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Electromagnetic radiation within the terahertz (THz) frequency range is of great interest for applications in remote sensing and time-domain spectroscopy. The laser-induced plasmas are promising mediums for generating THz radiation. It has been recently reported that focusing femtosecond Bessel pulses inside dielectrics induces a high aspect ratio over-critical plasmas. Here we show that the intense resonantly driven electrostatic fields at the so-called critical surface lead to THz radiation emission. Through three-dimensional particle-in-cell simulation and analytical derivation, we have investigated the emission of THz radiation. We show that the THz radiation is associated with a hot population of electrons trapped in ambipolar electric fields of the double layers., Comment: 10 pages, 4 figures, accepted for Physics of Plasmas

We examine the temporary evolution of axisymmetric magnetospheres around rapidly rotating black holes (BHs), by applying our two-dimensional particle-in-cell simulation code. Assuming a stellar-mass BH, we find that the created pairs fail to screen the electric field along the magnetic field, provided that the mass accretion rate is much small compared to the Eddington limit. Magnetic islands are created by reconnection near the equator and migrate toward the event horizon, expelling magnetic flux tubes from the BH vicinity during a large fraction of time. When the magnetic islands stick to the horizon due to redshift and virtually vanish, a strong magnetic field penetrates the horizon, enabling efficient extraction of energy from the BH. During this flaring phase, a BH gap appears around the inner light surface with a strong meridional return current toward the equator within the ergosphere. If the mass accretion rate is 0.025 percent of the Eddington limit, the BH's spin-down luminosity becomes 16-19 times greater than its analytical estimate during the flares, although its long-term average is only 6 percent of it. We demonstrate that the extracted energy flux concentrates along the magnetic field lines threading the horizon in the middle latitudes. It is implied that this meridional concentration of the Poynting flux may result in the formation of limb-brightened jets from low-accreting BH systems., Comment: Accepted for publication in ApJ; 25 pages, 17 figures, 1 movie (fig. 8, 18MB, filename=Aph_Npe_515.gif)

We investigate the temporal evolution of an axisymmetric magnetosphere around a rapidly rotating, stellar-mass black hole, applying a two-dimensional particle-in-cell simulation scheme. Adopting a homogeneous pair production, and assuming that the mass accretion rate is much less than the Eddington limit, we find that the black hole's rotational energy is preferentially extracted from the middle latitudes, and that this outward energy flux exhibits an enhancement that lasts approximately 160 dynamical time scales. It is demonstrated that the magnetohydrodynamic approximations cannot be justified in such a magnetically-dominated magnetosphere, because the Ohm's law completely breaks down, and because the charge-separated electron-positron plasmas are highly non-neutral. An implication is given regarding the collimation of relativistic jets., Comment: 32 pages, 12 figures; accepted for publication in ApJ

In this study we investigate jet interaction at a microscopic level in a cosmological environment, which responds to a key open question in the study of relativistic jets. Using small simulation systems during prior research, we initially studied the evolution of both electron-proton and electron-positron relativistic jets containing helical magnetic fields, by focusing on their interactions with an ambient plasma. Here, using larger jet radii, we have performed simulations of global jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability (kKHI) and the Mushroom instability (MI). We found that the evolution of global jets strongly depends on the size of the jet radius. For example, phase bunching of jet electrons, in particular in the electron-proton jet, is mixed with larger jet radius due to the more complicated structures of magnetic fields with excited kinetic instabilities. In our simulation study these kinetic instabilities lead to new types of instabilities in global jets. In the electron-proton jet simulation a modified recollimation occurs and jet electrons are strongly perturbed. In the electron-positron jet simulation mixed kinetic instabilities occur at early times followed by a turbulence-like structure. Simulations using much larger (and longer) systems are further required in order to thoroughly investigate the evolution of global jets containing helical magnetic fields., Comment: 7 pages, 4 figures, submitted to special issue "Polarised Emission from Astrophysical Jets", June 12-16, 2017, Ierapetra, Greece. arXiv admin note: substantial text overlap with arXiv:1609.09363

The epigenome, i.e. the whole of chromatin modifications, is transferred from mother to daughter cells during cell differentiation. When de novo chromatin modifications (establishment or erasure of, respectively, new or pre-existing DNA methylations and/or histone modifications) are made in a daughter cell, however, it has a different epigenome than its mother cell. Although de novo chromatin modifications are an important event that comprises elementary processes of cell differentiation, its molecular mechanism remains poorly understood. We argue in this Letter that a key to solving this problem lies in understanding the role of long non-coding RNAs (lncRNAs)- a type of RNA that is becoming increasingly prominent in epigenetic studies. Many studies show that lncRNAs form ribonucleo-protein complexes in the nucleus and are involved in chromatin modifications. However, chromatin-modifying enzymes lack the information about genomic positions on which they act. It is known, on the other hand, that a single-stranded RNA in general can bind to a double-stranded DNA to form a triple helix. If each lncRNA forms a ribonucleo-protein complex with chromatin-modifying enzymes on one hand and, at the same time, a triple helix with a genomic region based on its specific nucleotide sequence on the other hand, it can induce de novo chromatin modifications at specific sites. Thus, the great variety of lncRNAs can be explained by the requirement for the diversity of "genomic address codes" specific to their cognate genomic regions where de novo chromatin modifications take place., Comment: 12 pages, 1 figure

