Universal protein fluctuations in populations of microorganisms

The copy number of any protein fluctuates among cells in a population; characterizing and understanding these fluctuations is a fundamental problem in biophysics. We show here that protein distributions measured under a broad range of biological realizations collapse to a single non-Gaussian curve under scaling by the first two moments. Moreover in all experiments the variance is found to depend quadratically on the mean, showing that a single degree of freedom determines the entire distribution. Our results imply that protein fluctuations do not reflect any specific molecular or cellular mechanism, and suggest that some buffering process masks these details and induces universality

Physical Model of the Genotype-to-Phenotype Map of Proteins

How DNA is mapped to functional proteins is a basic question of living matter. We introduce and study a physical model of protein evolution which suggests a mechanical basis for this map. Many proteins rely on large-scale motion to function. We therefore treat protein as learning amorphous matter that evolves towards such a mechanical function: Genes are binary sequences that encode the connectivity of the amino acid network that makes a protein. The gene is evolved until the network forms a shear band across the protein, which allows for long-range, soft modes required for protein function. The evolution reduces the high-dimensional sequence space to a low-dimensional space of mechanical modes, in accord with the observed dimensional reduction between genotype and phenotype of proteins. Spectral analysis of the space of 10(6) solutions shows a strong correspondence between localization around the shear band of both mechanical modes and the sequence structure. Specifically, our model shows how mutations are correlated among amino acids whose interactions determine the functional mode

Diffusion of a Deformable Body in a random Flow

We consider a deformable body immersed in an incompressible liquid that is randomly stirred. Sticking to physical situations in which the body departs only slightly from its spherical shape, we calculate the diffusion constant of the body. We give explicitly the dependence of the diffusion constant on the velocity correlations in the liquid and on the size of the body. We emphasize the particular case in which the random velocity field follows from thermal agitation.Comment: 9 pages, 2 figures, late

Protein-DNA computation by stochastic assembly cascade

The assembly of RecA on single-stranded DNA is measured and interpreted as a stochastic finite-state machine that is able to discriminate fine differences between sequences, a basic computational operation. RecA filaments efficiently scan DNA sequence through a cascade of random nucleation and disassembly events that is mechanistically similar to the dynamic instability of microtubules. This iterative cascade is a multistage kinetic proofreading process that amplifies minute differences, even a single base change. Our measurements suggest that this stochastic Turing-like machine can compute certain integral transforms.Comment: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129313/ http://www.pnas.org/content/99/18/11589.abstrac

Turbulent Cells in Stars: I. Fluctuations in Kinetic Energy and Luminosity

Three-dimensional (3D) hydrodynamic simulations of shell oxygen burning (Meakin and Arnett, 2007b) exhibit bursty, recurrent fluctuations in turbulent kinetic energy. These are shown to be due to a general instability of the convective cell, requiring only a localized source of heating or cooling. Such fluctuations are shown to be suppressed in simulations of stellar evolution which use mixing-length theory (MLT). Quantitatively similar behavior occurs in the model of a convective roll (cell) of Lorenz (1963), which is known to have a strange attractor that gives rise to chaotic fluctuations in time of velocity and, as we show, luminosity. Study of simulations suggests that the behavior of a Lorenz convective roll may resemble that of a cell in convective flow. We examine some implications of this simplest approximation, and suggest paths for improvement. Using the Lorenz model as representative of a convective cell, a multiple-cell model of a convective layer gives total luminosity fluctuations which are suggestive of irregular variables (red giants and supergiants (Schwarzschild 1975)), and of the long secondary period feature in semi-regular AGB variables (Stothers 2010, Wood, Olivier and Kawaler 2004). This "tau-mechanism" is a new source for stellar variability, which is inherently non-linear (unseen in linear stability analysis), and one closely related to intermittency in turbulence. It was already implicit in the 3D global simulations of Woodward, Porter and Jacobs (2003). This fluctuating behavior is seen in extended 2D simulations of CNeOSi burning shells (Arnett and Meakin 2011b), and may cause instability which leads to eruptions in progenitors of core collapse supernovae PRIOR to collapse.Comment: 30 pages, 13 figure

Pattern Formation and Dynamics in Rayleigh-B\'{e}nard Convection: Numerical Simulations of Experimentally Realistic Geometries

Rayleigh-B\'{e}nard convection is studied and quantitative comparisons are made, where possible, between theory and experiment by performing numerical simulations of the Boussinesq equations for a variety of experimentally realistic situations. Rectangular and cylindrical geometries of varying aspect ratios for experimental boundary conditions, including fins and spatial ramps in plate separation, are examined with particular attention paid to the role of the mean flow. A small cylindrical convection layer bounded laterally either by a rigid wall, fin, or a ramp is investigated and our results suggest that the mean flow plays an important role in the observed wavenumber. Analytical results are developed quantifying the mean flow sources, generated by amplitude gradients, and its effect on the pattern wavenumber for a large-aspect-ratio cylinder with a ramped boundary. Numerical results are found to agree well with these analytical predictions. We gain further insight into the role of mean flow in pattern dynamics by employing a novel method of quenching the mean flow numerically. Simulations of a spiral defect chaos state where the mean flow is suddenly quenched is found to remove the time dependence, increase the wavenumber and make the pattern more angular in nature.Comment: 9 pages, 10 figure

Power-Law Behavior of Power Spectra in Low Prandtl Number Rayleigh-Benard Convection

The origin of the power-law decay measured in the power spectra of low Prandtl number Rayleigh-Benard convection near the onset of chaos is addressed using long time numerical simulations of the three-dimensional Boussinesq equations in cylindrical domains. The power-law is found to arise from quasi-discontinuous changes in the slope of the time series of the heat transport associated with the nucleation of dislocation pairs and roll pinch-off events. For larger frequencies, the power spectra decay exponentially as expected for time continuous deterministic dynamics.Comment: (10 pages, 6 figures