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PubMed2005

Electronic relaxation dynamics of Ni2+-ion aqueous solution: molecular-dynamics simulation.

Electronic relaxation dynamics of Ni2+-ion aqueous solution is investigated using molecular-dynamics (MD) simulations with the model-effective Hamiltonian developed previously. The nonadiabatic transition rates from the first three excited states to the ground state are evaluated by the golden rule formula with the adiabatic MD simulations. The MD simulations with the fewest-switch surface-hopping method are also carried out to obtain a more detailed description of the electronic relaxation dynamics among the excited states. We found out that the transitions among the three excited states are very fast, in the order of 10 fs, while the transition between the excited and ground states is slow, about 800 ps. These findings are consistent with the time scales of energy dissipation detected by the transient lens experiment. In both simulations, we explore the effects of the quantum decoherence, where the decoherence functions are derived by the energy-gap dynamics with the displaced harmonic-oscillator model.

Journal Article↗
PubMed2005

Infrared and molecular-dynamics studies of the rotational dynamics of water highly diluted in supercritical CO2.

Far-infrared (FIR) and mid-infrared (MIR) profiles of D2O infinitely dilute in supercritical CO2 have been studied using molecular-dynamics simulations. For this purpose, we have proposed an intermolecular potential model taking implicitly into account electron donor-acceptor (EDA) interactions between water and CO2 evaluated from ab initio calculations of the intermolecular potential-energy surface (IPS). Interaction-induced dipole mechanisms have been also taken into account in addition to the water permanent dipole to evaluate the simulated FIR profiles of water and CO2 polarizable molecules. They were found to play a minor role in the genesis of the FIR profiles of water/CO2 under supercritical conditions. The analysis of the reorientational dynamics of D2O shows that the rotational dynamics of water is weakly anisotropic due to the EDA interactions which affect more specifically the reorientational motions of the C2 symmetry axis of solute. These results have been used to assess the contribution of the vibrational relaxation in the experimental mid-infrared profiles associated with the nu1 symmetric and nu3 antisymmetric stretching and nu2 bending modes of D2O. It was found that the rotational dynamics mainly contribute to the broadening of the infrared (IR) profiles. Nevertheless, the vibrational processes play a role in the frequency shifts of the band centers and the relative intensity enhancements of the nu1 and nu3 modes of D2O. In particular, the EDA interactions between water and CO2 lead to the appearance of a well-defined IR band of the nu1 mode of D2O. Finally, a comparison with another model taking only into account dipole-quadrupole electrostatic interactions between water and CO2 molecules clearly reveals that EDA interactions have to be considered to reproduce both MIR and FIR measurements. From this point of view CO2 can be classified on a hydrophilic solvent scale based upon the solubility criterion as an intermediate solvent between "inert" xenon and carbon tetrachloride.

Journal Article↗
PubMed2005

Quantum dynamics driven by continuous laser fields under measurements: towards measurement-assisted quantum dynamics control.

We study quantum system dynamics driven by continuous laser fields under the measurement process. In order to take into account the system transition due to the measurement, we define the superoperator which eliminates the coherence relevant to the measured quantum states. We clarify that the dynamics of the measured states is frozen in the frequent measurement limit, while the space spanned by unmeasured states is isolated from the original system. We also derive the effective Liouvillian which governs incoherent population dynamics under the condition, in which measurements are frequently applied. We apply the formulation to two-level and Lambda-type three-level systems and clarify how the quantum measurements hinder the coherent population dynamics driven by the continuous laser fields in practical examples. Analysis on the laser field amplitude dependency of the final distribution in the t-->infinity limit suggests the possibility of the measurement-assisted quantum control.

Journal Article↗
PubMed2006

Dynamical properties of the soft sticky dipole-quadrupole-octupole water model: a molecular dynamics study.

