Related papers: Maximum Power Efficiency and Criticality in Random…
This paper presents the foundation for a decomposition theory for Boolean networks, a type of discrete dynamical system that has found a wide range of applications in the life sciences, engineering, and physics. Given a Boolean network…
Control problem in a biological system is the problem of finding an interventional policy for changing the state of the biological system from an undesirable state, e.g. disease, into a desirable healthy state. Boolean networks are utilized…
A model of cellular metabolism due to S. Kauffman is analyzed. It consists of a network of Boolean gates randomly assembled according to a probability distribution. It is shown that the behavior of the network depends very critically on…
The network inference problem arises in biological research when one needs to quantitatively choose the best protein-interaction model for explaining a phenotype. The diverse nature of the data and nonlinear dynamics pose significant…
We consider the effect of noise in sparse Boolean Networks with redundant functions. We show that they always exhibit a non-zero error level, and the dynamics undergoes a phase transition from non-ergodicity to ergodicity, as a function of…
We study the thermodynamic cost associated with the erasure of one bit of information over a finite amount of time. We present a general framework for minimizing the average work required when full control of a system's microstates is…
Battery powered transmitters face energy constraint, replenishing their energy by a renewable energy source (like solar or wind power) can lead to longer lifetime. We consider here the problem of finding the optimal power allocation under…
In thermodynamics one considers thermal systems and the maximization of entropy subject to the conservation of energy. A consequence is Landauer's erasure principle, which states that the erasure of 1 bit of information requires a minimum…
Dynamic processes on networks are fundamental to understanding modern-day phenomena such as information diffusion and opinion polarization on the internet or epidemics spreading through society. However, such processes are notoriously…
The co-evolution of network topology and dynamics is studied in an evolutionary Boolean network model that is a simple model of gene regulatory network. We find that a critical state emerges spontaneously resulting from interplay between…
Boolean Networks have been used to study numerous phenomena, including gene regulation, neural networks, social interactions, and biological evolution. Here, we propose a general method for determining the critical behavior of Boolean…
This thesis focuses on three fundamental aspects of biological systems; namely, entropy production, Bayesian mechanics, and the free-energy principle. The contributions are threefold: 1) We compute the entropy production for a greater class…
This paper underscores the conjecture that intrinsic computation is maximal in systems at the "edge of chaos." We study the relationship between dynamics and computational capability in Random Boolean Networks (RBN) for Reservoir Computing…
Recent work emphasizes that the maximum entropy principle provides a bridge between statistical mechanics models for collective behavior in neural networks and experiments on networks of real neurons. Most of this work has focused on…
We develop a general method to explore how the function performed by a biological network can constrain both its structural and dynamical network properties. This approach is orthogonal to prior studies which examine the functional…
Characterization of the differences between biological and random networks can reveal the design principles that enable the robust realization of crucial biological functions including the establishment of different cell types. Previous…
The problem of designing policies for in-network function computation with minimum energy consumption subject to a latency constraint is considered. The scaling behavior of the energy consumption under the latency constraint is analyzed for…
Living systems operate in a critical dynamical regime -- between order and chaos -- where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the established 'structural theory' of…
Landauer's erasure principle states that any irreversible erasure protocol of a single bit memory needs work of at least $k_B T ln2.$ Recent proof of concept experiments has demonstrated that the erasure protocols with work close to the…
We construct and investigate Boolean networks that follow a given reliable trajectory in state space, which is insensitive to fluctuations in the updating schedule, and which is also robust against noise. Robustness is quantified as the…