Signal Amplification in Highly Ordered Networks Is Driven by Geometry

Here, we hypothesize that, in biological systems such as cell surface receptors that relay external signals, clustering leads to substantial improvements in signaling efficiency. Representing cooperative signaling networks as planar graphs and applying Euler’s polyhedron formula, we can show that clustering may result in an up to a 200% boost in signaling amplitude dictated solely by the size and geometry of the network. This is a fundamental relationship that applies to all clustered systems regardless of its components. Nature has figured out a way to maximize the signaling amplitude in receptors that relay weak external signals. In addition, in cell-to-cell interactions, clustering both receptors and ligands may result in maximum efficiency and synchronization. The importance of clustering geometry in signaling efficiency goes beyond biological systems and can inform the design of amplifiers in nonbiological systems.

An Open Dynamical System Approach to Dissipative Quantum Dot Array Antennas

A new computational approach to quantum antennas based on first principle open stochastic quantum dynamics.<div><br></div><div>We develop a general computational approach for the analysis and design of quantum antenna systems comprised of coupled quantum dot arrays interacting with external fields and producing quantum radiation. The method is based on using the GKSL master equation to model quantum dissipation and decoherence. The density operator of a coupled two-level quantum dot (qbit) array, excited by classical external signals with variable amplitude and phase, is evolved in time using a quantum Liouville-like equation (the master equation). We illustrate the method in a numerical example where it is shown that manipulating the phase excitations of individual quantum dots may significantly enhance the directive radiation properties of the quantum dot antenna system<br></div>

An Open Dynamical System Approach to Dissipative Quantum Dot Array Antennas

A new computational approach to quantum antennas based on first principle open stochastic quantum dynamics.<div><br></div><div>We develop a general computational approach for the analysis and design of quantum antenna systems comprised of coupled quantum dot arrays interacting with external fields and producing quantum radiation. The method is based on using the GKSL master equation to model quantum dissipation and decoherence. The density operator of a coupled two-level quantum dot (qbit) array, excited by classical external signals with variable amplitude and phase, is evolved in time using a quantum Liouville-like equation (the master equation). We illustrate the method in a numerical example where it is shown that manipulating the phase excitations of individual quantum dots may significantly enhance the directive radiation properties of the quantum dot antenna system<br></div>

External signals regulate continuous transcriptional states in hematopoietic stem cells

Hematopoietic stem cells (HSCs) must ensure adequate blood cell production following distinct external stressors. A comprehensive understanding of in vivo heterogeneity and specificity of HSC responses to external stimuli is currently lacking. We performed single-cell RNA sequencing (scRNA-Seq) on functionally validated mouse HSCs and LSK (Lin-, c-Kit+, Sca1+) progenitors after in vivo pharmacological perturbation of niche signals interferon, granulocyte colony-stimulating factor (G-CSF), and prostaglandin. We identified six HSC states that are characterized by enrichment but not exclusive expression of marker genes. External signals induced rapid transitions between HSC states but transcriptional response varied both between external stimulants and within the HSC population for a given perturbation. In contrast to LSK progenitors, HSCs were characterized by a greater link between molecular signatures at baseline and in response to external stressors. Chromatin analysis of unperturbed HSCs and LSKs by scATAC-Seq suggested some HSC-specific, cell intrinsic predispositions to niche signals. We compiled a comprehensive resource of HSC- and LSK progenitor-specific chromatin and transcriptional features that represent determinants of signal receptiveness and regenerative potential during stress hematopoiesis.

MODELING THE PROPERTIES OF GAS SENSOR MATERIALS BASED ON ORGANIC SEMICONDUCTORS

An approach has been developed for modeling the gas-sensitive and physicochemical properties of materials based on organic semiconductors. The approach is based on the use of various modeling methods: linear, nonlinear regression analysis and neural networks. The parameters of the technological process of the formation of materials were selected as external signals for modeling: the mass fraction of metal in the film-forming solution, the temperature and time of the first and second stages of annealing.

The people behind the papers – Megan Rommelfanger and Adam MacLean

Cell fate decisions are dependent on both internal and external factors, but mathematical models of this process have often neglected the external signals. A new paper in Development describes a multiscale model that integrates intracellular gene regulatory networks with a cell-cell communication network at single-cell resolution. We caught up with the authors, PhD student Megan Rommelfanger and Adam MacLean, Assistant Professor at the University of Southern California, to find out more about their research.

