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PubMed2003

Common dynamic properties of biosignals during cognition: self-similarity and chaotic dynamics of both response times and EEG during movement imagery.

This study was undertaken to verify whether different output variables or biosignals, measured during performance of a cognitive task, manifest common dynamical properties. Nonlinear properties of both response times (RTs) and electroercephalograms (EEG) were tested. We asked subjects to generate mental images of actions following of auditorily presentation simple phrases suggesting the action. Analysis of RT series combined from many subjects and of EEG records from single subjects clearly manifested self-similarity and chaotic dynamics that provide insights into the self-organization of the brain/behavioral system.

Adult↗
PubMed2004

Model-free analysis of protein dynamics: assessment of accuracy and model selection protocols based on molecular dynamics simulation.

The popular model-free approach to analyze NMR relaxation measurements has been examined using artificial amide (15)N relaxation data sets generated from a 10 nanosecond molecular dynamics trajectory of a dihydrofolate reductase ternary complex in explicit water. With access to a detailed picture of the underlying internal motions, the efficacy of model-free analysis and impact of model selection protocols on the interpretation of NMR data can be studied. In the limit of uncorrelated global tumbling and internal motions, fitting the relaxation data to the model-free models can recover a significant amount of quantitative information on the internal dynamics. Despite a slight overestimation, the generalized order parameter is quite accurately determined. However, the model-free analysis appears to be insensitive to the presence of nanosecond time scale motions with relatively small magnitude. For such cases, the effective correlation time can be significantly underestimated. As a result, proteins appear to be more rigid than they really are. The model selection protocols have a major impact on the information one can reliably obtain. The commonly employed protocol based on step-up hypothesis testing has severe drawbacks of oversimplification and underfitting. The consequences are that the order parameter is more severely overestimated and the correlation time more severely underestimated. Instead, model selection based on Bayesian Information Criteria (BIC), recently introduced to the model-free analysis by d'Auvergne and Gooley (2003), provides a better balance between bias and variance. More appropriate models can be selected, leading to improved estimate of both the order parameter and correlation time. In addition, the computational cost is significantly reduced and subjective parameters such as the significance level are unnecessary.

Anisotropy↗
PubMed1991

Task dynamics and resource dynamics in the assembly of a coordinated rhythmic activity.

Task dynamics corresponding to rhythmic movements emerge from interactions among dynamical resources composed of the musculature, the link segments, and the nervous and circulatory systems. This article investigated whether perturbations of interlimb coordination might be effect over circulatory and nervous elements. Stiffness of wrist-pendulums oscillated at a common tempo and at 180 degrees relative phase was perturbed through the use of tonic activity about an ankle. Left and right stiffnesses, the common period, and the phase relation all changed. Stiffnesses increased with ankle torque in proportion to the wrist's inertial load. Despite different changes in stiffness at the two wrists, isochrony was preserved. The stability was shown to be consistent with the proportionality of changes in stiffness to the inertial loads. The phase departed from antiphase in proportion to the asymmetry of inertial loads. The size of departures decreased with increasing ankle torque. An account was developed in terms of muscular, circulatory, and nervous functions.

Adult↗
PubMed1982

Dynamic and biochemical responses to single and repeated doses of clonidine during dynamic physical activity.

Beta-adrenoceptor blockade increases serum K, which may be related to renin inhibition, hypoaldosteronism, and exercise-induced skeletal muscle release of serum K. We report on the dynamic and biochemical response to clonidine (C) after single (S) 0.2-mg and repeated (R) 0.1-mg bid doses of C to six normal subjects at rest, 2 hr after dosing and immediately before dynamic physical activity (DPA) on a treadmill, and at peak activity and 2 hr after DPA. Blood pressure (BP), heart rate (HR), plasma renin concentration (PRC), aldosterone (ALD), serum K, epinephrine (E), and norepinephrine (NE) were measured in standing subjects before and 2 hr after placebo or C (S or R), at peak DPA, and 2 hr after exercise. K, BP, and HR were also determined during all stages of DPA. Results show a parallel rise in K at peak over rest after C (S or R) and after placebo. NE, E, and PRC decreased after 1 wk of C (P less than 0.01), but the fall of ALD was only slight. The fall in NE at rest suggested a relationship to the decrease in systolic BP and rate pressure product after 1 wk on C. With DPA there is a normal yet smaller increase in systolic BP and also a smaller rise in HR with S- and R-dose C. There is no adverse rise in K in C-treated subjects during DPA.

