Multiscale Dynamic Modeling of Flexibility in Myosin V

2013 ◽  
Author(s):  
Mahdi Haghshenas-Jaryani ◽  
Alan Bowling
Keyword(s):  
Dynamic Modeling ◽  
Multiple Scales ◽  
Equations Of Motion ◽  
Experimental Studies ◽  
Physical Parameters ◽  
Myosin V ◽  
Step Size ◽  
Time Step ◽  
Time Step Size ◽  
Run Time

This paper presents a multiscale dynamic model for the simulation and analysis of flexibility in myosin V. A three dimensional (3D) flexible multibody model is developed to mechanically model the biological structure of myosin V. Experimental studies have shown that myosin’s neck domain can be considered as three pairs of tandem elements which can bend at junctures between them. Therefore, each neck is modeled by three rigid bodies connected by flexible spherical joints. One of the most important issues in dynamic modeling of micro-nanoscale sized biological structures, likes DNA and motor proteins, is the long simulation run time due to the disproportionality between physical parameters involved in their dynamics such as mass, drag coefficient, and stiffness. In order to address this issue, the mostly used models, based on the famous overdamped Langevin dynamics, omit the inertial terms in the equations of motion; that leads to a first order model which is inconsistent with the Newton’s second law. However, the proposed model uses the concept of the method of multiple scales (MMS) that brings all terms of the equations of motion into proportion with each other that helps to retain the inertia terms. This keeps consistency of the model with the physical laws and increases time step size of numerical integration from commonly used sub-femto seconds to sub-milli seconds. Therefore, simulation run time will be many orders of magnitude less than ones based on the other approaches. The simulation results obtained by the proposed multiscale model show more realistic dynamic behavior of myosin V in compared with other models.

Modeling Flexibility in Myosin V Using a Multiscale Articulated Multi-Rigid Body Approach

2014 ◽  
Vol 10 (1) ◽  
Author(s):  
Mahdi Haghshenas-Jaryani ◽  
Alan Bowling
Keyword(s):  
Multiple Scales ◽  
Equations Of Motion ◽  
Multiscale Model ◽  
Physical Parameters ◽  
Myosin V ◽  
Step Size ◽  
Finite Segment ◽  
Proposed Model ◽  
Run Time ◽  
Physical Laws

This paper presents a multiscale dynamic model for the simulation and analysis of flexibility in myosin V. A 3D finite segment model, a multirigid body model connected with torsional springs, is developed to mechanically model the biological structure of myosin V. The long simulation run time is one of the most important issues in the dynamic modeling of biomolecules and proteins due to the disproportionality between the physical parameters involved in their dynamics. In order to address this issue, the most-used models, based on the famous overdamped Langevin equation, omit the inertial terms in the equations of motion; that leads to a first order model that is inconsistent with Newton's second law. However, the proposed model uses the concept of the method of multiple scales (MMS) that brings all of the terms of the equations of motion into proportion with each other; that helps to retain the inertia terms. This keeps the consistency of the model with the physical laws and experimental observations. In addition, the numerical integration's step size can be increased from commonly used subfemtoseconds to submilliseconds. Therefore, the simulation run time is significantly reduced in comparison with other approaches. The simulation results obtained by the proposed multiscale model show a dynamic behavior of myosin V which is more consistent with experimental observations in comparison with other overdamped models.

A Strategy to Accelerate the Numerical Integration in the Dynamic Simulation of Multibody Systems

1997 ◽  
Author(s):  
Jesús Cardenal ◽  
Javier Cuadrado ◽  
Eduardo Bayo
Keyword(s):  
Multibody Systems ◽  
Equations Of Motion ◽  
Stiff Systems ◽  
Step Size ◽  
Step Method ◽  
Integral Of Motion ◽  
Time Step ◽  
Time Step Size ◽  
Variable Time ◽  
Numerical Integrator

Abstract This paper presents a multi-index variable time step method for the integration of the equations of motion of constrained multibody systems in descriptor form. The basis of the method is the augmented Lagrangian formulation with projections in index-3 and index-1. The method takes advantage of the better performance of the index-3 formulation for large time steps and of the stability of the index-1 for low time steps, and automatically switches from one method to the other depending on the required accuracy and values of the time step. The variable time stepping is accomplished through the use of an integral of motion, which in the case of conservative systems becomes the total energy. The error introduced by the numerical integrator in the integral of motion during consecutive time steps provides a good measure of the local integration error, and permits a simple and reliable strategy for varying the time step. Overall, the method is efficient and powerful; it is suitable for stiff and non-stiff systems, robust for all time step sizes, and it works for singular configurations, redundant constraints and topology changes. Also, the constraints in positions, velocities and accelerations are satisfied during the simulation process. The method is robust in the sense that becomes more accurate as the time step size decreases.

