Related papers: Combinatorial Algorithms for Control of Biological…
Given a conjunctive Boolean network (CBN) with $n$ state-variables, we consider the problem of finding a minimal set of state-variables to directly affect with an input so that the resulting conjunctive Boolean control network (CBCN) is…
Methods of modeling cellular regulatory networks as diverse as differential equations and Boolean networks co-exist, however, without any closer correspondence to each other. With the example system of the fission yeast cell cycle control…
Selecting a few available actuators to ensure the controllability of a linear system is a fundamental problem in control theory. Previous works either focus on optimal performance, simplifying the controllability issue, or make the system…
Engineering biology requires precise control of biomolecular circuits, and Cybergenetics is the field dedicated to achieving this goal. A significant challenge in developing controllers for cellular functions is designing systems that can…
We show that biological networks with serial regulation (each node regulated by at most one other node) are constrained to {\it direct functionality}, in which the sign of the effect of an environmental input on a target species depends…
We initiate a line of investigation into biological neural networks from an algorithmic perspective. We develop a simplified but biologically plausible model for distributed computation in stochastic spiking neural networks and study…
We show that under mild assumptions for a problem whose solutions admit a dynamic programming-like recurrence relation, we can still find a solution under additional packing constraints, which need to be satisfied approximately. The number…
In previous works, we introduced the notion of dominant vertices in the context of dynamical systems on networks. This is a set of nodes in the underlying network whose evolution determines the whole network's dynamics after a transient…
Despite their apparent simplicity, random Boolean networks display a rich variety of dynamical behaviors. Much work has been focused on the properties and abundance of attractors. The topologies of random Boolean networks with one input per…
We study experimentally the synchronization patterns in time-delayed directed Boolean networks of excitable systems. We observe a transition in the network dynamics when the refractory time of the individual systems is adjusted. When the…
We address the problem of minimal actuator placement in linear systems so that the volume of the set of states reachable with one unit or less of input energy is lower bounded by a desired value. First, following the recent work of…
The study of network structural controllability focuses on the minimum number of driver nodes needed to control a whole network. Despite intensive studies on this topic, most of them consider static networks only. It is well-known, however,…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
The emerging field at the intersection of quantitative biology, network modeling, and control theory has enjoyed significant progress in recent years. This Special Issue brings together a selection of papers on complementary approaches to…
In this paper, we propose to study on sufficient control of complex networks which is to control a sufficiently large portion of the network, where only the quantity of controllable nodes matters. To the best of our knowledge, this is the…
Controlling real-world networked systems, including ecological, biomedical, and engineered networks that exhibit higher-order interactions, remains challenging due to inherent nonlinearities and large system scales. Despite extensive…
Controlling a complex network towards a desire state is of great importance in many applications. Existing works present an approximate algorithm to find the driver nodes used to control partial nodes of the network. However, the driver…
The problem of placing or selecting sensors and control nodes plays a pivotal role in the operation of dynamic networks. This paper proposes optimal algorithms and heuristics to solve the simultaneous sensor and actuator selection problem…
This paper studies the problem of, given the structure of a linear-time invariant system and a set of possible inputs, finding the smallest subset of input vectors that ensures system's structural controllability. We refer to this problem…
Intracellular networks process cellular-level information and control cell fate. They can be computationally modeled using Boolean networks, which are implicit-time causal models of discrete binary events. These networks can be embedded in…