Distribution of label spacings for genome mapping in nanochannels

In genome mapping experiments, long DNA molecules are stretched by confining them to very narrow channels, so that the locations of sequence-specific fluorescent labels along the channel axis provide large-scale genomic information. It is difficult, however, to make the channels narrow enough so that the DNA molecule is fully stretched. In practice, its conformations may form hairpins that change the spacings between internal segments of the DNA molecule, and thus the label locations along the channel axis. Here, we describe a theory for the distribution of label spacings that explains the heavy tails observed in distributions of label spacings in genome mapping experiments.

Exponentially growing solutions in homogeneous Rayleigh-Bénard convection

It is shown that homogeneous Rayleigh-Bénard flow, i.e., Rayleigh-Bénard turbulence with periodic boundary conditions in all directions and a volume forcing of the temperature field by a mean gradient, has a family of exact, exponentially growing, separable solutions of the full nonlinear system of equations. These solutions are clearly manifest in numerical simulations above a computable critical value of the Rayleigh number. In our numerical simulations they are subject to secondary numerical noise and resolution dependent instabilities that limit their growth to produce statistically steady turbulent transport.

Macrophage response to Mycobacteriumtuberculosis infection

The immune response to Mycobacterium tuberculosis (Mtb) infection is the formation of multicellular lesions, or granolomas, in the lung of the individual. However, the structure of the granulomas and the spatial distribution of the immune cells within is not well understood. In this paper we develop a mathematical model investigating the early and initial immune response to Mtb. The model consists of coupled reaction-diffusion-advection partial differential equations governing the dynamics of the relevant macrophage and bacteria populations and a bacteria-produced chemokine. Our novel application of mathematical concepts of internal states and internal velocity allows us to begin to study this unique immunological structure. Volume changes resulting from proliferation and death terms generate a velocity field by which all cells are transported within the forming granuloma. We present numerical results for two distinct infection outcomes: controlled and uncontrolled granuloma growth. Using a simplified model we are able to analytically determine conditions under which the bacteria population decreases, representing early clearance of infection, or grows, representing the initial stages of granuloma formation.

Optimal signal-to-noise in digital phase lock amplifiers

We derive an expression for the optimal signal-to-noise ratio for linear phase lock amplifiers. In its digital form the optimal method can be implemented by real-time signal processing techniques. We analyze in detail the case of detector-noise-limited systems finding that the optimal technique can be used to eliminate effectively the detector's time constant from the set of parameters determining the overall efficiency. This has important implications for optical detection system design. We also report an experimental verification of the optimal method, thus establishing its practicality.