Finding weakly reversible realizations of chemical reaction networks using optimization

An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem statement can be traced back at least 30 years ago. The algorithm uses standard linear and mixed integer linear programming, and it is based on elementary graph theory and important former results on the dense realizations of CRNs. The proposed method is also capable of determining if no dynamically equivalent weakly reversible structure exists for a given reaction network with a previously fixed complex set.Comment: 18 pages, 9 figure

Conformational mechanism for the stability of microtubule-kinetochore attachments

Regulating the stability of microtubule(MT)-kinetochore attachments is fundamental to avoiding mitotic errors and ensure proper chromosome segregation during cell division. While biochemical factors involved in this process have been identified, its mechanics still needs to be better understood. Here we introduce and simulate a mechanical model of MT-kinetochore interactions in which the stability of the attachment is ruled by the geometrical conformations of curling MT-protofilaments entangled in kinetochore fibrils. The model allows us to reproduce with good accuracy in vitro experimental measurements of the detachment times of yeast kinetochores from MTs under external pulling forces. Numerical simulations suggest that geometrical features of MT-protofilaments may play an important role in the switch between stable and unstable attachments

A critical look at the role of the bare parameters in the renormalization of Phi-derivable approximations

We revisit the renormalization of Phi-derivable approximations from a slightly different point of view than the one which is usually followed in previous works. We pay particular attention to the question of the existence of a solution to the self-consistent equation that defines the two-point function in the Cornwall-Jackiw-Tomboulis formalism and to the fact that some of the ultraviolet divergences which appear if one formally expands the solution in powers of the bare coupling do not always appear as divergences at the level of the solution itself. We discuss these issues using a particular truncation of the Phi functional, namely the simplest truncation which brings non-trivial momentum and field dependence to the two-point function.Comment: 30 pages, 12 figure

Geometrodynamics in a spherically symmetric, static crossflow of null dust

The spherically symmetric, static spacetime generated by a crossflow of non-interacting radiation streams, treated in the geometrical optics limit (null dust) is equivalent to an anisotropic fluid forming a radiation atmosphere of a star. This reference fluid provides a preferred / internal time, which is employed as a canonical coordinate. Among the advantages we encounter a new Hamiltonian constraint, which becomes linear in the momentum conjugate to the internal time (therefore yielding a functional Schr\"{o}dinger equation after quantization), and a strongly commuting algebra of the new constraints.Comment: Section on boundary behavior and fall-off conditions of canonical variables added. New references, 1 new figure, 12 pages. Version accepted in Phys.Rev.

Estimations of orbital parameters of exoplanets from transit photometry by using dynamical constraints

The probability of the detection of Earth-like exoplanets may increase in the near future after the launch of the space missions using the transit photometry as observation method. By using this technique only the semi-major axis of the detected planet can be determined, and there will be no information on the upper limit of its orbital eccentricity. However, the orbital eccentricity is a very important parameter, not only from a dynamical point of view, since it gives also information on the climate and the habitability of the Earth-like planets. In this paper a possible procedure is suggested for confining the eccentricity of an exoplanet discovered by transit photometry if an already known giant planet orbits also in the system.Comment: 16 pages, 10 figures, accepted for Cel. Mech. Dyn. Astro