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At least 541 records · Page 30Linked to original sources
PubMed2005

Studying reactive processes with classical dynamics: rebinding dynamics in MbNO.

A new surface-crossing algorithm suitable for describing bond-breaking and bond-forming processes in molecular dynamics simulations is presented. The method is formulated for two intersecting potential energy manifolds which dissociate to different adiabatic states. During simulations, crossings are detected by monitoring an energy criterion. If fulfilled, the two manifolds are mixed over a finite number of time steps, after which the system is propagated on the second adiabat and the crossing is carried out with probability one. The algorithm is extensively tested (almost 0.5 mus of total simulation time) for the rebinding of NO to myoglobin. The unbound surface (Fe...NO) is represented using a standard force field, whereas the bound surface (Fe-NO) is described by an ab initio potential energy surface. The rebinding is found to be nonexponential in time, in agreement with experimental studies, and can be described using two time constants. Depending on the asymptotic energy separation between the manifolds, the short rebinding timescale is between 1 and 9 ps, whereas the longer timescale is about an order of magnitude larger. NO molecules which do not rebind within 1 ns are typically found in the Xenon-4 pocket, indicating the high affinity of NO to this region in the protein.

Algorithms↗
PubMedDate not supplied

Leaf litter dynamics and nitrous oxide emission in a Mediterranean riparian forest: implications for soil nitrogen dynamics.

Mediterranean riparian zones can experience severe drought periods that lead to low soil moisture content, which dramatically affects their performance as nitrate removal systems. In the Mediterranean riparian zone of this study, we determined that N2O emission was practically nil. To understand the role of forest floor processes in nitrogen retention of a Mediterranean riparian area, we studied leaf litter dynamics of two tree species, London planetree [Platanus x acerifolia (Aiton) Willd.] and alder [Alnus glutinosa (L.) Gaertn.], for two years, along with soil nitrogen mineralization rates. Annual leaf litter fall equaled 562.6 +/- 10.1 (standard error) g dry wt. m(-2), 68% of which was planetree and 32% of which was alder. The temporal distribution of litterfall showed a two-peak annual cycle, one occurring in midsummer, the other in autumn. Planetree provided the major input of organic nitrogen to the forest floor, and the amount of planetree leaves remaining on the forest floor was equivalent to approximately four years of stock. Leaf litter decomposition was three times higher for alder (decay coefficient [k] = 1.13 yr(-1)) than for planetree (k = 0.365 yr(-1)). Mineralization rates showed a seasonal pattern, with the maximum rate in summer (1.92 mg N kg(-1) d(-1)). Although the forest floor was an important sink for nitrogen due to planetree leaf accumulation, 7.5% of this leaf litter was scoured to the streambed by wind. This loss was irrelevant for alder leaves. Due to the litter quality, the forest floor of this Mediterranean riparian forest acts as a nitrogen sink.

Betulaceae↗
PubMed1984

Quantitative relationships between dynamics and kinetics of drugs: a systems dynamics approach.

The body is considered as a system composed of a number of subsystems. The response(s) of a drug is a complicated function of the concentration in the blood plasma, which in turn is some function of the dosage input. The dose-response curve of a drug in a subsystem (e.g., isolated organ) is, over a limited concentration range, a linear function of the logarithm of the concentration. The logarithm of the concentration in the plasma is, again over a limited range, a linear function of time. Time-effect curves in the intact organism may therefore be a linear function of time. In reality, the situation is far more complex, because of nonlinear kinetics, nonlinear kinetics of effects in the subsystems, and adaptation phenomena based on feedback regulation, as is illustrated by examples. It is concluded that one should not only consider the body as a system but also study it as a system; that is, apply the dynamic system approach in pharmacology.

Acetylcholine↗
PubMedDate not supplied

[Molecular dynamics of oligopeptides. 3. Maps of levels of free energy of modified dipeptides and dynamic correlation in amino acid residues].

