Two-step simulations of reaction systems by minimal ones

Reaction systems were introduced by Ehrenfeucht and Rozenberg with biochemical applications in mind. The model is suitable for the study of subset functions, that is, functions from the set of all subsets of a finite set into itself. In this study the number of resources of a reaction system is essential for questions concerning generative capacity. While all functions (with a couple of trivial exceptions) from the set of subsets of a finite set S into itself can be defined if the number of resources is unrestricted, only a specific subclass of such functions is defined by minimal reaction systems, that is, the number of resources is smallest possible. On the other hand, minimal reaction systems constitute a very elegant model. In this paper we simulate arbitrary reaction systems by minimal ones in two derivation steps. Various techniques for doing this consist of taking names of reactions or names of subsets as elements of the background set. In this way also subset functions not at all definable by reaction systems can be generated. We follow the original definition of reaction systems, where both reactant and inhibitor sets are assumed to be nonempty

Reaction mechanisms of pair transfer

The mechanisms of nuclear transfer reactions are described for the transfer of two nucleons from one nucleus to another. Two-nucleon overlap functions are defined in various coordinate systems, and their transformation coefficients given between coordinate systems. Post and prior couplings are defined for sequential transfer mechanisms, and it is demonstrated that the combination of `prior-post' couplings avoids non-orthogonality terms, but does not avoid couplings that do not have good zero-range approximations. The simultaneous and sequential mechanisms are demonstrated for the $^{124}$Sn(p,t)$^{122}$Sn reaction at 25 MeV using shell-model overlap functions. The interference between the various simultaneous and sequential amplitudes is shown.Comment: 14 pages, 3 figures, chapter 34 in "50 Years of Nuclear BCS", edited by R. A. Broglia and V. Zelevinsky: ISBN 978-981-4412-48-3 Uses WS macros (included). Corrected text and calculations as in the published versio

Exhibiting cross-diffusion-induced patterns for reaction-diffusion systems on evolving domains and surfaces

The aim of this manuscript is to present for the first time the application of the finite element method for solving reaction-diffusion systems with cross-diffusion on continuously evolving domains and surfaces. Furthermore we present pattern formation generated by the reaction-diffusion systemwith cross-diffusion on evolving domains and surfaces. A two-component reaction-diffusion system with linear cross-diffusion in both u and v is presented. The finite element method is based on the approximation of the domain or surface by a triangulated domain or surface consisting of a union of triangles. For surfaces, the vertices of the triangulation lie on the continuous surface. A finite element space of functions is then defined by taking the continuous functions which are linear affine on each simplex of the triangulated domain or surface. To demonstrate the role of cross-diffusion to the theory of pattern formation, we compute patterns with model kinetic parameter values that belong only to the cross-diffusion parameter space; these do not belong to the standard parameter space for classical reaction-diffusion systems. Numerical results exhibited show the robustness, flexibility, versatility, and generality of our methodology; the methodology can deal with complicated evolution laws of the domain and surface, and these include uniform isotropic and anisotropic growth profiles as well as those profiles driven by chemical concentrations residing in the domain or on the surface

Kramers problem for nonequilibrium current-induced chemical reactions

We discuss the use of tunneling electron current to control and catalyze chemical reactions. Assuming the separation of time scales for electronic and nuclear dynamics we employ the Langevin equation for the reaction coordinate. The Langevin equation contains current-induced forces and is used to define nonequilibrium, effective potential energy surface for current-carrying molecular systems. The current-induced forces are computed via Keldysh nonequilibrium Green's functions. Once the nonequilibrium, current-depended potential energy surface is defined, the chemical reaction is modeled as an escape of a Brownian particle from the potential well. We demonstrate that the barrier between the reactant and the product states can be controlled by the bias voltage. When the molecule is asymmetrically coupled to the electrodes, the reaction can be catalyzed or stopped depending on the polarity of the tunneling current.Comment: 4 pages, 2 figure