We study the interaction of relativistic jets with their environment, using 3-dimensional relativistic particle-in-cell simulations for two cases of jet composition: (i) electron-proton ($e^{-}-p^{+}$) and (ii) electron-positron ($e^{\pm}$) plasmas containing helical magnetic fields. We have performed simulations of "global" jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability and the Mushroom instability. We have found that these kinetic instabilities are suppressed and new types of instabilities can grow. For the $e^{-}-p^{+}$ jet, a recollimation-like instability occurs and jet electrons are strongly perturbed, whereas for the $e^{\pm}$ jet, a recollimation-like instability occurs at early times followed by kinetic instability and the general structure is similar to a simulation without a helical magnetic field. We plan to perform further simulations using much larger systems to confirm these new findings., Comment: 4 pages, 1 figure, New Frontiers in Black Hole Astrophysics, Proceedings of the IAU Symposium No. 324, A. Gomboc, ed

In the study of relativistic jets one of the key open questions is their interaction with the environment on the microscopic level. Here, we study the initial evolution of both electron$-$proton ($e^{-}-p^{+}$) and electron$-$positron ($e^{\pm}$) relativistic jets containing helical magnetic fields, focusing on their interaction with an ambient plasma. We have performed simulations of "global" jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability (kKHI) and the Mushroom instability (MI). In our initial simulation study these kinetic instabilities are suppressed and new types of instabilities can grow. In the $e^{-}-p^{+}$ jet simulation a recollimation-like instability occurs and jet electrons are strongly perturbed. In the $e^{\pm}$ jet simulation a recollimation-like instability occurs at early times followed by a kinetic instability and the general structure is similar to a simulation without helical magnetic field. Simulations using much larger systems are required in order to thoroughly follow the evolution of global jets containing helical magnetic fields., Comment: 9 pages, 6 figures, Blazars through Sharp Multi-Wavelength Eyes. Malaga (Spain). 30 May - 3 June 2016, movie is available at http://www.mpdi.com/link, Video S1

The course of non-thermal electron ejection in relativistic unmagnetized electron-ion shocks is investigated by performing self-consistent particle-in-cell simulations. The shocks are excited through the injection of relativistic jet into ambient plasma, leading to two distinct shocks (named as the trailing shock and leading shock) and a contact discontinuity. The Weibel-like instabilities heat the electrons up to approximately half of ion kinetic energy. The double layers formed in the trailing and leading edges then accelerated the electrons by the ion kinetic energy. The electron distribution function in the leading edge shows a clear non-thermal power-law tail which contains $\sim1\%$ of electrons and $\sim8\%$ of electron energy. Its power-law index is -2.6. The acceleration efficiency is $\sim23\%$ by number and $\sim50\%$ by energy and the power-law index is -1.8 for electron distribution function in the trailing edge. The effect of the dimensionality is examined by comparing results of 3D simulation with 2D ones. It exhibits that the electron acceleration is more efficient in 2D., Comment: 15 pages, 17 figurs, and one table. Accepted for publication in The Astrophysical Journal

For parameters that are applicable to the conditions at young supernova remnants, we present results of 2D3V particle-in-cell simulations of a non-relativistic plasma shock with a large-scale perpendicular magnetic field inclined at 45-deg angle to the simulation plane to approximate 3D physics. We developed an improved clean setup that uses the collision of two plasma slabs with different density and velocity, leading to the development of two distinctive shocks and a contact discontinuity. The shock formation is mediated by Weibel-type filamentation instabilities that generate magnetic turbulence. Cyclic reformation is observed in both shocks with similar period, for which we note global variations on account of shock rippling and local variations arising from turbulent current filaments. The shock rippling occurs on spatial and temporal scales given by gyro-motions of shock-reflected ions. The drift motion of electrons and ions is not a gradient drift, but commensurates with E x B drift. We observe a stable suprathermal tail in the ion spectra, but no electron acceleration because the amplitude of Buneman modes in the shock foot is insufficient for trapping relativistic electrons. We see no evidence of turbulent reconnection. A comparison with other 2D simulation results suggests that the plasma beta and the ion-to-electron mass ratio are not decisive for efficient electron acceleration, but pre-acceleration efficacy might be reduced with respect to the 2D results once three-dimensional effects are fully accounted for. Other microphysical factors may also be at play to limit the amplitude of Buneman waves or prevent return of electrons to the foot region., Comment: Astrophysical Journal, in press, some figures with low resolution

