Implementing a modeling software for animated protein-complex interactions using a physics simulation library

2014 ◽  
Vol 12 (06) ◽  
pp. 1442003 ◽  
Author(s):  
Yutaka Ueno ◽  
Shuntaro Ito ◽  
Akihiko Konagaya
Keyword(s):  
Three Dimensional ◽  
Rigid Body Dynamics ◽  
Dynamics Simulation ◽  
Molecular Models ◽  
Body Dynamics ◽  
Physics Simulation ◽  
Modeling Software ◽  
Physical Simulations ◽  
A Cell ◽  
Scripting Language

To better understand the behaviors and structural dynamics of proteins within a cell, novel software tools are being developed that can create molecular animations based on the findings of structural biology. This study proposes our method developed based on our prototypes to detect collisions and examine the soft-body dynamics of molecular models. The code was implemented with a software development toolkit for rigid-body dynamics simulation and a three-dimensional graphics library. The essential functions of the target software system included the basic molecular modeling environment, collision detection in the molecular models, and physical simulations of the movement of the model. Taking advantage of recent software technologies such as physics simulation modules and interpreted scripting language, the functions required for accurate and meaningful molecular animation were implemented efficiently.

Modeling a Flexible-Link Power Transmission System

1992 ◽  
Author(s):  
Maureen J. Murray ◽  
Thomas R. Canfield
Keyword(s):  
Power Transmission ◽  
Three Dimensional ◽  
Pilot Project ◽  
Rigid Body Dynamics ◽  
Computer Simulation Model ◽  
Flexible Link ◽  
Complex Action ◽  
3 Dimensional ◽  
Track System ◽  
Body Dynamics

Abstract The flexible link and sprocket system of a tracked vehicle was modeled as part of a supercomputing pilot project on a Cray X-MP supercomputer. This computer simulation model utilizes the ADAMS 3-dimensional rigid body dynamics code. Using this ADAMS model of the track system, engineers can simulate the complex action of this three dimensional mechanism, and, through the use of graphics, can illustrate the behavior of the interaction of the components in this track system.

scholarly journals Hamilton’s Equations With Euler Parameters for Rigid Body Dynamics Modeling

2004 ◽  
Vol 126 (1) ◽  
pp. 124-130 ◽  
Author(s):  
Ravishankar Shivarama ◽  
Eric P. Fahrenthold
Keyword(s):  
Rigid Body ◽  
Three Dimensional ◽  
Nonlinear Problems ◽  
Potential Energy Function ◽  
Rigid Body Dynamics ◽  
Dynamics Modeling ◽  
Euler Parameters ◽  
Strongly Nonlinear ◽  
Body Dynamics ◽  
General Potential

A combination of Euler parameter kinematics and Hamiltonian mechanics provides a rigid body dynamics model well suited for use in strongly nonlinear problems involving arbitrarily large rotations. The model is unconstrained, free of singularities, includes a general potential energy function and a minimum set of momentum variables, and takes an explicit state space form convenient for numerical implementation. The general formulation may be specialized to address particular applications, as illustrated in several three dimensional example problems.

DESIGN AND IMPLEMENTATION OF REAL-TIME PHYSICS SIMULATION ENGINE FOR e-ENTERTAINMENT

2013 ◽  
Vol 04 (supp01) ◽  
pp. 1340002
Author(s):  
MYUNGSOO BAE ◽  
YOUNG J. KIM
Keyword(s):  
Real Time ◽  
Computer Games ◽  
Rigid Body Dynamics ◽  
Dynamics Simulation ◽  
Scale Model ◽  
Simulation Engine ◽  
Physics Engine ◽  
Model Control ◽  
Physics Simulation ◽  
Functional Components

We present our recent research results regarding the designing and implementation of real-time physics simulation engines, which aim at developing physics-inspired e-entertainment such as computer games, mobile applications, interactive TV and other smart media in Korea. Our real-time physics engine consists of three functional components: rigid body dynamics simulation, deformable body simulation, and data-driven physics simulation. The core simulation techniques to realize these simulation components include real-time collision detection and response, large-scale model simulation, and character model control. In this paper, we highlight these features and demonstrate their performances. We also showcase some of the gaming applications that we have integrated our physics engine into.

scholarly journals Rotation of Lipids in Membranes: Molecular Dynamics Simulation, 31P Spin-Lattice Relaxation, and Rigid-Body Dynamics

2008 ◽  
Vol 94 (8) ◽  
pp. 3074-3083 ◽  
Author(s):  
Jeffery B. Klauda ◽  
Mary F. Roberts ◽  
Alfred G. Redfield ◽  
Bernard R. Brooks ◽  
Richard W. Pastor
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Rigid Body ◽  
Lattice Relaxation ◽  
Rigid Body Dynamics ◽  
Dynamics Simulation ◽  
Spin Lattice Relaxation ◽  
Spin Lattice ◽  
Body Dynamics

scholarly journals Towards Billion-Body Dynamics Simulation of Granular Material

2012 ◽  
Author(s):  
Rebecca Shotwell ◽  
Dan Negrut
Keyword(s):  
Granular Material ◽  
Software Package ◽  
Dynamics Simulation ◽  
Engine Simulation ◽  
Software Models ◽  
Body Dynamics ◽  
Modeling Software ◽  
Commercial Software Package ◽  
Two Bodies ◽  
Made In

