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https://read.qxmd.com/read/30603073/structural-colours-in-the-frond-of-microsorum-thailandicum
#1
Lisa Maria Steiner, Yu Ogawa, Villads Egede Johansen, Clive R Lundquist, Heather Whitney, Silvia Vignolini
Blue and near-ultraviolet structural colours have often been reported in understorey plants living in deep shade. While this intense blue coloration is very catchy to the eye of a human observer, there are cases in which structural colours can be hidden either by the scattered light interacting with pigments or because they are found in unexpected positions in the plants. Here, we show that the fronds of Microsorum thailandicum produce structural coloration on both the adaxial and abaxial epidermal surface...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603072/i-see-your-false-colours-how-artificial-stimuli-appear-to-different-animal-viewers
#2
Mary Caswell Stoddard, Audrey E Miller, Harold N Eyster, Derya Akkaynak
The use of artificially coloured stimuli, especially to test hypotheses about sexual selection and anti-predator defence, has been common in behavioural ecology since the pioneering work of Tinbergen. To investigate the effects of colour on animal behaviour, many researchers use paints, markers and dyes to modify existing colours or to add colour to synthetic models. Because colour perception varies widely across species, it is critical to account for the signal receiver's vision when performing colour manipulations...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603071/nonlinear-optical-spectroscopy-and-two-photon-excited-fluorescence-spectroscopy-reveal-the-excited-states-of-fluorophores-embedded-in-a-beetle-s-elytra
#3
Sébastien R Mouchet, Charlotte Verstraete, Dimitrije Mara, Stijn Van Cleuvenbergen, Ewan D Finlayson, Rik Van Deun, Olivier Deparis, Thierry Verbiest, Bjorn Maes, Pete Vukusic, Branko Kolaric
Upon illumination by ultraviolet light, many animal species emit light through fluorescence processes arising from fluorophores embedded within their biological tissues. Fluorescence studies in living organisms are however relatively scarce and so far limited to the linear regime. Multiphoton excitation fluorescence analyses as well as nonlinear optical techniques offer unique possibilities to investigate the effects of the local environment on the excited states of fluorophores. Herein, these techniques are applied for the first time to study of the naturally controlled fluorescence in insects...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603070/coherent-backscattering-of-light-by-an-anisotropic-biological-network
#4
Gianni Jacucci, Olimpia D Onelli, Antonio De Luca, Jacopo Bertolotti, Riccardo Sapienza, Silvia Vignolini
The scattering strength of a random medium relies on the geometry and spatial distribution of its components as well as on their refractive index. Anisotropy can, therefore, play a major role in the optimization of the scattering efficiency in both biological and synthetic materials. In this study, we show that, by exploiting the coherent backscattering phenomenon, it is possible to characterize the optical anisotropy in Cyphochilus beetle scales without the need to change their orientation or their thickness...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603069/quantitative-characterization-of-iridescent-colours-in-biological-studies-a-novel-method-using-optical-theory
#5
Hugo Gruson, Christine Andraud, Willy Daney de Marcillac, Serge Berthier, Marianne Elias, Doris Gomez
Iridescent colours are colours that change with viewing or illumination geometry. While they are widespread in many living organisms, most evolutionary studies on iridescence do not take into account their full complexity. Few studies try to precisely characterize what makes iridescent colours special: their angular dependency. Yet, it is likely that this angular dependency has biological functions and is therefore submitted to evolutionary pressures. For this reason, evolutionary biologists need a repeatable method to measure iridescent colours as well as variables to precisely quantify the angular dependency...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603068/functional-nanomaterials-to-augment-photosynthesis-evidence-and-considerations-for-their-responsible-use-in-agricultural-applications
#6
REVIEW
Thomas A Swift, Thomas A A Oliver, M Carmen Galan, Heather M Whitney
At the current population growth rate, we will soon be unable to meet increasing food demands. As a consequence of this potential problem, considerable efforts have been made to enhance crop productivity by breeding, genetics and improving agricultural practices. While these techniques have traditionally been successful, their efficacy since the 'green revolution' has begun to significantly plateau. This stagnation of gains combined with the negative effects of climate change on crop yields has prompted researchers to develop novel and radical methods to increase crop productivity...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603067/phenotypic-variation-in-heliconius-erato-crosses-shows-that-iridescent-structural-colour-is-sex-linked-and-controlled-by-multiple-genes
#7
Melanie N Brien, Juan Enciso-Romero, Andrew J Parnell, Patricio A Salazar, Carlos Morochz, Darwin Chalá, Hannah E Bainbridge, Thomas Zinn, Emma V Curran, Nicola J Nadeau
