Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System

The-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are all homogeneously distributed in the reaction compartments, which is not the case in some cellular processes. The MinCDE system in Escherichia coli, for example, relies on intricately controlled reaction, diffusion and localization of Min proteins on the membrane and in the cytoplasm compartments to inhibit cell division at the poles of the rod-shaped cell. To model such processes, we have extended the E-Cell System to support reaction-diffusion and dynamic localization of molecules in volume and surface compartments. We evaluated our method by modeling the in vivo dynamics of MinD and MinE and comparing their simulated localization patterns to the observations in experiments and previous computational work. In both cases, our simulation results are in good agreement

Efficient method for simulating quantum electron dynamics under the time dependent Kohn-Sham equation

A numerical scheme for solving the time-evolution of wave functions under the time dependent Kohn-Sham equation has been developed. Since the effective Hamiltonian depends on the wave functions, the wave functions and the effective Hamiltonian should evolve consistently with each other. For this purpose, a self-consistent loop is required at every time-step for solving the time-evolution numerically, which is computationally expensive. However, in this paper, we develop a different approach expressing a formal solution of the TD-KS equation, and prove that it is possible to solve the TD-KS equation efficiently and accurately by means of a simple numerical scheme without the use of any self-consistent loops.Comment: 5 pages, 3 figures. Physical Review E, 2002, in pres

Inhomogeneous distribution of flux pinning strength and its effecton irreversibility line and vortex glass-liquid transition line in Bi-2212 tapes

The irreversibility line and the vortex glass-liquid transition line under a magnetic field parallel to the c-axis are investigated for silver-sheathed and dip-coated Bi-2212 tape wires. It is found that the two characteristic lines for silver-sheathed tape is well explained by the flux creep-flow model assuming the distribution of pinning strength with a single peak. On the other hand, general agreements are obtained for these characteristic lines and the critical current density between experiments and theory only when two peaks are assumed in the distribution of flux pinning strength for the dip-coated tape. The causative structure in the dip-coated tape for the peak at small strength in the distribution is discusse

Disaster debris estimation using high-resolution polarimetric stereo-SAR

AbstractThis paper addresses the problem of debris estimation which is one of the most important initial challenges in the wake of a disaster like the Great East Japan Earthquake and Tsunami. Reasonable estimates of the debris have to be made available to decision makers as quickly as possible. Current approaches to obtain this information are far from being optimal as they usually rely on manual interpretation of optical imagery. We have developed a novel approach for the estimation of tsunami debris pile heights and volumes for improved emergency response. The method is based on a stereo-synthetic aperture radar (stereo-SAR) approach for very high-resolution polarimetric SAR. An advanced gradient-based optical-flow estimation technique is applied for optimal image coregistration of the low-coherence non-interferometric data resulting from the illumination from opposite directions and in different polarizations. By applying model based decomposition of the coherency matrix, only the odd bounce scattering contributions are used to optimize echo time computation. The method exclusively considers the relative height differences from the top of the piles to their base to achieve a very fine resolution in height estimation. To define the base, a reference point on non-debris-covered ground surface is located adjacent to the debris pile targets by exploiting the polarimetric scattering information. The proposed technique is validated using in situ data of real tsunami debris taken on a temporary debris management site in the tsunami affected area near Sendai city, Japan. The estimated height error is smaller than 0.6m RMSE. The good quality of derived pile heights allows for a voxel-based estimation of debris volumes with a RMSE of 1099m3. Advantages of the proposed method are fast computation time, and robust height and volume estimation of debris piles without the need for pre-event data or auxiliary information like DEM, topographic maps or GCPs

A q-analog of the ADHMN construction and axisymmetric multi-instantons

In the preceding paper (Phys. Lett. B463 (1999) 257), the authors presented a q-analog of the ADHMN construction and obtained a family of anti-selfdual configurations with a parameter q for classical SU(2) Yang-Mills theory in four-dimensional Euclidean space. The family of solutions can be seen as a q-analog of the single BPS monopole preserving (anti-)selfduality. Further discussion is made on the relation to axisymmetric ansatz on anti-selfdual equation given by Witten in the late seventies. It is found that the q-exponential functions familiar in q-analysis appear as analytic functions categorizing the anti-selfdual configurations yielded by axisymmetric ansatz.Comment: 11pages, Latex2e, to appear in Journal of Physics A: Mathematical and General as a `Special Issue/Difference Equations

Hypocretin/Orexin Peptides Alter Spike Encoding by Serotonergic Dorsal Raphe Neurons through Two Distinct Mechanisms That Increase the Late Afterhyperpolarization

