arXiv subjects

Jörg Langowski

Publications and source records attributed to Jörg Langowski.

7 recordsLinked to original sources

arXiv2011

Multiplexed multiple-τ auto- and cross- correlators on a single FPGA

Fluorescence correlation and cross-correlation spectroscopy (FCS, FCCS) are widely used techniques to study the diffusion properties and interactions of fluorescent molecules. Autocorrelation (ACFs) and cross-correlation functions (CCFs) are typically acquired with fast hardware correlators. Here we introduce a new multiple-τ hardware correlator design for computing ACFs and CCFs in real time. A scheduling algorithm minimizes the use of hardware resources by calculating the different segments of the correlation function on a single correlator block. The program was written in LabVIEW, enabling computation of two multiple-τ ACFs and two CCFs on a National Instruments FPGA card (NI 7833R) in real time with a minimal sampling time of 400 ns. Raw data are also stored with a time resolution of 50 ns for later analysis. The design can be adapted to other FPGA cards with only minor changes and extended to evaluate more inputs and correlation functions.

physics.optics↗

arXiv2011

FPGA implementation of a 32x32 autocorrelator array for analysis of fast image series

With the evolving technology in CMOS integration, new classes of 2D-imaging detectors have recently become available. In particular, single photon avalanche diode (SPAD) arrays allow detection of single photons at high acquisition rates (\geq 100 kfps), which is about two orders of magnitude higher than with currently available cameras. Here we demonstrate the use of a SPAD array for imaging fluorescence correlation spectroscopy (imFCS), a tool to create 2D maps of the dynamics of fluorescent molecules inside living cells. Time-dependent fluorescence fluctuations, due to fluorophores entering and leaving the observed pixels, are evaluated by means of autocorrelation analysis. The multi-τ correlation algorithm is an appropriate choice, as it does not rely on the full data set to be held in memory. Thus, this algorithm can be efficiently implemented in custom logic. We describe a new implementation for massively parallel multi-τ correlation hardware. Our current implementation can calculate 1024 correlation functions at a resolution of 10μs in real-time and therefore correlate real-time image streams from high speed single photon cameras with thousands of pixels.

physics.optics↗

arXiv2009

How proteins squeeze through polymer networks: a Cartesian lattice study

In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamic behaviour of single chains on the lattice is investigated and Rouse scaling is verified. Dynamical dense networks are created by a combined version of the bond fluctuation method and a Metropolis Monte Carlo algorithm. Semidilute behaviour of the dense chain networks is shown. By comparing diffusion of particles in a static and a dynamical chain network, we demonstrate that chain diffusion does not alter the diffusion process of small particles. However, we prove that a dynamical network facilitates the transport of large particles. By weighting the mean square displacement trajectories of particles in the static chain network data from the dynamical network can be reconstructed. Additionally, it is shown that subdiffusive behaviour of particles on short time scales results from trapping processes in the crowded environment of the chain network. In the presented model a protein with 30 nm diameter has an effective diffusion coefficient of 1.24E-11 m^2/s in a chromatin fiber network.

physics.bio-ph↗

arXiv2007

Modelling diffusional transport in the interphase cell nucleus

In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles, a random walk chain model, and a self avoiding random walk chain model with persistence length. By comparing a discrete and a continuous version of the random walk chain model, we demonstrate that lattice discretization does not alter particle diffusion. The influence of the 3D geometry of the fiber network on the particle diffusion is investigated in detail, while varying occupation volume, chain length, persistence length and walker size. It is shown that adjacency of the monomers, the excluded volume effect incorporated in the self avoiding random walk model, and, to a lesser extent, the persistence length, affect particle diffusion. It is demonstrated how the introduction of the effective chain occupancy, which is a convolution of the geometric chain volume with the walker size, eliminates the conformational effects of the network on the diffusion, i.e., when plotting the diffusion coefficient as a function of the effective chain volume, the data fall onto a master curve.

physics.bio-ph↗

arXiv2006

Facilitated diffusion of DNA-binding proteins: Simulation of large systems

The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be calibrated in numerical simulations inside a test system of moderate size. Once this is done, reaction times of systems of arbitrary dimensions are derived by extrapolation, with an accuracy of 10 to 15 percent. The achieved speed up, when compared to explicit simulations of the reaction process, is increasing proportional to the extrapolated volume of the cell.

physics.bio-ph↗

arXiv2005

Facilitated diffusion of DNA-binding proteins: Efficient simulation with the method of excess collisions (MEC)

In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing modes, a free diffusion and a DNA-sliding mode, to search for its specific binding site in the center of the cell. There is no need for a straightforward simulation of this process. Instead, an alternative and exact approach is shown to be essentially faster than explicit random-walk simulations. The speed-up of this novel simulation technique is rapidly growing with system size.

physics.bio-ph↗

arXiv2005

In silicio stretching of chromatin

We present Monte-Carlo (MC) simulations of the stretching of a single 30 nm chromatin fiber. The model approximates the DNA by a flexible polymer chain with Debye-Hückel electrostatics and uses a two-angle zig-zag model for the geometry of the linker DNA connecting the nucleosomes. The latter are represented by flat disks interacting via an attractive Gay-Berne potential. Our results show that the stiffness of the chromatin fiber strongly depends on the linker DNA length. Furthermore, changing the twisting angle between nucleosomes from 90 deg to 130 deg increases the stiffness significantly. An increase in the opening angle from 22 deg to 34 deg leads to softer fibers for small linker lengths. We observe that fibers containing a linker histone at each nucleosome are stiffer compared to those without the linker histone. The simulated persistence lengths and elastic moduli agree with experimental data. Finally, we show that the chromatin fiber does not behave as an isotropic elastic rod, but its rigidity depends on the direction of deformation: chromatin is much more resistant to stretching than to bending.

q-bio.BM↗