scholarly journals Synchrony and pattern formation of coupled genetic oscillators on a chip of artificial cells

2017 ◽  
Vol 114 (44) ◽  
pp. 11609-11614 ◽  
Author(s):  
Alexandra M. Tayar ◽  
Eyal Karzbrun ◽  
Vincent Noireaux ◽  
Roy H. Bar-Ziv
Keyword(s):  
Pattern Formation ◽  
Large Scale ◽  
Reaction Diffusion ◽  
Biochemical Networks ◽  
Artificial Cells ◽  
Diffusion Dynamics ◽  
Oscillatory Reactions ◽  
Potential Applications ◽  
On Chip ◽  
Genetic Oscillators

Understanding how biochemical networks lead to large-scale nonequilibrium self-organization and pattern formation in life is a major challenge, with important implications for the design of programmable synthetic systems. Here, we assembled cell-free genetic oscillators in a spatially distributed system of on-chip DNA compartments as artificial cells, and measured reaction–diffusion dynamics at the single-cell level up to the multicell scale. Using a cell-free gene network we programmed molecular interactions that control the frequency of oscillations, population variability, and dynamical stability. We observed frequency entrainment, synchronized oscillatory reactions and pattern formation in space, as manifestation of collective behavior. The transition to synchrony occurs as the local coupling between compartments strengthens. Spatiotemporal oscillations are induced either by a concentration gradient of a diffusible signal, or by spontaneous symmetry breaking close to a transition from oscillatory to nonoscillatory dynamics. This work offers design principles for programmable biochemical reactions with potential applications to autonomous sensing, distributed computing, and biomedical diagnostics.

scholarly journals Pattern formation in reaction–diffusion system on membrane with mechanochemical feedback

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Naoki Tamemoto ◽  
Hiroshi Noguchi
Keyword(s):  
Pattern Formation ◽  
Plasma Membranes ◽  
Reaction Diffusion ◽  
Living Cells ◽  
Nonequilibrium Dynamics ◽  
Membrane Deformation ◽  
Brusselator Model ◽  
Diffusion Dynamics ◽  
Curved Membranes ◽  
Membrane Shape

Abstract Shapes of biological membranes are dynamically regulated in living cells. Although membrane shape deformation by proteins at thermal equilibrium has been extensively studied, nonequilibrium dynamics have been much less explored. Recently, chemical reaction propagation has been experimentally observed in plasma membranes. Thus, it is important to understand how the reaction–diffusion dynamics are modified on deformable curved membranes. Here, we investigated nonequilibrium pattern formation on vesicles induced by mechanochemical feedback between membrane deformation and chemical reactions, using dynamically triangulated membrane simulations combined with the Brusselator model. We found that membrane deformation changes stable patterns relative to those that occur on a non-deformable curved surface, as determined by linear stability analysis. We further found that budding and multi-spindle shapes are induced by Turing patterns, and we also observed the transition from oscillation patterns to stable spot patterns. Our results demonstrate the importance of mechanochemical feedback in pattern formation on deforming membranes.

Fracture pattern formation in frictional, cohesive, granular material

2010 ◽  
Vol 368 (1910) ◽  
pp. 95-118 ◽  
Author(s):  
Alison Ord ◽  
Bruce E. Hobbs
Keyword(s):  
Pattern Formation ◽  
Granular Media ◽  
Large Scale ◽  
High Stress ◽  
Reaction Diffusion ◽  
Fracture Pattern ◽  
Reaction Diffusion Equations ◽  
Three Dimensions ◽  
Localized Deformation

Naturally, deformed rocks commonly contain crack arrays (joints) forming patterns with systematic relationships to the large-scale deformation. Kinematically, joints can be mode-1, -2 or -3 or combinations of these, but there is no overarching theory for the development of the patterns. We develop a model motivated by dislocation pattern formation in metals. The problem is formulated in one dimension in terms of coupled reaction–diffusion equations, based on computer simulations of crack development in deformed granular media with cohesion. The cracks are treated as interacting defects, and the densities of defects diffuse through the rock mass. Of particular importance is the formation of cracks at high stresses associated with force-chain buckling and variants of this configuration; these cracks play the role of ‘inhibitors’ in reaction–diffusion relationships. Cracks forming at lower stresses act as relatively mobile defects. Patterns of localized deformation result from (i) competition between the growth of the density of ‘mobile’ defects and the inhibition of these defects by crack configurations forming at high stress and (ii) the diffusion of damage arising from these two populations each characterized by a different diffusion coefficient. The extension of this work to two and three dimensions is discussed.

scholarly journals On-chip scalable mode-selective converter based on asymmetrical micro-racetrack resonators

