Reducibility of Gene Patterns in Ciliates using the Breakpoint Graph

Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the development of the theoretical models of gene assembly, and in particular we demonstrate the use of the concept of the breakpoint graph, known from another branch of DNA transformation research. More specifically: (1) we characterize the intermediate gene patterns that can occur during the transformation of a given micronuclear gene pattern to its macronuclear form; (2) we determine the number of applications of the loop recombination operation (the most basic of the three molecular operations that accomplish gene assembly) needed in this transformation; (3) we generalize previous results (and give elegant alternatives for some proofs) concerning characterizations of the micronuclear gene patterns that can be assembled using a specific subset of the three molecular operations.Comment: 30 pages, 13 figure

Building SSPs for climate policy analysis: a scenario elicitation methodology to map the space of possible future challenges to mitigation and adaptation

International audienceThe scientific community is now developing a new set of scenarios, referred to as Shared Socio-economic Pathways (SSPs) that will be contrasted along two axes: challenges to mitigation, and challenges to adaptation. This paper proposes a methodology to develop SSPs with a "backwards" approach based on (i) an a priori identification of potential drivers of mitigation and adaptation challenges; (ii) a modelling exercise to transform these drivers into a large set of scenarios; (iii) an a posteriori selection of a few SSPs among these scenarios using statistical cluster-finding algorithms. This backwards approach could help inform the development of SSPs to ensure the storylines focus on the driving forces most relevant to distinguishing between the SSPs. In this illustrative analysis, we find that energy sobriety, equity and convergence prove most important towards explaining future difference in challenges to adaptation and mitigation. The results also demonstrate the difficulty in finding explanatory drivers for a middle scenario (SSP2). We argue that methodologies such as that used here are useful for broad questions such as the definition of SSPs, and could also be applied to any specific decisions faced by decision-makers in the field of climate change

Membrane Systems with External Control

We consider the idea of controlling the evolution of a membrane system. In particular, we investigate a model of membrane systems using promoted rules, where a string of promoters (called the control string) “travels” through the regions, activating the rules of the system. This control string is present in the skin region at the beginning of the computation – one can interpret that it has been inserted in the system before starting the computation – and it is “consumed”, symbol by symbol, while traveling through the system. In this way, the inserted string drives the computation of the membrane system by controlling the activation of evolution rules. When the control string is entirely consumed and no rule can be applied anymore, then the system halts – this corresponds to a successful computation. The number of objects present in the output region is the result of such a computation. In this way, using a set of control strings (a control program), one generates a set of numbers. We also consider a more restrictive definition of a successful computation, and then study the corresponding model. In this paper we investigate the influence of the structure of control programs on the generative power. We demonstrate that different structures yield generative powers ranging from finite to recursively enumerable number sets. In determining the way that the control string moves through the regions, we consider two possible “strategies of traveling”, and prove that they are similar as far as the generative power is concerned

Membrane systems with proteins embedded in membranes

Membrane computing is a biologically inspired computational paradigm. Motivated by brane calculi we investigate membrane systems which differ from conventional membrane systems by the following features: (1) biomolecules (proteins) can move through the regions of the systems, and can attach onto (and de-attach from) membranes, and (2) membranes can evolve depending on the attached molecules. The evolution of membranes is performed by using rules that are motivated by the operation of pinocytosis (the pino rule) and the operation of cellular dripping (the drip rule) that take place in living cells. We show that such membrane systems are computationally universal. We also show that if only the second feature is used then one can generate at least the family of Parikh images of the languages generated by programmed grammars without appearance checking (which contains non-semilinear sets of vectors). If, moreover, the use of pino/drip rules is non-cooperative (i.e., not dependent on the proteins attached to membranes), then one generates a family of sets of vectors that is strictly included in the family of semilinear sets of vectors. We also consider a number of decision problems concerning reachability of configurations and boundness

Risk factors' prediction model for the investment evaluation

The article deals with the issue of increasing the competitiveness of enterprises and their long-term sustainability based on the efficiency of investment processes. Implementing new approaches to the company's decision-making processes will allow companies to overcome the pitfalls of the market environment created by the post-COVID period and the current energy crisis that has affected the world markets after the conflict between Ukraine and Russia. The article aims to verify the application of the methodology for increasing the competitiveness of enterprises based on the use of a model creating a fusion of traditional and sophisticated tools. The analyses carried out are based on the investment decisions of a real company operating in the Slovak Republic's territory in the production and supply of security products. Mathematical modelling and Monte Carlo simulation are based on the company's accounting and operational financial outputs (profit and loss statement, balance sheet). The methodology is based on mathematical modelling through static traditional financial approaches and their verification through sensitivity analysis, regression analysis and Monte Carlo simulation based on distributional distributions of risk factors. The output is the assessment of risk factors and their significance for the criterion value Net Present Value (NPV)

Reaction Cycles in Membrane Systems and Molecular Dynamics

We are considering molecular dynamics and (sequential) membrane systems from the viewpoint of Markov chain theory. The first step is to understand the structure of the configuration space, with respect to communicating classes. Instead of a reachability analysis by traditional methods, we use the explicit monoidal structure of this space with respect to rule applications. This leads to the notion of precycle, which is an element of the integer kernel of the stoichiometric matrix. The generators of the set of precycles can be effectively computed by an incremental algorithm due to Contejean and Devie. To arrive at a characterization of cycles, we introduce the notion of defect, which is a set of geometric constraints on a configuration to allow a precycle to be enabled, that is, be a cycle. An important open problem is the effcient calculation of the defects. We also discuss aspects of asymptotic behavior and connectivity, as well as give a biological example, showing the usefulness of the method for model checking

Membrane Systems with Marked Membranes

AbstractMembrane computing is a biologically inspired computational paradigm. Motivated by brane calculi we investigate membrane systems which differ from conventional membrane systems by the following features: (1) biomolecules (proteins) can move through the regions of the systems, and can attach onto (and de-attach from) membranes, and (2) membranes can evolve depending on the attached molecules. The evolution of membranes is performed by using rules that are motivated by the operation of pinocytosis (the pino rule) and the operation of cellular dripping (the drip rule) that take place in living cells. We show that such membrane systems are computationally universal. We also show that if only the second feature is used then one can generate at least the family of Parikh images of the languages generated by programmed grammars without appearance checking (which contains non-semilinear sets of vectors). If, moreover, the use of pino/drip rules is non-cooperative (i.e., not dependent on the proteins attached to membranes), then one generates a family of sets of vectors that is strictly included in the family of semilinear sets of vectors. We also consider a number of decision problems concerning reachability of configurations and boundness