The solution space of metabolic networks: producibility, robustness and fluctuations

Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of its main areas of application is the study of cellular metabolic networks. We briefly and selectively review the main approaches to this problem and then, building on recent work, we provide a characterization of the productive capabilities of the metabolic network of the bacterium E.coli in a specified growth medium in terms of the producible biochemical species. While a robust and physiologically meaningful production profile clearly emerges (including biomass components, biomass products, waste etc.), the underlying constraints still allow for significant fluctuations even in key metabolites like ATP and, as a consequence, apparently lay the ground for very different growth scenarios.Comment: 10 pages, prepared for the Proceedings of the International Workshop on Statistical-Mechanical Informatics, March 7-10, 2010, Kyoto, Japa

Theory of controlled quantum dynamics

We introduce a general formalism, based on the stochastic formulation of quantum mechanics, to obtain localized quasi-classical wave packets as dynamically controlled systems, for arbitrary anharmonic potentials. The control is in general linear, and it amounts to introduce additional quadratic and linear time-dependent terms to the given potential. In this way one can construct for general systems either coherent packets moving with constant dispersion, or dynamically squeezed packets whose spreading remains bounded for all times. In the standard operatorial framework our scheme corresponds to a suitable generalization of the displacement and scaling operators that generate the coherent and squeezed states of the harmonic oscillator.Comment: LaTeX, A4wide, 28 pages, no figures. To appear in J. Phys. A: Math. Gen., April 199

A cross impact methodology for the assessment of US telecommunications system with application to fiber optics development: Executive summary

A cross impact model of the U.S. telecommunications system was developed. For this model, it was necessary to prepare forecasts of the major segments of the telecommunications system, such as satellites, telephone, TV, CATV, radio broadcasting, etc. In addition, forecasts were prepared of the traffic generated by a variety of new or expanded services, such as electronic check clearing and point of sale electronic funds transfer. Finally, the interactions among the forecasts were estimated (the cross impacts). Both the forecasts and the cross impacts were used as inputs to the cross impact model, which could then be used to stimulate the future growth of the entire U.S. telecommunications system. By varying the inputs, technology changes or policy decisions with regard to any segment of the system could be evaluated in the context of the remainder of the system. To illustrate the operation of the model, a specific study was made of the deployment of fiber optics, throughout the telecommunications system

Symbolic computation of exact solutions expressible in hyperbolic and elliptic functions for nonlinear PDEs

Algorithms are presented for the tanh- and sech-methods, which lead to closed-form solutions of nonlinear ordinary and partial differential equations (ODEs and PDEs). New algorithms are given to find exact polynomial solutions of ODEs and PDEs in terms of Jacobi's elliptic functions. For systems with parameters, the algorithms determine the conditions on the parameters so that the differential equations admit polynomial solutions in tanh, sech, combinations thereof, Jacobi's sn or cn functions. Examples illustrate key steps of the algorithms. The new algorithms are implemented in Mathematica. The package DDESpecialSolutions.m can be used to automatically compute new special solutions of nonlinear PDEs. Use of the package, implementation issues, scope, limitations, and future extensions of the software are addressed. A survey is given of related algorithms and symbolic software to compute exact solutions of nonlinear differential equations.Comment: 39 pages. Software available from Willy Hereman's home page at http://www.mines.edu/fs_home/whereman

Adaptive drivers in a model of urban traffic

We introduce a simple lattice model of traffic flow in a city where drivers optimize their route-selection in time in order to avoid traffic jams, and study its phase structure as a function of the density of vehicles and of the drivers' behavioral parameters via numerical simulations and mean-field analytical arguments. We identify a phase transition between a low- and a high-density regime. In the latter, inductive drivers may surprisingly behave worse than randomly selecting drivers.Comment: 7 pages, final versio

A cross impact methodology for the assessment of US telecommunications system with application to fiber optics development, volume 2

The appendices for the cross impact methodology are presented. These include: user's guide, telecommunication events, cross impacts, projection of historical trends, and projection of trends in satellite communications

A cross impact methodology for the assessment of US telecommunications system with application to fiber optics development, volume 1

A cross impact model of the U.S. telecommunications system was developed. It was necessary to prepare forecasts of the major segments of the telecommunications system, such as satellites, telephone, TV, CATV, radio broadcasting, etc. In addition, forecasts were prepared of the traffic generated by a variety of new or expanded services, such as electronic check clearing and point of sale electronic funds transfer. Finally, the interactions among the forecasts were estimated (the cross impact). Both the forecasts and the cross impacts were used as inputs to the cross impact model, which could then be used to stimulate the future growth of the entire U.S. telecommunications system. By varying the inputs, technology changes or policy decisions with regard to any segment of the system could be evaluated in the context of the remainder of the system. To illustrate the operation of the model, a specific study was made of the deployment of fiber optics throughout the telecommunications system

Von Neumann's expanding model on random graphs

Within the framework of Von Neumann's expanding model, we study the maximum growth rate r achievable by an autocatalytic reaction network in which reactions involve a finite (fixed or fluctuating) number D of reagents. r is calculated numerically using a variant of the Minover algorithm, and analytically via the cavity method for disordered systems. As the ratio between the number of reactions and that of reagents increases the system passes from a contracting (r1). These results extend the scenario derived in the fully connected model (D\to\infinity), with the important difference that, generically, larger growth rates are achievable in the expanding phase for finite D and in more diluted networks. Moreover, the range of attainable values of r shrinks as the connectivity increases.Comment: 20 page

Rashba spin-orbit coupling and spin precession in carbon nanotubes

The Rashba spin-orbit coupling in carbon nanotubes and its effect on spin-dependent transport properties are analyzed theoretically. We focus on clean non-interacting nanotubes with tunable number of subbands $N$. The peculiar band structure is shown to allow in principle for Datta-Das oscillatory behavior in the tunneling magnetoresistance as a function of gate voltage, despite the presence of multiple bands. We discuss the conditions for observing Datta-Das oscillations in carbon nanotubes.Comment: 12 pages, published versio