Aldosterone↗
PubMed2006

Structure and dynamics of the [Zn(NH3)(H2O)5]2+ complex in aqueous solution obtained by an ab initio QM/MM molecular dynamics study.

A model complex of the hexahydrated zinc(ii) cation with one water substituted by ammonia in aqueous solution has been studied by hybrid ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) at the double-zeta Hartree-Fock (HF) quantum mechanical level. The first solvation shell, consisting of 5 + 1 ligand(s) at mean distances of 2.2 and 2.1 A, respectively, from the Zn(ii) ion, was found to remain stable with respect to exchange processes within the simulation time. The labile second shell consists on average of approximately 19 water molecules. For structural elucidation of the pentaaquozinc(ii) amine complex in aqueous solution several data sets such as radial distribution functions (RDF), coordination number distributions (CND) and different angular distributions (ADF, tilt and theta angle) were employed. Dynamics were characterised by the ligands' mean residence time (MRT), ion-ligand stretching frequencies and the vibrational and librational motions of water ligands. The labile second shell's MRT value decreases upon introduction of one NH(3) ligand to 7.2 ps from the 10.5 ps observed for the hexaaquozinc(ii) complex.

Journal Article↗
PubMed2001

Effectiveness of a new perforated 0.15 mm poly-p-dioxanon-foil versus titanium-dynamic mesh in reconstruction of the orbital floor.

Introduction: In recent years a new perforated PDS (poly-p-dioxanon) foil (0.15 mm) has become available and has not yet been proven to be successful in reconstruction of the orbital floor after blow-out-fractures in randomized studies. The main aim of this clinical trial is to compare this new PDS foil with titanium dynamic mesh (0.3 mm) (TD), which is well established in reconstruction of the orbital floor. Patients and Methods: In a prospective multicentre randomized trial, conducted between 1997 and 1998, out of 42 patients with fractures of the orbital floor, 28 patients needing material for reconstruction were randomized to receive either PDS foil or TD. In a comprehensive preoperative and postoperative protocol patients were monitored by the surgeon, radiologist and ophthalmologist with a postoperative follow-up of least 6 months. Results: Maximum defects of the orbital floor were comparable in both groups (PDS group: 13.3 mm, TD group: 13.9 mm). In both groups the surgical procedure was well tolerated, and functional and cosmetic results were evaluated as satisfactory by all patients. Ophthalmological evaluation, performed up to 6 months postoperatively, revealed double vision or vertical strabismus in nine patients (five PDS group, four titanium group). This was not confirmed subjectively in each single patient. Also ex- or enophthalmos, registered in seven patients of the PDS and four of the TD group (mainly +/-1 mm) were not considered as relevant by the patients. Conclusion: The new 0.15 mm perforated PDS foil was comparable to 0.3 mm titanium mesh concerning functional and cosmetic outcome. Obviously, persisting ophthalmometric disorders were compensated very well in both groups. PDS foil is felt to be the preferred material since it is bioresorbable and more convenient to handle. Copyright 2001 European Association for Cranio-Maxillofacial Surgery.

Journal Article↗
PubMed2001

[The dynamic treatment of intraarticular fractures of the base of the middle phalanx with the Suzuki dynamic fixator].

Between 1994 and 1998, we have treated eleven patients with intraarticular fractures of the base of the middle phalanx including impaction, dislocation, and pilon types of injuries. All patients were evaluated after a median follow-up period of 25.8 (8 to 57) months. Treatment was carried out according to Suzuki's technique with a dynamic PIP-joint distraction fixator consisting of Kirschner wires and rubber bands. In five cases, there was additional osteosynthesis (Kirschner wires, resorbable hemicerclage) or cancellous bone-grafting for reconstruction of the joint surface. Early mobilisation commenced with active exercises for the PIP joint on the day of surgery. The dynamic extension fixator was applied for an average duration of 28 (15 to 42) days. By the time of follow-up examinations, we found a range of motion on an average of 64 (0 to 105) degrees including a lack of extension of 11 (0 to 60) degrees and a median flexion capacity of 75 (30 to105) degrees. All fractures healed uneventfully with restored joint stability. Eight patients were completely painfree, three complained of mild occupational pain.

Adult↗
PubMed2004

A combined molecular dynamics+quantum mechanics method for investigation of dynamic effects on local surface structures.

