FERN – a Java framework for stochastic simulation and evaluation of reaction networks

<p>Abstract</p> <p>Background</p> <p>Stochastic simulation can be used to illustrate the development of biological systems over time and the stochastic nature of these processes. Currently available programs for stochastic simulation, however, are limited in that they either a) do not provide the most efficient simulation algorithms and are difficult to extend, b) cannot be easily integrated into other applications or c) do not allow to monitor and intervene during the simulation process in an easy and intuitive way. Thus, in order to use stochastic simulation in innovative high-level modeling and analysis approaches more flexible tools are necessary.</p> <p>Results</p> <p>In this article, we present FERN (Framework for Evaluation of Reaction Networks), a Java framework for the efficient simulation of chemical reaction networks. FERN is subdivided into three layers for network representation, simulation and visualization of the simulation results each of which can be easily extended. It provides efficient and accurate state-of-the-art stochastic simulation algorithms for well-mixed chemical systems and a powerful observer system, which makes it possible to track and control the simulation progress on every level. To illustrate how FERN can be easily integrated into other systems biology applications, plugins to Cytoscape and CellDesigner are included. These plugins make it possible to run simulations and to observe the simulation progress in a reaction network in real-time from within the Cytoscape or CellDesigner environment.</p> <p>Conclusion</p> <p>FERN addresses shortcomings of currently available stochastic simulation programs in several ways. First, it provides a broad range of efficient and accurate algorithms both for exact and approximate stochastic simulation and a simple interface for extending to new algorithms. FERN's implementations are considerably faster than the C implementations of gillespie2 or the Java implementations of ISBJava. Second, it can be used in a straightforward way both as a stand-alone program and within new systems biology applications. Finally, complex scenarios requiring intervention during the simulation progress can be modelled easily with FERN.</p

Optical control of internal electric fields in band-gap graded InGaN nanowires

InGaN nanowires are suitable building blocks for many future optoelectronic devices. We show that a linear grading of the indium content along the nanowire axis from GaN to InN introduces an internal electric field evoking a photocurrent. Consistent with quantitative band structure simulations we observe a sign change in the measured photocurrent as a function of photon flux. This negative differential photocurrent opens the path to a new type of nanowire-based photodetector. We demonstrate that the photocurrent response of the nanowires is as fast as 1.5 ps

The Complex Langevin method: When can it be trusted?

We analyze to what extent the complex Langevin method, which is in principle capable of solving the so-called sign problems, can be considered as reliable. We give a formal derivation of the correctness and then point out various mathematical loopholes. The detailed study of some simple examples leads to practical suggestions about the application of the method.Comment: 14 pages, including several eps figures and tables; clarification and minor corrections added, to appear in PR

Chemical Chaperones Improve Protein Secretion and Rescue Mutant Factor VIII in Mice with Hemophilia A.

nefficient intracellular protein trafficking is a critical issue in the pathogenesis of a variety of diseases and in recombinant protein production. Here we investigated the trafficking of factor VIII (FVIII), which is affected in the coagulation disorder hemophilia A. We hypothesized that chemical chaperones may be useful to enhance folding and processing of FVIII in recombinant protein production, and as a therapeutic approach in patients with impaired FVIII secretion. A tagged B-domain-deleted version of human FVIII was expressed in cultured Chinese Hamster Ovary cells to mimic the industrial production of this important protein. Of several chemical chaperones tested, the addition of betaine resulted in increased secretion of FVIII, by increasing solubility of intracellular FVIII aggregates and improving transport from endoplasmic reticulum to Golgi. Similar results were obtained in experiments monitoring recombinant full-length FVIII. Oral betaine administration also increased FVIII and factor IX (FIX) plasma levels in FVIII or FIX knockout mice following gene transfer. Moreover, in vitro and in vivo applications of betaine were also able to rescue a trafficking-defective FVIII mutant (FVIIIQ305P). We conclude that chemical chaperones such as betaine might represent a useful treatment concept for hemophilia and other diseases caused by deficient intracellular protein trafficking

