TY - JOUR AB - Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved. AU - Friedlander, Tamar AU - Mayo, Avraham AU - Tlusty, Tsvi AU - Alon, Uri ID - 1827 IS - 3 JF - PLoS Computational Biology TI - Evolution of bow-tie architectures in biology VL - 11 ER - TY - JOUR AB - Background: Indirect genetic effects (IGEs) occur when genes expressed in one individual alter the expression of traits in social partners. Previous studies focused on the evolutionary consequences and evolutionary dynamics of IGEs, using equilibrium solutions to predict phenotypes in subsequent generations. However, whether or not such steady states may be reached may depend on the dynamics of interactions themselves. Results: In our study, we focus on the dynamics of social interactions and indirect genetic effects and investigate how they modify phenotypes over time. Unlike previous IGE studies, we do not analyse evolutionary dynamics; rather we consider within-individual phenotypic changes, also referred to as phenotypic plasticity. We analyse iterative interactions, when individuals interact in a series of discontinuous events, and investigate the stability of steady state solutions and the dependence on model parameters, such as population size, strength, and the nature of interactions. We show that for interactions where a feedback loop occurs, the possible parameter space of interaction strength is fairly limited, affecting the evolutionary consequences of IGEs. We discuss the implications of our results for current IGE model predictions and their limitations. AU - Trubenova, Barbora AU - Novak, Sebastian AU - Hager, Reinmar ID - 1809 IS - 5 JF - PLoS One TI - Indirect genetic effects and the dynamics of social interactions VL - 10 ER - TY - GEN AU - Trubenova, Barbora AU - Novak, Sebastian AU - Hager, Reinmar ID - 9772 TI - Description of the agent based simulations ER - TY - GEN AU - Friedlander, Tamar AU - Mayo, Avraham E. AU - Tlusty, Tsvi AU - Alon, Uri ID - 9773 TI - Evolutionary simulation code ER - TY - JOUR AB - The tunability of topological surface states and controllable opening of the Dirac gap are of fundamental and practical interest in the field of topological materials. In the newly discovered topological crystalline insulators (TCIs), theory predicts that the Dirac node is protected by a crystalline symmetry and that the surface state electrons can acquire a mass if this symmetry is broken. Recent studies have detected signatures of a spontaneously generated Dirac gap in TCIs; however, the mechanism of mass formation remains elusive. In this work, we present scanning tunnelling microscopy (STM) measurements of the TCI Pb 1â'x Sn x Se for a wide range of alloy compositions spanning the topological and non-topological regimes. The STM topographies reveal a symmetry-breaking distortion on the surface, which imparts mass to the otherwise massless Dirac electrons-a mechanism analogous to the long sought-after Higgs mechanism in particle physics. Interestingly, the measured Dirac gap decreases on approaching the trivial phase, whereas the magnitude of the distortion remains nearly constant. Our data and calculations reveal that the penetration depth of Dirac surface states controls the magnitude of the Dirac mass. At the limit of the critical composition, the penetration depth is predicted to go to infinity, resulting in zero mass, consistent with our measurements. Finally, we discover the existence of surface states in the non-topological regime, which have the characteristics of gapped, double-branched Dirac fermions and could be exploited in realizing superconductivity in these materials. AU - Zeljkovic, Ilija AU - Okada, Yoshinori AU - Maksym Serbyn AU - Sankar, Raman AU - Walkup, Daniel AU - Zhou, Wenwen AU - Liu, Junwei AU - Chang, Guoqing AU - Wang, Yungjui AU - Hasan, Md Z AU - Chou, Fangcheng AU - Lin, Hsin AU - Bansil, Arun AU - Fu, Liang AU - Madhavan, Vidya ID - 981 IS - 3 JF - Nature Materials TI - Dirac mass generation from crystal symmetry breaking on the surfaces of topological crystalline insulators VL - 14 ER - TY - JOUR AB - We propose a new approach to probing ergodicity and its breakdown in one-dimensional quantum manybody systems based on their response to a local perturbation. We study the distribution of matrix elements of a local operator between the system's eigenstates, finding a qualitatively different behavior in the manybody localized (MBL) and ergodic phases. To characterize how strongly a local perturbation modifies the eigenstates, we introduce the parameter g(L) = (In (Vnm/δ)) which represents the disorder-averaged ratio of a typical matrix element of a local operator V to energy level spacing δ this parameter is reminiscent of the Thouless conductance in the single-particle localization. We show that the parameter g(L) decreases with system size L in the MBL phase and grows in the ergodic phase. We surmise that the delocalization transition occurs when g(L) is independent of system size, g(L)=gc ~ 1. We illustrate our approach by studying the many-body localization