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.

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.

Nonlinear Forced Vibration Analysis of Smart Curved CNTs Conveying Fluid

2021 ◽  
Author(s):  
Vahid Mohamadhashemi ◽  
Amir Jalali ◽  
Habib Ahmadi
Keyword(s):  
Carbon Nanotube ◽  
Velocity Vector ◽  
Multiple Scales ◽  
Fluid Velocity ◽  
Equations Of Motion ◽  
Primary Resonance ◽  
Maximum Amplitude ◽  
Beam Theory ◽  
Physical Parameters ◽  
Conveying Fluid

In this study, the nonlinear vibration of a curved carbon nanotube conveying fluid is analyzed. The nanotube is assumed to be covered by a piezoelectric layer and the Euler–Bernoulli beam theory is employed to establish the governing equations of motion. The influence of carbon nanotube curvature on structural modeling and fluid velocity vector is considered and the slip boundary conditions of CNT conveying fluid are included. The mathematical modeling of the structure is developed using Hamilton’s principle and then, the Galerkin procedure is employed to discretize the equation of motion. Furthermore, the frequency response of the system is extracted by applying the multiple scales method of perturbation. Finally, a comprehensive study is carried out on the primary resonance and piezoelectric-based parametric resonance of the system. It is shown that consideration of nanotube curvature may lead to an increase in nonlinearity. Implementing the fluid velocity vector in which nanotube curvature is included highly affects the maximum amplitude of the response and should not be ignored. Furthermore, different system parameters have evident impacts on the behavior of the system and therefore, selecting the reasonable geometrical and physical parameters of the system can be very useful to achieve a favorable response.

Development of the Finite Segment Method for Modeling Railroad Track Structures

2011 ◽  
Author(s):  
Martin B. Hamper ◽  
Khaled E. Zaazaa ◽  
Ahmed A. Shabana
Keyword(s):  
Sparse Matrix ◽  
Deformable Body ◽  
Contact Point ◽  
Equations Of Motion ◽  
Variable Step Size ◽  
Variable Order ◽  
Step Size ◽  
Finite Segment ◽  
Finite Segment Method ◽  
Railroad Vehicle

In the finite segment method, the dynamics of a deformable body is described using a set of rigid bodies that are connected by elastic force elements. This approach can be used, as demonstrated in this investigation, in the simulation of some rail movement scenarios. The purpose of this investigation is to develop a new track model that combines the absolute nodal coordinate formulation (ANCF) geometry and the finite segment method. The ANCF finite elements define the track geometry in the reference configuration as well as the change in the geometry due to the movement of the finite segments of the track. Using ANCF geometry and the finite segment kinematics, the location of the wheel/rail contact point is predicted online and used to update the creepage expressions due to the finite segment displacements and rotations. The location of the wheel/rail contact point and the updated creepage expressions are used to evaluate the creep forces. A three-dimensional elastic contact formulation (ECF-A), that allows for wheel/rail separation, is used in this investigation. The rail displacement due to the applied loads is modeled by a set of rigid finite segments that are connected by set of spring-damper elements. Each rail finite segment is assumed to have six rigid body degrees of freedom. The equations of motion of the finite segments are integrated with the railroad vehicle system equations of motion in a sparse matrix formulation. The resulting dynamic equations are solved using a predictor-corrector numerical integration method that has a variable order and variable step size. As shown in this paper, the finite segments may be used to model specific phenomena that occur in railroad vehicle applications, including rail rotations and gage widening. The procedure used in this investigation to implement the finite segment method in a general purpose multibody system (MBS) computer program is described. Four simple models are presented in order to demonstrate the implementation of the finite segment method in MBS algorithms. The limitations of using the finite segments approach for modeling the track structure and rail flexibility are also discussed.

