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PubMed2001

Combining the advantages of step-and-shoot and dynamic delivery of intensity-modulated radiotherapy by interrupted dynamic sequences.

PURPOSE: A hybrid between step-and-shoot and dynamic operation, called interrupted dynamic sequences, was investigated for prostate intensity-modulated radiotherapy (IMRT) delivered by a multisegment close-in technique. The new delivery mode was compared to the step-and-shoot mode concerning dose distribution. METHODS AND MATERIALS: Segments suitable for dynamic transition were selected using a system of segment classes. Transitions were only allowed between two segments of the same class, keeping intended sharp in-field dose gradients unchanged. Delivery was performed by an Elekta SLiplus (Crawley, UK) linear accelerator equipped with a dynamic multileaf collimator (MLC). Because no modeling of the dose during the transitions is made, accurate dose measurements were performed. Dose profiles were measured using a linear ion chamber array (LA48, PTW-Freiburg). The suitability of this detector for measurements in sharp dose gradients was investigated first. In addition, field flatness was examined for segments with a low monitor unit (MU) count. Uncertainties in dose output were investigated using an ionization chamber (30001, PTW-Freiburg). RESULTS: Because linear array measured penumbrae are only slightly broader (< or = 0.4 mm for MLC collimated field) than those obtained using a diamond detector, the array is a good device for profile measurements. Uncertainties related with the use of low MU beam segments are very small (< 1% for segments of minimum 3 MU), giving no contra-evidence for the step-and-shoot mode. Interrupted dynamic sequences are shown to introduce only small dosimetric differences as compared to the step-and-shoot delivery. CONCLUSION: Both delivery modes, step-and-shoot and interrupted dynamic sequences, result in similar dose distributions for the forward planned prostate class solution.

Humans↗
PubMed2002

Backbone dynamics of the ribonuclease binase active site area using multinuclear ((15)N and (13)CO) NMR relaxation and computational molecular dynamics.

The nano-pico second backbone dynamics of the ribonuclease binase, homologous to barnase, is investigated with (15)N, (13)C NMR relaxation at 11.74 and 18.78 T and with a 1.1 ns molecular dynamics simulation. The data are compared with the temperature factors reported for the X-ray structure of this enzyme. The molecular dynamics and X-ray data correspond well and predict motions in the loops 56-61 and 99-104 that contain residues that specifically recognize substrate and are catalytic (His101), respectively. In contrast, the (15)N relaxation data indicate that these loops are mostly ordered at the nano-pico second time scale. Nano-pico second motions in the recognition loop 56-61 are evident from (13)CO-(13)C cross relaxation data, but the mobility of the catalytic loop 99-104 is not detected by (13)CO cross relaxation either. From the results of this and previous work [Wang, L., Pang, Y., Holder, T., Brender, J. R., Kurochkin, A., and Zuiderweg, E. R. P. (2001) Proc. Natl. Acad. Sci. U.S.A., 98, 7684-7689], the following dynamical characterization of the active site area of binase emerges: a beta sheet, rigid at all probed time scales, supports the catalytic residue Glu 72. Both substrate-encapsulating loops are mobile on both fast and slow time scales, but the fast motions of the loop which contains the other catalytic residue, His 101, as predicted by B-factors and computational molecular dynamics is not detected by NMR relaxation. This work strongly argues for the use of several measures in the study of protein dynamics.

Amino Acid Sequence↗
PubMed2004

Methyl group dynamics as a probe of the protein dynamical transition.

Hydrated proteins undergo a dynamical transition around 200 K from glasslike to liquidlike motion. Molecular dynamics simulations have been used to study the temperature dependence of the dynamics of ribonuclease A in the hydrated crystal, a model dehydrated powder, and aqueous solution. Changes in the dynamics accompanying the transition throughout the protein have been quantified in terms of the mean-squared fluctuations (MSFs) of methyl hydrogen atoms on the 100 ps time scale. In solution at 300 K the MSFs span a broad distribution, consistent with NMR relaxation measurements. The MSF distribution in the hydrated crystal at 300 K is qualitatively similar to the solution result, except for a slight shift to lower values, and dehydration results in a dramatic shift of the MSFs to lower values. As the temperature is lowered, the whole distribution of methyl group fluctuations in the hydrated crystal shifts to lower values. Most of the methyl groups in the hydrated protein display a nonlinear temperature dependence with a dynamical transition at approximately 200 K, but most methyl groups do not undergo a transition in the dehydrated protein. We conclude that the dynamical transition occurs throughout most of the protein and that solvent is required for the transition.