A Comparative Analysis of Consumption: Evidence from a Cultural Goods Market

This study uniquely employs a fuzzy-set qualitative comparative analysis (fsQCA) technique to account for complex relationships in consumption. The fsQCA technique assumes that relationships are based on a set–subset relationship. This assumption is fundamental when decision-makers are affected by information asymmetry and are, thus, required to jointly evaluate the credibility and reliability of a range of external signals. This issue also affects consumers in markets for cultural goods, where the quality of products is not known with certainty in advance of the purchase decision. Our study uses fsQCA to establish the effect of different quality signals on consumption in the US market for video game software. Our results show that reviews from professional critics alongside brand extension and multi-platform release strategies act as signals of product quality and, therefore, lead to high sales performance.

Anti-$\mathcal{PT}$-symmetric Kerr gyroscope

Non-Hermitian systems can exhibit unconventional spectral singularities called exceptional points (EPs). Various EP sensors have been fabricated in recent years, showing strong spectral responses to external signals. Here we propose how to achieve a nonlinear anti-parity-time ($\mathcal{APT}$) gyroscope by spinning an optical resonator. We show that, in the absence of any nonlinearity, the sensitivity or optical mode splitting of the linear device can be magnified up to 3 orders than that of the conventional device without EPs. Remarkably, the $\mathcal{APT}$ symmetry can be broken when including the Kerr nonlinearity of the materials and, as the result, the detection threshold can be significantly lowered, i.e., much weaker rotations which are well beyond the ability of a linear gyroscope can now be detected with the nonlinear device. Our work shows the powerful ability of $\mathcal{APT}$ gyroscopes in practice to achieve ultrasensitive rotation measurement.

Two structurally different oomycete MAMPs induce distinctive plant immune responses.

Plants recognize a variety of external signals and induce appropriate mechanisms to increase their tolerance to biotic and abiotic stresses. Precise recognition of attacking pathogens and induction of effective resistance mechanisms are critical functions for plant survival. Some molecular patterns unique to a certain group of microbes (MAMPs, microbe-associated molecular patterns) are sensed by plant cells as non-self molecules via pattern recognition receptors. While a variety of MAMPs of bacterial and fungal origin have been identified, reports on MAMPs of oomycete pathogens are relatively limited. This study aimed to identify unique MAMP elicitors from the oomycete pathogen Phytophthora infestans, the causal agent of potato late blight. Using reactive oxygen species (ROS) production and phytoalexin production in potato as markers for the purification of oomycete elicitors, we identified two structurally different groups of elicitors, namely ceramides and diacylglycerols. P. infestans ceramide (Pi-Cer) elicitors induced ROS production, while diacylglycerol (Pi-DAG) elicitors, containing eicosapentaenoic acid (EPA) as a substructure, induced the formation of phytoalexins in potato. Pi-Cer and Pi-DAG are also contained in the mycelia of another oomycete pathogen Pythium aphanidermatum, indicating that they are MAMPs of oomycetes. When Arabidopsis was treated with Pi-Cer and EPA, partially overlapping but different sets of genes were induced. Furthermore, simultaneous treatment with Pi-Cer and EPA did not have a cumulative effect on induced genes, but rather the expression of some genes induced by EPA was attenuated by the co-treatment with Pi-Cer. These results indicate that plants may combine the signals from simultaneously recognized MAMP elicitors to specifically adapt the defense response to a particular pathogen.

Autoregulation of switching behavior by cellular compartment size

Many kinds of cellular compartments comprise decision making mechanisms that control growth and shrinkage of the compartment in response to external signals. Key examples include synaptic plasticity mechanisms that regulate the size and strength of synapses in the nervous system. However, when synaptic compartments and postsynaptic densities are small such mechanisms operate in a regime where chemical reactions are discrete and stochastic due to low copy numbers of the species involved. In this regime, fluctuations are large relative to mean concentrations, and inherent discreteness leads to breakdown of mass action kinetics. Understanding how synapses and other small compartments achieve reliable switching in the low copy number limit thus remains a key open problem. We propose a novel self regulating signaling motif that exploits the breakdown of mass action kinetics to generate a reliable size-regulated switch. We demonstrate this in simple two and three-species chemical reaction systems and uncover a key role for inhibitory loops among species in generating switching behavior. This provides an elementary motif that could allow size dependent regulation in more complex reaction pathways and may explain discrepant experimental results on well-studied biochemical pathways.