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PubMed2006

Path-integral centroid dynamics for general initial conditions: a nonequilibrium projection operator formulation.

The formulation of path-integral centroid dynamics is extended to the quantum dynamics of density operators evolving from general initial states by means of the nonequilibrium projection operator technique. It is shown that the new formulation provides a basis for applying the method of centroid dynamics to nonequilibrium situations and that it allows the derivation of new formal relations, which can be useful in improving current equilibrium centroid dynamics methods. A simple approximation of uniform relaxation for the unprojected portion of the Liouville space propagator leads to a class of practically solvable equations of motion for the centroid variables, but with an undetermined parameter of relaxation. This new class of equations encompasses the centroid molecular-dynamics (CMD) method as a limiting case, and can be applied to both equilibrium and nonequilibrium situations. Tests for the equilibrium dynamics of one-dimensional model systems demonstrate that the new equations with appropriate choice of the relaxation parameter are comparable to the CMD method.

Journal Article↗
PubMed2006

Does equilibrium polymerization describe the dynamic heterogeneity of glass-forming liquids?

A significant body of evidence indicates that particles with excessively high or low mobility relative to Brownian particles form in dynamic equilibrium in glass-forming liquids. We examine whether these "dynamic heterogeneities" can be identified with a kind of equilibrium polymerization. This correspondence is first checked by demonstrating the presence of a striking resemblance between the temperature dependences of the configurational entropy s(c) in both the theory of equilibrium polymerization and the generalized entropy theory of glass formation in polymer melts. Moreover, the multiple characteristic temperatures of glass formation are also shown to have analogs in the thermodynamics of equilibrium polymerization, supporting the contention that both processes are varieties of rounded thermodynamic transitions. We also find that the average cluster mass (or degree of polymerization) varies in nearly inverse proportionality to s(c). This inverse relation accords with the basic hypothesis of Adam-Gibbs that the number of particles in the cooperatively rearranging regions (CRR) of glass-forming liquids scales inversely to s(c) of the fluid. Our identification of the CRR with equilibrium polymers is further supported by simulations for a variety of glass-forming liquids that verify the existence of stringlike or polymeric clusters exhibiting collective particle motion. Moreover, these dynamical clusters have an exponential length distribution, and the average "string" length grows upon cooling according to the predictions of equilibrium polymerization theory. The observed scale of dynamic heterogeneity in glass-forming liquids is found to be consistent with this type of self-assembly process. Both experiments and simulations have revealed remarkable similarities between the dynamical properties of self-assembling and glass-forming liquids, suggesting that the development of a theory for the dynamics of self-assembling fluids will also enhance our understanding of relaxation in glass-forming liquids.

Journal Article↗
PubMed2002

Factors contributing to the implicit dynamic quality of static abstract designs.

Participants rated the dynamic quality of a set of twelve-element nonrepresentational or abstract visual designs each composed of one of four types of triangles or four types of quadrilaterals. We investigated the contribution to the perceived or implicit dynamics of the design of the four factors edge alignment of compositional elements, physical weight distribution about the horizontal axis, activity directions within the designs, and type of compositional element. It was found that edge alignment of elements was the most influential factor contributing to the dynamics both of triangle and of quadrilateral designs. In addition, dynamics was found to be positively correlated with the number of perceived activity directions within both types of stimuli. Triangle designs, but not quadrilateral ones, with greater structural weight above the horizontal axis were rated as more dynamic. Results suggest that implicit dynamics of nonrepresentational designs arises from a percept based on a global spatial analysis of the stimulus characteristics studied.

Adult↗
PubMed2005

Spread dynamics of invasive species.

Species invasions are a principal component of global change, causing large losses in biodiversity as well as economic damage. Invasion theory attempts to understand and predict invasion success and patterns of spread. However, there is no consensus regarding which species or community attributes enhance invader success or explain spread dynamics. Experimental and theoretical studies suggest that regulation of spread dynamics is possible; however, the conditions for its existence have not yet been empirically demonstrated. If invasion spread is a regulated process, the structure that accounts for this regulation will be a main determinant of invasion dynamics. Here we explore the existence of regulation underlying changes in the rate of new site colonization. We employ concepts and analytical tools from the study of abundance dynamics and show that spread dynamics are, in fact, regulated processes and that the regulation structure is notably consistent among invasions occurring in widely different contexts. We base our conclusions on the analysis of the spread dynamics of 30 species invasions, including birds, amphibians, fish, invertebrates, plants, and a virus, all of which exhibited similar regulation structures. In contrast to current beliefs that species invasions are idiosyncratic phenomena, here we provide evidence that general patterns do indeed exist.