Bright, highly reflective iridescent colours can be seen across nature and are produced by the scattering of light from nanostructures. Heliconius butterflies have been widely studied for their diversity and mimicry of wing colour patterns. Despite iridescence evolving multiple times in this genus, little is known about the genetic basis of the colour and the development of the structures which produce it. Heliconius erato can be found across Central and South America, but only races found in western Ecuador and Colombia have developed blue iridescent colour...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603066/thin-film-structural-coloration-from-simple-fused-scales-in-moths
#8
Cédric Kilchoer, Ullrich Steiner, Bodo D Wilts
The metallic coloration of insects often originates from diverse nanostructures ranging from simple thin films to complex three-dimensional photonic crystals. In Lepidoptera, structural coloration is widely present and seems to be abundant in extant species. However, even some basal moths exhibit metallic coloration. Here, we have investigated the origin of the vivid metallic colours of the wing scales of the basal moth Micropterix aureatella by spectrophotometry and scanning electron microscopy. The metallic gold-, bronze- and purple-coloured scales share a similar anatomy formed of a fused lower and upper lamina resulting in a single thin film...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603065/reflections-on-iridescent-neck-and-breast-feathers-of-the-peacock-pavo-cristatus
#9
Pascal Freyer, Bodo D Wilts, Doekele G Stavenga
The blue neck and breast feathers of the peacock are structurally coloured due to an intricate photonic crystal structure in the barbules consisting of a two-dimensionally ordered rectangular lattice of melanosomes (melanin rodlets) and air channels embedded in a keratin matrix. We here investigate the feather coloration by performing microspectrophotometry, imaging scatterometry and angle-dependent reflectance measurements. Using previously determined wavelength-dependent refractive indices of melanin and keratin, we interpret the spectral and spatial reflection characteristics by comparing the measured spectra to calculated spectra by effective-medium multilayer and full three-dimensional finite-difference time-domain modelling...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30603064/differences-in-the-optical-properties-of-valve-and-girdle-band-in-a-centric-diatom
#10
Johannes W Goessling, Yanyan Su, Christian Maibohm, Marianne Ellegaard, Michael Kühl
Diatoms are phototrophic single-celled microalgae encased in a cell wall (frustule) made of amorphous silicate. The frustule comprises two valves connected by a variable number of girdle bands, all exhibiting periodic micro/nanoporous structures. We studied the optical properties in water of girdle bands from the centric diatom Coscinodiscus granii , a frustule part that so far has received little attention by the scientific community. We show that valves and girdle bands exhibit different optical properties, as valves attenuate shorter wavelengths and girdle bands attenuate longer wavelengths of the visible light spectrum...
February 6, 2019: Interface Focus
https://read.qxmd.com/read/30443338/semantic-information-autonomous-agency-and-non-equilibrium-statistical-physics
#11
Artemy Kolchinsky, David H Wolpert
Shannon information theory provides various measures of so-called syntactic information, which reflect the amount of statistical correlation between systems. By contrast, the concept of 'semantic information' refers to those correlations which carry significance or 'meaning' for a given system. Semantic information plays an important role in many fields, including biology, cognitive science and philosophy, and there has been a long-standing interest in formulating a broadly applicable and formal theory of semantic information...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443337/haematopoietic-stem-cells-entropic-landscapes-of-differentiation
#12
K Wiesner, J Teles, M Hartnor, C Peterson
The metaphor of a potential epigenetic differentiation landscape broadly suggests that during differentiation a stem cell approaches a stable equilibrium state from a higher free energy towards a stable equilibrium state which represents the final cell type. It has been conjectured that there is an analogy to the concept of entropy in statistical mechanics. In this context, in the undifferentiated state, the entropy would be large since fewer constraints exist on the gene expression programmes of the cell. As differentiation progresses, gene expression programmes become more and more constrained and thus the entropy would be expected to decrease...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443336/intrinsic-limits-of-information-transmission-in-biochemical-signalling-motifs
#13
Ryan Suderman, Eric J Deeds
All living things have evolved to sense changes in their environment in order to respond in adaptive ways. At the cellular level, these sensing systems generally involve receptor molecules at the cell surface, which detect changes outside the cell and relay those changes to the appropriate response elements downstream. With the advent of experimental technologies that can track signalling at the single-cell level, it has become clear that many signalling systems exhibit significant levels of 'noise,' manifesting as differential responses of otherwise identical cells to the same environment...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443335/computational-modelling-unravels-the-precise-clockwork-of-cyanobacteria
#14
REVIEW
Nicolas M Schmelling, Ilka M Axmann