A study of collisionless external shocks in gamma-ray bursts is presented. The shock structure, electromagnetic fields, and process of electron acceleration are assessed by performing a self-consistent 3D particle-in-cell (PIC) simulation. In accordance with hydrodynamic shock systems, the shock consists of a reverse shock (RS) and forward shock (FS) separated by a contact discontinuity (CD). The development and structure are controlled by the ion Weibel instability. The ion filaments are sources of strong transverse electromagnetic fields at both sides of the double shock structure over a length of 30 - 100 ion skin depths. Electrons are heated up to a maximum energy $\epsilon_{\rm ele}\approx \sqrt{\epsilon_{\rm b}}$, where $\epsilon$ is the energy normalized to the total incoming energy. Jet electrons are trapped in the RS transition region due to the presence of an ambipolar electric field and reflection by the strong transverse magnetic fields in the shocked region. In a process similar to shock surfing acceleration (SSA) for ions, electrons experience drift motion and acceleration by ion filament transverse electric fields in the plane perpendicular to the shock propagation direction. Ultimately accelerated jet electrons are convected back into the upstream., Comment: 17 pages, 6 figures, Accepted for publication in The Astrophysical Journal

We have performed two-dimensional special-relativistic magnetohydrodynamic simulations of non-equilibrium over-pressured relativistic jets in cylindrical geometry. Multiple stationary recollimation shock and rarefaction structures are produced along the jet by the nonlinear interaction of shocks and rarefaction waves excited at the interface between the jet and the surrounding ambient medium. Although initially the jet is kinematically dominated, we have considered axial, toroidal and helical magnetic fields to investigate the effects of different magnetic-field topologies and strengths on the recollimation structures. We find that an axial field introduces a larger effective gas-pressure and leads to stronger recollimation shocks and rarefactions, resulting in larger flow variations. The jet boost grows quadratically with the initial magnetic field. On the other hand, a toroidal field leads to weaker recollimation shocks and rarefactions, modifying significantly the jet structure after the first recollimation rarefaction and shock. The jet boost decreases systematically. For a helical field, instead, the behaviour depends on the magnetic pitch, with a phenomenology that ranges between the one seen for axial and toroidal magnetic fields, respectively. In general, however, a helical magnetic field yields a more complex shock and rarefaction substructure close to the inlet that significantly modifies the jet structure. The differences in shock structure resulting from different field configurations and strengths may have observable consequences for disturbances propagating through a stationary recollimation shock., Comment: 14 pages, 15 figures and 1 table, accepted for publication in ApJ

We have investigated the influence of velocity shear and a radial density profile on the spatial development of the current driven kink instability along helically magnetized relativistic jets via three-dimensional relativistic magnetohydrodynamic simulations. In this study, we use a non-periodic computational box, the jet flow is initially established across the computational grid, and a precessional perturbation at the inlet triggers growth of the kink instability. If the velocity shear radius is located inside the characteristic radius of the helical magnetic field, a static non-propagating current driven kink is excited as the perturbation propagates down the jet. Temporal growth disrupts the initial flow across the computational grid not too far from the inlet. On the other hand, if the velocity shear radius is outside the characteristic radius of the helical magnetic field, the kink is advected with the flow and grows spatially down the jet. In this case flow is maintained to much larger distances from the inlet. The effect of different radial density profiles is more subtle. When the density increases with radius, the kink appears to saturate by the end of the simulation without apparent disruption of the helical twist. This behavior suggests that relativistic jets consisting of a tenuous spine surrounded by a denser medium with a velocity shear radius outside the radius of maximum toroidal magnetic field have a relatively stable configuration., Comment: 31 pages, 8 figures, and 2 tables, accepted for publication in ApJ

We have investigated via two-dimensional relativistic MHD simulations the long-term evolution of turbulence created by a relativistic shock propagating through an inhomogeneous medium. In the postshock region, magnetic field is strongly amplified by turbulent motions triggered by preshock density inhomogeneities. Using a long-simulation box we have followed the magnetic-field amplification until it is fully developed and saturated. The turbulent velocity is sub-relativistic even for a strong shock. Magnetic-field amplification is controled by the turbulent motion and saturation occurs when the magnetic energy is comparable to the turbulent kinetic energy. Magnetic-field amplification and saturation depend on the initial strength and direction of the magnetic field in the preshock medium, and on the shock strength. If the initial magnetic field is perpendicular to the shock normal, the magnetic field is first compressed at the shock and then can be amplified by turbulent motion in the postshock region. Saturation occurs when the magnetic energy becomes comparable to the turbulent kinetic energy in the postshock region. If the initial magnetic field in the preshock medium is strong, the postshock region becomes turbulent but significant field amplification does not occur. If the magnetic energy after shock compression is larger than the turbulent kinetic energy in the postshock region, significant field amplification does not occur. We discuss possible applications of our results to gamma-ray bursts and active galactic nuclei., Comment: 14 pages, 15 figures, accepted for publication in MNRAS

