Synthesizing and tuning chemical reaction networks with specified behaviours

We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First, we identify candidate CRNs that have the possibility to produce correct computations for a given finite set of inputs. We then optimise the reaction rates of each CRN using a combination of stochastic search techniques applied to the chemical master equation, simultaneously improving the of correct behaviour and ruling out spurious solutions. In addition, we use techniques from continuous time Markov chain theory to study the expected termination time for each CRN. We illustrate our approach by identifying CRNs for majority decision-making and division computation, which includes the identification of both known and unknown networks.Comment: 17 pages, 6 figures, appeared the proceedings of the 21st conference on DNA Computing and Molecular Programming, 201

The Computational Power of Beeps

In this paper, we study the quantity of computational resources (state machine states and/or probabilistic transition precision) needed to solve specific problems in a single hop network where nodes communicate using only beeps. We begin by focusing on randomized leader election. We prove a lower bound on the states required to solve this problem with a given error bound, probability precision, and (when relevant) network size lower bound. We then show the bound tight with a matching upper bound. Noting that our optimal upper bound is slow, we describe two faster algorithms that trade some state optimality to gain efficiency. We then turn our attention to more general classes of problems by proving that once you have enough states to solve leader election with a given error bound, you have (within constant factors) enough states to simulate correctly, with this same error bound, a logspace TM with a constant number of unary input tapes: allowing you to solve a large and expressive set of problems. These results identify a key simplicity threshold beyond which useful distributed computation is possible in the beeping model.Comment: Extended abstract to appear in the Proceedings of the International Symposium on Distributed Computing (DISC 2015

Passively Mobile Communicating Logarithmic Space Machines

We propose a new theoretical model for passively mobile Wireless Sensor Networks. We call it the PALOMA model, standing for PAssively mobile LOgarithmic space MAchines. The main modification w.r.t. the Population Protocol model is that agents now, instead of being automata, are Turing Machines whose memory is logarithmic in the population size n. Note that the new model is still easily implementable with current technology. We focus on complete communication graphs. We define the complexity class PLM, consisting of all symmetric predicates on input assignments that are stably computable by the PALOMA model. We assume that the agents are initially identical. Surprisingly, it turns out that the PALOMA model can assign unique consecutive ids to the agents and inform them of the population size! This allows us to give a direct simulation of a Deterministic Turing Machine of O(nlogn) space, thus, establishing that any symmetric predicate in SPACE(nlogn) also belongs to PLM. We next prove that the PALOMA model can simulate the Community Protocol model, thus, improving the previous lower bound to all symmetric predicates in NSPACE(nlogn). Going one step further, we generalize the simulation of the deterministic TM to prove that the PALOMA model can simulate a Nondeterministic TM of O(nlogn) space. Although providing the same lower bound, the important remark here is that the bound is now obtained in a direct manner, in the sense that it does not depend on the simulation of a TM by a Pointer Machine. Finally, by showing that a Nondeterministic TM of O(nlogn) space decides any language stably computable by the PALOMA model, we end up with an exact characterization for PLM: it is precisely the class of all symmetric predicates in NSPACE(nlogn).Comment: 22 page

Stable Leader Election in Population Protocols Requires Linear Time

A population protocol *stably elects a leader* if, for all $n$, starting from an initial configuration with $n$ agents each in an identical state, with probability 1 it reaches a configuration $\mathbf{y}$ that is correct (exactly one agent is in a special leader state $\ell$) and stable (every configuration reachable from $\mathbf{y}$ also has a single agent in state $\ell$). We show that any population protocol that stably elects a leader requires $\Omega(n)$ expected "parallel time" --- $\Omega(n^2)$ expected total pairwise interactions --- to reach such a stable configuration. Our result also informs the understanding of the time complexity of chemical self-organization by showing an essential difficulty in generating exact quantities of molecular species quickly.Comment: accepted to Distributed Computing special issue of invited papers from DISC 2015; significantly revised proof structure and intuitive explanation