The silicon trypanosome

African trypanosomes have emerged as promising unicellular model organisms for the next generation of systems biology. They offer unique advantages, due to their relative simplicity, the availability of all standard genomics techniques and a long history of quantitative research. Reproducible cultivation methods exist for morphologically and physiologically distinct life-cycle stages. The genome has been sequenced, and microarrays, RNA-interference and high-accuracy metabolomics are available. Furthermore, the availability of extensive kinetic data on all glycolytic enzymes has led to the early development of a complete, experiment-based dynamic model of an important biochemical pathway. Here we describe the achievements of trypanosome systems biology so far and outline the necessary steps towards the ambitious aim of creating a , a comprehensive, experiment-based, multi-scale mathematical model of trypanosome physiology. We expect that, in the long run, the quantitative modelling enabled by the Silicon Trypanosome will play a key role in selecting the most suitable targets for developing new anti-parasite drugs

Minimal Brownian Ratchet: An Exactly Solvable Model

We develop an exactly-solvable three-state discrete-time minimal Brownian ratchet (MBR), where the transition probabilities between states are asymmetric. By solving the master equations we obtain the steady-state probabilities. Generally the steady-state solution does not display detailed balance, giving rise to an induced directional motion in the MBR. For a reduced two-dimensional parameter space we find the null-curve on which the net current vanishes and detailed balance holds. A system on this curve is said to be balanced. On the null-curve, an additional source of external random noise is introduced to show that a directional motion can be induced under the zero overall driving force. We also indicate the off-balance behavior with biased random noise.Comment: 4 pages, 4 figures, RevTex source, General solution added. To be appeared in Phys. Rev. Let

New paradoxical games based on Brownian ratchets

Based on Brownian ratchets, a counter-intuitive phenomenon has recently emerged -- namely, that two losing games can yield, when combined, a paradoxical tendency to win. A restriction of this phenomenon is that the rules depend on the current capital of the player. Here we present new games where all the rules depend only on the history of the game and not on the capital. This new history-dependent structure significantly increases the parameter space for which the effect operates.Comment: 4 pages, 3 eps figures, revte

Generalized Smoluchowski equation with correlation between clusters

In this paper we compute new reaction rates of the Smoluchowski equation which takes into account correlations. The new rate K = KMF + KC is the sum of two terms. The first term is the known Smoluchowski rate with the mean-field approximation. The second takes into account a correlation between clusters. For this purpose we introduce the average path of a cluster. We relate the length of this path to the reaction rate of the Smoluchowski equation. We solve the implicit dependence between the average path and the density of clusters. We show that this correlation length is the same for all clusters. Our result depends strongly on the spatial dimension d. The mean-field term KMFi,j = (Di + Dj)(rj + ri)d-2, which vanishes for d = 1 and is valid up to logarithmic correction for d = 2, is the usual rate found with the Smoluchowski model without correlation (where ri is the radius and Di is the diffusion constant of the cluster). We compute a new rate: the correlation rate K_{i,j}^{C} (D_i+D_j)(r_j+r_i)^{d-1}M{\big(\frac{d-1}{d_f}}\big) is valid for d \leq 1(where M(\alpha) = \sum+\infty i=1i\alphaNi is the moment of the density of clusters and df is the fractal dimension of the cluster). The result is valid for a large class of diffusion processes and mass radius relations. This approach confirms some analytical solutions in d 1 found with other methods. We also show Monte Carlo simulations which illustrate some exact new solvable models

Detection of 6 November 1997 ground level event by Milagrito

Solar Energetic Particles (SEPs) with energies exceeding 10 GeV associated with the 6 November 1997 solar flare/CME (coronal mass ejection) have been detected with Milagrito, a prototype of the Milagro Gamma Ray Observatory. While SEP acceleration beyond 1 GeV is well established, few data exist for protons or ions beyond 10 GeV. The Milagro observatory, a ground based water Cherenkov detector designed for observing very high energy gamma ray sources, can also be used to study the Sun. Milagrito, which operated for approximately one year in 1997/98, was sensitive to solar proton and neutron fluxes above ∼4 GeV. In its scaler mode, Milagrito registered a rate increase coincident with the 6 November 1997 ground level event observed by Climax and other neutron monitors. A preliminary analysis suggests the presence of \u3e10 GeV particles

Search for Point Sources of Ultra-High Energy Cosmic Rays Above 40 EeV Using a Maximum Likelihood Ratio Test

We present the results of a search for cosmic ray point sources at energies above 40 EeV in the combined data sets recorded by the AGASA and HiRes stereo experiments. The analysis is based on a maximum likelihood ratio test using the probability density function for each event rather than requiring an a priori choice of a fixed angular bin size. No statistically significant clustering of events consistent with a point source is found.Comment: 7 pages, 7 figures. Accepted for publication in The Astrophysical Journa

Results from the Milagrito experiment

The Milagro water Cherenkov detector near Los Alamos, New Mexico is the first air shower detector capable of continuously monitoring the sky at energies between 500 GeV and 20 TeV. Preliminary results of the Milagro experiment are presented. A predecessor of the Milagro detector, Milagrito, was operational from February 1997 to May 1998. Milagrito consisted of 228 8″ photomultiplier tubes (PMTs) arranged in a grid with a 2.8 meter spacing and submerged in 1–2 meters of water. During its operation, Milagrito collected in excess of 9 billion events with a median energy of about 3 TeV. The detector’s sensitivity extends below 1 TeV for showers from near zenith. The results of an all sky search for the Milagrito data for both transient and DC sources will be presented, including the Crab Nebula and active galaxies Markarian 501 and 421, which are known sources of TeV gamma-rays. Also presented will be a study of the TeV emission from gamma ray bursts (GRBs) in Milagrito’s field of view detected by the BATSE experiment on the Compton Gamma-Ray Observatory

Milagrito Detection of TeV Emission from Mrk 501

The Milagro water Cherenkov detector near Los Alamos, New Mexico, has been operated as a sky monitor at energies of a few TeV between February 1997 and April 1998. Serving as a test run for the full Milagro detector, Milagrito has taken data during the strong and long-lasting 1997 flare of Mrk 501. We present results from the analysis of Mrk 501 and compare the excess and background rates with expectations from the detector simulations.Comment: 4 pages, submitted to XXVI International Cosmic Ray Conference, Salt Lake Cit

Calibration of the Milagro Cosmic Ray Telescope

The Milagro detector is an air shower array which uses the water Cherenkov technique and is capable of continuously monitoring the sky at energies near 1 TeV. The detector consists of 20000 metric tons of pure water instrumented with 723 photo-multiplier tubes (PMTs). The PMTs are arranged in a two-layer structure on a lattice of 3 m spacing covering 5000 $m^2$ area. The direction of the shower is determined from the relative timing of the PMT signals, necessitating a common time reference and amplitude slewing corrections to improve the time resolution. The calibration system to provide these consists of a pulsed laser driving 30 diffusing light sources deployed in the pond to allow cross-calibration of the PMTs. The system is capable of calibrating times and the pulse-heights from the PMTs using the time-over-threshold technique. The absolute energy scale is provided using single muons passing through the detector. The description of the calibration system of the Milagro detector and its prototype Milagrito will be presented.Comment: 4 pages, submitted to the XXVI International Cosmic Ray Conferenc