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At least 55 records · Page 3Linked to original sources
PubMed2002

Verification of dynamic and segmental IMRT delivery by dynamic log file analysis.

A program has been developed to evaluate the delivered fluence of step-and-shoot segmental and sliding window dynamic multileaf collimator (MLC) fields. To automate these checks, a number of tools have been developed using data available from the dynamic log files that can be created each time a dynamic delivery occurs. Experiments were performed with a Varian 2100EX with a 120 leaf MLC equipped with dynamic capabilities. A dynamic leaf sequence is delivered and measured with film or an amorphous silicon imager. After delivery, the dynamic log file is written by the accelerator control system. The file reports the expected and actual position for each leaf and the dose fraction every 0.055 seconds. Leaf trajectories are calculated from this data and expected and actual fluence images are created from the difference of opposing leaf trajectories. These images can be compared with the expected delivery, measurements, and calculations of fluence. Tools have been developed to investigate other aspects of the delivery, such as specific leaf errors, beam hold-off flags sent by the control system to the MLC, and gap widths. This program is part of a semi-automated quality assurance (QA) system for pretreatment fluence verification and daily treatment verification of dynamic multileaf collimation (DMLC) delivery.

Computer Simulation↗
PubMed2003

Detection of hepatocellular carcinoma: comparison of dynamic MR imaging with dynamic double arterial phase helical CT.

OBJECTIVE: Three-dimensional (3D) Fourier transformation-enhanced fast gradient-echo sequences with a special spectral inversion recovery pulse and fat suppression developed for abdominal imaging, including MR angiography, can show enhanced areas clearly. The purpose of this study was to evaluate the efficacy of dynamic MR imaging with the pulse sequences for the detection of hypervascular hepatocellular carcinoma by comparing it with that of dynamic helical CT with double arterial phase imaging. SUBJECTS AND METHODS: Fifty-three patients with 103 hypervascular hepatocellular carcinoma nodules who underwent both dynamic MR imaging with 3D Fourier transformation-enhanced fast gradient-echo sequences with a special spectral inversion recovery pulse and dynamic helical CT with double arterial phase imaging were enrolled in the study. For dynamic MR imaging, unenhanced, arterial, portal venous, and equilibrium phase images were obtained before and approximately 19, 60, and 120 sec, respectively, after injection of gadopentetate dimeglumine. Three observers independently interpreted the images obtained with each technique in a blinded manner and in random order. RESULTS: Mean sensitivity and positive predictive values of CT for hypervascular hepatocellular carcinoma (66% and 97%, respectively) were higher than those of MR imaging (63% and 96%, respectively), but there was no significant difference in detecting sensitivity among the observers (p < 0.05). CT and MR imaging were complementary, with some tumors undetected by CT but revealed on MR imaging. There was also no significant difference in A(z) values between CT (0.74) and MR imaging (0.71) (p < 0.05). CONCLUSION: Dynamic MR imaging with 3D Fourier transformation-enhanced fast gradient-echo sequences with a special spectral inversion recovery pulse is recommended to improve the detection of hypervascular hepatocellular carcinoma nodules in addition to the use of dynamic helical CT with double arterial phase imaging.

Aged↗
PubMed2001

Toward an interpretation of dynamic neural activity in terms of chaotic dynamical systems.

Using the concepts of chaotic dynamical systems, we present an interpretation of dynamic neural activity found in cortical and subcortical areas. The discovery of chaotic itinerancy in high-dimensional dynamical systems with and without a noise term has motivated a new interpretation of this dynamic neural activity, cast in terms of the high-dimensional transitory dynamics among "exotic" attractors. This interpretation is quite different from the conventional one, cast in terms of simple behavior on low-dimensional attractors. Skarda and Freeman (1987) presented evidence in support of the conclusion that animals cannot memorize odor without chaotic activity of neuron populations. Following their work, we study the role of chaotic dynamics in biological information processing, perception, and memory. We propose a new coding scheme of information in chaos-driven contracting systems we refer to as Cantor coding. Since these systems are found in the hippocampal formation and also in the olfactory system, the proposed coding scheme should be of biological significance. Based on these intensive studies, a hypothesis regarding the formation of episodic memory is given.

