The TATA-box binding protein (TBP) is required by all three eukaryotic RNA polymerases for the initiation of transcription from most promoters. TBP recognizes, binds to, and bends promoter sequences called "TATA-boxes" in the DNA. We present results from the study of individual Saccharomyces cerevisiae TBPs interacting with single DNA molecules containing a TATA-box. Using video microscopy, we ...

The sequence dependence of the conformational distribution of DNA under various levels of torsional stress is an important unsolved problem. Combining theory and coarse-grained simulations shows that the DNA sequence and a structural correlation due to topology constraints of a circle are the main factors that dictate the 3D structure of a 336 bp DNA minicircle under torsional stress. We found ...

We study the inflated phase of two dimensional lattice polygons, both convex and column-convex, with fixed area A and variable perimeter, when a weight μ exp[−Jb] is associated to a polygon with perimeter t and b bends. The mean perimeter is calculated as a function of the fugacity μ and the bending rigidity J . In the limit μ → 0, the mean perimeter has the asymptotic behaviour 〈t〉/4 √ A ≃ 1−K...

Slot waveguides allow for high optical confinement in a planar optical waveguide. Here we show a method for maintaining this high degree of confinement in slot waveguides with sharp bends. This high confinement can be achieved by using an asymmetric slot-based structure, where the mode in the bend remains localized in the slot region. We show that the relative power inside the slot can be as hi...

The survival of many animals depends in part on their ability to sense the flow of the surrounding fluid medium. To date, however, little is known about how terrestrial mammals sense airflow direction or speed. The present work analyzes the mechanical response of isolated rat macrovibrissae (whiskers) to airflow to assess their viability as flow sensors. Results show that the whisker bends prim...

An unexpected type of behavior in electroconvection (EC) has been detected in nematic liquid crystals (NLCs) under the condition of comparable time scales of the director relaxation and the period of the driving ac voltage. The studied NLCs exhibit standard EC (s-EC) at the onset of the instability, except one compound in which nonstandard EC (ns-EC) has been detected. In the relevant frequency...

The binding of many proteins to DNA is profoundly affected by DNA bending, twisting, and supercoiling. When protein binding alters DNA conformation, interaction between inherent and induced DNA conformation can affect protein binding affinity and specificity. Integration host factor (IHF), a sequence-specific, DNA-binding protein of Escherichia coli, strongly bends the DNA upon binding. To asse...

On a microgrooved substrate, cells migrate along the pattern, and at random positions, reverse their directions. Here, we demonstrate that these reversals can be controlled by introducing discontinuities to the pattern. On "V-shaped grating patterns", mouse osteogenic progenitor MC3T3-E1 cells reversed predominately at the bends and the ends. The patterns were engineered in a way that the combi...

We present vibrational configuration interaction calculations employing the Watson Hamiltonian and a multimode expansion. Results for the lowest 36 eigenvalues of the zero total angular momentum rovibrational spectrum of methane agree with the accurate benchmarks of Wang and Carrington to within a mean unsigned deviation of 0.68, 0.033, and 0.014 cm(-1) for 4-mode, 5-mode, and 6-mode representa...