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We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
Collective cell migration in response to a chemical cue occurs in many biological processes such as morphogenesis and cancer metastasis. Clusters of migratory cells in these systems are capable of responding to gradients of less than 1%…
Neural oscillations are universal phenomena and can be observed at different levels of neural systems, from single neuron to macroscopic brain. The frequency of those oscillations are related to the brain functions. However, little is know…
Mounting evidence shows that oscillatory activity is widespread in cell signaling. Here we review some of this recent evidence, focusing on both the molecular mechanisms that potentially underlie such dynamical behavior, and the potential…
The smart integrated systems of tomorrow would demand a combination of micromechanical components and traditional electronics. On-chip solutions will be the ultimate goal. One way of making such systems is to implement the mechanical parts…
Existing multi-behavior recommendations tend to prioritize performance at the expense of explainability, while current explainable methods suffer from limited generalizability due to their reliance on external information. Neuro-Symbolic…
A variety of complex mechanisms, from chemical reaction pathways to active fluctuations, orchestrate molecular transport in intracellular environments. Despite significant recent progress in visualizing and probing these processes, little…
Living cells must control the reading out or "expression" of information encoded in their genomes, and this regulation often is mediated by transcription factors--proteins that bind to DNA and either enhance or repress the expression of…
Timing is of fundamental importance in biology and our life. Borrowing ideas from mechanism, we map our clock signals onto a gear system, in pursuit of better depiction of a clock signal implemented with chemical reaction networks (CRNs).…
We introduce a novel gene regulatory network (GRN) inference method that integrates optimal transport (OT) with a deep-learning structural inference model. Advances in next-generation sequencing enable detailed yet destructive gene…
Cognitive Radios (CRs) build upon Software Defined Radios (SDRs) to allow for autonomous reconfiguration of communication architectures. In recent years, CRs have been identified as an enabler for Dynamic Spectrum Access (DSA) applications…
The adoption of deep learning techniques in genomics has been hindered by the difficulty of mechanistically interpreting the models that these techniques produce. In recent years, a variety of post-hoc attribution methods have been proposed…
In this contribution, a design of a synthetic calibration genetic circuit to characterize the relative strength of different sensing promoters is proposed and its specifications and performance are analyzed via an effective mathematical…
Cell polarization and directional cell migration can display random, persistent and oscillatory dynamic patterns. However, it is not clear if these polarity patterns can be explained by the same underlying regulatory mechanism. Here, we…
The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…
Characterizing and controlling nonlinear, multi-scale phenomena play important roles in science and engineering. Cluster-based reduced-order modeling (CROM) was introduced to exploit the underlying low-dimensional dynamics of complex…
We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying…
In this paper, a centralized Power Control (PC) scheme and an interference channel learning method are jointly tackled to allow a Cognitive Radio Network (CRN) access to the frequency band of a Primary User (PU) operating based on an…
Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular…
In this study, an algorithm to blind and automatic modulation classification has been proposed. It well benefits combined machine leaning and signal feature extraction to recognize diverse range of modulation in low signal power to noise…