From Network Structure to Dynamics and Back Again: Relating dynamical stability and connection topology in biological complex systems

The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from statistical physics and non-linear dynamics. In this paper, we look at a few examples of biological networks to see how similar questions can come up in very different contexts. We review some of our recent work that looks at how network structure (e.g., its connection topology) can dictate the nature of its dynamics, and conversely, how dynamical considerations constrain the network structure. We also see how networks occurring in nature can evolve to modular configurations as a result of simultaneously trying to satisfy multiple structural and dynamical constraints. The resulting optimal networks possess hubs and have heterogeneous degree distribution similar to those seen in biological systems.Comment: 15 pages, 6 figures, to appear in Proceedings of "Dynamics On and Of Complex Networks", ECSS'07 Satellite Workshop, Dresden, Oct 1-5, 200

Hydrodynamics of Binary Coalescence.I. Polytropes with Stiff Equations of State

We have performed a series of three-dimensional hydrodynamic calculations of binary coalescence using the smoothed particle hydrodynamics (SPH) method. The initial conditions are exact polytropic equilibrium configurations with \gam > 5/3, on the verge of dynamical instability. We calculate the emission of gravitational radiation in the quadrupole approximation. The fully nonlinear development of the instability is followed until a new equilibrium configuration is reached. We find that the properties of this final configuration depend sensitively on both the compressibility and mass ratio. An {\em axisymmetric} merged configuration is always produced when \gam\lo2.3. As a consequence, the emission of gravitational radiation shuts off abruptly right after the onset of dynamical instability. In contrast, {\em triaxial\/} merged configurations are obtained when \gam\go2.3, and the system continues to emit gravitational waves after the final coalescence. Systems with mass ratios $q\ne1$ typically become dynamically unstable before the onset of mass transfer. Stable mass transfer from one neutron star to another in a close binary is therefore probably ruled out. The maximum amplitude $h_{max}$ and peak luminosity $L_{max}$ of the gravitational waves emitted during the final coalescence are nearly independent of \gam, but depend very sensitively on the mass ratio $q$.Comment: 27 pages, uuencoded compressed postscript, 16 figures upon request from [email protected], IAS-AST-94-

On the Hamiltonian structure and three-dimensional instabilities of rotating liquid bridges

We consider a rotating inviscid liquid drop trapped between two parallel plates. The liquid–air interface is a free surface and the boundaries of the wetted regions in the plates are also free. We assume that the two contact angles at the plates are equal. We present drop shapes that generalize the catenoids, nodoids and unduloids in the presence of rotation. We describe profile curves of these drops and investigate their stability to three-dimensional perturbations. The instabilities are associated with degeneracies of eigenvalues of the corresponding Hamiltonian linear stability problem. We observe that these instabilities are present even in the case when the analogue of the Rayleigh criterion for two-dimensional stability is satisfie

Twin Binaries: Studies of Stability, Mass Transfer, and Coalescence

Motivated by suggestions that binaries with almost equal-mass components ("twins") play an important role in the formation of double neutron stars and may be rather abundant among binaries, we study the stability of synchronized close and contact binaries with identical components in circular orbits. In particular, we investigate the dependency of the innermost stable circular orbit on the core mass, and we study the coalescence of the binary that occurs at smaller separations. For twin binaries composed of convective main-sequence stars, subgiants, or giants with low mass cores (M_c <~0.15M, where M is the mass of a component), a secular instability is reached during the contact phase, accompanied by a dynamical mass transfer instability at the same or at a slightly smaller orbital separation. Binaries that come inside this instability limit transfer mass gradually from one component to the other and then coalesce quickly as mass is lost through the outer Lagrangian points. For twin giant binaries with moderate to massive cores (M_c >~0.15M), we find that stable contact configurations exist at all separations down to the Roche limit, when mass shedding through the outer Lagrangian points triggers a coalescence of the envelopes and leaves the cores orbiting in a central tight binary. In addition to the formation of binary neutron stars, we also discuss the implications of our results for the production of planetary nebulae with double degenerate central binaries.Comment: 17 pages, accepted to ApJ, final version includes discussion of planetary nebulae with central binaries and a new figure about shock heating, visualizations at http://webpub.allegheny.edu/employee/j/jalombar/movies

Fractal free energy landscapes in structural glasses

Glasses are amorphous solids whose constituent particles are caged by their neighbors and thus cannot flow. This sluggishness is often ascribed to the free energy landscape containing multiple minima (basins) separated by high barriers. Here we show, using theory and numerical simulation, that the landscape is much rougher than is classically assumed. Deep in the glass, it undergoes a "roughness transition" to fractal basins. This brings about isostaticity at jamming and marginality of glassy states near jamming. Critical exponents for the basin width, the weak force distribution, and the spatial spread of quasi-contacts at jamming can be analytically determined. Their value is found to be compatible with numerical observations. This advance therefore incorporates the jamming transition of granular materials into the framework of glass theory. Because temperature and pressure control which features of the landscape are experienced, glass mechanics and transport are expected to reflect the features of the topology we discuss here. Hitherto mysterious properties of low-temperature glasses could be explained by this approach.Comment: 13 pages, 4 figures. This version was initially submitted to Nature Communications in December 2013. The (much improved) final version is available on the Nature Communications website (see DOI below). A detailed version of this work is available on arXiv:1310.254