scholarly journals Emergent probability fluxes in confined microbial navigation

2021 ◽  
Vol 118 (39) ◽  
pp. e2024752118
Author(s):  
Jan Cammann ◽  
Fabian Jan Schwarzendahl ◽  
Tanya Ostapenko ◽  
Danylo Lavrentovich ◽  
Oliver Bäumchen ◽  
...  
Keyword(s):  
Self Organization ◽  
Complex Geometries ◽  
Length Scale ◽  
Universal Relation ◽  
Active Motion ◽  
Motile Cells ◽  
Flux Loops ◽  
Emergent Probability ◽  
Microbial Systems ◽  
Probability Flux

When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While most of our current understanding is based on bulk systems or idealized geometries, it remains elusive how and at which length scale self-organization emerges in complex geometries. Here, using experiments and analytical and numerical calculations, we study the motion of motile cells under controlled microfluidic conditions and demonstrate that probability flux loops organize active motion, even at the level of a single cell exploring an isolated compartment of nontrivial geometry. By accounting for the interplay of activity and interfacial forces, we find that the boundary’s curvature determines the nonequilibrium probability fluxes of the motion. We theoretically predict a universal relation between fluxes and global geometric properties that is directly confirmed by experiments. Our findings open the possibility to decipher the most probable trajectories of motile cells and may enable the design of geometries guiding their time-averaged motion.

scholarly journals Geometric Effect for Biological Reactors and Biological Fluids

2018 ◽  
Vol 5 (4) ◽  
pp. 110 ◽  
Author(s):  
Kazusa Beppu ◽  
Ziane Izri ◽  
Yusuke Maeda ◽  
Ryota Sakamoto
Keyword(s):  
Biological Fluids ◽  
Biological Systems ◽  
Self Organization ◽  
Active Matter ◽  
Confined Space ◽  
Self Organized ◽  
Motile Cells ◽  
Recent Developments ◽  
A Cell

As expressed “God made the bulk; the surface was invented by the devil” by W. Pauli, the surface has remarkable properties because broken symmetry in surface alters the material properties. In biological systems, the smallest functional and structural unit, which has a functional bulk space enclosed by a thin interface, is a cell. Cells contain inner cytosolic soup in which genetic information stored in DNA can be expressed through transcription (TX) and translation (TL). The exploration of cell-sized confinement has been recently investigated by using micron-scale droplets and microfluidic devices. In the first part of this review article, we describe recent developments of cell-free bioreactors where bacterial TX-TL machinery and DNA are encapsulated in these cell-sized compartments. Since synthetic biology and microfluidics meet toward the bottom-up assembly of cell-free bioreactors, the interplay between cellular geometry and TX-TL advances better control of biological structure and dynamics in vitro system. Furthermore, biological systems that show self-organization in confined space are not limited to a single cell, but are also involved in the collective behavior of motile cells, named active matter. In the second part, we describe recent studies where collectively ordered patterns of active matter, from bacterial suspensions to active cytoskeleton, are self-organized. Since geometry and topology are vital concepts to understand the ordered phase of active matter, a microfluidic device with designed compartments allows one to explore geometric principles behind self-organization across the molecular scale to cellular scale. Finally, we discuss the future perspectives of a microfluidic approach to explore the further understanding of biological systems from geometric and topological aspects.

scholarly journals Mastering Self-Organization of Functional Materials at Different Length Scale

2011 ◽  
Vol 21 (7) ◽  
pp. 1210-1211 ◽  
Author(s):  
Paolo Samorì ◽  
Ana Helman ◽  
Fabio Biscarini ◽  
Franco Cacialli
Keyword(s):  
Functional Materials ◽  
Self Organization ◽  
Length Scale

scholarly journals Element-splitting-invariant local-length-scale calculation in B-Spline meshes for complex geometries

2020 ◽  
Vol 30 (11) ◽  
pp. 2139-2174 ◽  
Author(s):  
Yuki Ueda ◽  
Yuto Otoguro ◽  
Kenji Takizawa ◽  
Tayfun E. Tezduyar
Keyword(s):  
Finite Element ◽  
Multiscale Methods ◽  
Complex Geometries ◽  
Length Scale ◽  
Element Discretization ◽  
B Spline ◽  
Parametric Space ◽  
Stabilized Methods ◽  
Physical Element ◽  
Isogeometric Discretization

