Exponential Replication of Patterns in the Signal Tile Assembly Model

Chemical self-replicators are of considerable interest in the field of nanomanufacturing and as a model for evolution. We introduce the problem of self-replication of rectangular two-dimensional patterns in the practically motivated Signal Tile Assembly Model (STAM) [9]. The STAM is based on the Tile Assembly Model (TAM) which is a mathematical model of self-assembly in which DNA tile monomers may attach to other DNA tile monomers in a programmable way. More abstractly, four-sided tiles are assigned glue types to each edge, and self-assembly occurs when singleton tiles bind to a growing assembly, if the glue types match and the glue binding strength exceeds some threshold. The signal tile extension of the TAM allows signals to be propagated across assemblies to activate glues or break apart assemblies. Here, we construct a pattern replicator that replicates a two-dimensional input pattern over some fixed alphabet of size φ with O(φ) tile types, O(φ) unique glues, and a signal complexity of O(1). Furthermore, we show that this replication system displays exponential growth in n, the number of replicates of the initial patterned assembly

Generation of NSE-MerCreMer Transgenic Mice with Tamoxifen Inducible Cre Activity in Neurons

To establish a genetic tool for conditional deletion or expression of gene in neurons in a temporally controlled manner, we generated a transgenic mouse (NSE-MerCreMer), which expressed a tamoxifen inducible type of Cre recombinase specifically in neurons. The tamoxifen inducible Cre recombinase (MerCreMer) is a fusion protein containing Cre recombinase with two modified estrogen receptor ligand binding domains at both ends, and is driven by the neural-specific rat neural specific enolase (NSE) promoter. A total of two transgenic lines were established, and expression of MerCreMer in neurons of the central and enteric nervous systems was confirmed. Transcript of MerCreMer was detected in several non-neural tissues such as heart, liver, and kidney in these lines. In the background of the Cre reporter mouse strain Rosa26R, Cre recombinase activity was inducible in neurons of adult NSE-MerCreMer mice treated with tamoxifen by intragastric gavage, but not in those fed with corn oil only. We conclude that NSE-MerCreMer lines will be useful for studying gene functions in neurons for the conditions that Cre-mediated recombination resulting in embryonic lethality, which precludes investigation of gene functions in neurons through later stages of development and in adult

Tube Formation in Nanoscale Materials

The formation of tubular nanostructures normally requires layered, anisotropic, or pseudo-layered crystal structures, while inorganic compounds typically do not possess such structures, inorganic nanotubes thus have been a hot topic in the past decade. In this article, we review recent research activities on nanotubes fabrication and focus on three novel synthetic strategies for generating nanotubes from inorganic materials that do not have a layered structure. Specifically, thermal oxidation method based on gas–solid reaction to porous CuO nanotubes has been successfully established, semiconductor ZnS and Nb2O5nanotubes have been prepared by employing sacrificial template strategy based on liquid–solid reaction, and an in situ template method has been developed for the preparation of ZnO taper tubes through a chemical etching reaction. We have described the nanotube formation processes and illustrated the detailed key factors during their growth. The proposed mechanisms are presented for nanotube fabrication and the important pioneering studies are discussed on the rational design and fabrication of functional materials with tubular structures. It is the intention of this contribution to provide a brief account of these research activities

Exploring strategies to bias sequence in natural and synthetic oligomers and polymers

Millions of years of biological evolution have driven the development of highly sophisticated molecular machinery found within living systems. These systems produce polymers such as proteins and nucleic acids with incredible fidelity and function. In nature, the precise molecular sequence is the factor that determines the function of these macromolecules. Given that the ability to precisely define sequence emerges naturally, the fact that biology achieves unprecedented control over the unit sequence of the monomers through evolved enzymatic catalysis is incredible. Indeed, the ability to engineer systems that allow polymer synthesis with precise sequence control is a feat that technology is yet to replicate in artificial synthetic systems. This is the case because, without access to evolutionary control for finely tuned biological catalysts, the inability to correct errors or harness multiple competing processes means that the prospects for digital control of polymerization have been firmly bootstrapped to biological systems or limited to stepwise synthetic protocols. In this Account, we give an overview of strategies that have been used over the last 5 years in efforts to program polymer synthesis with sequence control in the laboratory. We also briefly explore how the use of robotics, algorithms, and stochastic chemical processes might lead to new understanding, mechanisms, and strategies to achieve full digital control. The aim is to see whether it is possible to go beyond bootstrapping to biological polymers or stepwise chemical synthesis. We start by describing nonenzymatic techniques used to obtain sequence-controlled natural polymers, a field that lends itself to direct application of insights gleaned from biology. We discuss major advances, such as the use of rotaxane-based molecular machines and templated approaches, including the utilization of biological polymers as templates for purely synthetic chains. We then discuss synthetic polymer chemistry, whose array of techniques allows the production of polymers with enormous structural and functional diversity, but so far with only limited control over the unit sequence itself. Synthetic polymers can be subdivided into multiple classes depending on the nature of processes used to synthesize them, such as by addition or condensation. Consequently, varied approaches for sequence control have been demonstrated in the area, including but not limited to click reactions, iterative solid-phase chemistry, and exploiting the chemical affinity of the monomers themselves. In addition to those, we highlight the importance of environmental bias in possible control of polymerization at the single-unit level, such as using catalyst switching or external stimuli. Even the most successful experimental sequence control approach needs appropriate tools to verify its scope and validity; therefore, we devote part of the present Account to possible analytical approaches to sequence readout, starting with well-established tandem mass spectrometry techniques and touching on those more applicable to specific classes of processes, such as diffusion-ordered NMR spectroscopy. Finally, we discuss progress in modeling and automation of sequence-controlled polymers. We postulate that developments in analytical chemistry, bioinformatics, and computer modeling will lead to new ways of exploring the development of new strategies for the realization of sequence control by means of sequence bias. This is the case because treating the assembly of polymers as a network of chemical reactions will enable the development of control strategies that can bias the outcome of the polymer assembly. The grand aim would be the synthesis of complex polymers in one step with a precisely defined digital sequence

Time-resolved powder X-ray diffraction of the solvothermal crystallization of cobalt gallate spinel photocatalyst reveals transient layered double hydroxides

High energy X-ray diffraction is used to follow in situ the crystallization of a cobalt gallate from metallic gallium under solvothermal conditions in an aminoalcohol, revealing the formation and decay of transient metastable layered double hydroxides. Photocatalytic studies show the spinel product has activity as a water oxidation catalyst for oxygen evolution