Journal Article↗
PubMed2003

The RNA-protein complex: direct probing of the interfacial recognition dynamics and its correlation with biological functions.

The N protein from bacteriophage lambda is a key regulator of transcription antitermination. It specifically recognizes a nascent mRNA stem loop termed boxB, enabling RNA polymerase to read through downstream terminators processively. The stacking interaction between Trp-18 of WT N protein and A7 of boxB RNA is crucial for efficient antitermination. Here, we report on the direct probing of the dynamics for this interfacial binding and the correlation of the dynamics with biological functions. Specifically, we examined the influence of structural changes in four peptides on the femtosecond dynamics of boxB RNA (2-aminopurine labeled in different positions), through mutations of critical residues of N peptide (residues 1-22). We then compare their in vivo (Escherichia coli) transcription antitermination activities with the dynamics. The results demonstrate that the RNA-peptide complexes adopt essentially two dynamical conformations with the time scale for interfacial interaction in the two structures being vastly different, 1 ps for the stacked structure and nanosecond for the unstacked one; only the weighted average of the two is detected in NMR by nuclear Overhauser effect experiments. Strikingly, the amplitude of the observed ultrafast dynamics depends on the identity of the amino acid residues that are one helical turn away from Trp-18 in the peptides and is correlated with the level of biological function of their respective full-length proteins.

Bacteriophage lambda↗
PubMed2003

Biomolecular hydration: from water dynamics to hydrodynamics.

Thermally driven rotational and translational diffusion of proteins and other biomolecules is governed by frictional coupling to their solvent environment. Prediction of this coupling from biomolecular structures is a longstanding biophysical problem, which cannot be solved without knowledge of water dynamics in an interfacial region comparable to the dry protein in volume. Efficient algorithms have been developed for solving the hydrodynamic equations of motion for atomic-resolution biomolecular models, but experimental diffusion coefficients can be reproduced only by postulating hundreds of rigidly bound water molecules. This static picture of biomolecular hydration is fundamentally inconsistent with magnetic relaxation dispersion experiments and molecular dynamics simulations, which both reveal a highly dynamic interface where rotation and exchange of nearly all water molecules are several orders of magnitude faster than biomolecular diffusion. Here, we resolve this paradox by means of a dynamic hydration model that explicitly links protein hydrodynamics to hydration dynamics. With the aid of this model, bona fide structure-based predictions of global biomolecular dynamics become possible, as demonstrated here for a set of 16 proteins for which accurate experimental rotational diffusion coefficients are available.

Animals↗
PubMed2006

FTDP-17 mutations compromise the ability of tau to regulate microtubule dynamics in cells.

The neural microtubule-associated protein Tau binds directly to microtubules and regulates their dynamic behavior. In addition to being required for normal development, maintenance, and function of the nervous system, Tau is associated with several neurodegenerative diseases, including Alzheimer disease. One group of neurodegenerative dementias known as FTDP-17 (fronto-temporal dementia with Parkinsonism linked to chromosome 17) is directly linked genetically to mutations in the tau gene, demonstrating that Tau misfunction can cause neuronal cell death and dementia. These mutations result either in amino acid substitutions in Tau or in altered Tau mRNA splicing that skews the expression ratio of wild-type 3-repeat and 4-repeat Tau isoforms. Because wild-type Tau regulates microtubule dynamics, one possible mechanism underlying Tau-mediated neurodegeneration is aberrant regulation of microtubule behavior. In this study, we microinjected normal and mutated Tau protein into cultured cells expressing fluorescent tubulin and measured the effects on the dynamic instability of individual microtubules. We found that the FTDP-17 amino acid substitutions G272V (in both 3-repeat and 4-repeat Tau contexts), DeltaK280, and P301L all exhibited markedly reduced abilities to regulate dynamic instability relative to wild-type Tau. In contrast, the FTDP-17 R406W mutation (which maps in a regulatory region outside the microtubule binding domain of Tau) did not significantly alter the ability of 3-repeat or 4-repeat Tau to regulate microtubule dynamics. Overall, these data are consistent with a loss-of-function model in which both amino acid substitutions and altered mRNA splicing in Tau lead to neurodegeneration by diminishing the ability of Tau to properly regulate microtubule dynamics.

