for the fluctuation of the odour emission. Odour emission tended to increase over the fattening period f rom August to November 2000 by a factor of two to three, although temperature and air-flow rate decreased according to the seasons. Feeding caused a significant temporary rise in animal activity, dust and odour concentration resulting in an increase of odour emission. The sensor signals of an electronic odour sensor increased simultaneously and showed a good relation to the odour concentration. There is a promising potential of electronic odour sensors to detect the dynamic and the level of odour concentrations. Further investigation will be done, to ensure a standardised measuring protocol and to obtain a calibration of electronic odour sensor signals direct to odour concentrations.

Agriculture↗
PubMed2000

[Dynamics of soil P pool in a long-term fertilizing experiment of wheat-maize rotation. II. Dynamics of soil Olsen-P and inorganic P].

Studies on the dynamics of soil Olsen-P and different form inorganic P in the long-term fertilizing experiment of winter wheat-summer maize-->spring maize rotation showed that the contents of Olsen-P and inorganic P were changed by the accumulation and consumption of P in soil. In P0 treatments, Olsen-P decreased gradually, and then, trended to the critical level. When fertilizing amount was basically equal to the intake by crops, the balance of Olsen-P was dynamically maintained. The contents of Olsen-P and inorganic P were enhanced, when applied P was larger than the P intake by crops. The major contents of residual inorganic P were Ca2-P and Ca8-P, both accounting for 52.3% of total inorganic P in average, and Ca8-P accounting for 78.3%. Al-P and Fe-P accounted for 26.1%, and O-P and Ca10-P accounted for 20.4% of total inorganic P. The availability of fertilizer P was obviously increased by long-term applying fertilizer P together with manure, compared with applying fertilizer P alone.

China↗
PubMed2002

Days and knights discussing membrane dynamics in endocytosis: meeting report from the Euresco/EMBL Membrane Dynamics in Endocytosis, 6--11 October in Tomar, Portugal.

The Euresco/EMBL sponsored meeting on 'Membrane Dynamics in Endocytosis' took place on 6--11 October in Tomar, Portugal. Here we report on the 5 full days of exciting talks and active poster sessions that covered topics ranging from the mechanisms of clathrin-mediated endocytosis, the regulation of phagocytosis, caveolae dynamics and function, the role of lipids in regulating endocytic transport, the formation of and sorting into and out of multivesicular bodies, new links between the actin cytoskeleton and vesicular transport, and emerging roles for endocytic trafficking in signal transduction and development.

Actins↗
PubMedDate not supplied

[Molecular dynamics of oligopeptides. 4. Dynamic characteristics of frequently and rarely occurring dipeptide fragments of proteins].

The existence of differences in the dynamic organization of frequently and the rarely occurring dipeptide fragments in globular and membrane proteins was shown. The dynamic isomorphism and the collective degrees of freedom in these fragments were analyzed. A topological classification of the maps of the levels of free energy for pairs of dihedral angles of the main chain and side residues was carried out.

Algorithms↗
PubMed2005

Function of dynamic membrane in self-forming dynamic membrane coupled bioreactor.

The Self-Forming Dynamic Membrane Coupled Bioreactor (SFDMBR), which uses coarse pore-sized material to separate solid and liquid in bioreactors, has some advantages compared with MBR using micro-/ultra-filtration membranes, for example, low module cost and high flux. The cake layer and gel layer formed on the surface and in the pores of the material during filtration played an important role, called self-forming dynamic membrane (DM), which mainly consisted of activated sludge. In this study, the function of DM in pollutant removal was investigated. It was found that DM could remove some organic matter (12.6 mg L(-1) on average) and total nitrogen (3.01 mg L(-1) on average) in the supernatant. Colloids and organic nitrogen were partly removed by DM while DOC, ammonia nitrogen and nitrate nitrogen removal by DM varied from negative to positive, which resulted from the combination of various biological activities, e.g. nitrification, biological utilization and so on. DO concentration in DM decreased with the depth and reached zero at about 1.5-2.5 mm depth. The organic degradation activity and nitrification activity of the biomass suspended in the bioreactor were higher than those of the biomass in the cake layer, which might be caused by the low DO concentration and low organic pollutant content in DM.

Ammonia↗
PubMed1991

[A return to callus healing using dynamic osteosynthesis procedures. Principles, indications, complications, x-ray diagnosis of interlocking nailing and dynamic monofixators in comparison with conventional bone plates].

A disproportionately high rate of complications such as osteomyelitis, nonunion and refracture after plating have brought about a change in our understanding of the process of fracture healing. Locked nailing and dynamic external Monofixators, however, avoid fracture exposure obviate the necessity of arranging fragments and aim at callus healing of fractures. Fracture hematoma and axial micromovements of these dynamic stabilizing devices are two of the yet known elements to promote callus production.

Bone Nails↗
PubMed1993

[Dynamic fracture stabilization with the DYBASTAB--with the help of dynamic compensating stabilizers--DYNASTAB D-K--new outlook on treating fractures].

Dynamic stabilizer DYNASTAB D-K for functional, ambulatory treatment of fractures is presented. The possibility to include an active hinge enabling physiological movement of the injured or remaining in the injured zone joint allows for an early mobilization of the limb concerned. Solid, spatial screws anchoring enables early axial dynamization within the union zone. Plastic cubes reduce the weight and prevent disturbance of electrophysiology of the fracture healing. The hydraulic chamber pressure measurement taken at the load will permit the assessment of bony union consolidation.

Bone Screws↗