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  1. No Access

    Article

    Spatially resolved simulations of membrane reactions and dynamics: Multipolar reaction DPD

    Biophysical chemistry of mesoscale systems and quantitative modeling in systems biology now require a simulation methodology unifying chemical reaction kinetics with essential collective physics. This will ena...

    R. M. Füchslin, T. Maeke, J. S. McCaskill in The European Physical Journal E (2009)

  2. No Access

    Article

    Evolutionary stabilization of generous replicases by complex formation

    The importance of spatial organization for the evolutionary stability of trans-acting replicase systems ( $T\buildrel X \over \longrigh...

    R. M. Füchslin, S. Altmeyer, J. S. McCaskill in The European Physical Journal B - Condense… (2004)

  3. No Access

    Chapter and Conference Paper

    Advanced Simulation in the Configurable Massively Parallel Hardware MereGen

    Simulation of biological molecular systems or studies on self- organization are most suitably studied in spatially extended environments. The study of evolutionary systems, be they optimization problems, chemi...

    U. Tangen, Th. Maeke, J. S. McCaskill in Coupling of Biological and Electronic Systems (2002)

  4. No Access

    Chapter and Conference Paper

    Simulation of evolving systems using FPGA technology

    The theoretical study and simulation of biomolecular reaction systems is generally an extremely computationally intensive task. Especially studies treating evolutionary aspects, i.e. dealing with a variety of dif...

    R. M. Füchslin, S. Altmeyer, J. S. McCaskill in Coupling of Biological and Electronic Syst… (2002)

  5. No Access

    Chapter and Conference Paper

    Isothermal Biochemical Amplification in Miniaturized Reactors with Integrated Microvalves

    A microreactor of 64 nl volume with integrated micro membrane valves of 1.7 mm2 active area was designed for examination of biochemical reaction diffusion systems. The goal was to create a reactor with integrated...

    R. Bräutigam, D. Steen, R. Ehricht… in Microreaction Technology: Industrial Prosp… (2000)

  6. No Access

    Article

    In vitro DNA-based predator-prey system with oscillatory kinetics

    A coupled system of two isothermal in vitro DNA/RNA amplification reactions using different primers is modeled kinetically with realistic rate parameters and shown to exhibit oscillatory behavior in a flow reacto...

    J. Ackermann, B. Wlotzka, J. S. McCaskill in Bulletin of Mathematical Biology (1998)

  7. No Access

    Article

    RNA multi-structure landscapes

    Statistical properties of RNA folding landscapes obtained by the partition function algorithm (McCaskill 1990) are investigated in detail. The pair correlation of free energies as a function of the Hamming dis...

    S. Bonhoeffer, J. S. McCaskill, P. F. Stadler, P. Schuster in European Biophysics Journal (1993)

  8. No Access

    Chapter and Conference Paper

    Equilibrium Distribution of Secondary Structures for Large RNA

    The full distribution of secondary structures for a given RNA (length N < 500) has been available since 1988 using the partition function based calculation developed by the author (McCaskill 1990). All possible n...

    J. S. McCaskill in Computation of Biomolecular Structures (1993)

  9. No Access

    Article

    A stochastic theory of macromolecular evolution

    A stochastic theory of selection introduces the possibility of metastable distributions of macromolecular sequences, “metaspecies”, which succeed one another in a slowing optimization walk which may not reach ...

    J. S. McCaskill in Biological Cybernetics (1984)