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PubMedDate not supplied

Detection of hypervascular hepatocellular carcinoma by dynamic magnetic resonance imaging with double-echo chemical shift in-phase and opposed-phase gradient echo technique: comparison with dynamic helical computed tomography imaging with double arterial phase.

PURPOSE: The technique of double-echo chemical shift gradient echo magnetic resonance imaging (MRI) with the fast low-angle shot (double-echo FLASH) sequence provides in-phase and opposed-phase images in a single breath hold. The purpose of this study was to evaluate the efficacy of dynamic MRI with double-echo FLASH imaging for the detection of hypervascular hepatocellular carcinoma by comparing it with dynamic helical computed tomography (CT) imaging with double arterial phase. MATERIALS AND METHODS: Twenty-nine patients with 67 hypervascular hepatocellular carcinoma nodules who underwent both dynamic MRI with double-echo FLASH imaging (repetition time/echo time/flip angle: 160/3.6, 7.0/80 degrees ) and dynamic helical CT imaging with double arterial phase were enrolled in the study. For dynamic MRI, precontrast, arterial, portal venous, and equilibrium phase images were obtained before and approximately 19, 60, and 120 seconds, respectively, after intravenous injection of 0.1 mmol/kg of gadopentetate dimeglumine at a rate of 2 ml/s. For dynamic CT imaging, quadraphase images, including early arterial, late arterial, portal venous, and equilibrium phases, were obtained serially approximately 20, 30, 70, and 180 seconds, respectively, after intravenous administration of 2 ml/kg of 300 mgI/ml of nonionic contrast medium at a rate of 5 ml/s. Three masked observers independently interpreted images obtained with each technique in random order, separately and without patient identifiers. Sensitivity and positive predictive values as well as the area below the alternative-free response receiver operating characteristic curve (Az) for each imaging technique were calculated and compared statistically. RESULTS: Mean sensitivity and positive predictive values of MRI for hypervascular hepatocellular carcinoma were 48% and 94%, respectively, and those of CT imaging were 47% and 91%, respectively. In 11 (38%) of the 29 patients, at least one observer judged dynamic MRI to be superior, whereas in 5 patients (17%), dynamic CT was judged to be superior. There was no significant difference in the sensitivity and positive predictive values between these techniques (p > 0.05). There was no significant difference either in mean Az values between CT (0.55) and MRI (0.57) (p = 0.61). CONCLUSION: Dynamic MRI with double-echo FLASH imaging can detect hypervascular hepatocellular carcinoma as well as dynamic helical CT imaging with double arterial phase.

Adult↗
PubMed2005

Characterizing the amplitude dynamics of the human core-temperature circadian rhythm using a stochastic-dynamic model.

Two measures, amplitude and phase, have been used to describe the characteristics of the endogenous human circadian pacemaker, a biological clock located in the hypothalamus. Although many studies of change in circadian phase with respect to different stimuli have been conducted, the physiologic implications of the amplitude changes (dynamics) of the pacemaker are unknown. It is known that phase changes of the human circadian pacemaker have a significant impact on sleep timing and content, hormone secretion, subjective alertness and neurobehavioral performance. However, the changes in circadian amplitude with respect to different stimuli are less well documented. Although amplitude dynamics of the human circadian pacemaker are observed in physiological rhythms such as plasma cortisol, plasma melatonin and core temperature data, currently methods are not available to accurately characterize the amplitude dynamics from these rhythms. Of the three rhythms core temperature is the only reliable variable that can be monitored continuously in real time with a high sampling rate. To characterize the amplitude dynamics of the circadian pacemaker we propose a stochastic-dynamic model of core temperature data that contains both stochastic and dynamic characteristics. In this model the circadian component that has a dynamic characteristic is represented as a perturbation solution of the van der Pol equation and the thermoregulatory response in the data that has a stochastic characteristic is represented as a first-order autoregressive process. The model parameters are estimated using data with a maximum likelihood procedure and the goodness-of-fit measures along with the associated standard error of the estimated parameters provided inference about the amplitude dynamics of the pacemaker. Using this model we analysed core temperature data from an experiment designed to exhibit amplitude dynamics. We found that the circadian pacemaker recovers slowly to an equilibrium level following amplitude suppression. In humans this reaction to perturbation from equilibrium value has potential physiological implications.

