TY - JOUR A1 - Gong, Chen Chris A1 - Klumpp, Stefan T1 - Modeling sRNA-Regulated Plasmid Maintenance JF - PLoS one N2 - We study a theoretical model for the toxin-antitoxin (hok/sok) mechanism for plasmid maintenance in bacteria. Toxin-antitoxin systems enforce the maintenance of a plasmid through post-segregational killing of cells that have lost the plasmid. Key to their function is the tight regulation of expression of a protein toxin by an sRNA antitoxin. Here, we focus on the nonlinear nature of the regulatory circuit dynamics of the toxin-antitoxin mechanism. The mechanism relies on a transient increase in protein concentration rather than on the steady state of the genetic circuit. Through a systematic analysis of the parameter dependence of this transient increase, we confirm some known design features of this system and identify new ones: for an efficient toxin-antitoxin mechanism, the synthesis rate of the toxin’s mRNA template should be lower that of the sRNA antitoxin, the mRNA template should be more stable than the sRNA antitoxin, and the mRNA-sRNA complex should be more stable than the sRNA antitoxin. Moreover, a short half-life of the protein toxin is also beneficial to the function of the toxin-antitoxin system. In addition, we study a therapeutic scenario in which a competitor mRNA is introduced to sequester the sRNA antitoxin, causing the toxic protein to be expressed. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0169703 SN - 1932-6203 VL - 12 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Couto, Rafael C. A1 - Cruz, Vinicius V. A1 - Ertan, Emelie A1 - Eckert, Sebastian A1 - Fondell, Mattis A1 - Dantz, Marcus A1 - Kennedy, Brian A1 - Schmitt, Thorsten A1 - Pietzsch, Annette A1 - Guimaraes, Freddy F. A1 - Agren, Hans A1 - Odelius, Michael A1 - Kimberg, Victor A1 - Föhlisch, Alexander T1 - Selective gating to vibrational modes through resonant X-ray scattering JF - Nature Communications N2 - The dynamics of fragmentation and vibration of molecular systems with a large number of coupled degrees of freedom are key aspects for understanding chemical reactivity and properties. Here we present a resonant inelastic X-ray scattering (RIXS) study to show how it is possible to break down such a complex multidimensional problem into elementary components. Local multimode nuclear wave packets created by X-ray excitation to different core-excited potential energy surfaces (PESs) will act as spatial gates to selectively probe the particular ground-state vibrational modes and, hence, the PES along these modes. We demonstrate this principle by combining ultra-high resolution RIXS measurements for gas-phase water with state-of-the-art simulations. Y1 - 2017 U6 - https://doi.org/10.1038/ncomms14165 SN - 2041-1723 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Mardoukhi, Ahmad A1 - Mardoukhi, Yousof A1 - Hokka, Mikko A1 - Kuokkala, Veli-Tapani T1 - Effects of strain rate and surface cracks on the mechanical behaviour of Balmoral Red granite JF - Philosophical Transactions of the Royal Society of London, Series A : Mathematical, Physical and Engineering Sciences N2 - This work presents a systematic study on the effects of strain rate and surface cracks on the mechanical properties and behaviour of Balmoral Red granite. The tensile behaviour of the rock was studied at low and high strain rates using Brazilian disc samples. Heat shocks were used to produce samples with different amounts of surface cracks. The surface crack patterns were analysed using optical microscopy, and the complexity of the patterns was quantified by calculating the fractal dimensions of the patterns. The strength of the rock clearly drops as a function of increasing fractal dimensions in the studied strain rate range. However, the dynamic strength of the rock drops significantly faster than the quasi-static strength, and, because of this, also the strain rate sensitivity of the rock decreases with increasing fractal dimensions. This can be explained by the fracture behaviour and fragmentation during the dynamic loading, which is more strongly affected by the heat shock than the fragmentation at low strain rates. KW - split Hopkinson pressure bar KW - rock KW - granite KW - dynamic loading KW - fractal dimension KW - surface cracks Y1 - 2017 U6 - https://doi.org/10.1098/rsta.2016.0179 SN - 1364-503X SN - 1471-2962 VL - 375 IS - 2085 PB - Royal Society CY - London ER - TY - JOUR A1 - Goychuk, Igor T1 - Quantum ergodicity breaking in semi-classical electron transfer dynamics JF - Physical chemistry, chemical physics : a journal of European Chemical Societies N2 - Can the statistical properties of single-electron transfer events be correctly predicted within a common equilibrium ensemble description? This fundamental in nanoworld question of ergodic behavior is scrutinized within a very basic semi-classical curve-crossing problem. It is shown that in the limit of non-adiabatic electron transfer (weak tunneling) well-described by the Marcus-Levich-Dogonadze (MLD) rate the answer is yes. However, in the limit of the so-called solvent-controlled adiabatic electron transfer, a profound breaking of ergodicity occurs. Namely, a common description based on the ensemble reduced density matrix with an initial equilibrium distribution of the reaction coordinate is not able to reproduce the statistics of single-trajectory events in this seemingly classical regime. For sufficiently large activation barriers, the ensemble survival probability in a state remains nearly exponential with the inverse rate given by the sum of the adiabatic curve crossing (Kramers) time and the inverse MLD rate. In contrast, near to the adiabatic regime, the single-electron survival probability is clearly non-exponential, even though it possesses an exponential tail which agrees well with the ensemble description. Initially, it is well described by a Mittag-Leffler distribution with a fractional rate. Paradoxically, the mean transfer time in this classical on the ensemble level regime is well described by the inverse of the nonadiabatic quantum tunneling rate on a single particle level. An analytical theory is developed which perfectly agrees with stochastic simulations and explains our findings. Y1 - 2016 U6 - https://doi.org/10.1039/c6cp07206b SN - 1463-9076 SN - 1463-9084 VL - 19 SP - 3056 EP - 3066 PB - Royal Society of Chemistry CY - Cambridge ER - TY - JOUR A1 - Kunnus, Kristjan A1 - Josefsson, I. A1 - Schreck, Simon Frederik A1 - Quevedo, W. A1 - Miedema, P. S. A1 - Techert, S. A1 - de Groot, F. M. F. A1 - Föhlisch, Alexander A1 - Odelius, M. A1 - Wernet, Ph. T1 - Quantifying covalent interactions with resonant inelastic soft X-ray scattering BT - case study of Ni2+ aqua complex JF - Chemical physics letters N2 - We analyze the effects of covalent interactions in Ni 2p3d resonant inelastic X-ray scattering (RIXS) spectra from aqueous Ni2+ ions and find that the relative RIXS intensities of ligand-to-metal charge-transfer final states with respect to the ligand-field final states reflect the covalent mixing between Ni 3d and water orbitals. Specifically, the experimental intensity ratio at the Ni L-3-edge allows to determine that the Ni 3d orbitals have on average 5.5% of water character. We propose that 2p3d RIXS at the Ni L-3-edge can be utilized to quantify covalency in Ni complexes without the use of external references or simulations. KW - Transition-metal ion KW - Aqueous solution KW - Covalent interaction KW - Resonant inelastic X-ray scattering KW - Ligand-field state KW - Charge-transfer state Y1 - 2016 U6 - https://doi.org/10.1016/j.cplett.2016.12.046 SN - 0009-2614 SN - 1873-4448 VL - 669 SP - 196 EP - 201 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Vandewal, Koen A1 - Benduhn, Johannes A1 - Schellhammer, Karl Sebastian A1 - Vangerven, Tim A1 - Rückert, Janna E. A1 - Piersimoni, Fortunato A1 - Scholz, Reinhard A1 - Zeika, Olaf A1 - Fan, Yeli A1 - Barlow, Stephen A1 - Neher, Dieter A1 - Marder, Seth R. A1 - Manca, Jean A1 - Spoltore, Donato A1 - Cuniberti, Gianaurelio A1 - Ortmann, Frank T1 - Absorption Tails of Donor BT - C-60 Blends Provide Insight into Thermally Activated Charge-Transfer Processes and Polaron Relaxation JF - Journal of the American Chemical Society N2 - In disordered organic semiconductors, the transfer of a rather localized charge carrier from one site to another triggers a deformation of the molecular structure quantified by the intramolecular relaxation energy. A similar structural relaxation occurs upon population