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At least 253 records · Page 14Linked to original sources
PubMed2006

Dynamic intensity model calculation of vibronic oscillator strengths for Cs2NaNdCl6: A molecular dynamics study.

We present here a dynamic intensity model calculation of vibronic oscillator strengths for the Cs2NaNdCl6 compound by applying the method of molecular-dynamics simulation (MDS). The force field parameters used for the MDS reproduce the structure and several vibrational frequencies of Cs2NaNdCl6 very well. Both the static-coupling (SC) and dynamic-coupling (DC) mechanisms are taken into account for the intensity parameter calculations, in which the effective point charges and isotropic polarizabilities are optimized with respect to experimental energy levels. A comparison of intensity parameters and vibronic oscillator strengths between the two individual mechanisms indicates that the DC mechanism is operative. The calculated vibronic oscillator strengths for the combined SC and DC mechanism agree quite well with the available experimental values.

Journal Article↗
PubMed2006

Molecular dynamics simulation of liquid water confined inside graphite channels: dielectric and dynamical properties.

Electric and dielectric properties and microscopic dynamics of liquid water confined between graphite slabs are analyzed by means of molecular dynamics simulations for several graphite-graphite separations at ambient conditions. The electric potential across the interface shows oscillations due to water layering, and the overall potential drop is about -0.28 V. The total dielectric constant is larger than the corresponding value for the bulklike internal region of the system. This is mainly due to the preferential orientations of water nearest the graphite walls. Estimation of the capacitance of the system is reported, indicating large variations for the different adsorption layers. The main trend observed concerning water diffusion is 2-fold: on one hand, the overall diffusion of water is markedly smaller for the closest graphite-graphite separations, and on the other hand, water molecules diffuse in interfaces slightly slower than those in the bulklike internal areas. Molecular reorientational times are generally larger than those corresponding to those of unconstrained bulk water. The analysis of spectral densities revealed significant spectral shifts, compared to the bands in unconstrained water, in different frequency regions, and associated to confinement effects. These findings are important because of the scarce information available from experimental, theoretical, and computer simulation research into the dielectric and dynamical properties of confined water.

Journal Article↗
PubMed2006

Dynamics of changes in blood flow, volume, and oxygenation: implications for dynamic functional magnetic resonance imaging calibration.

Changes in cerebral blood flow (CBF), volume (CBV), and oxygenation (blood-oxygenation level dependent (BOLD)) during functional activation are important for calculating changes in cerebral metabolic rate of oxygen consumption (CMRo2) from calibrated functional MRI (fMRI). An important part of this process is the CBF/CBV relationship, which is signified by a power-law parameter: gamma=ln (1+DeltaCBV/CBV)/ln (1+DeltaCBF/CBF). Because of difficulty in measuring CBF and CBV with MRI, the value of gamma is therefore assumed to be approximately 0.4 from a prior primate study under hypercapnia. For dynamic fMRI calibration, it is important to know if the value of gamma varies after stimulation onset. We measured transient relationships between DeltaCBF, DeltaCBV, and DeltaBOLD by multimodal MRI with temporal resolution of 500 ms (at 7.0 T) from the rat somatosensory cortex during forepaw stimulation, where the stimulus duration ranged from 4 to 32 secs. Changes in CBF and BOLD were measured before the administration of the contrast agent for CBV measurements in the same subjects. We observed that the relationship between DeltaCBF and DeltaCBV varied dynamically from stimulation onset for all stimulus durations. Typically after stimulation onset and at the peak or plateau of the DeltaCBF, the value of gamma ranged between 0.1 and 0.2. However, after stimulation offset, the value of gamma increased to 0.4 primarily because of rapid and slow decays in DeltaCBF and DeltaCBV, respectively. These results suggest caution in using dynamic measurements of DeltaCBF and DeltaBOLD required for calculating DeltaCMRo2 for functional stimulation, when either DeltaCBV has not been accurately measured or a fixed value of gamma during hypercapnia perturbation is used.

Animals↗
PubMed2001

Investigation of nonlinear dynamical properties by the observed complex behaviour as a basis for construction of dynamical models of atmospheric photochemical systems.

