scholarly journals Angular measurements of the dynein ring reveal a stepping mechanism dependent on a flexible stalk

2017 ◽  
Vol 114 (23) ◽  
pp. E4564-E4573 ◽  
Author(s):  
Lisa G. Lippert ◽  
Tali Dadosh ◽  
Jodi A. Hadden ◽  
Vishakha Karnawat ◽  
Benjamin T. Diroll ◽  
...  
Keyword(s):  
Structural Dynamics ◽  
Total Internal Reflection ◽  
Angular Position ◽  
Dynamics Simulation ◽  
Power Stroke ◽  
Small Scale ◽  
Ring Rotation ◽  
Stepping Pattern ◽  
Angular Measurements ◽  
Stroke Mechanism

The force-generating mechanism of dynein differs from the force-generating mechanisms of other cytoskeletal motors. To examine the structural dynamics of dynein’s stepping mechanism in real time, we used polarized total internal reflection fluorescence microscopy with nanometer accuracy localization to track the orientation and position of single motors. By measuring the polarized emission of individual quantum nanorods coupled to the dynein ring, we determined the angular position of the ring and found that it rotates relative to the microtubule (MT) while walking. Surprisingly, the observed rotations were small, averaging only 8.3°, and were only weakly correlated with steps. Measurements at two independent labeling positions on opposite sides of the ring showed similar small rotations. Our results are inconsistent with a classic power-stroke mechanism, and instead support a flexible stalk model in which interhead strain rotates the rings through bending and hinging of the stalk. Mechanical compliances of the stalk and hinge determined based on a 3.3-μs molecular dynamics simulation account for the degree of ring rotation observed experimentally. Together, these observations demonstrate that the stepping mechanism of dynein is fundamentally different from the stepping mechanisms of other well-studied MT motors, because it is characterized by constant small-scale fluctuations of a large but flexible structure fully consistent with the variable stepping pattern observed as dynein moves along the MT.

scholarly journals Using SysML to Support Impact Analysis on Structural Dynamics Simulation Models

Procedia CIRP ◽  
2021 ◽  
Vol 100 ◽  
pp. 91-96
Author(s):  
Patrick Jagla ◽  
Georg Jacobs ◽  
Justus Siebrecht ◽  
Stefan Wischmann ◽  
Jonathan Sprehe
Keyword(s):  
Structural Dynamics ◽  
Impact Analysis ◽  
Simulation Models ◽  
Dynamics Simulation

scholarly journals Interaction of the Motor Protein SecA and the Bacterial Protein Translocation Channel SecYEG in the Absence of ATP

2019 ◽  
Author(s):  
Klemens Winkler ◽  
Andreas Karner ◽  
Andreas Horner ◽  
Christof Hannesschlaeger ◽  
Denis Knyazev ◽  
...  
Keyword(s):  
High Speed ◽  
Atp Hydrolysis ◽  
Protein Translocation ◽  
Resonance Energy Transfer ◽  
Motor Protein ◽  
Resonance Energy ◽  
Power Stroke ◽  
Secretory Proteins ◽  
Force Microscopy ◽  
Stroke Mechanism

ABSTRACTTranslocation of many secretory proteins through the bacterial plasma membrane is facilitated by a complex of the SecYEG channel with the motor protein SecA. The ATP-free complex is unstable in detergent, raising the question how SecA may perform several rounds of ATP hydrolysis without being released from the membrane embedded SecYEG. Here we show that dual recognition of (i) SecYEG and (ii) vicinal acidic lipids confers an apparent nanomolar affinity. High-speed atomic force microscopy visualizes the complexes between monomeric SecA and SecYEG as being stable for tens of seconds. These long-lasting events and complementary shorter ones both give rise to single ion channel openings of equal duration. Furthermore, luminescence resonance energy transfer reveals two conformations of the SecYEG-SecA complex that differ in the protrusion depth of SecA’s two-helix finger into SecYEG’s aqueous channel. Such movement of the finger is in line with the power stroke mechanism of protein translocation.

