SummaryMicrobial communities are increasingly utilized in biotechnology. Efficiency and productivity in many of these applications depends on the presence of cooperative interactions between members of the community. Two key processes underlying these interactions are the production of public goods and metabolic cross‐feeding, which can be understood in the general framework of ecological and evolutionary (eco‐evo) dynamics. In this review, we illustrate the relevance of cooperative interactions in microbial biotechnological processes, discuss their mechanistic origins and analyse their evolutionary resilience. Cooperative behaviours can be damaged by the emergence of ‘cheating’ cells that benefit from the cooperative interactions but do not contribute to them. Despite this, cooperative interactions can be stabilized by spatial segregation, by the presence of feedbacks between the evolutionary dynamics and the ecology of the community, by the role of regulatory systems coupled to the environmental conditions and by the action of horizontal gene transfer. Cooperative interactions enrich microbial communities with a higher degree of robustness against environmental stress and can facilitate the evolution of more complex traits. Therefore, the evolutionary resilience of microbial communities and their ability to constraint detrimental mutants should be considered to design robust biotechnological applications.

We consider here spiking neural P systems with a non-synchronized (i.e., asynchronous) use of rules: in any step, a neuron can apply or not apply its rules which are enabled by the number of spikes it contains (further spikes can come, thus changing the rules enabled in the next step). Because the time between two firings of the output neuron is now irrelevant, the result of a computation is the number of spikes sent out by the system, not the distance between certain spikes leaving the system. The additional non-determinism introduced in the functioning of the system by the nonsynchronization is proved not to decrease the computing power in the case of using extended rules (several spikes can be produced by a rule). That is, we obtain again the equivalence with Turing machines (interpreted as generators of sets of (vectors of) numbers). However, this problem remains open for the case of restricted spiking neural P systems, whose rules can only produce one spike. On the other hand we prove that asynchronous systems, with extended rules, and where each neuron is either bounded or unbounded, are not computationally complete. For these systems, the configuration reachability, membership (in terms of generated vectors), emptiness, infiniteness, and disjointness problems are shown to be decidable. However, containment and equivalence are undecidable. In short, an SN P system consists of a set of neurons placed in the nodes of a directed graph and sending signals (spikes, denoted in what follows by the symbol a) along the arcs of the graph (they are called synapses). Thus, the architecture is that of a tissue-like P system, with only one kind of object present in the cells (the reader is referred to [18] for an introduction to membrane computing and to [23] for the up-to-date information about this research area). The objects evolve by means of standard spiking rules, which are of the form E/a c → a; d, where E is a regular expression over {a} and c, d are natural numbers, c ≥ 1, d ≥ 0. The meaning is that a neuron containing k spikes such that a k ∈ L(E), k ≥ c, can consume c spikes and produce one spike, after a delay of d steps. This spike is sent to all neurons connected by an outgoing synapse from the neuron where the rule was applied. There also are forgetting rules, of the form a s → λ, with the meaning that s ≥ 1 spikes are removed, provided that the neuron contains exactly s spikes. Extended rules were considered in [4], [17]: these rules are of the form E/a c → a p ; d, with the meaning that when using the rule, c spikes are consumed and p spikes are produced. Because p can be 0 or greater than 0, we obtain a generalization of both standard spiking and forgetting rules. In this paper we consider extended spiking rules with restrictions on the type of the regular expressions used. In particular, we consider two types of rules. The first type are called bounded rules and are of the form a i /a c → a p ; d, where 1 ≤ c ≤ i, p ≥ 0, and d ≥ 0. We also consider unbounded rules of the form a i (a j) * /a c → a p ; d...

Social, biological and economic networks grow and decline with occasional fragmentation and re-formation, often explained in terms of external perturbations. We show that these phenomena can be a direct consequence of simple imitation and internal conflicts between ‘cooperators’ and ‘defectors’. We employ a game-theoretic model of dynamic network formation where successful individuals are more likely to be imitated by newcomers who adopt their strategies and copy their social network. We find that, despite using the same mechanism, cooperators promote well-connected highly prosperous networks and defectors cause the network to fragment and lose its prosperity; defectors are unable to maintain the highly connected networks they invade. Once the network is fragmented it can be reconstructed by a new invasion of cooperators, leading to the cycle of formation and fragmentation seen, for example, in bacterial communities and socio-economic networks. In this endless struggle between cooperators and defectors we observe that cooperation leads to prosperity, but prosperity is associated with instability. Cooperation is prosperous when the network has frequent formation and fragmentation.

