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PubMed2003

Compensatory changes in static and dynamic subjective visual vertical in patients following vestibular schwanoma surgery.

OBJECTIVE: Among patients with vestibular schwanoma (VS), vestibular function is nonhomogeneous, both before and after surgical removal of the VS. This paper reports investigations of neural changes, especially changes in the contribution of visual input to vestibular system integration, after VS surgery. METHODS: We examined 33 patients who underwent VS surgery via a middle fossa approach. Static and dynamic subjective visual vertical (SVV) was measured once after surgery and compared to those measured in control subjects. SVVs were assessed using a paradigm requiring the subject to manually adjust an image of a bar to the perceived vertical alignment. SVVs were measured when the background was stationary or rotating. RESULTS: In almost all patients, static SVV deviated toward the operated side. In VS subjects, the mean static SVV was 1.8+/-2.2 degrees; the amount of deviation in the dynamic SVV toward the operated side (11.7+/-8.3 degrees ) was significantly larger than that to the intact side (8.8+/-5.5 degrees ). In VS subjects, static SVV was correlated with dynamic SVV only in cases of bar adjustments toward the operated side (R=0.67, P<0.001), but not in cases of adjustments toward the intact, unoperated side. The axis of rotation was defined as the mean value of dynamic SVV for adjustments toward either side. There was only a weak correlation between the static SVV and the axis of rotation (R=0.31; P<0.05) in the control subjects. On the other hand, a more robust correlation between static SVV and axis of rotation was found (R=0.67, P<0.001) in VS subjects. There was no correlation between the static SVV and the deviation of dynamic SVV from static SVV for CCW and CW in control subjects. In contrast, there were significant correlations between static SVV and deviation of dynamic SVV from static SVV for adjustments made toward both operated (r=0.48, P<0.001) and intact sides (r=038, P<0.05). CONCLUSION: It is assumed that the amount of deviation in static SVV reflects the individual level of compensation. In addition, increased visual dependency evoked a symmetrical bias of the dynamic SVV from the measures at initial SVV assessment (i.e. static SVV or the center of tilt). As a result, we conclude that the contribution of visual inputs had changed after surgery, while at the same time, each patient used their static SVV as their reference point for orientation.

Adaptation, Physiological↗
PubMed2002

Application of dynamic MRI to differentiating odontogenic myxomas from ameloblastomas.

It is often difficult to radiographically distinguish odontogenic myxomas from ameloblastomas. In the present study, we tried to differentiate odontogenic myxomas from ameloblastomas using dynamic magnetic resonance imaging (dynamic MRI). Two cases of ameloblastoma with cystic components and two cases of odontogenic myxoma were compared by dynamic MRI. The dynamic MRI features of solid areas of ameloblastomas showed a rapid enhancement, reaching maximum contrast at 45-60 s, and maintained these enhancement levels or showed a gradual wash-out to 600 s thereafter; in contrast, those of the cystic areas of ameloblastomas showed no enhancement. The dynamic MRI features of the whole area of odontogenic myxomas (we considered the whole area to be the tumor substance in the odontogenic myxomas, as based on histopathological examinations) showed a gradual increase in enhancement at 500-600 s. The central portions of the odontogenic myxomas, which did not appear to be enhanced on Gd-T1 weighted images also showed a gradual increase in enhancement at 500-600 s, though the increase was minimal. These results indicate that the dynamic MRI features of odontogenic myxomas are different from those of ameloblastomas. Therefore, dynamic MRI may be a useful tool for diagnosis of myxoma.

Ameloblastoma↗
PubMed2003

Pulmonary hilar lymph nodes in lung cancer: assessment with 3D-dynamic contrast-enhanced MR imaging.

