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PubMed1994

Cardiac function and histological changes after non-dynamic cardiomyoplasty and preliminary study of dynamic cardiomyoplasty.

By means of histological method and ultrasound cardiographic (UCG) examination, the left-right ratio of transectional area of muscle fiber of latissimus dorsi muscle (LDM) after non-dynamic cardiomyoplasty was 77.4 +/- 11.7% in Group I (3 weeks after operation), and 78.4 +/- 11.6% atrophy and hyperplasia of LDM, but the basical structure was retained. The ejection fraction (EF) decreased significantly after operation (P < 0.05), but the difference between two groups was non- significant. Also, dynamic cardiomyoplasty was performed on a sheep. UCG showed the increased cardiac systolic function after operation. ATPase, succinodehydrogenase (SDH) and PAS examination implied the strengthening of fatigue-resistant ability in skeletal muscles after long-term electrical stimulation. So cardiomyoplasty is suggested to be a supplementary measure in treating end-stage heart failure.

Animals↗
PubMed2006

Dynamic-persistence of cooperation in public good games when group size is dynamic.

The evolution of cooperation is possible with a simple model of a population of agents that can move between groups. The agents play public good games within their group. The relative fitness of individuals within the whole population affects their number of offspring. Groups of cooperators evolve but over time are invaded by defectors which eventually results in the group's extinction. However, for small levels of migration and mutation, high levels of cooperation evolve at the population level. Thus, evolution of cooperation based on individual fitness without kin selection, indirect or direct reciprocity is possible. We provide an analysis of the parameters that affect cooperation, and describe the dynamics and distribution of population sizes over time.

Animals↗
PubMed2006

Dynamic and interactive generation of object handling behaviors by a small humanoid robot using a dynamic neural network model.

This study presents experiments on the learning of object handling behaviors by a small humanoid robot using a dynamic neural network model, the recurrent neural network with parametric bias (RNNPB). The first experiment showed that after the robot learned different types of ball handling behaviors using human direct teaching, the robot was able to generate adequate ball handling motor sequences situated to the relative position between the robot's hands and the ball. The same scheme was applied to a block handling learning task where it was shown that the robot can switch among learned different block handling sequences, situated to the ways of interaction by human supporters. Our analysis showed that entrainment of the internal memory structures of the RNNPB through the interactions of the objects and the human supporters are the essential mechanisms for those observed situated behaviors of the robot.

Algorithms↗
PubMed1997

EEG alpha dynamics as viewed from EEG dimension dynamics.

EEG alpha power covaries with changes in visual input and with changes in other aspects of cortical processing. We present an synopsis of three experiments that demonstrate these effects. A concurrent analysis of the EEG dimension indicates that the dynamics of EEG alpha may result from at least two different mechanisms.

Adolescent↗
PubMed1996

The influence of a protein on water dynamics in its vicinity investigated by molecular dynamics simulation.

A system containing the globular protein ubiquitin and 4,197 water molecules has been used for the analysis of the influence exerted by a protein on solvent dynamics in its vicinity. Using Voronoi polyhedra, the solvent has been divided into three subsets, i.e., the first and second hydration shell, and the remaining bulk, which is hardly affected by the protein. Translational motion in the first shell is retarded by a factor of 3 in comparison to bulk. Several molecules in the first shell do not reach the diffusive regime within 100 ps. Shell-averaged orientational autocorrelation functions, which are also subject to a retardation effect, cannot be modeled by a single exponential time law, but are instead well-described by a Kohlrausch-Williams-Watts (KWW) function. The underlying distribution of single-molecule rotational correlation times is both obtained directly from the simulation and derived theoretically. The temperature dependence of reorientation is characterized by a strongly varying correlation time, but a virtually temperature-independent KWW exponent. Thus, the coupling of water structure relaxation with the respective environment, which is characteristic of each solvation shell, is hardly affected by temperature. In other words, the functional form of the distributions of single-molecule rotational correlation times is not subject to a temperature effect. On average, a correlation between reorientation and lifetimes of neighborhood relations is observed.

Proteins↗
PubMed2003

Dynamic T1 estimation of brain tumors using double-echo dynamic MR imaging.

PURPOSE: To assess the clinical utility of a new method for real-time estimation of T1 during the first pass of contrast agent by using this method to examine brain tumors. MATERIALS AND METHODS: The multi-phase spoiled gradient-echo pulse sequence using the double-echo magnetic resonance (MR) technique was modified. In the first half of the pulse sequence, the flip angle was varied systematically. Then, static T1 values were calculated using differences in MR signal intensities between different flip angles. In the latter half of this sequence, changes in absolute T1 were calculated using differences in signal intensities before and after injection of contrast agent. The double-echo MR data were used to minimize the T2* effect. Five cases of neurinoma and seven cases of meningioma were examined. Changes in T1 during the first pass of contrast agent were compared between neurinoma and meningioma. RESULTS: Changes in absolute T1 were clearly demonstrated on the parametric map. Although the changes in absolute T1 during the first pass of contrast agent did not allow differentiation between the two types of tumors, the mean gradient after the first pass was statistically higher for neurinoma than for meningioma (P < 0.05; meningioma, 0.011 +/- 0.012 second(-1)/second; neurinoma, 0.034 +/- 0.020 second(-1)/second). CONCLUSION: The present method appears to be useful for estimation of dynamic T1 changes in brain tumors in clinical settings.

Adult↗
PubMed1994

Structure and dynamics of the active site gorge of acetylcholinesterase: synergistic use of molecular dynamics simulation and X-ray crystallography.

The active site of acetylcholinesterase (AChE) from Torpedo californica is located 20 A from the enzyme surface at the bottom of a narrow gorge. To understand the role of this gorge in the function of AChE, we have studied simulations of its molecular dynamics. When simulations were conducted with pure water filling the gorge, residues in the vicinity of the active site deviated quickly and markedly from the crystal structure. Further study of the original crystallographic data suggests that a bis-quaternary decamethonium (DECA) ion, acquired during enzyme purification, residues in the gorge. There is additional electron density within the gorge that may represent small bound cations. When DECA and 2 cations are placed within the gorge, the simulation and the crystal structure are dramatically reconciled. The small cations, more so than DECA, appear to stabilize part of the gorge wall through electrostatic interactions. This part of the gorge wall is relatively thin and may regulate substrate, product, and water movement through the active site.

Acetylcholinesterase↗
PubMed2004

Accurate and efficient description of protein vibrational dynamics: comparing molecular dynamics and Gaussian models.

Current all-atom potential based molecular dynamics (MD) allows the identification of a protein's functional motions on a wide-range of timescales, up to few tens of nanoseconds. However, functional, large-scale motions of proteins may occur on a timescale currently not accessible by all-atom potential based MD. To avoid the massive computational effort required by this approach, several simplified schemes have been introduced. One of the most satisfactory is the Gaussian network approach based on the energy expansion in terms of the deviation of the protein backbone from its native configuration. Here, we consider an extension of this model that captures in a more realistic way the distribution of native interactions due to the introduction of effective side-chain centroids. Since their location is entirely determined by the protein backbone, the model is amenable to the same exact and computationally efficient treatment as previous simpler models. The ability of the model to describe the correlated motion of protein residues in thermodynamic equilibrium is established through a series of successful comparisons with an extensive (14 ns) MD simulation based on the AMBER potential of HIV-1 protease in complex with a peptide substrate. Thus, the model presented here emerges as a powerful tool to provide preliminary, fast yet accurate characterizations of protein near-native motion.

Computer Simulation↗
PubMed1993

A comparison of 15N NMR relaxation measurements with a molecular dynamics simulation: backbone dynamics of the glucocorticoid receptor DNA-binding domain.

