Regime Switching Issues and Criteria for Coupled Static-Dynamic Atomistic Methods

2007 ◽  
Author(s):  
S. N. Medyanik ◽  
E. Guleryuz
Keyword(s):  
Regime Switching ◽  
Stable State ◽  
Coarse Graining ◽  
Slow Phase ◽  
Local Energy Minimum ◽  
Fast Phase ◽  
Static Modeling ◽  
Minimization Technique ◽  
Transition Event ◽  
Static Energy

Coupled static-dynamic atomistic method may be used for coarse graining time in temporal multi-scale atomistic modeling of nano-mechanical problems. This approach can be especially effective for mechanical processes that consist of two distinct phases: the slow phase when the system resides in one local energy minimum and the fast phase associated with a rapid transition from one meta-stable state to another. In this case, the slow phase can be effectively modeled using static energy minimization technique, while the fast phase corresponding to the state transition event may be modeled dynamically. In this case, dynamic modeling is necessary to capture the dynamic effects, such as thermal and inertial, that can not be accounted for in static modeling. One of the major issues of this type of method is to determine when the transitions between the two regimes have to be done. In this presentation, issues of switching between the static and dynamic regimes are outlined and criteria that can be used for effective switching between the two regimes are proposed. In particular, a dynamic-to-static switch based on the kinetic energy and static-to-dynamic switch based on the potential energy are discussed.

Possible cues driving context-specific adaptation of optocollic reflex in pigeons (Columba livia)

2012 ◽  
Vol 107 (2) ◽  
pp. 704-717 ◽  
Author(s):  
Henri Gioanni ◽  
Pierre-Paul Vidal
Keyword(s):  
Columba Livia ◽  
Motor Command ◽  
Slow Phase ◽  
Gaze Stabilization ◽  
Specific Adaptation ◽  
Body Vibration ◽  
Fast Phase ◽  
Context Specific ◽  
Context Cues

Context-specific adaptation (Shelhamer M, Clendaniel R. Neurosci Lett 332: 200–204, 2002) explains that reflexive responses can be maintained with different “calibrations” for different situations (contexts). Which context cues are crucial and how they combine to evoke context-specific adaptation is not fully understood. Gaze stabilization in birds is a nice model with which to tackle that question. Previous data showed that when pigeons ( Columba livia) were hung in a harness and subjected to a frontal airstream provoking a flying posture (“flying condition”), the working range of the optokinetic head response [optocollic reflex (OCR)] extended toward higher velocities compared with the “resting condition.” The present study was aimed at identifying which context cues are instrumental in recalibrating the OCR. We investigated that question by using vibrating stimuli delivered during the OCR provoked by rotating the visual surroundings at different velocities. The OCR gain increase and the boost of the fast phase velocity observed during the “flying condition” were mimicked by body vibration. On the other hand, the newly emerged relationship between the fast-phase and slow-phase velocities in the “flying condition” was mimicked by head vibration. Spinal cord lesion at the lumbosacral level decreased the effects of body vibration, whereas lesions of the lumbosacral apparatus had no effect. Our data suggest a major role of muscular proprioception in the context-specific adaptation of the stabilizing behavior, while the vestibular system could contribute to the context-specific adaptation of the orienting behavior. Participation of an efferent copy of the motor command driving the flight cannot be excluded.

Fast-phase transvascular fluid flux and the Fahraeus effect

1987 ◽  
Vol 62 (4) ◽  
pp. 1513-1520 ◽  
Author(s):  
W. N. Richardson ◽  
D. Bilan ◽  
M. Hoppensack ◽  
L. Oppenheimer
Keyword(s):  
Mechanical Properties ◽  
Slow Rate ◽  
Time Course ◽  
Rate Of Change ◽  
Distributed Model ◽  
Slow Phase ◽  
Fluid Flux ◽  
Fast Phase ◽  
Constant Rate ◽  
Fahraeus Effect

