Single-Molecule Analysis of i-motif Within Self-Assembled DNA Duplexes and Nanocircles

The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif–forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif–forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the topological environments play a key role on i-motif stability and dynamics. While the human telomere sequence (C3TAA)3C3 assumes i-motif structure at pH 5.5 regardless of topological constraint, it undergoes conformational dynamics among unfolded, partially folded and fully folded states at pH 6.5. The lifetimes of i-motif and the partially folded state at pH 6.5 were determined to be 6 ± 2 and 31 ± 11 s, respectively. Consistent with the partially folded state observed in fluorescence analysis, interrogation of current versus time traces obtained from nanopore analysis at pH 6.5 shows long-lived shallow blockades with a mean lifetime of 25 ± 6 s. Such lifetimes are sufficient for the i-motif and partially folded states to interact with proteins to modulate cellular processes

Sustaining supercooled mixed phase via resonant oscillations of the order parameter

We investigate the dynamics of a first order transition when the order parameter field undergoes resonant oscillations, driven by a periodically varying parameter of the free energy. This parameter could be a background oscillating field as in models of pre-heating after inflation. In the context of condensed matter systems, it could be temperature $T$, or pressure, external electric/magnetic field etc. We show that with suitable driving frequency and amplitude, the system remains in a type of mixed phase, without ever completing transition to the stable phase, even when the oscillating parameter of the free energy remains below the corresponding critical value (for example, with oscillating temperature, $T$ always remains below the critical temperature $T_c$). This phenomenon may have important implications. In cosmology, it will imply prolonged mixed phase in a first order transition due to coupling with background oscillating fields. In condensed matter systems, it will imply that using oscillating temperature (or, more appropriately, pressure waves) one may be able to sustain liquids in a mixed phase indefinitely at low temperatures, without making transition to the frozen phase.Comment: 17 pages, 7 figures, Expanded version with more detail

Chiral Properties of QCD Vacuum in Magnetars- A Nambu-Jona-Lasinio Model with Semi-Classical Approximation

The breaking of chiral symmetry of light quarks at zero temperature in presence of strong quantizing magnetic fiels is studied using Nambu-Jona-Lasinio (NJL) model with Thomas-Fermi type semi-classical formalism. It is found that the dynamically generated light quark mass can never become zero if the Landau levels are populated and the mass increases with the increase of magnetic field strength.Comment: REVTEX 11 Pages, One .eps figure (included

Viscous instabilities in flowing foams: A Cellular Potts Model approach

The Cellular Potts Model (CPM) succesfully simulates drainage and shear in foams. Here we use the CPM to investigate instabilities due to the flow of a single large bubble in a dry, monodisperse two-dimensional flowing foam. As in experiments in a Hele-Shaw cell, above a threshold velocity the large bubble moves faster than the mean flow. Our simulations reproduce analytical and experimental predictions for the velocity threshold and the relative velocity of the large bubble, demonstrating the utility of the CPM in foam rheology studies.Comment: 10 pages, 3 figures. Replaced with revised version accepted for publication in JSTA

Hinode Calibration for Precise Image Co-alignment between SOT and XRT (November 2006 -- April 2007)

To understand the physical mechanisms for activity and heating in the solar atmosphere, the magnetic coupling from the photosphere to the corona is an important piece of information from the Hinode observations, and therefore precise positional alignment is required among the data acquired by different telescopes. The Hinode spacecraft and its onboard telescopes were developed to allow us to investigate magnetic coupling with co-alignment accuracy better than 1 arcsec. Using the Mercury transit observed on 8 November 2006 and co-alignment measurements regularly performed on a weekly basis, we have determined the information necessary for precise image co-alignment and have confirmed that co-alignment better than 1 arcsec can be realized between Solar Optical Telescope (SOT) and X-Ray Telescope (XRT) with our baseline co-alignment method. This paper presents results from the calibration for precise co-alignment of CCD images from SOT and XRT.Comment: 8 pages, 9 figures, accepted for publication in PASJ (Hinode Special issue

Emission Characteristics of the Projectile Fragments at Relativistic Energy

A projectile (84^Kr_36) having kinetic energy around 1 A GeV was used to expose NIKFI BR-2 emulsion target. A total of 700 inelastic events are used in the present studies on projectile fragments. The emission angle of the projectile fragments are strongly affected by charge of the other projectile fragments emitted at same time with different emission angle is observed. The angular distribution studies show symmetrical nature for lighter charge projectile fragments. The symmetrical nature decreased with the charge of projectile fragments. At ~4o of emission angle for double charge projectile fragments, the momentum transfer during interaction is similar for various target species of emulsion were observed. We also observed a small but significant amplitude peaks on both side of the big peak for almost all light charge projectile fragments having different delta angle values. It reflects that there are few percent of projectile fragments that are coming from the decay of heavy projectile fragments or any other process.Comment: 32 pages, 17 Figure

Solving Medium-Density Subset Sum Problems in Expected Polynomial Time: An Enumeration Approach

The subset sum problem (SSP) can be briefly stated as: given a target integer $E$ and a set $A$ containing $n$ positive integer $a_j$, find a subset of $A$ summing to $E$. The \textit{density} $d$ of an SSP instance is defined by the ratio of $n$ to $m$, where $m$ is the logarithm of the largest integer within $A$. Based on the structural and statistical properties of subset sums, we present an improved enumeration scheme for SSP, and implement it as a complete and exact algorithm (EnumPlus). The algorithm always equivalently reduces an instance to be low-density, and then solve it by enumeration. Through this approach, we show the possibility to design a sole algorithm that can efficiently solve arbitrary density instance in a uniform way. Furthermore, our algorithm has considerable performance advantage over previous algorithms. Firstly, it extends the density scope, in which SSP can be solved in expected polynomial time. Specifically, It solves SSP in expected $O(n\log{n})$ time when density $d \geq c\cdot \sqrt{n}/\log{n}$, while the previously best density scope is $d \geq c\cdot n/(\log{n})^{2}$. In addition, the overall expected time and space requirement in the average case are proven to be $O(n^5\log n)$ and $O(n^5)$ respectively. Secondly, in the worst case, it slightly improves the previously best time complexity of exact algorithms for SSP. Specifically, the worst-case time complexity of our algorithm is proved to be $O((n-6)2^{n/2}+n)$, while the previously best result is $O(n2^{n/2})$.Comment: 11 pages, 1 figur

Doping of inorganic materials in microreactors – preparation of Zn doped Fe₃O₄ nanoparticles

Microreactor systems are now used more and more for the continuous production of metal nanoparticles and metal oxide nanoparticles owing to the controllability of the particle size, an important property in many applications. Here, for the first time, we used microreactors to prepare metal oxide nanoparticles with controlled and varying metal stoichiometry. We prepared and characterised Zn-substituted Fe₃O₄ nanoparticles with linear increase of Zn content (ZnxFe₃−xO₄ with 0 ≤ x ≤ 0.48), which causes linear increases in properties such as the saturation magnetization, relative to pure Fe₃O₄. The methodology is simple and low cost and has great potential to be adapted to the targeted doping of a vast array of other inorganic materials, allowing greater control on the chemical stoichiometry for nanoparticles prepared in microreactors