@misc{BaldKeller2014,
  author    = {Bald, Ilko and Keller, Adrian},
  title     = {Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {9},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47584},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-475843},
  pages     = {13803 -- 13823},
  year      = {2014},
  abstract  = {DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.},
  language  = {en}
}
@misc{BaldKopyraKeller2014,
  author    = {Bald, Ilko and Kopyra, Janina and Keller, Adrian},
  title     = {On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-73412},
  pages     = {6825 -- 6829},
  year      = {2014},
  abstract  = {Gemcitabine (2′,2′-difluorocytidine) is a well-known radiosensitizer routinely applied in concomitant chemoradiotherapy. During irradiation of biological media with high-energy radiation secondary low-energy (<10 eV) electrons are produced that can directly induce chemical bond breakage in DNA by dissociative electron attachment (DEA). Here, we investigate and compare DEA to the three molecules 2′-deoxycytidine, 2′-deoxy-5-fluorocytidine, and gemcitabine. Fluorination at specific molecular sites, i.e., nucleobase or sugar moiety, is found to control electron attachment and subsequent dissociation pathways. The presence of two fluorine atoms at the sugar ring results in more efficient electron attachment to the sugar moiety and subsequent bond cleavage. For the formation of the dehydrogenated nucleobase anion, we obtain an enhancement factor of 2.8 upon fluorination of the sugar, whereas the enhancement factor is 5.5 when the nucleobase is fluorinated. The observed fragmentation reactions suggest enhanced DNA strand breakage induced by secondary electrons when gemcitabine is incorporated into DNA.},
  language  = {en}
}
@misc{CherstvyChechkinMetzler2014,
  author    = {Cherstvy, Andrey G. and Chechkin, Aleksei V. and Metzler, Ralf},
  title     = {Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity},
  number    = {168},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-74021},
  pages     = {1591 -- 1601},
  year      = {2014},
  abstract  = {We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.},
  language  = {en}
}
@misc{CommingesFrascaSuetterlinetal.2014,
  author    = {Comminges, Cl{\´e}ment and Frasca, Stefano and S{\"u}tterlin, Martin and Wischerhoff, Erik and Laschewsky, Andr{\´e} and Wollenberger, Ursula},
  title     = {Surface modification with thermoresponsive polymer brushes for a switchable electrochemical sensor},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-99471},
  year      = {2014},
  abstract  = {Elaboration of switchable surfaces represents an interesting way for the development of a new generation of electrochemical sensors. In this paper, a method for growing thermoresponsive polymer brushes from a gold surface pre-modified with polyethyleneimine (PEI), subsequent layer-by-layer polyelectrolyte assembly and adsorption of a charged macroinitiator is described. We propose an easy method for monitoring the coil-to-globule phase transition of the polymer brush using an electrochemical quartz crystal microbalance with dissipation (E-QCM-D). The surface of these polymer modified electrodes shows reversible switching from the swollen to the collapsed state with temperature. As demonstrated from E-QCM-D measurements using an original signal processing method, the switch is operating in three reversible steps related to different interfacial viscosities. Moreover, it is shown that the one electron oxidation of ferrocene carboxylic acid is dramatically affected by the change from the swollen to the collapsed state of the polymer brush, showing a spectacular 86\% decrease of the charge transfer resistance between the two states.},
  language  = {en}
}
@misc{CywińskiNonoCharbonniereetal.2014,
  author    = {Cywiński, Piotr J. and Nono, Katia Nchimi and Charbonni{\`e}re, Lo{\"i}c J. and Hammann, Tommy and L{\"o}hmannsr{\"o}ben, Hans-Gerd},
  title     = {Photophysical evaluation of a new functional terbium complex in FRET-based time-resolved homogenous fluoroassays},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-95390},
  pages     = {6060 -- 6067},
  year      = {2014},
  abstract  = {A new functional luminescent lanthanide complex (LLC) has been synthesized with terbium as a central lanthanide ion and biotin as a functional moiety. Unlike in typical lanthanide complexes assembled via carboxylic moieties, in the presented complex, four phosphate groups are chelating the central lanthanide ion. This special chemical assembly enhances the complex stability in phosphate buffers conventionally used in biochemistry. The complex synthesis strategy and photophysical properties are described as well as the performance in time-resolved F{\"o}rster Resonance Energy Transfer (FRET) assays. In those assays, this biotin-LLC transferred energy either to acceptor organic dyes (Cy5 or AF680) labelled on streptavidin or to quantum dots (QD655 or QD705) surface-functionalised with streptavidins. The permanent spatial donor-acceptor proximity is assured through strong and stable biotin-streptavidin binding. The energy transfer is evidenced from the quenching observed in donor emission and from a decrease in donor luminescence decay, both associated with simultaneous increase in acceptor intensity and in the decay time. The dye-based assays are realised in TRIS and in PBS, whereas QD-based systems are studied in borate buffer. The delayed emission analysis allows for quantifying the recognition process and for auto-fluorescence-free detection, which is particularly relevant for application in bioanalysis. In accordance with F{\"o}rster theory, F{\"o}rster-radii (R0) were found to be around 60 {\AA} for organic dyes and around 105 {\AA} for QDs. The FRET efficiency (η) reached 80\% and 25\% for dye and QD acceptors, respectively. Physical donor-acceptor distances (r) have been determined in the range 45-60 {\AA} for organic dye acceptors, while for acceptor QDs between 120 {\AA} and 145 {\AA}. This newly synthesised biotin-LLC extends the class of highly sensitive analytical tools to be applied in the bioanalytical methods such as time-resolved fluoroimmunoassays (TR-FIA), luminescent imaging and biosensing.},
  language  = {en}
}