Transvascular fluid flux was induced in six isolated blood-perfused canine lobes by increasing and decreasing hydrostatic inflow pressure (Pi). Fluid flux was followed against the change in concentration of an impermeable tracer (Blue Dextran) measured directly with a colorimetric device. The time course of fluid flux was biphasic with an initial fast transient followed by a slow phase. Hematocrit changes unrelated to fluid flux occurred due to the Fahraeus effect, and their contribution to the total color signal was subtracted to determine the rate of fast fluid flux (Qf). Qf was related to Pi to derive fast-phase conductance (Kf). Slow-phase Kf was calculated from the constant rate of change of lobe weight. For a mean change in Pi of 7 cmH2O, 40% of the color signal was due to fluid flux. Fast- and slow-phase Kf's were 0.86 +/- 0.15 and 0.27 +/- 0.05 ml X min-1. cmH2O–1 X 100 g dry wt-1. The fast-phase Kf is smaller than that reported for plasma-perfused lobes. Possible explanations discussed are the nature of the perfusate, the mechanical properties of the interstitium, and the slow rate of rise of the driving pressure at the filtration site on the basis of a distributed model of pulmonary vascular compliance.

scholarly journals Mechanism of retraction of the trailing edge during fibroblast movement.

1981 ◽  
Vol 90 (1) ◽  
pp. 187-200 ◽  
Author(s):  
W T Chen
Keyword(s):  
Slow Component ◽  
Fast Component ◽  
Slow Phase ◽  
Main Body ◽  
Elastic Recoil ◽  
Forward Movement ◽  
Trailing Edge ◽  
Fast Phase ◽  
Focal Contacts

Retraction of the taut, trailing portion of a moving chick heart fibroblast in vitro is an abrupt dynamic process. Upon retraction, the fibroblast tail always ruptures, leaving a small amount of itself attached to the substratum by focal contacts. Time-lapse cinemicrography shows that retraction produces a sudden, massive movement of both surface and cytoplasmic material toward a cluster of focal contacts near the main body of the cell. The appearance of folds on the upper cell surface at this time and the absence of endocytotic vesicles are consistent with this forward movement. Retraction of the trailing edge, either occurring naturally or produced artificially with a microneedle, consists of an initial fast component followed and overlapped by a slow component. Upon artificial detachment in the presence of iodoacetate, dinitrophenol, and sodium fluoride, and at 4 degrees C, the slow component is strongly inhibited and the fast one only slightly inhibited. Moreover of the bundles of microfilaments oriented parallel to the long axis of the tail seen in TEM. Most of the birefringence is lost during the fast phase and the rest during the slow phase of retraction. Concurrently, the bundles of microfilaments disappear during the fast phase of retraction and are replaced by a microfilament meshwork. All of these results are consistent with the hypothesis that the initial fast component of retraction is a passive elastic recoil, associated with the oriented bundles of microfilaments, and that the slow component of retraction is an active contraction, associated with a meshwork of microfilaments.

scholarly journals The assembly of microtubule protein in vitro. The kinetic role in microtubule elongation of oligomeric fragments containing microtubule-associated proteins

1985 ◽  
Vol 227 (2) ◽  
pp. 439-455 ◽  
Author(s):  
P M Bayley ◽  
F M M Butler ◽  
D C Clark ◽  
E J Manser ◽  
S R Martin
Keyword(s):  
Self Assembly ◽  
Protein Concentration ◽  
Wavelength Dependence ◽  
Electrophoretic Analysis ◽  
Slow Phase ◽  
Condensation Polymerization ◽  
Fast Phase ◽  
Microtubule Protein ◽  
Kinetics Of

The kinetics of assembly were studied for bovine and pig microtubule protein in vitro over a range of conditions of pH, temperature, nucleotide and protein concentration. The kinetics are in general biphasic with two major processes of similar amplitude but separated in rate by one order of magnitude. Rates and amplitudes are complex functions of solution conditions. The rates of the fast phase and the slow phase attain limiting values as a function of increasing protein concentration, and are more stringently limited at pH 6.5 than pH 6.95. Such behaviour indicates that mechanisms other than the condensation polymerization of tubulin dimer become rate-limiting at higher protein concentration. The constancy of the wavelength-dependence of light-scattering and ultrastructural criteria indicate that microtubules of normal morphology are formed in both phases of the assembly process. Electrophoretic analysis of assembling microtubule protein shows that MAP- (microtubule-associated-protein-)rich microtubules are formed during the fast phase. The rate of dissociation of oligomeric species on dilution of microtubule protein closely parallels the fast-phase rate in magnitude and temperature-dependence. We propose that the rate of this process constitutes an upper limit to the rate of the fast phase of assembly. The kinetics of redistribution of MAPs from MAP-rich microtubules may be a factor limiting the slow-phase rate. A working model is derived for the self-assembly of microtubule protein incorporating the dissociation and redistribution mechanisms that impose upper limits to the rates of assembly attainable by bimolecular addition reactions. Key roles are assigned to MAP-containing fragments in both phases of microtubule elongation. Variations in kinetic behaviour with solution conditions are inferred to derive from the nature and properties of fragments formed from oligomeric species after the rapid temperature jump. The model accounts for the limiting rate behaviour and indicates experimental criteria to be applied in evaluating the relative contributions of alternative pathways.