Body Temperature Regulation↗
PubMed2006

A molecular dynamics study of Lys-Trp-Lys: structure and dynamics in solution following photoexcitation.

We report studies of the structure and dynamics of a tripeptide Lys-Trp-Lys (KWK) in aqueous solution following photoexcitation by molecular dynamics simulations. For ground-state KWK, we observe three stable conformations with free energy differences of less than 5.2 kJ/mol. Each conformer is stabilized by a pi-cation interaction between one of three protonated amino groups and the indole moiety. For the excited state of tryptophan in KWK, the simulated molecular dynamics of the three isomers are similar, all in good agreement with recent femtosecond experiments (J. Phys. Chem. B 2005, 109, 16901). Specifically, we observe: (1) the fluorescence anisotropy is dominated by a single-exponential component and decays in approximately 130 ps, (2) the total dynamic Stokes shift reaches approximately 2700 cm(-1), and (3) the excited state relaxation dynamics occurs on several time scales ranging from femtoseconds to tens of picoseconds. The relaxation dynamics involve rapid initial response of neighboring water, followed by local motions of flexible peptide chains. These processes drive global restructuring of the tripeptide on a rather flat energy surface, inducing slower dynamics evident in both the water and protein contributions to the stabilization energy of the photoexcited chromophore. The water and protein dynamics are strongly correlated. On a still longer time scale, we observe isomerization of two excited state conformers to the other most stable one, an analogue for evolution of trajectories along the funnel on the rugged free energy landscape to the final "native" state. Our studies suggest new experiments to detect this unique dynamics.

Isomerism↗
PubMed2004

On combining molecular dynamics and stochastic dynamics simulations to compute reaction rates in liquids.

An approach that combines molecular dynamics and stochastic dynamics calculations for obtaining reaction rates in liquids is investigated by studying the cis-->trans isomerization of HONO in liquid krypton. The isomerization rates are computed for several liquid densities by employing full-dimensional molecular-dynamics simulations. The rates are also computed by employing the stochastic dynamics method for a wide range of collision frequencies. Comparisons of the two sets of the computed rates show that for a wide range of liquid densities there is a simple linear relation between the liquid density rho and the collision frequency alpha, that is, alpha=crho. This suggests that once the constant c is determined from a molecular-dynamics calculation at a single density, the reaction rates can be obtained from stochastic dynamics calculations for the entire range of liquid densities where alpha=crho holds. The applicability of the combined molecular dynamics and stochastic dynamics approach provides a practical means for obtaining rate constants at considerable savings of computer time compared to that required by using full-dimensional molecular-dynamics simulations alone.

Journal Article↗
PubMed2005

Quantum wave packet ab initio molecular dynamics: an approach to study quantum dynamics in large systems.

A methodology to efficiently conduct simultaneous dynamics of electrons and nuclei is presented. The approach involves quantum wave packet dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator, in conjunction with ab initio molecular dynamics treatment of the electronic and classical nuclear degree of freedom. The latter may be achieved either by using atom-centered density-matrix propagation or by using Born-Oppenheimer dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. The quantum wave packet dynamics is made computationally robust by using adaptive grids to achieve optimized sampling. One notable feature of the approach is that important quantum dynamical effects including zero-point effects, tunneling, as well as over-barrier reflections are treated accurately. The electronic degrees of freedom are simultaneously handled at accurate levels of density functional theory, including hybrid or gradient corrected approximations. Benchmark calculations are provided for proton transfer systems and the dynamics results are compared with exact calculations to determine the accuracy of the approach.

Journal Article↗
PubMed2006

Influence of modulated structural dynamics on the kinetics of alpha-chymotrypsin catalysis. Insights through chemical glycosylation, molecular dynamics and domain motion analysis.

