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Modeling and simulation of complex dynamic musculoskeletal architectures.

ABSTRACT: Natural creatures, from fish and cephalopods to snakes and birds, combine neural control, sensory feedback and compliant mechanics to effectively operate across dynamic, uncertain environments. In order to facilitate the understanding of the biophysical mechanisms at play and to streamline their potential use in engineering applications, we present here a versatile numerical approach to the simulation of musculoskeletal architectures. It relies on the assembly of heterogenous, active and passive Cosserat rods into dynamic structures that model bones, tendons, ligaments, fibers and muscle connectivity. We demonstrate its utility in a range of problems involving biological and soft robotic scenarios across scales and environments: from the engineering of millimeter-long bio-hybrid robots to the synthesis and reconstruction of complex musculoskeletal systems. The versatility of this methodology offers a framework to aid forward and inverse bioengineering designs as well as fundamental discovery in the functioning of living organisms.

SUBMITTER: Zhang X

PROVIDER: S-EPMC6811595 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

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Modeling and simulation of complex dynamic musculoskeletal architectures.

Zhang Xiaotian X Chan Fan Kiat FK Parthasarathy Tejaswin T Gazzola Mattia M

Nature communications 20191023 1

Natural creatures, from fish and cephalopods to snakes and birds, combine neural control, sensory feedback and compliant mechanics to effectively operate across dynamic, uncertain environments. In order to facilitate the understanding of the biophysical mechanisms at play and to streamline their potential use in engineering applications, we present here a versatile numerical approach to the simulation of musculoskeletal architectures. It relies on the assembly of heterogenous, active and passive ...[more]

PMID: 31645555

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Project description:Understanding the mechanisms that trigger chromatin compaction, its patterns, and the factors they depend on, is a fundamental and still open question in Biology. Chromatin compacts and reinforces DNA and is a stable but dynamic structure, to make DNA accessible to proteins. In recent years, computational advances have provided larger amounts of data and have made large-scale simulations more viable. Experimental techniques for the extraction and reconstitution of chromatin fibers have improved, reinvigorating theoretical and experimental interest in the topic and stimulating debate on points previously considered as certainties regarding chromatin. A great assortment of approaches has emerged, from all-atom single-nucleosome or oligonucleosome simulations to various degrees of coarse graining, to polymer models, to fractal-like structures and purely topological models. Different fiber-start patterns have been studied in theory and experiment, as well as different linker DNA lengths. DNA is a highly charged macromolecule, making ionic and electrostatic interactions extremely important for chromatin topology and dynamics. Indeed, the repercussions of varying ionic concentration have been extensively examined at the computational level, using all-atom, coarse-grained, and continuum techniques. The presence of high-curvature AT-rich segments in DNA can cause conformational variations, attesting to the fact that the role of DNA is both structural and electrostatic. There have been some tentative attempts to describe the force fields governing chromatin conformational changes and the energy landscapes of these transitions, but the intricacy of the system has hampered reaching a consensus. The study of chromatin conformations is an intrinsically multiscale topic, influenced by a wide range of biological and physical interactions, spanning from the atomic to the chromosome level. Therefore, powerful modeling techniques and carefully planned experiments are required for an overview of the most relevant phenomena and interactions. The topic provides fertile ground for interdisciplinary studies featuring a synergy between theoretical and experimental scientists from different fields and the cross-validation of respective results, with a multi-scale perspective. Here, we summarize some of the most representative approaches, and focus on the importance of electrostatics and solvation, often overlooked aspects of chromatin modeling.

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Dataset Information

Modeling and simulation of complex dynamic musculoskeletal architectures.

Publications

Modeling and simulation of complex dynamic musculoskeletal architectures.

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