Alternative Splicing↗
PubMed2006

A conformational switch in vinculin drives formation and dynamics of a talin-vinculin complex at focal adhesions.

Dynamic interactions between the cytoskeleton and integrins control cell adhesion, but regulatory mechanisms remain largely undefined. Here, we tested the extent to which the autoinhibitory head-tail interaction (HTI) in vinculin regulates formation and lifetime of the talin-vinculin complex, a proposed mediator of integrin-cytoskeleton bonds. In an ectopic recruitment assay, mutational reduction of HTI drove assembly of talin-vinculin complexes, whereas ectopic complexes did not form between talin and wild-type vinculin. Moreover, reduction of HTI altered the dynamic assembly of vinculin and talin in focal adhesions. Using fluorescence recovery after photobleaching, we show that the focal adhesion residency time of vinculin was enhanced up to 3-fold by HTI mutations. The slow dynamics of vinculin correlated with exposure of its cryptic talin-binding site, and a talin-binding site mutation rescued the dynamics of activated vinculin. Significantly, HTI-deficient vinculin inhibited the focal adhesion dynamics of talin, but not paxillin or alpha-actinin. These data show that talin conformation in cells permits vinculin binding, whereas the autoinhibited conformation of vinculin constitutes the barrier to complex formation. Down-regulation of HTI in vinculin to Kd approximately 10(-7) is sufficient to induce talin binding, and HTI is essential to the dynamics of vinculin and talin at focal adhesions. We therefore conclude that vinculin conformation, as modulated by the strength of HTI, directly regulates the formation and lifetime of talin-vinculin complexes in cells.

Fluorescence↗
PubMed1992

Influence of body segment dynamics on loads at the lumbar spine during lifting.

Flexion-extension moments acting at the L5/S1 level and hip joints were calculated using three different techniques; a pure static analysis, a static analysis including the inertial force of the load, and a dynamic analysis. Ten subjects participated in the study and were asked to lift a box weighing either 50 N or 150 N, using a freestyle technique. The lifts were performed at normal and fast speed. The intra-subject lifting techniques were consistent when lifting the same loads. The moments predicted by the dynamic analysis and the static analysis were the same when holding weights in static postures. When performing the lifts, differences in the peak moments occurred between static and dynamic analyses. These differences were influenced by external load and by lifting speed. Taking the effect of the inertia of load into account in the static analysis resulted in an increase in the moment magnitude, but the predicted moment was still much less than in the dynamic analysis which yielded the largest moment magnitudes. The difference between dynamic and static analysis was greatest when lifting 50 N at fast speed; an 87% increase in L5/S1 moment and a 95% increase in hip moment was observed when replacing the pure static with a dynamic analysis.

Adult↗
PubMed2003

Is static spatial performance distinguishable from dynamic spatial performance? A latent-variable analysis.

There is disagreement among researchers about the distinction between dynamic and static spatial performance. Given that dynamic spatial performance is supposed to be important for some occupations, such as air traffic control (ATC), it is germane to have evidence about the likelihood of that distinction. In the present study, a battery of printed static spatial and reasoning tests were applied to 480 applicants for an ATC training course. Two dynamic spatial tests were also applied. Confirmatory factor analyses were performed for testing three models. In Model A, static and dynamic spatial tests were grouped, whereas in Model B, spatial tests were separated according to their static or dynamic character, and in Model C, spatial tests were segregated according to the construct they tapped (visualization or spatial relations). The authors found that Model B, which distinguished static and dynamic spatial tests, showed the best fit. They also discuss some implications of the findings.

Adult↗
PubMed1995

Nonlinear dynamical patterns as personality theory for neurobiology and psychiatry.

