In turbulent Rayleigh-Benard convection, a large-scale circulation (LSC) develops in a nearly vertical plane, and is maintained by rising and falling plumes detaching from the unstable thermal boundary layers. Rare but large fluctuations in the LSC a
mplitude can lead to extinction of the LSC (a cessation event), followed by the re-emergence of another LSC with a different (random) azimuthal orientation. We extend previous models of the LSC dynamics to include momentum and thermal diffusion in the azimuthal plane, and calculate the tails of the probability distributions of both the amplitude and azimuthal angle. Our analytical results are in very good agreement with experimental data.
Evolution is the fundamental physical process that gives rise to biological phenomena. Yet it is widely treated as a subset of population genetics, and thus its scope is artificially limited. As a result, the key issues of how rapidly evolution occur
s, and its coupling to ecology have not been satisfactorily addressed and formulated. The lack of widespread appreciation for, and understanding of, the evolutionary process has arguably retarded the development of biology as a science, with disastrous consequences for its applications to medicine, ecology and the global environment. This review focuses on evolution as a problem in non-equilibrium statistical mechanics, where the key dynamical modes are collective, as evidenced by the plethora of mobile genetic elements whose role in shaping evolution has been revealed by modern genomic surveys. We discuss how condensed matter physics concepts might provide a useful perspective in evolutionary biology, the conceptual failings of the modern evolutionary synthesis, the open-ended growth of complexity, and the quintessentially self-referential nature of evolutionary dynamics.
We use momentum transfer arguments to predict the friction factor $f$ in two-dimensional turbulent soap-film flows with rough boundaries (an analogue of three-dimensional pipe flow) as a function of Reynolds number Re and roughness $r$, considering s
eparately the inverse energy cascade and the forward enstrophy cascade. At intermediate Re, we predict a Blasius-like friction factor scaling of $fproptotextrm{Re}^{-1/2}$ in flows dominated by the enstrophy cascade, distinct from the energy cascade scaling of $textrm{Re}^{-1/4}$. For large Re, $f sim r$ in the enstrophy-dominated case. We use conformal map techniques to perform direct numerical simulations that are in satisfactory agreement with theory, and exhibit data collapse scaling of roughness-induced criticality, previously shown to arise in the 3D pipe data of Nikuradse.
We analyze a system-level model for lytic repression of lambda-phage in E. coli using reliability theory, showing that the repressor circuit comprises 4 redundant components whose failure mode is prophage induction. Our model reflects the specific bi
ochemical mechanisms involved in regulation, including long-range cooperative binding, and its detailed predictions for prophage induction in E. coli under ultra-violet radiation are in good agreement with experimental data.
A molecular dynamics calculation of the amino acid polar requirement is presented and used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code mo
re than any previously-known measure. These results strongly support the idea that the genetic code evolved from a communal state of life prior to the root of the modern ribosomal tree of life.
We simulate an individual-based model that represents both the phenotype and genome of digital organisms with predator-prey interactions. We show how open-ended growth of complexity arises from the invariance of genetic evolution operators with respe
ct to changes in the complexity, and that the dynamics which emerges is controlled by a non-equilibrium critical point. The mechanism is analogous to the development of the cascade in fluid turbulence.
A dynamical theory of geophysical precipitation pattern formation is presented and applied to irreversible calcium carbonate (travertine) deposition. Specific systems studied here are the terraces and domes observed at geothermal hot springs, such as
those at Yellowstone National Park, and speleothems, particularly stalactites and stalagmites. The theory couples the precipitation front dynamics with shallow water flow, including corrections for turbulent drag and curvature effects. In the absence of capillarity and with a laminar flow profile, the theory predicts a one-parameter family of steady state solutions to the moving boundary problem describing the precipitation front. These shapes match well the measured shapes near the vent at the top of observed travertine domes. Closer to the base of the dome, the solutions deviate from observations, and circular symmetry is broken by a fluting pattern, which we show is associated with capillary forces causing thin film break-up. We relate our model to that recently proposed for stalactite growth, and calculate the linear stability spectrum of both travertine domes and stalactites. Lastly, we apply the theory to the problem of precipitation pattern formation arising from turbulent flow down an inclined plane, and identify a linear instability that underlies scale-invariant travertine terrace formation at geothermal hot springs.