The dynamical properties of the soft sticky dipole-quadrupole-octupole (SSDQO) water model using SPC/E moments are calculated utilizing molecular dynamics simulations. This new potential for liquid water describes the water-water interactions by a Lennard-Jones term and a sticky potential, which is an approximate moment expansion with point dipole, quadrupole, and octupole moments, and reproduces radial distribution functions of pure liquid water using the moments of SPC/E [Ichiye and Tan, J. Chem. Phys. 124, 134504 (2006)]. The forces and torques of SSDQO water for the dipole-quadrupole, quadrupole-quadrupole, and dipole-octupole interactions are derived here. The simulations are carried out at 298 K in the microcanonical ensemble employing the Ewald method for the long-range dipole-dipole interactions. Here, various dynamical properties associated with translational and rotational motions of SSDQO water using the moments of SPC/E (SSDQO:SPC/E) water are compared with the results from SPC/E and also experiment. The self-diffusion coefficient of SSDQO:SPC/E water is found to be in excellent agreement with both SPC/E and experiment whereas the single particle orientational relaxation time for dipole vector is better than SPC/E water but it is somewhat smaller than experiment. The dielectric constant of SSDQO:SPC/E is essentially identical to SPC/E, and both are slightly lower than experiment. Also, molecular dynamics simulations of the SSDQO water model are found to be about twice as fast as three-site models such as SPC/E.

Computer Simulation↗
PubMed1993

How the transition frequencies of microtubule dynamic instability (nucleation, catastrophe, and rescue) regulate microtubule dynamics in interphase and mitosis: analysis using a Monte Carlo computer simulation.

Microtubules (MTs) in newt mitotic spindles grow faster than MTs in the interphase cytoplasmic microtubule complex (CMTC), yet spindle MTs do not have the long lengths or lifetimes of the CMTC microtubules. Because MTs undergo dynamic instability, it is likely that changes in the durations of growth or shortening are responsible for this anomaly. We have used a Monte Carlo computer simulation to examine how changes in the number of MTs and changes in the catastrophe and rescue frequencies of dynamic instability may be responsible for the cell cycle dependent changes in MT characteristics. We used the computer simulations to model interphase-like or mitotic-like MT populations on the basis of the dynamic instability parameters available from newt lung epithelial cells in vivo. We started with parameters that produced MT populations similar to the interphase newt lung cell CMTC. In the simulation, increasing the number of MTs and either increasing the frequency of catastrophe or decreasing the frequency of rescue reproduced the changes in MT dynamics measured in vivo between interphase and mitosis.

Animals↗
PubMed2002

Confirmation of anomalous dynamical arrest in attractive colloids: a molecular dynamics study.

Previous theoretical simulation and experimental studies have indicated that particles with a short-ranged attraction exhibit a range of dynamical arrest phenomena. These include very pronounced reentrance in the dynamical arrest curve, a logarithmic singularity in the density correlation functions, and the existence of "attractive" and "repulsive" glasses. Here we carry out extensive molecular dynamics calculations on dense systems interacting via a square-well potential. This is one of the simplest systems with the required properties, and may be regarded as canonical for interpreting the phase diagram, and now also the dynamical arrest. We confirm the theoretical predictions for reentrance, logarithmic singularity, and give a direct evidence of the existence, independent of theory, of two distinct glasses. We now regard the previous predictions of these phenomena as having been established.

Journal Article↗
PubMed2003

Dynamics of supercooled liquids confined to the pores of sol-gel glass: a dynamic light scattering study.

Dynamics of low molecular weight and polymeric glass forming liquids in confined geometries has been studied by means of depolarized dynamic light scattering: photon correlation spectroscopy and Fabry-Perot interferometry. The pore size of the glassy matrix amounted to 2.5, 5.0, and 7.5 nm. The glass transition temperature T(g) of these liquids in confined geometries has been measured using differential scanning calorimetry. A systematic decrease of T(g) (up to 25 K) with decreasing pore size has been observed. The relaxation times of the alpha process at constant temperature were decreasing with decreasing pore size (up to 6 orders of magnitude at T(g)), while the width of their distribution was increasing. The change of the relaxation times can be assigned to the change of T(g) in confined geometries. After correcting the activation plots for the shift of T(g) a master curve was obtained for all pore sizes and the bulk material. The effect of chemical modification of the surface of the porous matrix on the dynamics of ortho-terphenyl has also been studied. These dramatic changes of the T(g) and the relaxation time of confined liquids can be explained by simple thermodynamic arguments. There is no indication that they are related to the change of the correlation length of cooperative dynamics.

Journal Article↗
PubMed2002

Role of protein-water hydrogen bond dynamics in the protein dynamical transition.