A method of free energy maps for studying the dynamic correlations of fluctuations in molecules with conformational mobility is proposed. An agreement between the structure of the free energy level map and the type of the corresponding cross-correlation function (in the presence and absence of the correlation of fluctuations in conformational freedom degree in modified dipeptides) was established.

Amino Acids↗
PubMed1992

[Mathematical modeling of the dynamics of frequency of the mutation process. I. Age features of SA frequency dynamics tendency].

A mathematical method for modelling SA frequency dynamics tendencies, depending on age, for different fixation moments and in general for the whole interval of observation is suggested. The criteria of remainder dispersion attitude is used for choosing an optimal model. The initial hypothesis about discrepancies distribution law is used for checking adequateness of the optimal model to the research process. In addition, aposteriory trust intervals are built for the initial and forecast SA frequency values and the hit into them corresponding the experimental values of SA frequencies is controlled. An example of practical realization of the model proposed is considered and the results obtained analysed.

Models, Theoretical↗
PubMed1991

Conformational dynamics of the formyl peptide receptor: a prototype for studies of receptor dynamics and binding pocket structure.

We have used spectrofluorometric and flow cytometric techniques to examine the interactions of formyl peptide ligands (L) with their cell surface receptors (R). Kinetic studies suggest that L binds to R at a diffusion limited rate and that R undergoes rapid transitions involving three states (LR, LRG, the ternary complex of L and R with the G protein, and a desensitized receptor "LRX" which forms within seconds) prior to internalization. A spectroscopic analysis of the interaction between L and R show that the binding pocket of R is large enough to contain no more than 6 amino acids and that a fluorescein-labelled pentapeptide is quenched upon binding to R. We hypothesize that histidine 90 (putatively located in the extracellular loop connecting the second and third transmembrane domains) protonates L and quenches the probe. New technology will extend the analysis of structure and dynamics to low affinity peptide receptors of living biological systems. Such technology will have implications in the design of peptidomimetic ligand and drug molecules.

Animals↗
PubMed1985

[Mathematical modeling of the dynamics of the intensity of the mutation process. II. Dynamic evaluation of the frequencies of hereditary pathology].

Mathematical models were devised to evaluate the dynamics of hereditary pathology frequencies, based on registration of spontaneous abortions, congenital malformations and Down disease in the city of Angarsk during 12 years. The models provide an opportunity to detect the fact of the presence or absence of temporary tendencies. The average frequency of spontaneous abortions and units of hereditary pathology have not been changed for 12 years, the frequency of Down disease being decreased, while congenital malformations seem to change with certain periodicity. In cases of insufficient sample sizes, the prolongation of observation for a period of several years does not facilitate the task of construction of models which could adequately describe multifactor-conditioned processes.

Abortion, Spontaneous↗
PubMed1988

Integrated dynamic image of the liver: a new dynamic study for evaluation of liver disease.

A new method of hepatic dynamic imaging, which we designated an integrated image, is described. In this new method, the passage of the radiocolloid from the subclavian vein through the central circulation system to the abdominal organs and its accumulation in the liver was recorded on a single X-ray film. With this method, hepatic blood flow can be easily evaluated by comparison of the density between the liver and lung. Increased or decreased perfusion of the space-occupying lesions in the liver can also be evaluated. This method is very simple in technique and can be performed routinely in any hospital which has nuclear medicine facilities.

Adult↗
PubMed1978

[Age-related dynamics of outpatient forms of schizophrenia (on the age-related dynamics of so-called latent schizophrenia in light of late catamneses in senescence)].

The report contains a study of 45 patients aged 60--84 in whom during the entire life there were gradually increasing subclinical symptoms of schizophrenia: emotional shallowness, oddness, episodic rudimentary affective or paranoial disturbances. However, the level of adaptation and mental activity did not suffer significantly. The age-specific dynamics of such forms corresponded to general regularities in the development of schizophrenia: in the involutional period there was revivification of the above-mentioned symptoms of schizophrenia while in senescence only paranoial disorders and an increase of deficitary changes remained. The author discusses the question of justified diagnosis of latent schizophrenia in such cases.

