Cardiac side effects of antidepressant drugs are well recognized. Adverse effects precipitated by the tricyclic drug desipramine include prolonged QT intervals, torsade de pointes tachycardia, heart failure, and sudden cardiac death. QT prolongation has been primarily attributed to acute blockade of hERG/I(Kr) currents. This study was designed to provide a more complete picture of cellular effects associated with desipramine. hERG channels were expressed in Xenopus laevis oocytes and human embryonic kidney (HEK 293) cells, and potassium currents were recorded using patch clamp and two-electrode voltage clamp electrophysiology. Ventricular action potentials were recorded from guinea pig cardiomyocytes. Protein trafficking and cell viability were evaluated in HEK 293 cells and in HL-1 mouse cardiomyocytes by immunocytochemistry, Western blot analysis, or colorimetric MTT assay, respectively. We found that desipramine reduced hERG currents by binding to a receptor site inside the channel pore. hERG protein surface expression was reduced after short-term treatment, revealing a previously unrecognized mechanism. When long-term effects were studied, forward trafficking was impaired and hERG currents were decreased. Action potential duration was prolonged upon acute and chronic desipramine exposure. Finally, desipramine triggered apoptosis in cells expressing hERG channels. Desipramine exerts at least four different cellular effects: (1) direct hERG channel block, (2) acute reduction of hERG surface expression, (3) chronic disruption of hERG trafficking, and (4) induction of apoptosis. These data highlight the complexity of hERG-associated drug effects.

The purity of single-walled carbon nanotubes (SWNTs) is a key parameter for their integration in electronic, optoelectronic and photonic devices. Samples of pristine SWNTs are inhomogeneous in terms of electric behavior and diameter and contain a variety of amorphous carbon and catalyst residues. To obtain high performance devices, purification of SWNTs is required. Conjugated polymers have emerged as efficient solubilizing and sorting agents for small diameter SWNTs (HiPco tubes, 0.7 nm<Ø<1.1 nm). Nevertheless, reports on polymers able to efficiently sort large diameter SWNTs with Ø>1.1 nm are lacking. Several pyridine-containing copolymers were synthesized for this purpose and showed efficient and selective extraction of semiconducting large diameter SWNTs (PLV tubes, Ø>1.1 nm). High concentration and high purity suspensions are obtained without the use of ultracentrifugation, which gives an up-scaling potential of the method. The emission wavelength is in near infrared region around 1550 nm and fits with broadly used telecommunication wavelength window. The processes taking place at the interface were simulated by a newly designed hybrid coarse-grain model combining density functional theory and geometrical calculation to yield insights into the wrapping processes with an unprecedented level of details for such large diameter SWNTs.

The computational effort of biomolecular simulations can be significantly reduced by means of implicit solvent models in which the energy generally contains a correction depending on the surface area and/or the volume of the molecule. In this article, we present simple derivation of exact, easy-to-use analytical formulas for these quantities and their derivatives with respect to atomic coordinates. In addition, we provide an efficient, linear-scaling algorithm for the construction of the power diagram required for practical implementation of these formulas. Our approach is implemented in a C++ header-only template library.

Molecular simulation methods have increasingly contributed to our understanding of molecular and nanoscale systems. However, the family of Monte Carlo techniques has taken a backseat to molecular dynamics based methods, which is also reflected in the number of available simulation packages. Here, we report the development of a generic, versatile simulation package for stochastic simulations and demonstrate its application to protein conformational change, protein-protein association, small-molecule protein docking, and simulation of the growth of nanoscale clusters of organic molecules. Simulation of molecular and nanoscale systems (SIMONA) is easy to use for standard simulations via a graphical user interface and highly parallel both via MPI and the use of graphical processors. It is also extendable to many additional simulations types. Being freely available to academic users, we hope it will enable a large community of researchers in the life- and materials-sciences to use and extend SIMONA in the future. SIMONA is available for download under http://int.kit.edu/nanosim/simona.

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