No abstract

Abstract. In search for "realistic" bio-inspired computing models, we consider asynchronous spiking neural P systems, in the hope to get a class of computing devices with decidable properties. However, although the non-synchronization is known in general to decrease the computing power, in the case of using extended rules (several spikes can be produced by a rule) we obtain again the equivalence with Turing machines (interpreted as generators of sets of vectors of numbers). The problem remains open for the case of restricted spiking neural P systems, whose rules can only produce one spike. On the other hand, we prove that asynchronous spiking neural P systems, with a specific way of halting, using extended rules and where each neuron is either bounded or unbounded, are equivalent to partially blind counter machines and, therefore, have many decidable properties. Spiking Neural P Systems -An Informal PresentationIn the present paper we continue the investigation of spiking neural P systems (SN P systems, in short). A survey of results and the biological motivations for these systems can be found in [5] and [2]. In the meantime, two main research directions were particularly active in this area of membrane computing: looking for classes of systems with tractable (for instance, decidable) properties, and looking for the possibility of using SN P systems for efficiently solving computationally hard problems. Along the second research line are the investigations related to the possibility of simulating an SN P system by a Turing machine with a polynomial slowdown (preliminary results can be found in [3]) and those trying to improve the efficiency of SN P systems, e.g., by enhancing the parallelism of the system (see, for instance, [7]).In this paper we report several recent results concerning the first topic mentioned above -specifically, removing the synchronization (common in many membrane computing models), calling them asynchronous SN P systems. These

in various types of structured communities newcomers choose their interaction partners by selecting a role-model and copying their social networks. participants in these networks may be cooperators who contribute to the prosperity of the community, or cheaters who do not and simply exploit the cooperators. For newcomers it is beneficial to interact with cooperators but detrimental to interact with cheaters. However, cheaters and cooperators usually cannot be identified unambiguously and newcomers' decisions are often based on a combination of private and public information. We use evolutionary game theory and dynamical networks to demonstrate how the specificity and sensitivity of those decisions can dramatically affect the resilience of cooperation in the community. We show that promiscuous decisions (high sensitivity, low specificity) are advantageous for cooperation when the strength of competition is weak; however, if competition is strong then the best decisions for cooperation are risk-adverse (low sensitivity, high specificity). Opportune decisions based on private and public information can still support cooperation but suffer of the presence of information cascades that damage cooperation, especially in the case of strong competition. our research sheds light on the way the interplay of specificity and sensitivity in individual decision-making affects the resilience of cooperation in dynamical structured communities. Cooperation is widespread in the real world and can be observed at different scales of biological organization, ranging from genes to multi-cellular organisms and socio-technological systems 1-4. However, cooperators pay a cost to benefit others. The extent to which cooperators can thrive within the system apparently contradicts the idea that only selfish behaviors are rewarded during competition between individuals. The resilience of cooperation has been approached in different domains 5 and evolutionary game theory 6-8 provides a framework for studying the evolution of cooperation among unrelated individuals. The Prisoner's Dilemma (PD) in particular has been widely employed for investigating the sustainability of cooperation. The prisoner's dilemma stresses the key point of the conflict of interest between what is best for the individual and what is best for the group, and thus creates a social dilemma. To solve the dilemma, several mechanisms have been suggested to facilitate the spreading of cooperation such as direct reciprocity, indirect reciprocity, kin selection, group selection, and graph selection or spatial reciprocity, etc. 2. Much work has been dedicated to the spreading of cooperation in structured populations and networks, where the promotion of cooperation is associated with the formation of cooperative clusters 9-12. In this paper we use evolutionary game theory to study a model of dynamical networks to understand how attachment choices cascade down the generations and lead, or not, to a collapse of cooperation. In this model, when a new node (newcomer) joins the network, i...

In the commons, communities whose growth depends on public good, individuals often rely on surprisingly simple strategies, or heuristics, to decide whether to contribute to the shared resource (at risk of exploitation by free-riders). Although this appears a limitation, we show here how four heuristics lead to sustainable growth when coupled to specific ecological constraints. The two simplest ones—contribute permanently or switch stochastically between contributing or not—are first shown to bring sustainability when the public good efficiently promotes growth. If efficiency declines and the commons is structured in small groups, the most effective strategy resides in contributing only when a majority of individuals are also contributors. In contrast, when group size becomes large, the most effective behaviour follows a minimal-effort rule: contribute only when it is strictly necessary. Both plastic strategies are observed in natural scenarios across scales that present them as relevant social motifs for the sustainable management of public goods.

No abstract