Real-time dynamics of lattice gauge theories with a few-qubit quantum computer

Gauge theories are fundamental to our understanding of interactions between the elementary constituents of matter as mediated by gauge bosons. However, computing the real-time dynamics in gauge theories is a notorious challenge for classical computational methods. In the spirit of Feynman's vision of a quantum simulator, this has recently stimulated theoretical effort to devise schemes for simulating such theories on engineered quantum-mechanical devices, with the difficulty that gauge invariance and the associated local conservation laws (Gauss laws) need to be implemented. Here we report the first experimental demonstration of a digital quantum simulation of a lattice gauge theory, by realising 1+1-dimensional quantum electrodynamics (Schwinger model) on a few-qubit trapped-ion quantum computer. We are interested in the real-time evolution of the Schwinger mechanism, describing the instability of the bare vacuum due to quantum fluctuations, which manifests itself in the spontaneous creation of electron-positron pairs. To make efficient use of our quantum resources, we map the original problem to a spin model by eliminating the gauge fields in favour of exotic long-range interactions, which have a direct and efficient implementation on an ion trap architecture. We explore the Schwinger mechanism of particle-antiparticle generation by monitoring the mass production and the vacuum persistence amplitude. Moreover, we track the real-time evolution of entanglement in the system, which illustrates how particle creation and entanglement generation are directly related. Our work represents a first step towards quantum simulating high-energy theories with atomic physics experiments, the long-term vision being the extension to real-time quantum simulations of non-Abelian lattice gauge theories

Electrically and Magnetically Charged States and Particles in the 2+1-Dimensional Z_N-Higgs Gauge Model

Electrically as well as magnetically charged states are constructed in the 2+1-dimensional Euclidean Z_N-Higgs lattice gauge model, the former following ideas of Fredenhagen and Marcu and the latter using duality transformations on the algebra of observables. The existence of electrically and of magnetically charged particles is also established. With this work we prepare the ground for the constructive study of anyonic statistics of multiparticle scattering states of electrically and magnetically charged particles in this model (work in progress).Comment: 57 pages, Sfb 288 Preprint No. 109. To appear in Commun. Math. Phys. About the file: This is a uuencoded, "gzip-ed" postscript file. It is about 300kB large. The original ps file is about 700kB large. All figures are included. The LaTeX sources ou even hard copies can be required to the authors at [email protected] or Freie Universitaet Berlin. Institut fuer Theoretische Physik. Arnimallee 14. Berlin 14195 German

Cinacalcet-induced hypocalcemia in a cohort of European haemodialysis patients: predictors, therapeutic approaches and outcomes

BACKGROUND: Calcimimetic treatment of secondary hyperparathyroidism in chronic dialysis patients is often followed by hypocalcemia. METHODS: We investigated the frequency, predictors, consequences and therapeutic responses following cinacalcet-induced hypocalcemia in an incident European hemodialysis cohort of 1068 patients with a cinacalcet prescription. RESULTS: Of 905 normocalcemic patients initiating cinacalcet, 67% developed hypocalcemia within 12 months: 68% mild, 23% moderate, 9% severe. Compared to persistently normocalcemic patients, those with severe hypocalcemia were more often diabetic, overweight, had cardiovascular disease, shorter dialysis vintage, used a catheter dialysis access, had fewer active vitamin-D sterols, and exhibited higher CRP and iPTH and lower calcium levels. Multivariate predictors of hypocalcemia included a catheter for vascular access, low albumin and high iPTH. Generally, no therapeutic intervention to prevent hypocalcemia was taken prior to cinacalcet initiation. After the hypocalcemic event, the most common clinical response was no change of the dialysis or medical regimen. Following the hypocalcemic event, iPTH remained low even in those with severe hypocalcemia. The number of deaths and cardiovascular events did not differ between patients with and without hypocalcemia within six months following cinacalcet initiation. CONCLUSION: Two-thirds of cinacalcet initiated patients experienced hypocalcaemia with 9% being severe. Hypocalcemia was mostly asymptomatic, transient (with and without targeted intervention to correct it) and not associated with an increase in cardiovascular events or deaths