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To explain the differentiation of stem cells in terms of dynamical systems theory, models of interacting cells with intracellular protein expression dynamics are analyzed and simulated. Simulations were carried out for all possible protein…

Cell Behavior · Quantitative Biology 2015-06-15 Yusuke Goto , Kunihiko Kaneko

In vivo and in vitro systems of cells and extra-cellular matrix (ECM) systems are well known to form ordered patterns of orientationally aligned fibers. Here, we interpret them as active analogs of the (disordered) isotropic to the…

Soft Condensed Matter · Physics 2025-04-11 Haiqian Yang , Ming Guo , L. Mahadevan

In active matter systems, self-propelled particles can self-organize to undergo collective motion, leading to persistent dynamical behavior out of equilibrium. In cells, cytoskeletal filaments and motor proteins self-organize into complex…

Soft Condensed Matter · Physics 2020-05-19 Jeffrey M. Moore , Tyler N. Thompson , Matthew A. Glaser , Meredith D. Betterton

A non-negligible part of the biological reactions in the activated sludge process for treatment of wastewater takes place in secondary settling tanks that follow biological reactors. It is therefore of interest to develop models of…

Numerical Analysis · Mathematics 2023-04-18 Raimund Bürger , Julio Careaga , Stefan Diehl , Romel Pineda

In this work, we construct an effective continuum model for architected sheets that are composed of bulky tiles connected by slender elastic joints. Due to their mesostructure, these sheets feature quasi-mechanisms -- low-energy local…

Materials Science · Physics 2022-06-22 Connor McMahan , Andrew Akerson , Paolo Celli , Basile Audoly , Chiara Daraio

We argue that nucleation of brittle cracks in initially flawless soft elastic solids is preceded by a nonlinear elastic instability, which cannot be captured without accounting for geometrical precise description of finite elastic…

Soft Condensed Matter · Physics 2024-06-17 D. Riccobelli , P. Ciarletta , G. Vitale , C. Maurini , L. Truskinovsky

We determine stability boundaries for the wrinkling of highly uni-directionally stretched, finely thin, rectangular elastic sheets. For a given fine thickness and length, a stability boundary here is a curve in the parameter plane, aspect…

Soft Condensed Matter · Physics 2016-12-21 Qingdu Li , Timothy J. Healey

The polarisation of cells and tissues is fundamental for tissue morphogenesis during biological development and regeneration. A deeper understanding of biological polarity pattern formation can be gained from the consideration of pattern…

Cell Behavior · Quantitative Biology 2017-10-23 Karl B. Hoffmann , Anja Voss-Böhme , Jochen C. Rink , Lutz Brusch

Instabilities in thin elastic sheets, such as wrinkles, are of broad interest both from a fundamental viewpoint and also because of their potential for engineering applications. Nematic liquid crystal elastomers offer a new form of control…

Soft Condensed Matter · Physics 2019-10-03 Madison S. Krieger , Marcelo A. Dias

Unlike most synthetic materials, biological materials often stiffen as they are deformed. This nonlinear elastic response, critical for the physiological function of some tissues, has been documented since at least the 19th century, but the…

Soft Condensed Matter · Physics 2009-11-10 Cornelis Storm , Jennifer J. Pastore , Fred C. MacKintosh , Tom C. Lubensky , Paul A. Janmey

Soft-granular media, such as dense emulsions, foams or tissues, exhibit either fluid- or solid-like properties depending on the applied external stresses. Whereas bulk rheology of such materials has been thoroughly investigated, the…

Soft Condensed Matter · Physics 2024-07-04 Michal Bogdan , Jesus Pineda , Mihir Durve , Leon Jurkiewicz , Sauro Succi , Giovanni Volpe , Jan Guzowski

The impact of confinement on self-assembly of particles interacting with short-range attraction and long-range repulsion (SALR) potential is studied for thermodynamic states corresponding to local ordering of clusters or layers in the bulk.…

Soft Condensed Matter · Physics 2014-11-17 Jakub Pękalski , Alina Ciach , Noé G. Almarza

Spatially confined rigid membranes reorganize their morphology in response to the imposed constraints. A crumpled elastic sheet presents a complex pattern of random folds focusing the deformation energy while compressing a membrane resting…

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

Biomolecules · Quantitative Biology 2016-05-23 Karol Wołek , Marek Cieplak

We investigate stationary, spatially localized patterns in lattice dynamical systems that exhibit bistability. The profiles associated with these patterns have a long plateau where the pattern resembles one of the bistable states, while the…

Dynamical Systems · Mathematics 2022-03-23 Jason J. Bramburger , Bjorn Sandstede

The shapes of epithelial tissues result from a complex interplay of contractile forces in the cytoskeleta of the cells in the tissue, and adhesion forces between them. A host of discrete, cell-based models describe these forces by assigning…

Soft Condensed Matter · Physics 2019-02-27 Pierra A. Haas , Raymond E. Goldstein

The weighted extended B-spline method [Hoellig (2003)] is applied to bending and buckling problems of plates with different shapes and stiffener arrangements. The discrete equations are obtained from the energy contributions of the…

Numerical Analysis · Mathematics 2015-12-15 Joris C. G. Verschaeve

We study the mechanical stiffening behavior in two-dimensional (2D) cross-linked networks of semiflexible biopolymer filaments under simple shear. Filamental constituents immersed in a fluid undergo thermally excited bending motions.…

Biological Physics · Physics 2007-05-23 T. Van Dillen , P. R. Onck , E. Van der Giessen

Many engineering structures are composed of weakly coupled sectors assembled in a cyclic and ideally symmetric configuration, which can be simplified as forced Duffing oscillators. In this paper, we study the emergence of localized states…

Pattern Formation and Solitons · Physics 2018-11-14 A. Papangelo , F. Fontanela , A. Grolet , M. Ciavarella , N. Hoffmann

We constrast the dynamics in model unentangled polymer melts of chains of three different stiffnesses: flexible, intermediate, and rodlike. Flexible and rodlike chains, which readily solidify into close-packed crystals (respectively with…

Soft Condensed Matter · Physics 2016-11-23 Hong T. Nguyen , Robert S. Hoy
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