The Weismann barrier, or the impossibility of inheritance of acquired traits, comprises a foundation of modern biology, and it has been a major obstacle in establishing the connection between evolution and ontogenesis. We propose the cooperative model based on the assumption that evolution is achieved by a cooperation between genetic mutations and acquired changes (phenotypic plasticity). It is also assumed in this model that natural selection operates on phenotypes, rather than genotypes, of individuals, and that the relationship between phenotypes and genotypes is one-to-many. In the simulations based on these assumptions, individuals exhibited phenotypic changes in response to an environmental change, corresponding multiple genetic mutations were increasingly accumulated in individuals in the population, and phenotypic plasticity was gradually replaced with genetic mutations. This result suggests that Lamarck's law of use and disuse can effectively hold without conflicting the Weismann barrier, and thus evolution can be logically connected with ontogenesis., Comment: 23 pages, 1 figure

We have investigated the influence of jet rotation and differential motion on the linear and nonlinear development of the current-driven (CD) kink instability of force-free helical magnetic equilibria via three-dimensional relativistic magnetohydrodynamic simulations. In this study, we follow the temporal development within a periodic computational box. Displacement of the initial helical magnetic field leads to the growth of the CD kink instability. We find that, in accord with linear stability theory, the development of the instability depends on the lateral distribution of the poloidal magnetic field. If the poloidal field significantly decreases outwards from the axis, the initial small perturbations grow strongly, and if multiple wavelengths are excited non-linear interaction eventually disrupts the initial cylindrical configuration. When the profile of the poloidal field is shallow, the instability develops slowly and eventually saturates. We briefly discuss implications of our findings for Poynting dominated jets., Comment: 30 pages, 11 figures, and 1 table, accepted to ApJ

We have investigated the influence of a velocity shear surface on the linear and non-linear development of the CD kink instability of force-free helical magnetic equilibria in 3D. In this study we follow the temporal development within a periodic computational box and concentrate on flows that are sub-Alfvenic on the cylindrical jet's axis. Displacement of the initial force-free helical magnetic field leads to the growth of CD kink instability. We find that helically distorted density structure propagates along the jet with speed and flow structure dependent on the radius of the velocity shear surface relative to the characteristic radius of the helically twisted force-free magnetic field. At small velocity shear surface radius the plasma flows through the kink with minimal kink propagation speed. The kink propagation speed increases as the velocity shear radius increases and the kink becomes more embedded in the plasma flow. A decreasing magnetic pitch profile and faster flow enhance the influence of velocity shear. Simulations show continuous transverse growth in the nonlinear phase of the instability. The growth rate of the CD kink instability and the nonlinear behavior also depend on the velocity shear surface radius and flow speed, and the magnetic pitch radial profile. Larger velocity shear radius leads to slower linear growth, makes a later transition to the nonlinear stage, and with larger maximum amplitude than occur for a static plasma column. However, when the velocity shear radius is much greater than the characteristic radius of the helical magnetic field, linear and non-linear development can be similar to the development of a static plasma column., Comment: 38 pages, 18 figures, accepted for publication in ApJ

We have investigated the relaxation of a hydrostatic hot plasma column containing toroidal magnetic field by the Current-Driven (CD) kink instability as a model of pulsar wind nebulae. In our simulations the CD kink instability is excited by a small initial velocity perturbation and develops turbulent structure inside the hot plasma column. We demonstrate that, as envisioned by Begelman, the hoop stress declines and the initial gas pressure excess near the axis decreases. The magnetization parameter \sigma, the ratio of the Poynting to the kinetic energy flux, declines from an initial value of 0.3 to about 0.01 when the CD kink instability saturates. Our simulations demonstrate that axisymmetric models strongly overestimate the elongation of the pulsar wind nebulae. Therefore, the previous requirement for an extremely low pulsar wind magnetization can be abandoned. The observed structure of the pulsar wind nebulae do not contradict the natural assumption that the magnetic energy flux still remains a good fraction of the total energy flux after dissipation of alternating fields., Comment: 14 pages, 5 figures, accepted for publication in ApJ

