[en] DNA is the central storage molecule of genetic information in the cell, and reading that information is a central problem in biology. While sequencing technology has made enormous advances over the past decade, there is growing interest in platforms that can readout genetic information directly from long single DNA molecules, with the ultimate goal of single-cell, single-genome analysis. Such a capability would obviate the need for ensemble averaging over heterogeneous cellular populations and eliminate uncertainties introduced by cloning and molecular amplification steps (thus enabling direct assessment of the genome in its native state). In this review, we will discuss how the information contained in genomic-length single DNA molecules can be accessed via physical confinement in nanochannels. Due to self-avoidance interactions, DNA molecules will stretch out when confined in nanochannels, creating a linear unscrolling of the genome along the channel for analysis. We will first review the fundamental physics of DNA nanochannel confinement—including the effect of varying ionic strength—and then discuss recent applications of these systems to genomic mapping. Apart from the intense biological interest in extracting linear sequence information from elongated DNA molecules, from a physics view these systems are fascinating as they enable probing of single-molecule conformation in environments with dimensions that intersect key physical length-scales in the 1 nm to 100 µm range. (review article)

[en] We show here that the temperature dependence of the amide I band of myoglobin shows evidence for a low-lying self-trapped state at 6.15 μm. We have conducted a careful set of picosecond pump-probe experiments providing results as a function of temperature and wavelength and show that this low-lying state has a 30 ps lifetime at 50 K, much longer than the relaxation time of the main amide I band at 50 K. Fits of the temperature dependence of thermal occupation of this state yield the result that it lies 280 K below the main amide I band. Since the gap energy of this state is approximately equal to room temperature, this self-trapped state can act as a transient store of vibrational energy at physiological temperatures in biomolecules and can help to direct the path of energy flow in a biomolecule under biological conditions

[en] Upconverting nanoparticles (UCNPs) when excited in the near-infrared (NIR) region display anti-Stokes emission whereby the emitted photon is higher in energy than the excitation energy. The material system achieves that by converting two or more infrared photons into visible photons. The use of the infrared confers benefits to bioimaging because of its deeper penetrating power in biological tissues and the lack of autofluorescence. We demonstrate here sub-10 nm, upconverting rare earth oxide UCNPs synthesized by a combustion method that can be stably suspended in water when amine modified. The amine modified UCNPs show specific surface immobilization onto patterned gold surfaces. Finally, the low toxicity of the UCNPs is verified by testing on the multi-cellular C. elegans nematode.

[en] We revisit mid-IR pump–probe experiments at the FELIX picosecond Free Electron Laser which probed the vibrational dynamics of the α-helix rich protein in search of long-lived anharmonic trapped vibrational states (solitons). We analyze and try to understand something puzzling that we observed in the context of unusual ‘hidden’ quantum phenomena in proteins which probably are of no biological consequences, but bears re-examination. We observed in a narrow (0.5 cm"−"1) spectral range of the amide-I band a very large response in terms of degenerate 4-wave mixing scattering. We propose that this narrow but strong scattering signal is not due to anharmonic trapping but rather is the imaginary (index of refraction) component of a super-linear response of the amide I band to high levels of vibrational excitation. (topical articles)

[en] We have constructed a microfabricated circular corral for bacteria made of rings of concentric funnels which channel motile bacteria outwards via non-hydrodynamic interactions with the funnel walls. Initially bacteria do move rapidly outwards to the periphery of the corral. At the edge, nano-slits allow for the transport of nutrients into the device while keeping the bacteria from escaping. After a period of time in which the bacteria increase their cell density in this perimeter region, they are then able to defeat the physical constrains of the funnels by launching back-propagating collective waves. We present the basic data and some nonlinear modeling which can explain how bacterial population waves propagate through a physical funnel, and discuss possible biological implications. (paper)

[en] We have used a variety of different applied fields to control the density, growth, and structure of colloidal crystals. Gravity exerts a body force proportional to the buoyant mass and in equilibrium produces a height-dependent concentration profile. A similar body force can be obtained with electric fields on charged particles (electrophoresis), a temperature gradient on all particles, or an electric field gradient on uncharged particles (dielectrophoresis). The last is particularly interesting since its magnitude and sign can be changed by tuning the applied frequency. We study these effects in bulk (making 'dielectrophoretic bottles' or traps), to control concentration profiles during nucleation and growth and near surfaces. We also study control of non-spherical and optically anisotropic particles with the light field from laser tweezers