Computer Simulation↗
PubMed2005

Effects of solute-solvent proton exchange on polypeptide chain dynamics: a constant-pH molecular dynamics study.

A method for performing implicit-solvent molecular dynamics simulations at constant pH was applied to a pentapeptide acetyl-Ala-Asp-Ala-Lys-Ala-amide at pH 4. As a reference, molecular dynamics simulations were done for the same peptide with two variants of its fixed protonation patterns expected to dominate at pH 4, i.e., with a protonated and a deprotonated side chain of the Asp residue and the protonated Lys residue in both cases. The dynamic trajectories of the peptide were used to discuss the problem of the significance of the solute-solvent proton exchange phenomena for the dynamics and structural distributions of the polypeptide chain. The Asp-Lys distance was used as a probe of the overall molecular structure of the investigated pentapeptide. To characterize the dynamics, distributions of the "waiting" times for a transition from a "short" distance conformation to a "long" distance conformation were constructed, based on the generated molecular dynamics trajectories. We show that the relaxation time for the transitions, derived from the constant-pH simulations, is very close to the relaxation time characterizing a permanently protonated molecule, although the average protonation probability of the short-distance conformation is close to zero. However, the distribution of the Asp-Lys distances obtained from constant-pH simulations cannot be reproduced as a linear combination of the distributions resulting from the simulations with fixed protonation states.

Aspartic Acid↗
PubMed2006

Temperature effects on the structural and dynamical properties of the Zn(II)-water complex in aqueous solution: a QM/MM molecular dynamics study.

An ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulation at double-zeta restricted Hartree-Fock (RHF) level was performed at an elevated temperature of 363 K (90 degrees C) to study the temperature effects on the structural and dynamical properties of a Zn(II)-water complex in aqueous solution. The first hydration shell, consisting of 6 water molecules at a mean Zn-O distance of 2.16 A, was found to remain stable also at 90 degrees C with respect to exchange processes. The flexible second shell contains, in average, approximately 27 water ligands. To fully characterize the hydration structure, several other parameters such as radial and angular distribution functions (RDF and ADF) and tilt- and theta-angle distributions were evaluated and compared to data obtained at 298 K (25 degrees C). Temperature effects on the dynamics of the Zn(II)-water complex were studied in terms of water reorientations, mean ligand residence times (MRTs), and number of ligand exchange processes. To get further insight into the solute dynamics, additional data, in particular, librational and vibrational motions of water ligands and Zn-O stretching frequencies, were calculated. The second shell is considerably influenced by the elevated temperature, as the ligands' mean residence time is shortened to 4 ps from the value of 10.5 observed at room temperature. The values of the QM/MM MD simulation were also compared to the results of a classical molecular dynamics (CMD) simulation with two- plus three-body potential performed at 90 degrees C, revealing that an accurate description of the second shell and the dynamics of the Zn(II) hydrate needs the inclusion of quantum mechanics in the description.

Quantum Theory↗
PubMed2000

Conformational dynamics in mixed alpha/beta-oligonucleotides containing polarity reversals: a molecular dynamics study using time-averaged restraints.