@misc{EhlertUngerSaalfrank2014,
  author    = {Ehlert, Christopher and Unger, Wolfgang E. S. and Saalfrank, Peter},
  title     = {C K-edge NEXAFS spectra of graphene with physical and chemical defects},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-74429},
  pages     = {14083 -- 14095},
  year      = {2014},
  abstract  = {Recently, C K-edge Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra of graphite (HOPG) surfaces have been measured for the pristine material, and for HOPG treated with either bromine or krypton plasmas (Lippitz et al., Surf. Sci., 2013, 611, L1). Changes of the NEXAFS spectra characteristic for physical (krypton) and/or chemical/physical modifications of the surface (bromine) upon plasma treatment were observed. Their molecular origin, however, remained elusive. In this work we study by density functional theory, the effects of selected point and line defects as well as chemical modifications on NEXAFS carbon K-edge spectra of single graphene layers. For Br-treated surfaces, also Br 3d X-ray Photoelectron Spectra (XPS) are simulated by a cluster approach, to identify possible chemical modifications. We observe that some of the defects related to plasma treatment lead to characteristic changes of NEXAFS spectra, similar to those in experiment. Theory provides possible microscopic origins for these changes.},
  language  = {en}
}
@misc{ErmeydanCabaneGierlingeretal.2014,
  author    = {Ermeydan, Mahmut Ali and Cabane, Etienne and Gierlinger, Notburga and Koetz, Joachim and Burgert, Ingo},
  title     = {Improvement of wood material properties via in situ polymerization of styrene into tosylated cell walls},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-98736},
  pages     = {8},
  year      = {2014},
  abstract  = {As an engineering material derived from renewable resources, wood possesses excellent mechanical properties in view of its light weight but also has some disadvantages such as low dimensional stability upon moisture changes and low durability against biological attack. Polymerization of hydrophobic monomers in the cell wall is one of the potential approaches to improve the dimensional stability of wood. A major challenge is to insert hydrophobic monomers into the hydrophilic environment of the cell walls, without increasing the bulk density of the material due to lumen filling. Here, we report on an innovative and simple method to insert styrene monomers into tosylated cell walls (i.e. -OH groups from natural wood polymers are reacted with tosyl chloride) and carry out free radical polymerization under relatively mild conditions, generating low wood weight gains. In-depth SEM and confocal Raman microscopy analysis are applied to reveal the distribution of the polystyrene in the cell walls and the lumen. The embedding of polystyrene in wood results in reduced water uptake by the wood cell walls, a significant increase in dimensional stability, as well as slightly improved mechanical properties measured by nanoindentation.},
  language  = {en}
}
@misc{ErmeydanCabaneHassetal.2014,
  author    = {Ermeydan, Mahmut Ali and Cabane, Etienne and Hass, Philipp and Koetz, Joachim and Burgert, Ingo},
  title     = {Fully biodegradable modification of wood for improvement of dimensional stability and water absorption properties by poly(ε-caprolactone) grafting into the cell walls},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-97265},
  pages     = {3313 -- 3321},
  year      = {2014},
  abstract  = {Materials derived from renewable resources are highly desirable in view of more sustainable manufacturing. Among the available natural materials, wood is one of the key candidates, because of its excellent mechanical properties. However, wood and wood-based materials in engineering applications suffer from various restraints, such as dimensional instability upon humidity changes. Several wood modification treatments increase water repellence, but the insertion of hydrophobic polymers can result in a composite material which cannot be considered as renewable anymore. In this study, we report on the grafting of the fully biodegradable poly(ε-caprolactone) (PCL) inside the wood cell walls by Sn(Oct)2 catalysed ring-opening polymerization (ROP). The presence of polyester chains within the wood cell wall structure is monitored by confocal Raman imaging and spectroscopy as well as scanning electron microscopy. Physical tests reveal that the modified wood is more hydrophobic due to the bulking of the cell wall structure with the polyester chains, which results in a novel fully biodegradable wood material with improved dimensional stability.},
  language  = {en}
}
@misc{GhoshCherstvyMetzler2014,
  author    = {Ghosh, Surya K. and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Non-universal tracer diffusion in crowded media of non-inert obstacles},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-77128},
  pages     = {1847 -- 1858},
  year      = {2014},
  abstract  = {We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer-obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer-obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer-crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids.},
  language  = {en}
}
@misc{Laschewsky2014,
  author    = {Laschewsky, Andr{\´e}},
  title     = {Structures and synthesis of zwitterionic polymers},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1043},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-47616},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476167},
  pages     = {60},
  year      = {2014},
  abstract  = {The structures and synthesis of polyzwitterions ("polybetaines") are reviewed, emphasizing the literature of the past decade. Particular attention is given to the general challenges faced, and to successful strategies to obtain polymers with a true balance of permanent cationic and anionic groups, thus resulting in an overall zero charge. Also, the progress due to applying new methodologies from general polymer synthesis, such as controlled polymerization methods or the use of "click" chemical reactions is presented. Furthermore, the emerging topic of responsive ("smart") polyzwitterions is addressed. The considerations and critical discussions are illustrated by typical examples.},
  language  = {en}
}