Programing strand displacement reaction pathways using small molecular DNA binders

DNA has been used in nature as carriers of heredity information for billions of years. The last four decades have witnessed the success of DNA nanotechnology, an interdisciplinary research area in which DNA is used as a synthetic engineering tool rather than a carrier of genetic information. The growth of DNA nanotechnology crosses the boundaries between physics, chemistry, biology and computer science and enables DNA to function as an electronic component, substrate, drug delivery vector and data storage unit. The hybridization of DNA strictly follows the by Watson-Crick rule; thus, DNA base pairs are the most reliable and predictable building block in the true nanometer range. New methods and designs for controlling DNA hybridization have always provided the most essential momentum for the development of DNA nanotechnology. When small molecules bind to the double helical structure of DNA, either through intercalation or minor groove binding, the stability and functionality of DNA may be significantly altered, which is a fundamental basis for many therapeutic and sensing applications. Herein, we reveal, for the first time, that small molecular DNA binders may also be used to program the reaction pathways of toehold-mediated DNA strand displacement, an elementary building block in DNA nanotechnology

Small polaron with generic open boundary conditions revisit: exact solution via the off-diagonal Bethe ansatz

The small polaron, an one-dimensional lattice model of interacting spinless fermions, with generic non-diagonal boundary terms is studied by the off-diagonal Bethe ansatz method. The presence of the Grassmann valued non-diagonal boundary fields gives rise to a typical $U(1)$-symmetry-broken fermionic model. The exact spectra of the Hamiltonian and the associated Bethe ansatz equations are derived by constructing an inhomogeneous $T-Q$ relation.Comment: 12 pages, no figure, published versio

Robust Depth Linear Error Decomposition with Double Total Variation and Nuclear Norm for Dynamic MRI Reconstruction

Compressed Sensing (CS) significantly speeds up Magnetic Resonance Image (MRI) processing and achieves accurate MRI reconstruction from under-sampled k-space data. According to the current research, there are still several problems with dynamic MRI k-space reconstruction based on CS. 1) There are differences between the Fourier domain and the Image domain, and the differences between MRI processing of different domains need to be considered. 2) As three-dimensional data, dynamic MRI has its spatial-temporal characteristics, which need to calculate the difference and consistency of surface textures while preserving structural integrity and uniqueness. 3) Dynamic MRI reconstruction is time-consuming and computationally resource-dependent. In this paper, we propose a novel robust low-rank dynamic MRI reconstruction optimization model via highly under-sampled and Discrete Fourier Transform (DFT) called the Robust Depth Linear Error Decomposition Model (RDLEDM). Our method mainly includes linear decomposition, double Total Variation (TV), and double Nuclear Norm (NN) regularizations. By adding linear image domain error analysis, the noise is reduced after under-sampled and DFT processing, and the anti-interference ability of the algorithm is enhanced. Double TV and NN regularizations can utilize both spatial-temporal characteristics and explore the complementary relationship between different dimensions in dynamic MRI sequences. In addition, Due to the non-smoothness and non-convexity of TV and NN terms, it is difficult to optimize the unified objective model. To address this issue, we utilize a fast algorithm by solving a primal-dual form of the original problem. Compared with five state-of-the-art methods, extensive experiments on dynamic MRI data demonstrate the superior performance of the proposed method in terms of both reconstruction accuracy and time complexity

Study on the Reasonable Smoke Exhaust Rate of the Crossrange Exhaust Duct in Double-layer Shield Tunnel

AbstractThe research on the concentrated smoke extraction system of crossrange exhaust duct in double-layer shield tunnel is still very lack in the world. This paper is on the smoke extraction system of double-layer shield tunnel. It will provide the supports and references for the smoke control of tunnel fire and the determination of related technical parameters in the design of tunnel fire ventilation and smoke extraction, so it has important scientific value, practical significance and application prospects. This paper bases on the tunnel project of Slender West Lake in Yangzhou. By using the method of combining theory and numerical simulation, a conclusion can be drawn that the reasonable smoke exhaust rate of the upper tunnel is 140 m3/s

Task modules Partitioning, Scheduling and Floorplanning for Partially Dynamically Reconfigurable Systems Based on Modern Heterogeneous FPGAs

Modern field programmable gate array(FPGA) can be partially dynamically reconfigurable with heterogeneous resources distributed on the chip. And FPGA-based partially dynamically reconfigurable system(FPGA-PDRS) can be used to accelerate computing and improve computing flexibility. However, the traditional design of FPGA-PDRS is based on manual design. Implementing the automation of FPGA-PDRS needs to solve the problems of task modules partitioning, scheduling, and floorplanning on heterogeneous resources. Existing works only partly solve problems for the automation process of FPGA-PDRS or model homogeneous resource for FPGA-PDRS. To better solve the problems in the automation process of FPGA-PDRS and narrow the gap between algorithm and application, in this paper, we propose a complete workflow including three parts, pre-processing to generate the list of task modules candidate shapes according to the resources requirements, exploration process to search the solution of task modules partitioning, scheduling, and floorplanning, and post-optimization to improve the success rate of floorplan. Experimental results show that, compared with state-of-the-art work, the proposed complete workflow can improve performance by 18.7\%, reduce communication cost by 8.6\%, on average, with improving the resources reuse rate of the heterogeneous resources on the chip. And based on the solution generated by the exploration process, the post-optimization can improve the success rate of the floorplan by 14\%

Bethe ansatz solutions of the τ 2-model with arbitrary boundary fields

The quantum $\tau_2$-model with generic site-dependent inhomogeneity and arbitrary boundary fields is studied via the off-diagonal Bethe Ansatz method. The eigenvalues of the corresponding transfer matrix are given in terms of an inhomogeneous T-Q relation, which is based on the operator product identities among the fused transfer matrices and the asymptotic behavior of the transfer matrices. Moreover, the associated Bethe Ansatz equations are also obtained.Comment: 26 pages, no figures, published versio

In silico screening of transaminase using semi-empirical QM/MM approach

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