of intermolecular charge-transfer (CT) states formed at organic electron donor (D)-acceptor (A) interfaces. Weak CT absorption bands for D A complexes occur at photon energies below the optical gaps of both the donors and the C-60 acceptor as a result of optical transitions from the neutral ground state to the ionic CT state. In this work, we show that temperature-activated intramolecular vibrations of the ground state play a major role in determining the line shape of such CT absorption bands. This allows us to extract values for the relaxation energy related to the geometry change from neutral to ionic CT complexes. Experimental values for the relaxation energies of 20 D:C-60 CT complexes correlate with values calculated within density functional theory. These results provide an experimental method for determining the polaron relaxation energy in solid-state organic D-A blends and show the importance of a reduced relaxation energy, which we introduce to characterize thermally activated CT processes. Y1 - 2017 U6 - https://doi.org/10.1021/jacs.6b12857 SN - 0002-7863 VL - 139 IS - 4 SP - 1699 EP - 1704 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Henkel, Carsten T1 - Nanoscale Thermal Transfer BT - an Invitation to Fluctuation Electrodynamics JF - Zeitschrift für Naturforschung A N2 - An electromagnetic theory of thermal radiation is outlined, based on the fluctuation electrodynamics of Rytov and co-workers. We discuss the basic concepts and the status of different approximations. The physical content is illustrated with a few examples on near-field heat transfer. KW - Heat Transfer KW - Near-Field Optics KW - Thermal Radiation Y1 - 2017 U6 - https://doi.org/10.1515/zna-2016-0372 SN - 0932-0784 SN - 1865-7109 VL - 72 IS - 2 SP - 99 EP - 108 PB - De Gruyter CY - Berlin ER - TY - JOUR A1 - Sun, Ning-Chen A1 - de Grijs, Richard A1 - Subramanian, Smitha A1 - Cioni, Maria-Rosa L. A1 - Rubele, Stefano A1 - Bekki, Kenji A1 - Ivanov, Valentin D. A1 - Piatti, Andrés E. A1 - Ripepi, Vincenzo T1 - The VMC Survey. XXII. Hierarchical star formation in the 30 Doradus-N158-N159-N160 star-forming complex JF - The astrophysical journal : an international review of spectroscopy and astronomical physics N2 - We study the hierarchical stellar structures in a similar to 1.5 deg(2) area covering the 30. Doradus-N158-N159-N160 starforming complex with the VISTA Survey of. Magellanic Clouds. Based on the young upper main-sequence stars, we find that the surface densities cover a wide range of values, from log(Sigma.pc(2))less than or similar to -2.0 to log(Sigma. pc(2)) greater than or similar to 0.0. Their distributions are highly non-uniform, showing groups that frequently have subgroups inside. The sizes of the stellar groups do not exhibit characteristic values, and range continuously from several parsecs to more than 100. pc; the cumulative size distribution can be well described by a single power law, with the power-law index indicating a projected fractal dimension D-2 = 1.6 +/- 0.3. We suggest that the phenomena revealed here support a scenario of hierarchical star formation. Comparisons with other star-forming regions and galaxies are also discussed. KW - galaxies: clusters: general KW - infrared: stars KW - Magellanic Clouds KW - stars: formation Y1 - 2017 U6 - https://doi.org/10.3847/1538-4357/835/2/171 SN - 0004-637X SN - 1538-4357 VL - 835 IS - 2 PB - Institute of Physics Publ. CY - Bristol ER - TY - JOUR A1 - Koopman, Wouter-Willem Adriaan A1 - Natali, Marco A1 - Donati, Giovanni P. A1 - Muccini, Michele A1 - Toffanin, Stefano T1 - Charge-exciton interaction rate in organic field-effect transistors by means of transient photoluminescence electromodulated spectroscopy JF - ACS photonics N2 - Organic light-emitting transistors (OLETs) offer a huge potential for the design of highly integrated multifunctional optoelectronic systems and of intense nano scale light sources, such as the long-searched-for electrically pumped organic laser. In order to fulfill these promises, the efficiency and brightness of the current state-of-the-art devices have to be increased significantly. The dominating quenching process limiting the external quantum efficiency in OLETs is charge-exciton interaction. A comprehensive understanding