A Lattice Model on the Rate of DNA Hybridization

We develop a lattice model on the rate of hybridization of the complementary single-stranded DNAs (c-ssDNAs). Upon translational diffusion mediated collisions, c-ssDNAs interpenetrate each other to form correct (cc), incorrect (icc) and trap-correct contacts (tcc) inside the reaction volume. Correct contacts are those with exact registry matches which leads to nucleation and zipping. Incorrect contacts are the mismatch contacts which are less stable compared to tcc which can occur in the repetitive c-ssDNAs. Although tcc possess registry match within the repeating sequences, they are incorrect contacts in the view of the whole c-ssDNAs. The nucleation rate (kN) is directly proportional to the collision rate and the average number of correct-contacts (<ncc>) formed when both the c-ssDNAs interpenetrate each other. Detailed lattice model simulations suggest that 〈n_cc 〉∝L⁄V where L is the length of c-ssDNAs and V is the reaction volume. Further numerical analysis revealed the scaling for the average radius of gyration of c-ssDNAs (Rg) with their length as R_g∝√L. Since the reaction space will be approximately a sphere with radius equals to 2Rg and V∝L^(3⁄2), one obtains k_N∝1/√L. When c-ssDNAs are nonrepetitive, then the overall renaturation rate becomes as k_R∝k_N L and one finally obtains k_R∝√L in line with the experimental observations. When c-ssDNAs are repetitive with a complexity of c, then earlier models suggested the scaling k_R∝√L/c which breaks down at c = L. This clearly suggested the existence of at least two different pathways of renaturation in case of repetitive c-ssDNAs viz. via incorrect contacts and trap correct contacts. The trap correct contacts can lead to the formation of partial duplexes which can keep the complementary strands in the close vicinity for a prolonged timescale. This is essential for the extended 1D slithering, inchworm movements and internal displacement mechanisms which can accelerate the searching for the correct contacts. Clearly, the extent of slithering dynamics will be inversely proportional to the complexity. When the complexity is close to the length of c-ssDNAs, then the pathway via incorrect contacts will dominate. When the complexity is much lesser than the length of c-ssDNA, then pathway via trap correct contacts would be the dominating one.

CANDIDATE: A tool for generating anonymous participant-linking IDs in multi-session studies

Background To ensure the privacy of participants is an ethical and legal obligation for researchers. Yet, achieving anonymity can be technically difficult. When observing participants over time one needs mechanisms to link the data from the different sessions. Also, it is often necessary to expand the sample of participants during a project. Objectives To help researchers simplify the administration of such studies the CANDIDATE tool is proposed. This tool allows simple, unique, and anonymous participant IDs to be generated on the fly. Method Simulations were used to validate the uniqueness of the IDs as well as their anonymity. Results The tool can successfully generate IDs with a low collision rate while maintaining high anonymity. A practical compromise between integrity and anonymity was achieved when the ID space is about ten times the number of participants. Implications The tool holds potential for making it easier to collect more comprehensive empirical evidence over time that in turn will provide a more solid basis for drawing reliable conclusions based on research data. An open-source implementation of the tool that runs locally in a web-browser is made available.

In-Network Data Aggregation for Ad Hoc Clustered Cognitive Radio Wireless Sensor Network

In cognitive radio wireless sensor networks (CRSN), the nodes act as secondary users. Therefore, they can access a channel whenever its primary user (PU) is absent. Thus, the nodes are assumed to be equipped with a spectrum sensing (SS) module to monitor the PU activity. In this manuscript, we focus on a clustered CRSN, where the cluster head (CH) performs SS, gathers the data, and sends it toward a central base station by adopting an ad hoc topology with in-network data aggregation (IDA) capability. In such networks, when the number of clusters increases, the consumed energy by the data transmission decreases, while the total consumed energy of SS increases, since more CHs need to perform SS before transmitting. The effect of IDA on CRSN performance is investigated in this manuscript. To select the best number of clusters, a study is derived aiming to extend the network lifespan, taking the SS requirements, the IDA effect, and the energy consumed by both SS and transmission into consideration. Furthermore, the collision rate between primary and secondary transmissions and the network latency are theoretically derived. Numerical results corroborate the efficiency of IDA to extend the network lifespan and minimize both the collision rate and the network latency.

