Zero tension Kardar-Parisi-Zhang equation in (d+1)- Dimensions

The joint probability distribution function (PDF) of the height and its gradients is derived for a zero tension $d+1$-dimensional Kardar-Parisi-Zhang (KPZ) equation. It is proved that the height`s PDF of zero tension KPZ equation shows lack of positivity after a finite time $t_{c}$. The properties of zero tension KPZ equation and its differences with the case that it possess an infinitesimal surface tension is discussed. Also potential relation between the time scale $t_{c}$ and the singularity time scale $t_{c, \nu \to 0}$ of the KPZ equation with an infinitesimal surface tension is investigated.Comment: 18 pages, 8 figure

Intermittency of Height Fluctuations and Velocity Increment of The Kardar-Parisi-Zhang and Burgers Equations with infinitesimal surface tension and Viscosity in 1+1 Dimensions

The Kardar-Parisi-Zhang (KPZ) equation with infinitesimal surface tension, dynamically develops sharply connected valley structures within which the height derivative is not continuous. We discuss the intermittency issue in the problem of stationary state forced KPZ equation in 1+1--dimensions. It is proved that the moments of height increments $C_a =$ behave as $|x_1 -x_2|^{\xi_a}$ with $\xi_a = a$ for length scales $|x_1-x_2| << \sigma$. The length scale $\sigma$ is the characteristic length of the forcing term. We have checked the analytical results by direct numerical simulation.Comment: 13 pages, 9 figure

Exact Analysis of Level-Crossing Statistics for (d+1)-Dimensional Fluctuating Surfaces

We carry out an exact analysis of the average frequency $\nu_{\alpha x_i}^+$ in the direction $x_i$ of positive-slope crossing of a given level $\alpha$ such that, $h({\bf x},t)-\bar{h}=\alpha$, of growing surfaces in spatial dimension $d$. Here, $h({\bf x},t)$ is the surface height at time $t$, and $\bar{h}$ is its mean value. We analyze the problem when the surface growth dynamics is governed by the Kardar-Parisi-Zhang (KPZ) equation without surface tension, in the time regime prior to appearance of cusp singularities (sharp valleys), as well as in the random deposition (RD) model. The total number $N^+$ of such level-crossings with positive slope in all the directions is then shown to scale with time as $t^{d/2}$ for both the KPZ equation and the RD model.Comment: 22 pages, 3 figure

Entropy Production Rate is Maximized in Non-Contractile Actomyosin

The actin cytoskeleton is an active semi-flexible polymer network whose non-equilibrium properties coordinate both stable and contractile behaviors to maintain or change cell shape. While myosin motors drive the actin cytoskeleton out-of-equilibrium, the role of myosin-driven active stresses in the accumulation and dissipation of mechanical energy is unclear. To investigate this, we synthesize an actomyosin material in vitro whose active stress content can tune the network from stable to contractile. Each increment in activity determines a characteristic spectrum of actin filament fluctuations which is used to calculate the total mechanical work and the production of entropy in the material. We find that the balance of work and entropy does not increase monotonically and, surprisingly, the entropy production rate is maximized in the non-contractile, stable state. Our study provides evidence that the origins of system entropy production and activity-dependent dissipation arise from disorder in the molecular interactions between actin and myosinComment: 31 pages, 5 figure

Dynamics and Selective Remodeling of the DNA-binding Domains of RPA

Replication protein A (RPA) coordinates important DNA metabolic events by stabilizing single-stranded DNA (ssDNA) intermediates, activating the DNA-damage response and handing off ssDNA to the appropriate downstream players. Six DNA-binding domains (DBDs) in RPA promote high-affinity binding to ssDNA yet also allow RPA displacement by lower affinity proteins. We generated fluorescent versions of Saccharomyces cerevisiae RPA and visualized the conformational dynamics of individual DBDs in the context of the full-length protein. We show that both DBD-A and DBD-D rapidly bind to and dissociate from ssDNA while RPA remains bound to ssDNA. The recombination mediator protein Rad52 selectively modulates the dynamics of DBD-D. These findings reveal how RPA-interacting proteins with lower ssDNA binding affinities can access the occluded ssDNA and remodel individual DBDs to replace RPA

Gauge Equivalence in Two--Dimensional Gravity

Two-dimensional quantum gravity is identified as a second-class system which we convert into a first-class system via the Batalin-Fradkin (BF) procedure. Using the extended phase space method, we then formulate the theory in most general class of gauges. The conformal gauge action suggested by David, Distler and Kawai is derived from a first principle. We find a local, light-cone gauge action whose Becchi-Rouet-Stora-Tyutin invariance implies Polyakov's curvature equation $\partial_{-}R=\partial_{-}^{3}g_{++}=0$, revealing the origin of the $SL(2,R)$ Kac-Moody symmetry. The BF degree of freedom turns out be dynamically active as the Liouville mode in the conformal gauge, while in the light-cone gauge the conformal degree of freedom plays that r{\^o}le. The inclusion of the cosmological constant term in both gauges and the harmonic gauge-fixing are also considered.Comment: 30 pages, KANAZAWA 93-

