Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “dynamics”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 415 records · Page 23Linked to original sources
PubMed1993

Isomerization reaction dynamics and equilibrium at the liquid-vapor interface of water. A molecular-dynamics study.

The gauche-trans isomerization reaction of 1,2-dichloroethane at the liquid-vapor interface of water is studied using molecular-dynamics computer simulations. The solvent bulk and surface effects on the torsional potential of mean force and on barrier recrossing dynamics are computed. The isomerization reaction involves a large change in the electric dipole moment, and as a result the trans/gauche ratio is considerably affected by the transition from the bulk solvent to the surface. Reactive flux correlation function calculations of the reaction rate reveal that deviation from the transition-state theory due to barrier recrossing is greater at the surface than in the bulk water. This suggests that the system exhibits non-Rice-Ramsperger-Kassel-Marcus behavior due to the weak solvent-solute coupling at the water liquid-vapor interface.

Carbon↗
PubMed2002

Molecular dynamic study of orotidine-5'-monophosphate decarboxylase in ground state and in intermediate state: a role of the 203-218 loop dynamics.

Molecular dynamics simulations have been used to derive the structures of ground (orotidine-5'-monophosphate decarboxylase x orotidine 5'-monophosphate; ODC x OMP) and intermediate (ODC x intermediate; ODC x I(-)) states in the ODC-catalyzed decarboxylation of OMP. For comparison, a molecular dynamics simulation of the conformers of OMP dissolved in water was also studied. This structural information is unavailable from present crystal structures. The electrostatic network in the active site around the carboxylate moiety of OMP exhibits remarkable stability. The conformation of enzyme-bound OMP is very similar to the conformation of OMP in water. Thus, the proposed Circe effect mechanism for ODC catalysis is unlikely. Comparison of ground state and intermediate state structures shows that on decarboxylation C6 takes the position of the carboxylate O8. This significant movement of the ligand is accompanied by a placement of the C6 carbanion in the vicinity of the protonated Lys-93 and is enforced by a change of the 203-218 loop from an unstructured form to an ordered beta-hairpin. Previously proposed mechanisms involving protonation at O2, O4, or C5 have in common internal stabilization of the anionic intermediate by conjugation with positive charge on the pyrimidine ring. These mechanisms are not supported because there are no proton sources near O2, O4, and C5. We propose that the stabilization of intermediate ODC x I(-) is achieved by movement of the carbanion toward the external cation Lys-93 on decarboxylation and organization of the 203-218 loop. Because the intermediate and transition state are energetically similar, stabilization of the former decreases the free energy content of the latter.

Binding Sites↗
PubMed2006

Structural and dynamical properties of a full-length HIV-1 integrase: molecular dynamics simulations.

The structural and dynamical properties of the complete full-length structure of HIV-1 integrase were investigated using Molecular Dynamics approach. Simulations were carried out for the three systems, core domain only (CORE), full-length structure without (FULL) and with a Mg2+ (FULL+ION) in its active site, aimed to investigate the difference in the molecular properties of the full-length models due to their different construction procedures as well as the effects of the two ends, C- and N-terminal, on those properties in the core domain. The full-length structure was prepared from the two experimental structures of two-domain fragment. The following properties were observed to differ significantly from the previous reports: (i) relative topology formed by an angle between the three domains; (ii) the cavity size defined by the catalytic triad, Asp64, Asp116, and Glu152; (iii) distances and solvation of the Mg2+; and (iv) conformation of the catalytic residues. In addition, the presence of the two terminal domains decreases the mobility of the central core domain significantly.

Binding Sites↗
PubMed2001

Structure and dynamics of adenosine loops in RNA bulge duplexes as revealed by linked application of thermodynamics, spectrofluorimetry and simulation of molecular dynamics.

Structure and dynamics of adenosine loops in RNA bulge duplexes was studied using time-resolved spectrofluorimetry and in aqua simulation of molecular dynamics. Thermodynamics revealed that 2-aminopurine riboside is an non-invasive fluorescent probe when built within the bulge region of chemically synthesized RNA duplexes.