ADVANCES in the theory of nonlinear differential equations and their statistical representations have yielded a powerful, qualitatively descriptive yet quantitative language that captures characteristic patterns of behavior (what the psychoanalyst Roy Schafer calls "continuity, coherence, and consistency of action") that has begun to influence studies of complex systems in motion as diverse in specifics as signatory patterns of discharge of neurochemically defined single neurons and the dynamical structures characteristic of a particular composer's music. What might be called personality theories of neurobiological dynamics have arisen to replace neurobiological theories of personality. It is in this way that rigorously proven and powerful general mathematical insights have changed the face of determinism in research in brain and behavior. Two examples: (1) Very complicated looking behavior of neurobiological forced-dissipative (expanding and contracting) systems over time take place on low dimensional abstract surfaces on which only a few underlying abstract parameters control the action. (2) Independent of specific details (chemical, electrical, and/or behavioral), there exist a relatively few fundamental categories of behavior in time and transitions, among them a property called universality. Results from this new theoretical, in contrast with experimental, reductionism yield analogies with and new approaches to historically important dynamic ideas about personality and character patterns that are equally relevant to micro and macrocomplex systems such as neural membrane receptor proteins and individual personality styles. Research findings achieved over the past decade and a half in our laboratory and others in neurochemistry, neurophysiology, and animal and human behavior, as well as the results of a new demonstration experiment involving the prediction of dynamical category membership from abstract expressive motion in humans, are used to exemplify this use of a quantitative dynamic category theory across disciplinary levels in brain and behavior. Multiple measures of complexity adapted from current research in the statistical properties of chaos on unobtrusively observed and reconstructed orbits on the computer screen made by non-premorbid subjects executing content-free, computer-game-like tasks with a mouse, were used to reliably differentiate the "signatures" of two Axis II diagnoses as established using SCID-II criteria. Whereas the techniques of nonlinear systems have achieved some success in quantifying and stimulating the dynamical styles of relatively local phenomena such as the spontaneous behavior of neuronal membrane conductances, single neurons, neural networks, and field electrical events, we think that the real power of these techniques lies in their quantitative description and statistical prediction of global patterns of behavior of entire systems. For example, since the late 1970s our work has shown that these measures could be used to discriminate categories of drug action and dose when applied to patterns of rat exploratory behavior in space and time. The combination of abstract generality and quantitative precision of these methods suggests their usefulness as a cross-disciplinary language for fields like psychiatry that deal with complicated behavior of both neurobiological elements and "the whole person."

Behavior↗
PubMed2005

Strength training: isometric training at a range of joint angles versus dynamic training.

Strength training with isometric contractions produces large but highly angle-specific adaptations. To contrast the contractile mode of isometric versus dynamic training, but diminish the strong angle specificity effect, we compared the strength gains produced by isometric training at four joint angles with conventional dynamic training. Thirty-three recreationally active healthy males aged 18 - 30 years completed 9 weeks of strength training of the quadriceps muscle group three times per week. An intra-individual design was adopted: one leg performed purely isometric training at each of four joint angles (isometrically trained leg); the other leg performed conventional dynamic training, lifting and lowering (dynamically trained leg). Both legs trained at similar relative loads for the same duration. The quadriceps strength of each leg was measured isometrically (at four angles) and isokinetically (at three velocities) pre and post training. After 9 weeks of training, the increase in isokinetic strength was similar in both legs (pooled data from three velocities: dynamically trained leg, 10.7%; isometrically trained leg, 10.5%). Isometric strength increases were significantly greater for the isometrically trained leg (pooled data from four angles: dynamically trained leg, 13.1%; isometrically trained leg, 18.0%). This may have been due to the greater absolute torque involved with isometric training or a residual angle specificity effect despite the isometric training being divided over four angles.

Adaptation, Physiological↗
PubMedDate not supplied

Quantitative evaluation of the dynamics of external factors influencing canine gastric electrical activity before and after uncoupling.

