Direct Measurement of Hydrodynamic Cross Correlations between Two Particles in an External Potential

We report a direct measurement of the hydrodynamic interaction between two colloidal particles. Two micron-sized latex beads were held at varying distances in optical tweezers while their Brownian displacements were measured. In spite of the fact that fluid systems at low Reynolds number are generally considered to have no “memory,” the cross-correlation function of the bead positions shows a pronounced, time-delayed anticorrelation. We show that the anticorrelations can be understood in terms of the standard Oseen tensor hydrodynamic coupling

A Generalized Theory of DNA Looping and Cyclization

We have developed a generalized semi-analytic approach for efficiently computing cyclization and looping $J$ factors of DNA under arbitrary binding constraints. Many biological systems involving DNA-protein interactions impose precise boundary conditions on DNA, which necessitates a treatment beyond the Shimada-Yamakawa model for ring cyclization. Our model allows for DNA to be treated as a heteropolymer with sequence-dependent intrinsic curvature and stiffness. In this framework, we independently compute enthlapic and entropic contributions to the $J$ factor and show that even at small length scales $(\sim \ell_{p})$ entropic effects are significant. We propose a simple analytic formula to describe our numerical results for a homogenous DNA in planar loops, which can be used to predict experimental cyclization and loop formation rates as a function of loop size and binding geometry. We also introduce an effective torsional persistence length that describes the coupling between twist and bending of DNA when looped.Comment: 6 pages, 4 figures, submitted to EP

Topologic mixing on a microfluidic chip

Mixing two liquids on a microfluidic chip is notoriously hard because the small dimensions and velocities on the chip effectively prevent turbulence. We present a topological mixing scheme that exploits the laminarity of the flow to repeatedly fold the flow and exponentially increase the concentration gradients to obtain fast and efficient mixing by diffusion. It is based on helical flow channels with opposite chiralities that split, rotate, and recombine the fluid stream in a topology reminiscent of a series of Möbius bands. This geometry is realized in a simple six-stage, two-layer elastomer structure with a footprint of 400 μm×300 μm400μm×300μm per stage that mixes two solutions efficiently at Reynolds numbers between 0.1 and 2. This represents more than an order of magnitude reduction in the size of microfluidic mixers that can be manufactured in standard multilayer soft lithography techniques. © 2004 American Institute of Physics.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69745/2/APPLAB-84-12-2193-1.pd

All-Optical Constant-Force Laser Tweezers

AbstractOptical tweezers are a powerful tool for the study of single biomolecules. Many applications require that a molecule be held under constant tension while its extension is measured. We present two schemes based on scanning-line optical tweezers to accomplish this, providing all-optical alternatives to force-clamp traps that rely on electronic feedback to maintain constant-force conditions for the molecule. In these schemes, a laser beam is rapidly scanned along a line in the focal plane of the microscope objective, effectively creating an extended one-dimensional optical potential over distances of up to 8μm. A position-independent lateral force acting on a trapped particle is created by either modulating the laser beam intensity during the scan or by using an asymmetric beam profile in the back focal plane of the microscope objective. With these techniques, forces of up to 2.69 pN have been applied over distances of up to 3.4μm with residual spring constants of <26.6fN/μm. We used these techniques in conjunction with a fast position measurement scheme to study the relaxation of λ-DNA molecules against a constant external force with submillisecond time resolution. We compare the results to predictions from the wormlike chain model

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

Состав углеводородов в продуктах синтеза из окиси углерода и водяного пара

Исследован состав продукта синтеза из окиси углерода и водяного пара методами газожидкостной хроматографии. Показано, что продукт представлен смесью углеводородов C5-C20, спиртами и кислотами состава C1-C12; наряду с н-парафинами и а-олефинами присутствуют соединения изостроения. Определен индивидуальный состав фракции С5-С8, где обнаружено 83 компонента

Interference of Clocks: A Quantum Twin Paradox

The phase of matter waves depends on proper time and is therefore susceptible to special-relativistic (kinematic) and gravitational time dilation (redshift). Hence, it is conceivable that atom interferometers measure general-relativistic time-dilation effects. In contrast to this intuition, we show that light-pulse interferometers without internal transitions are not sensitive to gravitational time dilation, whereas they can constitute a quantum version of the special-relativistic twin paradox. We propose an interferometer geometry isolating the effect that can be used for quantum-clock interferometry.Comment: 9 Pages, 2 Figure

Femtonewton Force Spectroscopy of Single Extended DNA Molecules

We studied the thermal fluctuations of single DNA molecules with a novel optical tweezer based force spectroscopy technique. This technique combines femtonewton sensitivity with millisecond time resolution, surpassing the sensitivity of previous force measurements in aqueous solution with comparable bandwidth by a hundredfold. Our data resolve long-standing questions concerning internal hydrodynamics of the polymer and anisotropy in the molecular relaxation times and friction coefficients. The dynamics at high extension show interesting nonlinear behavior

Characterising the sea ice environment using a newly developed sensor array mounted on an under-ice trawl

One of the most pronounced impacts of climate change is the changing sea ice cover, which has implications for sea ice-associated ecosystems that depend on carbon produced by ice-associated algae. In order to fully understand these ecosystems there is a need to understand both the physical and biological components. We present preliminary results from Polarstern cruises to the Eastern Central Arctic Ocean (summer 2012) and Weddell Sea (fall-winter 2013). Biological samples were acquired from the under-ice environment using the Surface and Under-Ice Trawl (SUIT) and from within the ice by extracting ice cores. Biophysical properties of sea ice and under-ice environments were characterized using a sensor array mounted on the SUIT that measured ice thickness, under-ice light spectra, water properties and chlorophyll a biomass (in- and under-ice). Modal ice thicknesses were between 0.45-1.38 m (Arctic) and 0.23-0.70 m (Weddell Sea). Sea ice properties were related to the distribution of some key under-ice species (e.g. Polar Cod and Antarctic Krill). Previous studies have used under-ice light spectra to derive ice-algal biomass but were limited to local-scale point measurements. We present a new method for calculating ice-algal biomass from under-ice spectra on local- to meso-scales and compare the results using both methods