transition and resolving the many-body mobility edge in a disordered one-dimensional XXZ spin-1=2 chain using exact diagonalization and time-evolving block-decimation methods. Our criterion for the MBL transition gives insights into microscopic details of transition. Its direct physical consequences, in particular, logarithmically slow transport at the transition and extensive entanglement entropy of the eigenstates, are consistent with recent renormalization-group predictions. AU - Maksym Serbyn AU - Papić, Zlatko AU - Abanin, Dmitry A ID - 982 IS - 4 JF - Physical Review X TI - Criterion for many-body localization-delocalization phase transition VL - 5 ER - TY - JOUR AB - Quasiparticle excitations can compromise the performance of superconducting devices, causing high-frequency dissipation, decoherence in Josephson qubits, and braiding errors in proposed Majorana-based topological quantum computers. Quasiparticle dynamics have been studied in detail in metallic superconductors but remain relatively unexplored in semiconductor-superconductor structures, which are now being intensely pursued in the context of topological superconductivity. To this end, we use a system comprising a gate-confined semiconductor nanowire with an epitaxially grown superconductor layer, yielding an isolated, proximitized nanowire segment. We identify bound states in the semiconductor by means of bias spectroscopy, determine the characteristic temperatures and magnetic fields for quasiparticle excitations, and extract a parity lifetime (poisoning time) of the bound state in the semiconductor exceeding 10 ms. AU - Higginbotham, Andrew P AU - Albrecht, S M AU - Kiršanskas, Gediminas AU - Chang, W AU - Kuemmeth, Ferdinand AU - Krogstrup, Peter AU - Jespersen, Thomas AU - Nygård, Jesper AU - Flensberg, Karsten AU - Marcus, Charles ID - 99 IS - 12 JF - Nature Physics TI - Parity lifetime of bound states in a proximitized semiconductor nanowire VL - 11 ER - TY - JOUR AB - In this note, we consider the dynamics associated to a perturbation of an integrable Hamiltonian system in action-angle coordinates in any number of degrees of freedom and we prove the following result of ``micro-diffusion'': under generic assumptions on $ h$ and $ f$, there exists an orbit of the system for which the drift of its action variables is at least of order $ \sqrt {\varepsilon }$, after a time of order $ \sqrt {\varepsilon }^{-1}$. The assumptions, which are essentially minimal, are that there exists a resonant point for $ h$ and that the corresponding averaged perturbation is non-constant. The conclusions, although very weak when compared to usual instability phenomena, are also essentially optimal within this setting. AU - Bounemoura, Abed AU - Kaloshin, Vadim ID - 8495 IS - 4 JF - Proceedings of the American Mathematical Society SN - 0002-9939 TI - A note on micro-instability for Hamiltonian systems close to integrable VL - 144 ER - TY - JOUR AB - Proteases play important roles in many biologic processes and are key mediators of cancer, inflammation, and thrombosis. However, comprehensive and quantitative techniques to define the substrate specificity profile of proteases are lacking. The metalloprotease ADAMTS13 regulates blood coagulation by cleaving von Willebrand factor (VWF), reducing its procoagulant activity. A mutagenized substrate phage display library based on a 73-amino acid fragment of VWF was constructed, and the ADAMTS13-dependent change in library complexity was evaluated over reaction time points, using high-throughput sequencing. Reaction rate constants (kcat/KM) were calculated for nearly every possible single amino acid substitution within this fragment. This massively parallel enzyme kinetics analysis detailed the specificity of ADAMTS13 and demonstrated the critical importance of the P1-P1' substrate residues while defining exosite binding domains. These data provided empirical evidence for the propensity for epistasis within VWF and showed strong correlation to conservation across orthologs, highlighting evolutionary selective pressures for VWF. AU - Kretz, Colin A AU - Dai, Manhong AU - Soylemez, Onuralp AU - Yee, Andrew AU - Desch, Karl C AU - Siemieniak, David R AU - Tomberg, Kärt AU - Fyodor Kondrashov AU - Meng, Fan AU - Ginsburg, David B ID - 866 IS - 30 JF - PNAS TI - Massively parallel enzyme kinetics reveals the substrate recognition landscape of the metalloprotease ADAMTS13 VL - 112 ER - TY - JOUR AB - The factors that determine the tempo and mode of protein evolution continue to be a central question in molecular evolution. Traditionally, studies of protein evolution focused on the rates of amino acid substitutions. More recently, with the availability of sequence data and advanced experimental techniques, the focus of attention has shifted toward the study of evolutionary trajectories and the overall layout of protein fitness landscapes. In this review we describe the effect of epistasis on the topology of evolutionary pathways that are likely to be found in fitness landscapes and develop a simple theory to