On the origin of the unusual behavior in the stretching of single-stranded DNA

Force extension curves (FECs), which quantify the response of a variety of biomolecules subject to mechanical force ($f$), are often quantitatively fit using worm-like chain (WLC) or freely-jointed chain (FJC) models. These models predict that the chain extension, $x$, normalized by the contour length increases linearly at small $f$ and at high forces scale as $x \sim (1 - f^{-\alpha})$ where $\alpha$= 0.5 for WLC and unity for FJC. In contrast, experiments on ssDNA show that over a range of $f$ and ionic concentration, $x$ scales as $x\sim\ln f$, which cannot be explained using WLC or FJC models. Using theory and simulations we show that this unusual behavior in FEC in ssDNA is due to sequence-independent polyelectrolyte effects. We show that the $x\sim \ln f$ arises because in the absence of force the tangent correlation function, quantifying chain persistence, decays algebraically on length scales on the order of the Debye length. Our theory, which is most appropriate for monovalent salts, quantitatively fits the experimental data and further predicts that such a regime is not discernible in double stranded DNA.Comment: Accepted for publication in JC

Kinetics of Loop Formation in Polymer Chains

We investigate the kinetics of loop formation in flexible ideal polymer chains (Rouse model), and polymers in good and poor solvents. We show for the Rouse model, using a modification of the theory of Szabo, Schulten, and Schulten, that the time scale for cyclization is $\tau_c\sim \tau_0 N^2$ (where $\tau_0$ is a microscopic time scale and $N$ is the number of monomers), provided the coupling between the relaxation dynamics of the end-to-end vector and the looping dynamics is taken into account. The resulting analytic expression fits the simulation results accurately when $a$, the capture radius for contact formation, exceeds $b$, the average distance between two connected beads. Simulations also show that, when $a < b$, $\tau_c\sim N^{\alpha_\tau}$, where $1.5<{\alpha_\tau}\le 2$ in the range $7<N<200$ used in the simulations. By using a diffusion coefficient that is dependent on the length scales $a$ and $b$ (with $a<b$), which captures the two-stage mechanism by which looping occurs when $a < b$, we obtain an analytic expression for $\tau_c$ that fits the simulation results well. The kinetics of contact formation between the ends of the chain are profoundly affected when interactions between monomers are taken into account. Remarkably, for $N < 100$ the values of $\tau_c$ decrease by more than two orders of magnitude when the solvent quality changes from good to poor. Fits of the simulation data for $\tau_c$ to a power law in $N$ ($\tau_c\sim N^{\alpha_\tau}$) show that $\alpha_\tau$ varies from about 2.4 in a good solvent to about 1.0 in poor solvents. Loop formation in poor solvents, in which the polymer adopts dense, compact globular conformations, occurs by a reptation-like mechanism of the ends of the chain.Comment: 30 pages, 9 figures. Revised version includes a new figure (8) and minor changes to the tex

The Current Adoption of Dry-Direct Seeding Rice (DDSR) in Thailand and Lessons Learned for Mekong River Delta of Vietnam

The paper documents the joint study trip, organized by CCAFS Southeast Asia for Vietnamese rice researchers, extension workers, as well as local decision makers, to visit Thailand in April 2018. The goal of the study trip was to observe and learn the experience of Thai farmers on the large-scale adoption process of dry-direct seeding rice (DDSR), a viable alternative to address regional scarcity of fresh water in irrigation caused by the drought and salinity intrusion in the Mekong River Delta

Presence of e-EDCs in surface water and effluents of pollution sources in Sai Gon and Dong Nai river basin

© 2016 This study aimed to assess the presence of estrogenic endocrine disrupting compounds (e-EDCs) including estriol, bisphenol A (BPA), atrazine (ATZ), octylphenol, octylphenol diethoxylate, octylphenol triethoxylate, nonylphenol, Nonylphenol triethoxylate (NPE3), nonylphenol diethoxylate (NPE2) and 17β-estradiol in: (i) Sai Gon and Dong Nai river waters which have been major raw water sources for drinking water supply for Ho Chi Minh City (HCMC) and neighbouring provinces, and (ii) water pollution sources located in their catchment basin. NPE3 and NPE2 were detected in most of the surface water samples. Concentrations of NPE3 were in a range of less than 5.9–235 ng L−1, whereas BPA was detected at significantly high concentrations in the dry season in canals in HCMC. In the upstream of Sai Gon and Dong Nai Rivers, ATZ concentrations were observed at water intake of water treatment plants served for HCMC water supply system. Similarly, high potential risk of NPE2 and NPE3 contamination at Phu Cuong Bridge near Hoa Phu water intake was identified. The significant correlation between NPE2, dissolved organic carbon and total nitrogen was found. Estrogenic equivalent or estrogenic activity of Sai Gon and Dong Nai Rivers was lower than those of the previous studies. Compared with other studies, e-EDCs of pollution in Sai Gon river basin were relatively low

Remark on the Entropy Production of Adaptive Run-and-Tumble Chemotaxis

Chemotactic active particles, such as bacteria and cells, exhibit an adaptive run-and-tumble motion, giving rise to complex emergent behaviors in response to external chemical fields. This motion is generated by the conversion of internal chemical energy into self-propulsion, allowing each agent to sustain a steady-state far from thermal equilibrium and perform works. The rate of entropy production serves as an indicates of how extensive these agents operate away from thermal equilibrium, providing a measure for estimating maximum obtainable power. Here we present the general framework for calculating the entropy production rate created by such population of agents from the first principle, using the minimal model of bacterial adaptive chemotaxis, as they execute the most basic collective action -- the mass transport

Flexural-strengthening efficiency of cfrp sheets for unbonded post-tensioned concrete T-beams

There has been a limited number of studies about the flexural behavior of unbonded post-tensioned concrete (UPC) beams strengthened with carbon fibre reinforced polymer (CFRP) and these studies have not systematically examined the effect of CFRP sheets on the tendon strain as well as the strengthening efficiency. Moreover, current design guides for the FRP strengthening techniques have not provided any design procedure for UPC structures. This study, thus, investigates the influence of CFRP sheet ratio on the flexural behavior of CFRP-strengthened UPC T-beams and quantifies its effect upon tendon behavior in this kind of UPC beams. The testing program consisted of nine large-scale UPC T-beams strengthened by different layers of CFRP sheets with or without CFRP U-wrapped anchors. The experimental results have shown that the use of CFRP sheets and CFRP U-wrapped anchors significantly affected the tendon strain. The FRP reinforcement ratio governed the flexural capacity, the crack width, the mid-span displacement, and the ductility of the beams in which the strengthening efficiency reduces with the increased number of CFRP layers. The configuration of the CFRP U-wrapped anchors affected the strain of the CFRP sheets, the failure mode and thus the beam behavior. In addition, semi-empirical equations were proposed to estimate the actual strain of unbonded tendons in which the effect of the CFRP sheets and CFRP U-wrapped anchors have been taken into consideration. The proposed equations, which are simple to use, yield reliable predictions with a small variation

Enhanced UV/blue fluorescent sensing using metal-dielectric-metal aperture nanoantenna arrays

Subwavelength aperture antenna arrays are designed and fabricated for potential applications in fluorescence sensing in the near UV/blue range. They are designed using finite-difference time-domain (FDTD) simulation, fabricated using focused ion beam etching and characterised using angular Fourier spectroscopy. The aperture arrays are formed in the top layer of an aluminum-silica-aluminum trilayer and produce a maximum simulated field intensity enhancement of 5.8 times at 406 nm and highly directive emission with a beamwidth of 8.3 deg. The normal incidence reflection response has been measured and shows reasonable agreement with modelled results. In addition, to investigate higher field intensity enhancements, bowtie aperture arrays are simulated and the influence of parameters such as dielectric gap, position of dipole source, and aperture shape and size are discussed and show enhancements up to 67 times are possible

Inferring the effective thickness of polyelectrolytes from stretching measurements at various ionic strengths: applications to DNA and RNA

By resorting to the thick-chain model we discuss how the stretching response of a polymer is influenced by the self-avoidance entailed by its finite thickness. The characterization of the force versus extension curve for a thick chain is carried out through extensive stochastic simulations. The computational results are captured by an analytic expression that is used to fit experimental stretching measurements carried out on DNA and single-stranded RNA (poly-U) in various solutions. This strategy allows us to infer the apparent diameter of two biologically-relevant polyelectrolytes, namely DNA and poly-U, for different ionic strengths. Due to the very different degree of flexibility of the two molecules, the results provide insight into how the apparent diameter is influenced by the interplay between the (solution-dependent) Debye screening length and the polymers' ``bare'' thickness. For DNA, the electrostatic contribution to the effective radius, $\Delta$, is found to be about 5 times larger than the Debye screening length, consistently with previous theoretical predictions for highly-charged stiff rods. For the more flexible poly-U chains the electrostatic contribution to $\Delta$ is found to be significantly smaller than the Debye screening length.Comment: iopart, 14 pages, 13 figures, to appear in J. Phys.: Condens. Matte

Structural assessment based on vibration measurement test combined with an artificial neural network for the steel truss bridge

Damage assessment is one of the most crucial issues for bridge engineers during the operational and maintenance phase, especially for existing steel bridges. Among several methodologies, the vibration measurement test is a typical approach, in which the natural frequency variation of the structure is monitored to detect the existence of damage. However, locating and quantifying the damage is still a big challenge for this method, due to the required human resources and logistics involved. In this regard, an artificial intelligence (AI)-based approach seems to be a potential way of overcoming such obstacles. This study deployed a comprehensive campaign to determine all the dynamic parameters of a predamaged steel truss bridge structure. Based on the results for mode shape, natural frequency, and damping ratio, a finite element model (FEM) was created and updated. The artificial intelligence network’s input data from the damage cases were then analysed and evaluated. The trained artificial neural network model was curated and evaluated to confirm the approach’s feasibility. During the actual operational stage of the steel truss bridge, this damage assessment system showed good performance, in terms of monitoring the structural behaviour of the bridge under some unexpected accidents.This research was funded by FCT/MCTES through national funds (PIDDAC) from the R&D Unit Institute for Sustainability and Innovation in Structural Engineering (ISISE), under the reference UIDB/04029/2020, and from the Associate Laboratory Advanced Production and Intelligent Systems ARISE, under the reference LA/P/0112/2020, as well as financial support of the project research “B2022-GHA-03” from the Ministry of Education and Training. And The APC was funded by ANI (“Agência Nacional de Inovação”) through the financial support given to the R&D Project “GOA Bridge Management System—Bridge Intelligence”, with reference POCI-01-0247-FEDER069642, which was cofinanced by the European Regional Development Fund (FEDER) through the Operational Competitiveness and Internationalisation Program (POCI)