Interplay between excitation kinetics and reaction-center dynamics in purple bacteria

Photosynthesis is arguably the fundamental process of Life, since it enables energy from the Sun to enter the food-chain on Earth. It is a remarkable non-equilibrium process in which photons are converted to many-body excitations which traverse a complex biomolecular membrane, getting captured and fueling chemical reactions within a reaction-center in order to produce nutrients. The precise nature of these dynamical processes -- which lie at the interface between quantum and classical behaviour, and involve both noise and coordination -- are still being explored. Here we focus on a striking recent empirical finding concerning an illumination-driven transition in the biomolecular membrane architecture of {\it Rsp. Photometricum} purple bacteria. Using stochastic realisations to describe a hopping rate model for excitation transfer, we show numerically and analytically that this surprising shift in preferred architectures can be traced to the interplay between the excitation kinetics and the reaction center dynamics. The net effect is that the bacteria profit from efficient metabolism at low illumination intensities while using dissipation to avoid an oversupply of energy at high illumination intensities.Comment: 21 pages, 13 figures, accepted for publication in New Journal of Physic

Quantum inequalities for the free Rarita-Schwinger fields in flat spacetime

Using the methods developed by Fewster and colleagues, we derive a quantum inequality for the free massive spin-${3\over 2}$ Rarita-Schwinger fields in the four dimensional Minkowski spacetime. Our quantum inequality bound for the Rarita-Schwinger fields is weaker, by a factor of 2, than that for the spin-${1\over 2}$ Dirac fields. This fact along with other quantum inequalities obtained by various other authors for the fields of integer spin (bosonic fields) using similar methods lead us to conjecture that, in the flat spacetime, separately for bosonic and fermionic fields, the quantum inequality bound gets weaker as the the number of degrees of freedom of the field increases. A plausible physical reason might be that the more the number of field degrees of freedom, the more freedom one has to create negative energy, therefore, the weaker the quantum inequality bound.Comment: Revtex, 11 pages, to appear in PR

Towards an embedding of Graph Transformation in Intuitionistic Linear Logic

Linear logics have been shown to be able to embed both rewriting-based approaches and process calculi in a single, declarative framework. In this paper we are exploring the embedding of double-pushout graph transformations into quantified linear logic, leading to a Curry-Howard style isomorphism between graphs and transformations on one hand, formulas and proof terms on the other. With linear implication representing rules and reachability of graphs, and the tensor modelling parallel composition of graphs and transformations, we obtain a language able to encode graph transformation systems and their computations as well as reason about their properties

Scalar Field Quantum Inequalities in Static Spacetimes

We discuss quantum inequalities for minimally coupled scalar fields in static spacetimes. These are inequalities which place limits on the magnitude and duration of negative energy densities. We derive a general expression for the quantum inequality for a static observer in terms of a Euclidean two-point function. In a short sampling time limit, the quantum inequality can be written as the flat space form plus subdominant correction terms dependent upon the geometric properties of the spacetime. This supports the use of flat space quantum inequalities to constrain negative energy effects in curved spacetime. Using the exact Euclidean two-point function method, we develop the quantum inequalities for perfectly reflecting planar mirrors in flat spacetime. We then look at the quantum inequalities in static de~Sitter spacetime, Rindler spacetime and two- and four-dimensional black holes. In the case of a four-dimensional Schwarzschild black hole, explicit forms of the inequality are found for static observers near the horizon and at large distances. It is show that there is a quantum averaged weak energy condition (QAWEC), which states that the energy density averaged over the entire worldline of a static observer is bounded below by the vacuum energy of the spacetime. In particular, for an observer at a fixed radial distance away from a black hole, the QAWEC says that the averaged energy density can never be less than the Boulware vacuum energy density.Comment: 27 pages, 2 Encapsulated Postscript figures, uses epsf.tex, typeset in RevTe

Resource-Bound Quantification for Graph Transformation

Graph transformation has been used to model concurrent systems in software engineering, as well as in biochemistry and life sciences. The application of a transformation rule can be characterised algebraically as construction of a double-pushout (DPO) diagram in the category of graphs. We show how intuitionistic linear logic can be extended with resource-bound quantification, allowing for an implicit handling of the DPO conditions, and how resource logic can be used to reason about graph transformation systems

