Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites

Surviving in a diverse environment requires corresponding organism responses. At the cellular level, such adjustment relies on the transcription factors (TFs) which must rapidly find their target sequences amidst a vast amount of non-relevant sequences on DNA molecules. Whether these transcription factors locate their target sites through a 1D or 3D pathway is still a matter of speculation. It has been suggested that the optimum search time is when the protein equally shares its search time between 1D and 3D diffusions. In this paper, we study the above problem using a Monte Carlo simulation by considering a very simple physical model. A 1D strip, representing a DNA, with a number of low affinity sites, corresponding to non-target sites, and high affinity sites, corresponding to target sites, is considered and later extended to a 2D strip. We study the 1D and 3D exploration pathways, and combinations of the two modes by considering three different types of molecules: a walker that randomly walks along the strip with no dissociation; a jumper that represents dissociation and then re-association of a TF with the strip at later time at a distant site; and a hopper that is similar to the jumper but it dissociates and then re-associates at a faster rate than the jumper. We analyze the final probability distribution of molecules for each case and find that TFs can locate their targets fast enough even if they spend 15% of their search time diffusing freely in the solution. This indeed agrees with recent experimental results obtained by Elf et al. 2007 and is in contrast with theoretical expectation.Comment: 24 pages, 9 figure

Mechanisms of photoluminescence from silicon nanocrystals formed by pulsed-laser deposition in argon and oxygen ambient

We have investigated the different mechanisms of photoluminescence (PL) of silicon nanocrystals due to the quantum confinement effect (QCE) and interface states. Si nanocrystals were formed by pulsed-laser deposition in inert argon and reactive oxygen gas. The collisions between the ejected species greatly influence the morphology of the Si nanocrystals and cause a transition from a film structure to a porous cauliflower-like structure, as the ambient gas pressure increases from 1 mTorr to 1 Torr. The oxygen content of the Si nanocrystals increases with increasing O2 ambient pressure, and nearly SiO2 stoichiometry is obtained when the O2 pressure is higher than 100 mTorr. Broad PL spectra are observed from Si nanocrystals. The peak position and intensity of the PL band at 1.8–2.1 eV vary with ambient gas pressure, while intensity changes and blueshifts are observed after oxidation and annealing. The PL band at 2.55 eV shows vibronic structures with periodic spacing of 9769 meV, while no peak shift is found before and after oxidation and annealing. Raman and transmission electron microscope measurements show consistent results in crystal size while more accurate atomic force microscope measurements reveal a smaller crystal size. X-ray diffraction reveals a polycrystal structure in the Si nanocrystals and the crystallinity improves after annealing. Combined with the PL spectra of Si nanocrystals obtained by crumbling electrochemically etched porous Si layer, the results clearly demonstrate that the PL band at 1.8–2.1 eV is due to the QCE in the Si nanocrystal core, while the PL band at 2.55 eV is related to localized surface states at the SiOx /Si interface

Raman theory of quantum wires. Evidence of ripples in Raman spectra of thin wall Si nanotubes

In the present paper we develop for the first time a general theory calculating the Raman spectrum of a quantum wire, using the phonon modes active in the wire. No Raman theory is at present available for quantum wires. In fact, to date only phenomenological models with arbitrary parameters, or unidimensional approaches have been published specifically for quantum dots. In our approach the confinement effects due to the reduced size are introduced directly by means of the Heisenberg Uncertainty Principle. The present theory, applied to silicon nanowires, permits the evaluation of Raman frequency shift and linewidth broadening as a function of the size. The results obtained by this model for Si nanowires are in close agreement with the few experimental data available in the literature. The model also shows evidence of ripples in the Raman spectra of thin wall Si nanotubes. This theory can be applied as well to any semiconductor of known phonon branches

Transpiration on the rebound in lowland Sumatra

Following large-scale conversion of rainforest, rubber and oil palm plantations dominate lowland Sumatra (Indonesia) and other parts of South East Asia today, with potentially far-reaching ecohydrological consequences. We assessed how such land-use change affects plant transpiration by sap flux measurements at 42 sites in selectively logged rainforests, agroforests and rubber and oil palm monoculture plantations in the lowlands of Sumatra. Site-to-site variability in stand-scale transpiration and tree-level water use were explained by stand structure, productivity, soil properties and plantation age. Along a land-use change trajectory forest-rubber-oil palm, time-averaged transpiration decreases by 43 ± 11% from forest to rubber monoculture plantations, but rebounds with conversion to smallholder oil palm plantations. We uncovered that particularly commercial, intensive oil palm cultivation leads to high transpiration (827 ± 77 mm yr−1), substantially surpassing rates at our forest sites (589 ± 52 mm yr−1). Compared to smallholder oil palm, land-use intensification leads to 1.7-times higher transpiration in commercial plantations. Combined with severe soil degradation, the high transpiration may cause periodical water scarcity for humans in oil palm-dominated landscapes. As oil palm is projected to further expand, severe shifts in water cycling after land-cover change and water scarcity due to land-use intensification may become more widespread