Protein-mediated DNA Loop Formation and Breakdown in a Fluctuating Environment

Living cells provide a fluctuating, out-of-equilibrium environment in which genes must coordinate cellular function. DNA looping, which is a common means of regulating transcription, is very much a stochastic process; the loops arise from the thermal motion of the DNA and other fluctuations of the cellular environment. We present single-molecule measurements of DNA loop formation and breakdown when an artificial fluctuating force, applied to mimic a fluctuating cellular environment, is imposed on the DNA. We show that loop formation is greatly enhanced in the presence of noise of only a fraction of $k_B T$, yet find that hypothetical regulatory schemes that employ mechanical tension in the DNA--as a sensitive switch to control transcription--can be surprisingly robust due to a fortuitous cancellation of noise effects

Preventing transition to turbulence: a viscosity stratification does not always help

In channel flows a step on the route to turbulence is the formation of streaks, often due to algebraic growth of disturbances. While a variation of viscosity in the gradient direction often plays a large role in laminar-turbulent transition in shear flows, we show that it has, surprisingly, little effect on the algebraic growth. Non-uniform viscosity therefore may not always work as a flow-control strategy for maintaining the flow as laminar.Comment: 9 pages, 8 figure

Transient Analysis of Warm Electron Injection Programming of Double Gate SONOS Memories by means of Full Band Monte Carlo Simulation

In this paper we investigate "Warm Electron Injection" as a mechanism for NOR programming of double-gate SONOS memories through 2D full band Monte Carlo simulations. Warm electron injection is characterized by an applied VDS smaller than 3.15 V, so that electrons cannot easily accumulate a kinetic energy larger than the height of the Si/SiO2 barrier. We perform a time-dependent simulation of the program operation where the local gate current density is computed with a continuum-based method and is adiabatically separated from the 2D full Monte Carlo simulation used for obtaining the electron distribution in the phase space. In this way we are able to compute the time evolution of the charge stored in the nitride and of the threshold voltages corresponding to forward and reverse bias. We show that warm electron injection is a viable option for NOR programming in order to reduce power supply, preserve reliability and CMOS logic level compatibility. In addition, it provides a well localized charge, offering interesting perspectives for multi-level and dual bit operation, even in devices with negligible short channel effects

Acoustic Energy and Momentum in a Moving Medium

By exploiting the mathematical analogy between the propagation of sound in a non-homogeneous potential flow and the propagation of a scalar field in a background gravitational field, various wave ``energy'' and wave ``momentum'' conservation laws are established in a systematic manner. In particular the acoustic energy conservation law due to Blokhintsev appears as the result of the conservation of a mixed co- and contravariant energy-momentum tensor, while the exchange of relative energy between the wave and the mean flow mediated by the radiation stress tensor, first noted by Longuet-Higgins and Stewart in the context of ocean waves, appears as the covariant conservation of the doubly contravariant form of the same energy-momentum tensor.Comment: 25 Pages, Late

Experimental verification of strong rotational dependence of fluorescence and predissociation yield in the b ¹Πᵤ(v = 1) level of ¹⁴N₂

New, rotationally resolved fluorescence-excitation spectra confirm coupled-channel Schrödinger-equation predictions of strong rotational dependence of the fluorescence and predissociation yields in the b(v = 1) level of ¹⁴N₂.This work was supported by the National Science Foundation grant AST-0906158 and the Australian Research Council grants DP0558962, DP0773050, and LX0882438

The Cerenkov effect revisited: from swimming ducks to zero modes in gravitational analogs

We present an interdisciplinary review of the generalized Cerenkov emission of radiation from uniformly moving sources in the different contexts of classical electromagnetism, superfluid hydrodynamics, and classical hydrodynamics. The details of each specific physical systems enter our theory via the dispersion law of the excitations. A geometrical recipe to obtain the emission patterns in both real and wavevector space from the geometrical shape of the dispersion law is discussed and applied to a number of cases of current experimental interest. Some consequences of these emission processes onto the stability of condensed-matter analogs of gravitational systems are finally illustrated.Comment: Lecture Notes at the IX SIGRAV School on "Analogue Gravity" in Como, Italy from May 16th-21th, 201

Heteroresistance to the model antimicrobial peptide polymyxin B in the emerging Neisseria meningitidis lineage 11.2 urethritis clade: mutations in the pilMNOPQ operon

Clusters of Neisseria meningitidis (Nm) urethritis among primarily heterosexual males in multiple US cities have been attributed to a unique non‐encapsulated meningococcal clade (the US Nm urethritis clade, US_NmUC) within the hypervirulent clonal complex 11. Resistance to antimicrobial peptides (AMPs) is a key feature of urogenital pathogenesis of the closely related species, Neisseria gonorrhoeae. The US_NmUC isolates were found to be highly resistant to the model AMP, polymyxin B (PmB, MICs 64–256 µg ml–1). The isolates also demonstrated stable subpopulations of heteroresistant colonies that showed near total resistant to PmB (MICs 384–1024 µg ml–1) and colistin (MIC 256 µg ml–1) as well as enhanced LL‐37 resistance. This is the first observation of heteroresistance in N. meningitidis. Consistent with previous findings, overall PmB resistance in US_NmUC isolates was due to active Mtr efflux and LptA‐mediated lipid A modification. However, whole genome sequencing, variant analyses and directed mutagenesis revealed that the heteroresistance phenotypes and very high‐level AMP resistance were the result of point mutations and IS1655 element movement in the pilMNOPQ operon, encoding the type IV pilin biogenesis apparatus. Cross‐resistance to other classes of antibiotics was also observed in the heteroresistant colonies. High‐level resistance to AMPs may contribute to the pathogenesis of US_NmUC

Comparison of two-phase pipe flow in openFOAM with a mechanistic model

Two-phase pipe flow is a common occurrence in many industrial applications such as power generation and oil and gas transportation. Accurate prediction of liquid holdup and pressure drop is of vast importance to ensure effective design and operation of fluid transport systems. In this paper, a Computational Fluid Dynamics (CFD) study of a two-phase flow of air and water is performed using OpenFOAM. The two-phase solver, interFoam is used to identify flow patterns and generate values of liquid holdup and pressure drop, which are compared to results obtained from a two-phase mechanistic model developed by Petalas and Aziz (2002). A total of 60 simulations have been performed at three separate pipe inclinations of 0°, +10° and -10° respectively. A three dimensional, 0.052m diameter pipe of 4m length is used with the Shear Stress Transport (SST) k - turbulence model to solve the turbulent mixtures of air and water. Results show that the flow pattern behaviour and numerical values of liquid holdup and pressure drop compare reasonably well to the mechanistic model