PURPOSE: We performed 3D-dynamic MRI on patients with primary lung cancer to identify its usefulness for detecting hilar adenopathy shown at surgery. METHODS AND MATERIALS: 30 consecutive patients with peripheral lung cancer underwent preoperative 3D-dynamic Gd-DTPA-enhanced MRI. Two thoracic radiologists blinded to histopathologic findings reviewed those studies independently for hilar adenopathy visualization. The results were correlated with surgical and histopathologic findings. Interreader agreement for the detection of hilar adenopathy was assessed by means of the kappa statistic. RESULTS: Dynamic MRI demonstrated hilar adenopathy, with or without metastasis revealed at surgery, in all of 15 patients. Adenopathy without metastasis was shown in four patients. Dynamic MRI also revealed metastatic adenopathy in 11 of 12 patients with pathologically proven metastasis. There was only one case with lymph node metastasis that did not have adenopathy either on MRI or even at surgery. The diagnostic accuracy of dynamic MRI for adenopathy with or without metastases revealed at surgery were as follows; sensitivity, 100%; specificity, 100%; positive predictive value, 100%; and negative predictive value, 100%, respectively. The diagnostic accuracy of dynamic MRI for hilar lymph nodes metastasis were as follows; sensitivity, 92%; specificity, 78%; positive predictive value, 73%; and negative predictive value, 93%. Interreader agreement was substantial (kappa=0.73) for detection of hilar adenopathy. CONCLUSION: Hilar adenopathy on 3D-dynamic MRI correlated well with that of surgical finding on patients with primary lung cancer. It may have the potential to make an accurate preoperative evaluation of hilar lymph node metastasis from lung cancer.

Adenocarcinoma↗
PubMed1998

Investigation of multiaxial molecular dynamics by 2H MAS NMR spectroscopy.

The technique of 2H MAS NMR spectroscopy is presented for the investigation of multiaxial molecular dynamics. To evaluate the effects of discrete random reorientation a Lie algebraic formalism based on the stochastic Liouville-von Neumann equation is developed. The solution to the stochastic Liouville-von Neumann equation is obtained both in the presence and absence of rf irradiation. This allows effects of molecular dynamics to be evaluated during rf pulses and extends the applicability of the formalism to arbitrary multiple pulse experiments. Theoretical methods are presented for the description of multiaxial dynamics with particular emphasis on the application of vector parameters to represent molecular rotations. Numerical time and powder integration algorithms are presented that are both efficient and easy to implement computationally. The applicability of 2H MAS NMR spectroscopy for investigating molecular dynamics is evaluated from theoretical spectra. To demonstrate the potential of the technique the dynamics of thiourea-2H4 is investigated experimentally. From a series of variable temperature MAS and quadrupole echo spectra it has been found that the dynamics can be described by composite rotation about the CS and CN bonds. Both experiments are sensitive to the fast CS rotation which is shown to be described by the Arrhenius parameters E(CS) = 46.4 +/- 2.3 kJ mol(-1) and ln(A(CS))= 32.6 +/- 0.9. The MAS experiment represents a significant improvement by simultaneously allowing the dynamics of the slow CN rotation to be fully characterized in terms of E(CN) = 56.3 +/- 3.4 kJ mol(-1) and ln(A(CN)) = 25.3 +/- 1.1.

Magnetic Resonance Spectroscopy↗
PubMedDate not supplied

Dynamical coding of sensory information with competitive networks.

Based on experiments with the locust olfactory system, we demonstrate that model sensory neural networks with lateral inhibition can generate stimulus specific identity-temporal patterns in the form of stimulus-dependent switching among small and dynamically changing neural ensembles (each ensemble being a group of synchronized projection neurons). Networks produce this switching mode of dynamical activity when lateral inhibitory connections are strongly non-symmetric. Such coding uses 'winner-less competitive' (WLC) dynamics. In contrast to the well known winner-take-all competitive (WTA) networks and Hopfield nets, winner-less competition represents sensory information dynamically. Such dynamics are reproducible, robust against intrinsic noise and sensitive to changes in the sensory input. We demonstrate the validity of sensory coding with WLC networks using two different formulations of the dynamics, namely the average and spiking dynamics of projection neurons (PN).

Animals↗
PubMed1997

Backbone dynamics of homologous fibronectin type III cell adhesion domains from fibronectin and tenascin.

