Charge carrier dynamics in an organic semiconductor can often be described in terms of charge hopping between localized states. The hopping rates depend on electronic coupling elements, reorganization energies, and driving forces, which vary as a function of position and orientation of the molecules. The exact evaluation of these contributions in a molecular assembly is computationally prohibitive. Various, often semiempirical, approximations are employed instead. In this work, we review some of these approaches and introduce a software toolkit which implements them. The purpose of the toolkit is to simplify the workflow for charge transport simulations, provide a uniform error control for the methods and a flexible platform for their development, and eventually allow in silico prescreening of organic semiconductors for specific applications. All implemented methods are illustrated by studying charge transport in amorphous films of tris-(8-hydroxyquinoline)aluminum, a common organic semiconductor.

Coarse-graining is a systematic way of reducing the number of degrees of freedom representing a system of interest. Several coarse-graining techniques have so far been developed, such as iterative Boltzmann inversion, force-matching, and inverse Monte Carlo. However, there is no unified framework that implements these methods and that allows their direct comparison. We present a versatile object-oriented toolkit for coarse-graining applications (VOTCA) that implements these techniques and that provides a flexible modular platform for the further development of coarse-graining techniques. All methods are illustrated and compared by coarse-graining the SPC/E water model, liquid methanol, liquid propane, and a single molecule of hexane.

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Predictions of charge-carrier mobilities in amorphous semiconductors often rely on charge transport simulations in microscopically sized systems, where transport is dispersive and mobilities are system-size dependent. We propose a method for extrapolating a macroscopic nondispersive mobility from the temperature dependence of a microscopic one. The method is tested on an amorphous phase of tris͑8-hydroxyquinoline͒ aluminum, for which the temperature dependence of a microscopic hole mobility is obtained by combining molecular-dynamics simulations for generating material morphologies, electronic-structure calculations for determining charge hopping rates, and kinetic Monte Carlo simulations for studying charge dynamics. The extracted value of the nondispersive mobility and its electric field dependence agree well with the results of time-of-flight experiments.

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The effect of the force‐field parameters on the morphology and charge dynamics is assessed for amorphous films of tris(8‐hydroxyquinolinato)aluminium. Two force‐fields are used for non‐bonded parameters, OPLS and Williams 99, whereas bonded interactions are obtained from first‐principles calculations. By comparing densities and glass transition temperatures we conclude that the OPLS‐based force field provides a better description of the amorphous morphology. At the same time, the difference in molecular packing does not significantly affect the distribution of charge hopping rates or charge carrier mobility.

A bottom-up coarse-graining procedure for peptides in aqueous solution is presented, where the interactions in the coarse-grained (CG) model are determined such that the CG peptide samples conformations according to a high-resolution (atomistic) model. It is shown that important aspects of conformational sampling, such as correlated degrees of freedom (DOF) which play an important role in secondary structure formation, can be reproduced in the CG description. In some cases, microscopic structural/conformational details are lost in the coarse-graining process. We show that these "lost" properties can be recovered in a backmapping procedure which reintroduces atomistic DOF into CG structures - as long as the overall conformational sampling of the molecule is correctly represented in the CG level of resolution. Thus, it is possible to link an existing all-atom model of a biomolecular system with a CG description such that after inverse mapping one can recover structures at high resolution with the correctly sampled (according to the atomistic model) conformational properties.

Рассматривается иммобилизация клеток оксигенных фототрофных микроорганиз-мов -цианобактерий и эукариотических микроводорослей -в природе и в искусствен-ных системах. В обзоре подчеркивается, что существование клеток микроорганизмов в прикрепленном состоянии, например, в составе биопленок, является широко распро-страненной в природе стратегией, обеспечивающей выживание клеток. Таким образом, искусственно иммобилизованные клетки оксигенных фототрофных микроорганизмов можно рассматривать как особую группу биомиметических материалов. Особое внимание уделено изучению влияния различных способов иммобилизации на физиологическое состояние клеток цианобактерий и микроводорослей, их устойчивость к стрессовым воз-действиям, а также продуктивность культур, находящихся в иммобилизованном состоя-нии. В обзоре проводится анализ преимуществ и недостатков современных методов им-мобилизации и используемых в настоящее время носителей. Освещаются возможности применения иммобилизованных культур оксигенных фототрофных микроорганизмов в различных областях биотехнологии, таких как получение биомассы и ценных метаболи-тов, сбор биомассы, очистка водных акваторий и сточных вод от тяжелых металлов, из-бытка биогенных элементов и органических загрязнителей.