The excited-state intramolecular proton transfer process in 3-hydroxyflavone is investigated based on the computed structural parameters and energetics of stationary points of vibronically coupled S1-S2 potential energy surfaces. A conical intersection close to the Franck-Condon point on S1 is identified. The minimum energy of the conical intersection is found to be near-degenerate with the equilibrium minimum of S2. Quantum nuclear wavepacket simulations revealed a small population transfer from the “bright” S1 to “dark” S2 on a time scale shorter than the O—H stretching vibrational period. Such a nonadiabatic transition opens up the possibility of new photophysical and photochemical pathways, including the proton transfer via S2.

Covalent organic frameworks (COFs) are potential candidates for applications in optoelectronic devices and solar cells due to their ability to transport charge through their aromatic molecular units. The highly ordered pi-conjugated TP-COF, consisting of pyrene and triphenylene functional units alternately linked in a mesoporous hexagonal skeleton, is known as the first semiconducting COF. In this paper, we investigate the transport of holes as charge carriers in TP-COF through the pi-stacked pyrene units with a multiscale technique, which combines classical molecular dynamics simulations, quantum chemical calculations, and carrier dynamics simulations. To efficiently estimate the charge transfer integrals from quantum chemical calculations, we developed the FMO-DFTB/LCMO approach by combining the fragment molecular orbital (FMO), density-functional tight-binding (DFTB), and linear-combination of fragment molecular orbitals (LCMO) methods. We observed that the thermal motions of TP-COF cause substantial fluctuations of the transfer integrals. To evaluate the charge carrier diffusion, we performed Ehrenfest dynamics and kinetic Monte Carlo simulations, including the fluctuations of the transfer integrals. Using both simulation approaches, we obtained high carrier mobilities of ca. 2 cm(2) V-1 s(-1). We found that the characteristics of charge transport in COFs are similar to that of oligoacene crystals, suggesting a common mechanism associated with "band-like" transport.

Evolution often diversifies a peptide hormone family into multiple subfamilies, which exert distinct activities by exclusive interaction with specific receptors. Here we show that systematic swapping of pre-existing variation in a subfamily of plant CLE peptide hormones leads to a synthetic bifunctional peptide that exerts activities beyond the original subfamily by interacting with multiple receptors. This approach provides new insights into the complexity and specificity of peptide signalling.

Bright fluorescent molecules with long fluorescence lifetimes are important for the development of lifetime-based fluorescence imaging techniques. Herein, a molecular design is described for simultaneously attaining long fluorescence lifetime (τ) and high brightness (ΦF ×ɛ) in a system that features macrocyclic dimerization of fluorescent π-conjugated skeletons with flexible linkers. An alkylene-linked macrocyclic dimer of bis(thienylethynyl)anthracene was found to show excimer emission with a long fluorescence lifetime (τ≈19 ns) in solution, while maintaining high brightness. A comparison with various relevant derivatives revealed that the macrocyclic structure and the length of the alkylene chains play crucial roles in attaining these properties. In vitro time-gated imaging experiments were conducted as a proof-of-principle for the superiority of this macrocyclic fluorophore relative to the commercial fluorescent dye Alexa Fluor 488.

Abstract With ArmarX we introduce a robot programming environment that has been developed in order to ease the realization of higher level capabilities needed by complex robotic systems such as humanoid robots. ArmarX is built upon the idea that consistent disclosure of the system state strongly facilitates the development process of distributed robot applications. We show the applicability of ArmarX by introducing a robot architecture for a humanoid system and discuss essential aspects based on an exemplary pick and place task. With several tools that are provided by the ArmarX framework, such as graphical user interfaces (GUI) or statechart editors, the programmer is enabled to efficiently build and inspect component based robotics software systems.

The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle-mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) electron-induced repair of a DNA lesion. Also discussed is the further development of the framework, regarding mostly the options for parallelization. (c) 2015 Wiley Periodicals, Inc.

The robot development environment (RDE) ArmarX aims at providing an infrastructure for developing a customized robot framework that allows realizing distributed robot software components. This includes communication properties, start-up and error handling, mechanisms for state implementations, interface definitions and concepts for the structured development of robot programs. In addition to this core functionality, we will show in this paper that ArmarX provides customizable building blocks for high level robot control and how these components can be used to build a generic backbone of the robot software architecture. ArmarX provides standard interfaces and ready-to-use implementations of several core components which are needed to setup a distributed robot software framework.

Charge transfer in peptides and proteins can occur on different pathways, depending on the energetic landscape as well as the coupling between the involved orbitals. Since details of the mechanism and pathways are difficult to access experimentally, different modeling strategies have been successfully applied to study these processes in the past. These can be based on a simple empirical pathway model, efficient tight binding type atomic orbital Hamiltonians or ab initio and density functional calculations. An interesting strategy, which allows an efficient calculations of charge transfer parameters, is based on a fragmentation of the system into functional units. While this works well for systems like DNA, where the charge transfer pathway is naturally divided into distinct molecular fragments, this is less obvious for charge transfer along peptide and protein backbones. In this work, we develop and access a strategy for an effective fragmentation approach, which allows one to compute electronic couplings for large systems along nanosecond time scale molecular dynamics trajectories. The new methodology is applied to a solvated peptide, for which charge transfer properties have been studied recently using an empirical pathway model. As could be expected, dynamical effects turn out to be important, which emphasizes the importance of using effective quantum approaches which allow for sufficient sampling. However, the computed rates are orders of magnitude smaller than experimentally determined, which indicates the shortcomings of present modeling approaches.