scholarly journals A Lie group variational integration approach to the full discretization of a constrained geometrically exact Cosserat beam model

2021 ◽  
Author(s):  
Stefan Hante ◽  
Denise Tumiotto ◽  
Martin Arnold
Keyword(s):  
Lie Group ◽  
Group Structure ◽  
Equations Of Motion ◽  
Second Order ◽  
The Body ◽  
Benchmark Problems ◽  
Beam Model ◽  
Step Size ◽  
Time Step ◽  
Time Step Size

AbstractIn this paper, we will consider a geometrically exact Cosserat beam model taking into account the industrial challenges. The beam is represented by a framed curve, which we parametrize in the configuration space $\mathbb{S}^{3}\ltimes \mathbb{R}^{3}$ S 3 ⋉ R 3 with semi-direct product Lie group structure, where $\mathbb{S}^{3}$ S 3 is the set of unit quaternions. Velocities and angular velocities with respect to the body-fixed frame are given as the velocity vector of the configuration. We introduce internal constraints, where the rigid cross sections have to remain perpendicular to the center line to reduce the full Cosserat beam model to a Kirchhoff beam model. We derive the equations of motion by Hamilton’s principle with an augmented Lagrangian. In order to fully discretize the beam model in space and time, we only consider piecewise interpolated configurations in the variational principle. This leads, after approximating the action integral with second order, to the discrete equations of motion. Here, it is notable that we allow the Lagrange multipliers to be discontinuous in time in order to respect the derivatives of the constraint equations, also known as hidden constraints. In the last part, we will test our numerical scheme on two benchmark problems that show that there is no shear locking observable in the discretized beam model and that the errors are observed to decrease with second order with the spatial step size and the time step size.

scholarly journals Multi-Degree of Freedom Propeller Force Models Based on a Neural Network and Regression

2020 ◽  
Vol 8 (2) ◽  
pp. 89 ◽  
Author(s):  
Bradford Knight ◽  
Kevin Maki
Keyword(s):  
Neural Network ◽  
Stokes Equations ◽  
Equations Of Motion ◽  
Open Water ◽  
Small Time ◽  
Training Data ◽  
Step Size ◽  
Time Step ◽  
Neural Network Approach ◽  
Time Step Size

Accurate and efficient prediction of the forces on a propeller is critical for analyzing a maneuvering vessel with numerical methods. CFD methods like RANS, LES, or DES can accurately predict the propeller forces, but are computationally expensive due to the need for added mesh discretization around the propeller as well as the requisite small time-step size. One way of mitigating the expense of modeling a maneuvering vessel with CFD is to apply the propeller force as a body force term in the Navier–Stokes equations and to apply the force to the equations of motion. The applied propeller force should be determined with minimal expense and good accuracy. This paper examines and compares nonlinear regression and neural network predictions of the thrust, torque, and side force of a propeller both in open water and in the behind condition. The methods are trained and tested with RANS CFD simulations. The neural network approach is shown to be more accurate and requires less training data than the regression technique.

Scaling of Constraints and Augmented Lagrangian Formulations in Multibody Dynamics Simulations

2009 ◽  
Vol 4 (2) ◽  
Author(s):  
Olivier A. Bauchau ◽  
Alexander Epple ◽  
Carlo L. Bottasso
Keyword(s):  
Physical Properties ◽  
Augmented Lagrangian ◽  
Equations Of Motion ◽  
Time Integration ◽  
Differential Algebraic Equations ◽  
Algebraic Equations ◽  
Step Size ◽  
Time Step ◽  
Time Step Size ◽  
Integration Schemes

This paper addresses practical issues associated with the numerical enforcement of constraints in flexible multibody systems, which are characterized by index-3 differential algebraic equations (DAEs). The need to scale the equations of motion is emphasized; in the proposed approach, they are scaled based on simple physical arguments, and an augmented Lagrangian term is added to the formulation. Time discretization followed by a linearization of the resulting equations leads to a Jacobian matrix that is independent of the time step size, h; hence, the condition number of the Jacobian and error propagation are both O(h0): the numerical solution of index-3 DAEs behaves as in the case of regular ordinary differential equations (ODEs). Since the scaling factor depends on the physical properties of the system, the proposed scaling decreases the dependency of this Jacobian on physical properties, further improving the numerical conditioning of the resulting linearized equations. Because the scaling of the equations is performed before the time and space discretizations, its benefits are reaped for all time integration schemes. The augmented Lagrangian term is shown to be indispensable if the solution of the linearized system of equations is to be performed without pivoting, a requirement for the efficient solution of the sparse system of linear equations. Finally, a number of numerical examples demonstrate the efficiency of the proposed approach to scaling.

