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The results of Brownian dynamics simulations of a single DNA molecule in shear flow are presented taking into account the effect of internal viscosity. The dissipative mechanism of internal viscosity is proved necessary in the research of DNA dynamics. A stochastic model is derived on the basis of the balance equation for forces acting on the chain. The Euler method is applied to the solution of the model. The extensions of DNA molecules for different Weissenberg numbers are analyzed. Comparison with the experimental results available in the literature is carried out to estimate the contribution of the effect of internal viscosity.

In the past decades, DNA has been intensely studied and exploited in different research areas of nanoscience and nanotechnology. At first glance, DNA-based nanophotonics seems to deviate quite far from the original goal of Nadrian Seeman, the founder of DNA nanotechnology, who hoped to organize biological entities using DNA in high-resolution crystals. As a matter of fact, DNA-based nanophotonics does closely follow his central spirit. That is, apart from being a genetic material for inheritance, DNA is also an ideal material for building molecular devices.

The idea of computing with DNA was given by Tom Head in 1987, however in 1994 in a seminal paper, the actual successful experiment for DNA computing was performed by Adleman. The heart of the DNA computing is the DNA hybridization, however, it is also the source of errors. Thus the success of the DNA computing depends on the error control techniques. The classical coding theory techniques have provided foundation for the current information and communication technology (ICT). Thus it is natural to expect that coding theory will be the foundational subject for the DNA computing paradigm. For the successful experiments with DNA computing usually we design DNA strings which are sufficiently dissimilar. This leads to the construction of a large set of DNA strings which satisfy certain combinatorial and thermodynamic constraints. Over the last 16 years, many approaches such as combinatorial, algebraic, computational have been used to construct such DNA strings. In this work, we survey this interesting area of DNA coding theory by providing key ideas of the area and current known results.

We introduce $\textit{scadnano}$ (https://scadnano.org) (short for "scriptable cadnano"), a computational tool for designing synthetic DNA structures. Its design is based heavily on cadnano, the most widely-used software for designing DNA origami, with three main differences: 1. scadnano runs entirely in the browser, with $\textit{no software installation}$ required. 2. scadnano designs, while they can be edited manually, can also be created and edited by a $\textit{well-documented Python scripting library}$, to help automate tedious tasks. 3. The scadnano file format is $\textit{easily human-readable}$. This goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. The format is also somewhat more expressive than that of cadnano, able to describe a broader range of DNA structures than just DNA origami.

The proton-magnetic reaction is commonly used in MRI machines with a strong magnetic field of over 1 T, while this study hypothesized that the electron magnetic reaction of hydrogen could affect the hydrogen bonds of double-stranded DNA (dsDNA) at a low magnetic field below 0.01 T. The goal is to develop a hydrogen bonding magnetic reaction-based gene regulation (HBMR-GR) system. The polarities of DNA base pairs are derived from the relative electrostatic charge between purines and pyrimidines, which become positively and negatively charged, respectively. The Pyu dsDNAs with pyrimidine(s)-purine(s) sequences, ds3T3A, ds3C3G, and ds3C3A, showed stronger DNA hybridization potential, increased infrared absorption at 3400-3200 cm-1, and a unique DNA conformation in HPLC analysis compared to the corresponding Puy dsDNAs. To target the three-dimensional structure of dsDNA based on the DNA base pair polarities, one can use cyclic electromagnetic DNA simulation (CEDS) with approximately 25% efficiency for randomly oriented dsDNAs. CEDS was found to induce sequence-specific hybridization of target oligo-dsDNAs in 0.005M NaCl solution and sequence-specific conformation of oligo-dsDNAs in 0.1M NaCl solution. It was found that the Pyu oligo-dsDNAs were more responsible for the hybridization and conformational changes by CEDS than the Puy oligo-dsDNAs. CEDS decreased ethidium bromide (EtBr) DNA intercalation and spermidine DNA condensation depending on CEDS time in the binding assay. The results also included that the Pyu oligo-dsDNAs were more responsible for CEDS by forming stable and unique conformation of oligo-dsDNA than the Therefore, it is postulated that the low-level HBMR-based CEDS can enhance the hybridization potential of oligo-dsDNAs and subsequently lead to the unique DNA conformation required for the initiation of various DNA functions.