Statocyst-Induced Eye Movements in the Crab Scylla Serrata

1973 ◽  
Vol 59 (1) ◽  
pp. 17-38
Author(s):  
D. C. SANDEMAN ◽  
A. OKAJIMA
Keyword(s):  
Eye Movement ◽  
Contralateral Side ◽  
Scylla Serrata ◽  
Slow Phase ◽  
Fast Phase ◽  
Preferred Direction ◽  
Sensory Axons ◽  
Proprioceptive Input ◽  
Motor Neurones ◽  
The Brain

1. The sensory axons of the thread hair receptors, free hook hair receptors and most receptors of the statolith area of the crab statocyst all project to the same dorsolateral part of the brain. Large sensory receptors which innervate some hairs surrounding the statolith project to a more ventral site, and send some branches across to the contralateral side of the brain. 2. The central projections of oculomotor neurones have a characteristically open branch pattern and their dendritic field corresponds closely with that of the thread hairs. There are no branches extending to the contralateral side of the brain. 3. Intracellular responses from the motor neurones of horizontal eye-movement muscles during nystagmus show that they are probably directly inhibited during a fast-phase movement of the eye opposite to the direction in which they act. During a slow-phase eye movement opposite to their preferred direction the input to the motor neurones is diminished pre-synaptically. 4. Sets of antagonist motor neurones maintain a fairly rigid relationship to one another so that an increase in activity of one set leads to a decrease in the antagonists. Neither this, nor the onset of the fast phase of nystagmus, is governed by proprioceptive input or by the frequency of discharge of the motor neurones themselves.

scholarly journals Comparison of the Vertical Distributions of Cloud Properties from Idealized Extratropical Deep Convection Simulations Using Various Horizontal Resolutions

2018 ◽  
Vol 146 (3) ◽  
pp. 833-851 ◽  
Author(s):  
Wei Huang ◽  
J.-W. Bao ◽  
Xu Zhang ◽  
Baode Chen
Keyword(s):  
Deep Convection ◽  
Wrf Model ◽  
Coarse Graining ◽  
Vertical Flux ◽  
Coarse Grained ◽  
Moist Static Energy ◽  
Grid Spacing ◽  
Eddy Simulation ◽  
Cloud Properties ◽  
Static Energy

ABSTRACT The authors coarse-grained and analyzed the output from a large-eddy simulation (LES) of an idealized extratropical supercell storm using the Weather Research and Forecasting (WRF) Model with various horizontal resolutions (200 m, 400 m, 1 km, and 3 km). The coarse-grained physical properties of the simulated convection were compared with explicit WRF simulations of the same storm at the same resolution of coarse-graining. The differences between the explicit simulations and the coarse-grained LES output increased as the horizontal grid spacing in the explicit simulation coarsened. The vertical transport of the moist static energy and total hydrometeor mixing ratio in the explicit simulations converged to the LES solution at the 200-m grid spacing. Based on the analysis of the coarse-grained subgrid vertical flux of the moist static energy, the authors confirmed that the nondimensional subgrid vertical flux of the moist static energy varied with the subgrid fractional cloudiness according to a function of fractional cloudiness, regardless of the box size. The subgrid mass flux could not account for most of the total subgrid vertical flux of the moist static energy because the eddy-transport component associated with the internal structural inhomogeneity of convective clouds was of a comparable magnitude. This study highlights the ongoing challenge in developing scale-aware parameterizations of subgrid convection.