2-Aminopurine↗
PubMed1996

A molecular dynamics study of the effect of carbon tetrachloride on enzyme structure and dynamics: subtilisin.

Developing enzymes that are functional in highly concentrated halocarbon solutions, such as carbon tetrachloride, may prove useful in the development of new strategies for environmental remediation and monitoring of pollutant plumes, as well as in developing 'green' processes. Doing so will require gaining an understanding of the underlying structural and dynamic effects on enzymes induced by such solvents. Herein we report a 714 ps molecular dynamics simulation of the enzyme subtilisin Carlsberg and its waters of crystallization in a periodic box of carbon tetrachloride. The crystal structure from aqueous solution was used as the starting structure for our simulation using the AMBER program and forcefield. The calculated time-averaged structure is similar to the aqueous X-ray structure except for significant differences in loop (or turn) regions, resulting in many extra intra-protein hydrogen bonding interactions. Since carbon tetrachloride is a non-polar solvent and cannot interact strongly with the protein and water molecules, the water molecules stay very close to the protein surface throughout the simulation. The mobility of most of the waters was therefore very low. A few water molecules underwent significant lateral motion during the simulation, but never wandered far from the protein surface. Waters were either hydrogen bonded to protein polar groups, other water and/or counterions. Some of the surface waters participated in the formation of water-mediated hydrogen bonding networks. The increase in total number of intra-protein hydrogen bonds and the formation of water-mediated hydrogen bonding networks in carbon tetrachloride is consistent with the generally observed increase in thermostability and reduced flexibility of proteins in non-aqueous solutions. Several possible carbon tetrachloride binding sites on the protein surface are predicted.

Binding Sites↗
PubMedDate not supplied

Intrahepatic peripheral cholangiocarcinoma: comparison of dynamic CT and dynamic MRI.

PURPOSE: The purpose of this work was to compare dynamic MRI (D-MRI) with dynamic CT (D-CT) for the diagnosis of peripheral cholangiocarcinoma (PCC) of the liver. METHOD: Twenty patients with PCC underwent both D-CT and D-MRI during the early, middle, and delayed phase after contrast medium administration. The findings from D-MRI were compared with those from D-CT. RESULTS: D-CT and D-MRI exhibited a similar tumoral enhancement pattern, and this enhancement was more conspicuous on D-MRI. A wedge-like enhancement area peripheral to the tumor was observed in 9 (45%) patients on D-CT and 11 (55%) patients on D-MRI. Ductal dilatation was found in 13 (65%) patients on both techniques. Vascular involvement and extrahepatic invasion were seen in nine (45%) and two (10%) patients, respectively. The relationship of the tumor to the vessels and surrounding organs was more easily evaluated on D-CT. CONCLUSION: Both D-CT and D-MRI can provide important information for the diagnosis of PCC. D-CT is better than D-MRI for demonstrating vascular involvement and extrahepatic invasion. D-MRI gives more conspicuous enhancement.

Aged↗
PubMed1995

A mechanical comparison of the dynamic compression plate, limited contact-dynamic compression plate, and point contact fixator.

Cortical bone porosis associated with the dynamic compression plate (DCP) prompted the development of the limited-contact dynamic compression plate (LC-DCP) and the point-contact fixator (PC-Fix) to increase bone vascularity. However, the comparative fixation characteristics of the three designs are unknown. Transverse fractures were physiologically created in paired cadaveric sheep tibiae, which were plated before torsion testing and four-point bending to failure. The tibiae were grouped randomly and compared as follows: DCP versus LC-DCP, DCP versus PC-Fix, and LC-DCP versus PC-Fix. Mean torque to failure demonstrated no significant difference between the three plates (p < 0.33). Mean bending stiffness, gap opening, and moment to failure also demonstrated no significant difference between the three designs with p < 0.29, < 0.13, and < 0.16, respectively. The LC-DCP and PC-Fix have torsion and bending properties comparable with the DCP in the fixation of simple transverse diaphyseal fractures.

Animals↗
PubMed1999

Dynamical regimes in the dissipative particle dynamics model.

We discuss theoretically the behavior of the velocity autocorrelation function in the dissipative particle dynamics (DPD) model. Two dynamical regimes are identified depending on the dimensionless model parameters. For low values of the dimensional friction, a mean field behavior is observed in which the kinetic theory for the DPD model provides good predictions. For high values of the friction, collective hydrodynamic effects are dominant. We have performed numerical simulations that validate the theory presented.

Journal Article↗
PubMed2001

Conformational dynamics of an alanine dipeptide analog: an ab initio molecular dynamics study.

An ab initio molecular dynamics (MD) simulation technique employing the Born-Oppenheimer approach in the framework of a Gaussian implementation of Kohn-Sham density functional theory is used to study the gas-phase conformational dynamics of an alanine dipeptide analog. It is found that conformational transformation between C5 and C7(eq) occurs on the picosecond time scale. Classical MD simulations using most of the popular force fields do not yield a transition even after nanoseconds. An analysis is given of the difference, for this small gas-phase system, between ab initio MD and traditional MD simulation using force fields.

Alanine↗
PubMed2001

Molecular dynamics simulation of the fragile glass former orthoterphenyl: a flexible molecule model. II. Collective dynamics.

We present a molecular dynamics study of the collective dynamics of a model for the fragile glass former orthoterphenyl. In this model, introduced by Mossa, Di Leonardo, Ruocco, and Sampoli [Phys. Rev. E 62, 612 (2000)], the intramolecular interaction among the three rigid phenyl rings is described by a set of force constants whose value has been fixed in order to obtain a realistic isolated molecule spectrum. The interaction between different molecules is described by a Lennard Jones site-site potential. We study the behavior of the coherent scattering functions F(t)(q,t), considering the density fluctuations of both molecular and phenyl-ring centers of mass; moreover we directly simulate the neutron scattering spectra taking into account both the contributions due to carbon and hydrogens atoms. We compare our results with the main predictions of the mode-coupling theory and with the available coherent neutron scattering experimental data.

Journal Article↗
PubMed2002

Rotational dynamics of propane in Na-Y zeolite: a molecular dynamics and quasielastic neutron-scattering study.

We report results from molecular dynamics (MD) simulations and quasielastic neutron-scattering (QENS) measurements on the rotational dynamics of propane in Na-Y zeolite at room temperature with a loading of four molecules per alpha cage. Rotational part of the intermediate scattering function F(Q,t) obtained from the MD simulation suggests that rotational motion is faster relative to the translational motion. Various rotational models fitted to the MD data suggest that rotation is isotropic. It is found that the hydrogen atoms lie, on the average, on a sphere of radius 1.88+/-0.05 A, which is also the average distance of the hydrogen atoms from the center of mass of the propane molecule. Results from QENS measurements are in excellent agreement with those obtained from MD, suggesting that the intermolecular potential employed in the MD simulation provides a realistic description of propane motion within faujasite. The rotational diffusion constant D(R) is 1.05+/-0.09 x 10(12) sec(-1) from the QENS data, which may be compared with that obtained from the MD data (0.82+/-0.05 x 10(12) sec(-1)).

Journal Article↗
PubMed2003

Collective ionic dynamics in the liquid Na-Cs alloy: an ab initio molecular dynamics study.

We present results for several structural and dynamical properties of the liquid Na-Cs alloy. The study has been carried out by means of the orbital-free ab initio molecular dynamics method, combined with local ionic pseudopotentials constructed within the same framework. The results show good agreement with the available experimental data, reproducing the homocoordinating tendency exhibited by this alloy.

Journal Article↗
PubMed2003

Test of mean-field equations for two types of hard-sphere systems by a Brownian-dynamics simulation and a molecular-dynamics simulation.

A mean-field nonlinear equation for the mean-square displacement, recently proposed by one of the present authors [M. Tokuyama, Phys. Rev. E 62, R5915 (2000); Physica A 289, 57 (2001)], for concentrated, equilibrium suspensions of hard spheres is extended to describe equilibrium atomic systems of hard spheres. The validity of two types of mean-field equations is investigated by two kinds of computer simulations; a Brownian-dynamics simulation on suspensions of hard spheres and a molecular-dynamics simulation on atomic systems of hard spheres. A good agreement between the mean-field equations and simulations is then shown for different volume fractions. The two types of model systems of hard spheres are thus shown to be identical to each other on the study of the liquid-solid transition. However, analyses suggest that a new interaction is indispensable to understand the mechanism for the liquid-glass transition in both systems.