The importance of the investigation of nonlinear dynamical properties (NDPs) of the atmospheric photochemical systems (PCSs) was demonstrated in ref. 1 and 2 (A. M. Feigin and I. B. Konovalov, J. Geophys. Res., 1996, 101 (D20), 26038; 1. B. Konovalov, A. M. Feigin and A. Y. Mukhina, J. Geophys. Res., 1999, 104 (D3), 3669). The only known way to study NDPs of any natural dynamical system (including atmospheric PCSs) is to construct a mathematical model of the system. The key point here is adequacy of the NDPs of the constructed model to the system observed. We propose a new approach to construction of such an adequate model for systems manifesting nonstationary chaotic behaviour and describe an algorithm based exclusively on nonlinear dynamical analysis of the observed time series (TS) without invoking any a priori knowledge about the properties of the system observed. Potentialities of the algorithm are demonstrated with the aid of a computer model of the mesospheric PCS. The duration of the "observed" TS is limited so that the system demonstrates only one--chaotic--type of behaviour, without any bifurcations throughout the observed TS. The proposed algorithm enabled us to make a correct prognosis of bifurcation sequences and calculate probabilities to reveal, at the time instant of interest, predicted regimes of the system's behaviour for times much greater than the length of the initial TS.

Journal Article↗
PubMed2006

Dynamics of rotating paramagnetic particles simulated by lattice Boltzmann and particle dynamics methods.

Novel biochemical sensors consisting of rotating chains of microscale paramagnetic particles have been proposed that would enable convenient, sensitive analyte detection. Predicting the dynamics of these particles is required to optimise their design. The results of lattice Boltzmann (LB) and particle dynamics (PD) simulations are reported, where the LB approach provides a verified solution of the complete Navier-Stokes equations, including the hydrodynamic interactions among the particles. On the other hand, the simpler PD approach neglects hydrodynamic interactions, and does not compute the fluid motion. It is shown that macroscopic properties, like the number of aggregated particles, depend only on the drag force and not on the total hydrodynamic force, making PD simulations yield reasonably accurate predictions. Relatively good agreement between the LB and PD simulations, and qualitative agreement with experimental data, are found for the number of aggregated particles as a function of the Mason number. The drag force on a rotating cylinder is significantly different from that on particle chains calculated from both simulations, demonstrating the different dynamics between the two cases. For microscopic quantities like the detailed force distributions on each particle, the complete Navier-Stokes solution, here represented by the LB simulation, is required.

Computer Simulation↗
PubMed2000

Dynamic anal endosonography may challenge defecography for assessing dynamic anorectal disorders: results of a prospective pilot study.

BACKGROUND AND STUDY AIMS: The diagnosis of anorectal dynamic disorders and perineal insufficiency has been mainly based up to now on the use of defecography. Here, we performed a prospective blinded study to evaluate the accuracy of a new procedure, dynamic anorectal endosonography (DAE), by comparing it with defecography. PATIENTS AND METHODS: A total of 43 women (mean age 53), presenting with outlet obstruction, were prospectively enrolled in our study. The DAE was performed with a 7.5-Mhz linear probe (Toshiba, Tokyo, Japan) with basal and straining recordings. None of the DAE or defecography operators was informed about the results of the respective other investigation. RESULTS: Defecography showed a descending perineum in 29 patients (68%), a rectocele in 25 patients (58%), and a rectal intussusception in eight patients (18%). The rate of concordance between the diagnosis of descending urinary bladder at DAE and descending perineum at defecography was 35/43 (80%), and that between the descending puborectal muscle at DAE and descending perineum at defecography was 40/43 (93 %). The rates of concordance between DAE and defecography for the diagnosis of rectocele and rectal intussusception were 27/43 patients (57%) and 34/43 patients (80%), respectively. In the last 15 patients, the DAE technique was adapted in order to improve the accuracy for diagnosing rectocele by filling the rectum with water. This improved sensitivity from 36 to 86% and accuracy from 57 to 87%. CONCLUSIONS: DAE is a new imaging approach to anorectal dynamic disorders, providing a highly reliable means of diagnosing perineal insufficiency as well as rectocele. DAE should be substituted for previous methods since it makes it possible at the same time to assess the anal sphincters and to avoid pelvic irradiation.