We perform two-dimensional relativistic magnetohydrodynamic simulations of a mildly relativistic shock propagating through an inhomogeneous medium. We show that the postshock region becomes turbulent owing to preshock density inhomogeneity, and the magnetic field is strongly amplified due to the stretching and folding of field lines in the turbulent velocity field. The amplified magnetic field evolves into a filamentary structure in two-dimensional simulations. The magnetic energy spectrum is flatter than the Kolmogorov spectrum and indicates that a so-called small-scale dynamo is occurring in the postshock region. We also find that the amount of magnetic-field amplification depends on the direction of the mean preshock magnetic field, and the time scale of magnetic-field growth depends on the shock strength., Comment: 22 pages, 9 figures, accepted for publication in ApJ

An algorithm is presented that incorporates the tensor form of Maxwell's equations in a general relativistic electromagnetic particle-in-cell code. The code simplifies to Schwartzschild space-time for a non-spinning central mass. The particle advance routine uses a fourth-order Runge-Kutta algorithm to integrate the four-velocity form of Lorentz force. The current density is calculated using the curved space-time of the metric., Comment: 17 pages, 8 figures

We have investigated the development of current-driven (CD) kink instability through three-dimensional relativistic MHD simulations. A static force-free equilibrium helical magnetic configuration is considered in order to study the influence of the initial configuration on the linear and nonlinear evolution of the instability. We found that the initial configuration is strongly distorted but not disrupted by the kink instability. The instability develops as predicted by linear theory. In the non-linear regime the kink amplitude continues to increase up to the terminal simulation time, albeit at different rates, for all but one simulation. The growth rate and nonlinear evolution of the CD kink instability depends moderately on the density profile and strongly on the magnetic pitch profile. The growth rate of the kink mode is reduced in the linear regime by an increase in the magnetic pitch with radius and the non-linear regime is reached at a later time than for constant helical pitch. On the other hand, the growth rate of the kink mode is increased in the linear regime by a decrease in the magnetic pitch with radius and reaches the non-linear regime sooner than the case with constant magnetic pitch. Kink amplitude growth in the non-linear regime for decreasing magnetic pitch leads to a slender helically twisted column wrapped by magnetic field. On the other hand, kink amplitude growth in the non-linear regime nearly ceases for increasing magnetic pitch., Comment: 24 pages, 10 figures, and 1 table, submitted to ApJ

We solve the Riemann problem for the deceleration of an arbitrarily magnetized relativistic flow injected into a static unmagnetized medium in one dimension. We find that for the same initial Lorentz factor, the reverse shock becomes progressively weaker with increasing magnetization \sigma (the Poynting-to kinetic energy flux ratio), and the shock becomes a rarefaction wave when \sigma exceeds a critical value, \sigma_c, defined by the balance between the magnetic pressure in the flow and the thermal pressure in the forward shock. In the rarefaction wave regime, we find that the rarefied region is accelerated to a Lorentz factor that is significantly larger than the initial value. This acceleration mechanism is due to the strong magnetic pressure in the flow. We discuss the implications of these results for models of gamma-ray bursts and active galactic nuclei., Comment: 13 pages, 3 figures, Accepted to publication in ApJ Letters

We performed relativistic magnetohydrodynamic simulations of the hydrodynamic boosting mechanism for relativistic jets explored by Aloy & Rezzolla (2006) using the RAISHIN code. Simulation results show that the presence of a magnetic field changes the properties of the shock interface between the tenuous, overpressured jet ($V^z_j$) flowing tangentially to a dense external medium. Magnetic fields can lead to more efficient acceleration of the jet, in comparison to the pure-hydrodynamic case. A ``poloidal'' magnetic field ($B^z$), tangent to the interface and parallel to the jet flow, produces both a stronger outward moving shock and a stronger inward moving rarefaction wave. This leads to a large velocity component normal to the interface in addition to acceleration tangent to the interface, and the jet is thus accelerated to larger Lorentz factors than those obtained in the pure-hydrodynamic case. Likewise, a strong ``toroidal'' magnetic field ($B^y$), tangent to the interface but perpendicular to the jet flow, also leads to stronger acceleration tangent to the shock interface relative to the pure-hydrodynamic case. Overall, the acceleration efficiency in the ``poloidal'' case is less than that of the ``toroidal'' case but both geometries still result in higher Lorentz factors than the pure-hydrodynamic case. Thus, the presence and relative orientation of a magnetic field in relativistic jets can significant modify the hydrodynamic boost mechanism studied by Aloy & Rezzolla (2006)., Comment: 25 pages, 10 figures, accepted for publication in ApJ