Electrical uncoupling could be a major source of gastric motility abnormalities. Non-invasive recognition of the onsets of gastric electrical uncoupling could become an avenue for early detection of gastric motor abnormalities. Cutaneous recordings of gastric electrical activity (GEA), known as electrogastrograms (EGG), are dynamically influenced by a variety of external factors, jeopardizing their reliability. In the present study the dynamics of external factors influencing both internal GEA and EGG during surgically induced gastric electrical uncoupling are quantitatively explored. Sixteen anaesthesized dogs underwent implantation of six stainless steel pairs of bipolar electrodes, positioned among the sites for future divisions of the stomach into three equal sections. In the basal state and after each surgical cut, simultaneous 30-min recordings of six internal GEA and eight EGG channels were performed in each dog. The signals were filtered, conditioned and digitized to obtain their one-dimensional representations in the sampled time domain. These representations were regarded as particular projections of multidimensional dynamic vectors located in the phase space, which incorporated both the dynamics of the electrical processes taking place in the stomach and the dynamic interactions between the external factors influencing the recordings. Embedding dimensions in the phase space were considered quantitative expressions of all these factors. Comparative statistical evaluation of the dynamics of the embedding dimensions for both internal GEA and EGG channels was performed. Although the number of embedding dimensions did not change significantly with the introduction of gradual uncoupling both in the internal GEA and in the EGG channels, opposite tendencies towards increment in the former and decrement in the latter were noted. After the introduction of severe uncoupling, cutaneous embedding dimensions became very similar to the internal ones. A significant number of external factors influencing EGG recordings preclude reliable recognition of mild electrical uncoupling from EGG.

Animals↗
PubMed2000

Dynamics of a double stranded DNA oligomer: mode-coupling diffusion approach and reduced rigid fragment models.

The local dynamics of a double stranded DNA fragment [d(CpGpCpApApApTpTpTpGpCpG)]2 of twelve base pairs is obtained to second order in the mode-coupling expansion of the Smoluchowski diffusion theory. The DNA is considered a fluctuating three-dimensional (3D) structure undergoing rotational diffusion. The starting structure for the calculations is the B canonical structure of the fragment, while the fluctuations are evaluated using molecular dynamics simulations, with the ensemble averages approximated by time averages along a trajectory of length 1.5 ns. The rotational dynamics of the bonds along the double strands are calculated and compared to experimental NMR relaxation rates of different 13C along the sequence: R(Cz), R(Cxy) and R(Hz-->Cz). For a fluctuating 3D structure the mode-coupling diffusion theory is found to be in good agreement with several relative characteristics of the experimental relaxation parameters, while motivations are given for the few differences which are due mainly to poor statistics or to inaccuracies in the diffusion model. With a view to application to larger DNA fragments, discussion is dedicated to the validity of reducing the number of degrees of freedom in the double helix statistics by grouping the atoms in rigid fragments (e.g. the backbone atoms, the sugar atoms and the base atoms of each nucleotide). Consideration is given to the effect on local dynamics properties of reduced descriptions that include only three or four rigid bodies per nucleotide as well as five rigid bodies per base pair. It is found that in general these approximations almost uniformly produce slight increase in the correlation time pattern, which grows as the rigidity in the model increases. The relative effects on the dynamic pattern for the most accurate rigid body models are modest. The errors in C1' and C5' mobilities are more significant if C5' is included in the backbone rigid body. These results offer new tools to analyse NMR relaxation behaviour and new perspectives in studying the role of dynamics in biological macromolecules.

Algorithms↗
PubMed2002

Significance of respiratory dynamics of the lung tissue in pulmonary drug permeation.

There are two main objectives in this study. One is to investigate the roles of respiration, i.e., the dynamic change of the lung tissue, on drug transport across the air-blood barrier. The others is to establish the quantitative relationship between the effect of respiration and the physicochemical properties of drugs. To achieve these objectives, progesterone and a group of its hydroxy derivatives with varying hydrophilicity were used as the model drugs and their permeation kinetics studies were conducted under simulated respiratory dynamics using the in vitro pulmonary permeation system developed earlier in this laboratory. The physiological respiratory dynamics were successfully simulated and found to enhance significantly the transpulmonary permeation of progesterone and its hydroxy derivatives through bullfrog lung membrane, a model air-blood barrier. The extent of enhancement in the rate of drug permeation was observed to depend on the pattern of pressure application. As a pressure of the same magnitude was applied, the respiratory pressure was found to have a greater effect than a constant pressure. The results suggested that respiration has increased not only the surface area of lung membrane for permeation, but also dramatically affected the permeability of the lung membrane. Furthermore, the enhancement in permeation rate produced by respiration was observed to be in a linear correlation with the hydrophilicity of penetrants. The effect of variation in various respiratory parameters on drug permeation was also evaluated, and the results suggested that the dynamic change of the lung tissue generated by respiration plays an important role in the transpulmonary permeation of drugs. A possible mechanism involved could be attributed to the formation of transitional pores in lung membrane during the dynamic process of respiration. Therefore, it is necessary to bear in mind and take the respiratory dynamics into consideration for studying the transpulmonary permeation of drugs, especially when the drug has hydrophilic characteristics.

