An Emerging O(N) Model and Algorithm for Virtual Prototyping of Dynamics of Molecular Conformation

2008 ◽  
Author(s):  
Andrew Ries ◽  
Shanzhong Shawn Duan
Keyword(s):  
Degrees Of Freedom ◽  
Molecular Conformation ◽  
Molecular System ◽  
Equations Of Motion ◽  
Integration Step ◽  
Computational Costs ◽  
System A ◽  
Hard Constraints ◽  
Solution Of Equations ◽  
Computationally Intensive

Molecular dynamics is effective for nano-scale phenomenon analysis. There are two major computational steps associated with computer simulation of dynamics of molecular conformation and they are the calculation of the interatomic forces and the formation and solution of the equations of motion. Currently, these two computational steps are treated separately, but in this paper an O(N) (order N) procedure is presented for an integration between these computational steps. For computational costs associated with calculating the interatomic forces, an internal coordinate method (ICM) approach is used for determining potentials due to both the bonding and non-bonding interactions. Thus, the potential gradients can be expressed as a combination of the potential in absolute and relative coordinates. For computational costs associated with the formation and solution of the equations of motion for the system, a constraint method that is used in computational multibody dynamics is utilized. This frees some degrees of freedom so that Kane’s method can be applied for the recursive formation and solution of equations of motion for the atomistic molecular system. Because the inclusion of lightly excited high frequency degrees of freedom, such as inter-atomic oscillations and rotation about double bonds would force the use of very small integration step sizes, holonomic constraints are introduced to freeze these “uninteresting” degrees of freedom. By introducing these hard constraints the time scale can be appropriately sized for to provide a less computationally intensive dynamic simulation of molecular conformation. The algorithm developed improves computational speed significantly when compared with any traditional O(N3) procedure.

An Efficient O(N) Algorithm for Computer Simulation of Rigid Body Molecular Dynamics

2007 ◽  
Author(s):  
Shanzhong Duan ◽  
Andrew Ries
Keyword(s):  
Molecular Dynamics ◽  
Computer Simulation ◽  
Degrees Of Freedom ◽  
Molecular System ◽  
Equations Of Motion ◽  
Interaction Forces ◽  
High Frequencies ◽  
Coordinate Method ◽  
Computational Costs ◽  
Solution Of Equations

Molecular dynamics is effective for a nano-scale phenomenon analysis. There are two major computational costs associated with computer simulation of atomistic molecular dynamics. They are calculation of the interaction forces and formation/solution of equations of motion. In this paper, an O(N) (order N) procedure is presented for calculation of the interaction forces and formation/solution of equations of motion. For computational costs associated with potentials or interaction forces, an internal coordinate method is used. Use of the internal coordinate method makes application of multi-rigid body molecular dynamics to an atomistic molecular system become possible. The algorithm based on the method makes the calculation considerably more practical for large-scale problems encountered in molecular dynamics such as conformation dynamics of polymers. For computational costs associated with formation/solution of equations of motion, Kane method and the internal coordinate method are used for recursive formation and solution of equations of motion of an atomistic molecular system. However, in computer simulation of atomistic molecular dynamics, the inclusion of lightly excited all degrees of freedom of an atom, such as inter-atomic oscillations and rotation about double bonds with high frequencies, introduces limitations to the simulation. The high frequencies of these degrees of freedom force the use of very small integration step sizes, which severely limit the time scales for the atomic molecular simulation over long periods of time. To improve this, holonomic constraints such as strictly constant bond lengths and bond angles are introduced to freeze these high frequency degrees of freedom since they have insignificant effect on long time scale processes in conformational dynamics. In this way, the procedure developed in multibody dynamics can be utilized to achieve higher computing efficiency and an O(N) computational performance can be realized for formation/solution of equations of motion.

Implementation of an Efficient Algorithm for Virtual Prototyping of Dynamics of Molecular Conformation

2009 ◽  
Author(s):  
Shanzhong Shawn Duan ◽  
Andrew Ries
Keyword(s):  
High Frequency ◽  
Efficient Algorithm ◽  
Molecular Conformation ◽  
Molecular System ◽  
Molecular Model ◽  
Virtual Prototyping ◽  
Molecular Chain ◽  
Integration Step ◽  
Computational Performance ◽  
Macro Scale