BACKGROUND: Fibronectin type III domains are found as autonomously-folded domains in a large variety of multidomain proteins, including extracellular matrix proteins. A subset of these domains employ an Arg-Gly-Asp (RGD) tripeptide motif to mediate contact with cell-surface receptors (integrins). This motif mediates protein-protein interactions in a diverse range of biological processes, such as in tissue development, would healing and metastasis. The molecular basis for affinity and specificity of cell adhesion via type III domains has not been clearly established. The tenth type III domain from fibronectin (FNfn10) and the third type III domain from tenascin-C (TNfn3) have 27% sequence identity and share the same overall protein fold, but present the RGD motifs in different structural contexts. The dynamical properties of the RGD motifs may affect the specificity and affinity of the FNfn10 and TNfn3 domains. Structure-dynamics correlations for these structurally homologous proteins may reveal common molecular features which are important to the dynamical properties of proteins. RESULTS: The intramolecular dynamics of the protein backbones of FNfn10 and TNfn3 have been studied by 15N nuclear spin relaxation. The FG loop in FNfn10, which contains the RGD motif, exhibits extensive flexibility on picosecond to nanosecond timescales, but motions on microsecond to millisecond timescales are not observed. The equivalent region in TNfn3 is as rigid as regular elements of secondary structure. The CC' loop also is more flexible on picosecond-nanosecond timescales in FNfn10 than in TNfn3. Conformational exchange, reflecting flexibility on microsecond-millisecond timescales, is observed in beta strands A and B of both FNfn10 and TNfn3. CONCLUSIONS: Comparison of the structures of the FNfn10 and TNfn3 reveals several features related to their different dynamical properties. The larger amplitude motions of loops in FNfn10 are consistent with the hypothesis that flexibility of these regions facilitates induced-fit recognition of fibronectin by multiple receptors. Similarly, the more rigid loops of TNfn3 may reflect greater specificity for particular integrins. The correlations observed between structural features and dynamical properties of the homologous type III domains indicate the influence of hydrogen bonding and hydrophobic packing on dynamical fluctuations in proteins.

Amino Acid Sequence↗
PubMed2004

Comparisons of dynamic retinoscopy measurements with a print card, a video display terminal, and a PRIO System Tester as test targets.

BACKGROUND: Dynamic retinoscopy is a common clinical test for assessment of visual function in patients with symptoms related to computer use. It has been suggested that performing dynamic retinoscopy with a fixation target resembling a computer screen may be valuable in the examination of computer users. However, such targets differ in luminance and other characteristics from the printed paper test cards typically used for dynamic retinoscopy. METHOD: To address the effect of varying test targets on dynamic retinoscopy results, this study compared lag of accommodation results from dynamic retinoscopy with three different fixation targets: (a) a printed paper target, (b) a video display terminal, and (c) the PRIO vision testing device, which is designed to simulate a computer screen. MEM (monocular estimate method) dynamic retinoscopy was performed with the print target and with the PRIO device. RESULTS: The difference between results with the different test conditions were generally small, with a statistically significant 0.32 D lower lag found on MEM retinoscopy with the PRIO target IMEM-PRIO) than on MEM retinoscopy with a print target (MEM-PRINT). Mean lag measurements on MEM with a print target and on Nott retinoscopy with the video display terminal (NOTT-VDT) were only 0.04 D different. The 95% limits of agreement for the difference between MEM-PRINT and MEM-PRIO (+/- 0.6 D) was similar to the 95% limits of agreement for the interexaminer reliability of the two procedures (+/- 0.6 D for MEM-PRINT and +/- 0.7 D for MEM-PRIO). CONCLUSION: There was a small but statistically significant difference in lag of accommodation measured with MEM dynamic retinoscopy on the PRIO testing device when compared to a print card.

Accommodation, Ocular↗
PubMed2001

Hydride transfer in liver alcohol dehydrogenase: quantum dynamics, kinetic isotope effects, and role of enzyme motion.

The quantum dynamics of the hydride transfer reaction catalyzed by liver alcohol dehydrogenase (LADH) are studied with real-time dynamical simulations including the motion of the entire solvated enzyme. The electronic quantum effects are incorporated with an empirical valence bond potential, and the nuclear quantum effects of the transferring hydrogen are incorporated with a mixed quantum/classical molecular dynamics method in which the transferring hydrogen nucleus is represented by a three-dimensional vibrational wave function. The equilibrium transition state theory rate constants are determined from the adiabatic quantum free energy profiles, which include the free energy of the zero point motion for the transferring nucleus. The nonequilibrium dynamical effects are determined by calculating the transmission coefficients with a reactive flux scheme based on real-time molecular dynamics with quantum transitions (MDQT) surface hopping trajectories. The values of nearly unity for these transmission coefficients imply that nonequilibrium dynamical effects such as barrier recrossings are not dominant for this reaction. The calculated deuterium and tritium kinetic isotope effects for the overall rate agree with experimental results. These simulations elucidate the fundamental nature of the nuclear quantum effects and provide evidence of hydrogen tunneling in the direction along the donor-acceptor axis. An analysis of the geometrical parameters during the equilibrium and nonequilibrium simulations provides insight into the relation between specific enzyme motions and enzyme activity. The donor-acceptor distance, the catalytic zinc-substrate oxygen distance, and the coenzyme (NAD(+)/NADH) ring angles are found to strongly impact the activation free energy barrier, while the donor-acceptor distance and one of the coenzyme ring angles are found to be correlated to the degree of barrier recrossing. The distance between VAL-203 and the reactive center is found to significantly impact the activation free energy but not the degree of barrier recrossing. This result indicates that the experimentally observed effect of mutating VAL-203 on the enzyme activity is due to the alteration of the equilibrium free energy difference between the transition state and the reactant rather than nonequilibrium dynamical factors. The promoting motion of VAL-203 is characterized in terms of steric interactions involving THR-178 and the coenzyme.