Adult↗
PubMed2004

Ab initio centroid path integral molecular dynamics: application to vibrational dynamics of diatomic molecular systems.

An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.

Journal Article↗
PubMed2004

Dynamical behavior of one-dimensional water molecule chains in zeolites: nanosecond time-scale molecular dynamics simulations of bikitaite.

Nanosecond scale molecular dynamics simulations of the behavior of the one-dimensional water molecule chains adsorbed in the parallel nanochannels of bikitaite, a rare lithium containing zeolite, were performed at different temperatures and for the fully and partially hydrated material. New empirical potential functions have been developed for representing lithium-water interactions. The structure and the vibrational spectrum of bikitaite were in agreement both with experimental data and Car-Parrinello molecular dynamics results. Classical molecular dynamics simulations were extended to the nanosecond time scale in order to study the flip motion of water molecules around the hydrogen bonds connecting adjacent molecules in the chains, which has been observed by NMR experiments, and the dehydration mechanism at high temperature. Computed relaxation times of the flip motion follow the Arrhenius behavior found experimentally, but the activation energy of the simulated system is slightly underestimated. Based on the results of the simulations, it may be suggested that the dehydration proceeds by a defect-driven stepwise diffusion. The diffusive mechanism appears as a single-file motion: the molecules never pass one another, even at temperatures as high as about 1000 K, nor can they switch between different channels. However, the mean square displacement (MSD) of the molecules, computed with respect to the center of mass of the simulated system, shows an irregular trend from which the single-file diffusion cannot be clearly evidenced. If the MSDs are evaluated with respect to the center of mass of the molecules hosted in each channel, the expected dependence on the square root of time finally appears.

Journal Article↗
PubMed2004

A molecular dynamics simulation study of the alpha-relaxation in a 1,4-polybutadiene melt as probed by the coherent dynamic structure factor.

The dynamic coherent structure factor Scoh(q,t) for a 1,4-polybutadiene (PBD) melt has been investigated using atomistic molecular dynamics simulations. The relaxation of Scoh(q,t) at q = 1.44 angstroms(-1) and q = 2.72 angstroms(-1), corresponding to the first and second peaks in the static structure factor for PBD, was studied in detail over a wide range of temperature. It was found that time-temperature superposition holds for the alpha-relaxation for both q values over a wide temperature range and that the alpha-relaxation can be well described by a stretched (Kohlrauch-William-Watts) exponential with temperature independent but q dependent amplitude and stretching exponent. The alpha-relaxation times for both q values were found to exhibit the same non-Arrhenius temperature dependence, indicating that the same physical processes are responsible for relaxation on both length scales. The alpha-relaxation time was found to depend strongly upon the dynamical range of data utilized in determining the relaxation time, accounting for qualitative discrepancies between alpha-relaxation times reported here and those extracted for PBD from experimentally measured Scoh(q,t).

Journal Article↗
PubMed2004

Dynamic light scattering study of the dynamics of a gelled polymeric micellar system.

The dynamics of the E(92)B(18)/water system are studied by dynamic light scattering (DLS) in the liquid, soft gel, and hard gel phases. Both the liquid and the soft gel phases are micellar phases, although the structural order is higher in the soft gel phase than in the liquid phase. The hard gel phase corresponds to a face-centered cubic arrangement of micelles. DLS results show that the dilute liquid phase is characterized by a single characteristic time tau(1) associated with the diffusion of the micelles. In addition, a second characteristic time tau(2) associated with the presence of micellar clusters in the system is identified in the concentrated liquid and in the soft gel phases. According to these results, DLS suggests that the structure of the soft gel phase comprises micellar clusters coexisting with micellar fluid, in good agreement with hypotheses from our previous work. The dynamics of the system slows down as the hard gel phase is approached and a plateau is observed in the DLS correlation function. The structure of the hard gel is "softened" upon increasing temperature and/or decreasing concentration.

Journal Article↗
PubMed2005

Quantum dynamics in the highly discrete, commensurate Frenkel Kontorova model: a path-integral molecular dynamics study.