Brain↗
PubMed2002

Assessment of the RR versus QT relation by a new symbolic dynamics method. Gender differences in repolarization dynamics.

A new method based on symbolic dynamics was applied to assess RR-QT dynamics and to compare gender differences. Segments of 10,000 RR and QT from the night were selected. The values of RR and QT were coded as follows. Each RR and QT interval was compared with their means in the last 50 beats [xRR, xQT]; when the interval was larger than x + delta then it was coded as a "2", where delta is the tolerance parameter; when it was less than x - delta-the code was a "0"; when it was larger than x-delta and and the less than x+delta-then it was coded as a "1." The tolerance parameter "delta" was equal to 10 ms for RR and 4 ms for QT. We obtained pairs of symbols representing the values of RR and QT-symbolic words. The results were presented in form of the probability density of the symbolic words. Mean RR, mean QT, SDRR, SDQT, QTc (Bazett formula) were also calculated. Electrocardiogram data of healthy individuals: 20 women and 20 men (mean age 39 +/- 12) were analyzed. There were significant gender differences in RR-QT dynamics. During heart rate acceleration the probability of QT shortening (the probability of the word "00") was higher in men than in women (P =.003). During heart rate deceleration QT lengthening (the word "22") was more frequently observed in men than in women (P =.003) as well. The QT reaction to RR interval changes is less complex in women than in men. In discriminant analysis, when QTc was ignored in the model, the RR-QT dynamics separated genders with 67% accuracy (chi(2) = 9.1, P <.003). RR-QT dynamics can be analyzed with symbolic dynamics methods. The gender differences in repolarization are not only due to QTc duration alone but also result from the dependence of the duration of QT on the RR duration.

Adult↗
PubMed2005

Link between population dynamics and dynamics of Darwinian evolution.

We provide the link between population dynamics and the dynamics of Darwinian evolution via studying the joint population dynamics of similar populations. Similarity implies that the relative dynamics of the populations is slow compared to, and decoupled from, their aggregated dynamics. The relative dynamics is simple, and captured by a Taylor expansion in the difference between the populations. The emerging evolution is directional, except at the singular points of the evolutionary state space. Here "evolutionary branching" may occur. The diversification of life forms thus is demonstrated to be a natural consequence of the Darwinian process.

Biodiversity↗
PubMed2001

Effect of glycosylation on structure and dynamics of MHC class I glycoprotein: a molecular dynamics study.

Complex carbohydrates linked to glycoproteins are recently being implicated to play a variety of biological roles. The lack of well-resolved crystallographic coordinates of the carbohydrates makes it difficult to assess the contributions of the glycan chain on protein structure and dynamics. We have modeled two different oligosaccharides NeuNAc2Gal3Man3GlcNAc5Fuc and Man3GlcNAc4 to generate two glycosylation variants of major histocompatibility complex (MHC) class I glycoprotein. Molecular dynamics simulations of the isolated fourteen- and seven-residue oligosaccharides have been done in vacuo and in solution. The dynamics of the two glycoforms of MHC class I protein have been simulated in solution in the free as well as in the peptide-bound form. Good agreement between the calculated solution conformations of the oligosaccharides in isolated and conjugated forms and the average conformations obtained from x-ray or NMR data was observed for most of the glycosidic linkages. These molecular dynamics simulations of the isolated glycan chains and the glycoconjugates reveal the details of the conformational flexibility of the glycan chains; they also provide atomic level details of protein-carbohydrate interactions and the effect of the ligand binding on the carbohydrate structure and dynamics. It was found that though there is some flexibility in some of the glycosidic linkages in the isolated oligosaccharides, in the protein-conjugated form the linkages adopt more restricted conformations. The glycan chains protrude out into the solvent and might hinder the lateral association of the proteins. The presence of the bulky glycan chains does not affect the average backbone fold of the protein but induces local changes in protein structure and dynamics. It has been noted that the extent of the changes depends upon the nature of the attached glycan chain. The glycan chains do not appear to influence the peptide binding property of the protein directly, but may stabilize the protein residues that are involved in ligand binding.

