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Tile displacement is a newly-recognized mechanism in DNA nanotechnology that exploits principles analogous to toehold-mediated strand displacement but within the context of self-assembled DNA origami tile arrays. Here, we formulate an abstract model of tile displacement for the simplest case: individual assemblies interacting with monomer tiles in solution. We give several constructions for programmable computation by tile displacement, from circuits to cellular automata, that vary in how they use energy (or not) to drive the system forward (or not), how much space and how many tile types they require, and whether their computational power is limited to PTIME or PSPACE with respect to the size of the system. In particular, we show that tile displacement systems are Turing universal and can simulate arbitrary two-dimensional synchronous block cellular automata, where each transition rule for updating the state of a 2 by 2 neighborhood is implemented by just a single tile.

Gastric cancer is one of the most common malignancies worldwide and vasculogenic mimicry (VM) is considered to be the leading cause for the failure of anti-angiogenesis therapy in advanced gastric cancer patients. In the present study, we investigate the role of tenascin-c (TNC) in the formation of VM in gastric cancer and found that TNC was upregulated in gastric cancer tissue than in the corresponding adjacent tissues and correlated with VM and poor prognosis of gastric cancer. Furthermore, knockdown of TNC significantly inhibited VM formation and proliferation of gastric cancer cells in vitro and in vivo, with a reduction in cell migration and invasion. Mechanistically, TNC knockdown suppressed the phosphorylation of ERK and subsequently inhibited the process of EMT, both of which play an important role in VM formation. Our results indicated that TNC plays an important role in VM formation in gastric cancer. Combining inhibition of TNC and ERK may be a potential therapeutic approach to inhibit gastric cancer growth and metastasis and decrease antiangiogenic therapeutic resistance.

In molecular programming, the Chemical Reaction Network model is often used to describe real or hypothetical systems. Often, an interesting computational task can be done with a known hypothetical Chemical Reaction Network, but often such networks have no known physical implementation. One of the important breakthroughs in the field was that any Chemical Reaction Network can be physically implemented, approximately, using DNA strand displacement mechanisms. This allows us to treat the Chemical Reaction Network model as a programming language and the implementation schemes as its compiler. This also suggests that it would be useful to optimize the result of such a compilation, and in general to find effective ways to design better DNA strand displacement systems. We discuss DNA strand displacement systems in terms of "motifs", short sequences of elementary DNA strand displacement reactions. We argue that describing such motifs in terms of their inputs and outputs, then building larger systems out of the abstracted motifs, can be an efficient way of designing DNA strand displacement systems. We discuss four previously studied motifs in this abstracted way, and present a new motif based on cooperative 4-way strand exchange. We then show how Chemical Reaction Network implementations can be built out of abstracted motifs, discussing existing implementations as well as presenting two new implementations based on 4-way strand exchange, one of which uses the new cooperative motif. The new implementations both have two desirable properties not found in existing implementations, namely both use only at most 2-stranded DNA complexes for signal and fuel complexes and both are physically reversible. There are reasons to believe that those properties may make them more robust and energy-efficient, but at the expense of using more fuel complexes than existing implementation schemes.

Japanese traditional rice production technique features “sparse seeding, long cultivation, scattered planting and limited transplanting”, and scientific rice production methods of deep plowing, fertilization, weeding, irrigation and drainage are employed. This technique has reversed the common practice of “dense seeding and planting” in rice paddies and changed the history of growing rice spikes purely out of stems, thus enabling stable and high yields of several tillering grain crops including rice. The technique can provide a useful reference for developing modern rice production in warm areas.

Models of well-mixed chemical reaction networks (CRNs) have provided a solid foundation for the study of programmable molecular systems, but the importance of spatial organization in such systems has increasingly been recognized. In this paper, we explore an alternative chemical computing model introduced by Qian & Winfree in 2014, the surface CRN, which uses molecules attached to a surface such that each molecule only interacts with its immediate neighbours. Expanding on the constructions in that work, we first demonstrate that surface CRNs can emulate asynchronous and synchronous deterministic cellular automata and implement continuously active Boolean logic circuits. We introduce three new techniques for enforcing synchronization within local regions, each with a different trade-off in spatial and chemical complexity. We also demonstrate that surface CRNs can manufacture complex spatial patterns from simple initial conditions and implement interesting swarm robotic behaviours using simple local rules. Throughout all example constructions of surface CRNs, we highlight the trade-off between the ability to precisely place molecules and the ability to precisely control molecular interactions. Finally, we provide a Python simulator for surface CRNs with an easy-to-use web interface, so that readers may follow along with our examples or create their own surface CRN designs.