Agrobacterium-mediated transformation of kabocha squash (Cucurbita moschata Duch) induced by wounding with aluminum borate whiskers

An efficient genetic transformation method for kabocha squash (Cucurbita moschata Duch cv. Heiankogiku) was established by wounding cotyledonary node explants with aluminum borate whiskers prior to inoculation with Agrobacterium. Adventitious shoots were induced from only the proximal regions of the cotyledonary nodes and were most efficiently induced on Murashige–Skoog agar medium with 1 mg/L benzyladenine. Vortexing with 1% (w/v) aluminum borate whiskers significantly increased Agrobacterium infection efficiency in the proximal region of the explants. Transgenic plants were screened at the T0 generation by sGFP fluorescence, genomic PCR, and Southern blot analyses. These transgenic plants grew normally and T1 seeds were obtained. We confirmed stable integration of the transgene and its inheritance in T1 generation plants by sGFP fluorescence and genomic PCR analyses. The average transgenic efficiency for producing kabocha squashes with our method was about 2.7%, a value sufficient for practical use

Transmission electron microscopic observations of nanobubbles and their capture of impurities in wastewater

Unique properties of micro- and nanobubbles (MNBs), such as a high adsorption of impurities on their surface, are difficult to verify because MNBs are too small to observe directly. We thus used a transmission electron microscope (TEM) with the freeze-fractured replica method to observe oxygen (O2) MNBs in solutions. MNBs in pure water and in 1% NaCl solutions were spherical or oval. Their size distribution estimated from TEM images close to that of the original solution is measured by light-scattered methods. When we applied this technique to the observation of O2 MNBs formed in the wastewater of a sewage plant, we found the characteristic features of spherical MNBs that adsorbed surrounding impurity particles on their surface

Synthesis of Gemini cationic surfactants based on natural nicotinic acid and evaluation of their inhibition performance at C-steel/1 M HCl interface: Electrochemical and computational investigations

Herein, we prepare effective Gemini cationic surfactants (CSII, CSIV) and characterize them using FT-IR and 1HNMR spectroscopy. The adsorptive properties of CSII and CSIV at HCl/air and C-steel/HCl interfaces were examined with surface tension and electrochemical parameters, respectively. The critical micelle concentration (CMC) of the CSII and CSIV indicated their adsorption affinity at the HCl/air interface. Where, aliphatic chains increase surface coverage percentage and aid in surfactant adsorption. The electrochemical parameters of C-steel in 1 M HCl were studied using electrochemical impedance spectroscopy (EIS) and potentiodynamic polarization (PDP) at different temperatures. The charge transfer resistance of the C-steel electrode was enhanced from 28.2 Ω.cm2 to 770.79 and 831.45 Ω.cm2 after adding 5 × 10−4 M of CSII and CSIV, respectively. Both CSII and CSIV act as mixed inhibitors with inhibition performance exceeding 97% due to their highly adsorption affinity. The chemical adsorption affinity of these compounds is suggested by the higher adsorption energy (∆G*ads) values (>−40 kJ mol−1) according to the Langmuir isotherm model. The theoretical calculations including DFT, and Monte Carlo simulation (MCs) provide insight into the relationship between corrosion inhibition and molecular structure, where the calculated parameters agree with the experimental results

Improved accuracy of multiple ncRNA alignment by incorporating structural information into a MAFFT-based framework

<p>Abstract</p> <p>Background</p> <p>Structural alignment of RNAs is becoming important, since the discovery of functional non-coding RNAs (ncRNAs). Recent studies, mainly based on various approximations of the Sankoff algorithm, have resulted in considerable improvement in the accuracy of pairwise structural alignment. In contrast, for the cases with more than two sequences, the practical merit of structural alignment remains unclear as compared to traditional sequence-based methods, although the importance of multiple structural alignment is widely recognized.</p> <p>Results</p> <p>We took a different approach from a straightforward extension of the Sankoff algorithm to the multiple alignments from the viewpoints of accuracy and time complexity. As a new option of the MAFFT alignment program, we developed a multiple RNA alignment framework, X-INS-i, which builds a multiple alignment with an iterative method incorporating structural information through two components: (1) pairwise structural alignments by an external pairwise alignment method such as SCARNA or LaRA and (2) a new objective function, Four-way Consistency, derived from the base-pairing probability of every sub-aligned group at every multiple alignment stage.</p> <p>Conclusion</p> <p>The BRAliBASE benchmark showed that X-INS-i outperforms other methods currently available in the sum-of-pairs score (SPS) criterion. As a basis for predicting common secondary structure, the accuracy of the present method is comparable to or rather higher than those of the current leading methods such as RNA Sampler. The X-INS-i framework can be used for building a multiple RNA alignment from any combination of algorithms for pairwise RNA alignment and base-pairing probability. The source code is available at the webpage found in the Availability and requirements section.</p