Alcohol Dehydrogenase↗
PubMed2002

Deuterium spin probes of side-chain dynamics in proteins. 2. Spectral density mapping and identification of nanosecond time-scale side-chain motions.

In the previous paper in this issue we have demonstrated that it is possible to measure the five different relaxation rates of a deuteron in (13)CH(2)D methyl groups of (13)C-labeled, fractionally deuterated proteins. The extensive set of data acquired in these experiments provides an opportunity to investigate side-chain dynamics in proteins at a level of detail that heretofore was not possible. The data, acquired on the B1 domain of peptostreptococcal protein L, include 16 (9) relaxation measurements at 4 (2) different magnetic field strengths, 25 degrees C (5 degrees C). These data are shown to be self-consistent and are analyzed using a spectral density mapping procedure which allows extraction of values of the spectral density function at a number of frequencies with no assumptions about the underlying dynamics. Dynamics data from 31 of 35 methyls in the protein for which data could be obtained were well-fitted using the two-parameter Lipari-Szabo model (Lipari, G.; Szabo, A. J. Am. Chem. Soc. 1982, 104, 4546). The data from the remaining 4 methyls can be fitted using a three-parameter version of the Lipari-Szabo model that takes into account, in a simple manner, additional nanosecond time-scale local dynamics. This interpretation is supported by analysis of a molecular dynamics trajectory where spectral density profiles calculated for side-chain methyl sites reflect the influence of slower (nanosecond) time-scale motions involving jumps between rotameric wells. A discussion of the minimum number of relaxation measurements that are necessary to extract the full complement of dynamics information is presented along with an interpretation of the extracted dynamics parameters.

Bacterial Proteins↗
PubMed2005

Sensitivity of polar solvation dynamics to the secondary structures of aqueous proteins and the role of surface exposure of the probe.

The structure and dynamics of water around a protein is expected to be sensitive to the details of the adjacent secondary structure of the protein. In this article, we explore this sensitivity by calculating both the orientational dynamics of the surface water molecules and the equilibrium solvation time correlation function of the polar amino acid residues in each of the three helical segments of the protein HP-36, using atomistic molecular dynamics simulations. The solvation dynamics of polar amino acid residues in helix-2 is found to be faster than that of the other two helices (the average time constant is smaller by a factor of 2), although the interfacial water molecules around helix-2 exhibit much slower orientational dynamics than that around the other two helices. A careful analysis shows that the origin of such a counterintuitive behavior lies in the dependence of the solvation time correlation function on the surface exposure of the probe-the more exposed is the probe, the faster the solvation dynamics. We discuss that these results are useful in explaining recent solvation dynamics experiments.

Binding Sites↗
PubMed2005

Dynamic effects in MAS and MQMAS NMR spectra of half-integer quadrupolar nuclei: calculations and an application to the double perovskite cryolite.

Dynamic processes such as chemical exchange or rotations between inequivalent orientations can affect the magic-angle spinning (MAS) and the multiple-quantum (MQ) MAS NMR spectra of half-integer quadrupolar nuclei. The present paper discusses such dynamic multisite MAS and MQMAS effects and applies them to study the dynamic processes that occur in the double perovskite cryolite, Na3AlF6. Dynamic line shape simulations invoking a second-order broadening of the central transition and relying on the semiclassical Bloch-McConnell formalism for chemical exchange were performed for a variety of exchange models possessing different symmetries. Fitting experimental variable-temperature cryolite 23Na NMR data with this formalism revealed that the two inequivalent sodium sites in this mineral undergo an exchange characterized by a broad distribution of rates. To further assess this dynamic process a variety of 27Al and 19F MAS NMR studies were also undertaken; quantitative 27Al-19F dipolar coupling measurements then revealed a dynamic motion of the AlF6 octahedra that were qualitatively consistent with predictions stemming from molecular dynamic simulations on this double perovskite.