Although the chemical nature of the catalytic mechanism of the serine protease alpha-chymotrypsin (alpha-CT) is largely understood, the influence of the enzyme's structural dynamics on its catalysis remains uncertain. Here we investigate whether alpha-CT's structural dynamics directly influence the kinetics of enzyme catalysis. Chemical glycosylation [Solá RJ & Griebenow K (2006) FEBS Lett 580, 1685-1690] was used to generate a series of glycosylated alpha-CT conjugates with reduced structural dynamics, as determined from amide hydrogen/deuterium exchange kinetics (k(HX)). Determination of their catalytic behavior (K(S), k(2), and k(3)) for the hydrolysis of N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (Suc-Ala-Ala-Pro-Phe-pNA) revealed decreased kinetics for the catalytic steps (k(2) and k(3)) without affecting substrate binding (K(S)) at increasing glycosylation levels. Statistical correlation analysis between the catalytic (DeltaG( not equal)k(i)) and structurally dynamic (DeltaG(HX)) parameters determined revealed that the enzyme acylation and deacylation steps are directly influenced by the changes in protein structural dynamics. Molecular modelling of the alpha-CT glycoconjugates coupled with molecular dynamics simulations and domain motion analysis employing the Gaussian network model revealed structural insights into the relation between the protein's surface glycosylation, the resulting structural dynamic changes, and the influence of these on the enzyme's collective dynamics and catalytic residues. The experimental and theoretical results presented here not only provide fundamental insights concerning the influence of glycosylation on the protein biophysical properties but also support the hypothesis that for alpha-CT the global structural dynamics directly influence the kinetics of enzyme catalysis via mechanochemical coupling between domain motions and active site chemical groups.

Catalysis↗
PubMed1994

Dynamics and evolution: evolutionarily stable attractors, invasion exponents and phenotype dynamics.

We extend the ideas of evolutionary dynamics and stability to a very broad class of biological and other dynamical systems. We simultaneously develop the general mathematical theory and a discussion of some illustrative examples. After developing an appropriate formulation for the dynamics, we define the notion of an evolutionary stable attractor (ESA) and give some samples of ESAS with simple and complex dynamics. We discuss the relationship between our theory and that for ESSS in classical linear evolutionary game theory by considering some dynamical extensions. We then introduce and develop our main mathematical tool, the invasion exponent. This allows analytical and numerical analysis of relatively complex situations, such as the coevolution of multiple species with chaotic population dynamics. Using this, we introduce the notion of differential selective pressure which for generic systems is nonlinear and characterizes internal ESAS. We use this to analytically determine the ESAS in our previous examples. Then we introduce the phenotype dynamics which describe how a population with a distribution of phenotypes changes in time with or without mutations. We discuss the relation between the asymptotic states of this and the ESAS. Finally, we use our mathematical formulation to analyse a non-reproductive form of evolution in which various learning rules compete and evolve. We give a very tentative economic application which has interesting ESAS and phenotype dynamics.

Animals↗
PubMed1994

Inverse dynamic optimization including muscular dynamics, a new simulation method applied to goal directed movements.

This paper presents a new method for estimating muscular force and activation from experimental kinematic data. The method combines conventional inverse dynamics with optimization utilizing a dynamic muscle model. The method uses only very limited computational power, which makes it a useful tool especially for complex systems like the shoulder or the locomotor system. The net torques/forces are calculated by using conventional inverse dynamics. A solution of the load sharing problem is determined by minimization of the weighted sum of squared muscle forces. The load sharing problem is solved with a dynamic constraint reflecting physiological muscle properties. This constraint takes into account the nonlinear dynamics of the contractile element (CE) and the series elastic element (SE), active state dynamics and neural excitation dynamics. This physiological constraint is determined with an inverse muscle model. With this model, muscular states and neural inputs are also estimated. The method of inverse dynamics requires position, velocity and acceleration signals as input. A method to prepare such signals from noisy measured data is presented.

Acceleration↗
PubMed2004

Brownian Dynamics, Molecular Dynamics, and Monte Carlo modeling of colloidal systems.

