抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

A digital computer is generally believed to be an efficient universal computing device; that is, it is believed able to simulate any physical computing device with an increase in computation time by at most a polynomial factor. This may not be true when quantum mechanics is taken into consideration. This paper considers factoring integers and finding discrete logarithms, two problems which are generally thought to be hard on a classical computer and which have been used as the basis of several proposed cryptosystems. Efficient randomized algorithms are given for these two problems on a hypothetical quantum computer. These algorithms take a number of steps polynomial in the input size, e.g., the number of digits of the integer to be factored.

Polynomial-Time Algorithms for Prime Factorization and Discrete Logarithms on a Quantum Computer

Planning algorithms are impacting technical disciplines and industries around the world, including robotics, computer-aided design, manufacturing, computer graphics, aerospace applications, drug design, and protein folding. This coherent and comprehensive book unifies material from several sources, including robotics, control theory, artificial intelligence, and algorithms. The treatment is centered on robot motion planning but integrates material on planning in discrete spaces. A major part of the book is devoted to planning under uncertainty, including decision theory, Markov decision processes, and information spaces, which are the “configuration spaces” of all sensor-based planning problems. The last part of the book delves into planning under differential constraints that arise when automating the motions of virtually any mechanical system. Developed from courses taught by the author, the book is intended for students, engineers, and researchers in robotics, artificial intelligence, and control theory as well as computer graphics, algorithms, and computational biology.

Planning Algorithms: Introductory Material

'Bottom-up fabrication', which exploits the intrinsic properties of atoms and molecules to direct their self-organization, is widely used to make relatively simple nanostructures. A key goal for this approach is to create nanostructures of high complexity, matching that routinely achieved by 'top-down' methods. The self-assembly of DNA molecules provides an attractive route towards this goal. Here I describe a simple method for folding long, single-stranded DNA molecules into arbitrary two-dimensional shapes. The design for a desired shape is made by raster-filling the shape with a 7-kilobase single-stranded scaffold and by choosing over 200 short oligonucleotide 'staple strands' to hold the scaffold in place. Once synthesized and mixed, the staple and scaffold strands self-assemble in a single step. The resulting DNA structures are roughly 100 nm in diameter and approximate desired shapes such as squares, disks and five-pointed stars with a spatial resolution of 6 nm. Because each oligonucleotide can serve as a 6-nm pixel, the structures can be programmed to bear complex patterns such as words and images on their surfaces. Finally, individual DNA structures can be programmed to form larger assemblies, including extended periodic lattices and a hexamer of triangles (which constitutes a 30-megadalton molecular complex).

/pdf/folding-dna-to-create-nanoscale-shapes-and-patterns-1liv7u73y0.pdf

Folding DNA to create nanoscale shapes and patterns

A DNA nanostructure consisting of four four-arm junctions oriented with a square aspect ratio was designed and constructed. Programmable self-assembly of 4 × 4 tiles resulted in two distinct lattice morphologies: uniform-width nanoribbons and two-dimensional nanogrids, which both display periodic square cavities. Periodic protein arrays were achieved by templated self-assembly of streptavidin onto the DNA nanogrids containing biotinylated oligonucleotides. On the basis of a two-step metallization procedure, the 4 × 4 nanoribbons acted as an excellent scaffold for the production of highly conductive, uniform-width, silver nanowires.

https://www.phy.duke.edu/%7Egleb/Pdf_FILES/DNA_science.pdf

DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires

Complexity of the Mover's Problem and Generalizations Extended Abstract

Recent work1,2,3 has demonstrated the self-assembly of designed periodic two-dimensional arrays composed of DNA tiles, in which the intermolecular contacts are directed by ‘sticky’ ends. In a mathematical context, aperiodic mosaics may be formed by the self-assembly of ‘Wang’ tiles4, a process that emulates the operation of a Turing machine. Macroscopic self-assembly has been used to perform computations5; there is also a logical equivalence between DNA sticky ends and Wang tile edges6,7. This suggests that the self-assembly of DNA-based tiles could be used to perform DNA-based computation8. Algorithmic aperiodic self-assembly requires greater fidelity than periodic self-assembly, because correct tiles must compete with partially correct tiles. Here we report a one-dimensional algorithmic self-assembly of DNA triple-crossover molecules9 that can be used to execute four steps of a logical (cumulative XOR) operation on a string of binary bits.

/pdf/logical-computation-using-algorithmic-self-assembly-of-dna-49uk1s5uar.pdf

Logical computation using algorithmic self-assembly of DNA triple-crossover molecules

This paper concerns the problem of moving a polyhedron through Euclidean space while avoiding polyhedral obstacles.

/pdf/complexity-of-the-mover-s-problem-and-generalizations-fpucxxfax1.pdf

Complexity of the mover's problem and generalizations

This paper extends the study and prototyping of unusual DNA motifs, unknown in nature, but founded
on principles derived from biological structures. Artificially designed DNA complexes show promise as building
blocks for the construction of useful nanoscale structures, devices, and computers. The DNA triple crossover
(TX) complex described here extends the set of experimentally characterized building blocks. It consists of
four oligonucleotides hybridized to form three double-stranded DNA helices lying in a plane and linked by
strand exchange at four immobile crossover points. The topology selected for this TX molecule allows for the
presence of reporter strands along the molecular diagonal that can be used to relate the inputs and outputs of
DNA-based computation. Nucleotide sequence design for the synthetic strands was assisted by the application
of algorithms that minimize possible alternative base-pairing structures. Synthetic oligonucleotides were purified,
stoichiometric mixtures were annealed by slow cooling, and the resulting DNA structures were analyzed by
nondenaturing gel electrophoresis and heat-induced unfolding. Ferguson analysis and hydroxyl radical
autofootprinting provide strong evidence for the assembly of the strands to the target TX structure. Ligation
of reporter strands has been demonstrated with this motif, as well as the self-assembly of hydrogen-bonded
two-dimensional crystals in two different arrangements. Future applications of TX units include the construction
of larger structures from multiple TX units, and DNA-based computation. In addition to the presence of reporter
strands, potential advantages of TX units over other DNA structures include space for gaps in molecular arrays,
larger spatial displacements in nanodevices, and the incorporation of well-structured out-of-plane components
in two-dimensional arrays.

John H. Reif

Papers

DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires

Complexity of the Mover's Problem and Generalizations Extended Abstract

Logical computation using algorithmic self-assembly of DNA triple-crossover molecules

Complexity of the mover's problem and generalizations

Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes