Recursiveness, Switching, and Fluctuations in a Replicating Catalytic Network

A protocell model consisting of mutually catalyzing molecules is studied in order to investigate how chemical compositions are transferred recursively through cell divisions under replication errors. Depending on the path rate, the numbers of molecules and species, three phases are found: fast switching state without recursive production, recursive production, and itinerancy between the above two states. The number distributions of the molecules in the recursive states are shown to be log-normal except for those species that form a core hypercycle, and are explained with the help of a heuristic argument.Comment: 4 pages (with 7 figures (6 color)), submitted to PR

Orbital-dependent modifications of electronic structure across magneto-structural transition in BaFe2As2

Laser angle-resolved photoemission spectroscopy (ARPES) is employed to investigate the temperature (T) dependence of the electronic structure in BaFe2As2 across the magneto-structural transition at TN ~ 140 K. A drastic transformation in Fermi surface (FS) shape across TN is observed, as expected by first-principles band calculations. Polarization-dependent ARPES and band calculations consistently indicate that the observed FSs at kz ~ pi in the low-T antiferromagnetic (AF) state are dominated by the Fe3dzx orbital, leading to the two-fold electronic structure. These results indicate that magneto-structural transition in BaFe2As2 accompanies orbital-dependent modifications in the electronic structure.Comment: 13 pages, 4 figures. accepted by Physical Review Letter

Doping-dependence of nodal quasiparticle properties in high-TcT_{\rm c} cuprates studied by laser-excited angle-resolved photoemission spectroscopy

We investigate the doping dependent low energy, low temperature ($T$ = 5 K) properties of nodal quasiparticles in the d-wave superconductor Bi$_{2.1}$Sr$_{1.9}$CaCu$_2$O$_{8+\delta}$ (Bi2212). By utilizing ultrahigh resolution laser-excited angle-resolved photoemission spectroscopy, we obtain precise band dispersions near $E_{F}$, mean free paths and scattering rates ($\Gamma$) of quasiparticles. For optimally and overdoped, we obtain very sharp quasiparticle peaks of 8 meV and 6 meV full-width at half-maximum, respectively, in accord with terahertz conductivity. For all doping levels, we find the energy-dependence of $\Gamma \sim |\omega |$, while $\Gamma$($\omega =0$) shows a monotonic increase from overdoping to underdoping. The doping dependence suggests the role of electronic inhomogeneity on the nodal quasiparticle scattering at low temperature (5 K \lsim 0.07T_{\rm c}), pronounced in the underdoped region

Transitions Induced by the Discreteness of Molecules in a Small Autocatalytic System

Autocatalytic reaction system with a small number of molecules is studied numerically by stochastic particle simulations. A novel state due to fluctuation and discreteness in molecular numbers is found, characterized as extinction of molecule species alternately in the autocatalytic reaction loop. Phase transition to this state with the change of the system size and flow is studied, while a single-molecule switch of the molecule distributions is reported. Relevance of the results to intracellular processes are briefly discussed.Comment: 5 pages, 4 figure

Bulk and surface-sensitive high-resolution photoemission study of Mott-Hubbard systems SrVO3_3 and CaVO3_3

We study the electronic structure of Mott-Hubbard systems SrVO$_{3}$ and CaVO$_3$ with bulk and surface-sensitive high-resolution photoemission spectroscopy (PES), using a VUV laser, synchrotron radiation and a discharge lamp ($h\nu$ = 7 - 21 eV). A systematic suppression of the density of states (DOS) within $\sim$ 0.2 eV of the Fermi level ($E_F$) is found on decreasing photon energy i.e. on increasing bulk sensitivity. The coherent band in SrVO$_{3}$ and CaVO$_3$ is shown to consist of surface and bulk derived features, separated in energy. The stronger distortion on surface of CaVO$_{3}$ compared to SrVO$_{3}$ leads to higher surface metallicity in the coherent DOS at $E_F$, consistent with recent theory.Comment: 4 pages 5 figures (including 2 auxiliary figures); A complete analysis of the spectra based on the surface and bulk analysis shows in auxiliary figures Fig. A1 and A

Creation and Reproduction of Model Cells with Semipermeable Membrane

A high activity of reactions can be confined in a model cell with a semipermeable membrane in the Schl\"ogl model. It is interpreted as a model of primitive metabolism in a cell. We study two generalized models to understand the creation of primitive cell systems conceptually from the view point of the nonlinear-nonequilibrium physics. In the first model, a single-cell system with a highly active state confined by a semipermeable membrane is spontaneously created from an inactive homogeneous state by a stochastic jump process. In the second model, many cell structures are reproduced from a single cell, and a multicellular system is created.Comment: 11 pages, 7 figure

Nonlinearity of Mechanochemical Motions in Motor Proteins

The assumption of linear response of protein molecules to thermal noise or structural perturbations, such as ligand binding or detachment, is broadly used in the studies of protein dynamics. Conformational motions in proteins are traditionally analyzed in terms of normal modes and experimental data on thermal fluctuations in such macromolecules is also usually interpreted in terms of the excitation of normal modes. We have chosen two important protein motors - myosin V and kinesin KIF1A - and performed numerical investigations of their conformational relaxation properties within the coarse-grained elastic network approximation. We have found that the linearity assumption is deficient for ligand-induced conformational motions and can even be violated for characteristic thermal fluctuations. The deficiency is particularly pronounced in KIF1A where the normal mode description fails completely in describing functional mechanochemical motions. These results indicate that important assumptions of the theory of protein dynamics may need to be reconsidered. Neither a single normal mode, nor a superposition of such modes yield an approximation of strongly nonlinear dynamics.Comment: 10 pages, 6 figure

Photoelectron Angular Distributions for Two-photon Ionization of Helium by Ultrashort Extreme Ultraviolet Free Electron Laser Pulses

Phase-shift differences and amplitude ratios of the outgoing $s$ and $d$ continuum wave packets generated by two-photon ionization of helium atoms are determined from the photoelectron angular distributions obtained using velocity map imaging. Helium atoms are ionized with ultrashort extreme-ultraviolet free-electron laser pulses with a photon energy of 20.3, 21.3, 23.0, and 24.3 eV, produced by the SPring-8 Compact SASE Source test accelerator. The measured values of the phase-shift differences are distinct from scattering phase-shift differences when the photon energy is tuned to an excited level or Rydberg manifold. The difference stems from the competition between resonant and non-resonant paths in two-photon ionization by ultrashort pulses. Since the competition can be controlled in principle by the pulse shape, the present results illustrate a new way to tailor the continuum wave packet.Comment: 5 pages, 1 table, 3 figure