The commensurate Frenkel Kontorova (FK) model is studied using path-integral molecular dynamics (PIMD). We focus on the highly discrete case, in which the embedding potential has a much greater maximum curvature than the harmonic potential connecting two particles in the FK chain. When efficient sampling methods are used, the dynamical interpretation of adiabatic PIMD appears to represent quite accurately the true time correlation functions of this highly correlated many-body system. We have found that the discrete, quantum FK model shows different behavior than its continuum version. The spectral density does not show the characteristic omega-2Theta(omega-omegac) cusp of the continuum solution in the pinned phase (m>m(c)). We also identify a dynamical quantum hysteresis in addition to the regular classical hysteresis when an external force is applied to the FK chain. In the unpinned phase (m<or=m(c)), we find a linear response damping coefficient which is finite and only weakly dependent on temperature T at small values of T.

Journal Article↗
PubMed2005

Non-Fickian interdiffusion of dynamically asymmetric species: a molecular-dynamics study.

We use molecular dynamics combined with dissipative particle dynamics to construct a model of a binary mixture where the two species differ only in their dynamic properties (friction coefficients). For an asymmetric mixture of slow and fast particles we study the interdiffusion process. The relaxation of the composition profile is investigated in terms of its Fourier coefficients. While for weak asymmetry we observe Fickian behavior, a strongly asymmetric system exhibits clear indications of anomalous diffusion, which occurs in a crossover region between cases I (Fickian) and II (sharp front moving with constant velocity), and is close to the case II limit.

Journal Article↗
PubMed2005

Static and dynamical properties of heavy water at ambient conditions from first-principles molecular dynamics.

The static and dynamical properties of heavy water have been studied at ambient conditions with extensive Car-Parrinello molecular-dynamics simulations in the canonical ensemble, with temperatures ranging between 325 and 400 K. Density-functional theory, paired with a modern exchange-correlation functional (Perdew-Burke-Ernzerhof), provides an excellent agreement for the structural properties and binding energy of the water monomer and dimer. On the other hand, the structural and dynamical properties of the bulk liquid show a clear enhancement of the local structure compared to experimental results; a distinctive transition to liquidlike diffusion occurs in the simulations only at the elevated temperature of 400 K. Extensive runs of up to 50 ps are needed to obtain well-converged thermal averages; the use of ultrasoft or norm-conserving pseudopotentials and the larger plane-wave sets associated with the latter choice had, as expected, only negligible effects on the final result. Finite-size effects in the liquid state are found to be mostly negligible for systems as small as 32 molecules per unit cell.

Journal Article↗
PubMed2005

Speed up of dynamic observables in coarse-grained molecular-dynamics simulations of unentangled polymers.

Coarse-grained models that preserve atomistic detail display faster dynamics than atomistic systems alone. We show that this " indirect speed up" is robust: coarse-grained dynamic observables computed with time scaled by a constant factor are in excellent agreement with their underlying atomistic counterparts. Borrowing from accelerated dynamics methods used in the field of rare events, we predict the scaling factor within 7%, based on reduced intermolecular attraction yielding faster neighbor cage escapes.

Journal Article↗
PubMed2005

Mean-field dynamics with stochastic decoherence (MF-SD): a new algorithm for nonadiabatic mixed quantum/classical molecular-dynamics simulations with nuclear-induced decoherence.

The key factors that distinguish algorithms for nonadiabatic mixed quantum/classical (MQC) simulations from each other are how they incorporate quantum decoherence-the fact that classical nuclei must eventually cause a quantum superposition state to collapse into a pure state-and how they model the effects of decoherence on the quantum and classical subsystems. Most algorithms use distinct mechanisms for modeling nonadiabatic transitions between pure quantum basis states ("surface hops") and for calculating the loss of quantum-mechanical phase information (e.g., the decay of the off-diagonal elements of the density matrix). In our view, however, both processes should be unified in a single description of decoherence. In this paper, we start from the density matrix of the total system and use the frozen Gaussian approximation for the nuclear wave function to derive a nuclear-induced decoherence rate for the electronic degrees of freedom. We then use this decoherence rate as the basis for a new nonadiabatic MQC molecular-dynamics (MD) algorithm, which we call mean-field dynamics with stochastic decoherence (MF-SD). MF-SD begins by evolving the quantum subsystem according to the time-dependent Schrodinger equation, leading to mean-field dynamics. MF-SD then uses the nuclear-induced decoherence rate to determine stochastically at each time step whether the system remains in a coherent mixed state or decoheres. Once it is determined that the system should decohere, the quantum subsystem undergoes an instantaneous total wave-function collapse onto one of the adiabatic basis states and the classical velocities are adjusted to conserve energy. Thus, MF-SD combines surface hops and decoherence into a single idea: decoherence in MF-SD does not require the artificial introduction of reference states, auxiliary trajectories, or trajectory swarms, which also makes MF-SD much more computationally efficient than other nonadiabatic MQC MD algorithms. The unified definition of decoherence in MF-SD requires only a single ad hoc parameter, which is not adjustable but instead is determined by the spatial extent of the nonadiabatic coupling. We use MF-SD to solve a series of one-dimensional scattering problems and find that MF-SD is as quantitatively accurate as several existing nonadiabatic MQC MD algorithms and significantly more accurate for some problems.