The rapid motions of the backbone of the DNA-binding domain of the glucocorticoid receptor (GR DBD) have been investigated using proton-detected heteronuclear NMR experiments on 15N-labeled protein at pH 6.0 and with a 200 psec molecular dynamics simulation of hydrated GR DBD. The experimental data were interpreted in terms of a generalized order parameter (S2) and an effective correlation time (tau e) for the internal motion of each amide bond. A back calculation, using the same model, yielded the [1H]-14N nuclear Overhauser effects (NOEs) and the 15N spin-lattice relaxation times (T1) from the simulated data. The rapid motions of the backbone turned out to be rather limited and uniform throughout the protein, with a somewhat reduced mobility in the two major alpha-helical regions and a slightly enhanced flexibility for some residues in the first zinc coordinating region. The agreement between the experimental and simulated S2-values was as good as quantitative for most of the residues, except for some residues that were subject to a more large-scale, and in the simulation thus poorly sampled, motion. Examples of such motions that were found in the simulation include jumps of the amide bond of Ile-487 between the charged oxygens of the side chain of Asp-485 and less distinct large scale motions for some of the residues in the extended regions, that were shown to give rise to noisy and/or fast decaying internal reorientational correlation functions. For these residues large differences in the simulated and experimental tau e-values were found, indicating that motions on different time scales were dominating in the experimental and simulated values. The lower (< 0.7) experimental NOEs for these residues could not be reproduced in the simulation and were shown to be a consequence of the lower tau e-values estimated in the simulation. By combining information from the simulation and the experiment a more complete picture of the motions for these residues can be obtained as is illustrated with an estimation of the jump angle and jump frequency for the amide bond of Ile-487.

Amino Acid Sequence↗
PubMed1997

Rheology and Dynamics of Water-in-Oil Emulsions under Steady and Dynamic Shear Flow

The fundamental aspects governing the rheology of water-in-oil emulsions, such as viscosity ratio and morphology were considered. The model developed here is based on the early work of Pal and Rhodes (1989) for viscosity equation, combined with the theory of Lee and Park (1994) for the morphological contributions. Thus, the proposed conception enables us to predict not only the degree of flocculation but also viscosity ratio and morphological effects. The contribution of secondary morphology caused by the flocculation of droplets on the viscosity of dispersed emulsions has been found by using the factor, -alpha'q'xy/gamma; (where alpha' is the interfacial tension, q'xy is xy-component of anisotropy tensor, and gamma; is shear rate). However, this approach is only useful for system below the maximum random packing concentration. Experimentally, the bulk rheological properties have been examined under steady and dynamic shear flow to investigate the structure of emulsion. The flocculation-deflocculation transition was observed during the shear rate sweep, resulting in instant dilatancy of viscosity near the critical shear rate gamma; approximately 100 s-1.

Journal Article↗
PubMed2002

Development of effective Stokesian dynamics method for ferromagnetic colloidal dispersions (cluster-based Stokesian dynamics method).

We have developed a new Stokesian dynamics (SD) method for nondilute colloidal dispersions, which enables us to reduce drastically the computation time. To verify the validity of the present method, which is called the "cluster-based SD method," three-dimensional simulations of a ferromagnetic colloidal dispersion have been carried out for a simple shear flow. The correlation function and viscosity have been evaluated to compare the results obtained by the present method with those obtained by the ordinary SD method and by the method of ignoring hydrodynamic interactions between particles. The results obtained here are summarized as follows. The transient properties from an initial state obtained by the present method agree well with those obtained by the ordinary method, even if a radius r(clstr), which defines the cluster formation, is taken as a small value such as r(clstr)=1.2d (d is the particle diameter). Also, the equilibrium properties such as the pair correlation function and viscosity obtained by the present cluster-based method are in satisfactory agreement with those obtained by the ordinary SD method. Furthermore, the cluster-based method drastically reduces the computation time to about one-fourteenth to one-seventieth that of the ordinary method. It is clear from these results that the cluster-based SD method is significantly superior to the ordinary SD method for ferromagnetic colloidal dispersions for which a large model system such as N=1000 or 10,000 is indispensable in simulations.

Journal Article↗
PubMed1993

How consistent are molecular dynamics simulations? Comparing structure and dynamics in reduced and oxidized Escherichia coli thioredoxin.