This paper serves as an introductory review of Brownian Dynamics (BD), Molecular Dynamics (MD), and Monte Carlo (MC) modeling techniques. These three simulation methods have proven to be exceptional investigative solutions for probing discrete molecular, ionic, and colloidal motions at their basic microscopic levels. The review offers a general study of the classical theories and algorithms that are foundational to Brownian Dynamics, Molecular Dynamics, and Monte Carlo simulations. Important topics of interest include fundamental theories that govern Brownian motion, the Langevin equation, the Verlet algorithm, and the Metropolis method. Brownian Dynamics demonstrates advantages over Molecular Dynamics as pertaining to the issue of time-scale separation. Monte Carlo methods exhibit strengths in terms of ease of implementation. Hybrid techniques that combine these methods and draw from these efficacies are also presented. With their rigorous microscopic approach, Brownian Dynamics, Molecular Dynamics, and Monte Carlo methods prove to be especially viable modeling methods for problems with challenging complexities such as high-level particle concentration and multiple particle interactions. These methods hold promising potential for effective modeling of transport in colloidal systems.

Journal Article↗
PubMed1996

Dynamic delay and maximal dynamic error in continuous biosensors.

When biosensors are operated continuously, a dynamic delay and a dynamic error relate the sensor signal to the changing analyte concentration. The dynamic delay is the temporal displacement of the signal, or the lag, and is specified solely by properties of the biosensor and external mass transfer. The dynamic error is the difference between the actual concentration and the simultaneous reported concentration and is the product of the dynamic delay and the instantaneous rate of concentration change. In real-time operation of sensors, a maximal dynamic error based on the maximal expected rate of concentration change must be employed to estimate the worst-case error because the actual instantaneous rate is not independently known. Values of dynamic delay and maximal dynamic error that are acceptable in particular monitoring situations can be used in the design of acceptable continuous biosensors. This analysis suggests experimental alternatives to the standard response time approach for sensor characterization that are particularly advantageous for continuously operated biosensors. The concepts are applied here to in vitro operation of a continuous glucose sensor.

Biosensing Techniques↗
PubMedDate not supplied

Reorganization of dynamic self-assemblies of cellulose diacetate in solution: dynamical critical-like fluctuations in the lower critical solution temperature system.

Dynamics of cellulose diacetate (CDA, the total degree of substitution (TDS) = 2.44) in dimethylacetamide (DMAc) in dilute solution was investigated at 2, 10, 20, 30, 40, 49.7, and 61.5 degrees C through dynamic light scattering in the quiescent state. The following three facts were made clear. First, CDA existed in three types of structures in the polar solvent, DMAc; one is a single CDA chain, and the others are dynamic structures, or self-assemblies, which were formed temporarily and locally by the solvent-mediated hydrogen bonding between the intermolecular C-6 position hydroxyls of the anhydroglucose units in the CDA backbone. Second, CDA showed a nature of low-temperature solubility in DMAc, that is, CDA is expected to dissolve molecularly below -12 degrees C but to take a phase separation above 65 degrees C, where two structures such as collapses of a single CDA chain and an aggregate appear. Third, a reorganization in the dynamic structures was detected at the temperature T = 33.8 degrees C. At this temperature, two dynamic structures showed the discontinuity in their correlation lengths, whereas the single CDA realized an uncorrelated chain state in the dynamical sense. In view of the low-temperature solubility of CDA in DMAc, this abnormal behavior around T was explained by dynamical critical-like fluctuations if T were treated as a kind of lower critical solution temperature (LCST) in the CDA/DMAc system. Here, the self-assemblies arise as the dynamical fluctuations under the spinodal decomposition situation and the competition between the hydrogen bonding (HB) and the hydrophobic interaction (HPhI) makes the conformation of CDA chains change drastically. In this scheme, the solvent-mediated HB and HPhI play important roles in the structure reorganization of cellulose derivatives in strong electronegative solvents, though HB and HPhI cooperate with the inherent chain helicality.

Cellulose↗
PubMed2006

Nonadiabatic molecular dynamics simulations of correlated electrons in solution. 1. Full configuration interaction (CI) excited-state relaxation dynamics of hydrated dielectrons.