Application of the Modified Rosenbrock Algorithm for Transient Rotordynamic Analysis

2012 ◽  
Author(s):  
Anand Srinivasan ◽  
Dhruv Kumar
Keyword(s):  
Numerical Integration ◽  
Equations Of Motion ◽  
Mathematical Formulation ◽  
Single Step ◽  
Degree Of Freedom ◽  
Step Size ◽  
Time Step ◽  
Time Step Size ◽  
Forcing Function ◽  
Transient Simulations

It is well known that transient rotordynamic analyses involve numerical integration of the equations of motion in order to study the response of the system under an applied forcing function. A common problem that arises in such simulations is the choice of step-size that needs to be used to obtain numerically stable results. Traditional numerical integration techniques such as the Runge-Kutta algorithms not only require splitting up second order differential equations as two first order equations, but also necessitate multiple integrations at each time-step, thus increasing the solution time. The Newmark-beta and Wilson-theta algorithms are some of the prevalent methods that have been used for transient simulations in rotordynamics. However, those single-step methods are only conditionally stable, and require iterations to converge to a solution at each time step, thus making it pseudosingle-step. In the more recent years, a modified form of the Rosenbrock algorithm has been proposed as a numerically stable and true single-step mathematical formulation for the integration of structural dynamics problems. In this paper, the modified Rosenbrock algorithm has been applied to a transient start-up multi-degree-of-freedom rotordynamics problem. A constant time step-size algorithm has been used for the simulations, and results of the transient analysis have been presented. The fact that a multi-degree-of-freedom system can be solved without condensation of the higher order modes makes the superior numerical damping characteristics of the algorithm become evident.

scholarly journals Analysis of a Decoupled Time-Stepping Scheme for Evolutionary Micropolar Fluid Flows

2016 ◽  
Vol 2016 ◽  
pp. 1-13 ◽  
Author(s):  
S. S. Ravindran
Keyword(s):  
Micropolar Fluid ◽  
Stokes Equations ◽  
Fluid Model ◽  
Navier Stokes ◽  
Optimal Order ◽  
Step Size ◽  
Time Step ◽  
Order Error ◽  
Time Step Size ◽  
Time Stepping

Micropolar fluid model consists of Navier-Stokes equations and microrotational velocity equations describing the dynamics of flows in which microstructure of fluid is important. In this paper, we propose and analyze a decoupled time-stepping algorithm for the evolutionary micropolar flow. The proposed method requires solving only one uncoupled Navier-Stokes and one microrotation subphysics problem per time step. We derive optimal order error estimates in suitable norms without assuming any stability condition or time step size restriction.

On the Influence of Inflow Model Selection for Time-Domain Tiltrotor Aeroelastic Analysis

2021 ◽  
Author(s):  
Ethan Corle ◽  
Matthew Floros ◽  
Sven Schmitz
Keyword(s):  
Experimental Data ◽  
Particle Method ◽  
Comprehensive Analysis ◽  
Solution Stability ◽  
Step Size ◽  
Time Step ◽  
Time Step Size ◽  
Vortex Particle Method ◽  
Whirl Flutter ◽  
Vortex Particle

The methods of using the viscous vortex particle method, dynamic inflow, and uniform inflow to conduct whirl-flutter stability analysis are evaluated on a four-bladed, soft-inplane tiltrotor model using the Rotorcraft Comprehensive Analysis System. For the first time, coupled transient simulations between comprehensive analysis and a vortex particle method inflow model are used to predict whirl-flutter stability. Resolution studies are performed for both spatial and temporal resolution in the transient solution. Stability in transient analysis is noted to be influenced by both. As the particle resolution is refined, a reduction in simulation time-step size must also be performed. An azimuthal time step size of 0.3 deg is used to consider a range of particle resolutions to understand the influence on whirl-flutter stability predictions. Comparisons are made between uniform inflow, dynamic inflow, and the vortex particle method with respect to prediction capabilities when compared to wing beam-bending frequency and damping experimental data. Challenges in assessing the most accurate inflow model are noted due to uncertainty in experimental data; however, a consistent trend of increasing damping with additional levels of fidelity in the inflow model is observed. Excellent correlation is observed between the dynamic inflow predictions and the vortex particle method predictions in which the wing is not part of the inflow model, indicating that the dynamic inflow model is adequate for capturing damping due to the induced velocity on the rotor disk. Additional damping is noted in the full vortex particle method model, with the wing included, which is attributed to either an interactional aerodynamic effect between the rotor and the wing or a more accurate representation of the unsteady loading on the wing due to induced velocities.

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