scholarly journals A Framework for Stochastic Optimization of Parameters for Integrative Modeling of Macromolecular Assemblies

Life ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 1183
Author(s):  
Satwik Pasani ◽  
Shruthi Viswanath
Keyword(s):  
Stochastic Optimization ◽  
Degrees Of Freedom ◽  
Rigid Bodies ◽  
Simultaneous Optimization ◽  
Coarse Grained ◽  
High Dimensions ◽  
Optimization Of Parameters ◽  
Stochastic Sampling ◽  
Macromolecular Assemblies ◽  
Integrative Modeling

Integrative modeling of macromolecular assemblies requires stochastic sampling, for example, via MCMC (Markov Chain Monte Carlo), since exhaustively enumerating all structural degrees of freedom is infeasible. MCMC-based methods usually require tuning several parameters, such as the move sizes for coarse-grained beads and rigid bodies, for sampling to be efficient and accurate. Currently, these parameters are tuned manually. To automate this process, we developed a general heuristic for derivative-free, global, stochastic, parallel, multiobjective optimization, termed StOP (Stochastic Optimization of Parameters) and applied it to optimize sampling-related parameters for the Integrative Modeling Platform (IMP). Given an integrative modeling setup, list of parameters to optimize, their domains, metrics that they influence, and the target ranges of these metrics, StOP produces the optimal values of these parameters. StOP is adaptable to the available computing capacity and converges quickly, allowing for the simultaneous optimization of a large number of parameters. However, it is not efficient at high dimensions and not guaranteed to find optima in complex landscapes. We demonstrate its performance on several examples of random functions, as well as on two integrative modeling examples, showing that StOP enhances the efficiency of sampling the posterior distribution, resulting in more good-scoring models and better sampling precision.

scholarly journals Quantum information probes of charge fractionalization in large-N gauge theories

2021 ◽  
Vol 2021 (5) ◽  
Author(s):  
Brandon S. DiNunno ◽  
Niko Jokela ◽  
Juan F. Pedraza ◽  
Arttu Pönni
Keyword(s):  
Degrees Of Freedom ◽  
Gauge Theories ◽  
Entanglement Entropy ◽  
Coarse Grained ◽  
Strongly Coupled ◽  
Information Theoretic ◽  
Large N ◽  
Wide Range ◽  
Charge Fractionalization ◽  
Electric Flux

Abstract We study in detail various information theoretic quantities with the intent of distinguishing between different charged sectors in fractionalized states of large-N gauge theories. For concreteness, we focus on a simple holographic (2 + 1)-dimensional strongly coupled electron fluid whose charged states organize themselves into fractionalized and coherent patterns at sufficiently low temperatures. However, we expect that our results are quite generic and applicable to a wide range of systems, including non-holographic. The probes we consider include the entanglement entropy, mutual information, entanglement of purification and the butterfly velocity. The latter turns out to be particularly useful, given the universal connection between momentum and charge diffusion in the vicinity of a black hole horizon. The RT surfaces used to compute the above quantities, though, are largely insensitive to the electric flux in the bulk. To address this deficiency, we propose a generalized entanglement functional that is motivated through the Iyer-Wald formalism, applied to a gravity theory coupled to a U(1) gauge field. We argue that this functional gives rise to a coarse grained measure of entanglement in the boundary theory which is obtained by tracing over (part) of the fractionalized and cohesive charge degrees of freedom. Based on the above, we construct a candidate for an entropic c-function that accounts for the existence of bulk charges. We explore some of its general properties and their significance, and discuss how it can be used to efficiently account for charged degrees of freedom across different energy scales.

Configuration Robustness Analysis of the Optimal Design of Cable-Driven Manipulators

2016 ◽  
Vol 8 (6) ◽  
Author(s):  
Joshua T. Bryson ◽  
Xin Jin ◽  
Sunil K. Agrawal
Keyword(s):  
Optimal Design ◽  
Stochastic Optimization ◽  
High Dimension ◽  
Degrees Of Freedom ◽  
Robustness Analysis ◽  
Optimal Solution ◽  
Design Parameters ◽  
Robot Leg ◽  
Robot Performance

Designing an effective cable architecture for a cable-driven robot becomes challenging as the number of cables and degrees of freedom of the robot increase. A methodology has been previously developed to identify the optimal design of a cable-driven robot for a given task using stochastic optimization. This approach is effective in providing an optimal solution for robots with high-dimension design spaces, but does not provide insights into the robustness of the optimal solution to errors in the configuration parameters that arise in the implementation of a design. In this work, a methodology is developed to analyze the robustness of the performance of an optimal design to changes in the configuration parameters. This robustness analysis can be used to inform the implementation of the optimal design into a robot while taking into account the precision and tolerances of the implementation. An optimized cable-driven robot leg is used as a motivating example to illustrate the application of the configuration robustness analysis. Following the methodology, the effect on robot performance due to design variations is analyzed, and a modified design is developed which minimizes the potential performance degradations due to implementation errors in the design parameters. A robot leg is constructed and is used to validate the robustness analysis by demonstrating the predicted effects of variations in the design parameters on the performance of the robot.