Nucleic acid duplexes featuring a single alpha-anomeric thymidine inserted into each DNA strand via 3'-3' and 5'-5' phosphodiester linkages exhibit local conformational dynamics that are not adequately depicted by conventional restrained molecular dynamics (rMD) methods. We have used molecular dynamics with time-averaged NMR restraints (MDtar) to explore its applicability to describing the conformational dynamics of two alpha-containing duplexes--d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2 and d(ATGG-3'-3'-alphaT-5'-5'-GCTC) x r(gagcaccau). In contrast to rMD, enforcing NOE-based distance restraints over a period of time in MDtar rather than instantaneously results in better agreement with the experimental NOE and J-data. This conclusion is based on the dramatic decreases in average distance and coupling constant violations (delta d(av), J(rms), and delta J(av)) and improvements in sixth-root R-factors (R(X)). In both duplexes, the deoxyribose ring puckering behavior predicted independently by pseudorotation analysis is portrayed remarkably well using this approach compared to rMD. This indicates that the local dynamic behavior is encoded within the NOE data, although this is not obvious from the local R(X) values. In both systems, the backbone torsion angles comprising the 3'-3' linkage as well as the (high S-) sugars of the alpha-nucleotide and preceding residue (alpha - 1) are relatively static, while the conformations of the 5'-5' linkage and the sugar in the neighboring beta-nucleotide (alpha + 1) show enhanced flexibility. To reduce the large ensembles generated by MDtar to more manageable clusters we utilized the PDQPRO program. The resulting PDQPRO clusters (in both cases, 13 structures and associated probabilities extracted from a pool of 300 structures) adequately represent the structural and dynamic characteristics predicted by the experimental data.

Base Pair Mismatch↗
PubMed2005

Molecular dynamics investigation of dynamical properties of phosphatidylethanolamine lipid bilayers.

We describe the dynamic behavior of a 1-stearoyl-2-oleoyl-phosphatidylethanolamine (SOPE) bilayer from a 20 ns molecular dynamics simulation. The dynamics of individual molecules are characterized in terms of (2)H spin-lattice relaxation rates, nuclear overhauser enhancement spectroscopy (NOESY) cross-relaxation rates, and lateral diffusion coefficients. Additionally, we describe the dynamics of hydrogen bonding through an analysis of hydrogen bond lifetimes and the time evolution of clusters of hydrogen bonded lipids. The simulated trajectory is shown to be consistent with experimental measures of internal, intermolecular, and diffusive motion. Consistent with our analysis of SOPE structure in the companion paper, we see hydrogen bonding dominating the dynamics of the interface region. Comparison of (2)H T(1) relaxation rates for chain methylene segments in phosphatidylcholine and phosphatidylethanolamine bilayers indicates that slower motion resulting from hydrogen bonding extends at least three carbons into the hydrophobic core. NOESY cross-relaxation rates compare well with experimental values, indicating the observed hydrogen bonding dynamics are realistic. Calculated lateral diffusion rates (4 +/ -1 x 10(-8) cm(2)s) are comparable, though somewhat lower than, those determined by pulsed field gradient NMR methods.

Algorithms↗
PubMed2006

Cluster dynamics transcending chemical dynamics toward nuclear fusion.

Ultrafast cluster dynamics encompasses femtosecond nuclear dynamics, attosecond electron dynamics, and electron-nuclear dynamics in ultraintense laser fields (peak intensities 10(15)-10(20) W.cm(-2)). Extreme cluster multielectron ionization produces highly charged cluster ions, e.g., (C(4+)(D(+))(4))(n) and (D(+)I(22+))(n) at I(M) = 10(18) W.cm(-2), that undergo Coulomb explosion (CE) with the production of high-energy (5 keV to 1 MeV) ions, which can trigger nuclear reactions in an assembly of exploding clusters. The laser intensity and the cluster size dependence of the dynamics and energetics of CE of (D(2))(n), (HT)(n), (CD(4))(n), (DI)(n), (CD(3)I)(n), and (CH(3)I)(n) clusters were explored by electrostatic models and molecular dynamics simulations, quantifying energetic driving effects, and kinematic run-over effects. The optimization of table-top dd nuclear fusion driven by CE of deuterium containing heteroclusters is realized for light-heavy heteroclusters of the largest size, which allows for the prevalence of cluster vertical ionization at the highest intensity of the laser field. We demonstrate a 7-orders-of-magnitude enhancement of the yield of dd nuclear fusion driven by CE of light-heavy heteroclusters as compared with (D(2))(n) clusters of the same size. Prospective applications for the attainment of table-top nucleosynthesis reactions, e.g., (12)C(P,gamma)(13)N driven by CE of (CH(3)I)(n) clusters, were explored.

Journal Article↗
PubMed2002

Theoretical framework for a dynamic cone-beam reconstruction algorithm based on a dynamic particle model.