Advances are being made in the simulation of granular material, such that billion- body simulations are, perhaps, feasible using a combination of existing hardware and new modeling software technology. This capability is predicted to lead to a better understanding of granular materials, contributing to many areas of research. However, these capabilities are only useful if they are shown to agree well with reality. Beginning at a simple level, a study was conducted to compare the simulation of primitive joints in the Chrono::Engine simulation package with the MSC/ADAMS commercial software package. This simple effort provides a measure for the accuracy with which the software models the interaction of a joint and one or two bodies. This allows more complex analyses to be carried out with knowledge of the software’s accuracy at this level. 

Research on Dynamic Balance of Linkage Considering the Influence of Elastic Deformation Based on Simulation

2012 ◽  
Vol 217-219 ◽  
pp. 1465-1470
Author(s):  
Qi Bing Li ◽  
Yu Huang
Keyword(s):  
Objective Function ◽  
Elastic Deformation ◽  
Dynamic Balance ◽  
Three Dimensional ◽  
Geometrical Shape ◽  
Three Dimensional Modeling ◽  
Dimensional Modeling ◽  
Body Dynamics ◽  
Modeling Software ◽  
Multi Body

A method based on mechanical kinetics, Virtual Prototype technology and Finite Element Method (FEM) is proposed, aiming at the dynamic balance of planar linkage with elastic deformation. The method applies to the situation that the elastic deformation of the components can’t be neglected. Translate the key components to flexible bodies by FEM; Build the rigid-flexible multi-body dynamics model by dynamic analysis software, and synthetically optimize the dynamic balance of the model by using the comprehensive indicator which includes input torque, shaking force and moment as the objective function; Finally, according to the parameter result of the previous optimization, the component’s geometrical shape was designed in three-dimensional modeling software. Taking a kind of crank-slide mechanism as an example, it uses this method to optimize a crank-slide mechanism’s dynamic balance and to make the objective function value declined by about 9.2%. The mechanism’s vibration characteristic is improved, so the method is proved to be practical and effective.

Validation of a Computational Musculoskeletal Model of the Elbow

2007 ◽  
Author(s):  
Justin P. Fisk ◽  
Jennifer S. Wayne
Keyword(s):  
Rigid Body ◽  
Degrees Of Freedom ◽  
Three Dimensional ◽  
Rigid Body Dynamics ◽  
Clinical Tool ◽  
Element Analysis ◽  
Reconstructive Procedures ◽  
Biomechanical Models ◽  
Musculoskeletal Models ◽  
Body Dynamics

Musculoskeletal computational modeling can be a powerful and useful tool to study joint behavior, examine muscle and ligament function, measure joint contact pressures, simulate injury, and analyze the biomechanical results of reconstructive procedures. Commonly, biomechanical models are based on either finite element analysis (FEA) or three-dimensional rigid body dynamics. While each approach has advantages for specific applications, rigid body dynamics algorithms are highly efficient [1], thus significantly reducing solution time. Many musculoskeletal models of the elbow have been developed [2, 3], but all have constrained the articulations to have particular degrees of freedom and ignored the effects of ligaments. An accurate and robust model without these limitations has potential as a clinical tool to predict the outcome of injuries and/or surgical procedures. This work develops and validates an accurate computational model of the elbow joint whereby joint kinematics are dictated by three-dimensional bony geometry contact, ligamentous constraints, and muscle loading.

Vibrating Simulation of Diesel Engine Based on Multi-Body Dynamics

2011 ◽  
Vol 97-98 ◽  
pp. 706-711 ◽  
Author(s):  
Kang Shao ◽  
Chang Wen Liu ◽  
Fong Rong Bi ◽  
Xian Feng Du ◽  
Xia Wang ◽  
...  
Keyword(s):  
Diesel Engine ◽  
System Analysis ◽  
Simulation Analysis ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Main Bearing ◽  
Engine Vibration ◽  
Body Dynamics ◽  
Flexible Body Dynamics ◽  
Multi Body

Taking example of a four-cylinder inline diesel engine that used in vehicle, this paper makes an assembly engine of three-dimensional that based on virtual prototype technology. While using the flexible-body dynamics simulation, the main bearing load that effect engine’s vibration will be gained. And the key point vibration response will be gained when the support part constrained. The experimental results coincide with the simulation results shows the correction of the simulation analysis. The initial stage of the vibration can be predicted by using the method of multi-body system analysis, and this guide the designer to identify the engine vibration.

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