Holger Merlitz

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A Brownian dynamics (BD) model described in the accompanying paper (Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA, and other wormlike chain polyelectrolytes. Biophys. J. 74:000-000) has been used for computing the end-to-end distance distribution function, the cyclization(More)
The development of simulation techniques that can elucidate the function of biomolecular nanodevices is still in its infancy. In this paper we summarize our approach to the investigation of structural properties of biomolecular systems with stochastic optimization methods. We briefly review the stochastic tunnelling method and summarize applications in two(More)
In this paper a lattice model for the diffusional transport of particles in the interphase cell nucleus is proposed. The dynamical behavior 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(More)
We report results for the in-silico screening of a database of 10000 flexible compounds against various crystal structures of the thymidine kinase receptor complexed with 10 known inhibitors. The ligands were docked with the stochastic tunneling method using a first-principle based scoring function. Using a rigid receptor we find large deviations in the(More)
Using a cascadic version of the stochastic tunneling method we perform an all-atom database screen over 186,000 flexible ligands of the NCI 3D database against the thymidine kinase receptor. By analyzing the errors in the binding energy we demonstrate how the cascadic technique is superior to conventional sequential docking techniques and how reliable(More)
Thermal rectifiers whose forward heat fluxes are greater than reverse counterparts have been extensively studied. Here we have discovered, idealized, and derived the ultimate limit of such rectification ratios, which are partially validated by numerical simulations, experiments, and micro-scale Hamiltonian-oscillator analyses. For rectifiers whose thermal(More)
Pulse implementation or switching-off (PISO) of electrical currents has become a common operation in junction-temperature (Tj) measurements for semiconductor devices since 2004. Here we have experimentally discovered a substantial discrepancy between Tj values with, and without, PISO (e.g., 36.8 °C versus 76.5 °C above the ambient temperature at 25.0 °C).(More)
Intermediate filament (IF) elongation proceeds via full-width "mini-filaments", referred to as "unit-length" filaments (ULFs), which instantaneously form by lateral association of extended coiled-coil complexes after assembly is initiated. In a comparatively much slower process, ULFs longitudinally interact end-to-end with other ULFs to form short(More)
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