Orexins (hypocretins) are neuropeptides that regulate multiple homeostatic processes, including reward and arousal, in part by exciting serotonergic dorsal raphe neurons, the major source of forebrain serotonin. Here, using mouse brain slices, we found that, instead of simply depolarizing these neurons, orexin-A altered the spike encoding process by increasing the postspike afterhyperpolarization (AHP) via two distinct mechanisms. This orexin-enhanced AHP (oeAHP) was mediated by both OX1 and OX2 receptors, required Ca(2+) influx, reversed near EK, and decayed with two components, the faster of which resulted from enhanced SK channel activation, whereas the slower component decayed like a slow AHP (sAHP), but was not blocked by UCL2077, an antagonist of sAHPs in some neurons. Intracellular phospholipase C inhibition (U73122) blocked the entire oeAHP, but neither component was sensitive to PKC inhibition or altered PKA signaling, unlike classical sAHPs. The enhanced SK current did not depend on IP3-mediated Ca(2+) release but resulted from A-current inhibition and the resultant spike broadening, which increased Ca(2+) influx and Ca(2+)-induced-Ca(2+) release, whereas the slower component was insensitive to these factors. Functionally, the oeAHP slowed and stabilized orexin-induced firing compared with firing produced by a virtual orexin conductance lacking the oeAHP. The oeAHP also reduced steady-state firing rate and firing fidelity in response to stimulation, without affecting the initial rate or fidelity. Collectively, these findings reveal a new orexin action in serotonergic raphe neurons and suggest that, when orexin is released during arousal and reward, it enhances the spike encoding of phasic over tonic inputs, such as those related to sensory, motor, and reward events. SIGNIFICANCE STATEMENT: Orexin peptides are known to excite neurons via slow postsynaptic depolarizations. Here we elucidate a significant new orexin action that increases and prolongs the postspike afterhyperpolarization (AHP) in 5-HT dorsal raphe neurons and other arousal-system neurons. Our mechanistic studies establish involvement of two distinct Ca(2+)-dependent AHP currents dependent on phospholipase C signaling but independent of IP3 or PKC. Our functional studies establish that this action preserves responsiveness to phasic inputs while attenuating responsiveness to tonic inputs. Thus, our findings bring new insight into the actions of an important neuropeptide and indicate that, in addition to producing excitation, orexins can tune postsynaptic excitability to better encode the phasic sensory, motor, and reward signals expected during aroused states

Effective mass staircase and the Fermi liquid parameters for the fractional quantum Hall composite fermions

Effective mass of the composite fermion in the fractional quantum Hall system, which is of purely interaction originated, is shown, from a numerical study, to exhibit a curious nonmonotonic behavior with a staircase correlated with the number (=2,4,...) of attached flux quanta. This is surprising since the usual composite-fermion picture predicts a smooth behavior. On top of that, significant interactions are shown to exist between composite fermions, where the excitation spectrum is accurately reproduced in terms of Landau's Fermi liquid picture with negative (i.e., Hund's type) orbital and spin exchange interactions.Comment: 4 pages, 3 figures, REVTe

The HI content of star-forming galaxies at z = 0.24

We use observations from the Giant Metrewave Radio Telescope (GMRT) to measure the atomic hydrogen gas content of star-forming galaxies at z = 0.24 (i.e. a look-backtime of ~3 Gyr). The sample of galaxies studied were selected from Halpha-emitting field galaxies detected in a narrow-band imaging survey with the Subaru Telescope. The Anglo-Australian Telescope was used to obtain precise optical redshifts for these galaxies. We then coadded the HI 21 cm emission signal for all the galaxies within the GMRT spectral line data cube. From the coadded signal of 121 galaxies, we measure an average atomic hydrogen gas mass of (2.26 +- 0.90)*10^9 solar masses. We translate this HI signal into a cosmic density of neutral gas at z = 0.24 of Omega_gas = (0.91 +- 0.42)*10^-3. This is the current highest redshift at which Omega_gas has been constrained from 21 cm emission and our value is consistent with that estimated from damped Lyman-alpha systems around this redshift. We also find that the correlations between the Halpha luminosity and the radio continuum luminosity and between the star formation rate and the HI gas content in star-forming galaxies at z = 0.24 are consistent with the correlations found at z = 0. These two results suggest that the star formation mechanisms in field galaxies ~3 Gyr ago were not substantially different from the present, even though the star formation rate is 3 times higher.Comment: 11 pages, contains 9 figures and 1 table. Accepted for publishing in MNRAS 2007 January 22. Received 2007 January 22; in original form 2006 November 3

Magnetohydrodynamics in full general relativity: Formulation and tests

A new implementation for magnetohydrodynamics (MHD) simulations in full general relativity (involving dynamical spacetimes) is presented. In our implementation, Einstein's evolution equations are evolved by a BSSN formalism, MHD equations by a high-resolution central scheme, and induction equation by a constraint transport method. We perform numerical simulations for standard test problems in relativistic MHD, including special relativistic magnetized shocks, general relativistic magnetized Bondi flow in stationary spacetime, and a longterm evolution for self-gravitating system composed of a neutron star and a magnetized disk in full general relativity. In the final test, we illustrate that our implementation can follow winding-up of the magnetic field lines of magnetized and differentially rotating accretion disks around a compact object until saturation, after which magnetically driven wind and angular momentum transport inside the disk turn on.Comment: 28 pages, to be published in Phys. Rev.