Torsion Angle Refinement and Dynamics as a Tool to Aid Crystallographic Structure Determination

2009 ◽  
Author(s):  
Ralf W. Grosse-Kunstleve ◽  
Nigel W. Moriarty ◽  
Paul D. Adams
Keyword(s):  
Torsion Angle ◽  
Data Bank ◽  
Optimization Methods ◽  
Rigid Body Dynamics ◽  
Optimization Techniques ◽  
Conformational Space ◽  
Crystallographic Structure ◽  
Local Minima ◽  
Body Dynamics ◽  
Angle Space

Crystallographic methods using experimental diffraction data have produced about 85% of the macromolecular structures in the Protein Data Bank. Before deposition, nearly all crystal structures are refined with gradient-driven optimization techniques. Refinement is typically performed with iterative local optimization methods. A common problem is convergence to local minima. Reparameterization of the model in torsion angle space reduces the number of parameters. This in itself can help to escape from local minima. Combination with rigid-body dynamics algorithms results in an important tool for sampling conformational space. This paper presents the torsion angle refinement and dynamics algorithms implemented for the phenix.refine program and the results of various tests.

scholarly journals Slipping–rolling transitions of a body with two contact points

2021 ◽  
Author(s):  
Mate Antali ◽  
Gabor Stepan
Keyword(s):  
Rigid Body ◽  
Contact Point ◽  
Static Friction ◽  
Rigid Body Dynamics ◽  
Contact Forces ◽  
Friction Forces ◽  
Contact Points ◽  
Body Dynamics ◽  
Coulomb Model ◽  
Rigid Surfaces

AbstractIn this paper, the general kinematics and dynamics of a rigid body is analysed, which is in contact with two rigid surfaces in the presence of dry friction. Due to the rolling or slipping state at each contact point, four kinematic scenarios occur. In the two-point rolling case, the contact forces are undetermined; consequently, the condition of the static friction forces cannot be checked from the Coulomb model to decide whether two-point rolling is possible. However, this issue can be resolved within the scope of rigid body dynamics by analysing the nonsmooth vector field of the system at the possible transitions between slipping and rolling. Based on the concept of limit directions of codimension-2 discontinuities, a method is presented to determine the conditions when the two-point rolling is realizable without slipping.

Time-Accurate Simulation of Longitudinal Flight Mechanics with Control by CFD/RBD Coupling

2012 ◽  
Vol 226-228 ◽  
pp. 788-792 ◽  
Author(s):  
Dong Guo ◽  
Min Xu ◽  
Shi Lu Chen
Keyword(s):  
Computational Study ◽  
Rigid Motion ◽  
Rigid Body Dynamics ◽  
Flight Mechanics ◽  
Control Surface ◽  
Free Flight ◽  
Body Dynamics ◽  
Computational Fluid Dynamics Cfd ◽  
Coupled Solution ◽  
Surface Deflections

This paper describes a multidisciplinary computational study undertaken to compute the flight trajectories and simultaneously predict the unsteady free flight aerodynamics of aircraft in time domain using an advanced coupled computational fluid dynamics (CFD)/rigid body dynamics (RBD) technique. This incorporation of the flight mechanics equations and controller into the CFD solver loop and the treatment of the mesh, which must move with both the control surface deflections and the rigid motion of the aircraft, are illustrated. This work is a contribution to a wider effort towards the simulation of aeroelastic and flight stability in regions where nonlinear aerodynamics, and hence potentially CFD, can play a key role. Results demonstrating the coupled solution are presented.

New solutions of classical problems in rigid body dynamics

2015 ◽  
Vol 69 ◽  
pp. 40-44
Author(s):  
H.M. Yehia ◽  
E. Saleh ◽  
S.F. Megahid
Keyword(s):  
Rigid Body ◽  
Rigid Body Dynamics ◽  
Body Dynamics

scholarly journals In Silico Single-Molecule Manipulation of DNA with Rigid Body Dynamics

2014 ◽  
Vol 10 (2) ◽  
pp. e1003456 ◽  
Author(s):  
Pascal Carrivain ◽  
Maria Barbi ◽  
Jean-Marc Victor
Keyword(s):  
Rigid Body ◽  
Single Molecule ◽  
In Silico ◽  
Rigid Body Dynamics ◽  
Body Dynamics ◽  
Single Molecule Manipulation

Optimal Design of a 4-DOF SCARA Type Parallel Robot Using Dynamic Performance Indices and Angular Constraints

2012 ◽  
Vol 4 (3) ◽  
Author(s):  
Songtao Liu ◽  
Tian Huang ◽  
Jiangping Mei ◽  
Xueman Zhao ◽  
Panfeng Wang ◽  
...  
Keyword(s):  
Optimal Design ◽  
Dynamic Performance ◽  
Parallel Robot ◽  
Singularity Analysis ◽  
Rigid Body Dynamics ◽  
Performance Indices ◽  
Global Dynamic ◽  
Transmission Angle ◽  
Body Dynamics ◽  
Rigid Design

This paper deals with the optimal design of a 4-DOF SCARA type (three translations and one rotation) parallel robot using dynamic performance indices and angular constraints within and amongst limbs. The architecture of the robot is briefly addressed with emphasis on the mechanical realization of the articulated traveling plate for achieving a lightweight yet rigid design. On the basis of the kinematic singularity analysis, two types of transmission angle constraints are considered to ensure the kinematic performance. A simplified model of rigid body dynamics is then formulated, with which two global dynamic performance indices are proposed for minimization by taking into account both inertial and centrifugal/Coriolis effects. In addition, the servomotor specifications are estimated using the Extended Adept Cycle. The proposed approach has successfully been employed to develop a prototype machine.

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 Easy Tracking of UAV Using PID Controller

2018 ◽  
Vol 47 (3) ◽  
pp. 171-177 ◽  
Author(s):  
Satla Zouaoui ◽  
Elajrami Mohamed ◽  
Bendine Kouider
Keyword(s):  
Pid Controller ◽  
Controller Design ◽  
Rigid Body Dynamics ◽  
Simulation Studies ◽  
Simple Strategy ◽  
Matlab Program ◽  
Fluid Velocities ◽  
Body Dynamics ◽  
Pid Controller Design ◽  
Surrounding Fluid

The main objective of the present paper is to design a mathematical model to estimate the behavior of flying robots with four motors (quadcopters) controlled by three algorithms; P depends on the present errors; I on the accumulation of past errors, and D a prediction of future errors (PID controller design) with simple strategy. In this regard, a governing equation of motion based on Newton Euler’s formularies for rigid body dynamics is presented. In order to design the control algorithm some assumptions are made such as the ignorance of the blade flapping, surrounding fluid velocities. This exclusion of parameters makes the model flexible, simple, and allows the control to be more efficiency and easy to designed without the need of expensive computation. The simulation studies are carried out using MATLAB program.

On so‐called singular constraints in rigid‐body dynamics

1986 ◽  
Vol 54 (7) ◽  
pp. 585-586
Author(s):  
Stephen F. Felszeghy
Keyword(s):  
Rigid Body ◽  
Rigid Body Dynamics ◽  
Body Dynamics
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