Thermal expansion within a chain of magnetic colloidal particles

We study the thermal expansion of chains formed by self-assembly of magnetic colloidal particles in a magnetic field. Using video-microscopy, complete positional data of all the particles of the chains is obtained. By changing the ionic strength of the solution and the applied magnetic field, the interaction potential can be tuned. We analyze the thermal expansion of the chain using a simple model of a one dimensional anharmonic crystal of finite size.Comment: 5 pages and 3 figure

A Relative Tolerance Relation of Rough Set (RTRS) for potential fish yields in Indonesia

The sea is essential to life on earth, including regulating the climate, producing oxygen, providing medicines, providing habitats for marine animals, and feeding millions of people. It must be ensured that the sea continues to meet the needs of life without sacrificing the people of future generations. The sea regulates the planet’s climate and is a significant source of nutrients. The sea becomes an essential part of global commerce, while the contents of the ocean become the solution of human energy needs today and the future. The wealth and potential of the sea as a source of energy for humans today and the future needs to be mapped and described to provide a picture of marine potential to all concerned. As part of the government, the Ministry of Marine Affairs and Fisheries is responsible for the process of formulating, determining, and implementing policies in the field of marine and fisheries based on the results of mapping and extracting information from existing conditions. The results of this information can be used to predict the marine potential in a marine area. This prediction process can be developed using data-mining techniques such as applying the association rule by looking at the relationship between the quantity of fish based on the plankton abundance index. However, this association rules data-mining techniques that require complete data, which are data sets with no missing values to generate interesting rules for detection systems. The problem is often that required marine data are not available or that marine data are available, but they contain incomplete data. To address this problem, this paper introduces a Relative Tolerance Relation of Rough Set (RTRS). Novelty RTRS differs from previous rough approaches that use tolerance relationships, nonsymmetric equation relationships, and limited tolerance relationships. The RTRS approach is based on a limited tolerance relationship considering the relative precision between two objects; therefore, this is the first job to use relative precision. In addition, this paper presents the mathematical approach of the RTRS and compares it with other existing approaches using the marine real dataset to classify the marine potential level of the region. The results show that the proposed approach is better than the existing approach in terms of accuracy

Stochastic dynamics of macromolecular-assembly networks

The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current computational methods strongly limited for understanding how the physical interactions between cellular components give rise to systemic properties of cells. Here we present a stochastic approach to study the dynamics of networks formed by macromolecular complexes in terms of the molecular interactions of their components. Exploiting key thermodynamic concepts, this approach makes it possible to both estimate reaction rates and incorporate the resulting assembly dynamics into the stochastic kinetics of cellular networks. As prototype systems, we consider the lac operon and phage lambda induction switches, which rely on the formation of DNA loops by proteins and on the integration of these protein-DNA complexes into intracellular networks. This cross-scale approach offers an effective starting point to move forward from network diagrams, such as those of protein-protein and DNA-protein interaction networks, to the actual dynamics of cellular processes.Comment: Open Access article available at http://www.nature.com/msb/journal/v2/n1/full/msb4100061.htm

SEQuel: improving the accuracy of genome assemblies

Motivation: Assemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the assembly process. We develop SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model

Wavefront predictions for the automated assembly of optical systems

Industrial assembly of optical systems is still a tedious and cost-intensive task that is mostly dominated by manual labor. Positional fine-adjustment of optical components is pivotal to ensure a desired performance of the optical device at hand. In this paper, we use wavefront predictions to aim for fully automated assembly procedures. Wavefront measurements along with position identification methods can be utilized to continuously update a simulation model which in turn allows for predictions on future wavefront errors. This enables to take according correction measures during the assembly process if a certain wavefront tolerance specification is not met. In order to demonstrate the efficacy of the proposed approach and methods, a beam expander is sequentially assembled. The setup consists of a laser, two bi-convex lenses, and a Shack-Hartmann wavefront sensor and has to satisfy a certain wavefront tolerance specification after its assembly. © 2018 SPIE

High accuracy transfer printing of single-mode membrane silicon photonic devices

A transfer printing (TP) method is presented for the micro-assembly of integrated photonic devices from suspended membrane components. Ultra thin membranes with thickness of 150nm are directly printed without the use of mechanical support and adhesion layers. By using a correlation alignment scheme vertical integration of single-mode silicon waveguides is achieved with an average placement accuracy of 100±70nm. Silicon (Si) μ-ring resonators are also fabricated and show controllable optical coupling by varying the lateral absolute position to an underlying Si bus waveguide