Algorithms in nature: the convergence of systems biology and computational thinking

Biologists rely on computational methods to analyze and integrate large data sets, while several computational methods were inspired by the high-level design principles of biological systems. This Perspectives discusses the recent convergence of these two ways of thinking

Fault tolerant pulse synchronization

Pulse synchronization is the evolution of spontaneous firing action across a network of sensor nodes. In the pulse synchronization model all nodes across a network produce a pulse, or "fire", at regular intervals even without access to a shared global time. Previous researchers have proposed the Reachback Firefly algorithm for pulse synchronization, in which nodes react to the firings of other nodes by changing their period. We propose an extension to this algorithm for tolerating arbitrary or Byzantine faults of nodes. Our algorithm queues up all the firings heard in the current cycle and discards outliers at the end of the cycle. An adjustment is computed with the remaining values and used as a starting point of the next cycle. Through simulation we validate the performance of our algorithm and study the overhead in terms of convergence time and periodicity. The simulation considers two specific kinds of Byzantine faults, the No Jump model where faulty nodes follow their own firing cycle without reacting to firings heard from other nodes and the Random Jump model where faulty nodes fire at any random time in their cycle

Self-Stabilizing TDMA Algorithms for Dynamic Wireless Ad-hoc Networks

In dynamic wireless ad-hoc networks (DynWANs), autonomous computing devices set up a network for the communication needs of the moment. These networks require the implementation of a medium access control (MAC) layer. We consider MAC protocols for DynWANs that need to be autonomous and robust as well as have high bandwidth utilization, high predictability degree of bandwidth allocation, and low communication delay in the presence of frequent topological changes to the communication network. Recent studies have shown that existing implementations cannot guarantee the necessary satisfaction of these timing requirements. We propose a self-stabilizing MAC algorithm for DynWANs that guarantees a short convergence period, and by that, it can facilitate the satisfaction of severe timing requirements, such as the above. Besides the contribution in the algorithmic front of research, we expect that our proposal can enable quicker adoption by practitioners and faster deployment of DynWANs that are subject changes in the network topology

Fault-Tolerant Self-Stabilizing Distributed Clock Synchronization Protocol for Arbitrary Digraphs

A self-stabilizing network in the form of an arbitrary, non-partitioned digraph includes K nodes having a synchronizer executing a protocol. K-1 monitors of each node may receive a Sync message transmitted from a directly connected node. When the Sync message is received, the logical clock value for the receiving node is set to between 0 and a communication latency value (gamma) if the clock value is less than a minimum event-response delay (D). A new Sync message is also transmitted to any directly connected nodes if the clock value is greater than or equal to both D and a graph threshold (T(sub S)). When the Sync message is not received the synchronizer increments the clock value if the clock value is less than a resynchronization period (P), and resets the clock value and transmits a new Sync message to all directly connected nodes when the clock value equals or exceeds P

TRIX: Low-Skew Pulse Propagation for Fault-Tolerant Hardware

The vast majority of hardware architectures use a carefully timed reference signal to clock their computational logic. However, standard distribution solutions are not fault-tolerant. In this work, we present a simple grid structure as a more reliable clock propagation method and study it by means of simulation experiments. Fault-tolerance is achieved by forwarding clock pulses on arrival of the second of three incoming signals from the previous layer. A key question is how well neighboring grid nodes are synchronized, even without faults. Analyzing the clock skew under typical-case conditions is highly challenging. Because the forwarding mechanism involves taking the median, standard probabilistic tools fail, even when modeling link delays just by unbiased coin flips. Our statistical approach provides substantial evidence that this system performs surprisingly well. Specifically, in an "infinitely wide" grid of height~$H$, the delay at a pre-selected node exhibits a standard deviation of $O(H^{1/4})$ ($\approx 2.7$ link delay uncertainties for $H=2000$) and skew between adjacent nodes of $o(\log \log H)$ ($\approx 0.77$ link delay uncertainties for $H=2000$). We conclude that the proposed system is a very promising clock distribution method. This leads to the open problem of a stochastic explanation of the tight concentration of delays and skews. More generally, we believe that understanding our very simple abstraction of the system is of mathematical interest in its own right.Comment: 16 pages, 11 figure

{TRIX}: {L}ow-Skew Pulse Propagation for Fault-Tolerant Hardware

The vast majority of hardware architectures use a carefully timed reference signal to clock their computational logic. However, standard distribution solutions are not fault-tolerant. In this work, we present a simple grid structure as a more reliable clock propagation method and study it by means of simulation experiments. Fault-tolerance is achieved by forwarding clock pulses on arrival of the second of three incoming signals from the previous layer. A key question is how well neighboring grid nodes are synchronized, even without faults. Analyzing the clock skew under typical-case conditions is highly challenging. Because the forwarding mechanism involves taking the median, standard probabilistic tools fail, even when modeling link delays just by unbiased coin flips. Our statistical approach provides substantial evidence that this system performs surprisingly well. Specifically, in an "infinitely wide" grid of height~$H$, the delay at a pre-selected node exhibits a standard deviation of $O(H^{1/4})$ ($\approx 2.7$ link delay uncertainties for $H=2000$) and skew between adjacent nodes of $o(\log \log H)$ ($\approx 0.77$ link delay uncertainties for $H=2000$). We conclude that the proposed system is a very promising clock distribution method. This leads to the open problem of a stochastic explanation of the tight concentration of delays and skews. More generally, we believe that understanding our very simple abstraction of the system is of mathematical interest in its own right