Kinetic Theory Approach to Modeling of Cellular Repair Mechanisms under Genome Stress

Under acute perturbations from outer environment, a normal cell can trigger cellular self-defense mechanism in response to genome stress. To investigate the kinetics of cellular self-repair process at single cell level further, a model of DNA damage generating and repair is proposed under acute Ion Radiation (IR) by using mathematical framework of kinetic theory of active particles (KTAP). Firstly, we focus on illustrating the profile of Cellular Repair System (CRS) instituted by two sub-populations, each of which is made up of the active particles with different discrete states. Then, we implement the mathematical framework of cellular self-repair mechanism, and illustrate the dynamic processes of Double Strand Breaks (DSBs) and Repair Protein (RP) generating, DSB-protein complexes (DSBCs) synthesizing, and toxins accumulating. Finally, we roughly analyze the capability of cellular self-repair mechanism, cellular activity of transferring DNA damage, and genome stability, especially the different fates of a certain cell before and after the time thresholds of IR perturbations that a cell can tolerate maximally under different IR perturbation circumstances

Discovery (theoretical prediction and experimental observation) of a large-gap topological-insulator class with spin-polarized single-Dirac-cone on the surface

Recent theories and experiments have suggested that strong spin-orbit coupling effects in certain band insulators can give rise to a new phase of quantum matter, the so-called topological insulator, which can show macroscopic entanglement effects. Such systems feature two-dimensional surface states whose electrodynamic properties are described not by the conventional Maxwell equations but rather by an attached axion field, originally proposed to describe strongly interacting particles. It has been proposed that a topological insulator with a single spin-textured Dirac cone interfaced with a superconductor can form the most elementary unit for performing fault-tolerant quantum computation. Here we present an angle-resolved photoemission spectroscopy study and first-principle theoretical calculation-predictions that reveal the first observation of such a topological state of matter featuring a single-surface-Dirac-cone realized in the naturally occurring Bi$_2$Se$_3$ class of materials. Our results, supported by our theoretical predictions and calculations, demonstrate that undoped compound of this class of materials can serve as the parent matrix compound for the long-sought topological device where in-plane surface carrier transport would have a purely quantum topological origin. Our study further suggests that the undoped compound reached via n-to-p doping should show topological transport phenomena even at room temperature.Comment: 3 Figures, 18 pages, Submitted to NATURE PHYSICS in December 200

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2008-2009 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

The genome and transcriptome of Trichormus sp NMC-1: insights into adaptation to extreme environments on the Qinghai-Tibet Plateau

The Qinghai-Tibet Plateau (QTP) has the highest biodiversity for an extreme environment worldwide, and provides an ideal natural laboratory to study adaptive evolution. In this study, we generated a draft genome sequence of cyanobacteria Trichormus sp. NMC-1 in the QTP and performed whole transcriptome sequencing under low temperature to investigate the genetic mechanism by which T. sp. NMC-1 adapted to the specific environment. Its genome sequence was 5.9 Mb with a G+C content of 39.2% and encompassed a total of 5362 CDS. A phylogenomic tree indicated that this strain belongs to the Trichormus and Anabaena cluster. Genome comparison between T. sp. NMC-1 and six relatives showed that functionally unknown genes occupied a much higher proportion (28.12%) of the T. sp. NMC-1 genome. In addition, functions of specific, significant positively selected, expanded orthogroups, and differentially expressed genes involved in signal transduction, cell wall/membrane biogenesis, secondary metabolite biosynthesis, and energy production and conversion were analyzed to elucidate specific adaptation traits. Further analyses showed that the CheY-like genes, extracellular polysaccharide and mycosporine-like amino acids might play major roles in adaptation to harsh environments. Our findings indicate that sophisticated genetic mechanisms are involved in cyanobacterial adaptation to the extreme environment of the QTP

Topological Crystalline Insulators in the SnTe Material Class

Topological crystalline insulators are new states of matter in which the topological nature of electronic structures arises from crystal symmetries. Here we predict the first material realization of topological crystalline insulator in the semiconductor SnTe, by identifying its nonzero topological index. We predict that as a manifestation of this nontrivial topology, SnTe has metallic surface states with an even number of Dirac cones on high-symmetry crystal surfaces such as {001}, {110} and {111}. These surface states form a new type of high-mobility chiral electron gas, which is robust against disorder and topologically protected by reflection symmetry of the crystal with respect to {110} mirror plane. Breaking this mirror symmetry via elastic strain engineering or applying an in-plane magnetic field can open up a continuously tunable band gap on the surface, which may lead to wide-ranging applications in thermoelectrics, infrared detection, and tunable electronics. Closely related semiconductors PbTe and PbSe also become topological crystalline insulators after band inversion by pressure, strain and alloying.Comment: submitted on Feb. 10, 2012; to appear in Nature Communications; 5 pages, 4 figure

Massively parallel computing on an organic molecular layer

Current computers operate at enormous speeds of ~10^13 bits/s, but their principle of sequential logic operation has remained unchanged since the 1950s. Though our brain is much slower on a per-neuron base (~10^3 firings/s), it is capable of remarkable decision-making based on the collective operations of millions of neurons at a time in ever-evolving neural circuitry. Here we use molecular switches to build an assembly where each molecule communicates-like neurons-with many neighbors simultaneously. The assembly's ability to reconfigure itself spontaneously for a new problem allows us to realize conventional computing constructs like logic gates and Voronoi decompositions, as well as to reproduce two natural phenomena: heat diffusion and the mutation of normal cells to cancer cells. This is a shift from the current static computing paradigm of serial bit-processing to a regime in which a large number of bits are processed in parallel in dynamically changing hardware.Comment: 25 pages, 6 figure

An Unbiased ALMA Spectral Survey of the LkCa 15 and MWC 480 Protoplanetary Disks

The volatile contents of protoplanetary disks both set the potential for planetary chemistry and provide valuable probes of defining disk system characteristics such as stellar mass, gas mass, ionization, and temperature structure. Current disk molecular inventories are fragmented, however, giving an incomplete picture: unbiased spectral line surveys are needed to assess the volatile content. We present here an overview of such a survey of the protoplanetary disks around the Herbig Ae star MWC 480 and the T Tauri star LkCa 15 in ALMA Band 7, spanning ~36 GHz from 275 to 317 GHz and representing an order of magnitude increase in sensitivity over previous single-dish surveys. We detect 14 molecular species (including isotopologues), with five species (C34S, 13CS, H2CS, DNC, and C2D) detected for the first time in protoplanetary disks. Significant differences are observed in the molecular inventories of MWC 480 and LkCa 15, and we discuss how these results may be interpreted in light of the different physical conditions of these two disk systems

Superlattice in austenitic Ni-Mn-Ga shape memory microwires

The link between microstructure evolution, micromodulated domain and the structure transformation of Ni-Mn-Ga shape memory microwires prepared with rapid solidification is studied systematically by TEM and HRTEM. Multiple microdomain structures are determined according to the corresponding diffraction spots. The domain structure with a periodic distortion is a kind of characteristic of premartensitic phase. When cooling below the martensitic transformation temperature, the austenitic phase transforms to modulated 5M martensite, and the sequence of phase transformation can finally be confirmed from austenite to premartensite to 5M martensite during cooling. The characterization of micromodulated domain and the structure characteristics of austenite at atomic scale provide comprehensive understanding on the martensitic phase transformation route. (C) 2018 Published by Elsevier B.V.</p