Journal Article↗
PubMed2006

Simultaneous determination of protein backbone structure and dynamics from residual dipolar couplings.

Determination of protein structure classically results in a single average configuration that takes no account of conformational fluctuation. Dynamics are, however, inherently linked to structure and crucial to our understanding of biological function. In this study we have used analytical descriptions of dynamic averaging of residual dipolar couplings (RDCs) to simultaneously determine the backbone structure and dynamics of protein GB3. RDCs alone are used to determine an ultrahigh-resolution structure that compares very closely with a refined X-ray structure (rmsd of 0.34 A overall backbone residues). Dynamic amplitudes reporting on motions up to the millisecond time scale reproduce the main characteristics of dynamics previously determined in conjunction with the crystal structure. The use of RDCs alone allows a bias-free comparison with a purely static approach to structure determination. Extensive cross validation clearly demonstrates that the dynamic description is superior to the static approximation. The demonstration that this level of structural resolution and dynamic detail can be extracted from RDCs supports previous indications that these parameters contain extremely precise information about biomolecular conformational sampling.

Models, Molecular↗
PubMed2005

Dynamic behavior of water within a polymer electrolyte fuel cell membrane at low hydration levels.

Protonic conduction across the membrane of a polymer electrolyte fuel cell is intimately related to the dynamic behavior of water present within the membrane. To further the understanding of water dynamics in these materials, quasielastic neutron scattering (QENS) has been used to investigate the picosecond dynamic behavior of water within a perfluorosulfonated ionomer (PFSI) membrane under increasing hydration levels from dry to saturation. Evaluation of the elastic incoherent structure factor (EISF) reveals an increase in the characteristic length-scale of confinement as the number of water molecules in the membrane increases, tending to an asymptotic value at saturation. The fraction of elastic incoherent scattering observed at high Q over all hydration levels is well fit by a simple model that assumes a single, nondiffusing hydronium ion per membrane sulfonic acid site. The quasielastic component of the fitted data indicates confined dynamic behavior for scattering vectors less than 0.7 A(-1). As such, the dynamic behavior was interpreted using continuous diffusion confined within a sphere at Q < 0.7 A(-1) and random unconstrained jump diffusion at Q > 0.7 A(-1). As the number of water molecules in the membrane increases, the characteristic residence times obtained from both models is reduced. The increased dynamical frequency is further reflected in the diffusion coefficients predicted by both models. Between low hydration (2 H2O/SO3H) and saturation (16 H2O/SO3H), the continuous spherical diffusion coefficient changes from 0.46 +/- 0.12 to 1.04 +/- 0.12 (10(-5) cm2/s) and jump diffusion indicates an increase from 1.21 +/- 0.03 to 2.14 +/- 0.08 (10(-5) cm2/s). Overall, the dynamic behavior of water has been quantified over different length scale regimes, the results of which may be rationalized on the basis of the formation of water clusters in the hydrophilic domain that expand toward an asymptotic upper limit with increased hydration.

Journal Article↗
PubMed2006

Dynamics in the presence of attractive patchy interactions.

We report extensive Monte Carlo and event-driven molecular dynamics simulations of a liquid composed of particles interacting via hard-sphere interactions complemented by four tetrahedrally coordinated short-range attractive ("sticky") spots, a model introduced several years ago by Kolafa and Nezbeda (Kolafa, J.; Nezbeda, I. Mol. Phys. 1987, 87, 161). To access the dynamic properties of the model, we introduce and implement a new event-driven molecular dynamics algorithm suited to study the evolution of hard bodies interacting, beside the repulsive hard-core, with a short-ranged interpatch square well potential. We evaluate the thermodynamic properties of the model in deep supercooled states, where the bond network is fully developed, providing evidence of density anomalies. Different from models of spherically symmetric interacting particles, the liquid can be supercooled without encountering the gas-liquid spinodal in a wide region of packing fractions phi. Around an optimal phi, a stable fully connected tetrahedral network of bonds develops. By analyzing the dynamics of the model we find evidence of anomalous behavior: around the optimal packing, dynamics accelerate on both increasing and decreasing phi. We locate the shape of the isodiffusivity lines in the (phi - T) plane and establish the shape of the dynamic arrest line in the phase diagram of the model. Results are discussed in connection with colloidal dispersions of sticky particles and gel-forming proteins and their ability to form dynamically arrested states.