connect the number of maladapted genotypes to the topology of fitness landscapes with epistatic interactions. Finally, we review recent studies that have probed the extent of epistatic interactions and have begun to chart the fitness landscapes in protein sequence space. AU - Kondrashov, Dmitry A AU - Fyodor Kondrashov ID - 886 IS - 1 JF - Trends in Genetics TI - Topological features of rugged fitness landscapes in sequence space VL - 31 ER - TY - JOUR AB - MCM2 is a subunit of the replicative helicase machinery shown to interact with histones H3 and H4 during the replication process through its N-terminal domain. During replication, this interaction has been proposed to assist disassembly and assembly of nucleosomes on DNA. However, how this interaction participates in crosstalk with histone chaperones at the replication fork remains to be elucidated. Here, we solved the crystal structure of the ternary complex between the histone-binding domain of Mcm2 and the histones H3-H4 at 2.9 Å resolution. Histones H3 and H4 assemble as a tetramer in the crystal structure, but MCM2 interacts only with a single molecule of H3-H4. The latter interaction exploits binding surfaces that contact either DNA or H2B when H3-H4 dimers are incorporated in the nucleosome core particle. Upon binding of the ternary complex with the histone chaperone ASF1, the histone tetramer dissociates and both MCM2 and ASF1 interact simultaneously with the histones forming a 1:1:1:1 heteromeric complex. Thermodynamic analysis of the quaternary complex together with structural modeling support that ASF1 and MCM2 could form a chaperoning module for histones H3 and H4 protecting them from promiscuous interactions. This suggests an additional function for MCM2 outside its helicase function as a proper histone chaperone connected to the replication pathway. AU - Richet, Nicolas AU - Liu, Danni AU - Legrand, Pierre AU - Velours, Christophe AU - Corpet, Armelle AU - Gaubert, Albane AU - Bakail, May M AU - Moal-Raisin, Gwenaelle AU - Guerois, Raphael AU - Compper, Christel AU - Besle, Arthur AU - Guichard, Berengère AU - Almouzni, Genevieve AU - Ochsenbein, Françoise ID - 9017 IS - 3 JF - Nucleic Acids Research SN - 1362-4962 TI - Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork VL - 43 ER - TY - JOUR AB - This paper presents a numerical study of a Capillary Pumped Loop evaporator. A two-dimensional unsteady mathematical model of a flat evaporator is developed to simulate heat and mass transfer in unsaturated porous wick with phase change. The liquid-vapor phase change inside the porous wick is described by Langmuir's law. The governing equations are solved by the Finite Element Method. The results are presented then for a sintered nickel wick and methanol as a working fluid. The heat flux required to the transition from the all-liquid wick to the vapor-liquid wick is calculated. The dynamic and thermodynamic behavior of the working fluid in the capillary structure are discussed in this paper. AU - Boubaker, Riadh AU - Platel, Vincent AU - Bergès, Alexis AU - Bancelin, Mathieu AU - Hannezo, Edouard B ID - 924 JF - Applied Thermal Engineering TI - Dynamic model of heat and mass transfer in an unsaturated porous wick of capillary pumped loop VL - 76 ER - TY - JOUR AB - An essential question of morphogenesis is how patterns arise without preexisting positional information, as inspired by Turing. In the past few years, cytoskeletal flows in the cell cortex have been identified as a key mechanism of molecular patterning at the subcellular level. Theoretical and in vitro studies have suggested that biological polymers such as actomyosin gels have the property to self-organize, but the applicability of this concept in an in vivo setting remains unclear. Here, we report that the regular spacing pattern of supracellular actin rings in the Drosophila tracheal tubule is governed by a self-organizing principle. We propose a simple biophysical model where pattern formation arises from the interplay of myosin contractility and actin turnover. We validate the hypotheses of the model using photobleaching experiments and report that the formation of actin rings is contractility dependent. Moreover, genetic and pharmacological perturbations of the physical properties of the actomyosin gel modify the spacing of the pattern, as the model predicted. In addition, our model posited a role of cortical friction in stabilizing the spacing pattern of actin rings. Consistently, genetic depletion of apical extracellular matrix caused strikingly dynamic movements of actin rings, mirroring our model prediction of a transition from steady to chaotic actin patterns at low cortical friction. Our results therefore demonstrate quantitatively that a hydrodynamical instability of the actin cortex can trigger regular pattern formation and drive morphogenesis in an in vivo setting. AU - Hannezo, Edouard B AU - Dong, Bo AU - Recho, Pierre AU - Joanny, Jean AU - Hayashi, Shigeo ID - 929 IS - 28 JF - PNAS TI - Cortical instability drives periodic supracellular actin