P Systems with Anti-Matter

After a short introduction to the area of membrane computing (a branch of natural computing), we introduce the concept of anti-matter in membrane computing. First we consider spiking neural P systems with anti-spikes, and then we show the power of anti-matter in cell-like P systems. As expected, the use of anti-matter objects and especially of matter/anti-matter annihilation rules, turns out to be rather powerful: computational completeness of P systems with anti-matter is obtained immediately, even without using catalysts. Finally, some open problems are formulated, too

(Tissue) P Systems with Anti-Membranes

The concept of a matter object being annihilated when meeting its corresponding anti-matter object is taken over for membranes as objects and anti-membranes as the corresponding annihilation counterpart in P systems. Natural numbers can be represented by the corresponding number of membranes with a speci c label. Computational completeness in this setting then can be obtained with using only elementary membrane division rules, without using objects. A similar result can be obtained for tissue P systems with cell division rules and cell / anti-cell annihilation rules. In both cases, as derivation modes we may take the standard maximally parallel derivation modes as well as any of the maximally parallel set derivation modes (non-extendable (multi)sets of rules, (multi)sets with maximal number of rules, (multi)sets of rules a ecting the maximal number of objects)

P Systems: from Anti-Matter to Anti-Rules

The concept of a matter object being annihilated when meeting its corresponding anti-matter object is taken over for rule labels as objects and anti-rule labels as the corresponding annihilation counterpart in P systems. In the presence of a corresponding anti-rule object, annihilation of a rule object happens before the rule that the rule object represents, can be applied. Applying a rule consumes the corresponding rule object, but may also produce new rule objects as well as anti-rule objects, too. Computational completeness in this setting then can be obtained in a one-membrane P system with non-cooperative rules and rule / anti-rule annihilation rules when using one of the standard maximally parallel derivation modes as well as any of the maximally parallel set derivation modes (i.e., non-extendable (multi)sets of rules, (multi)sets with maximal number of rules, (multi)sets of rules a ecting the maximal number of objects). When using the sequential derivation mode, at least the computational power of partially blind register machines is obtained

The Bilayer Collective Properties Govern the Interaction of an HIV-1 Antibody with the Viral Membrane

Efficient engagement with the envelope glycoprotein membrane-proximal external region (MPER) results in robust blocking of viral infection by a class of broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV). Developing an accommodation surface that engages with the viral lipid envelope appears to correlate with the neutralizing potency displayed by these bnAbs. The nature of the interactions established between the antibody and the lipid is nonetheless a matter of debate, with some authors arguing that anti-MPER specificity arises only under pathological conditions in autoantibodies endowed with stereospecific binding sites for phospholipids. However, bnAb-lipid interactions are often studied in systems that do not fully preserve the biophysical properties of lipid bilayers, and therefore, questions on binding specificity and the effect of collective membrane properties on the interaction are still open. Here, to evaluate the specificity of lipid interactions of an anti-MPER bnAb (4E10) in an intact membrane context, we determine quantitatively its association with lipid bilayers by means of scanning fluorescence correlation spectroscopy and all-atom molecular dynamic simulations. Our data support that 4E10 establishes electrostatic and hydrophobic interactions with the viral membrane surface and that the collective physical properties of the lipid bilayer influence 4E10 dynamics therein. We conclude that establishment of peripheral, nonspecific electrostatic interactions with the viral membrane through accommodation surfaces may assist high-affinity binding of HIV-1 MPER epitope at membrane interfaces. These findings highlight the importance of considering antibody-lipid interactions in the design of antibody-based anti-HIV strategies.</p

Biomimetic monolayer films of digalactosyldiacylglycerol incorporating plastoquinone