The role of water in protein dynamics has been investigated using molecular dynamics simulations of crystals and a dehydrated powder. On the 100 ps time scale, the anharmonic and diffusive motions involved in the protein structural relaxation are correlated with the protein-water hydrogen bond dynamics. The complete structural relaxation of the protein requires relaxation of the hydrogen bond network via solvent translational displacement. Inhibiting the solvent translational mobility, and therefore the protein-water hydrogen bond dynamics, has an effect on the protein relaxation similar to dehydration.

Cold Temperature↗
PubMed2004

Spatially heterogeneous dynamics and dynamic facilitation in a model of viscous silica.

We perform molecular dynamics simulations to study the structural relaxation dynamics of a model of viscous silica, the prototype of a strong glass former. We find that the melt dynamics are spatially heterogeneous regardless of whether the bulk relaxation is non-Arrhenius or Arrhenius, and cannot be understood as a statistical bondbreaking process. Further, we show that stringlike motion is suppressed by the covalent bondings, yet high particle mobility propagates continuously, supporting the concept of dynamic facilitation emphasized in recent theoretical work.

Journal Article↗
PubMed2005

A statistical approach to the interpretation of molecular dynamics simulations of calmodulin equilibrium dynamics.

A sample of 35 independent molecular dynamics (MD) simulations of calmodulin (CaM) equilibrium dynamics was prepared from different but equally plausible initial conditions (20 simulations of the wild-type protein and 15 simulations of the D129N mutant). CaM's radius of gyration and backbone mean-square fluctuations were analyzed for the effect of the D129N mutation, and simulations were compared with experiments. Statistical tests were employed for quantitative comparisons at the desired error level. The computational model predicted statistically significant compaction of CaM relative to the crystal structure, consistent with the results of small-angle X-ray scattering (SAXS) experiments. This effect was not observed in several previously reported studies of (Ca2+)(4)-CaM, which relied on a single MD run. In contrast to radius of gyration, backbone mean-square fluctuations showed a distinctly non-normal and positively skewed distribution for nearly all residues. Furthermore, the D129N mutation affected the backbone dynamics in a complex manner and reduced the mobility of Glu123, Met124, Ile125, Arg126, and Glu127 located in the adjacent alpha-helix G. The implications of these observations for the comparisons of MD simulations with experiments are discussed. The proposed approach may be useful in studies of protein equilibrium dynamics where MD simulations fall short of properly sampling the conformational space, and when the comparison with experiments is affected by the reproducibility of the computational model.

Calmodulin↗
PubMed1997

A molecular dynamics study in explicit water of the reduced and oxidized forms of yeast iso-1-cytochrome c--solvation and dynamic properties of the two oxidation states.

Molecular dynamics calculations have been performed over long trajectories with the inclusion of explicit solvent molecules on the reduced and the oxidized states of yeast iso-1-cytochrome c. The resulting structures have been analyzed and compared both in terms of structural properties and dynamical behavior. The structure of the buried water molecules around the heme has been also analyzed for the two oxidation states and compared with the experimental observations on the X-ray and the solution NMR structures. From the overall analysis we learn that, as also observed experimentally through NMR, no significant differences are present between the structures of the two oxidation states beside the arrangement of a few side chains. Also the internal mobility is similar for the two oxidation states, even if interesting differences are observed for some residues, as for Tyr67, a residue present at the heme site. The location and the mobility of the ordered water molecules, observed in solution by NMR, are completely reproduced in the molecular dynamics simulations, which have been able to predict the different displacements of the catalytically relevant water molecule WAT166, similar to those observed in solution for the two oxidation states, at variance with that observed in the starting crystallographic structures. The relevance of these findings with respect to the prediction of structural and dynamical properties is discussed.

Computer Simulation↗
PubMed1993

Islet cell tumors: comparison of dynamic contrast-enhanced CT and MR imaging with dynamic gadolinium enhancement and fat suppression.

