Related papers: The coherent feed-forward loop acts as an efficien…
Network structures are extremely important to the study of political science. Much of the data in its subfields are naturally represented as networks. This includes trade, diplomatic and conflict relationships. The social structure of…
Recent progress in experimental techniques has enabled us to quantitatively study stochastic and flexible behavior of biological systems. For example, gene regulatory networks perform stochastic information processing and their…
BACKGROUND. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmental signals in the…
The purpose of this paper is to study the dynamics of a quantum coherent feedback network composed of two two-level systems (qubits) driven by two counter-propagating photons, one in each input channel. The coherent feedback network…
Feed-forward layers constitute two-thirds of a transformer model's parameters, yet their role in the network remains under-explored. We show that feed-forward layers in transformer-based language models operate as key-value memories, where…
In order to transmit biochemical signals, biological regulatory systems dissipate energy with concomitant entropy production. Additionally, signaling often takes place in challenging environmental conditions. In a simple model regulatory…
A single gene, regulating its own expression via a positive feedback loop, constitutes a common motif in gene regulatory networks and signalling cascades. Recent experiments on the development of competence in the bacterial population…
We explore the critical behaviors in the dynamics of information transfer of a biologically-inspired system by an individual-based model. "Quorum response", a type of social interaction which has been recognized taxonomically in animal…
Signal transduction in biological cells is effected by signaling pathways that typically include multiple feedback loops. Here we analyze information transfer through a prototypical signaling module with biochemical feedback. The module…
Biochemical networks related to similar functional pathways are often correlated due to cross-talk among the homologous proteins in the different networks. Using a stochastic framework, we address the functional significance of the…
Protein design often begins with the knowledge of a desired function from a motif which motif-scaffolding aims to construct a functional protein around. Recently, generative models have achieved breakthrough success in designing scaffolds…
Signal transduction, the information processing mechanism in biological cells, is carried out by a network of biochemical reactions. The dynamics of driven biochemical reactions can be studied in terms of nonequilibrium statistical physics.…
In this paper, we introduce a new model for RF-powered cognitive radio networks with the aim to improve the performance for secondary systems. In our proposed model, when the primary channel is busy, the secondary transmitter is able either…
As the need for higher performance from biological and electronic sensors continues to outpace current technologies, new strategies for designing, developing, and implementing novel sensor systems are emerging. A recently introduced…
Rhythmic gait patterns in animal locomotion are widely believed to be produced by a central pattern generator (CPG), a network of neurons that drives the muscle groups. In previous papers we have discussed how phase-synchronous signals can…
Biochemical networks can respond to temporal characteristics of time-varying signals. To understand how reliably biochemical networks can transmit information we must consider how an input signal as a function of time--the input…
Deep learning has successfully been leveraged for medical image segmentation. It employs convolutional neural networks (CNN) to learn distinctive image features from a defined pixel-wise objective function. However, this approach can lead…
Understanding why some cellular components are conserved across species, while others evolve rapidly is a key question of modern biology. Here we demonstrate that in S. cerevisiae proteins organized in cohesive patterns of interactions are…
In this paper, we consider a continuous-time model with discrete and dis-tributed delays to describe how two pieces of information interact in online social networks. Sufficient conditions are carried out to illustrate the stability of each…
In this paper, we consider bidirectional relaying between two diffusion-based molecular transceivers (bio-nodes). As opposed to existing literature, we incorporate the effect of direct diffusion links between the nodes and leverage it to…