ProtoFold: Part I — Nanokinematics for Analysis of Protein Molecules

2004 ◽  
Author(s):  
Kazem Kazerounian ◽  
Khalid Latif ◽  
Kimberly Rodriguez ◽  
Carlos Alvarado
Keyword(s):  
Three Dimensional ◽  
Linear Structure ◽  
Rigid Bodies ◽  
Dynamics Simulation ◽  
Kinematic Chains ◽  
Simulation Techniques ◽  
Revolute Joints ◽  
Zero Position ◽  
Ab Initio Prediction ◽  
Protein Molecules

Proteins are evolution’s mechanisms of choice. Study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. ProtoFold is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In this paper, we present the methods utilized in the kinematics notion and kinematics analysis of protein molecules. The kinematics portion of ProtoFold incorporates the Zero-Position Analysis Method and draws upon other recent advances in robot manipulation theories. We claim that the methodology presented is a computationally superior and more stable alternative to traditional molecular dynamics simulation techniques.

Nano-Kinematics for Analysis Of Protein Molecules

2004 ◽  
Vol 127 (4) ◽  
pp. 699-711 ◽  
Author(s):  
Kazem Kazerounian ◽  
Khalid Latif ◽  
Kimberly Rodriguez ◽  
Carlos Alvarado
Keyword(s):  
Software Package ◽  
Three Dimensional ◽  
Computer Software ◽  
Linear Structure ◽  
Data Bank ◽  
Kinematic Parameter ◽  
Rigid Bodies ◽  
Protein Chain ◽  
Kinematic Chains ◽  
Protein Molecules

Proteins are evolution’s mechanisms of choice. The study of nano-mechanical systems must encompass an understanding of the geometry and conformation of protein molecules. Proteins are open or closed loop kinematic chains of miniature rigid bodies connected by revolute joints. The Kinematics community is in a unique position to extend the boundaries of knowledge in nano biomechanical systems. In this work, we have presented a comprehensive methodology for kinematics notation and direct kinematics for protein molecules. These methods utilize the zero-position analysis method and draws upon other recent advances in robot manipulation theories. The procedures involved in finding the coordinates of every atom in the protein chain as a function of the dihedral and Rotamer angles are computationally the most efficient formulation developed to date. The notation and the methodologies of this paper are incorporated in the computer software package PROTOFOLD and will be made available to individuals interested in using it. PROTOFOLD is a software package that implements novel and comprehensive methodologies for ab initio prediction of the final three-dimensional conformation of a protein, given only its linear structure. In addition to the new kinematics methodologies mentioned above, we have also included all the basic kinematic parameter values that are needed in any kinematic analysis involving proteins. While these values are based on a body of knowledge recorded in the protein data bank, they are presented in a form conducive to kinematics.

Evaluation of a Possible Role of Stigmatella aurantiaca ACE in Aβ Peptide Degradation: A Molecular Modeling Approach

2015 ◽  
Vol 25 (1) ◽  
pp. 26-36 ◽  
Author(s):  
Chidambar B. Jalkute ◽  
Kailas D. Sonawane
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Three Dimensional ◽  
Amyloid Β ◽  
Dynamics Simulation ◽  
Aβ Peptide ◽  
Three Dimensional Model ◽  
Aβ Peptides ◽  
Simulation Techniques ◽  
Stigmatella Aurantiaca

Amyloid-β (Aβ)-degrading enzymes are known to degrade Aβ peptides, a causative agent of Alzheimer's disease. These enzymes are responsible for maintaining Aβ concentration. However, loss of such enzymes or their Aβ-degrading activity because of certain genetic as well as nongenetic reasons initiates the accumulation of Aβ peptides in the human brain. Considering the limitations of the human enzymes in clearing Aβ peptide, the search for microbial enzymes that could cleave Aβ is necessary. Hence, we built a three-dimensional model of angiotensin-converting enzyme (ACE) from <i>Stigmatella aurantiaca</i> using homology modeling technique. Molecular docking and molecular dynamics simulation techniques were used to outline the possible cleavage mechanism of Aβ peptide. These findings suggest that catalytic residue Glu 434 of the model could play a crucial role to degrade Aβ peptide between Asp 7 and Ser 8. Thus, ACE from <i>S. aurantiaca</i> might cleave Aβ peptides similar to human ACE and could be used to design new therapeutic strategies against Alzheimer's disease.

Self-Collision Detection in Spatial Closed Chains

2008 ◽  
Vol 130 (9) ◽  
Author(s):  
John S. Ketchel ◽  
Pierre M. Larochelle
Keyword(s):  
Motion Planning ◽  
Finite Length ◽  
Collision Detection ◽  
Three Dimensional ◽  
Detection Algorithm ◽  
Rigid Bodies ◽  
Three Dimensions ◽  
Circular Cylinders ◽  
Infinite Length ◽  
Kinematic Chains

A novel methodology for detecting self-collisions in spatial closed kinematic chains is presented. In general these chains generate complex three dimensional motions in which their own links will collide with each other (i.e., a self-collision) without effective motion planning. The self-collision detection is accomplished via a novel algorithm for definitively detecting collisions of right circular, cylindrically shaped, rigid bodies moving in three dimensions. The algorithm uses line geometry and dual number algebra to exploit the geometry of right circular cylindrical objects to facilitate the detection of collisions. In the first stage of the algorithm, cylindrically shaped rigid bodies are modeled by infinite length right circular cylinders. Sufficient and necessary conditions are then used to determine if a pair of infinite length cylinders collide. If the actual finite length rigid bodies collide, then it is necessary that their associate infinite length cylinder models collide, and we proceed to the next stage of the algorithm where the bodies are modeled with finite length cylinders and a definitive necessary and sufficient collision detection algorithm is employed. The result is an efficient approach of detecting collisions of cylindrically shaped bodies moving in three dimensions that has applications in spatial mechanism design and motion planning. A case study examining a spatial 4C mechanism for self-collisions is included.

Dynamics Simulation and Fatigue Life Study of the Drive System of Rack and Pinion Climbing Vertical Shiplift

2013 ◽  
Vol 456 ◽  
pp. 155-158
Author(s):  
Xiao Qing Sun ◽  
Yang Zhang ◽  
Duan Wei Shi
Keyword(s):  
Fatigue Life ◽  
Three Dimensional ◽  
Dynamics Simulation ◽  
Combination Method ◽  
Bending Stress ◽  
Assembly Model ◽  
Load History ◽  
Life Study ◽  
Simulation Techniques ◽  
Design Requirements

A combination method of virtual simulation techniques was proposed for fatigue life of vertical shiplifts big modulus gear. A Three-dimensional assembly model of rack and pinion mechanism was established by SolidWorks and its plug GearTrax, then dynamics simulation was conducted based on ADAMS, the relative error between simulation results and static load was 2.2%, indicating the accuracy of the simulation. Bending stress of the big modulus gear was analysed by ANSYS, the error was 1.6% compared with the theoretical value. Using the obtained load history data and bending stress results, the big modulus gears fatigue life was predicted based on nominal stress method, the result showed that the big modulus gear could well meet the design requirements.

Three-dimensional predator–prey interactions: a computer simulation of bird flocks and aircraft

1986 ◽  
Vol 64 (11) ◽  
pp. 2624-2633 ◽  
Author(s):  
Peter F. Major ◽  
Lawrence M. Dill ◽  
David M. Eaves
Keyword(s):  
Computer Simulation ◽  
Prey Species ◽  
Three Dimensional ◽  
Aircraft Engine ◽  
Aquatic Environments ◽  
Aircraft Engines ◽  
Predator Prey ◽  
Simulation Techniques ◽  
Computer Simulation Techniques ◽  
Individual Prey

Three-dimensional interactions between grouped aerial predators (frontal discs of aircraft engines), either linearly arrayed or clustered, and flocks of small birds were studied using interactive computer simulation techniques. Each predator modelled was orders of magnitude larger than an individual prey, but the prey flock was larger than each predator. Expected numbers of individual prey captured from flocks were determined for various predator speeds and trajectories, flock–predator initial distances and angles, and flock sizes, shapes, densities, trajectories, and speeds. Generally, larger predators and clustered predators caught more prey. The simulation techniques employed in this study may also prove useful in studies of predator–prey interactions between schools or swarms of small aquatic prey species and their much larger vertebrate predators, such as mysticete cetaceans.The study also provides a method to study problems associated with turbine aircraft engine damage caused by the ingestion of small flocking birds, as well as net sampling of organisms in open aquatic environments.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

Design and operation of a tripod walking robot via dynamics simulation

Robotica ◽  
2010 ◽  
Vol 29 (5) ◽  
pp. 733-743 ◽  
Author(s):  
Conghui Liang ◽  
Hao Gu ◽  
Marco Ceccarelli ◽  
Giuseppe Carbone
Keyword(s):  
Mechanical Design ◽  
Low Cost ◽  
Three Dimensional ◽  
The Body ◽  
Dynamics Simulation ◽  
Walking Ability ◽  
Walking Robot ◽  
Three Dimensional Model ◽  
Software Environment ◽  
Leg Mechanisms

SUMMARYA mechanical design and dynamics walking simulation of a novel tripod walking robot are presented in this paper. The tripod walking robot consists of three 1-degree-of-freedom (DOF) Chebyshev–Pantograph leg mechanisms with linkage architecture. A balancing mechanism is mounted on the body of the tripod walking robot to adjust its center of gravity (COG) during walking for balancing purpose. A statically stable tripod walking gait is performed by synchronizing the motions of the three leg mechanisms and the balancing mechanism. A three-dimensional model has been elaborated in SolidWorks® engineering software environment for a characterization of a feasible mechanical design. Dynamics simulation has been carried out in the MSC.ADAMS® environment with the aim to characterize and to evaluate the dynamic walking performances of the proposed design with low-cost easy-operation features. Simulation results show that the proposed tripod walking robot with proper input torques, gives limited reaction forces at the linkage joints, and a practical feasible walking ability on a flatten ground.

Modeling of a dry low nitrogen oxides burner using a three-dimensional computational fluid dynamics simulation

2021 ◽  
pp. 095440892110355
Author(s):  
Guodong Sun ◽  
Xuejing Duan ◽  
Bo Hao ◽  
Afshin Davarpanah
Keyword(s):  
Nitrogen Oxides ◽  
Greenhouse Gases ◽  
Power Plants ◽  
Three Dimensional ◽  
Control Policy ◽  
Dynamics Simulation ◽  
Weather Patterns ◽  
United Nations General ◽  
Fluent Software ◽  
Low Nitrogen

Nitrogen oxides are considered as one of the greenhouse gases. Among the most significant emission sources for this gas is a natural gas-fired power plant. The United Nations General assembly suggested in 1988 that human activities can negatively impact weather patterns, and thus they should be controlled. This control policy can improve the efficiency of final consumers such as power plants, cars, or other energy-intensive industries. In this paper, the existing strategies and explicitly making the dry low nitrogen oxides burner reduce greenhouse gases in power plants are explored. The geometry of the burner has been produced in a three-dimensional form in GAMBIT software, and the results of the simulation have been expressed through FLUENT software. Contours of pressure, temperature, and velocity of the fluid in the furnace are also derived. It is concluded that the dry low nitrogen oxides burners plan has a better result compared with other strategies.

Sign in / Sign up

Export Citation Format

Share Document