Dynamic cone-beam reconstruction algorithms are required to reconstruct three-dimensional (3D) image sequences on dynamic 3D CT combining multi-row two-dimensional (2D) detectors and sub-second scanners. The speed-up of the rotating gantry allows one to improve the temporal resolution of the image sequence, but at the same time, it implies increase in the dose delivered during a given time period to keep constant the signal-to-noise ratio associated with each frame. The alternative solution proposed in this paper is to process data acquisition on several half-turns in order to reduce the dose delivered per rotation with the same signal-to-noise ratio. In order to compensate for time evolution and motion artefacts, we propose to use a dynamic particle model to describe the object evolution during the scan. In this article, we first introduce the dynamic particle model and the dynamic CT acquisition model. Then, we explain the principle of the proposed dynamic cone-beam reconstruction algorithm. Lastly, we present preliminary results on simulated data.

Algorithms↗
PubMed2004

Dynamical motifs: building blocks of complex dynamics in sparsely connected random networks.

Spatiotemporal network dynamics is an emergent property of many complex systems that remains poorly understood. We suggest a new approach to its study based on the analysis of dynamical motifs-small subnetworks with periodic and chaotic dynamics. We simulate randomly connected neural networks and, with increasing density of connections, observe the transition from quiescence to periodic and chaotic dynamics. This transition is explained by the appearance of dynamical motifs in the structure of these networks. We also observe domination of periodic dynamics in simulations of spatially distributed networks with local connectivity and explain it by the absence of chaotic and the presence of periodic motifs in their structure.

Brain↗
PubMed2006

Functional dynamics of plant growth and photosynthesis--from steady-state to dynamics--from homogeneity to heterogeneity.

Plants are much more dynamic than we usually expect them to be. This dynamic behaviour is of paramount importance for their performance under natural conditions, when resources are distributed heterogeneously in space and time. However, plants are not only the cue ball of their physical and chemical environment. Endogenous rhythms and networks controlling photosynthesis and growth buffer plant processes from external fluctuations. This review highlights recent evidence of the importance of dynamic temporal and spatial organization of photosynthesis and of growth in leaves and roots. These central processes for plant performance differ strongly in their dependence on environmental impact and endogenous properties, respectively. Growth involves a wealth of processes ranging from the supply of resources from external and internal sources to the growth processes themselves. In contrast, photosynthesis can only take place when light and CO2 are present and thus clearly requires 'input from the environment'. Nevertheless, growth and photosynthesis are connected to each other via mechanisms that are still not fully understood. Recent advances in imaging technology have provided new insights into the dynamics of plant-environment interactions. Such processes do not only play a crucial role in understanding stress response of plants under extreme environmental conditions. Dynamics of plants under modest growth conditions rise from endogenous mechanisms as well as exogenous impact too. It is thus an important task for future research to identify how dynamic external conditions interact with plant-internal signalling networks to optimize plant behaviour in real time and to understand how plants have adapted to characteristic spatial and temporal properties of the resources from their environment, on which they depend on.

Adaptation, Physiological↗
PubMed1992

Long-term changes after brief dynamic psychotherapy: symptomatic versus dynamic assessments.

Dynamic change in psychotherapy, as measured by theory-related or mode-specific instruments, have been criticized for being too intercorrelated with symptomatic change measures. In this study, long-term changes after brief dynamic psychotherapy were studied in 45 moderately disturbed neurotic patients by a reliable outcome battery. The factor structure of all the change variables suggested that they tapped 2 distinct and stable sources of variance: dynamic and symptomatic change. The categories of overall dynamic change were different from categories of change on the Global Assessment Scale. A small systematic difference was found between the categories of overall dynamic change and the categories of target complaints change also, due to false solutions of dynamic conflicts.

Adult↗
PubMed2003

Dorsal capsulodesis and ligamentoplasty for chronic pre-dynamic and dynamic scapholunate dissociation.