The hydrated dielectron is composed of two excess electrons dissolved in liquid water that occupy a single cavity; in both its singlet and triplet spin states there is a significant exchange interaction so the two electrons cannot be considered to be independent. In this paper and the following paper,we present the results of mixed quantum/classical molecular dynamics simulations of the nonadiabatic relaxation dynamics of photoexcited hydrated dielectrons, where we use full configuration interaction (CI) to solve for the two-electron wave function at every simulation time step. To the best of our knowledge, this represents the first systematic treatment of excited-state solvation dynamics where the multiple-electron problem is solved exactly. The simulations show that the effects of exchange and correlation contribute significantly to the relaxation dynamics. For example, spin-singlet dielectrons relax to the ground state on a time scale similar to that of single electrons excited at the same energy, but spin-triplet dielectrons relax much faster. The difference in relaxation dynamics is caused by exchange and correlation: The Pauli exclusion principle imposes very different electronic structure when the electrons' spins are singlet paired than when they are triplet paired, altering the available nonadiabatic relaxation pathways. In addition, we monitor how electronic correlation changes dynamically during nonadiabatic relaxation and show that solvent dynamics cause electron correlation to evolve quite differently for singlet and triplet dielectrons. Despite such differences, our calculations show that both spin states are stable to excited-state dissociation, but that the excited-state stability has different origins for the two spin states. For singlet dielectrons, the stability depends on whether the solvent structure can rearrange to create a second cavity before the ground state is reached. For triplet dielectrons, in contrast, electronic correlation ensures that the two electrons do not dissociate, even if the dielectron is artificially kept from reaching the ground state. In addition, both singlet and triplet dielectrons change shape dramatically during relaxation, so that linear response fails to describe the solvation dynamics for either spin state. In the following paper (Larsen, R. E.; Schwartz, B. J. J. Phys. Chem. B 2006, 110, 9692), we use these simulations to calculate the pump-probe spectroscopic signal expected for photoexcited hydrated dielectrons and to predict an experiment to observe hydrated dielectrons directly.

Computer Simulation↗
PubMed2004

Stochastic dynamics and the dynamic phase transition in thin ferromagnetic films.

The dynamic phase behavior of a classical Heisenberg spin system with a bilinear exchange anisotropy in a planar thin film geometry has been investigated by Monte Carlo simulations using different forms for the stochastic dynamics. In simulations of the dynamic phase transition (DPT) in films subject to a pulsed oscillatory external field with competing surface fields, both Glauber and Metropolis dynamics show a continuous DPT. But while the field amplitude dependence of the DPT is similar in both cases, the transition region for the DPT as a function of temperature is more extended with Metropolis dynamics. The difference arises from a decoupling of the surface and bulk responses of the film near the dynamic phase transition with Metropolis dynamics that is not evident for Glauber dynamics.

Journal Article↗
PubMed2001

Dynamic regimes and correlated structural dynamics in native and denatured alpha-lactalbumin.

Understanding the mechanisms of protein folding requires knowledge of both the energy landscape and the structural dynamics of a protein. We report a neutron-scattering study of the nanosecond and picosecond dynamics of native and the denatured alpha-lactalbumin. The quasielastic scattering intensity shows that there are alpha-helical structure and tertiary-like side-chain interactions fluctuating on sub-nanosecond time-scales under extremely denaturing conditions and even in the absence of disulfide bonds. Based on the length-scale dependence of the decay rate of the measured correlation functions, the nanosecond dynamics of the native and the variously denatured proteins have three dynamic regimes. When 0.05 1.0 A(-1) is a regime that displays the local dynamic behavior of individual residues, Gamma proportional to Q(1.8+/-0.3). The picosecond time-scale dynamics shows that the potential barrier to side-chain proton jump motion is reduced in the molten globule and in the denatured proteins when compared to that of the native protein. Our results provide a dynamic view of the native-like topology established in the early stages of protein folding.

Animals↗
PubMed2006

Coupling between lysozyme and trehalose dynamics: microscopic insights from molecular-dynamics simulations.

We have carried out molecular-dynamics simulations on fully flexible all-atom models of the protein lysozyme immersed in trehalose, an effective biopreservative, with the purpose of exploring the nature and extent of the dynamical coupling between them. Our study shows a strong coupling over a wide range of temperatures. We found that the onset of anharmonic behavior was dictated by changes in the dynamics and relaxation processes in the trehalose glass. The physical origin of protein-trehalose coupling was traced to the hydrogen bonds formed at the interface between the protein and the solvent. Moreover, protein-solvent hydrogen bonding was found to control the structural relaxation of the protein. The dynamics of the protein was found to be heterogeneous; the motions of surface and core atoms had different dependencies on temperature and, in addition, the surface atoms were more sensitive to the dynamics of the solvent than the core atoms. From the solvent perspective we found that the dynamics near the protein surface showed an unexpected enhanced mobility compared to the bulk. These results shed some light on the microscopic origins of the dynamical coupling in protein-solvent systems.