Journal Article↗
PubMed2006

Dynamics of energy transfer in collisions of O(3P) atoms with a 1-decanethiol self-assembled monolayer surface.

Chemical dynamics simulations are reported of energy transfer in collisions of O(3P) atoms with a 300 K 1-decanethiol self-assembled monolayer (H-SAM) surface. The simulations are performed with a nonreactive potential energy surface, developed from PMP2/aug-cc-pVTZ calculations of the O(3P) + H-SAM intermolecular potential, and the simulation results represent the energy transfer dynamics in the absence of O(3P) reaction. Collisions energies E(i) of 0.12, 2.30, 11.2, 75.0, and 120.5 kcal/mol and incident angles theta(i) of 15, 30, 45, 60, and 75 degrees were considered in the study (theta(i) = 0 degrees is the surface normal). The translational energy distribution of the scattered O(3P) atoms, P(E(f)), may be deconvoluted into Boltzmann and non-Boltzmann components, with the former fraction identified as f(B). The trajectories are also analyzed in terms of three types; that is, direct scattering from and physisorption on the top of the H-SAM and penetration of the H-SAM. There are three energy regimes in the scattering dynamics. For the low E(i) values of 0.12 and 2.30 kcal/mol, physisorption is important and both f(B) and the average final translational energy of the scattered O(3P) atom, E(f), are nearly independent of the incident angle. The dynamics is much different for hyperthermal energies of 75.0 and 120.5 kcal/mol, where penetration of the surface is important. For hyperthermal collisions, the penetration probability decreases as theta(i) is increased, with a significant transition between theta(i) of 60 and 75 degrees . Hyperthermal penetration occurs upon initial surface impact and is more probable if the impinging O(3P) atom may move down a channel between the chains. For E(i) = 120.5 kcal/mol, 90% of the trajectories penetrate at theta(i) = 15 degrees , while only 3% penetrate at theta(i) = 75 degrees. For the former theta(i), the energy transfer to the surface is efficient with E(f) = 4.04 kcal/mol, but for the latter theta(i), E(f) = 85.3 kcal/mol! Particularly interesting penetrating trajectories are those in which O(3P) is trapped in the H-SAM for times exceeding 60 ps, linger near the Au substrate, and strike the Au substrate and scatter directly. For E(i) = 11.2 kcal/mol, there is a transition between the scattering dynamics for the low and hyperthermal collision energies. Additional detail in the energy transfer dynamics is obtained from the final polar and azimuthal angles, the residence time on/in the H-SAM, the minimum height with respect to the Au substrate, and the number of inner turning points in the O-atom's velocity. Calculated values of E(f) vs the final polar angle, theta(f), are in qualitative agreement with experiment. The O(3P) + H-SAM nonreactive energy transfer dynamics, for E(i) of 11.2 kcal/mol and lower, are very similar to previously reported Ne + H-SAM simulations.

Journal Article↗
PubMed2006

Exploring the role of decoherence in condensed-phase nonadiabatic dynamics: a comparison of different mixed quantum/classical simulation algorithms for the excited hydrated electron.

Mixed quantum/classical (MQC) molecular dynamics simulation has become the method of choice for simulating the dynamics of quantum mechanical objects that interact with condensed-phase systems. There are many MQC algorithms available, however, and in cases where nonadiabatic coupling is important, different algorithms may lead to different results. Thus, it has been difficult to reach definitive conclusions about relaxation dynamics using nonadiabatic MQC methods because one is never certain whether any given algorithm includes enough of the necessary physics. In this paper, we explore the physics underlying different nonadiabatic MQC algorithms by comparing and contrasting the excited-state relaxation dynamics of the prototypical condensed-phase MQC system, the hydrated electron, calculated using different algorithms, including: fewest-switches surface hopping, stationary-phase surface hopping, and mean-field dynamics with surface hopping. We also describe in detail how a new nonadiabatic algorithm, mean-field dynamics with stochastic decoherence (MF-SD), is to be implemented for condensed-phase problems, and we apply MF-SD to the excited-state relaxation of the hydrated electron. Our discussion emphasizes the different ways quantum decoherence is treated in each algorithm and the resulting implications for hydrated-electron relaxation dynamics. We find that for three MQC methods that use Tully's fewest-switches criterion to determine surface hopping probabilities, the excited-state lifetime of the electron is the same. Moreover, the nonequilibrium solvent response function of the excited hydrated electron is the same with all of the nonadiabatic MQC algorithms discussed here, so that all of the algorithms would produce similar agreement with experiment. Despite the identical solvent response predicted by each MQC algorithm, we find that MF-SD allows much more mixing of multiple basis states into the quantum wave function than do other methods. This leads to an excited-state lifetime that is longer with MF-SD than with any method that incorporates nonadiabatic effects with the fewest-switches surface hopping criterion.

