Optimization problem and efficient partitioning algorithm for transitions to finer-scale models in adaptive resolution simulation of articulated biopolymers

Adaptive coarse graining of highly complex biomolecular systems is conducted by either imposing constraints on the system model to generate a coarser model, or releasing certain constraints from it to create a higher fidelity one. This paper addresses some of the challenges of transitions to finer-s...

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Bibliographic Details
Published in:Multibody system dynamics Vol. 42; no. 1; pp. 97 - 117
Main Authors: Poursina, Mohammad, Anderson, Kurt S.
Format: Journal Article
Language:English
Published: Dordrecht Springer Netherlands 01.01.2018
Springer Nature B.V
Subjects:
Adaptive systems
Automotive Engineering
Biopolymers
Computer simulation
Computing time
Constraint modelling
Control
Dynamical Systems
Electrical Engineering
Engineering
Granulation
Jacobi matrix method
Kinetic energy
Mechanical Engineering
Mechanical systems
Optimization
Parallel processing
Partitioning
Scale models
Vibration
Molecular dynamics
Adaptive coarse graining
Model transition
Optimization
Divide-and-conquer algorithm
ISSN:1384-5640, 1573-272X
Online Access:Get full text
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Summary:Adaptive coarse graining of highly complex biomolecular systems is conducted by either imposing constraints on the system model to generate a coarser model, or releasing certain constraints from it to create a higher fidelity one. This paper addresses some of the challenges of transitions to finer-scale models. It is shown that the kinetic energy associated with ignored modes of motion during the coarse graining process must be estimated and put back into the simulation. As such, unlike real mechanical systems, transitioning back to a finer biomolecular model may result in an infinite number of solutions. Herein, an optimization-based approach subject to the satisfaction of impulse–momentum balance and desired kinetic energy is presented to arrive at a physically meaningful state of the system immediately after the transition. In order to reduce the cost of formulating and solving this optimization problem, generalized velocities of the system are partitioned into two categories: independent joint velocities associated with the released joints, and dependent joint velocities associated with the rest of the joints. This paper further develops a divide-and-conquer algorithm to efficiently perform this partitioning process and express dependent velocities in terms of independent ones. The presented method is highly parallelizable and avoids the construction of the mass and Jacobian matrices of the entire system, resulting in a significant improvement in computational efficiency.
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ISSN:1384-5640
1573-272X
DOI:10.1007/s11044-017-9603-6