pattern formation in epithelial tubes VL - 112 ER - TY - JOUR AB - Although collective cell motion plays an important role, for example during wound healing, embryogenesis, or cancer progression, the fundamental rules governing this motion are still not well understood, in particular at high cell density. We study here the motion of human bronchial epithelial cells within a monolayer, over long times. We observe that, as the monolayer ages, the cells slow down monotonously, while the velocity correlation length first increases as the cells slow down but eventually decreases at the slowest motions. By comparing experiments, analytic model, and detailed particle-based simulations, we shed light on this biological amorphous solidification process, demonstrating that the observed dynamics can be explained as a consequence of the combined maturation and strengthening of cell-cell and cell-substrate adhesions. Surprisingly, the increase of cell surface density due to proliferation is only secondary in this process. This analysis is confirmed with two other cell types. The very general relations between the mean cell velocity and velocity correlation lengths, which apply for aggregates of self-propelled particles, as well as motile cells, can possibly be used to discriminate between various parameter changes in vivo, from noninvasive microscopy data. AU - García, Simón AU - Hannezo, Edouard B AU - Elgeti, Jens AU - Joanny, Jean AU - Silberzan, Pascal AU - Gov, Nir ID - 933 IS - 50 JF - PNAS TI - Physics of active jamming during collective cellular motion in a monolayer VL - 112 ER - TY - JOUR AB - Genomic imprinting, an inherently epigenetic phenomenon defined by parent of origin-dependent gene expression, is observed in mammals and flowering plants. Genome-scale surveys of imprinted expression and the underlying differential epigenetic marks have led to the discovery of hundreds of imprinted plant genes and confirmed DNA and histone methylation as key regulators of plant imprinting. However, the biological roles of the vast majority of imprinted plant genes are unknown, and the evolutionary forces shaping plant imprinting remain rather opaque. Here, we review the mechanisms of plant genomic imprinting and discuss theories of imprinting evolution and biological significance in light of recent findings. AU - Rodrigues, Jessica A. AU - Zilberman, Daniel ID - 9532 IS - 24 JF - Genes and Development SN - 0890-9369 TI - Evolution and function of genomic imprinting in plants VL - 29 ER - TY - JOUR AB - The size dependence of the strength of nano- and micron-sized crystals is studied using a new simulation approach in which the dynamics of the density functions of dislocations are modeled. Since any quantity of dislocations can be represented by a density, this approach can handle large systems containing large quantities of dislocations, which may handicap discrete dislocation dynamics schemes due to the excessive computation time involved. For this reason, pillar sizes spanning a large range, from the sub-micron to micron regimes, can be simulated. The simulation results reveal the power-law relationship between strength and specimen size up to a certain size, beyond which the strength varies much more slowly with size. For specimens smaller than ~4000b, their strength is found to be controlled by the dislocation depletion condition, in which the total dislocation density remains almost constant throughout the loading process. In specimens larger than ~4000b, the initial dislocation distribution is of critical importance since the presence of dislocation entanglements is found to obstruct deformation in the neighboring regions within a distance of ~2000b. This length scale suggests that the effects of dense dislocation clusters are greater in intermediate-sized specimens (e.g. 4000b and 8000b) than in larger specimens (e.g. 16 000b), according to the weakest-link concept. AU - Leung, P S S AU - Leung, H S AU - Cheng, Bingqing AU - Ngan, A H W ID - 9684 IS - 3 JF - Modelling and Simulation in Materials Science and Engineering SN - 0965-0393 TI - Size dependence of yield strength simulated by a dislocation-density function dynamics approach VL - 23 ER - TY - JOUR AB - Deposits of misfolded proteins in the human brain are associated with the development of many neurodegenerative diseases. Recent studies show that these proteins have common traits even at the monomer level. Among them, a polyglutamine region that is present in huntingtin is known to exhibit a correlation between the length of the chain and the severity as well as the earliness of the onset of Huntington disease. Here, we apply bias exchange molecular dynamics to generate structures of polyglutamine expansions of several lengths and characterize the resulting independent conformations. We compare the properties of these conformations to those of the standard proteins, as well as to other homopolymeric tracts. We find that, similar to the previously studied polyvaline chains, the set of possible transient folds is much broader than the set of