Determinants of relaxation rate in skinned frog skeletal muscle fibers

1998 ◽  
Vol 274 (6) ◽  
pp. C1608-C1615 ◽  
Author(s):  
Philip A. Wahr ◽  
J. David Johnson ◽  
Jack. A. Rall
Keyword(s):  
Skeletal Muscle ◽  
Muscle Fibers ◽  
Slow Phase ◽  
Frog Skeletal Muscle ◽  
Force Of Contraction ◽  
Thin Filaments ◽  
Fast Phase ◽  
Skeletal Muscle Fibers ◽  
Kinetics Of ◽  
Overall Kinetics

The influences of sarcomere uniformity and Ca2+ concentration on the kinetics of relaxation were examined in skinned frog skeletal muscle fibers induced to relax by rapid sequestration of Ca2+ by the photolysis of the Ca2+ chelator, diazo-2, at 10°C. Compared with an intact fiber, diazo-2-induced relaxation exhibited a faster and shorter initial slow phase and a fast phase with a longer tail. Stabilization of the sarcomeres by repeated releases and restretches during force development increased the duration of the slow phase and slowed its kinetics. When force of contraction was decreased by lowering the Ca2+concentration, the overall kinetics of relaxation was accelerated, with the slow phase being the most sensitive to Ca2+ concentration. Twitchlike contractions were induced by photorelease of Ca2+ from a caged Ca2+ (DM-Nitrophen), with subsequent Ca2+ sequestration by intact sarcoplasmic reticulum or Ca2+ rebinding to caged Ca2+. These twitchlike responses exhibited relaxation kinetics that were about twofold slower than those observed in intact fibers. Results suggest that the slow phase of relaxation is influenced by the degree of sarcomere homogeneity and rate of Ca2+ dissociation from thin filaments. The fast phase of relaxation is in part determined by the level of Ca2+ activation.

scholarly journals Kinematic Principles of Primate Rotational Vestibulo-Ocular Reflex II. Gravity-Dependent Modulation of Primary Eye Position

1997 ◽  
Vol 78 (4) ◽  
pp. 2203-2216 ◽  
Author(s):  
Bernhard J. M. Hess ◽  
Dora E. Angelaki
Keyword(s):  
Slow Phase ◽  
Head Orientation ◽  
Eye Position ◽  
Single Plane ◽  
Fast Phase ◽  
Ocular Reflex ◽  
Listing's Plane ◽  
Vestibulo Ocular Reflex ◽  
Torsional Component ◽  
Listing’S Plane

Hess, Bernhard J. M. and Dora E. Angelaki. Kinematic principles of primate rotational vestibulo-ocular reflex. II. Gravity-dependent modulation of primary eye position. J. Neurophysiol. 78: 2203–2216, 1997. The kinematic constraints of three-dimensional eye positions were investigated in rhesus monkeys during passive head and body rotations relative to gravity. We studied fast and slow phase components of the vestibulo-ocular reflex (VOR) elicited by constant-velocity yaw rotations and sinusoidal oscillations about an earth-horizontal axis. We found that the spatial orientation of both fast and slow phase eye positions could be described locally by a planar surface with torsional variation of <2.0 ± 0.4° (displacement planes) that systematically rotated and/or shifted relative to Listing's plane. In supine/prone positions, displacement planes pitched forward/backward; in left/right ear-down positions, displacement planes were parallel shifted along the positive/negative torsional axis. Dynamically changing primary eye positions were computed from displacement planes. Torsional and vertical components of primary eye position modulated as a sinusoidal function of head orientation in space. The torsional component was maximal in ear-down positions and approximately zero in supine/prone orientations. The opposite was observed for the vertical component. Modulation of the horizontal component of primary eye position exhibited a more complex dependence. In contrast to the torsional component, which was relatively independent of rotational speed, modulation of the vertical and horizontal components of primary position depended strongly on the speed of head rotation (i.e., on the frequency of oscillation of the gravity vector component): the faster the head rotated relative to gravity, the larger was the modulation. Corresponding results were obtained when a model based on a sinusoidal dependence of instantaneous displacement planes (and primary eye position) on head orientation relative to gravity was fitted to VOR fast phase positions. When VOR fast phase positions were expressed relative to primary eye position estimated from the model fits, they were confined approximately to a single plane with a small torsional standard deviation (∼1.4–2.6°). This reduced torsional variation was in contrast to the large torsional spread (well >10–15°) of fast phase positions when expressed relative to Listing's plane. We conclude that primary eye position depends dynamically on head orientation relative to space rather than being fixed to the head. It defines a gravity-dependent coordinate system relative to which the torsional variability of eye positions is minimized even when the head is moved passively and vestibulo-ocular reflexes are evoked. In this general sense, Listing's law is preserved with respect to an otolith-controlled reference system that is defined dynamically by gravity.