Affective Symptoms↗
PubMed1996

[Usefulness of functional image of dynamic computed tomography (FID-CT) on acute cerebral ischemic disease: correlation between parameters of dynamic CT and angiographical findings].

We reported the correlation between the angiographical findings and parameters of the functional images of dynamic CT (FID-CT) in ten patients with cerebral ischemic disease. Six of these ten patients with an abnormal area on corrected mean transit time (CM) and time to peak (TP) had complete occlusion of intracerebral main arteries with poor collateral cerebral blood flow or no collateral flow on the angiography. Four patients with prolonged time only in the TP area, but not in the CM area, had stenosis or occlusion of the main trunk with satisfactory anterograde cerebral blood flow on the angiography. FID-CT is easy to apply for clinical use and said to be useful to predict arterial trunk occlusion or infarction volume. It might also be helpful to get further information about the intracerebral circulation disorders in the acute stage of cerebral ischemic disease.

Acute Disease↗
PubMed1996

[Dynamic magnetic resonance imaging versus dynamic echography in the staging of Peyronie's disease].

Clinical examination and ultrasonography are often the only evaluation needed for patient with Peyronie's disease. Magnetic resonance angiography (MRA), a new magnetic resonance imaging (MRI), improves tissue contrast between the fibrous plaque and the near structures. A total of 25 patients with Peyronie's disease underwent palpation, ultrasonography and MRI after dynamic improvement with intrapenile 10 micrograms prostaglandin E1. The patients were studied with conventional ultrasonography (US) (7.5 MHz) and with 1.5 T superconductive magnet (two-dimensional Fourier transform gradient-echo time-of-flight, 2DFT-TOF, sequences and conventional T1 and T2 spin echo (SE) sequences). The US evaluation demonstrated the presence of plaques in 18/25 patients (72%). The SE sequences revealed evidence of plaques in 10/25 patients (40%). MR angiograph enabled the correct evaluation of plaques in 23/25 patients (92%), and identified the involvement of the septum intercavernosum, that was not detected on both US and SE images. MRA provides accurate preoperative information fo correct evaluation of plaque extension in IPP.

Alprostadil↗
PubMed2006

Dynamic multipopulation and density dependent evolutionary games related to replicator dynamics. A metasimplex concept.

This paper contains the basic extensions of classical evolutionary games (multipopulation and density dependent models). It is shown that classical bimatrix approach is inconsistent with other approaches because it does not depend on proportion between populations. The main conclusion is that interspecific proportion parameter is important and must be considered in multipopulation models. The paper provides a synthesis of both extensions (a metasimplex concept) which solves the problem intrinsic in the bimatrix model. It allows us to model interactions among any number of subpopulations including density dependence effects. We prove that all modern approaches to evolutionary games are closely related. All evolutionary models (except classical bimatrix approaches) can be reduced to a single population general model by a simple change of variables. Differences between classic bimatrix evolutionary games and a new model which is dependent on interspecific proportion are shown by examples.

Biological Evolution↗
PubMed1993

[Dynamics of infectious disease transmission: a particular expression of predator-prey dynamics].

Infectious diseases in human populations are seldom seen as part of a permanently occurring phenomenon in natural ecosystems. Their relationships to predator-prey or host-parasite systems are not evident. The conceptual relationships between these systems is established through a basic deterministic model in this note, with special reference to populational fluctuations and epidemic recurrence.

Chile↗
PubMed1999

Incidental detection of acute myocardial infarction during routine performance of three-dimensional dynamic MR angiographic study with dynamic injection of gadolinium.

We report on the MR appearance of acute myocardial infarction in a 61-year-old man with Ehlers-Danlos syndrome using motion-independent, T2-weighted echo train spin echo and immediate post-gadolinium three-dimensional gradient echo imaging performed as an MRI angiographic study of the aortic arch. The region of acute infarction was of high signal intensity on the T2-weighted images and demonstrated greatly diminished enhancement on the immediate post-gadolinium three-dimensional gradient echo images. MRI findings showed good correlation with autopsy specimens obtained within 24 hours of the MRI study.

Aorta, Thoracic↗