Journal Article↗
PubMed2006

Surface phase transition of C12E1 at the air/water interface: a study by dynamic surface tension, external RA FT-IR, and 2D IR correlation methods.

The surface conformational states of the Gibbs monolayer of ethylene glycol mono-n-dodecyl ether (C(12)E(1)) at the air/water interface was studied using dynamic surface tension, external reflection-absorption FT-IR spectroscopy (ERA FT-IR), and two-dimensional infrared (2D IR) correlation methods at constant temperature. The dynamic surface tensions were measured at different bulk concentrations of C(12)E(1), and it was observed that a constant surface tension region appears at approximately 38.5 mN m(-1) in a dynamic surface tension profile at concentrations higher than 11 micromol kg(-1). This constant surface tension region corresponds to the surface phase transition from liquid expanded (LE) to liquid condensed (LC). Two sets of ERA FT-IR spectra were collected, one at different bulk concentrations but after equilibrium time (equilibrium measurements) and another at constant bulk concentration (m = 16 micromol kg(-1)) but at different times (dynamic measurements). The first set of these measurements show that the peak area increases in the range of 11 < m < or = 16 micromol kg(-1), which means the increase in the number of surfactant molecules at the air/water interface. Also, the wavenumber of antisymmetric CH(2) stretching decreases gradually from approximately 2923 cm(-1) (for 10 and 11 micromol kg(-1)) to approximately 2918 cm(-1) (for m > or = 16 micromol kg(-1)) with increasing concentration. The wavenumbers of 2923 and 2918 cm(-1) were assigned to LE and LC phases, respectively, and the decrease of wavenumber in the concentration range of 11 < m < or = 16 micromol kg(-1) were correlated to the surface phase transition (LE --> LC), or in other words, in the mentioned concentration range, two phases coexist. The dynamic ERA FT-IR measurements at 16 micromol kg(-1) also confirm the surface phase transition from LE to LC. The 2D IR correlation method was applied to the both equilibrium and dynamic IR spectra of the C(12)E(1) monolayer. The synchronous correlation maps show two strong autopeaks at approximately 2922 and approximately 2851 cm(-1) and also show a strong correlation (cross-peaks) between antisymmetric CH(2) stretching (nu(a)) and symmetric CH(2) stretching (nu(s)). The asynchronous correlation maps show that both observed bands of nu(a) and nu(s) in one-dimensional IR split into two components with the characteristic of overlapped bands, which reveals the coexistence of two phases (LE and LC) at the interface at 11 < m < or = 16 micromol kg(-1). The synchronous and asynchronous maps that were obtained from dynamic IR spectra closely resembled the equilibrium map.

Journal Article↗
PubMedDate not supplied

Evolution and analysis of model CPGs for walking: I. Dynamical modules.

Can one develop an abstract description of the dynamics of pattern generators that provides quantitative insight into their operation? We explored this question by examining the dynamics of a model central pattern generator that was created using an evolutionary algorithm. We propose an abstract description based on the concept of a dynamical module, a set of neurons that simultaneously make their transitions from one quasistable state to another while the synaptic inputs that they receive from other neurons remain essentially constant, thus temporarily reducing the dimensionality of the circuit dynamics. Using the mathematical tools of dynamical systems theory, we describe a method for identifying dynamical modules and demonstrate that this concept can be used to quantitatively characterize constraints on neural architecture, account for phase durations, and predict the effects of parameter changes. Moreover, this abstract description reveals coordinated parameter changes that leave the overall circuit dynamics essentially unchanged. In a companion article we employ this abstract description to examine the relationship between general principles and individual variability in large populations of evolved model pattern generators.

Gait↗