This paper presents an O(N) algorithm and its preliminary computer simulation results for virtual prototyping of molecular systems with a simple chain structure. The algorithm is based on proper integration between an internal coordinate method (ICM) and a multibody molecular model. ICM method makes the use of recursive relations possible between two adjacent subsets within a molecular system. The multibody molecular model takes the benefits of freezing degrees of freedom of some lightly excited high frequency bonds. Because these high frequency bonds would force the use of very small integration step sizes, which severely limits the time scales for virtual prototyping of dynamics of molecular conformation over long periods of time. Thus a new multiscale model and efficient algorithm is produced to increase computational efficiency for virtual prototyping of dynamical behaviors of molecular confirmation. This paper will be initially directed towards introduction of the new model and algorithm. Then attention will be turned to the implementation of the algorithm at macro scale, which can be used to demonstrate the validity of the procedure and algorithm. Final focus will be turned to the implementation of the algorithm to a simple molecular chain at micro scale. The algorithm gives an O(N) computational performance for formation/solution of equations of motion for a molecular chain system.

Effect of the mathematical model and integration step on the accuracy of the results of computation of artillery projectile flight parameters

2013 ◽  
Vol 61 (2) ◽  
pp. 475-484 ◽  
Author(s):  
L. Baranowski
Keyword(s):  
Mathematical Model ◽  
Mathematical Models ◽  
Degrees Of Freedom ◽  
Equations Of Motion ◽  
Integration Step ◽  
Six Degrees Of Freedom ◽  
Applied Model ◽  
Flight Parameters ◽  
The Mathematical Model ◽  
Artillery Projectile

Abstract In the paper the three different mathematical models of motion of a spin-stabilized, conventional artillery projectile, possessing at least trigonal symmetry, have been introduced. The vector six-degrees-of-freedom (6-DOF) differential equations of motion are an updated edition of those published by Lieske and McCoy and are consistent with STANAG 4355 (Ed. 3). The mathematical models have been used to developing software for simulating the flight of the Denel 155mm Assegai M2000 series artillery projectile and to conduct comprehensive research of the influence of the applied model and integration step on the accuracy and time of computation of projectile trajectory.

An Integrated Procedure for Computer Simulation of Dynamics of Multibody Molecular Structures in Polymers and Biopolymers

2015 ◽  
Author(s):  
Shanzhong (Shawn) Duan
Keyword(s):  
Computer Simulation ◽  
Molecular System ◽  
Fast Multipole Method ◽  
Equations Of Motion ◽  
Molecular Structures ◽  
Tree Structure ◽  
Fast Multipole ◽  
Computational Costs ◽  
Multipole Method ◽  
Multipole Methods

Though computational molecular dynamics is an effective tool for nano-scale phenomenon analysis, computational costs associated with its computer simulation are extremely high. There are two major computational steps associated with computer simulation of dynamics of molecular structures. They are calculation of interatomic forces and formation and solution of the equations of motion. Currently, these two computational steps are treated separately in most commonly-used methods. For example, Fast Multipole Method (FMM) and Cell Multipole Method (CMM) have been used for calculation of interatomic forces, and Cartesian Coordinate Method (CCM) and Internal Coordinate Molecular Dynamics Method (ICMD) have been created for the formation and solution of equations of motion of an atomistic molecular system. In this paper, a new procedure is presented through a proper integration between multibody molecular algorithms (MMA) and fast multipole methods to improve computational efficiency for computer simulation of the dynamical behaviors of multibody molecular structures in polymers and biopolymers. For the computational costs associated with interatomic forces, a fast multipole method is used to calculate the interatomic forces due to the potentials. For the computational costs associated with formation and solution of equations of motion, a multibody molecular algorithm developed by the author in his previous work will be utilized to integrate with fast multipole methods. The algorithm significantly improves computational efficiency when comparing with its counterpart procedures. The fast multipole method begins by scaling all atoms into a box with coordinate ranges to ensure numerical stability of subsequent operations. The parent box is then divided into half in the direction of each Cartesian axis and each child box is then subdivided to form a computational family tree. The flow of calculations is carried out along the tree structure with five passes. The fast multipole method has been improved and modified to achieve better effectiveness and higher efficiency since it was created. The multibody molecular algorithm starts with numbering subsets, forming bond graph, and developing three computing passes along the tree structure of an atomistic molecular system. Computing data flows in the fast multipole method and the multibody molecular algorithm will properly line up with the parent-child recursive relationship along the configuration of the tree structure due to linear recursive natures of both fast multipole method and multibody molecular algorithm. Then the time spent on the recursive simulation passes in the fast multipole method for computing forces may overlap with the time spent on the three recursive computational passes in the multibody molecular algorithm for forming and solving equations of motion.