Animals↗
PubMed1995

The role of microtubule dynamics in growth cone motility and axonal growth.

The growth cone contains dynamic and relatively stable microtubule populations, whose function in motility and axonal growth is uncharacterized. We have used vinblastine at low doses to inhibit microtubule dynamics without appreciable depolymerization to probe the role of these dynamics in growth cone behavior. At doses of vinblastine that interfere only with dynamics, the forward and persistent movement of the growth cone is inhibited and the growth cone wanders without appreciable forward translocation; it quickly resumes forward growth after the vinblastine is washed out. Direct visualization of fluorescently tagged microtubules in these neurons shows that in the absence of dynamic microtubules, the remaining mass of polymer does not invade the peripheral lamella and does not undergo the usual cycle of bundling and splaying and the growth cone stops forward movement. These experiments argue for a role for dynamic microtubules in allowing microtubule rearrangements in the growth cone. These rearrangements seem to be necessary for microtubule bundling, the subsequent coalescence of the cortex around the bundle to form new axon, and forward translocation of the growth cone.

Animals↗
PubMed1997

Astral microtubule dynamics in yeast: a microtubule-based searching mechanism for spindle orientation and nuclear migration into the bud.

Localization of dynein-green fluorescent protein (GFP) to cytoplasmic microtubules allowed us to obtain one of the first views of the dynamic properties of astral microtubules in live budding yeast. Several novel aspects of microtubule function were revealed by time-lapse, three-dimensional fluorescence microscopy. Astral microtubules, about four to six in number for each pole, exhibited asynchronous dynamic instability throughout the cell cycle, growing at approximately 0.3-1.5 micron/min toward the cell surface then switching to shortening at similar velocities back to the spindle pole body (SPB). During interphase, a conical array of microtubules trailed the SPB as the nucleus traversed the cytoplasm. Microtubule disassembly by nocodozole inhibited these movements, indicating that the nucleus was pushed around the interior of the cell via dynamic astral microtubules. These forays were evident in unbudded G1 cells, as well as in late telophase cells after spindle disassembly. Nuclear movement and orientation to the bud neck in S/G2 or G2/M was dependent on dynamic astral microtubules growing into the bud. The SPB and nucleus were then pulled toward the bud neck, and further microtubule growth from that SPB was mainly oriented toward the bud. After SPB separation and central spindle formation, a temporal delay in the acquisition of cytoplasmic dynein at one of the spindle poles was evident. Stable microtubule interactions with the cell cortex were rarely observed during anaphase, and did not appear to contribute significantly to spindle alignment or elongation into the bud. Alterations of microtubule dynamics, as observed in cells overexpressing dynein-GFP, resulted in eventual spindle misalignment. These studies provide the first mechanistic basis for understanding how spindle orientation and nuclear positioning are established and are indicative of a microtubule-based searching mechanism that requires dynamic microtubules for nuclear migration into the bud.

Anaphase↗
PubMed1999

Yeast Bim1p promotes the G1-specific dynamics of microtubules.

Microtubule dynamics vary during the cell cycle, and microtubules appear to be more dynamic in vivo than in vitro. Proteins that promote dynamic instability are therefore central to microtubule behavior in living cells. Here, we report that a yeast protein of the highly conserved EB1 family, Bim1p, promotes cytoplasmic microtubule dynamics specifically during G1. During G1, microtubules in cells lacking BIM1 showed reduced dynamicity due to a slower shrinkage rate, fewer rescues and catastrophes, and more time spent in an attenuated/paused state. Human EB1 was identified as an interacting partner for the adenomatous polyposis coli (APC) tumor suppressor protein. Like human EB1, Bim1p localizes to dots at the distal ends of cytoplasmic microtubules. This localization, together with data from electron microscopy and a synthetic interaction with the gene encoding the kinesin Kar3p, suggests that Bim1p acts at the microtubule plus end. Our in vivo data provide evidence of a cell cycle-specific microtubule-binding protein that promotes microtubule dynamicity.

Cell Cycle Proteins↗