Related papers: Computers from plants we never made. Speculations

Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…

A powerful experimental approach for investigating computation in networks of biological neurons is the use of cultured dissociated cortical cells grown into networks on a multi-electrode array. Such preparations allow investigation of…

Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…

Phylogenetic network is an evolutionary model that uses a rooted directed acyclic graph (instead of a tree) to model an evolutionary history of species in which reticulate events (e.g., hybrid speciation or horizontal gene transfer)…

Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…

Digital computers implement computations using circuits, as do many naturally occurring systems (e.g., gene regulatory networks). The topology of any such circuit restricts which variables may be physically coupled during the operation of a…

We investigate computational issues in the distributed model Amoebots of programmable matter. In this model, the computational entities, called particles, are anonymous finite-state machines that operate and move on an hexagonal tasselation…

In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…

Motivated by a potential application in economics, we investigate a simple dynamical scheme to produce planted solutions in optimization problems with continuous variables. We consider the perceptron model as a prototypical model. Starting…

Organic solar cells have the potential for widespread usage due to their promise of low cost, roll-to-roll manufacturability, and mechanical flexibility. However, deployment is impeded by their relatively low power conversion efficiencies.…

This paper addresses the trajectory-tracking problem for a class of electromechanical systems. To this end, the dynamics of the plants are modeled in the so-called port-Hamiltonian framework. Then, the notion of contraction is exploited to…

We present a form of algebraic reasoning for computational objects which are expressed as graphs. Edges describe the flow of data between primitive operations which are represented by vertices. These graphs have an interface made of…

Navigating topological transitions in cellular mechanical systems is a significant challenge for existing simulation methods. While abstract models lack predictive capabilities at the cellular level, explicit network representations…

The design of new devices and experiments in science and engineering has historically relied on the intuitions of human experts. This credo, however, has changed. In many disciplines, computer-inspired design processes, also known as…

Working with tree graphs is always easier than with loopy ones and spanning trees are the closest tree-like structures to a given graph. We find a correspondence between the solutions of random K-satisfiability problem and those of spanning…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…

We introduce an algorithm to generate (not solve) spin-glass instances with planted solutions of arbitrary size and structure. First, a set of small problem patches with open boundaries is solved either exactly or with a heuristic, and then…

Control of complex processes is a major goal of network analyses. Most approaches to control nonlinearly coupled systems require the network topology and/or network dynamics. Unfortunately, neither the full set of participating nodes nor…