A Logarithmic Complexity Divide-and-Conquer Algorithm for Multi-flexible Articulated Body Dynamics

2006 ◽  
Vol 2 (1) ◽  
pp. 10-21 ◽  
Author(s):  
Rudranarayan M. Mukherjee ◽  
Kurt S. Anderson
Keyword(s):  
Degrees Of Freedom ◽  
Temporal Integration ◽  
Equations Of Motion ◽  
Turnaround Time ◽  
Divide And Conquer ◽  
Dynamics Simulation ◽  
Flexible Body ◽  
Integration Step ◽  
Large Rotations ◽  
Nonlinear Equations Of Motion

This paper presents an efficient algorithm for the dynamics simulation and analysis of multi-flexible-body systems. This algorithm formulates and solves the nonlinear equations of motion for mechanical systems with interconnected flexible bodies subject to the limitations of modal superposition, and body substructuring, with arbitrarily large rotations and translations. The large rotations or translations are modelled as rigid body degrees of freedom associated with the interconnecting kinematic joint degrees of freedom. The elastic deformation of the component bodies is modelled through the use of modal coordinates and associated admissible shape functions. Apart from the approximation associated with the elastic deformations, this algorithm is exact, non-iterative, and applicable to generalized multi-flexible chain and tree topologies. In its basic form, the algorithm is both time and processor optimal in its treatment of the nb joint variables, providing O(log(nb)) turnaround time per temporal integration step, achieved with O(nb) processors. The actual cost associated with the parallel treatment of the nf flexible degrees of freedom depends on the specific parallel method chosen for dealing with the individual coefficient matrices which are associated locally with each flexible body.

Simplified FEM Model of Paper Machine Roll for Multibody Rolling Contact Analyses

2001 ◽  
Author(s):  
Veli-Matti Järvenpää ◽  
Erno K. Keskinen
Keyword(s):  
Finite Element ◽  
Degrees Of Freedom ◽  
Equations Of Motion ◽  
Element Model ◽  
Rolling Contact ◽  
Fe Model ◽  
Test Model ◽  
Paper Machine ◽  
Element Analysis ◽  
Computational Costs

Abstract In this paper a finite element model of a rotating paper machine roll for nip unit rolling contact analyses is discussed. This work presented here is based on the earlier work of the authors presented in [1] and [2]. The major motivations for developing a tailored FE-model including the large spin rotation are firstly to include the complex vibration phenomena as the shell vibrations of the roll structure in the analyses and secondly to reduce the computational costs of the numerical simulations due to the large number of degrees of freedom. The approach used is the use of the modal analysis i.e. to express the dynamics of the roll in terms of the lowest eigenmodes. The equations of motion are at first written in the rotating coordinates and then in addition to this the equations are expressed by using the modal coordinates. Numerical tests executed show that this modeling technique reduces computational costs significantly. Furthermore, use of the (semidefinite) eigenmode basis maintains the vibration characteristics of the roll structure. For verification purposes a test model was constructed and these simulation results were compared to the standard geometrically non-linear finite element analysis.

The motion of a lunar orbiter

1966 ◽  
Vol 25 ◽  
pp. 373
Author(s):  
Y. Kozai
Keyword(s):  
Degrees Of Freedom ◽  
Dimensional Space ◽  
Artificial Satellite ◽  
Equations Of Motion ◽  
Triaxial Ellipsoid ◽  
The Moon ◽  
Secular Motion ◽  
The Earth ◽  
Close Satellite ◽  
The Mean

The motion of an artificial satellite around the Moon is much more complicated than that around the Earth, since the shape of the Moon is a triaxial ellipsoid and the effect of the Earth on the motion is very important even for a very close satellite.The differential equations of motion of the satellite are written in canonical form of three degrees of freedom with time depending Hamiltonian. By eliminating short-periodic terms depending on the mean longitude of the satellite and by assuming that the Earth is moving on the lunar equator, however, the equations are reduced to those of two degrees of freedom with an energy integral.Since the mean motion of the Earth around the Moon is more rapid than the secular motion of the argument of pericentre of the satellite by a factor of one order, the terms depending on the longitude of the Earth can be eliminated, and the degree of freedom is reduced to one.Then the motion can be discussed by drawing equi-energy curves in two-dimensional space. According to these figures satellites with high inclination have large possibilities of falling down to the lunar surface even if the initial eccentricities are very small.The principal properties of the motion are not changed even if plausible values ofJ3andJ4of the Moon are included.This paper has been published in Publ. astr. Soc.Japan15, 301, 1963.