Variational multiscale methods and their precursors, stabilized methods, which are sometimes supplemented with discontinuity-capturing (DC) methods, have been playing their core-method role in flow computations increasingly with isogeometric discretization. The stabilization and DC parameters embedded in most of these methods play a significant role. The parameters almost always involve some local-length-scale expressions, most of the time in specific directions, such as the direction of the flow or solution gradient. Until recently, local-length-scale expressions originally intended for finite element discretization were being used also for isogeometric discretization. The direction-dependent expressions introduced in [Y. Otoguro, K. Takizawa and T. E. Tezduyar, Element length calculation in B-spline meshes for complex geometries, Comput. Mech. 65 (2020) 1085–1103, https://doi.org/10.1007/s00466-019-01809-w ] target B-spline meshes for complex geometries. The key stages of deriving these expressions are mapping the direction vector from the physical element to the parent element in the parametric space, accounting for the discretization spacing along each of the parametric coordinates, and mapping what has been obtained back to the physical element. The expressions are based on a preferred parametric space and a transformation tensor that represents the relationship between the integration and preferred parametric spaces. Element splitting may be a part of the computational method in a variety of cases, including computations with T-spline discretization and immersed boundary and extended finite element methods and their isogeometric versions. We do not want the element splitting to influence the actual discretization, which is represented by the control or nodal points. Therefore, the local length scale should be invariant with respect to element splitting. In element definition, invariance of the local length scale is a crucial requirement, because, unlike the element definition choices based on implementation convenience or computational efficiency, it influences the solution. We provide a proof, in the context of B-spline meshes, for the element-splitting invariance of the local-length-scale expressions introduced in the above reference.

Multiple length scale self-organization in liquid crystalline block copolymers

1997 ◽  
Vol 117 (1) ◽  
pp. 141-152 ◽  
Author(s):  
Christopher K. Ober ◽  
Jianguo Wang ◽  
Guoping Mao ◽  
Edward J. Kramer ◽  
John T. Chen ◽  
...  
Keyword(s):  
Block Copolymers ◽  
Liquid Crystalline ◽  
Self Organization ◽  
Length Scale ◽  
Multiple Length Scale

Modulated polarization microscopy displays the dynamics of cytoskeletal structures in living, motile cells

1995 ◽  
Vol 53 ◽  
pp. 902-903
Author(s):  
J. R. Kuhn ◽  
M. Poenie
Keyword(s):  
Mitotic Spindle ◽  
Actin Filaments ◽  
Cell Shape ◽  
Dynamic Structure ◽  
Living Cells ◽  
Cytoskeletal Proteins ◽  
Polarization Microscopy ◽  
Video Enhancement ◽  
Ultrastructural Studies ◽  
Motile Cells

Cell shape and movement are controlled by elements of the cytoskeleton including actin filaments an microtubules. Unfortunately, it is difficult to visualize the cytoskeleton in living cells and hence follow it dynamics. Immunofluorescence and ultrastructural studies of fixed cells while providing clear images of the cytoskeleton, give only a static picture of this dynamic structure. Microinjection of fluorescently Is beled cytoskeletal proteins has proved useful as a way to follow some cytoskeletal events, but long terry studies are generally limited by the bleaching of fluorophores and presence of unassembled monomers.Polarization microscopy has the potential for visualizing the cytoskeleton. Although at present, it ha mainly been used for visualizing the mitotic spindle. Polarization microscopy is attractive in that it pro vides a way to selectively image structures such as cytoskeletal filaments that are birefringent. By combing ing standard polarization microscopy with video enhancement techniques it has been possible to image single filaments. In this case, however, filament intensity depends on the orientation of the polarizer and analyzer with respect to the specimen.

Biomimetic materials: An introduction

1992 ◽  
Vol 50 (2) ◽  
pp. 1020-1021 ◽  
Author(s):  
M. Sarikaya ◽  
J. T. Staley ◽  
I. A. Aksay
Keyword(s):  
Self Assembly ◽  
Structural Control ◽  
Hierarchical Structures ◽  
Ceramic Composites ◽  
Advanced Materials ◽  
Length Scale ◽  
Spider Webs ◽  
Biomimetic Materials ◽  
Synthetic Materials ◽  
All Ceramic

Biomimetics is an area of research in which the analysis of structures and functions of natural materials provide a source of inspiration for design and processing concepts for novel synthetic materials. Through biomimetics, it may be possible to establish structural control on a continuous length scale, resulting in superior structures able to withstand the requirements placed upon advanced materials. It is well recognized that biological systems efficiently produce complex and hierarchical structures on the molecular, micrometer, and macro scales with unique properties, and with greater structural control than is possible with synthetic materials. The dynamism of these systems allows the collection and transport of constituents; the nucleation, configuration, and growth of new structures by self-assembly; and the repair and replacement of old and damaged components. These materials include all-organic components such as spider webs and insect cuticles (Fig. 1); inorganic-organic composites, such as seashells (Fig. 2) and bones; all-ceramic composites, such as sea urchin teeth, spines, and other skeletal units (Fig. 3); and inorganic ultrafine magnetic and semiconducting particles produced by bacteria and algae, respectively (Fig. 4).

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