We investigate here the effects of plasma instabilities driven by rapid electron/positron pair cascades, which arise in the environment of GRB sources as a result of back-scattering of a seed fraction of the original spectrum. The injection of electron/positron pairs induces strong streaming motions in the ambient medium. One therefore expects the pair-enriched medium ahead of the forward shock to be strongly sheared on length scales comparable to the radiation front thickness. Using three-dimensional particle-in-cell simulations, we show that plasma instabilities driven by these streaming electron/positron pairs are responsible for the excitation of near-equipartition, turbulent magnetic fields. Our results reveal the importance of the electromagnetic filamentation instability in ensuring an effective coupling between electron/positron pairs and ions, and may help explain the origin of large upstream fields in GRB shocks., Comment: ApJ in press, 13 pages, 9 figs

A new general relativistic magnetohydrodynamics (GRMHD) code ``RAISHIN'' used to simulate jet generation by rotating and non-rotating black holes with a geometrically thin Keplarian accretion disk finds that the jet develops a spine-sheath structure in the rotating black hole case. Spine-sheath structure and strong magnetic fields significantly modify the Kelvin-Helmholtz (KH) velocity shear driven instability. The RAISHIN code has been used in its relativistic magnetohydrodynamic (RMHD) configuration to study the effects of strong magnetic fields and weakly relativistic sheath motion, c/2, on the KH instability associated with a relativistic, Lorentz factor equal 2.5, jet spine-sheath interaction. In the simulations sound speeds up to c/1.7 and Alfven wave speeds up to 0.56 c are considered. Numerical simulation results are compared to theoretical predictions from a new normal mode analysis of the RMHD equations. Increased stability of a weakly magnetized system resulting from c/2 sheath speeds and stabilization of a strongly magnetized system resulting from c/2 sheath speeds is found., Comment: 5 pages, 5 figures, accepted for publication in Astrophysics and Space Science

Multicanonical molecular dynamics (MD) is a powerful technique for sampling conformations on rugged potential surfaces such as protein. However, it is notoriously difficult to estimate the multicanonical temperature effectively. Wang and Landau developed a convenient method for estimating the density of states based on a multicanonical Monte Carlo method. In their method, the density of states is calculated autonomously during a simulation. In this paper we develop a set of techniques to effectively apply the Wang-Landau method to MD simulations. In the multicanonical MD, the estimation of the derivative of the density of states is critical. In order to estimate it accurately, we devise two original improvements. First, the correction for the density of states is made smooth by using the Gaussian distribution obtained by a short canonical simulation. Second, an approximation is applied to the derivative, which is based on the Gaussian distribution and the multiple weighted histogram technique. A test of this method was performed with small polypeptides, Met-enkephalin and Trp-cage, and it is demonstrated that Wang-Landau MD is consistent with replica exchange MD but can sample much larger conformational space., Comment: 8 pages, 7 figures, accepted for publication in Physical Review E

Numerical simulations of weakly magnetized and strongly magnetized relativistic jets embedded in a weakly magnetized and strongly magnetized stationary or weakly relativistic (v = c/2) sheath have been performed. A magnetic field parallel to the flow is used in these simulations performed by the new GRMHD numerical code RAISHIN used in its RMHD configuration. In the numerical simulations the Lorentz factor $\gamma = 2.5$ jet is precessed to break the initial equilibrium configuration. In the simulations sound speeds are $\lesssim c/\sqrt 3$ in the weakly magnetized simulations and $\lesssim 0.3c$ in the strongly magnetized simulations. The Alfven wave speed is $\lesssim 0.07c$ in the weakly magnetized simulations and $\lesssim 0.56c$ in the strongly magnetized simulations. The results of the numerical simulations are compared to theoretical predictions from a normal mode analysis of the linearized relativistic magnetohydrodynamic (RMHD) equations capable of describing a uniform axially magnetized cylindrical relativistic jet embedded in a uniform axially magnetized relativistically moving sheath. The theoretical dispersion relation allows investigation of effects associated with maximum possible sound speeds, Alfven wave speeds near light speed and relativistic sheath speeds. The prediction of increased stability of the weakly magnetized system resulting from c/2 sheath speeds and the stabilization of the strongly magnetized system resulting from c/2 sheath speeds is verified by the numerical simulation results., Comment: 31 pages, 8 figures, accepted for publicatin in ApJ. A paper with high resolution figures available at http://gammaray.nsstc.nasa.gov/~mizuno/research_new.html