Carbohydrate Conformation↗
PubMed1991

Dynamic light scattering from weakly bending rods: estimation of the dynamic bending rigidity of the M13 virus.

A theory is presented for the dynamic structure factor [S(K,t]) of weakly bending rods. This treatment is based on a discrete bead model for the Brownian dynamics in which all bead motions associated with bending are constrained to occur in a plane perpendicular to the end-to-end vector, thus prohibiting extension or contraction along that axis. Preset hydrodynamic interactions are incorporated in a numerically exact manner. The predicted normalized dynamic structure factor S(K,t)/S(K,0) should be valid for short times t such that the rms rotation of the end-to-end vector around any transverse axis is much less than 1.0 radian. With geometrical parameters appropriate for the M13 virus, the intensity autocorrelation function G(2) (K,t) = 1 + magnitude of S(K,t)/S(K,0)2 is calculated over a range of times and scattering vectors K for selected values of the persistence length P. The calculated G(2) (K,t) are fitted to a single exponential with unit baseline over the same range of times as the experimental photon correlation functions, and the apparent diffusion coefficients Dapp (K) are obtained from the best-fit relaxation times. For the sake of completeness, an exact expression is derived for the apparent diffusion coefficient obtained from the initial slope of the dynamic structure factor. However, this does not reduce to the known correct result in the rigid rod limit. To obtain the correct result, the limit of infinite bending rigidity must be taken before the limit of zero time. For this and other reasons, the initial slope value of Dapp (K) is not useful for weakly bending rods. Photon correlation functions are measured for the M13 virus, which is virtually identical to the often-studied fd virus. The experimental photon correlation functions are fitted over 8 relaxation times to a single-exponential plus baseline, and the Dapp (K) are calculated from the best-fit relaxation times. Theoretical curves of Dapp (K) vs K2 for selected values of P are compared with the experimental data, which are satisfactorily reproduced when P = 22000 +/- 2000 A. This dynamic value is close to the static value, P = 20000 +/- 2000 A, reported for the very similar fd virus. The most recent theories of Maeda and Fujime and their dynamic light scattering studies of fd virus are compared with the present results in some detail. Their optimum value of P is in surprisingly good agreement with the present value.

Bacteriophages↗
PubMed1999

Conformational dynamics and molecular recognition: backbone dynamics of the estrogen receptor DNA-binding domain.

We examined the internal mobility of the estrogen receptor DNA-binding domain (ER DBD) using NMR15N relaxation measurements and compared it to that of the glucocorticoid receptor DNA-binding domain (GR DBD). The studied protein fragments consist of residues Arg183-His267 of the human ER and residues Lys438-Gln520 of the rat GR. The15N longitudinal (R1) and transverse (R2) relaxation rates and steady state {1H}-15N nuclear Overhauser enhancements (NOEs) were measured at 30 degrees C at1H NMR frequencies of 500 and 600 MHz. The NOE versus sequence profile and calculated order parameters for ER DBD backbone motions indicate enhanced internal dynamics on pico- to nanosecond time-scales in two regions of the core DBD. These are the extended strand which links the DNA recognition helix to the second zinc domain and the larger loop region of the second zinc domain. The mobility of the corresponding regions of the GR DBD, in particular that of the second zinc domain, is more limited. In addition, we find large differences between the ER and GR DBDs in the extent of conformational exchange mobility on micro- to millisecond time-scales. Based on measurements of R2as a function of the15N refocusing (CPMG) delay and quantitative (Lipari-Szabo-type) analysis, we conclude that conformational exchange occurs in the loop of the first zinc domain and throughout most of the second zinc domain of the ER DBD. The conformational exchange dynamics in GR DBD is less extensive and localized to two sites in the second zinc domain. The different dynamical features seen in the two proteins is consistent with previous studies of the free state structures in which the second zinc domain in the ER DBD was concluded to be disordered whereas the corresponding region of the GR DBD adopts a stable fold. Moreover, the regions of the ER DBD that undergo conformational dynamics on the micro- to millisecond time-scales in the free state are involved in intermolecular protein-DNA and protein-protein interactions in the dimeric bound state. Based on the present data and the previously published dynamical and DNA binding properties of a GR DBD triple mutant which recognize an ER binding site on DNA, we argue that the free state dynamical properties of the nuclear receptor DBDs is an important element in molecular recognition upon DNA binding.