Nanophotonics ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1447-1455
Author(s):  
Huifu Xiao ◽  
Zhenfu Zhang ◽  
Junbo Yang ◽  
Xu Han ◽  
Wenping Chen ◽  
...  
Keyword(s):  
Large Scale ◽  
Optical Network ◽  
Monochromatic Light ◽  
Network On Chip ◽  
Silicon On Insulator ◽  
Intelligent Network ◽  
Silicon Waveguides ◽  
Mode Division Multiplexing ◽  
Potential Applications ◽  
On Chip

AbstractMode division multiplexing (MDM) technology has been well known to researchers for its ability to increase the link capacity of photonic network. While various mode processing devices were demonstrated in recent years, the reconfigurability of multi-mode processing devices, which is vital for large-scale multi-functional networks, is rarely developed. In this paper, we first propose and experimentally demonstrate a scalable mode-selective converter using asymmetrical micro-racetrack resonators (MRRs) for optical network-on-chip. The proposed device, composed of cascaded MRRs, is able to convert the input monochromatic light to an arbitrary supported mode in the output waveguide as required. Thermo-optical effect of silicon waveguides is adopted to tune the working states of the device. To test the utility, a device for proof-of-concept is fabricated and experimentally demonstrated based on silicon-on-insulator substrate. The measured spectra of the device show that the extinction ratios of MRRs are larger than 18 dB, and modal crosstalk for selected modes are all less than −16.5 dB. The switching time of the fabricated device is in the level of about 40 μs. The proposed device is believed to have potential applications in multi-functional and intelligent network-on-chip, especially in reconfigurable MDM networks.

scholarly journals The human EDAR 370V/A polymorphism affects tooth root morphology potentially through the modification of a reaction–diffusion system

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Keiichi Kataoka ◽  
Hironori Fujita ◽  
Mutsumi Isa ◽  
Shimpei Gotoh ◽  
Akira Arasaki ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Computational Study ◽  
Reaction Diffusion ◽  
Human Migration ◽  
Reaction Diffusion System ◽  
Diffusion System ◽  
Tooth Root ◽  
Computed Tomography Images ◽  
Diffusion Dynamics ◽  
Root Morphogenesis

AbstractMorphological variations in human teeth have long been recognized and, in particular, the spatial and temporal distribution of two patterns of dental features in Asia, i.e., Sinodonty and Sundadonty, have contributed to our understanding of the human migration history. However, the molecular mechanisms underlying such dental variations have not yet been completely elucidated. Recent studies have clarified that a nonsynonymous variant in the ectodysplasin A receptor gene (EDAR370V/A; rs3827760) contributes to crown traits related to Sinodonty. In this study, we examined the association between theEDARpolymorphism and tooth root traits by using computed tomography images and identified that the effects of theEDARvariant on the number and shape of roots differed depending on the tooth type. In addition, to better understand tooth root morphogenesis, a computational analysis for patterns of tooth roots was performed, assuming a reaction–diffusion system. The computational study suggested that the complicated effects of theEDARpolymorphism could be explained when it is considered that EDAR modifies the syntheses of multiple related molecules working in the reaction–diffusion dynamics. In this study, we shed light on the molecular mechanisms of tooth root morphogenesis, which are less understood in comparison to those of tooth crown morphogenesis.

scholarly journals C4 Bacterial Volatiles Improve Plant Health

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 682
Author(s):  
Bruno Henrique Silva Dias ◽  
Sung-Hee Jung ◽  
Juliana Velasco de Castro Oliveira ◽  
Choong-Min Ryu
Keyword(s):  
Plant Growth ◽  
Volatile Compounds ◽  
Large Scale ◽  
Growth Promotion ◽  
Plant Growth Promoting Rhizobacteria ◽  
Plant Health ◽  
Systemic Resistance ◽  
Potential Applications ◽  
Plant Growth Promoting ◽  
Bacterial Volatiles

Plant growth-promoting rhizobacteria (PGPR) associated with plant roots can trigger plant growth promotion and induced systemic resistance. Several bacterial determinants including cell-wall components and secreted compounds have been identified to date. Here, we review a group of low-molecular-weight volatile compounds released by PGPR, which improve plant health, mostly by protecting plants against pathogen attack under greenhouse and field conditions. We particularly focus on C4 bacterial volatile compounds (BVCs), such as 2,3-butanediol and acetoin, which have been shown to activate the plant immune response and to promote plant growth at the molecular level as well as in large-scale field applications. We also disc/ uss the potential applications, metabolic engineering, and large-scale fermentation of C4 BVCs. The C4 bacterial volatiles act as airborne signals and therefore represent a new type of biocontrol agent. Further advances in the encapsulation procedure, together with the development of standards and guidelines, will promote the application of C4 volatiles in the field.

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