In this study we have examined several parameters that can be used for checking the consistency and accuracy of protein structures and molecular dynamics simulations. This is done by comparing: (1) three X-ray structures of oxidized Escherichia coli thioredoxin (Trx-S2); (2) 14 NMR structures of reduced E. coli thioredoxin (Trx-(SH)2); and (3) 30 different simulations, 15 of Trx-S2 and 15 of Trx-(SH)2. The energy, the agreement with NOE data, the root-mean-square deviation between structures, and the surface characteristics of all these structures are analyzed. The 30 simulations, four water simulations, 20 standard vacuum simulations and six alternative vacuum simulations, are examined with respect to mobility, temperature factors and aromatic side-chain mobility. It is shown that although vacuum simulations may reproduce some parameters, all the features of a water simulation cannot be reproduced in any of these simulations. Several of the parameters described above are shown to be good for discriminating between an accurate and an inaccurate simulation. It is also shown that 100 ps is too short a time to obtain statistically certain temperature factors and correlation functions of aromatic side-chain motions. The results also suggest that performing ten 100 ps simulations spans the conformation space better than one 1 ns simulation.

Computer Simulation↗
PubMed1999

Nucleosome dynamics. III. Histone tail-dependent fluctuation of nucleosomes between open and closed DNA conformations. Implications for chromatin dynamics and the linking number paradox. A relaxation study of mononucleosomes on DNA minicircles.

The mean linking number ( ) of the topoisomer equilibrium distribution obtained upon relaxation of DNA minicircles with topoisomerase I did not increase linearly, but rather in a step wise fashion, with DNA size between 351 and 366 bp. As a consequence, the corresponding linking number difference ( ) did not remain equal to 0, but rather oscillated between +/-0.3 with the periodicity of the double helix. This oscillation, not observed with plasmid-size DNA, is an expected consequence of the stiffness of short DNA. When minicircles were reconstituted with a nucleosome, the associated oscillated between approximately -1.4 +/-0. 2. This oscillation appears to result from the combined effects of DNA stiffness, and nucleosome ability to thermally fluctuate between three distinct DNA conformational states. Two of these states, a closed approximately 1.75-turn DNA conformation with negatively crossed entering and exiting DNAs, and an open approximately 1.4-turn conformation with uncrossed DNAs, are well known, whereas the third state, with a closed DNA conformation and DNAs tending to cross positively rather than negatively, is less familiar. Access to both closed "negative" and "positive" states appears to be mediated by histone N-terminal tails, as shown by specific alterations to the oscillation caused by histone acetylation and phosphate ions, a potent tail destabilizator. These results extend previous observations of ethidium bromide fluorescence titration in the accompanying article, which have pointed to an histone tail-dependent flexibility of entering and exiting DNAs to positive crossing. They also show that DNA wrapping around the histones occurred without twist alteration compared to the DNA free in solution, and reveal an intriguing new facet of the "linking-number-paradox" problem: the possibility for linkers in chromatin to adopt different crossing status within an overall dynamic equilibrium which may be regulated by histone acetylation.

Acetylation↗
PubMed2002

Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA.

Fourteen genetic neurodegenerative diseases and three fragile sites have been associated with the expansion of (CTG)n (CAG)n, (CGG)n (CCG)n, or (GAA)n (TTC)n repeat tracts. Different models have been proposed for the expansion of triplet repeats, most of which presume the formation of alternative DNA structures in repeat tracts. One of the most likely structures, slipped strand DNA, may stably and reproducibly form within triplet repeat sequences. The propensity to form slipped strand DNA is proportional to the length and homogeneity of the repeat tract. The remarkable stability of slipped strand DNA may, in part, be due to loop-loop interactions facilitated by the sequence complementarity of the loops and the dynamic structure of three-way junctions formed at the loop-outs.

DNA↗
PubMed1999

The dynamics of the vestibulo-ocular reflex after peripheral vestibular damage. II. Comparison with dynamics after optically induced learning.

The vestibulo-ocular reflex (VOR) stabilizes gaze adequately under a variety of conditions because it is capable of a simple form of motor learning. Learning is induced by changed visual conditions or to compensate for vestibular sensory loss. We asked whether the mechanisms that are triggered by visual signals can fully account for recovery from vestibular damage. We addressed this question by comparing the effects of optically induced motor learning (i.e., changes in gain induced by telescopic lenses) and recovery from a unilateral horizontal canal plug on the dynamics of the cat VOR. Optically induced learning modified the gain of the VOR more effectively for rotation at low frequencies (below 5 Hz) than for higher-frequency stimuli. During recovery from a plug, the gain of the VOR increased at all frequencies tested, with a similar time course for all frequencies. After recovery the gain for rotation at 5 Hz or above was relatively enhanced. After recovery reached its upper limit, optically induced learning could bring about further changes in gain. The results are interpreted with respect to partially (but not completely) shared mechanisms for optically induced learning and recovery after a unilateral canal plug.