Analysis of Reaction Network Systems Using Tropical Geometry

We discuss a novel analysis method for reaction network systems with polynomial or rational rate functions. This method is based on computing tropical equilibrations defined by the equality of at least two dominant monomials of opposite signs in the differential equations of each dynamic variable. In algebraic geometry, the tropical equilibration problem is tantamount to finding tropical prevarieties, that are finite intersections of tropical hypersurfaces. Tropical equilibrations with the same set of dominant monomials define a branch or equivalence class. Minimal branches are particularly interesting as they describe the simplest states of the reaction network. We provide a method to compute the number of minimal branches and to find representative tropical equilibrations for each branch.Comment: Proceedings Computer Algebra in Scientific Computing CASC 201

Gauge-boson propagator in out of equilibrium quantum-field system and the Boltzmann equation

We construct from first principles a perturbative framework for studying nonequilibrium quantum-field systems that include gauge bosons. The system of our concern is quasiuniform system near equilibrium or nonequilibrium quasistationary system. We employ the closed-time-path formalism and use the so-called gradient approximation. No further approximation is introduced. We construct a gauge-boson propagator, with which a well-defined perturbative framework is formulated. In the course of construction of the framework, we obtain the generalized Boltzmann equation (GBE) that describes the evolution of the number-density functions of gauge-bosonic quasiparticles. The framework allows us to compute the reaction rate for any process taking place in the system. Various processes, in turn, cause an evolution of the systems, which is described by the GBE.Comment: 28 page

Intrinsic tethering activity of endosomal Rab proteins.

Rab small G proteins control membrane trafficking events required for many processes including secretion, lipid metabolism, antigen presentation and growth factor signaling. Rabs recruit effectors that mediate diverse functions including vesicle tethering and fusion. However, many mechanistic questions about Rab-regulated vesicle tethering are unresolved. Using chemically defined reaction systems, we discovered that Vps21, a Saccharomyces cerevisiae ortholog of mammalian endosomal Rab5, functions in trans with itself and with at least two other endosomal Rabs to directly mediate GTP-dependent tethering. Vps21-mediated tethering was stringently and reversibly regulated by an upstream activator, Vps9, and an inhibitor, Gyp1, which were sufficient to drive dynamic cycles of tethering and detethering. These experiments reveal a previously undescribed mode of tethering by endocytic Rabs. In our working model, the intrinsic tethering capacity Vps21 operates in concert with conventional effectors and SNAREs to drive efficient docking and fusion

RIOJA (Repository Interface to Overlaid Journal Archives) project: final report

RIOJA (Repository Interface to Overlaid Journal Archives) was a 18-month partnership between UCL (University College London), Imperial College London, and the Universities Glasgow, Cambridge and Cornell. The project was funded by the JISC (Joint Information Systems Committee, UK). The project team worked with the Astrophysics community investigate aspects of overlay journals. For the purposes of the project, an overlay was defined as a quality-assured journal whose content is deposited to and resides more open access repositories. The project had both technical aims and supporting, non-technical aims. The primary technical deliverable from the project was a toolkit for the creation and maintenance overlay journals. The toolkit supports the exchange of data between a repository and piece of journal software. It supports functions such as author validation, metadata extraction from the source repository, and submission tracking. The toolkit is platform-neutral and could, in theory, be employed by any journal using content from any number repositories, in any discipline. The project also implemented a demonstrator overlay applying the RIOJA toolkit to the arXiv subject repository, and a demonstrator implementation of the RIOJA tool for GNU EPrints. Aside from creating the demonstrator and its underlying tools, the project aimed to acceptibility and feasibility of the overlay model. First, a large-scale survey of the Astrophysics community was undertaken. The survey collected data about research publishing practices within this community, and probed its reaction to the principle publishing. Second, the views of editors and publishers in this discipline were sought through interviews. These views were added to findings from the literature and summarised in a more general report on issues around the sustainability of an overlay journal