Chaos in the BMN matrix model

We study classical chaotic motions in the Berenstein-Maldacena-Nastase (BMN) matrix model. For this purpose, it is convenient to focus upon a reduced system composed of two-coupled anharmonic oscillators by supposing an ansatz. We examine three ans\"atze: 1) two pulsating fuzzy spheres, 2) a single Coulomb-type potential, and 3) integrable fuzzy spheres. For the first two cases, we show the existence of chaos by computing Poincar\'e sections and a Lyapunov spectrum. The third case leads to an integrable system. As a result, the BMN matrix model is not integrable in the sense of Liouville, though there may be some integrable subsectors.Comment: 23 pages, 15 figures, v2: further clarifications and references adde

Chaotic strings in a near Penrose limit of AdS5×T1,1_5\times T^{1,1}

We study chaotic motions of a classical string in a near Penrose limit of AdS$_5\times T^{1,1}$. It is known that chaotic solutions appear on $R\times T^{1,1}$, depending on initial conditions. It may be interesting to ask whether the chaos persists even in Penrose limits or not. In this paper, we show that sub-leading corrections in a Penrose limit provide an unstable separatrix, so that chaotic motions are generated as a consequence of collapsed Kolmogorov-Arnold-Moser (KAM) tori. Our analysis is based on deriving a reduced system composed of two degrees of freedom by supposing a winding string ansatz. Then, we provide support for the existence of chaos by computing Poincare sections. In comparison to the AdS$_5\times T^{1,1}$ case, we argue that no chaos lives in a near Penrose limit of AdS$_5\times$S$^5$, as expected from the classical integrability of the parent system.Comment: 19 pages, 9 figures, LaTeX, v2: typos corrected and some clarifications adde

Fusing enzymes to transcription activator LuxR for the rapid creation of metabolite sensors

Metabolite sensors have been applied for high-throughput screening for improved biosynthetic pathways, as well as for dynamic control of the metabolic networks. Obviously, however, current repertoire of natural sensors covers only a small fraction of the known metabolite. We have been developing the new robust workflow for the rapid creation of metabolite sensors where biosynthetic enzymes can be adopted as the sensory (recognizing) components. Most of the known metabolites act as the direct substrates of some enzymes, and they are recognized and converted by these enzymes in physiologically relevant concentrations. Thus, ever-increasing repertoire of available enzymes is a rich and reliable source of sensory units. We found that the transcription activator LuxR can be fused with various biosynthetic enzymes without losing its function. By adding moderately de-stabilizing mutations, typically by random mutagenesis of the resultant fusion proteins followed by screening a small number (~100) of variants, we could have quickly isolated variants that can activate LuxR-dependent promoter in response to the substrates of the enzymes fused to LuxR. In this presentation, we demonstrate various metabolites can be detected by this manner. Detailed analysis of the thus-obtained fusion proteins indicated that function of LuxR is dependent on the substrate binding-induced stabilization of the enzymes. The biosensors with this mode of action exhibited various unique features. For instance, we found that the sensitivity (EC50) and dynamic range of these sensors to the target metabolites can be flexibly altered by the concentration of homoserine lactones, the cognate ligand of LuxR, in the media. Also, this provides unique opportunity to indirectly visualizing the substrate-binding to the enzyme in high-throughput manner. Indeed, multi-round mutagenesis and screening of the fusion protein of isopentenyl diphosphate isomerase (IDI) with LuxR variant (IDI-LuxR) revealed that many of the mutations that improved sensory performance of IDI-LuxR also elevated the catalytic performance of IDI. Some of such mutations turned out to elevate IDI activity even without fusion partner LuxR. Altogether, by fusing to LuxR, random mutagenesis, and traditional reporter (fluorescence)-based screening, one can not only adopt a variety of biosynthetic enzymes as sensor components but also laboratory evolve their catalytic functions

Non-Equilibrium Ionization States of GRB Environments

Iron spectral features are thought to be the best tracer of a progenitor of gamma-ray bursts (GRBs). The detections of spectral features such as an iron line and/or a Radiative Recombination edge and Continuum (RRC) were reported in four X-ray afterglows of GRBs. However their properties were different each other burst by burst. For example, Chandra observation of GRB 991216 reported both the strong H-like iron line together with its RRC. On the contrary, Yoshida et al. (2001) report only a detection of the strong RRC in GRB 970828 with ASCA. Since it is difficult to produce the strong RRC, we have to consider special condition for the line and/or the RRC forming region. In this paper, we point out a possibility of a ``non-equilibrium ionization state'' for the line and the RRC forming region.Comment: 10pages, 2figures. Accepted for ApJL. This is a companion paper by A.Yoshida et. a