Related papers: Designing sequential transcription logic: a simple…
Animals often receive information about errors and rewards after a significant delay. For example, there is typically a delay of tens to hundreds of milliseconds between motor actions and visual feedback. The standard approach to handling…
Superconductor electronics (SCE) is competing to become a platform for efficient implementations of neuromorphic computing and deep learning algorithms (DLAs) with projects mostly concentrating on searching for gates that would better mimic…
Synaptic plasticity is metabolically expensive, yet animals continuously update their internal models without exhausting energy reserves. However, when artificial neural networks are trained, the network parameters are typically updated on…
We study the versatile performance of networks of coupled circuits. Each of these circuits is composed of a positive and a negative feedback loop in a motif that is frequently found in genetic and neural networks. When two of these circuits…
Auto-regulation, a process wherein a protein negatively regulates its own production, is a common motif in gene expression networks. Negative feedback in gene expression plays a critical role in buffering intracellular fluctuations in…
Memristive devices are commonly benchmarked by the multi-level programmability of their resistance states. Neural networks utilizing memristor crossbar arrays as synaptic layers largely rely on this feature. However, the dynamical…
Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of…
It has been repeatedly proposed to expand the scope for SETI, and one of the suggested alternatives to radio is the biological media. Genomic DNA is already used on Earth to store non-biological information. Though smaller in capacity, but…
Behavior can be described as a temporal sequence of actions driven by neural activity. To learn complex sequential patterns in neural networks, memories of past activities need to persist on significantly longer timescales than the…
We model the transcription factor based regulation network of yeast using a content-based network model that mimicks the recognition of binding motifs on the regulatory regions of the genes. We are thereby able to faithfully reproduce many…
Logic Programming languages and combinational circuit synthesis tools share a common "combinatorial search over logic formulae" background. This paper attempts to reconnect the two fields with a fresh look at Prolog encodings for the…
We demonstrate the advantages of feedforward loops using a Boolean network, which is one of the discrete dynamical models for transcriptional regulatory networks. After comparing the dynamical behaviors of network embedded feedback and…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need…
Synthetic genetic circuits are implemented in living cells for their operation. During gene expression, proteins are produced from the respective genes, by formation of complexes through the process of transcription and translation. In…
A biological circuit is a neural or biochemical cascade, taking inputs and producing outputs. How have biological circuits learned to solve environmental challenges over the history of life? The answer certainly follows Dobzhansky's famous…
We present a novel classification-based method for learning to predict gene regulatory response. Our approach is motivated by the hypothesis that in simple organisms such as Saccharomyces cerevisiae, we can learn a decision rule for…
Genetic circuit design is a well-studied problem in synthetic biology. Ever since the first genetic circuits -- the repressilator and the toggle switch -- were designed and implemented, many advances have been made in this area of research.…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
We study a system of dynamical units, each of which shows excitable or oscillatory behavior, depending on the choice of parameters. When we couple these units with repressive bonds, we can control the duration of collective oscillations for…