Membrane Computing as a Modelling Tool: Looking Back and Forward from Sevilla

This paper is a tribute to Prof. Mario de Jesús Pérez- Jiménez. An overview of modelling applications in membrane computing has been compiled, trying to narrate it from a historical perspective and including numerous bibliographical references. Since being exhaustive was obviously out of scope, this quick tour on almost two decades of applications is biased, paying special attention to the contributions in which Prof. Pérez-Jiménez and members of his research group were involved.Ministerio de Economía y Competitividad TIN2017-89842-

Roadmap on semiconductor-cell biointerfaces.

This roadmap outlines the role semiconductor-based materials play in understanding the complex biophysical dynamics at multiple length scales, as well as the design and implementation of next-generation electronic, optoelectronic, and mechanical devices for biointerfaces. The roadmap emphasizes the advantages of semiconductor building blocks in interfacing, monitoring, and manipulating the activity of biological components, and discusses the possibility of using active semiconductor-cell interfaces for discovering new signaling processes in the biological world

Approximating Non-discrete P Systems

The main goal of this paper is to propose some geometric approaches to the computations of non-discrete P systems. The behavior of this kind of P systems is similar to that of classic systems, with the difference that the contents of the membranes are represented by non-discrete multisets (the multiplicities can be non-integers) and, consequently, also the number of applications of a rule in a transition step can be non-integer.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

New Proposals for the Formalization of Membrane Proteins

This paper presents three new proposals to take advantage, in the framework of P systems, from proteins acting in bacteria. One attempt aims to focus on the transport protein that act as a logic AND gate at the cell membrane. The multiplicity of type of transporters involved in maintaining osmotic pressure within physiological values, both at short and long term level are also presented, as an example of parallelism occurring in living cell. Finally, the change of enzyme activity by reversible aggregation could be important for P systems as a new rule to follow, and process to model

A Study of the Robustness of the EGFR Signalling Cascade Using Continuous Membrane Systems

Many approaches to anticancer treatment have had a limited success. A fundamental hurdle to cancer therapy is the robustness of the signalling networks involved in tumourgenesis. The complexity of net- works of biological signalling pathways is such that the development of simplifying models is essential in trying to understand the wide-ranging cellular responses they can generate. In this paper a model of the epider- mal growth factor receptor signalling cascade is developed using contin- uous membrane systems. This model is used to study the robustness of this signalling cascade which is known to play a key role in tumour cell proliferation, angiogenesis and metastasis.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Membrane systems with limited parallelism

Membrane computing is an emerging research field that belongs to the more general area of molecular computing, which deals with computational models inspired from bio-molecular processes. Membrane computing aims at defining models, called membrane systems or P systems, which abstract the functioning and structure of the cell. A membrane system consists of a hierarchical arrangement of membranes delimiting regions, which represent various compartments of a cell, and with each region containing bio-chemical elements of various types and having associated evolution rules, which represent bio-chemical processes taking place inside the cell. This work is a continuation of the investigations aiming to bridge membrane computing (where in a compartmental cell-like structure the chemicals to evolve are placed in compartments defined by membranes) and brane calculi (where one considers again a compartmental cell-like structure with the chemicals/proteins placed on the membranes themselves). We use objects both in compartments and on membranes (the latter are called proteins), with the objects from membranes evolving under the control of the proteins. Several possibilities are considered (objects only moved across membranes or also changed during this operation, with the proteins only assisting the move/change or also changing themselves). Somewhat expected, computational universality is obtained for several combinations of such possibilities. We also present a method for solving the NP-complete SAT problem using P systems with proteins on membranes. The SAT problem is solved in O(nm) time, where n is the number of boolean variables and m is the number of clauses for an instance written in conjunctive normal form. Thus, we can say that the solution for each given instance is obtained in linear time. We succeeded in solving SAT by a uniform construction of a deterministic P system which uses rules involving objects in regions, proteins on membranes, and membrane division. Then, we investigate the computational power of P systems with proteins on membranes in some particular cases: when only one protein is placed on a membrane, when the systems have a minimal number of rules, when the computation evolves in accepting or computing mode, etc. This dissertation introduces also another new variant of membrane systems that uses context-free rewriting rules for the evolution of objects placed inside compartments of a cell, and symport rules for communication between membranes. The strings circulate across membranes depending on their membership to regular languages given by means of regular expressions. We prove that these rewriting-symport P systems generate all recursively enumerable languages. We investigate the computational power of these newly introduced P systems for three particular forms of the regular expressions that are used by the symport rules. A characterization of ET0L languages is obtained in this context

Modelling EGFR signalling cascade using continuous membrane systems

The complexity of networks of biological signalling pathways is such that the development of simplifying models is essential in trying to understand the wide-ranging cellular responses they can generate. In this paper a continuous variant of membrane systems is introduced and used to model the epidermal growth factor receptor signalling network which is known to play a key role in tumour cell proliferation, angiogenesis and metastasis.Ministerio de Ciencia y Tecnología TIC2002-04220-C03-0

Characterization of tryptophan oxidation affecting D1 degradation by FtsH in the photosystem II quality control of chloroplasts

Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH