A new approach to the mechanics of DNA: Atoms-to-beam homogenization

Kalliauer, Johannes; Kahl, Gerhard; Scheiner, Stefan; Hellmich, Christian

doi:10.1016/j.jmps.2020.104040

Cited by 8 publications

(3 citation statements)

References 69 publications

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“…Because of limitations in computational resources, even the slowest stretching velocities used in simulations are higher in magnitude than those used in equivalent AFM experiments [54]. From the computational point of view, the coarse-grained (CG) MD approach [55] and atoms-to-beam homogenization approach [56] are reported as the most promising approaches to predict structural features while achieving computational efficiency, i.e. lowering production times.…”

Section: (B) Steered Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular basis of conformational changes and mechanics of integrins

Gaikwad,

Jaswandkar,

Katti

et al. 2023

Phil. Trans. R. Soc. A.

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Integrin, as a mechanotransducer, establishes the mechanical reciprocity between the extracellular matrix (ECM) and cells at integrin-mediated adhesion sites. This study used steered molecular dynamics (SMD) simulations to investigate the mechanical responses of integrin α v β 3 with and without 10th type III fibronectin (FnIII 10 ) binding for tensile, bending and torsional loading conditions. The ligand-binding integrin confirmed the integrin activation during equilibration and altered the integrin dynamics by changing the interface interaction between β-tail, hybrid and epidermal growth factor domains during initial tensile loading. The tensile deformation in integrin molecules indicated that fibronectin ligand binding modulates its mechanical responses in the folded and unfolded conformation states. The bending deformation responses of extended integrin models reveal the change in behaviour of integrin molecules in the presence of Mn 2+ ion and ligand based on the application of force in the folding and unfolding directions of integrin. Furthermore, these SMD simulation results were used to predict the mechanical properties of integrin underlying the mechanism of integrin-based adhesion. The evaluation of integrin mechanics provides new insights into understanding the mechanotransmission (force transmission) between cells and ECM and contributes to developing an accurate model for integrin-mediated adhesion. This article is part of a discussion meeting issue ‘Supercomputing simulations of advanced materials’.

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Section: (B) Steered Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular basis of conformational changes and mechanics of integrins

Gaikwad,

Jaswandkar,

Katti

et al. 2023

Phil. Trans. R. Soc. A.

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“…The PVP is a fundamental exposition and can be applied for various applications ranging from, for instance, modeling DNA macromolecules to elastic foundations (Kalliauer et al. 2020 ; Höller et al. 2019 ).…”

Section: A Brief Review Of Fundamental Conceptsmentioning

confidence: 99%

Thermodynamically consistent concurrent material and structure optimization of elastoplastic multiphase hierarchical systems

Gangwar,

Schillinger

2023

Struct Multidisc Optim

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The concept of concurrent material and structure optimization aims at alleviating the computational discovery of optimum microstructure configurations in multiphase hierarchical systems, whose macroscale behavior is governed by their microstructure composition that can evolve over multiple length scales from a few micrometers to centimeters. It is based on the split of the multiscale optimization problem into two nested sub-problems, one at the macroscale (structure) and the other at the microscales (material). In this paper, we establish a novel formulation of concurrent material and structure optimization for multiphase hierarchical systems with elastoplastic constituents at the material scales. Exploiting the thermomechanical foundations of elastoplasticity, we reformulate the material optimization problem based on the maximum plastic dissipation principle such that it assumes the format of an elastoplastic constitutive law and can be efficiently solved via modified return mapping algorithms. We integrate continuum micromechanics based estimates of the stiffness and the yield criterion into the formulation, which opens the door to a computationally feasible treatment of the material optimization problem. To demonstrate the accuracy and robustness of our framework, we define new benchmark tests with several material scales that, for the first time, become computationally feasible. We argue that our formulation naturally extends to multiscale optimization under further path-dependent effects such as viscoplasticity or multiscale fracture and damage.

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“…This use of the PVP to explore equilibrium conditions (or in the dynamic case, motion rules) is the target already of the original paper of Germain [9], where he covered classical and second-order continua. This example has been followed by very many examples from different branches of the rich field of mechanics and beyond, such as second-order fluid-solid interaction or poromechanics [39,40], structural mechanics [41][42][43], bio-macromolecule homogenization [44], or elastic parameter homogenization [45].…”

Section: A C K N O W L E D G M E N T Smentioning

confidence: 99%

Stress average rule derived through the principle of virtual power

2022

Self Cite

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Stress and strain average rules are the key conceptual pillars of the wide field of continuum micromechanics of materials. The aforementioned rules express that the spatial average of (micro‐)stress and (micro‐)strain fields throughout a microscopically finite representative volume element (RVE) are equal to the (macro‐)stress and (macro‐)strain values associated with the corresponding macroscopically infinitesimal volume element (macroscopic material point). According to the famous contribution of Hashin, stress and strain average rules are derived from equilibrium and compatibility conditions, together with (micro‐)displacement and (micro‐)traction boundary conditions associated with homogeneous (macro‐)strains and (macro‐)stresses, respectively. However, as, strictly speaking, only displacements or tractions can be described at the boundary, the remaining average rule turns out as a mere definition. We here suggest a way to do without such a definition, by resorting to the principle of virtual power (PVP) as a means to guarantee mechanical equilibrium: at the boundary of the RVE, we prescribe virtual (micro‐)velocities, which are linked to arbitrary, but homogeneous virtual (macro‐)velocities and (macro‐)strain rates, while the latter are also linked, in a multilinear fashion, with the microscopic virtual strain rate fields inside the RVE. Considering, under these conditions, equivalence of the macroscopic and the microscopic expressions for the virtual power densities of the internal and the external forces yields the well‐known stress average rule and, in case of microscopically uniform force fields, a volume force average rule. The same strategy applied to an RVE hosting single forces between atomistic mass points, readily yields the macroscopic “internal virial stress tensor.”

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A new approach to the mechanics of DNA: Atoms-to-beam homogenization

Cited by 8 publications

References 69 publications

Molecular basis of conformational changes and mechanics of integrins

Molecular basis of conformational changes and mechanics of integrins

Thermodynamically consistent concurrent material and structure optimization of elastoplastic multiphase hierarchical systems

Stress average rule derived through the principle of virtual power

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