149,775 research outputs found
Stationary waves on nonlinear quantum graphs: General framework and canonical perturbation theory
In this paper we present a general framework for solving the stationary
nonlinear Schr\"odinger equation (NLSE) on a network of one-dimensional wires
modelled by a metric graph with suitable matching conditions at the vertices. A
formal solution is given that expresses the wave function and its derivative at
one end of an edge (wire) nonlinearly in terms of the values at the other end.
For the cubic NLSE this nonlinear transfer operation can be expressed
explicitly in terms of Jacobi elliptic functions. Its application reduces the
problem of solving the corresponding set of coupled ordinary nonlinear
differential equations to a finite set of nonlinear algebraic equations. For
sufficiently small amplitudes we use canonical perturbation theory which makes
it possible to extract the leading nonlinear corrections over large distances.Comment: 26 page
Exploration of Reaction Pathways and Chemical Transformation Networks
For the investigation of chemical reaction networks, the identification of
all relevant intermediates and elementary reactions is mandatory. Many
algorithmic approaches exist that perform explorations efficiently and
automatedly. These approaches differ in their application range, the level of
completeness of the exploration, as well as the amount of heuristics and human
intervention required. Here, we describe and compare the different approaches
based on these criteria. Future directions leveraging the strengths of chemical
heuristics, human interaction, and physical rigor are discussed.Comment: 48 pages, 4 figure
The Michaelis-Menten-Stueckelberg Theorem
We study chemical reactions with complex mechanisms under two assumptions:
(i) intermediates are present in small amounts (this is the quasi-steady-state
hypothesis or QSS) and (ii) they are in equilibrium relations with substrates
(this is the quasiequilibrium hypothesis or QE). Under these assumptions, we
prove the generalized mass action law together with the basic relations between
kinetic factors, which are sufficient for the positivity of the entropy
production but hold even without microreversibility, when the detailed balance
is not applicable. Even though QE and QSS produce useful approximations by
themselves, only the combination of these assumptions can render the
possibility beyond the "rarefied gas" limit or the "molecular chaos"
hypotheses. We do not use any a priori form of the kinetic law for the chemical
reactions and describe their equilibria by thermodynamic relations. The
transformations of the intermediate compounds can be described by the Markov
kinetics because of their low density ({\em low density of elementary events}).
This combination of assumptions was introduced by Michaelis and Menten in 1913.
In 1952, Stueckelberg used the same assumptions for the gas kinetics and
produced the remarkable semi-detailed balance relations between collision rates
in the Boltzmann equation that are weaker than the detailed balance conditions
but are still sufficient for the Boltzmann -theorem to be valid. Our results
are obtained within the Michaelis-Menten-Stueckelbeg conceptual framework.Comment: 54 pages, the final version; correction of a misprint in Attachment
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
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