Precisely timing the regulation of gene expression by anticipating recurring environmental changes is a fundamental part of global gene regulation. Circadian clocks are one form of this regulation, which is found in both eukaryotes and prokaryotes, providing a fitness advantage for these organisms. Whereas many different eukaryotic groups harbour circadian clocks, cyanobacteria are the only known oxygenic phototrophic prokaryotes to regulate large parts of their genes in a circadian fashion. A decade of intensive research on the mechanisms and functionality using computational and mathematical approaches in addition to the detailed biochemical and biophysical understanding make this the best understood circadian clock...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443334/a-thermodynamically-consistent-model-of-finite-state-machines
#15
Dominique Chu, Richard E Spinney
Finite-state machines (FSMs) are a theoretically and practically important model of computation. We propose a general, thermodynamically consistent model of FSMs and characterize the resource requirements of these machines. We model FSMs as time-inhomogeneous Markov chains. The computation is driven by instantaneous manipulations of the energy levels of the states. We calculate the entropy production of the machine, its error probability, and the time required to complete one update step. We find that a sequence of generalized bit-setting operations is sufficient to implement any FSM...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443333/thermodynamic-efficiency-of-contagions-a-statistical-mechanical-analysis-of-the-sis-epidemic-model
#16
Nathan Harding, Ramil Nigmatullin, Mikhail Prokopenko
We present a novel approach to the study of epidemics on networks as thermodynamic phenomena, quantifying the thermodynamic efficiency of contagions, considered as distributed computational processes. Modelling SIS dynamics on a contact network statistical-mechanically, we follow the maximum entropy (MaxEnt) principle to obtain steady-state distributions and derive, under certain assumptions, relevant thermodynamic quantities both analytically and numerically. In particular, we obtain closed-form solutions for some cases, while interpreting key epidemic variables, such as the reproductive ratio of a SIS model, in a statistical mechanical setting...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443332/something-has-to-give-scaling-combinatorial-computing-by-biological-agents-exploring-physical-networks-encoding-np-complete-problems
#17
REVIEW
Falco C M J M van Delft, Giulia Ipolitti, Dan V Nicolau, Ayyappasamy Sudalaiyadum Perumal, Ondřej Kašpar, Sara Kheireddine, Sebastian Wachsmann-Hogiu, Dan V Nicolau
On-chip network-based computation, using biological agents, is a new hardware-embedded approach which attempts to find solutions to combinatorial problems, in principle, in a shorter time than the fast, but sequential electronic computers. This analytical review starts by describing the underlying mathematical principles, presents several types of combinatorial (including NP-complete) problems and shows current implementations of proof of principle developments. Taking the subset sum problem as example for in-depth analysis, the review presents various options of computing agents, and compares several possible operation 'run modes' of network-based computer systems...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443331/from-statistical-inference-to-a-differential-learning-rule-for-stochastic-neural-networks
#18
Luca Saglietti, Federica Gerace, Alessandro Ingrosso, Carlo Baldassi, Riccardo Zecchina
Stochastic neural networks are a prototypical computational device able to build a probabilistic representation of an ensemble of external stimuli. Building on the relationship between inference and learning, we derive a synaptic plasticity rule that relies only on delayed activity correlations, and that shows a number of remarkable features. Our delayed-correlations matching (DCM) rule satisfies some basic requirements for biological feasibility: finite and noisy afferent signals, Dale's principle and asymmetry of synaptic connections, locality of the weight update computations...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443330/towards-fungal-computer
#19
Andrew Adamatzky
We propose that fungi Basidiomycetes can be used as computing devices: information is represented by spikes of electrical activity, a computation is implemented in a mycelium network and an interface is realized via fruit bodies. In a series of scoping experiments, we demonstrate that electrical activity recorded on fruits might act as a reliable indicator of the fungi's response to thermal and chemical stimulation. A stimulation of a fruit is reflected in changes of electrical activity of other fruits of a cluster, i...
December 6, 2018: Interface Focus
https://read.qxmd.com/read/30443329/membrane-remodelling-by-a-lipidated-endosomal-sorting-complex-required-for-transport-iii-chimera-in-vitro
#20
C J Marklew, A Booth, P A Beales, B Ciani
The complexity of eukaryotic cells is underscored by the compartmentalization of chemical signals by phospholipid membranes. A grand challenge of synthetic biology is building life from the 'bottom-up', for the purpose of generating systems simple enough to precisely interrogate biological pathways or for adapting biology to perform entirely novel functions. Achieving compartmentalization of chemistries in an addressable manner is a task exquisitely refined by nature and embodied in a unique membrane remodelling machinery that pushes membranes away from the cytosol, the ESCRT-III (endosomal sorting complex required for transport-III) complex...
October 6, 2018: Interface Focus
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