Prediction of Load and Shear of Ultra-Thin Multi-Species Surface Films

2012 ◽  
Author(s):  
W. W. F. Chong ◽  
M. Teodorescu ◽  
H. Rahnejat
Keyword(s):  
Thin Film ◽  
Intermolecular Forces ◽  
Dynamics Simulation ◽  
Small Scale ◽  
Solid Boundary ◽  
Surface Films ◽  
Micro Scale ◽  
Molecular Forces ◽  
Simplified Solution ◽  
Ultra Thin Film

Unless protected by an inert gas atmosphere, micro-scale conjunctions are often separated by molecularly-thin adhered films. Therefore, predicting contact load, friction or adhesion, must consider the contribution of this layer to the overall contact problem. The contribution of an adhered layer can be accounted for using a simplified solution (e.g. an adjustment to the energy of adhesion to account for the liquid film). However, these methods cannot account for layers consisting of multiple species of molecules. The most common approach, which accounts for inter-molecular forces between molecules of various species, is a molecular dynamics simulation. However, this is time consuming, and therefore, often limited for small volumes of fluid and small scale contacts. The current paper proposes an alternative approach, where the pressure and shear between two smooth surfaces separated by an ultra-thin film is predicted using a statistical mechanics based model. This method accounts for the chemical structure of each species of molecules comprising the ultra-thin film, their concentration, intermolecular forces and adsorption to the wall. This approach is very fast, therefore, it can be easily included in a larger scale code predicting the behavior of the entire micro-scale mechanism. It was found that for a specified material of the solid boundary the model can predict the optimal concentration of each species of molecule in the intervening ultra-thin film, to minimize friction or adhesion.

Computational fluid dynamics study of Savonius rotors using OpenFOAM

2020 ◽  
pp. 0309524X2092495
Author(s):  
Federico González Madina ◽  
Alejandro Gutiérrez ◽  
Pedro Galione
Keyword(s):  
Fluid Dynamics ◽  
Computational Fluid Dynamics ◽  
Vertical Axis ◽  
Aerodynamic Performance ◽  
Dynamics Simulation ◽  
Power Coefficient ◽  
Small Scale ◽  
Two Dimensional ◽  
Discretization Schemes ◽  
Set Up

In this work, two-dimensional models of Savonius rotors are simulated using OpenFOAM® in order to predict the aerodynamic performance of small-scale vertical-axis wind turbines. The results are reported analyzing the aerodynamic performance and forces acting on the rotors. Power coefficient, [Formula: see text], is compared with experimental data for each operation point, and for three different geometries. Simulations with first- and second-order discretization schemes are carried out and compared, both quantitative and qualitative. Since usual grid dimensions result not to be suitable for simulations of Savonius rotors, an analysis of different domains is performed and compared. Finally, a set up for computational fluid dynamics simulation of two-dimensional Savonius rotors is proposed. The fluid–rotor interaction is analyzed and the vortex shedding is correlated with [Formula: see text] values and wake description.

The relationship between leg stepping pattern and yaw torque oscillations in curve walking of two crayfish species

1999 ◽  
Vol 202 (22) ◽  
pp. 3069-3080 ◽  
Author(s):  
P. Domenici ◽  
J. Schmitz ◽  
M. Jamon
Keyword(s):  
Procambarus Clarkii ◽  
Open Loop ◽  
Power Stroke ◽  
Main Body ◽  
Astacus Leptodactylus ◽  
Stepping Pattern ◽  
Leg Coordination ◽  
Torque Curve ◽  
The Relationship ◽  
Step Amplitude