Compared to conventional imaging spectrometry,computational imaging spectrometry has the advantages of high throughput snapshot imaging etc.But because of the presence of the dispersive element,computational imaging spectrometry suffers the effect of spectral line bending.To study the effect of spectral line bending on signal acquisition,spatial-spectral aliasing and reconstructed result in computational imaging spectrometry,combined with the principle of computational imaging spectrometry and reconstruction algorithm,the relative peak signal-to-noise ratio of the reconstructed image and the maximal error of the reconstructed spectral curve with different spectral offset were calculated and analyzed.The experimental result showed that spectral offset of the signal acquired by the detector will change the degree of spatialspectral aliasing.The reconstructed results with spectral line bending exhibit distinct errors compared with no spectral line bending.And both sides of the reconstructed spectral curve tend to smooth.In order to reconstruct the object scene with high accuracy,spectral offset should be no more than half a pixel for computational imaging spectrometry with 10nm resolution.

The rural commodity economy in the Edo period developed by leaps and bounds under the influence of institution, policy, technology and other factors. From the mid-17th century, the specific area of cash crops gradually took shape in Japan and the large-scale cultivation of cash crops greatly promoted the development of rural handicrafts, thereby creating the conditions for the initiation of the capitalist relations of production. The development of rural commodity economy not only changed the traditional mode of operation and production of Japanese farmers, but also accelerated the class differentiation, shook and disintegrated the economic foundation and class basis of Bakuhan society, and created the preconditions for the later Meiji Restoration.

The rural commodity economy in the Edo period developed by leaps and bounds under the influence of institution, policy, technology and other factors. From the mid-17th century, the specific area of cash crops gradually took shape in Japan and the large-scale cultivation of cash crops greatly promoted the development of rural handicrafts, thereby creating the conditions for the initiation of the capitalist relations of production. The development of rural commodity economy not only changed the traditional mode of operation and production of Japanese farmers, but also accelerated the class differentiation, shook and disintegrated the economic foundation and class basis of Bakuhan society, and created the preconditions for the later Meiji Restoration.

Coded aperture snapshot spectral imaging (CASSI) has been discussed in recent years. It has the remarkable advantages of high optical throughput, snapshot imaging, etc. The entire spatial-spectral data-cube can be reconstructed with just a single two-dimensional (2D) compressive sensing measurement. On the other hand, for less spectrally sparse scenes, the insufficiency of sparse sampling and aliasing in spatial-spectral images reduce the accuracy of reconstructed three-dimensional (3D) spectral cube. To solve this problem, this paper extends the improved CASSI. A band-pass filter array is mounted on the coded mask, and then the first image plane is divided into some continuous spectral sub-band areas. The entire 3D spectral cube could be captured by the relative movement between the object and the instrument. The principle analysis and imaging simulation are presented. Compared with peak signal-to-noise ratio (PSNR) and the information entropy of the reconstructed images at different numbers of spectral sub-band areas, the reconstructed 3D spectral cube reveals an observable improvement in the reconstruction fidelity, with an increase in the number of the sub-bands and a simultaneous decrease in the number of spectral channels of each sub-band.

In chemistry, synthesis is the process in which a target compound is produced in a step-wise manner from given base compounds. A recent, promising approach for carrying out these reactions is DNA-templated synthesis, since, as opposed to more traditional methods, this approach leads to a much higher effective molarity and makes much desired one-pot synthesis possible. With this method, compounds are tagged with DNA sequences and reactions can be controlled by bringing two compounds together via their tags. This leads to new cost optimization problems of minimizing the number of different tags or strands to be used under various conditions. We identify relevant optimization criteria, provide the first computational approach to automatically inferring DNA-templated programs, and obtain optimal and near-optimal results.

International audience; Strand displacement and tile assembly systems are designed to follow prescribed kinetic rules (i.e., exhibit a specific time-evolution). However, the expected behavior in the limit of infinite time--known as thermodynamic equilibrium--is often incompatible with the desired computation. Basic physical chemistry implicates this inconsistency as a source of unavoidable error. Can the thermodynamic equilibrium be made consistent with the desired computational pathway? In order to formally study this question, we introduce a new model of molecular computing in which computation is driven by the thermodynamic driving forces of enthalpy and entropy. To ensure greatest generality we do not assume that there are any constraints imposed by geometry and treat monomers as unstructured collections of binding sites. In this model we design Boolean AND/OR formulas, as well as a self-assembling binary counter, where the thermodynamically favored states are exactly the desired final output configurations. Though inspired by DNA nanotechnology, the model is sufficiently general to apply to a wide variety of chemical systems.

In molecular self-assembly such as DNA origami, a circular strand’s topological routing determines the feasibility of a design to assemble to a target. In this regard, the Chinese-postman DNA scaffold routings of Benson et al. (2015) only ensure the unknottedness of the scaffold strand for triangulated topological spheres. In this paper, we present a cubic-time 53−approximation algorithm to compute unknotted Chinese-postman scaffold routings on triangulated orientable surfaces of higher genus. Our algorithm guarantees every edge is routed at most twice, hence permitting low-packed designs suitable for physiological conditions.