The formation mechanism of operons remains controversial despite the proposal of many models. Although acquisition of genes from other species, horizontal gene transfer, is considered to occur, definitive concrete cases have been unavailable. It is desirable to select horizontally transferred genes reliably and examine their relationship to operons. We here developed a method to identify candidates of horizontally transferred genes based on minimization of gene cluster insertions/deletions. To select a benchmark set of positively horizontally transferred genes against which the candidate set can be appraised, we devised another procedure using intergenetic alignments. Comparison with the benchmark set of horizontally transferred genes demonstrated the absence of a significant number of false positives in the candidates, showing that the method identifies horizontally transferred genes with a high degree of confidence. Horizontally transferred genes constitute at least 5.5% of the genes in Escherichia, Shigella, and Salmonella and ~46% of which originate from other gamma-proteobacteria. Not only informational genes, but also operational genes (those involved in housekeeping) are horizontally transferred less frequently than expected. A gene-cluster analysis of Escherichia coli K-12 operons revealed that horizontal transfer produced four entire operons and expanded two operons, but deletion of intervening genes accounts for the formation of no operons. We propose that operons generally form by horizontal gene transfer. We further suggest that genes with related essential functions tend to reside in conserved operons, while genes in nonconserved operons generally confer slight advantage to the organisms and frequently undergo horizontal transfer and decay., Comment: 22 pages, 7 figures

We have performed several simulations of black hole systems (non-rotating, black hole spin parameter a=0.0 and rapidly rotating, a=0.95) with a geometrically thin Keplerian disk using the newly developed RAISHIN code. The simulation results show the formation of jets driven by the Lorentz force and the gas pressure gradient. The jets have mildly relativistic speed (\sim 0.4c). The matter is continuously supplied from the accretion disk and the jet propagates outward until each applicable terminal simulation time (non-rotating: t/\tau_S = 275 and rotating: t/tau_S = 200, \tau_S \equiv r_S/c). It appears that a rotating black hole creates an additional, faster, and more collimated matter-dominated inner outflow (\sim 0.5c) formed and accelerated by the twisted magnetic field resulting from frame-dragging in the black hole ergosphere. This is the first known simulation confirming the formation of an inner magnetically-driven, matter-dominated jet by the frame-dragging effect from a black hole co-rotating with a thin Keplerian disk threaded by a vertical magnetic field. This result indicates that jet kinematic structure depends on black hole rotation and on the initial magnetic field configuration and strength., Comment: 12 pages, 3 figures, revised version based on referee's comments

We have developed a new three-dimensional general relativistic magnetohydrodynamic (GRMHD) code, RAISHIN, using a conservative, high resolution shock-capturing scheme. The numerical fluxes are calculated using the Harten, Lax, & van Leer (HLL) approximate Riemann solver scheme. The flux-interpolated, constrained transport scheme is used to maintain a divergence-free magnetic field. In order to examine the numerical accuracy and the numerical efficiency, the code uses four different reconstruction methods: piecewise linear methods with Minmod and MC slope-limiter function, convex essentially non-oscillatory (CENO) method, and piecewise parabolic method (PPM) using multistep TVD Runge-Kutta time advance methods with second and third-order time accuracy. We describe code performance on an extensive set of test problems in both special and general relativity. Our new GRMHD code has proven to be accurate in second order and has successfully passed with all tests performed, including highly relativistic and magnetized cases in both special and general relativity., Comment: 42 pages, 1 tables, 18 figures. Submitted to ApJS. A paper with high resolution figures available at http://gammaray.nsstc.nasa.gov/~mizuno/research_new.html

Background: One-dimensional protein structures such as secondary structures or contact numbers are useful for three-dimensional structure prediction and helpful for intuitive understanding of the sequence-structure relationship. Accurate prediction methods will serve as a basis for these and other purposes. Results: We implemented a program CRNPRED which predicts secondary structures, contact numbers and residue-wise contact orders. This program is based on a novel machine learning scheme called critical random networks. Unlike most conventional one-dimensional structure prediction methods which are based on local windows of an amino acid sequence, CRNPRED takes into account the whole sequence. CRNPRED achieves, on average per chain, Q3 = 81% for secondary structure prediction, and correlation coefficients of 0.75 and 0.61 for contact number and residue-wise contact order predictions, respectively. Conclusion: CRNPRED will be a useful tool for computational as well as experimental biologists who need accurate one-dimensional protein structure predictions., Comment: 10 pages, 1 figure, 2 tables

This paper was withdrawn by the authors., Comment: This paper has been withdrawn

Prediction of one-dimensional protein structures such as secondary structures and contact numbers is useful for the three-dimensional structure prediction and important for the understanding of sequence-structure relationship. Here we present a new machine-learning method, critical random networks (CRNs), for predicting one-dimensional structures, and apply it, with position-specific scoring matrices, to the prediction of secondary structures (SS), contact numbers (CN), and residue-wise contact orders (RWCO). The present method achieves, on average, $Q_3$ accuracy of 77.8% for SS, correlation coefficients of 0.726 and 0.601 for CN and RWCO, respectively. The accuracy of the SS prediction is comparable to other state-of-the-art methods, and that of the CN prediction is a significant improvement over previous methods. We give a detailed formulation of critical random networks-based prediction scheme, and examine the context-dependence of prediction accuracies. In order to study the nonlinear and multi-body effects, we compare the CRNs-based method with a purely linear method based on position-specific scoring matrices. Although not superior to the CRNs-based method, the surprisingly good accuracy achieved by the linear method highlights the difficulty in extracting structural features of higher order from amino acid sequence beyond that provided by the position-specific scoring matrices., Comment: 20 pages, 1 figure, 5 tables; minor revision; accepted for publication in BIOPHYSICS