Nonlinear Vibrations of Two-Span Composite Laminated Plates with Equal and Unequal Subspan Lengths

2017 ◽  
Vol 9 (6) ◽  
pp. 1485-1505
Author(s):  
Lingchang Meng ◽  
Fengming Li
Keyword(s):  
Multiple Scales ◽  
Equations Of Motion ◽  
Primary Resonance ◽  
Laminated Plates ◽  
Laminated Plate ◽  
Composite Laminated Plate ◽  
Vibration Localization ◽  
Composite Laminated Plates ◽  
Localization Phenomenon ◽  
Harmonic Resonance

AbstractThe nonlinear transverse vibrations of ordered and disordered two-dimensional (2D) two-span composite laminated plates are studied. Based on the von Karman's large deformation theory, the equations of motion of each-span composite laminated plate are formulated using Hamilton's principle, and the partial differential equations are discretized into nonlinear ordinary ones through the Galerkin's method. The primary resonance and 1/3 sub-harmonic resonance are investigated by using the method of multiple scales. The amplitude-frequency relations of the steady-state responses and their stability analyses in each kind of resonance are carried out. The effects of the disorder ratio and ply angle on the two different resonances are analyzed. From the numerical results, it can be concluded that disorder in the length of the two-span 2D composite laminated plate will cause the nonlinear vibration localization phenomenon, and with the increase of the disorder ratio, the vibration localization phenomenon will become more obvious. Moreover, the amplitude-frequency curves for both primary resonance and 1/3 sub-harmonic resonance obtained by the present analytical method are compared with those by the numerical integration, and satisfactory precision can be obtained for engineering applications and the results certify the correctness of the present approximately analytical solutions.

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.

TSDT theory for free vibration of functionally graded plates with various material properties

2021 ◽  
Vol 8 (4) ◽  
pp. 691-704
Author(s):  
M. Janane Allah ◽  
◽  
Y. Belaasilia ◽  
A. Timesli ◽  
A. El Haouzi ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
Volume Fraction ◽  
Equations Of Motion ◽  
Shear Deformation Theory ◽  
Functionally Graded ◽  
Third Order ◽  
Implicit Algorithm ◽  
Proposed Model ◽  
Graded Material ◽  
Composite Modeling

In this work, an implicit algorithm is used for analyzing the free dynamic behavior of Functionally Graded Material (FGM) plates. The Third order Shear Deformation Theory (TSDT) is used to develop the proposed model. In this contribution, the formulation is written without any homogenization technique as the rule of mixture. The Hamilton principle is used to establish the resulting equations of motion. For spatial discretization based on Finite Element Method (FEM), a quadratic element with four and eight nodes is adopted using seven degrees of freedom per node. An implicit algorithm is used for solving the obtained problem. To study the accuracy and the performance of the proposed approach, we present comparisons with literature and laminate composite modeling results for vibration natural frequencies. Otherwise, we examine the influence of the exponent of the volume fraction which reacts the plates "P-FGM" and "S-FGM". In addition, we study the influence of the thickness on "E-FGM" plates.

scholarly journals A Study of the Stability of a Plate-Like Load Towed beneath a Helicopter

1971 ◽  
Vol 13 (5) ◽  
pp. 330-343 ◽  
Author(s):  
D. F. Sheldon
Keyword(s):  
Equations Of Motion ◽  
Physical Parameters ◽  
Recent Experience ◽  
Wind Tunnel Testing ◽  
Stability Derivatives ◽  
Direct Indication ◽  
Metric Dimensions ◽  
Set Up ◽  
The Stability ◽  
Derivative Information

Recent experience has shown that a plate-like load suspended beneath a helicopter moving in horizontal forward flight has unstable characteristics at both low and high forward speeds. These findings have prompted a theoretical analysis to determine the longitudinal and lateral dynamic stability of a suspended pallet. Only the longitudinal stability is considered here. Although it is strictly a non-linear problem, the usual assumptions have been made to obtain linearized equations of motion. The aerodynamic derivative data required for these equations have been obtained, where possible, for the appropriate ranges of Reynolds and Strouhal number by means of static and dynamic wind tunnel testing. The resulting stability equations (with full aerodynamic derivative information) have been set up and solved, on a digital computer, to give direct indication of a stable or unstable system for a combination of physical parameters. These results have indicated a longitudinal unstable mode for all practical forward speeds. Simultaneously the important stability derivatives were found for this instability and modifications were made subsequently in the suspension system to eliminate the instabilities in the longitudinal sense. Throughout this paper, all metric dimensions are given approximately.

scholarly journals Numerical Model for the Analysis of Thermal Transients in District Heating Networks