Scapholunate (SL) instability is the most common cause of carpal instability. Pre-dynamic and dynamic type SL instability is difficult to diagnose and treat. This series reviews 17 soldiers with pre-dynamic or dynamic SL instability diagnosed by midcarpal arthroscopy and treated with dorsal capsulodesis and augmentation ligamentoplasty with partial dorsal radiocarpal (DRC) ligament procedure between 1997 and 2000. The sample included 14 males and three females. The dominant hand was involved in 15 patients. Moreover, the average patient age was 29.3 years (range 19-36 years). The diagnosis was based on clinical and arthroscopic criteria. Fifteen patients were followed up at our clinic regularly, with the follow-up period ranging from 12 to 39 months (mean 25.2 months). Fourteen patients had excellent or good results, and one patient had poor result based on Mayo Modified Wrist Score. Wrist motion in the flexion-extension plane loss averaged 18.4 degrees. Grip force increased significantly following treatment, with improvement totaling 15% of normal side. No complications were found in this series. Consequently, dorsal capsulodesis and ligamentoplasty with partial DRC ligament is considered a valuable therapeutic option for cases of pre-dynamic and dynamic SL instability.

Adult↗
PubMed1996

Analysis of dynamic spectra in ferret primary auditory cortex. II. Prediction of unit responses to arbitrary dynamic spectra.

1. Responses of single units and multiunit clusters were recorded in the ferret primary auditory cortex (AI) with the use of broadband complex dynamic spectra. Previous work has demonstrated that simpler spectra consisting of single moving ripples (i.e., sinusoidally modulated spectral profiles that travel at a constant velocity along the logarithmic frequency axis) could be used effectively to characterize the response fields and transfer functions of AI cells. 2. A complex dynamic spectral profile can be thought of as being the sum of moving ripple spectra. Such a decomposition can be computed from a two-dimensional spectrotemporal Fourier transform of the dynamic spectral profile with moving ripples as the basis function. 3. Therefore, if AI units were essentially linear, satisfying the superposition principle, then their responses to arbitrary dynamic spectra could be predicted from the responses to single moving ripples, i.e., from the units' response fields and transfer functions (spectral and temporal impulse response functions, respectively). 4. This conjecture was tested and confirmed with data from 293 combinations of moving ripples, involving complex spectra composed of up to 15 moving ripples of different ripple frequencies and velocities. For each case, response predictions based on the unit transfer functions were compared with measured responses. The correlation between predicted and measured responses was found to be consistently high (84% with rho > 0.6). 5. The distribution of response parameters suggests that AI cells may encode the profile of a dynamic spectrum by performing a multiscale spectrotemporal decomposition of the dynamic spectral profile in a largely linear manner.

Acoustic Stimulation↗
PubMed1979

Comparison of cardiovascular responses to static-dynamic effort and dynamic effort alone in patients with chronic ischemic heart disease.

Thirty men, mean age 55 years, known to have treadmill-induced ischemic ST-segment depression, performed static and dynamic effort, i.e., forearm lifting and treadmill exercise, separately and combined. Static effort was sustained at 20%, 25% or 30% of maximal forearm lifting capacity. Two symptom-limited treadmill tests, one with and one without added static effort, were performed on each of two visits. Compared with dynamic effort alone, combined static-dynamic effort decreased treadmill work load and increased heart rate, systolic blood pressure and rate-pressure product at the onset of ischemic ST-segment depression or angina pectoris: 7.1 +/- 0.4 vs 8.0 +/- 0.5 (SEM) multiples of resting oxygen consumption (mets), estimated; 141 +/- 3 vs 134 +/- 3 beats/min; 170 +/- 4 vs. 162 +/- 4 mm Hg and 239 +/- 8 vs 218 +/- 9 (p less than 0.001). The prevalence of angina pectoris was significantly less with combined static-dynamic effort than with dynamic effort alone. Static effort causes a resetting of the threshold at which ischemic abnormalities appear during dynamic effort.

Angina Pectoris↗
PubMed1989

A simple formulation of microtubule dynamics: quantitative implications of the dynamic instability of microtubule populations in vivo and in vitro.