of this quenching process is therefore of paramount importance. The present article reports a systematic investigation of charge-exciton interaction in organic transistors employing time resolved photoluminescence electro-modulation (PLEM) spectroscopy on the picosecond time scale. The results show that the injected charges reduce the exciton radiative recombination in two ways: (i) charges may prevent the generation of excitons and (ii) charges activate a further nonradiative channel for the exciton decay. Moreover, the transient PLEM measurements clearly reveal that not only trapped charges, as already reported in literature, but rather the entire injected charge density contributes to the quenching of the exciton population. KW - photoluminescence quenching KW - charge density KW - exciton dynamics KW - organic KW - field-effect transistor KW - light emission KW - optical spectroscopy Y1 - 2017 U6 - https://doi.org/10.1021/acsphotonics.6b00573 SN - 2330-4022 VL - 4 IS - 2 SP - 282 EP - 291 PB - American Chemical Society CY - Washington, DC ER - TY - JOUR A1 - Almeida, Leonardo A. A1 - Sana, H. A1 - Taylor, W. A1 - Barbá, Rodolfo A1 - Bonanos, Alceste Z. A1 - Crowther, Paul A1 - Damineli, Augusto A1 - de Koter, A. A1 - de Mink, Selma E. A1 - Evans, C. J. A1 - Gieles, Mark A1 - Grin, Nathan J. A1 - Hénault-Brunet, V. A1 - Langer, Norbert A1 - Lennon, D. A1 - Lockwood, Sean A1 - Maíz Apellániz, Jesús A1 - Moffat, A. F. J. A1 - Neijssel, C. A1 - Norman, C. A1 - Ramírez-Agudelo, O. H. A1 - Richardson, N. D. A1 - Schootemeijer, Abel A1 - Shenar, Tomer A1 - Soszyński, Igor A1 - Tramper, Frank A1 - Vink, J. S. T1 - The tarantula massive binary monitoring BT - I. Observational campaign and OB-type spectroscopic binaries JF - Astronomy and astrophysics : an international weekly journal N2 - Context: Massive binaries play a crucial role in the Universe. Knowing the distributions of their orbital parameters is important for a wide range of topics from stellar feedback to binary evolution channels and from the distribution of supernova types to gravitational wave progenitors, yet no direct measurements exist outside the Milky Way. Aims: The Tarantula Massive Binary Monitoring project was designed to help fill this gap by obtaining multi-epoch radial velocity (RV) monitoring of 102 massive binaries in the 30 Doradus region. Methods: In this paper we analyze 32 FLAMES/GIRAFFE observations of 93 O- and 7 B-type binaries. We performed a Fourier analysis and obtained orbital solutions for 82 systems: 51 single-lined (SB1) and 31 double-lined (SB2) spectroscopic binaries. Results: Overall, the binary fraction and orbital properties across the 30 Doradus region are found to be similar to existing Galactic samples. This indicates that within these domains environmental effects are of second order in shaping the properties of massive binary systems. A small difference is found in the distribution of orbital periods, which is slightly flatter (in log space) in 30 Doradus than in the Galaxy, although this may be compatible within error estimates and differences in the fitting methodology. Also, orbital periods in 30 Doradus can be as short as 1.1 d, somewhat shorter than seen in Galactic samples. Equal mass binaries (q> 0.95) in 30 Doradus are all found outside NGC 2070, the central association that surrounds R136a, the very young and massive cluster at 30 Doradus’s core. Most of the differences, albeit small, are compatible with expectations from binary evolution. One outstanding exception, however, is the fact that earlier spectral types (O2–O7) tend to have shorter orbital periods than later spectral types (O9.2–O9.7). Conclusions: Our results point to a relative universality of the incidence rate of massive binaries and their orbital properties in the metallicity range from solar (Z⊙) to about half solar. This provides the first direct constraints on massive binary properties in massive star-forming galaxies at the Universe’s peak of star formation at redshifts z ~ 1 to 2 which are estimated to have Z ~ 0.5 Z⊙. KW - stars: early-type KW - stars: massive KW - binaries: spectroscopic KW - binaries: close Y1 - 2017 U6 - https://doi.org/10.1051/0004-6361/201629844 SN - 1432-0746 VL - 598 PB - EDP Sciences CY - Les Ulis ER -