Ten patients with 11 islet cell tumors underwent dynamic contrast material-enhanced computed tomography (CT) and magnetic resonance (MR) imaging within a 1-month period. MR imaging depicted all 11 tumors, and CT depicted seven of the 11 tumors. CT did not depict four of seven tumors that measured 2.5 cm in diameter or less. Islet cell tumors had low signal intensity on T1-weighted fat-suppressed MR images, and gastrinomas were best shown with this technique. Two of three insulinomas less than 1.5 cm in diameter were best shown on dynamic contrast-enhanced fast low-angle shot (FLASH) images as uniform areas of high signal intensity. Hepatic metastases were seen in five patients and showed peripheral ringlike enhancement best demonstrated on dynamic gadolinium-enhanced FLASH images. Hepatic lesions were most conspicuous on T2-weighted fat-suppressed spin-echo images. MR imaging with dynamic gadolinium enhancement and fat suppression is a promising tool in the investigation of islet cell tumors.

Adenoma, Islet Cell↗
PubMed2006

Dynamic phenotypes: time series analysis techniques for characterizing neuronal and behavioral dynamics.

We consider quantitative measures of behavioral and neuronal dynamics as a means of characterizing phenotypes. Such measures are important from a scientific perspective; because understanding brain function is contingent on understanding the link between the dynamics of the nervous system and behavioral dynamics. They are also important from a biomedical perspective because they provide a contrast to purely psychological characterizations of phenotype or characterizations via static brain images or maps, and are a potential means for differential diagnoses of neuropsychiatric illnesses. After a brief presentation of background work and some current advances, we suggest that more attention needs to be paid to dynamic characterizations of phenotypes. We will discuss some of the relevant time series analysis tools.

Action Potentials↗
PubMed2005

Conformational dynamics of the ligand-binding domain of inward rectifier K channels as revealed by molecular dynamics simulations: toward an understanding of Kir channel gating.

Inward rectifier (Kir) potassium channels are characterized by two transmembrane helices per subunit, plus an intracellular C-terminal domain that controls channel gating in response to changes in concentration of various ligands. Based on the crystal structure of the tetrameric C-terminal domain of Kir3.1, it is possible to build a homology model of the ATP-binding C-terminal domain of Kir6.2. Molecular dynamics simulations have been used to probe the dynamics of Kir C-terminal domains and to explore the relationship between their dynamics and possible mechanisms of channel gating. Multiple simulations, each of 10 ns duration, have been performed for Kir3.1 (crystal structure) and Kir6.2 (homology model), in both their monomeric and tetrameric forms. The Kir6.2 simulations were performed with and without bound ATP. The results of the simulations reveal comparable conformational stability for the crystal structure and the homology model. There is some decrease in conformational flexibility when comparing the monomers with the tetramers, corresponding mainly to the subunit interfaces in the tetramer. The beta-phosphate of ATP interacts with the side chain of K185 in the Kir6.2 model and simulations. The flexibility of the Kir6.2 tetramer is not changed greatly by the presence of bound ATP, other than in two loop regions. Principal components analysis of the simulated dynamics suggests loss of symmetry in both the Kir3.1 and Kir6.2 tetramers, consistent with "dimer-of-dimers" motion of subunits in C-terminal domains of the corresponding Kir channels. This is suggestive of a gating model in which a transition between exact tetrameric symmetry and dimer-of-dimers symmetry is associated with a change in transmembrane helix packing coupled to gating of the channel. Dimer-of-dimers motion of the C-terminal domain tetramer is also supported by coarse-grained (anisotropic network model) calculations. It is of interest that loss of exact rotational symmetry has also been suggested to play a role in gating in the bacterial Kir homolog, KirBac1.1, and in the nicotinic acetylcholine receptor channel.

Adenosine Triphosphate↗
PubMed2005

Determination of the orientation and dynamics of ergosterol in model membranes using uniform 13C labeling and dynamically averaged 13C chemical shift anisotropies as experimental restraints.