Curve walking in two species of crayfish, Procambarus clarkii and Astacus leptodactylus, was investigated to test whether the mechanism underlying curve walking is the synchronous action of a centrally pre-programmed leg tripod or whether it is the action of one principal leg that produces the main body yaw torque. Curve walking was induced by an optomotor visual stimulus, and the yaw torque produced by the tethered animals was measured in open-loop conditions. Our main results suggest that the yaw torque oscillations in both P. clarkii and A. leptodactylus are related to the movement of outer leg 4 (i.e. leg 4 on the outside of the turn). That is, the peaks in the yaw torque occur, on average, in synchrony with the power stroke of outer leg 4. When comparing the results of this open-loop experiment on P. clarkii with results previously obtained for curve walking in untethered individuals of the same species, we found a much higher variability in leg coordination in the open-loop situation. Similarly, here we did not find the same level of synchrony in the tripod (formed by outer leg 4 and inner legs 2 and 5) observed during untethered free walking. Therefore, we suggest that tethered conditions may diminish the need for stability and thus allow outer leg 4 to produce a body rotation regardless of the leg stepping configuration. The characteristics of leg 4 are in line with its major role in turning. According to previous studies, legs 4 provide the largest force and the largest step amplitude during walking, and their force includes both a pulling and a pushing component which can facilitate the control of turning. Although it is apparent that outer leg 4 is not the only leg that can produce an inward yaw torque, its major role in modulating the yaw torque suggests that there may be a specific, centrally generated control of outer leg 4 during curve walking in crayfish.

Vibration and Load Suppression of Offshore Floating Wind Turbine

2014 ◽  
Vol 1025-1026 ◽  
pp. 891-896 ◽  
Author(s):  
Er Ming He ◽  
Ya Qi Hu ◽  
Yang Zhang ◽  
Ge Liang Yin
Keyword(s):  
Wind Turbine ◽  
Structural Dynamics ◽  
Wind Turbines ◽  
Structural Control ◽  
Offshore Wind ◽  
Dynamics Simulation ◽  
Type Model ◽  
Simulation Code ◽  
Offshore Wind Turbines ◽  
Floating Wind Turbine

The application of tuned mass dampers (TMDs) to offshore wind turbines has a huge potential to suppress the large vibration responses of these systems. Control module of TMDs is added into the wind turbine structural dynamics simulation code FAST and fully coupled aero-hydro-TMD-structural dynamics model of the 5MW Barge-type floating wind turbine by National Renewable Energy Laboratory (NREL) is established. A multi-parameter optimization study is performed to determine the optimal parameters of a fore-aft TMD system in the Barge-type model. The wind turbine model equipped with the optimal TMD is then simulated under five typical load conditions and the performance of the new system is evaluated. The results show that longitudinal loads at tower base and deflections at tower top reductions of up to 50% and longitudinal loads at blade root and deflections at blade tip reductions of up to 40% are achieved, which indicates that the optimal TMD can be used to suppress the vibration response of offshore wind turbines and also demonstrates the potential for TMD structural control approaches.

An Experiment for the Study of Free-Flying Supercavitating Projectiles

2011 ◽  
Vol 133 (2) ◽  
Author(s):  
Peter J. K. Cameron ◽  
Peter H. Rogers ◽  
John W. Doane ◽  
David H. Gifford
Keyword(s):  
High Speed ◽  
Degrees Of Freedom ◽  
Measurement Techniques ◽  
Theoretical Models ◽  
Dynamics Simulation ◽  
Small Scale ◽  
Successful Operation ◽  
Six Degrees Of Freedom ◽  
Impact Location ◽  
Simulation Based

Applications and research utilizing supercavitation for high-speed underwater flight has motivated study of the phenomenon. In this work, a small scale laboratory experiment for studying supercavitating projectiles has been designed, built, and tested. Similar existing experimental work has been documented in literature but using large, elaborate facilities, or has been presented with ambiguous conclusions from test results. The projectiles were 63.5 mm in length and traveled at speeds on the order of 145 m/s. Measurement techniques are discussed and used to record projectile speed, supercavity dimensions, and target impact location. Experimental observations are compared with a six degrees-of-freedom dynamics simulation based on theoretical models presented in literature for predicting supercavity shape and hydrodynamic forces on the supercavitating projectile during flight. Experimental observations are discussed qualitatively, along with quantitative statistics of the measurements made. Successful operation of the experiment has been demonstrated and verified by agreement with theoretical models.

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