Algebraic totality, towards completeness

Finiteness spaces constitute a categorical model of Linear Logic (LL) whose objects can be seen as linearly topologised spaces, (a class of topological vector spaces introduced by Lefschetz in 1942) and morphisms as continuous linear maps. First, we recall definitions of finiteness spaces and describe their basic properties deduced from the general theory of linearly topologised spaces. Then we give an interpretation of LL based on linear algebra. Second, thanks to separation properties, we can introduce an algebraic notion of totality candidate in the framework of linearly topologised spaces: a totality candidate is a closed affine subspace which does not contain 0. We show that finiteness spaces with totality candidates constitute a model of classical LL. Finally, we give a barycentric simply typed lambda-calculus, with booleans ${\mathcal{B}}$ and a conditional operator, which can be interpreted in this model. We prove completeness at type ${\mathcal{B}}^n\to{\mathcal{B}}$ for every n by an algebraic method

A quantum weak energy inequality for the Dirac field in two-dimensional flat spacetime

Fewster and Mistry have given an explicit, non-optimal quantum weak energy inequality that constrains the smeared energy density of Dirac fields in Minkowski spacetime. Here, their argument is adapted to the case of flat, two-dimensional spacetime. The non-optimal bound thereby obtained has the same order of magnitude, in the limit of zero mass, as the optimal bound of Vollick. In contrast with Vollick's bound, the bound presented here holds for all (non-negative) values of the field mass.Comment: Version published in Classical and Quantum Gravity. 7 pages, 1 figur

`Operational' Energy Conditions

I show that a quantized Klein-Gordon field in Minkowski space obeys an `operational' weak energy condition: the energy of an isolated device constructed to measure or trap the energy in a region, plus the energy it measures or traps, cannot be negative. There are good reasons for thinking that similar results hold locally for linear quantum fields in curved space-times. A thought experiment to measure energy density is analyzed in some detail, and the operational positivity is clearly manifested. If operational energy conditions do hold for quantum fields, then the negative energy densities predicted by theory have a will-o'-the-wisp character: any local attempt to verify a total negative energy density will be self-defeating on account of quantum measurement difficulties. Similarly, attempts to drive exotic effects (wormholes, violations of the second law, etc.) by such densities may be defeated by quantum measurement problems. As an example, I show that certain attempts to violate the Cosmic Censorship principle by negative energy densities are defeated. These quantum measurement limitations are investigated in some detail, and are shown to indicate that space-time cannot be adequately modeled classically in negative energy density regimes.Comment: 18 pages, plain Tex, IOP macros. Expanded treatment of measurement problems for space-time, with implications for Cosmic Censorship as an example. Accepted by Classical and Quantum Gravit

Hybrid Session Verification through Endpoint API Generation

© Springer-Verlag Berlin Heidelberg 2016.This paper proposes a new hybrid session verification methodology for applying session types directly to mainstream languages, based on generating protocol-specific endpoint APIs from multiparty session types. The API generation promotes static type checking of the behavioural aspect of the source protocol by mapping the state space of an endpoint in the protocol to a family of channel types in the target language. This is supplemented by very light run-time checks in the generated API that enforce a linear usage discipline on instances of the channel types. The resulting hybrid verification guarantees the absence of protocol violation errors during the execution of the session. We implement our methodology for Java as an extension to the Scribble framework, and use it to specify and implement compliant clients and servers for real-world protocols such as HTTP and SMTP

Propositions as Sessions

Continuing a line of work by Abramsky (1994), by Bellin and Scott (1994), and by Caires and Pfenning (2010), among others, this paper presents CP, a calculus in which propositions of classical linear logic correspond to session types. Continuing a line of work by Honda (1993), by Honda, Kubo, and Vasconcelos (1998), and by Gay and Vasconcelos (2010), among others, this paper presents GV, a linear functional language with session types, and presents a translation from GV into CP. The translation formalises for the first time a connection between a standard presentation of session types and linear logic, and shows how a modification to the standard presentation yield a language free from deadlock, where deadlock freedom follows from the correspondence to linear logic. Note. Please read this paper in colour! The paper uses colour to highlight the relation of types to terms and source to target. 1