Reversibly Sampling Conformations and Binding Modes Using Molecular Darting

2020 ◽  
Author(s):  
Samuel C. Gill ◽  
David Mobley
Keyword(s):  
Monte Carlo ◽  
Ligand Binding ◽  
Binding Sites ◽  
Degrees Of Freedom ◽  
Dynamics Simulation ◽  
Hiv Integrase ◽  
Binding Modes ◽  
System A ◽  
Multiple Binding ◽  
Internal Degrees Of Freedom

<div>Sampling multiple binding modes of a ligand in a single molecular dynamics simulation is difficult. A given ligand may have many internal degrees of freedom, along with many different ways it might orient itself a binding site or across several binding sites, all of which might be separated by large energy barriers. We have developed a novel Monte Carlo move called Molecular Darting (MolDarting) to reversibly sample between predefined binding modes of a ligand. Here, we couple this with nonequilibrium candidate Monte Carlo (NCMC) to improve acceptance of moves.</div><div>We apply this technique to a simple dipeptide system, a ligand binding to T4 Lysozyme L99A, and ligand binding to HIV integrase in order to test this new method. We observe significant increases in acceptance compared to uniformly sampling the internal, and rotational/translational degrees of freedom in these systems.</div>

The Influence of Loading Position in A Priori High Stress Detection using Mode Superposition

2020 ◽  
Vol 1 (1) ◽  
pp. 93-102
Author(s):  
Carsten Strzalka ◽  
◽  
Manfred Zehn ◽  
Keyword(s):  
Finite Element ◽  
Degrees Of Freedom ◽  
Equations Of Motion ◽  
A Priori ◽  
High Stress ◽  
Von Mises Stress ◽  
Detailed Knowledge ◽  
Variable Loading ◽  
Numerical Effort ◽  
Von Mises

For the analysis of structural components, the finite element method (FEM) has become the most widely applied tool for numerical stress- and subsequent durability analyses. In industrial application advanced FE-models result in high numbers of degrees of freedom, making dynamic analyses time-consuming and expensive. As detailed finite element models are necessary for accurate stress results, the resulting data and connected numerical effort from dynamic stress analysis can be high. For the reduction of that effort, sophisticated methods have been developed to limit numerical calculations and processing of data to only small fractions of the global model. Therefore, detailed knowledge of the position of a component’s highly stressed areas is of great advantage for any present or subsequent analysis steps. In this paper an efficient method for the a priori detection of highly stressed areas of force-excited components is presented, based on modal stress superposition. As the component’s dynamic response and corresponding stress is always a function of its excitation, special attention is paid to the influence of the loading position. Based on the frequency domain solution of the modally decoupled equations of motion, a coefficient for a priori weighted superposition of modal von Mises stress fields is developed and validated on a simply supported cantilever beam structure with variable loading positions. The proposed approach is then applied to a simplified industrial model of a twist beam rear axle.

Optimization of Operation Parameters for Direct Spring Loaded Pressure Relief Valve in a Pipeline System

2018 ◽  
Vol 140 (5) ◽  
Author(s):  
Hyunjun Kim ◽  
Sanghyun Kim ◽  
Youngman Kim ◽  
Jonghwan Kim
Keyword(s):  
Pressure Relief Valve ◽  
Pipeline System ◽  
Relief Valve ◽  
Pressure Relief ◽  
Computational Costs ◽  
Constant Degree ◽  
System A ◽  
Disk Mass ◽  
Analysis Scheme ◽  
Surge Control

A direct spring loaded pressure relief valve (DSLPRV) is an efficient hydraulic structure used to control a potential water hammer in pipeline systems. The optimization of a DSLPRV was explored to consider the instability issue of a valve disk and the surge control for a pipeline system. A surge analysis scheme, named the method of characteristics, was implemented into a multiple-objective genetic algorithm to determine the adjustable factors in the operation of the DSLPRV. The forward transient analysis and multi-objective optimization of adjustable factors, such as the spring constant, degree of precompression, and disk mass, showed substantial relaxation in the surge pressure and oscillation of valve disk in a hypothetical pipeline system. The results of the regression analysis of surge were compared with the optimization results to demonstrate the potential of the developed method to substantially reduce computational costs.

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