A combined molecular dynamics (MD)+quantum mechanics (QM) method for studying processes on ionic surfaces is presented. Through the combination of classical MD and ab initio embedded-cluster calculations, this method allows the modeling of surface processes involving both the structural and dynamic features of the substrate, even for large-scale systems. The embedding approach used to link the information from the MD simulation to the cluster calculation is presented, and rigorous tests have been carried out to ensure the feasibility of the method. The electrostatic potential and electron density resulting from our embedded-cluster model have been compared with periodic slab results, and confirm the satisfying quality of our embedding scheme as well as the importance of applying embedding in our combined MD+QM approach. We show that a highly accurate representation of the Madelung potential becomes a prerequisite when the embedded-cluster approach is applied to temperature-distorted surface snapshots from the MD simulation.

Journal Article↗
PubMed2004

Molecular orientation via a dynamically induced pulse-train: wave packet dynamics of NaI in a static electric field.

We regard the rovibrational wave packet dynamics of NaI in a static electric field after femtosecond excitation to its first electronically excited state. The following quasibound nuclear wave packet motion is accompanied by a bonding situation changing from covalent to ionic. At times when the charge separation is present, i.e., when the bond-length is large, a strong dipole moment exists and rotational excitation takes place. Upon bond contraction, the then covalently bound molecule does not experience the external field. This scenario repeats itself periodically. Thus, the vibrational dynamics causes a situation which is comparable to the interaction of the molecule with a train of pulses where the pulse separation is determined by the vibrational period.

Journal Article↗
PubMed2004

Photoinduced dynamics of ethene in the N, V, and Z valence states: a six-dimensional nonadiabatic quantum dynamics investigation.

The photoinduced dynamics of ethene following pi-->pi(*) excitation is investigated by quantum wave-packet dynamics on three coupled six-dimensional diabatic potential-energy surfaces representing the N, V, and Z valence states, which have been developed previously. The C-C stretching and torsion, as well as the pyramidalization and scissoring of both CH(2) groups are included in this description. The wave-packet calculations have been performed using the multiconfigurational time-dependent Hartree method for a time period up to 100 fs. While a small amount of population transfer to the electronic ground state is found within this period, the overall population decay time of the V state is found to exceed the 100 fs range significantly. The autocorrelation function of the wave packet and the stationary absorption spectrum of the V state also have been calculated. It is found that both the torsional mode as well as the C-C stretching mode contribute to the very extended vibrational structure of the absorption spectrum, and that both modes are strongly coupled. At least on the present ab initio surface of limited dimensionality, the speed of pyramidalization of 90 degrees twisted ethene appears as the bottleneck for the ultrafast radiationless decay of the V state.

Journal Article↗
PubMed2005

Dynamics of coupled Bohmian and phase-space variables: a moment approach to mixed quantum-classical dynamics.

The theoretical framework of the mixed quantum-classical description given by Burghardt and Parlant [J. Chem. Phys. 120, 3055 (2004)] is detailed. A representation in terms of partial hydrodynamic moments is developed, the dynamics of which is determined by a hierarchy of equations derived from the quantum Liouville equation. Exact equations of motion are obtained, whose quantum-classical approximants are associated with a fluid-dynamical trajectory representation which couples classical variables to quantum hydrodynamic variables. The latter evolve under a generalized hydrodynamic force which also depends upon the classical phase-space variables. The hydrodynamic moment description is shown to be closely connected to mixed quantum-classical phase-space methods.

Journal Article↗
PubMed2005

Dynamics of fluids near the consolute critical point: a molecular-dynamics study of the Widom-Rowlinson mixture.

Molecular-dynamics simulations are presented for the dynamic behavior of the Widom-Rowlinson mixture [B. Widom, and J. S. Rowlinson, J. Chem. Phys. 52, 1670 (1970)] at its critical point. This model consists of two components where like species do not interact and unlike species interact via a hard-core potential. Critical exponents are obtained from a finite-size scaling analysis. The self-diffusion coefficient shows no anomalous behavior near the critical point. The shear viscosity and thermal conductivity show no divergent behavior for the system sizes considered, although there is a significant critical enhancement. The mutual diffusion coefficient, D(AB), vanishes as D(AB) approximately xi(-1.26 +/- 0.08), where xi is the correlation length. This is different from the renormalization-group (D(AB) approximately xi(-1.065)) mode coupling theory (D(AB) approximately xi(-1)) predictions. The theories and simulations can be reconciled if we assume that logarithmic corrections to scaling are important.

Journal Article↗
PubMed2005

Foldamer dynamics expressed via Markov state models. I. Explicit solvent molecular-dynamics simulations in acetonitrile, chloroform, methanol, and water.