Amino Acid Sequence↗
PubMed2000

The dynamics of protein hydration water: a quantitative comparison of molecular dynamics simulations and neutron-scattering experiments.

We present results from an extensive molecular dynamics simulation study of water hydrating the protein Ribonuclease A, at a series of temperatures in cluster, crystal, and powder environments. The dynamics of protein hydration water appear to be very similar in crystal and powder environments at moderate to high hydration levels. Thus, we contend that experiments performed on powder samples are appropriate for discussing hydration water dynamics in native protein environments. Our analysis reveals that simulations performed on cluster models consisting of proteins surrounded by a finite water shell with free boundaries are not appropriate for the study of the solvent dynamics. Detailed comparison to available x-ray diffraction and inelastic neutron-scattering data shows that current generation force fields are capable of accurately reproducing the structural and dynamical observables. On the time scale of tens of picoseconds, at room temperature and high hydration, significant water translational diffusion and rotational motion occur. At low hydration, the water molecules are translationally confined but display appreciable rotational motion. Below the protein dynamical transition temperature, both translational and rotational motions of the water molecules are essentially arrested. Taken together, these results suggest that water translational motion is necessary for the structural relaxation that permits anharmonic and diffusive motions in proteins. Furthermore, it appears that the exchange of protein-water hydrogen bonds by water rotational/librational motion is not sufficient to permit protein structural relaxation. Rather, the complete exchange of protein-bound water molecules by translational displacement seems to be required.

Computer Simulation↗
PubMed1999

Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution.

We have examined the temperature dependence of motions in a cryosolution of the enzyme glutamate dehydrogenase (GDH) and compared these with activity. Dynamic neutron scattering was performed with two instruments of different energy resolution, permitting the separate determination of the average dynamical mean square displacements on the sub-approximately 100 ps and sub-approximately 5 ns time scales. The results demonstrate a marked dependence on the time scale of the temperature profile of the mean square displacement. The lowest temperature at which anharmonic motion is observed is heavily dependent on the time window of the instrument used to observe the dynamics. Several dynamical transitions (inflexions of the mean squared displacement) are observed in the slower dynamics. Comparison with the temperature profile of the activity of the enzyme in the same solvent reveals dynamical transitions that have no effect on GDH function.

Calorimetry, Differential Scanning↗
PubMed1999

Long-time dynamics of Met-enkephalin: comparison of theory with Brownian dynamics simulations.

A recent theory for the long time dynamics of flexible chain molecules is applied for the first time to a peptide of biological importance, the neurotransmitter met-enkephalin. The dynamics of met-enkephalin is considerably more complicated than that of the previously studied glycine oligomers; met-enkephalin contains the interesting motions of phenyl groups and of side chains relative to the backbone, motions that are present in general flexible peptides. The theory extends the generalized Rouse (GR) model used to study the dynamics of polymers by providing a systematic procedure for including the contributions from the memory function matrices neglected in the GR theory. The new method describes the dynamics by time correlation functions instead of individual trajectories. These correlation functions are analytically expressed in terms of a set of equilibrium averages and the eigenvalues and eigenfunctions of the diffusion operator. The predictions of the theory are compared with Brownian dynamics (BD) simulations, so that both theory and simulation use identical potential functions and solvent models. The theory thus contains no adjustable parameters. Inclusion of the memory function contributions profoundly affects the dynamics. The theory produces very good agreement with the BD simulations for the global motions of met-enkephalin. It also correctly predicts the long-time relaxation rate for local motions.

Biophysical Phenomena↗