Journal Article↗
PubMed2006

Dynamic bond constraints in protein Langevin dynamics.

Bond constraint algorithms for molecular dynamics typically take, as the target constraint lengths, the values of the equilibrium bond lengths defined in the potential. In Langevin form, the equations of motion are temperature dependent, which gives the average value for the individual bond lengths a temperature dependence. In addition to this, locally constant force fields can shift the local equilibrium bond lengths. To restore the average bond lengths in constrained integration to their unconstrained values, we suggest changing the constraint length used by popular constraint methods such as RATTLE [H. C. Andersen, J. Comput. Phys. 52, 23 (1983)] at each step. This allows us to more accurately capture the equilibrium bond length changes (with respect to the potential) due to the local equilibration and temperature effects. In addition, the approximations to the unconstrained nonbonded energies are closer using the dynamic constraint method than a traditional fixed constraint algorithm. The mechanism for finding the new constrained lengths involves one extra calculation of the bonded components of the force, and therefore adds O(N) time to the constraint algorithm. Since most molecular dynamics calculations are dominated by the O(N2) nonbonded forces, this new method does not take significantly more time than a fixed constraint algorithm.

Algorithms↗
PubMed2006

Dynamical pruning of static localized basis sets in time-dependent quantum dynamics.

We investigate the viability of dynamical pruning of localized basis sets in time-dependent quantum wave packet methods. Basis functions that have a very small population at any given time are removed from the active set. The basis functions themselves are time independent, but the set of active functions changes in time. Two different types of localized basis functions are tested: discrete variable representation (DVR) functions, which are localized in position space, and phase-space localized (PSL) functions, which are localized in both position and momentum. The number of functions active at each point in time can be as much as an order of magnitude less for dynamical pruning than for static pruning, in reactive scattering calculations of H2 on the Pt(211) stepped surface. Scaling of the dynamically pruned PSL (DP-PSL) bases with dimension is considerably more favorable than for either the primitive (direct product) or DVR bases, and the DP-PSL basis set is predicted to be three orders of magnitude smaller than the primitive basis set in the current state-of-the-art six-dimensional reactive scattering calculations.

Journal Article↗
PubMed2006

Femtosecond study on the isomerization dynamics of NK88. II. Excited-state dynamics.

The molecule 3,3(')-diethyl-2,2(')-thiacyanine isomerizes after irradiation with light of the proper wavelength. After excitation, it undergoes a transition, in which one or more conical intersections are involved, back to the ground state to form different product photoisomers. The dynamics before and directly after the transition back to the ground state is investigated by transient absorption spectroscopy in a wavelength region of 360-950 nm, as well as by fluorescence upconversion. It is shown that the excited-state dynamics are governed by two time scales: a short one with a decay time of less than 2 ps and a long one with about 9 ps. A thorough comparison of the experimental results with those of configuration interaction singles and time-dependent density functional theory calculations suggests that these dynamics are related to two competing pathways differing in the molecular twisting on the excited surface after photoexcitation. From the experimental point of view this picture arises taking into account the time scales for ground-state bleach, excited-state absorption, stimulated emission, fluorescence, and assumed hot ground-state absorption both in the solvent methanol and ethylene glycol.

Absorption↗