Humanoid robotics research has made significant progress and will continue to play central role in robotics research and many applications of the 21st cen-tury. In our research we investigate the engineering of humanoid robots able to act in the real world, learn from human observation, interact and collaborate with humans. In this paper we present recent advances in humanoid grasping and manipulation. We describe the grasping and manipulation system implemented on the humanoid robots ARMAR-IIIa and ARMAR-IIIb [1] to endow these robots with the capability of grasping and manipulating known and unknown objects in real world tasks. Further, we present a new grasping representation in the task space which can be learned from human grasping demonstration and adapted for execution on the robot while taking the grasping task and object specific constraints into consideration.

The first proton transfer in the bacteriorhodopsin photocycle takes place during the L → M transition. Structural details of the pre proton transfer L intermediate have been investigated using experiments and computations. Here, we assess L-state structural models by performing hybrid quantum mechanical/molecular mechanical molecular dynamics and excitation energy calculations. The computations suggest that a water-bridged twisted retinal structure gives the closest agreement with the experimental L/bR shift in the excitation energy.

Channelrhodopsin-2 is a light-gated ion channel, which has been studied intensively over the last decade. Vibrational spectroscopic experiments started to shed light on the structural changes, that occur during the photocycle, especially in the hydrogen-bonded network surrounding the protonated D156 and C128 - the DC gate. However, the interpretation of these experiments was only based on homology models. Since then, an X-ray structure and better computational models became available. In this article, we show that in combination with a recent reparametrization, the approximate DFT method, DFTB, is able to describe the effects of hydrogen bonding on the C=O stretch vibration in carboxylic acids reliably and agrees well with full DFT results. We apply DFTB in a QM/MM framework to perform vibrational analysis of buried aspartic acids in bacteriorhodopsin and channelrhodopsin-2. Using this approach, we can simulate the FTIR spectral difference between D115 in the dark-adapted and K states of bacteriorhodopsin. The FTIR experiments on the DC gate in channelrhodopsin-2 are well described using an indirect model, where D156 and C128 are bridged via a water molecule.

Channelrhodopsins (ChRs) are light-gated cation channels that mediate ion transport across membranes in microalgae (vectorial catalysis). ChRs gain increasing attention as useful tools for the analysis of neural networks in tissues and living animals (optogenetics). In fact, various mutagenesis approaches have realized practical applications with high reliability by enhancement of the expression level, channel kinetics control, and color tuning. Furthermore, the recently published x-ray structure has provided valuable information for further atomistic studies and engineering ChRs for a wider application. The present study is a computational attempt to describe the functional mechanism at the atomic level based on the x-ray structure. We present several structural characteristics that are highly involved in ion channel gating and ion transport, including (1) water distribution, (2) cation binding sites, (3) intrahelical hydrogen bond, (4) DC gate, and (5) active site.

A major strength of humanoid robotics platforms consists in their potential to perform a wide range of manipulation tasks in human-centered environments thanks to their anthropomorphic design. Further, they offer active head-eye systems which allow to extend the observable workspace by employing active gaze control. In this work, we address the question where to look during manipulation tasks while exploiting these two key capabilities of humanoid robots. We present a solution to the gaze selection problem, which takes into account constraints derived from manipulation tasks. Thereby, three different subproblems are addressed: the representation of the acquired visual input, the calculation of saliency based on this representation, and the selection of the most suitable gaze direction. As representation of the visual input, a probabilistic environmental model is discussed, which allows to take into account the dynamic nature of manipulation tasks. At the core of the gaze selection mechanism, a novel saliency measure is proposed that includes accuracy requirements from the manipulation task in the saliency calculation. Finally, an iterative procedure based on spherical graphs is developed in order to decide for the best gaze direction. The feasibility of the approach is experimentally evaluated in the context of bimanual manipulation tasks on the humanoid robot ARMAR-III.

Providing autonomous humanoid robots with the abilities to react in an adaptive and intelligent manner involves low level control and sensing as well as high level reasoning. However, the integration of both levels still remains challenging due to the representational gap between the continuous state space on the sensorimotor level and the discrete symbolic entities used in high level reasoning. In this work, we approach the problem of learning a representation of the space which is applicable on both levels. This representation is grounded on the sensorimotor level by means of exploration and on the language level by making use of common sense knowledge. We demonstrate how spatial knowledge can be extracted from these two sources of experience. Combining the resulting knowledge in a systematic way yields a solution to the grounding problem which has the potential to substantially decrease the learning effort.

Channelrhodopsins (ChRs) are light-gated cation channels that mediate ion transport across membranes in microalgae (vectorial catalysis). ChRs are now widely used for the analysis of neural networks in tissues and living animals with light (optogenetics). For elucidation of functional mechanisms at the atomic level, as well as for further engineering and application, a detailed structure is urgently needed. In the absence of an experimental structure, here we develop a structural ChR model based on several molecular computational approaches, capitalizing on characteristic patterns in amino acid sequences of ChR1, ChR2, Volvox ChRs, Mesostigma ChR, and the recently identified ChR of the halophilic alga Dunaliella salina. In the present model, we identify remarkable structural motifs that may explain fundamental electrophysiological properties of ChR2, ChR1, and their mutants, and in a crucial validation of the model, we successfully reproduce the excitation energy predicted by absorption spectra.

Here, we document the performance of different DFT and DFTB methods with respect to the C−O stretch vibration, both in terms of absolute frequencies and effects of hydrogen bonds on the frequencies. We demonstrate, that PBE/def2-TZVP is a suitable reference for the C−O stretch frequency in carboxylic acids. In the following text, the abbreviations ME (mean error), MAE (mean absolute error), MSE (mean squared error) and GGA (generalized gradient approximation) are used.