From Cellular Attractor Selection to Adaptive Signal Control for Traffic Networks.
Ontology highlight
ABSTRACT:
SUBMITTER: Tian D
PROVIDER: S-EPMC4789751 | biostudies-other | 2016 Mar
REPOSITORIES: biostudies-other
Similar Datasets
Project description:BackgroundThe experimental observations and numerical studies with dissipative metabolic networks have shown that cellular enzymatic activity self-organizes spontaneously leading to the emergence of a Systemic Metabolic Structure in the cell, characterized by a set of different enzymatic reactions always locked into active states (metabolic core) while the rest of the catalytic processes are only intermittently active. This global metabolic structure was verified for Escherichia coli, Helicobacter pylori and Saccharomyces cerevisiae, and it seems to be a common key feature to all cellular organisms. In concordance with these observations, the cell can be considered a complex metabolic network which mainly integrates a large ensemble of self-organized multienzymatic complexes interconnected by substrate fluxes and regulatory signals, where multiple autonomous oscillatory and quasi-stationary catalytic patterns simultaneously emerge. The network adjusts the internal metabolic activities to the external change by means of flux plasticity and structural plasticity.Methodology/principal findingsIn order to research the systemic mechanisms involved in the regulation of the cellular enzymatic activity we have studied different catalytic activities of a dissipative metabolic network under different external stimuli. The emergent biochemical data have been analysed using statistical mechanic tools, studying some macroscopic properties such as the global information and the energy of the system. We have also obtained an equivalent Hopfield network using a Boltzmann machine. Our main result shows that the dissipative metabolic network can behave as an attractor metabolic network.Conclusions/significanceWe have found that the systemic enzymatic activities are governed by attractors with capacity to store functional metabolic patterns which can be correctly recovered from specific input stimuli. The network attractors regulate the catalytic patterns, modify the efficiency in the connection between the multienzymatic complexes, and stably retain these modifications. Here for the first time, we have introduced the general concept of attractor metabolic network, in which this dynamic behavior is observed.
| S-EPMC3598861 | biostudies-literature
Project description:Cells switch between various stable genetic programs (attractors) to accommodate environmental conditions. Signal transduction machineries efficiently convey environmental changes to the gene regulation apparatus in order to express the appropriate genetic program. However, since the number of environmental conditions is much larger than that of available genetic programs so that the cell may utilize the same genetic program for a large set of conditions, it may not have evolved a signaling pathway for every environmental condition, notably those that are rarely encountered. Here we show that in the absence of signal transduction, switching to the appropriate attractor state expressing the genes that afford adaptation to the external condition can occur. In a synthetic bistable gene switch in Escherichia coli in which mutually inhibitory operons govern the expression of two genes required in two alternative nutritional environments, cells reliably selected the "adaptive attractor" driven by gene expression noise. A mathematical model suggests that the "non-adaptive attractor" is avoided because in unfavorable conditions, cellular activity is lower, which suppresses mRNA metabolism, leading to larger fluctuations in gene expression. This, in turn, renders the non-adaptive state less stable. Although attractor selection is not as efficient as signal transduction via a dedicated cascade, it is simple and robust, and may represent a primordial mechanism for adaptive responses that preceded the evolution of signaling cascades for the frequently encountered environmental changes.
| S-EPMC1762378 | biostudies-literature
Project description:Current transportation management systems rely on physical sensors that use traffic volume and queue-lengths. These physical sensors incur significant capital and maintenance costs. The ubiquity of mobile devices has made possible access to accurate and cheap traffic delay data. However, current traffic signal control algorithms do not accommodate the use of such data. In this paper, we propose a novel parsimonious model to utilize real-time crowdsourced delay data for traffic signal management. We demonstrate the versatility and effectiveness of the data and the proposed model on seven different intersections across three cities and two countries. This signal system provides an opportunity to leapfrog from physical sensors to low-cost, reliable crowdsourced data.
| S-EPMC7138299 | biostudies-literature
Project description:Traffic congestion has become common in urban areas worldwide. To solve this problem, the method of searching a solution using artificial intelligence has recently attracted widespread attention because it can solve complex problems such as traffic signal control. This study developed two traffic signal control models using reinforcement learning and a microscopic simulation-based evaluation for an isolated intersection and two coordinated intersections. To develop these models, a deep Q-network (DQN) was used, which is a promising reinforcement learning algorithm. The performance was evaluated by comparing the developed traffic signal control models in this research with the fixed-time signal optimized by Synchro model, which is a traffic signal optimization model. The evaluation showed that the developed traffic signal control model of the isolated intersection was validated, and the coordination of intersections was superior to that of the fixed-time signal control method.
| S-EPMC8412290 | biostudies-literature
Project description:As an effective method to alleviate traffic congestion, traffic signal coordination control has been applied in many cities to manage queues and to regulate traffic flow under oversaturated traffic condition. However, the previous methods are usually based on two hypotheses. One is that traffic demand is constant. The other assumes that the velocity of vehicle is immutable when entering the downstream section. In the paper, we develop a novel traffic coordination control method to control the traffic flow along oversaturated two-way arterials without both these hypotheses. The method includes two modules: intersection coordination control and arterial coordination control. The green time plan for all intersections can be obtained by the module of intersection coordination control. The module of arterial coordination control can optimize offset plan for all intersections along oversaturated two-way arterials. The experiment results verify that the proposed method can effectively control the queue length under the oversaturated traffic state. In addition, the delay in this method can be decreased by 5.4% compared with the existing delay minimization method and 13.6% compared with the traffic coordination control method without offset optimization. Finally, the proposed method can balance the delay level of different links along oversaturated arterial, which can directly reflect the efficiency of the proposed method on the traffic coordination control under oversaturated traffic condition.
| S-EPMC7924511 | biostudies-literature
Project description:The complex connectivity of the cerebral cortex suggests that inter-regional communication is a primary function. Using computational modeling, we show that anatomical connectivity may be a major determinant for global information flow in brain networks. A macaque brain network was implemented as a communication network in which signal units flowed between grey matter nodes along white matter paths. Compared to degree-matched surrogate networks, information flow on the macaque brain network was characterized by higher loss rates, faster transit times and lower throughput, suggesting that neural connectivity may be optimized for speed rather than fidelity. Much of global communication was mediated by a "rich club" of hub regions: a sub-graph comprised of high-degree nodes that are more densely interconnected with each other than predicted by chance. First, macaque communication patterns most closely resembled those observed for a synthetic rich club network, but were less similar to those seen in a synthetic small world network, suggesting that the former is a more fundamental feature of brain network topology. Second, rich club regions attracted the most signal traffic and likewise, connections between rich club regions carried more traffic than connections between non-rich club regions. Third, a number of rich club regions were significantly under-congested, suggesting that macaque connectivity actively shapes information flow, funneling traffic towards some nodes and away from others. Together, our results indicate a critical role of the rich club of hub nodes in dynamic aspects of global brain communication.
| S-EPMC3886893 | biostudies-literature
Project description:BackgroundBoolean networks (BNs) provide an effective modelling formalism for various complex biochemical phenomena. Their long term behaviour is represented by attractors-subsets of the state space towards which the BN eventually converges. These are then typically linked to different biological phenotypes. Depending on various logical parameters, the structure and quality of attractors can undergo a significant change, known as a bifurcation. We present a methodology for analysing bifurcations in asynchronous parametrised Boolean networks.ResultsIn this paper, we propose a computational framework employing advanced symbolic graph algorithms that enable the analysis of large networks with hundreds of Boolean variables. To visualise the results of this analysis, we developed a novel interactive presentation technique based on decision trees, allowing us to quickly uncover parameters crucial to the changes in the attractor landscape. As a whole, the methodology is implemented in our tool AEON. We evaluate the method's applicability on a complex human cell signalling network describing the activity of type-1 interferons and related molecules interacting with SARS-COV-2 virion. In particular, the analysis focuses on explaining the potential suppressive role of the recently proposed drug molecule GRL0617 on replication of the virus.ConclusionsThe proposed method creates a working analogy to the concept of bifurcation analysis widely used in kinetic modelling to reveal the impact of parameters on the system's stability. The important feature of our tool is its unique capability to work fast with large-scale networks with a relatively large extent of unknown information. The results obtained in the case study are in agreement with the recent biological findings.
| S-EPMC9092939 | biostudies-literature
Project description:Neural computations underlying cognitive functions require calibration of the strength of excitatory and inhibitory synaptic connections and are associated with modulation of gamma frequency oscillations in network activity. However, principles relating gamma oscillations, synaptic strength and circuit computations are unclear. We address this in attractor network models that account for grid firing and theta-nested gamma oscillations in the medial entorhinal cortex. We show that moderate intrinsic noise massively increases the range of synaptic strengths supporting gamma oscillations and grid computation. With moderate noise, variation in excitatory or inhibitory synaptic strength tunes the amplitude and frequency of gamma activity without disrupting grid firing. This beneficial role for noise results from disruption of epileptic-like network states. Thus, moderate noise promotes independent control of multiplexed firing rate- and gamma-based computational mechanisms. Our results have implications for tuning of normal circuit function and for disorders associated with changes in gamma oscillations and synaptic strength.
| S-EPMC4508578 | biostudies-literature
Project description:This paper proposes an emergency Traffic Adaptive MAC (eTA-MAC) protocol for WBANs based on Prioritization. The main advantage of the protocol is to provide traffic ranking through a Traffic Class Prioritization-based slotted-Carrier Sense Multiple Access/Collision Avoidance (TCP-CSMA/CA) scheme. The emergency traffic is handled through Emergency Traffic Class Provisioning-based slotted-CSMA/CA (ETCP-CSMA/CA) scheme. The emergency-based traffic adaptivity is provided through Emergency-based Traffic Adaptive slotted-CSMA/CA (ETA-CSMA/CA) scheme. The TCP-CSMA/CA scheme assigns a distinct, minimized and prioritized backoff period range to each traffic class in every backoff during channel access in Contention Access Period (CAP). The ETCP-CSMA/CA scheme delivers the sporadic emergency traffic that occurs at a single or multiple BMSN(s) instantaneously, with minimum delay and packet loss. It does this while being aware of normal traffic in the CAP. Then, the ETA-CSMA/CA scheme creates a balance between throughput and energy in the sporadic emergency situation with energy preservation of normal traffic BMSNs. The proposed protocol is evaluated using NS-2 simulator. The results indicate that the proposed protocol is better than the existing Medium Access Control (MAC) protocols by 86% decrease in packet delivery delay, 61% increase in throughput, and a 76% decrease in energy consumption.
| S-EPMC6886830 | biostudies-literature
Project description:Continuous attractor models of working-memory store continuous-valued information in continuous state-spaces, but are sensitive to noise processes that degrade memory retention. Short-term synaptic plasticity of recurrent synapses has previously been shown to affect continuous attractor systems: short-term facilitation can stabilize memory retention, while short-term depression possibly increases continuous attractor volatility. Here, we present a comprehensive description of the combined effect of both short-term facilitation and depression on noise-induced memory degradation in one-dimensional continuous attractor models. Our theoretical description, applicable to rate models as well as spiking networks close to a stationary state, accurately describes the slow dynamics of stored memory positions as a combination of two processes: (i) diffusion due to variability caused by spikes; and (ii) drift due to random connectivity and neuronal heterogeneity. We find that facilitation decreases both diffusion and directed drifts, while short-term depression tends to increase both. Using mutual information, we evaluate the combined impact of short-term facilitation and depression on the ability of networks to retain stable working memory. Finally, our theory predicts the sensitivity of continuous working memory to distractor inputs and provides conditions for stability of memory.
| S-EPMC6493776 | biostudies-literature