All-atomistic molecular dynamics study of the glass transition of amorphous polymers

2021 ◽  
Author(s):  
Zhiye Tang ◽  
Susumu Okazaki
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
Spatial Scale ◽  
Degrees Of Freedom ◽  
Main Chain ◽  
Polymer Materials ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Radius Of Gyration ◽  
Chemical Structures

Glass transition is an important phenomenon of polymer materials and it has been intensively studied over the past a few decades. However, the influencing factors arising from the chemical structures of the polymers are often ignored due to a continuous or coarse-grained description of the polymer. Here, we approached this phenomenon using all-atomistic molecular dynamics (MD) simulations and two conventionally used polymer materials, polycarbonate (PC) and poly-(methyl methacrylate) (PMMA). We reproduced the glass transition temperatures (Tg) of the two materials reasonably well. Then we characterized and investigated the glass transition process by looking at the changes of potential energy, dihedral transition, and thermal fluctuation of the individual degrees of freedom in the systems, over the entire temperature range of glass transition. As previously reported, the dihedral angles stop their conformational changes gradually at the Tg, especially for the main chain dihedrals, and sidechain rotations immediately rooting from the main chain. The volumetric change during the temperature decrease is confirmed to be because of conformational adjustment, probably due to the tendency of chain stretching for the maintenance of the radius of gyration, and the loss of thermal energy. The strength of motions of single degrees of freedom and polymer chains, and overall slow motions obtained by normal mode analysis (NMA) shows that different motions at different spatial scale may gradually stop at distinct temperature in the MD simulation temporal and spatial scales. Presumably, the small spatial scale do not contribute to the glass transition at the experimental scale since the timescale is much longer than their relaxation time.

scholarly journals An Efficient Contact Model for the Simulation of Cargo Airdrop Extraction Phase

2018 ◽  
Vol 2018 ◽  
pp. 1-13
Author(s):  
Leiming Ning ◽  
Jichang Chen ◽  
Mingbo Tong
Keyword(s):  
Degrees Of Freedom ◽  
Friction Model ◽  
Rigid Bodies ◽  
Contact Dynamics ◽  
Moving Frame ◽  
Contact Friction ◽  
Practical Implementation ◽  
Contact Formulation ◽  
Efficient Code ◽  
Extraction Phase

A high-fidelity cargo airdrop simulation requires the accurate modeling of the contact dynamics between an aircraft and its cargo. This paper presents a general and efficient contact-friction model for the simulation of aircraft-cargo coupling dynamics during an airdrop extraction phase. The proposed approach has the same essence as the finite element node-to-segment contact formulation, which leads to a flexible, straightforward, and efficient code implementation. The formulation is developed under an arbitrary moving frame with both aircraft and cargo treated as general six degrees-of-freedom rigid bodies, thus eliminating the restrictions of lateral symmetric assumptions in most existing methods. Moreover, the aircraft-cargo coupling algorithm is discussed in detail, and some practical implementation details are presented. The accuracy and capability of the present method are demonstrated through four numerical examples with increasing complexity and fidelity.

scholarly journals An Asymptotically Optimal NMPC Core for Multi Degrees of Freedom Rigid Bodies

2012 ◽  
Vol 45 (17) ◽  
pp. 207-212
Author(s):  
Chyon Hae Kim ◽  
Shimon Sugawara ◽  
Shigeki Sugano
Keyword(s):  
Degrees Of Freedom ◽  
Rigid Bodies ◽  
Asymptotically Optimal

Generalized Abbe Principle: Position Error Propagation in Machine Elements

1996 ◽  
Author(s):  
Joseph Pegna
Keyword(s):  
Error Propagation ◽  
Degrees Of Freedom ◽  
Rigid Bodies ◽  
Statistical Characterization ◽  
Physical Limit ◽  
Potential Applications ◽  
Machine Elements ◽  
Tolerance Verification ◽  
Precision Machines

Abstract In the quest for ever finer levels of technology integration, mechanical linkages reach their precision limits at about 5micrometers per meter of workspace. Beyond this physical limit, all six dimensional degrees of freedom need to be precisely ascertained to account for mechanical imperfections. This paper substantiates Wu’s vision of “precision machines without precision machinery.” A formulation and statistical characterization of position and orientation error propagation in rigid bodies are presented for two extreme models of measurement. It is shown that error distribution is uniquely dependent upon the design of the measurement plan. The theoretical foundations presented were evolved in the course of designing precision machinery. Other potential applications include: fixture design, metrology, and geometric tolerance verification.

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