Anomalously slow phase transitions in self-gravitating systems

Kinetics of collapse and explosion transitions in microcanonical self-gravitating ensembles is analyzed. A system of point particles interacting via an attractive soft Coulomb potential and confined to a spherical container is considered. We observed that for 100--200 particles collapse takes $10^3$ -- $10^4$ particle crossing times to complete, i. e., it is by 2-3 orders of magnitude slower than velocity relaxation. In addition, it is found that the collapse time decreases rapidly with the increase of the softcore radius. We found that such an anomalously long collapse time is caused by the slow energy exchange between a higher-temperature compact core and relatively cold diluted halo. The rate of energy exchange between the faster modes of the core particles and slower-moving particles of the halo is exponentially small in the ratio of the frequencies of these modes. As the softcore radius increases, and the typical core modes become slower, the ratio of core and halo frequencies decreases and the collapse accelerates. Implications to astrophysical systems and phase transition kinetics are discussed.Comment: 6 pages, 5 figure

Finding mesoscopic communities in sparse networks

We suggest a fast method to find possibly overlapping network communities of a desired size and link density. Our method is a natural generalization of the finite-$T$ superparamegnetic Potts clustering introduced by Blatt, Wiseman, and Domany (Phys. Rev. Lett. v.76, 3251 (1996) and the recently suggested by Reichard and Bornholdt (Phys. Rev. Lett. v.93, 21870 (2004)) annealing of Potts model with global antiferromagnetic term. Similarly to both preceding works, the proposed generalization is based on ordering of ferromagnetic Potts model; the novelty of the proposed approach lies in the adjustable dependence of the antiferromagnetic term on the population of each Potts state, which interpolates between the two previously considered cases. This adjustability allows to empirically tune the algorithm to detect the maximum number of communities of the given size and link density. We illustrate the method by detecting protein complexes in high-throughput protein binding networks.Comment: 8 pages, 2 figure, typos corrected, 1 figure adde

Propagation of fluctuations in interaction networks governed by the law of mass action

Using an example of physical interactions between proteins, we study how perturbations propagate in interconnected networks whose equilibrium state is governed by the law of mass action. We introduce a comprehensive matrix formalism which predicts the response of this equilibrium to small changes in total concentrations of individual molecules, and explain it using a heuristic analogy to a current flow in a network of resistors. Our main conclusion is that on average changes in free concentrations exponentially decay with the distance from the source of perturbation. We then study how this decay is influenced by such factors as the topology of a network, binding strength, and correlations between concentrations of neighboring nodes. An exact analytic expression for the decay constant is obtained for the case of uniform interactions on the Bethe lattice. Our general findings are illustrated using a real biological network of protein-protein interactions in baker's yeast with experimentally determined protein concentrations.Comment: 4 pages; 2 figure

Binaries and core-ring structures in self-gravitating systems

Low energy states of self-gravitating systems with finite angular momentum are considered. A constraint is introduced to confine cores and other condensed objects within the system boundaries by gravity alone. This excludes previously observed astrophysically irrelevant asymmetric configurations with a single core. We show that for an intermediate range of a short-distance cutoff and small angular momentum, the equilibrium configuration is an asymmetric binary. For larger angular momentum or for a smaller range of the short distance cutoff, the equilibrium configuration consists of a central core and an equatorial ring. The mass of the ring varies between zero for vanishing rotation and the full system mass for the maximum angular momentum $L_{max}$ a localized gravitationally bound system can have. The value of $L_{max}$ scales as $\sqrt{\ln(1/x_0)}$, where $x_0$ is a ratio of a short-distance cutoff range to the system size. An example of the soft gravitational potential is considered; the conclusions are shown to be valid for other forms of short-distance regularization.Comment: 6 pages, 3 figure

Collapses and explosions in self-gravitating systems

Collapse and reverse to collapse explosion transition in self-gravitating systems are studied by molecular dynamics simulations. A microcanonical ensemble of point particles confined to a spherical box is considered; the particles interact via an attractive soft Coulomb potential. It is observed that the collapse in the particle system indeed takes place when the energy of the uniform state is put near or below the metastability-instability threshold (collapse energy), predicted by the mean-field theory. Similarly, the explosion in the particle system occurs when the energy of the core-halo state is increased above the explosion energy, where according to the mean field predictions the core-halo state becomes unstable. For a system consisting of 125 -- 500 particles, the collapse takes about $10^5$ single particle crossing times to complete, while a typical explosion is by an order of magnitude faster. A finite lifetime of metastable states is observed. It is also found that the mean-field description of the uniform and the core-halo states is exact within the statistical uncertainty of the molecular dynamics data.Comment: 9 pages, 14 figure