Residue-wise contact order (RWCO) is a new kind of one-dimensional protein structures which represents the extent of long-range contacts. We have recently shown that a set of three types of one-dimensional structures (secondary structure, contact number, and RWCO) contains sufficient information for reconstructing the three-dimensional structure of proteins. Currently, there exist prediction methods for secondary structure and contact number from amino acid sequence, but none exists for RWCO. Also, the properties of amino acids that affect RWCO is not clearly understood. Here, we present a linear regression-based method to predict RWCO from amino acid sequence, and analyze the regression parameters to identify the properties that correlates with the RWCO. The present method achieves the significant correlation of 0.59 between the native and predicted RWCOs on average. An unusual feature of the RWCO prediction is the remarkably large optimal half window size of 26 residues. The regression parameters for the central and near-central residues of the local sequence segment highly correlate with those of the contact number prediction, and hence with hydrophobicity., Comment: 22 pages, 5 figures, 2 tables, manuscript submitted

Protein one-dimensional (1D) structures such as secondary structure and contact number provide intuitive pictures to understand how the native three-dimensional (3D) structure of a protein is encoded in the amino acid sequence. However, it has not been clear whether a given set of 1D structures contains sufficient information for recovering the underlying 3D structure. Here we show that the 3D structure of a protein can be recovered from a set of three types of 1D structures, namely, secondary structure, contact number and residue-wise contact order which is introduced here for the first time. Using simulated annealing molecular dynamics simulations, the structures satisfying the given native 1D structural restraints were sought for 16 proteins of various structural classes and of sizes ranging from 56 to 146 residues. By selecting the structures best satisfying the restraints, all the proteins showed a coordinate RMS deviation of less than 4\AA{} from the native structure, and for most of them, the deviation was even less than 2\AA{}. The present result opens a new possibility to protein structure prediction and our understanding of the sequence-structure relationship., Comment: Corrected title. No Change In Contents

Plasma outflows from gamma-ray bursts, supernovae, and relativistic jets, in general, interact with the surrounding medium through collisionless shocks. The microphysics of such shocks are still poorly understood, which, potentially, can introduce uncertainties in the interpretation of observations. It is now well established that the Weibel two-stream instability is capable of generating strong electromagnetic fields in the transition region between the jet and the ambient plasma. However, the parameter space of collisionless shocks is vast and still remains unexplored. In this Letter, we focus on how an ambient magnetic field affects the evolution of the electron Weibel instability and the associated shock. Using a particle-in-cell code, we have performed three-dimensional numerical experiments on such shocks. We compare simulations in which a jet is injected into an unmagnetized plasma with simulations in which the jet is injected into a plasma with an ambient magnetic field both parallel and perpendicular to the jet flow. We find that there exists a threshold of the magnetic field strength below which the Weibel two-stream instability dominates, and we note that the interstellar medium magnetic field strength lies well below this value. In the case of a strong magnetic field parallel to the jet, the Weibel instability is quenched. In the strong perpendicular case, ambient and jet electrons are strongly accelerated because of the charge separation between deflected jet electrons and less deflected jet ions. Also, the electromagnetic topologies become highly non-linear and complex with the appearance of anti-parallel field configurations., Comment: 4 pages with five figures. Accepted for publication in ApJ Letters

The International Space Station (ISS) continues to be a world-class space research laboratory after over 15 years of operations, and it has proven to be a fantastic resource for observing spacecraft floating potential variations related to high voltage solar array operations in Low Earth Orbit (LEO). Measurements of the ionospheric electron density and temperature along the ISS orbit and variations in the ISS floating potential are obtained from the Floating Potential Measurement Unit (FPMU). In particular, rapid variations in ISS floating potential during solar array operations on time scales of tens of milliseconds can be recorded due to the 128 Hz sample rate of the Floating Potential Probe (FPP) pro- viding interesting insight into high voltage solar array interaction with the space plasma environment. Comparing the FPMU data with the ISS operations timeline and solar array data provides a means for correlating some of the more complex and interesting transient floating potential variations with mission operations. These complex variations are not reproduced by current models and require further study to understand the underlying physical processes. In this paper we present some of the floating potential transients observed over the past few years along with the relevant space environment parameters and solar array operations data.