Adaptation, Physiological↗
PubMed2002

HIV-1(Lai) genomic RNA: combined used of NMR and molecular dynamics simulation for studying the structure and internal dynamics of a mutated SL1 hairpin.

The genome of all retroviruses consists of two identical copies of an RNA sequence associated in a non-covalent dimer. A region upstream from the splice donor (SL1) comprising a self-complementary sequence is responsible for the initiation of the dimerization. This region is able to dimerize in two conformations: a loop-loop complex or an extended duplex. Here, we solve by 2D NMR techniques the solution structure of a 23-nucleotide sequence corresponding to HIV-1 SL1(Lai) in which the mutation G12-->A12 is included to prevent dimerization. It is shown that this monomer adopts a stem-loop conformation with a seven base pairs stem and a nine nucleotide loop containing the G10 C11 A12 C13 G14 C15 sequence. The stem is well structured in an A-form duplex, while the loop is more flexible even though elements of structure are evident. We show that the structure adopted by the stem can be appreciably different from its relaxed structure when the adenines A8, A9 and A16 in the loop are mechanically constrained. This point could be important for the efficiency of the dimerization. This experimental study is complemented with a 10 ns molecular dynamics simulation in the presence of counterions and explicit water molecules. This simulation brings about information on the flexibility of the loop, such as a hinge motion between the stem and the loop and a labile lattice of hydrogen bonds in the loop. The bases of the nucleotides G10 to C15 were found outside of the loop during a part of the trajectory, which is certainly necessary to initiate the dimerization process of the genuine SL1(Lai) sequence.

Base Sequence↗
PubMed1993

Dynamical properties of bovine pancreatic trypsin inhibitor from a molecular dynamics simulation at 5000 atm.

Molecular dynamics simulations of bovine pancreatic trypsin inhibitor in water have been performed with coupling to pressure baths at 1 atm and at 5000 atm. The positional fluctuations of atoms in the alpha- and gamma-positions are slightly decreased at 5000 atm. The mobility of the backbone phi- and psi-angles is not affected with respect to the root mean square fluctuations and the rate of torsional angle transitions. The amplitude of libration of sidechain chi-angles remains nearly the same for both pressures, but the rate of torsional angle transitions decreases on average by 30% when increasing the hydrostatic pressure to 5000 atm.

Amino Acid Sequence↗
PubMed1991

Dynamic Monte Carlo simulations of a new lattice model of globular protein folding, structure and dynamics.

A long-standing problem of molecular biology is the prediction of globular protein tertiary structure from the primary sequence. In the context of a new, 24-nearest-neighbor lattice model of proteins that includes both alpha and beta-carbon atoms, the requirements for folding to a unique four-member beta-barrel, four-helix bundles and a model alpha/beta-bundle have been explored. A number of distinct situations are examined, but the common requirements for the formation of a unique native conformation are tertiary interactions plus the presence of relatively small (but not irrelevant) intrinsic turn preferences that select out the native conformer from a manifold of compact states. When side-chains are explicitly included, there are many conformations having the same or a slightly greater number of side-chain contacts as in the native conformation, and it is the local intrinsic turn preferences that produce the conformational selectivity on collapse. The local preference for helix or beta-sheet secondary structure may be at odds with the secondary structure ultimately found in the native conformation. The requisite intrinsic turn populations are about 0.3% for beta-proteins, 2% for mixed alpha/beta-proteins and 6% for helix bundles. In addition, an idealized model of an allosteric conformational transition has been examined. Folding occurs predominantly by a sequential on-site assembly mechanism with folding initiating either at a turn or from an isolated helix or beta-strand (where appropriate). For helical and beta-protein models, similar folding pathways were obtained in diamond lattice simulations, using an entirely different set of local Monte Carlo moves. This argues strongly that the results are universal; that is, they are independent of lattice, protein model or the particular realization of Monte Carlo dynamics. Overall, these simulations demonstrate that the folding of all known protein motifs can be achieved in the context of a single class of lattice models that includes realistic backbone structures and idealized side-chains.

Algorithms↗