In this article, we analyze the folding dynamics of an all-atom model of a polyphenylacetylene (pPA) 12-mer in explicit solvent for four common organic and aqueous solvents: acetonitrile, chloroform, methanol, and water. The solvent quality has a dramatic effect on the time scales in which pPA 12-mers fold. Acetonitrile was found to manifest ideal folding conditions as suggested by optimal folding times on the order of approximately 100-200 ns, depending on temperature. In contrast, chloroform and water were observed to hinder the folding of the pPA 12-mer due to extreme solvation conditions relative to acetonitrile; chloroform denatures the oligomer, whereas water promotes aggregation and traps. The pPA 12-mer in a pure methanol solution folded in approximately 400 ns at 300 K, compared relative to the experimental 12-mer folding time of approximately 160 ns measured in a 1:1 v/v THF/methanol solution. Requisite in drawing the aforementioned conclusions, analysis techniques based on Markov state models are applied to multiple short independent trajectories to extrapolate the long-time scale dynamics of the 12-mer in each respective solvent. We review the theory of Markov chains and derive a method to impose detailed balance on a transition-probability matrix computed from simulation data.

Acetonitriles↗
PubMed2005

A comparative study between dissipative particle dynamics and molecular dynamics for simple- and complex-geometry flows.

The purpose of this study is to compare the results from molecular-dynamics and dissipative particle dynamics (DPD) simulations of Lennard-Jones (LJ) fluid and determine the quantitative effects of DPD coarse graining on flow parameters. We illustrate how to select the conservative force coefficient, the cut-off radius, and the DPD time scale in order to simulate a LJ fluid. To show the effects of coarse graining and establish accuracy in the DPD simulations, we conduct equilibrium simulations, Couette flow simulations, Poiseuille flow simulations, and simulations of flow around a periodic array of square cylinders. For the last flow problem, additional comparisons are performed against continuum simulations based on the spectral/hp element method.

Journal Article↗
PubMed2006

Femtosecond study on the isomerization dynamics of NK88. I. Ground-state dynamics after photoexcitation.

Recently, optimal control of a photoisomerization reaction in the liquid phase was demonstrated for the first time on the system 3,3(')-diethyl-2,2(')-thiacyanine (NK88). Additionally, the class of cyanines to which the molecule NK88 belongs draws a lot of attention in different recent theoretical publications. Therefore, a better understanding of the molecular dynamics of this molecular system is of special interest. Experiments using the femtosecond pump-supercontinuum probe technique with an excitation wavelength of 400 nm and a spectral range from 370 to 620 nm for the probe beam have been performed. In order to analyze the dynamics properly the time window has been chosen to comprise the characteristic times of the contributing processes, additionally we have employed two solvents, methanol and ethylene glycol, and have conducted anisotropy measurements. The spectroscopic data have been assigned to different molecular states with the help of density functional theory and second-order Moller-Plesset perturbation theory calculations. The analysis of the data has revealed in the most likely model that three different isomers exist with different lifetimes. On the basis of experimental and theoretical data, a conclusive scheme of the isomerization reaction is presented.

Anisotropy↗
PubMed2006

Vibrational dynamics of DNA. III. Molecular dynamics simulations of DNA in water and theoretical calculations of the two-dimensional vibrational spectra.

A theoretical description of the vibrational excitons in DNA is presented by using the vibrational basis mode theory developed in Papers I and II. The parameters obtained from the density functional theory calculations, such as vibrational coupling constants and basis mode frequencies, are used to numerically simulate two-dimensional (2D) IR spectra of dG(n):dC(n) and dA(n):dT(n) double helices with n varying from 1 to 10. From the molecular dynamics simulations of dG(5)C(5) and dA(5)T(5) double helices in D(2)O solution, it is found that the thermally driven internal motions of these systems in an aqueous solution do not induce strong fluctuations of basis mode frequencies nor vibrational couplings. In order to construct the two-exciton Hamiltonian, the vibrational anharmonicities of eight basis modes are obtained by carrying out B3LYP6-31G(*) calculations for the nine basis modes. The simulated 2D IR spectra of dG(n):dC(n) double helix in D(2)O solution are directly compared with closely related experimental results. The 2D IR spectra of dG(n):dC(n) and dA(n):dT(n) are found to be weakly dependent on the number of base pairs. The present work demonstrates that the computational procedure combining quantum chemistry calculation and molecular dynamics simulation methods can be of use to predict 2D IR spectra of nucleic acids in solutions.

Base Pairing↗
PubMed2006

Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

Benzene↗