Related papers: Distributed delay stabilizes bistable genetic netw…
Synthetic biology is a growing interdisciplinary field, with far-reaching applications, which aims to design biochemical systems that behave in a desired manner. With the advancement of strand-displacement DNA computing, a large class of…
Biological functions in living cells are controlled by protein interaction and genetic networks. These molecular networks should be dynamically stable against various fluctuations which are inevitable in the living world. In this paper, we…
Significant variations of delays among connecting neurons cause an inevitable disadvantage of asynchronous brain dynamics compared to synchronous deep learning. However, this study demonstrates that this disadvantage can be converted into a…
We analyze the convergence of gradient-based optimization algorithms that base their updates on delayed stochastic gradient information. The main application of our results is to the development of gradient-based distributed optimization…
Time lags occur in a vast range of real-world dynamical systems due to finite reaction times or propagation speeds. Here we derive an analytical approach to determine the asymptotic stability of synchronous states in networks of coupled…
Mathematical models of stem cell differentiation are commonly based upon the concept of subsequent cell fate decisions, each controlled by a gene regulatory network. These networks exhibit a multistable behavior and cause the system to…
We present three examples of delayed bifurcations for spike solutions of reaction-diffusion systems. The delay effect results as the system passes slowly from a stable to an unstable regime, and was previously analysed in the context of…
Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence…
This paper studies the stability of synchronized states in networks where couplings between nodes are characterized by some distributed time delay, and develops a generalized master stability function approach. Using a generic example of…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the…
The state of many physical, biological and socio-technical systems evolves by combining smooth local transitions and abrupt resetting events to a set of reference values. The inclusion of the resetting mechanism not only provides the…
We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their…
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because…
Evolving biomolecular networks have to combine the stability against perturbations with flexibility allowing their constituents to assume new roles in the cell. Gene duplication followed by functional divergence of associated proteins is a…
Signal duration (e.g. the time scales over which an active signaling intermediate persists) is a key regulator of biological decisions in myriad contexts such as cell growth, proliferation, and developmental lineage commitments.…
How to model distribution of sequential data, including but not limited to speech and human motions, is an important ongoing research problem. It has been demonstrated that model capacity can be significantly enhanced by introducing…
We study a stochastic model of protein dynamics that explicitly includes delay in the degradation. We rigorously derive the master equation for the processes and solve it exactly. We show that the equations for the mean values obtained…
Genetic regulatory networks with adaptive responses are widely studied in biology. Usually, models consisting only of a few nodes have been considered. They present one input receptor for activation and one output node where the adaptive…
Biological structure and function depend on complex regulatory interactions between many genes. A wealth of gene expression data is available from high-throughput genome-wide measurement technologies, but effective gene regulatory network…
This paper investigates the stabilization of probabilistic Boolean networks (PBNs) via a novel pinning control strategy based on network structure. In a PBN, the evolution equation of each gene switches among a collection of candidate…