Pre-steady-state phosphorylation and dephosphorylation of detergent-purified plasma-membrane Ca2+-ATPase

2002 ◽  
Vol 361 (2) ◽  
pp. 355-361 ◽  
Author(s):  
Luis M. BREDESTON ◽  
Alcides F. REGA
Keyword(s):  
Plasma Membrane ◽  
Steady State ◽  
Time Course ◽  
Slow Phase ◽  
Fast Phase ◽  
Lauryl Ether ◽  
Phosphorylation Reaction ◽  
Steady Level ◽  
Biexponential Kinetics ◽  
Acidic Phospholipids

Pre-steady-state phosphorylation and dephosphorylation of purified and phospholipid-depleted plasma-membrane Ca2+-ATPase (PMCA) solubilized in the detergent polyoxyethylene 10 lauryl ether were studied at 25°C. The time course of phosphorylation with ATP of the enzyme associated with Ca2+, probably the true phosphorylation reaction, showed a fast phase (kapp near 400s−1) followed by a slow phase (kapp = 23s−1). With asolectin or acidic phosphatidylinositol, the concentration of phosphoenzyme (EP) increased at as high a rate as before, passed through a maximum at 4ms and stabilized at a steady level that was approx. half that without lipids. Calmodulin (CaM) did not change the rate of the fast phase, accelerated the slow phase (kapp = 93s−1) and increased [EP] with small changes in the shape of the time course. Dephosphorylation was slow (kapp = 30s−1) and insensitive to CaM. Asolectin accelerated dephosphorylation, which followed biexponential kinetics with fast (kapp = 220s−1) and slow (kapp = 20s−1) components. CaM stimulated the fast component by nearly 50%. The results show that the behaviour of the PMCA is complex, and suggest that acidic phospholipids and CaM activate PMCA through different mechanisms. Acceleration of dephosphorylation seems relevant during activation of the PMCA by acidic phospholipids.

scholarly journals Two Temporal Phases of Light Adaptation in Retinal Rods

2002 ◽  
Vol 119 (2) ◽  
pp. 129-146 ◽  
Author(s):  
Peter D. Calvert ◽  
Victor I. Govardovskii ◽  
Vadim Y. Arshavsky ◽  
Clint L. Makino
Keyword(s):  
Binding Sites ◽  
Time Course ◽  
Light Adaptation ◽  
Dynamic Range ◽  
Continuous Illumination ◽  
Slow Phase ◽  
Fast Phase ◽  
Slow Adaptation ◽  
Adaptation Phase

Vertebrate rod photoreceptors adjust their sensitivity as they adapt during exposure to steady light. Light adaptation prevents the rod from saturating and significantly extends its dynamic range. We examined the time course of the onset of light adaptation in bullfrog rods and compared it with the projected onset of feedback reactions thought to underlie light adaptation on the molecular level. We found that adaptation developed in two distinct temporal phases: (1) a fast phase that operated within seconds after the onset of illumination, which is consistent with most previous reports of a 1–2-s time constant for the onset of adaptation; and (2) a slow phase that engaged over tens of seconds of continuous illumination. The fast phase desensitized the rods as much as 80-fold, and was observed at every light intensity tested. The slow phase was observed only at light intensities that suppressed more than half of the dark current. It provided an additional sensitivity loss of up to 40-fold before the rod saturated. Thus, rods achieved a total degree of adaptation of ∼3,000-fold. Although the fast adaptation is likely to originate from the well characterized Ca2+-dependent feedback mechanisms regulating the activities of several phototransduction cascade components, the molecular mechanism underlying slow adaptation is unclear. We tested the hypothesis that the slow adaptation phase is mediated by cGMP dissociation from noncatalytic binding sites on the cGMP phosphodiesterase, which has been shown to reduce the lifetime of activated phosphodiesterase in vitro. Although cGMP dissociated from the noncatalytic binding sites in intact rods with kinetics approximating that for the slow adaptation phase, this hypothesis was ruled out because the intensity of light required for cGMP dissociation far exceeded that required to evoke the slow phase. Other possible mechanisms are discussed.

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