A new strategy was established to determine the average orientation and dynamics of ergosterol in dimyristoylphosphatidylcholine model membranes. It is based on the analysis of chemical shift anisotropies (CSAs) averaged by the molecular dynamics. Static (13)C CSA tensors were computed by quantum chemistry, using the gauge-including atomic-orbital approach within Hartree-Fock theory. Uniformly (13)C-labeled ergosterol was purified from Pichia pastoris cells grown on labeled methanol. After reconstitution into dimyristoylphosphatidylcholine lipids, the complete (1)H and (13)C assignment of ergosterol's resonances was performed using a combination of magic-angle spinning two-dimensional experiments. Dynamically averaged CSAs were determined by standard side-band intensity analysis for isolated (13)C resonances (C(3) and ethylenic carbons) and by off-magic-angle spinning experiments for other carbons. A set of 18 constraints was thus obtained, from which the sterol's molecular order parameter and average orientation could be precisely defined. The validity of using computed CSAs in this strategy was verified on cholesterol model systems. This new method allowed us to quantify ergosterol's dynamics at three molar ratios: 16 mol % (Ld phase), 30 mol % (Lo phase), and 23 mol % (mixed phases). Contrary to cholesterol, ergosterol's molecular diffusion axis makes an important angle (14 degrees) with the inertial axis of the rigid four-ring system.

Anisotropy↗
PubMed2005

Probing the local dynamics of nucleotide-binding pocket coupled to the global dynamics: myosin versus kinesin.

Based on the elastic network model, we develop a new analysis for protein complexes, which probes the local dynamics of a subsystem that is elastically coupled to a fluctuating environment. This method is applied to a comparative dynamical analysis of the nucleotide-binding pocket of two motor proteins-myosins and kinesins. In myosins, the observed structural changes in the nucleotide-pocket from the transition state to the rigorlike state are dominated by the lowest normal mode that involves significant movements in both switch I and switch II; in kinesins, the measured conformational changes in the nucleotide-pocket are also dominated by the lowest mode, which, however, only involves large movement in switch I. We then compute the global structural changes induced by the nucleotide-pocket deformations as described by the dominant pocket-mode, which yield encouraging results: in myosins, multiple hinge motions involving the opening/closing of the cleft between the upper and lower 50 -kDa subdomains and the swinging movement of the converter are induced, which are dominated by precisely the same global mode that has been recently identified by us as important to the dynamical correlations among the nucleotide-pocket, the actin-binding site, and the converter; in kinesins, the induced global conformational changes are well described by a highly collective global mode which hints for a dynamical pathway spanning from the nucleotide-pocket to the neck-linker via the H6 helix.

Actins↗
PubMed1989

[Analysis of the denture dynamics in R.P.D.'s. 1. Methods for analyzing the denture dynamics of free-end-saddle].

Excess denture movement during function may cause to jeopardize the resorption of the residual ridges and the mechanical trauma on the abutments in the partially dentate mouth. A removable partial denture (R.P.D.'s) should be so constructed that the artificial teeth on the denture base will be stabilized in their spatial position by way of the compensatory support due to the remaining abutments and the residual ridges. In this pilot study, the ordinary denture movement, that is the denture dynamics in function of the free end saddle R.P.D.'s was measured in the test denture assembly. The denture dynamics was assessed in two ways: The displacement sensors revealed the vertical and the horizontal movement of the denture base during function. They were based on the field magnetic effect and with good lineality. Tiny accerelometer was attached to the denture base to detect the accerelation during function. Ordinary mastication was not interefered by both methods. The Author has already reported the palpation test for diagnosing the denture dynamics of the free end saddles in clinics. This method was discussed objectively against the accerelometry on fifty patients. Two methods have revealed the good coincidence with each other to detect the dynamics of the free end saddles.

Alveolar Bone Loss↗
PubMed2003

Coordination dynamics in Parkinson's disease patients and healthy subjects quantified by the coordination dynamics recording method and sEMG.

Coordination dynamics were measured in Parkinson's disease patients to quantify central nervous system (CNS) dysfunction. The low-load coordination dynamics in the patients were impaired by 56% for forward and 44% for backward moving in comparison to a control group of similar age. Exercising at higher load was only partly possible. When the disease preferentially affected one side of the body, the coordination dynamics were worse for the affected side. A dexterity test showed that coordination of hand and arm movements could be improved in the short-term memory when exercising on the special coordination dynamics recording and therapy device. Simultaneously taken surface EMG (sEMG) showed that the motor pattern was impaired in the Parkinson's disease patients. sEMG recordings showed further that the fast fatigable muscle fibre activation was impaired. FF-type muscle fibres were already activated for low load in one and not at all in another muscle. In conclusion, coordination between motoneuron firings and between arm and leg movements were found to be impaired in Parkinson's disease patients.

Aged↗