The photosynthesis is the process used by plants and bacteria cells to convert inorganic matter in organic thanks to the light energy. This process consist on several steps, being one of them the electronic transport from the photosystem II to the cytochrome thanks to plastoquinone-9 (PQ). Here we prepare membranes that mimic the characteristics and composition of natural photosynthetic cell membranes and we characterize them in order to obtain the PQ molecules position in the membrane and their electrochemical behaviour. The selected galactolipid is digalactosyldiacylglycerol (DGDG) that represents the 30% of the thylakoid membrane lipid content. The results obtained are worthful for several science fields due to the relevance of galactolipids as anti-algal, anti-viral, anti-tumor and anti-inflammatory agents and the antioxidant and free radical scavenger properties of prenylquinones.; Both pure components (DGDG and PQ) and the DGDG:PQ mixtures have been studied using surface pressure-area isotherms. These isotherms give information about the film stability and indicate the thermodynamic behaviour of the mixture and their physical state. The Langmuir-Blodgett (LB) film has been transferred forming a monolayer that mimics the bottom layer of the biological membranes. This monolayer on mica has been topo-graphically characterized using AFM and both the height and the physical state that they present have been obtained. Moreover, these monolayers have been transferred onto ITO that is a hydrophilic substrate with good optical and electrical features, so that, it is suitable for studying the electrochemical behaviour of these systems and it is a good candidate for energy producing devices. (C) 2015 Elsevier B.V. All rights reserved.Peer ReviewedPostprint (author’s final draft

The Bilayer Collective Properties Govern the Interaction of an HIV-1 Antibody with the Viral Membrane

Efficient engagement with the envelope glycoprotein membrane-proximal external region (MPER) results in robust blocking of viral infection by a class of broadly neutralizing antibodies (bnAbs) against human immunodeficiency virus (HIV). Developing an accommodation surface that engages with the viral lipid envelope appears to correlate with the neutralizing potency displayed by these bnAbs. The nature of the interactions established between the antibody and the lipid is nonetheless a matter of debate, with some authors arguing that anti-MPER specificity arises only under pathological conditions in autoantibodies endowed with stereospecific binding sites for phospholipids. However, bnAb-lipid interactions are often studied in systems that do not fully preserve the biophysical properties of lipid bilayers, and therefore, questions on binding specificity and the effect of collective membrane properties on the interaction are still open. Here, to evaluate the specificity of lipid interactions of an anti-MPER bnAb (4E10) in an intact membrane context, we determine quantitatively its association with lipid bilayers by means of scanning fluorescence correlation spectroscopy and all-atom molecular dynamic simulations. Our data support that 4E10 establishes electrostatic and hydrophobic interactions with the viral membrane surface and that the collective physical properties of the lipid bilayer influence 4E10 dynamics therein. We conclude that establishment of peripheral, nonspecific electrostatic interactions with the viral membrane through accommodation surfaces may assist high-affinity binding of HIV-1 MPER epitope at membrane interfaces. These findings highlight the importance of considering antibody-lipid interactions in the design of antibody-based anti-HIV strategies.Supported by Ministerio de Economı´a y Competitividad in Spain grants (BIO2015-64221-R (MINECO/AEI/FEDER UE) and BFU2015-65625-P (MINECO/FEDER UE), Ministerio de Ciencia, Innovacio´n y Universidades in Spain grant RTI2018-095624-B-C21 (MCIU/AEI/FEDER UE), Basque Government grant IT1196-19, doctoral studentships to E.R., and a doctoral scholarship to A.G.V. (FPU2016-01727). P.C. also acknowledges a research associate contract at the University of the Basque Country (DOCREC18/01) and a postdoctoral fellowship from the Basque Government (POS_2018_1_0066). L.D. acknowledges ANII (Agencia Nacional de Investigacio´n e Innovacio´n) and the Institut Pasteur de Montevideo for funding his postdoctoral fellowship.Peer reviewe

Brane versus shell cosmologies in Einstein and Einstein-Gauss-Bonnet theories

We first illustrate on a simple example how, in existing brane cosmological models, the connection of a 'bulk' region to its mirror image creates matter on the 'brane'. Next, we present a cosmological model with no $Z_2$ symmetry which is a spherical symmetric 'shell' separating two metrically different 5-dimensional anti-de Sitter regions. We find that our model becomes Friedmannian at late times, like present brane models, but that its early time behaviour is very different: the scale factor grows from a non-zero value at the big bang singularity. We then show how the Israel matching conditions across the membrane (that is either a brane or a shell) have to be modified if more general equations than Einstein's, including a Gauss-Bonnet correction, hold in the bulk, as is likely to be the case in a low energy limit of string theory. We find that the membrane can then no longer be treated in the thin wall approximation. However its microphysics may, in some instances, be simply hidden in a renormalization of Einstein's constant, in which cases Einstein and Gauss-Bonnet membranes are identical.Comment: 15 pages, submitted to Phys. Rev.