A Study of Standardizing Frequencies Using Channel Raster for Underwater Wireless Acoustic Sensor Networks

In this paper, we propose the method to standardize acoustic frequencies for underwater wireless acoustic sensor networks (UWASNs) by applying the channel raster used in the terrestrial mobile communications. The standardization process includes: (1) Setting the available acoustic frequency band where a channel raster is employed via the frequency specification analysis of the state-of-the art underwater acoustic communication modems. (2) Defining the center frequencies and the channel numbers as a function of channel raster, and the upper limit of the value of channel raster. (3) Determining the value of the channel raster suitable for the available acoustic frequency band via simulations. To set the value, three performance metrics are considered: the collision rate, the idle spectrum rate, and the receiver computational complexity. The simulation results show that the collision rate and the idle spectrum rate according to the value of channel raster have a trade-off relationship, but the influence of channel raster on the two performance metrics is insignificant. However, the receiver computational complexity is enhanced remarkably as the value of channel raster increases. Therefore, setting the value of channel raster close to its upper limit is the most adequate in respect of mitigating the occurrence of a collision and enhancing the reception performance. The standardized frequencies based on channel raster can guarantee the frequency compatibility required for the emerging technologies like the Internet of Underwater Things (IoUT) or the underwater cognitive radio, but also improves the network performance by avoiding the arbitrary use of frequencies.

Polymerization and Collision in High Concentrations for Brownian Coagulation

Aggregation always occurs in industrial processes with fractal-like particles, especially in dense systems (the volume fraction, ϕ>1%). However, the classic aggregation theory, established by Smoluchowski in 1917, cannot sufficiently simulate the particle dynamics in dense systems, particularly those of generat ed fractal-like particles. In this article, the Langevin dynamic was applied to study the collision rate of aggregations as well as the structure of aggregates affected by different volume fractions. It is shown that the collision rate of highly concentrated particles is progressively higher than that of a dilute concentration, and the SPSD (self-preserving size distribution) is approached (σg,n≥1.5). With the increase in volume fraction, ϕ, the SPSD broadens, and the geometric standard is 1.54, 1.98, and 2.73 at ϕ= 0.1, 0.2, and 0.3. When the volume fraction, ϕ, is higher, the radius of gyration is smaller with the same cluster size (number-based), which means the particle agglomerations are in a tighter coagulation. The fractal-like property Df is in the range of 1.60–2.0 in a high-concentration system. Knowing the details of the collision progress in a high-concentration system can be useful for calculating the dynamics of coagulating fractal-like particles in the industrial process.

White dwarf–main sequence star collisions from wide triples in the field

ABSTRACT Multiple star systems interact strongly with galactic field stars when the outer semi-major axis of a triple or multiple star is &gt;103 AU. Stable triples composed of two white-dwarfs (WD) and a low-mass main sequence (MS) star in a wide outer orbit can thus be destabilized by gravitational interactions with random field stars. Such interactions excite the eccentricity of the distant third star sufficiently so that it begins to interact significantly with the inner binary. When this occurs, the triple undergoes multiple binary-single resonant encounters. These encounters may result either in a collision between the non-degenerate component and a WD, or the breakup of the triple into a compact binary and a third object which is ejected. The compact binary can be either a MS–WD pair which survives, or collides or a double WD (DWD), which may inspiral through gravitational wave emission. We calculate the collision rate between a MS and WD star, and the merger rate of DWDs. Additionally, we describe the prospects of detectability of such a collision, which may resemble a sub-luminous supernovae event.