Journal Article↗
PubMed2003

Structure, dynamics, and energetics of water at the surface of a small globular protein: a molecular dynamics simulation.

The dynamics of water around a biomolecular surface has attracted a lot of attention recently. We report here protein-solvent simulation studies of the small globular protein ubiquitin (human). The simulations are run unconstrained, without freezing the bonds. The mean square displacements of the water oxygen atoms show a sublinear trend with time. The diffusion coefficient data indicate that the water in the first hydration layer behaves like water at a temperature that is roughly 12 degrees C lower than the average temperature of the system (27 degrees C). Both the dipolar second-rank relaxation and the survival time correlation function of the water layers show two decay constants, indicating contributions from fast and slow dynamics. A calculation of the interaction energy between the water layers and protein indicates that the interaction energy sharply decreases beyond 4 A from the protein surface.

Biophysical Phenomena↗
PubMed2003

Dissipative particle dynamics: a useful thermostat for equilibrium and nonequilibrium molecular dynamics simulations.

We discuss dissipative particle dynamics as a thermostat to molecular dynamics, and highlight some of its virtues: (i) universal applicability irrespective of the interatomic potential; (ii) correct and unscreened reproduction of hydrodynamic correlations; (iii) stabilization of the numerical integration of the equations of motion; and (iv) the avoidance of a profile bias in boundary-driven nonequilibrium simulations of shear flow. Numerical results on a repulsive Lennard-Jones fluid illustrate our arguments.

Journal Article↗
PubMed2004

Coevolution of dynamical states and interactions in dynamic networks.

We explore the coupled dynamics of the internal states of a set of interacting elements and the network of interactions among them. Interactions are modeled by a spatial game and the network of interaction links evolves adapting to the outcome of the game. As an example, we consider a model of cooperation in which the adaptation is shown to facilitate the formation of a hierarchical interaction network that sustains a highly cooperative stationary state. The resulting network has the characteristics of a small world network when a mechanism of local neighbor selection is introduced in the adaptive network dynamics. The highly connected nodes in the hierarchical structure of the network play a leading role in the stability of the network. Perturbations acting on the state of these special nodes trigger global avalanches leading to complete network reorganization.

Journal Article↗
PubMed2005

Dynamic regimes of fluids simulated by multiparticle-collision dynamics.

We investigate the hydrodynamic properties of a fluid simulated with a mesoscopic solvent model. Two distinct regimes are identified, the "particle regime" in which the dynamics is gaslike and the "collective regime" where the dynamics is fluidlike. This behavior can be characterized by the Schmidt number, which measures the ratio between viscous and diffusive transport. Analytical expressions for the tracer diffusion coefficient, which have been derived on the basis of a molecular-chaos assumption, are found to describe the simulation data very well in the particle regime, but important deviations are found in the collective regime. These deviations are due to hydrodynamic correlations. The model is then extended in order to investigate self-diffusion in colloidal dispersions. We study first the transport properties of heavy pointlike particles in the mesoscopic solvent, as a function of their mass and number density. Second, we introduce excluded-volume interactions among the colloidal particles and determine the dependence of the diffusion coefficient on the colloidal volume fraction for different solvent mean-free paths. In the collective regime, the results are found to be in good agreement with previous theoretical predictions based on Stokes hydrodynamics and the Smoluchowski equation.

Journal Article↗
PubMed2005

Equation-free dynamic renormalization: self-similarity in multidimensional particle system dynamics.

We present an equation-free dynamic renormalization approach to the computational study of coarse-grained, self-similar dynamic behavior in multidimensional particle systems. The approach is aimed at problems for which evolution equations for coarse-scale observables (e.g., particle density) are not explicitly available. Our illustrative example involves Brownian particles in a 2D Couette flow; marginal and conditional inverse cumulative distribution functions (ICDFs) constitute the macroscopic observables of the evolving particle distributions.

Journal Article↗