Related papers: A population-based microbial oscillator
Mixed positive and negative feedback loops are often found in biological systems which support oscillations. In this work we consider a prototype of such systems, which has been recently found at the core of many genetic circuits showing…
In biochemical signaling, information is often encoded in oscillatory signals. However, the advantages of such a coding strategy over an amplitude encoding scheme of constant signals remain unclear. Here we study the dynamics of a simple…
We consider the problem of efficiently simulating population protocols. In the population model, we are given a distributed system of $n$ agents modeled as identical finite-state machines. In each time step, a pair of agents is selected…
The simplest ring oscillator is made from three strongly nonlinear elements repressing each other unidirectionally resulting in the emergence of a limit cycle. A popular implementation of this scheme uses repressive genes in bacteria…
Oscillator models are central to the study of system properties such as entrainment or synchronization. Due to their nonlinear nature, few system-theoretic tools exist to analyze those models. The paper develops a sensitivity analysis for…
Using a Multi-agent systems paradigm, the present project develops, validates and exploits a computational $\textit{testbed}$ that simulates micro-biological complex systems, namely the aggregation patterns of the social amoeba…
Population protocols are a model of distributed computation intended for the study of networks of independent computing agents with dynamic communication structure. Each agent has a finite number of states, and communication opportunities…
Heterologous gene expression draws resources from host cells. These resources include vital components to sustain growth and replication, and the resulting cellular burden is a widely recognised bottleneck in the design of robust circuits.…
For practical construction of complex synthetic genetic networks able to perform elaborate functions it is important to have a pool of relatively simple "bio-bricks" with different functionality which can be compounded together. To…
The majority of pulsar population synthesis studies performed to date have focused on isolated pulsar evolution. Those that have incorporated pulsar evolution within binary systems have tended to either treat binary evolution poorly of…
In order to analyze data from cancer genome sequencing projects, we need to be able to distinguish causative, or "driver," mutations from "passenger" mutations that have no selective effect. Toward this end, we prove results concerning the…
Vibration rendering is essential for creating realistic tactile experiences in human-virtual object interactions, such as in video game controllers and VR devices. By dynamically adjusting vibration parameters based on user actions, these…
We study synchronization dynamics in populations of coupled phase oscillators with higher-order interactions and community structure. We find that the combination of these two properties gives rise to a number of states unsupported by…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
Networks of coupled dynamical systems provide a powerful way to model systems with enormously complex dynamics, such as the human brain. Control of synchronization in such networked systems has far reaching applications in many domains,…
This study investigates remote synchronization in arbitrary network clusters of coupled nonlinear oscillators, a phenomenon inspired by neural synchronization in the brain. Employing a multi-faceted approach encompassing analytical,…
Our interest is in multiplex network data with multiple network samples observed across the same set of nodes. Examples originate from a variety of fields, including brain connectivity, international trade networks, and social networks,…
We study the dynamics of phase synchronization in growing populations of discrete phase oscillatory systems when the division process is coupled to the distribution of oscillator phases. Using mean field theory, linear stability analysis,…
Interest in non-algorithmic, unconventional computing is rising in recent years due to more and more apparent short comings of classic stored-program digital computers, such as energy efficiency, degree of parallelism in computations, clock…
Chronic diseases can greatly benefit from bioelectronic medicine approaches. Neuromorphic electronic circuits present ideal characteristics for the development of brain-inspired low-power implantable processing systems that can be…