2020 ◽  
Vol 197 ◽  
pp. 01004
Author(s):  
Martina Capone ◽  
Elisa Guelpa ◽  
Vittorio Verda
Keyword(s):  
Carbon Dioxide Emissions ◽  
Renewable Energy Sources ◽  
Management Strategies ◽  
District Heating ◽  
Equivalent Model ◽  
Computational Time ◽  
Physical Parameters ◽  
Thermal Transients ◽  
Proposed Model ◽  
Wide Range

As District Heating (DH) networks are experiencing an evolution towards the so-called 4th generation, there is a need to update the currently used models to take into account the ever-increasing complexity of this technology. Indeed, to further improve the reduction in energy consumption and carbon-dioxide emissions, a wide range of technologies and management strategies are being introduced within district heating, such as a large exploitation of Renewable Energy Sources (RES). As a consequence, thermal transients assume a major importance, posing the need to redefine the relevant physical parameters and to develop a model which accurately describes their behaviour. In this framework, this paper proposes a quantitative analysis of the influence of the pipe heat-capacity on the model. Moreover, an equivalent-model, which is able to take into account the two heat capacities of steel and water in just one equation, is proposed and compared with two commonly used approaches. One of the features of the proposed model is the suitability for application to large networks. To prove its capabilities, an application to the Turin district heating network, which is among the largest systems in Europe, is proposed. Results show significant improvements in terms of accuracy over computational time ratio.

scholarly journals A Multidimensional and Multiscale Model for Pressure Analysis in a Reservoir-Pipe-Valve System

2018 ◽  
Author(s):  
Feng Jie Zheng ◽  
Fu Zheng Qu ◽  
Xue Guan Song
Keyword(s):  
Pressure Fluctuation ◽  
Large Scale ◽  
Three Dimensional ◽  
Industrial Process ◽  
Multiscale Model ◽  
Computational Time ◽  
Small Scale ◽  
Cfd Model ◽  
Computationally Efficient ◽  
Proposed Model

Reservoir-pipe-valve (RPV) systems are widely used in many industrial process. The pressure in an RPV system plays an important role in the safe operation of the system, especially during the sudden operation such as rapid valve opening/closing. To investigate the pressure especially the pressure fluctuation in an RPV system, a multidimensional and multiscale model combining the method of characteristics (MOC) and computational fluid dynamics (CFD) method is proposed. In the model, the reservoir is modeled by a zero-dimensional virtual point, the pipe is modeled by a one-dimensional MOC, and the valve is modeled by a three-dimensional CFD model. An interface model is used to connect the multidimensional and multiscale model. Based on the model, a transient simulation of the turbulent flow in an RPV system is conducted, in which not only the pressure fluctuation in the pipe but also the detailed pressure distribution in the valve are obtained. The results show that the proposed model is in good agreement with the full CFD model in both large-scale and small-scale spaces. Moreover, the proposed model is more computationally efficient than the CFD model, which provides a feasibility in the analysis of complex RPV system within an affordable computational time.

scholarly journals Fast Iterative model for Sequential-Selection-Based Applications

2014 ◽  
Vol 12 (7) ◽  
pp. 3689-3696 ◽  
Author(s):  
Khosrow Amirizadeh ◽  
Rajeswari Mandava
Keyword(s):  
Confidence Bound ◽  
Adaptive Model ◽  
Step Size ◽  
Simple Task ◽  
Iterative Model ◽  
Lack Of Information ◽  
Sequential Selection ◽  
Proposed Model ◽  
On Line ◽  
Upper Confidence Bound

Accelerated multi-armed bandit (MAB) model in Reinforcement-Learning for on-line sequential selection problems is presented. This iterative model utilizes an automatic step size calculation that improves the performance of MAB algorithm under different conditions such as, variable variance of reward and larger set of usable actions. As result of these modifications, number of optimal selections will be maximized and stability of the algorithm under mentioned conditions may be amplified. This adaptive model with automatic step size computation may attractive for on-line applications in which,  variance of observations vary with time and re-tuning their step size are unavoidable where, this re-tuning is not a simple task. The proposed model governed by upper confidence bound (UCB) approach in iterative form with automatic step size computation. It called adaptive UCB (AUCB) that may use in industrial robotics, autonomous control and intelligent selection or prediction tasks in the economical engineering applications under lack of information.

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