BioNetGen is an open-source software package for rule-based modeling of complex biochemical systems. Version 2.2 of the software introduces numerous new features for both model specification and simulation. Here, we report on these additions, discuss
ing how they facilitate the construction, simulation, and analysis of larger and more complex models than previously possible.
The study of neutrino-nucleus interactions has recently seen rapid development with a new generation of accelerator-based neutrino experiments employing medium and heavy nuclear targets for the study of neutrino oscillations. A few unexpected results
in the study of quasi-elastic scattering and single photon production have spurred a revisiting of the underlying nuclear physics and connections to electron-nucleus scattering. A thorough understanding and resolution of these issues is essential for future progress in the study of neutrino oscillations. A recent workshop hosted by the Institute of Nuclear Theory at the University of Washington (INT-13-54W) examined experimental and theoretical developments in neutrino-nucleus interactions and related measurements from electron and pion scattering. We summarize the discussions at the workshop pertaining to the aforementioned issues in quasi-elastic scattering and single photon production, particularly where there was consensus on the highest priority issues to be resolved and the path towards resolving them.
Detailed modeling and simulation of biochemical systems is complicated by the problem of combinatorial complexity, an explosion in the number of species and reactions due to myriad protein-protein interactions and post-translational modifications. Ru
le-based modeling overcomes this problem by representing molecules as structured objects and encoding their interactions as pattern-based rules. This greatly simplifies the process of model specification, avoiding the tedious and error prone task of manually enumerating all species and reactions that can potentially exist in a system. From a simulation perspective, rule-based models can be expanded algorithmically into fully-enumerated reaction networks and simulated using a variety of network-based simulation methods, provided that the network is not exceedingly large. Alternatively, rule-based models can be simulated directly using particle-based kinetic Monte Carlo methods. This network-free approach produces exact stochastic trajectories with a computational cost that is independent of network size. However, memory and run time costs increase with the number of particles, limiting the size of system that can be feasibly simulated. Here, we present a hybrid particle/population simulation method that combines the best attributes of both the network-based and network-free approaches. The method takes as input a rule-based model and a user-specified subset of species to treat as population variables rather than as particles. The model is then transformed by a process of partial network expansion into a dynamically equivalent form that can be simulated using a population-adapted network-free simulator. The transformation method has been implemented within the open-source rule-based modeling platform BioNetGen, and resulting hybrid models can be simulated using the particle-based simulator NFsim.
A Large Quasar Group (LQG) of particularly large size and high membership has been identified in the DR7QSO catalogue of the Sloan Digital Sky Survey. It has characteristic size (volume^1/3) ~ 500 Mpc (proper size, present epoch), longest dimension ~
1240 Mpc, membership of 73 quasars, and mean redshift <z> = 1.27. In terms of both size and membership it is the most extreme LQG found in the DR7QSO catalogue for the redshift range 1.0 <= z <= 1.8 of our current investigation. Its location on the sky is ~ 8.8 deg north (~ 615 Mpc projected) of the Clowes & Campusano LQG at the same redshift, <z> = 1.28, which is itself one of the more extreme examples. Their boundaries approach to within ~ 2 deg (~ 140 Mpc projected). This new, huge LQG appears to be the largest structure currently known in the early universe. Its size suggests incompatibility with the Yadav et al. scale of homogeneity for the concordance cosmology, and thus challenges the assumption of the cosmological principle.
A preceding paper demonstrated that explicit asymptotic methods generally work much better for extremely stiff reaction networks than has previously been shown in the literature. There we showed that for systems well removed from equilibrium explicit
asymptotic methods can rival standard implicit codes in speed and accuracy for solving extremely stiff differential equations. In this paper we continue the investigation of systems well removed from equilibrium by examining quasi-steady-state (QSS) methods as an alternative to asymptotic methods. We show that for systems well removed from equilibrium, QSS methods also can compete with, or even exceed, standard implicit methods in speed, even for extremely stiff networks, and in many cases give somewhat better integration speed than for asymptotic methods. As for asymptotic methods, we will find that QSS methods give correct results, but with non-competitive integration speed as equilibrium is approached. Thus, we shall find that both asymptotic and QSS methods must be supplemented with partial equilibrium methods as equilibrium is approached to remain competitive with implicit methods.
Results based on 106 M $psi$ events and about 226 M $J/psi$ events acquired with the BESIII detector at BEPCII are reported, including a confirmation of the BESII $pbar{p}$ threshold enhancement in $J/psi to gamma pbar{p}$, branching ratios for $chi_
{cJ} to pi^0 pi^0$ and $eta eta$, and first measurements of the branching ratios for $psi to pi^0 h_c$ and $h_c to gamma eta_c$, as well as measurements of the mass and width of the $h_c$. Also reported are first observations of the two photon process $psi to gamma gamma J/psi$ and $f_0(980) - a_0(980)$ mixing.
There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial inhomogeneities and diffusion. This is particularly true in biology and
nanoscale materials science, where the common assumptions of deterministic dynamics and well-mixed reaction volumes often break down. In this article, we present a spatial version of the partitioned-leaping algorithm (PLA), a multiscale accelerated-stochastic simulation approach built upon the tau-leaping framework of Gillespie. We pay special attention to the details of the implementation, particularly as it pertains to the time step calculation procedure. We point out conceptual errors that have been made in this regard in prior implementations of spatial tau-leaping and illustrate the manifestation of these errors through practical examples. Finally, we discuss the fundamental difficulties associated with incorporating efficient exact-stochastic techniques, such as the next-subvolume method, into a spatial-leaping framework and suggest possible solutions.
Leaping methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address this issue usi
ng the partitioned leaping algorithm (PLA) [L.A. Harris and P. Clancy, J. Chem. Phys. 125, 144107 (2006)], a recently-introduced multiscale leaping approach. We use the PLA to investigate stochastic effects in two model biochemical reaction networks. The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to be generally representative of real biological systems. We demonstrate how the PLA allows us to quantify subtle effects of stochasticity in these systems that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly-used exact stochastic methods. We also illustrate bottlenecks that can hinder the approach and exemplify and discuss possible strategies for overcoming them. Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while at the same time elucidating obstacles that are often encountered in practice.
During the last few years there has been a renaissance in charm and charmonium spectroscopy with higher precision measurements at the $psi^{}$ and $psi(3770)$ coming from BESII and CLEOc and many new discoveries coming from B-factories. In this paper
, I review some new results on classical charmonium and $e^+ e^- to$ hadrons using B-factory Initial State Radiation and two photon events.
A Time of Flight monitoring system has been developed for BES3. The light source is a 442-443 nm laser diode, which is stable and provides a pulse width as narrow as 50 ps and a peak power as large as 2.6 W. Two optical-fiber bundles with a total o
f 512 optical fibers, including spares, are used to distribute the light pulses to the Time of Flight counters. The design, operation, and performance of the system are described.