A simple formulation of microtubule dynamic instability is presented, which is based on the experimental observations by T. Horio and H. Hotani of coexisting, interconverting growing and shrinking microtubules. Employing only three independent, experimentally determined parameters for a given microtubule end, this treatment accounts quantitatively for the principal features of the observed dynamic behaviour of steady-state tubulin microtubules in vitro. Experimental data are readily reproduced for microtubule length redistribution, and for the kinetics of tubulin exchange processes, including pulse-chase properties. The relative importance of dynamic incorporation and that due to treadmilling are assessed. Dynamic incorporation is found to dominate the overall exchange properties; polarized incorporation due to treadmilling generally becomes significant only when the dynamics are largely suppressed. This treatment also permits simulation of certain cellular phenomena, showing how microtubule renucleation can control microtubule growth, by means of changes in microtubule number concentration in a system at constant microtubule mass. A relatively simple extension of the formulation accounts quantitatively for non-steady-state microtubule properties, e.g. dilution-induced rapid disassembly and the oscillatory mode of microtubule assembly. The principles relating dynamic instability and oscillatory behaviour are clearly indicated. Possible mechanisms of the switching of microtubules are briefly discussed.

Animals↗
PubMed1990

[Analysis of the denture dynamics in R.P.D.'s. 2. Influence of retainers on the dynamics of free-end-saddle].

The ordinary denture movement during function is defined as the "Denture dynamics" in R.P.D.'s. by K. H. Körber (1975). The Author has already reported the evaluating method of the denture dynamics objectively by two ways: The displacement sensors of magnetoresistors detected the vertical and horizontal movements of denture saddle in free end situation. Tiny accerelometer also detected the accerelation during the movements. In this present study, the correlations among the retainers used, the extent of the denture dynamics in displacement and accerelation, the occluding force and the abutment tooth mobility induced by the denture support were correlatively evaluated in two patients with class I free end R.P.D.'s. with interchangeable retainers by above methods. All the data were collected simultaneously by the electronic measuring and recording apparatus. Following results were obtained: 1. The denture dynamics depended on the selection of retainers examined. The extent of the dynamics reduced from the denture with the wrought wire clasps, the denture with the cast clasps, then to the denture with cone crown telescopes in sequence. 2. The occluding force increased just as the changes in sequence of the denture dynamics. 3. The abutment tooth moved to the distal in each case. The highest value of the mobility was found in the denture with the cast clasps, then in the denture with the wrought wire clasps. The least value of the tooth mobility was found in the denture with the cone crown telescopes. These results will strongly support the concept of the free end saddle R.P.D.'s anchored and supported rigidly by the abutments and the residual ridges in clinics.

Dental Abutments↗
PubMed2002

Dynamic sonography of pancreatic tumors: comparison with dynamic CT.

OBJECTIVE: The aim of this study was to examine the usefulness of dynamic sonography in the characterization of pancreatic tumors. MATERIALS AND METHODS: IV contrast-enhanced pancreatic sonography (dynamic sonography) with Levovist was performed in 43 patients with pancreatic mass lesions (32 with pancreatic adenocarcinomas, four with inflammatory pancreatic masses, three with islet cell tumors, two with serous cystadenomas, one with a solid and cystic tumor, and one with metastatic pancreatic cancer). We calculated a contrast index using a time-intensity curve: contrast index equals elevation of intensity in the tumor divided by elevation of intensity in the pancreatic parenchyma. We classified the tumors into three groups according to the contrast index: a slightly enhanced group (contrast index < 0.5), a moderately enhanced group (contrast index = 0.5-1.5), and a well-enhanced group (contrast index > 1.5), and we compared these results with those from dynamic CT. RESULTS: The contrast indexes of 32 adenocarcinomas, four inflammatory pancreatic masses, three islet cell tumors, two serous cystadenomas, one solid and cystic tumor, and one metastatic tumor were, respectively, 0.12 +/- 0.095 (mean +/- SD), 0.54 +/- 0.420, 1.74 +/- 0.555, 1.09 +/- 1.380, 1.67, and 2.07. Thirty-five tumors, including all 32 adenocarcinomas, were classified in the slightly enhanced group, three were classified in the moderately enhanced group, and five were classified in the well-enhanced group. In 93% (40/43) of tumors, the grade of enhancement on dynamic sonography was closely correlated with the grade of enhancement on dynamic CT. CONCLUSION: Dynamic sonography can assist in the characterization of pancreatic tumors.

Adenocarcinoma↗