Computer Simulation↗
PubMed2003

Dynamic heterogeneities in the out-of-equilibrium dynamics of simple spherical spin models.

The response of spherical two-spin interaction models, the spherical ferromagnet (s-FM) and the spherical Sherrington-Kirkpatrick (s-SK) model, is calculated for the protocol of the so-called nonresonant hole burning (NHB) experiment for temperatures below the respective critical temperatures. It is shown that it is possible to select dynamic features in the out-of-equilibrium dynamics of both models, one of the hallmarks of dynamic heterogeneities. The behavior of the s-SK model and the s-FM model in three dimensions is very similar, showing dynamic heterogeneities in the long-time behavior, i.e., in the aging regime. The appearance of dynamic heterogeneities in the s-SK model explicitly demonstrates that these are not necessarily related to spatial heterogeneities. For the s-FM model, it is shown that the nature of the dynamic heterogeneities changes as a function of dimensionality. With the increasing dimension, the frequency selectivity of the NHB diminishes and the dynamics in the mean-field limit of the s-FM model becomes homogeneous.

Journal Article↗
PubMed2005

Dynamics of poly(ethylene oxide) in a blend with poly(methyl methacrylate): a quasielastic neutron scattering and molecular dynamics simulations study.

In this paper, we have addressed the question of the dynamic miscibility in a blend characterized by very different glass-transition temperatures, Tg, for the components: poly(ethylene oxide) and poly(methyl methacrylate) (PEO/PMMA). The combination of quasielastic neutron scattering with isotopic labeling and fully atomistic molecular dynamics simulations has allowed us to selectively investigate the dynamics of the two components in the picosecond-10 nanoseconds scale at temperatures close and above the Tg of the blend. The main focus was on the PEO component, i.e., that of the lowest Tg, but first we have characterized the dynamics of the other component in the blend and of the pure PEO homopolymer as reference. In the region investigated, the dynamics of PMMA in the blend is strongly affected by the alpha-methyl rotation; an additional process detected in the experimental window 65 K above the blend-Tg can be identified as the merged alphabeta process of this component that shows strong deviations from Gaussian behavior. On the other hand, pure PEO displays entropy driven dynamics up to very large momentum transfers. Such kind of motion seems to freeze when the PEO chains are in the blend. There, we have directly observed a very heterogeneous and moreover confined dynamics for the PEO component. The presence of the hardly moving PMMA matrix leads to the creation of little pockets of mobility where PEO can move. The characteristic size of such confined islands of mobility might be estimated to be of approximately 1 nm. These findings are corroborated by the simulation study, which has been an essential support and guide in our data analysis procedure.

Journal Article↗
PubMed2000

Dynamics of the Hck-SH3 domain: comparison of experiment with multiple molecular dynamics simulations.

Molecular dynamics calculations provide a method by which the dynamic properties of molecules can be explored over timescales and at a level of detail that cannot be obtained experimentally from NMR or X-ray analyses. Recent work (Philippopoulos M, Mandel AM, Palmer AG III, Lim C, 1997, Proteins 28:481-493) has indicated that the accuracy of these simulations is high, as measured by the correspondence of parameters extracted from these calculations to those determined through experimental means. Here, we investigate the dynamic behavior of the Src homology 3 (SH3) domain of hematopoietic cell kinase (Hck) via 5N backbone relaxation NMR studies and a set of four independent 4 ns solvated molecular dynamics calculations. We also find that molecular dynamics simulations accurately reproduce fast motion dynamics as estimated from generalized order parameter (S2) analysis for regions of the protein that have experimentally well-defined coordinates (i.e., stable secondary structural elements). However, for regions where the coordinates are not well defined, as indicated by high local root-mean-square deviations among NMR-determined structural family members or high B-factors/low electron density in X-ray crystallography determined structures, the parameters calculated from a short to moderate length (less than 5-10 ns) molecular dynamics trajectory are dependent on the particular coordinates chosen as a starting point for the simulation.

Crystallography, X-Ray↗