Properties of tug-of-war model for cargo transport by molecular motors

Molecular motors are essential components for the biophysical functions of the cell. Our current quantitative understanding of how multiple motors move along a single track is not complete; even though models and theories for single motor chemomechanics abound. Recently, M.J.I. M$\ddot{\rm u}$ller {\em et al.} have developed a tug-of-war model to describe the bidirectional movement of the cargo (PNAS(2008) 105(12) P4609-4614). Through Monte Carlo simulations, they discovered that the tug-of-war model exhibits several qualitative different motility regimes, which depend on the precise value of single motor parameters, and they suggested the sensitivity can be used by a cell to regulate its cargo traffic. In the present paper, we carry out a thorough analysis of the tug-of-war model. All the stable, i.e., biophysically observable, steady states are obtained. Depending on several parameters, the system exhibits either uni-, bi- or tristability. Based on the separating boundary of the different stable states and the initial numbers of the different motor species that are bound to the track, the steady state of the cargo movement can be predicted, and consequently the steady state velocity can be obtained. It is found that, the velocity, even the direction, of the cargo movement change with the initial numbers of the motors which are bound to the track and several other parameters

Off-Axis Afterglow Light Curves from High-Resolution Hydrodynamical Jet Simulations

Numerical jet simulations serve a valuable role in calculating gamma-ray burst afterglow emission beyond analytical approximations. Here we present the results of high resolution 2D simulations of decelerating relativistic jets performed using the RAM adaptive mesh refinement relativistic hydrodynamics code. We have applied a separate synchrotron radiation code to the simulation results in order to calculate light curves at frequencies varying from radio to X-ray for observers at various angles from the jet axis. We provide a confirmation from radio light curves from simulations rather than from a simplified jet model for earlier results in the literature finding that only a very small number of local Ibc supernovae can possibly harbor an orphan afterglow. Also, recent studies have noted an unexpected lack of observed jet breaks in the Swift sample. Using a jet simulation with physical parameters representative for an average Swift sample burst, such as a jet half opening angle of 0.1 rad and a source redshift of z = 2.23, we have created synthetic light curves at 1.5 keV with artificial errors while accounting for Swift instrument biases as well. A large set of these light curves have been generated and analyzed using a Monte Carlo approach. Single and broken power law fits are compared. We find that for increasing observer angle, the jet break quickly becomes hard to detect. This holds true even when the observer remains well within the jet opening angle. We find that the odds that a Swift light curve from a randomly oriented 0.1 radians jet at z = 2.23 will exhibit a jet break at the 3 sigma level are only 12 percent. The observer angle therefore provides a natural explanation for the lack of perceived jet breaks in the Swift sample.Comment: 4 pages, 3 figures. First of two contributions to proceedings GRB2010 Maryland conference. Editors: McEnery, Racusin and Gehrels. The data from this paper is publicly available from http://cosmo.nyu.edu/afterglowlibrary

An on-line library of afterglow light curves

Numerical studies of gamma-ray burst afterglow jets reveal significant qualitative differences with simplified analytical models. We present an on-line library of synthetic afterglow light curves and broadband spectra for use in interpreting observational data. Light curves have been calculated for various physics settings such as explosion energy and circumburst structure, as well as differing jet parameters and observer angle and redshift. Calculations gave been done for observer frequencies ranging from low radio to X-ray and for observer times from hours to decades after the burst. The light curves have been calculated from high-resolution 2D hydrodynamical simulations performed with the RAM adaptive-mesh refinement code and a detailed synchrotron radiation code. The library will contain both generic afterglow simulations as well as specific case studies and will be freely accessible at http://cosmo.nyu.edu/afterglowlibrary . The synthetic light curves can be used as a check on the accuracy of physical parameters derived from analytical model fits to afterglow data, to quantitatively explore the consequences of varying parameters such as observer angle and for accurate predictions of future telescope data.Comment: 4 pages, 2 figures. Second of two contributions to proceedings GRB2010 Maryland conference. Editors: McEnery, Racusin and Gehrels. The data from this paper is publicly available from http://cosmo.nyu.edu/afterglowlibrary

Sensitivity dependent model of protein-protein interaction networks

The scale free structure p(k)~k^{-gamma} of protein-protein interaction networks can be reproduced by a static physical model in simulation. We inspect the model theoretically, and find the key reason for the model to generate apparent scale free degree distributions. This explanation provides a generic mechanism of "scale free" networks. Moreover, we predict the dependence of gamma on experimental protein concentrations or other sensitivity factors in detecting interactions, and find experimental evidence to support the prediction.Comment: organization improved, and experimental evidence of predicted dependence on sensitivity is addresse

Study of X-ray Radiation Damage in Silicon Sensors

The European X-ray Free Electron Laser (XFEL) will deliver 30,000 fully coherent, high brilliance X-ray pulses per second each with a duration below 100 fs. This will allow the recording of diffraction patterns of single complex molecules and the study of ultra-fast processes. Silicon pixel sensors will be used to record the diffraction images. In 3 years of operation the sensors will be exposed to doses of up to 1 GGy of 12 keV X-rays. At this X-ray energy no bulk damage in silicon is expected. However fixed oxide charges in the insulating layer covering the silicon and interface traps at the Si-SiO2 interface will be introduced by the irradiation and build up over time. We have investigated the microscopic defects in test structures and the macroscopic electrical properties of segmented detectors as a function of the X-ray dose. From the test structures we determine the oxide charge density and the densities of interface traps as a function of dose. We find that both saturate (and even decrease) for doses between 10 and 100 MGy. For segmented sensors the defects introduced by the X-rays increase the full depletion voltage, the surface leakage current and the inter-pixel capacitance. We observe that an electron accumulation layer forms at the Si-SiO2 interface. Its width increases with dose and decreases with applied bias voltage. Using TCAD simulations with the dose dependent parameters obtained from the test structures, we are able to reproduce the observed results. This allows us to optimize the sensor design for the XFEL requirements