known-to-date folds, although the conformations have different structures. We show that the mechanical stability is not related to any simple geometrical characteristics of the structures. We demonstrate that long polyglutamine expansions result in higher mechanical stability than the shorter ones. They also have a longer life span and are substantially more prone to form knotted structures. The knotted region has an average length of 35 residues, similar to the typical threshold for most polyglutamine-related diseases. Similarly, changes in shape and mechanical stability appear once the total length of the peptide exceeds this threshold of 35 glutamine residues. We suggest that knotted conformers may also harm the cellular machinery and thus lead to disease. AU - Gómez Sicilia, Àngel AU - Sikora, Mateusz K AU - Cieplak, Marek AU - Carrión Vázquez, Mariano ID - 1566 IS - 10 JF - PLoS Computational Biology TI - An exploration of the universe of polyglutamine structures VL - 11 ER - TY - GEN AU - Tugrul, Murat AU - Paixao, Tiago AU - Barton, Nicholas H AU - Tkačik, Gašper ID - 9712 TI - Other fitness models for comparison & for interacting TFBSs ER - TY - GEN AU - Gómez Sicilia, Àngel AU - Sikora, Mateusz K AU - Cieplak, Marek AU - Carrión Vázquez, Mariano ID - 9714 TI - An exploration of the universe of polyglutamine structures - submission to PLOS journals ER - TY - GEN AU - Trubenova, Barbora AU - Novak, Sebastian AU - Hager, Reinmar ID - 9715 TI - Mathematical inference of the results ER - TY - JOUR AB - The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. AU - Konrad, Matthias AU - Grasse, Anna V AU - Tragust, Simon AU - Cremer, Sylvia ID - 1993 IS - 1799 JF - Proceedings of the Royal Society of London Series B Biological Sciences SN - 0962-8452 TI - Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host VL - 282 ER - TY - GEN AB - Repeated pathogen exposure is a common threat in colonies of social insects, posing selection pressures on colony members to respond with improved disease-defense performance. We here tested whether experience gained by repeated tending of low-level fungus-exposed (Metarhizium robertsii) larvae may alter the performance of sanitary brood care in the clonal ant, Platythyrea punctata. We trained ants individually over nine consecutive trials to either sham-treated or fungus-exposed larvae. We then compared the larval grooming behavior of naive and trained ants and measured how effectively they removed infectious fungal conidiospores from the fungus-exposed larvae. We found that the ants changed the duration of larval grooming in response to both, larval treatment and their level of experience: (1) sham-treated larvae received longer grooming than the fungus-exposed larvae and (2) trained ants performed less self-grooming but longer larval grooming than naive ants, which was true for both, ants trained to fungus-exposed and also to sham-treated larvae. Ants that groomed the fungus-exposed larvae for longer periods removed a higher number of fungal conidiospores from the surface of the fungus-exposed larvae. As experienced ants performed longer larval grooming, they were more effective in fungal removal, thus making them better caretakers under pathogen attack of the colony. By studying this clonal ant, we can thus conclude that even in the absence of genetic variation between colony members, differences in experience levels of brood care may affect performance of sanitary brood care in social insects. AU - Westhus, Claudia AU - Ugelvig, Line V AU - Tourdot, Edouard AU - Heinze, Jürgen AU - Doums, Claudie AU - Cremer, Sylvia ID - 9742 TI - Data from: Increased grooming after repeated brood care provides sanitary benefits in a clonal ant ER - TY - GEN AU - Chevereau, Guillaume AU - Lukacisinova, Marta AU - Batur, Tugce AU - Guvenek, Aysegul AU - Ayhan, Dilay Hazal AU - Toprak, Erdal AU - Bollenbach, Mark Tobias ID - 9765 TI - Gene ontology enrichment analysis for the most sensitive gene deletion strains for all drugs ER - TY - JOUR AB - The hydrology of high-elevation watersheds of the Hindu Kush-Himalaya region (HKH) is poorly known. The correct representation of internal states and process dynamics in glacio-hydrological models can often not be verified due to missing in situ measurements. We use a new set of detailed ground data from the upper Langtang valley in Nepal to systematically guide a state-of-the art glacio-hydrological model through a parameter assigning process with the aim to understand the hydrology of the catchment and contribution of snow and ice processes to runoff. 14 parameters are directly calculated on the basis of local data, and 13 parameters are calibrated against 5 different datasets of in situ or remote sensing data. Spatial fields of debris thickness are reconstructed through a novel approach that employs data from an Unmanned Aerial Vehicle (UAV), energy balance modeling and statistical techniques. The model is validated against measured catchment runoff (Nash–Sutcliffe efficiency 0.87) and modeled snow cover is compared to Landsat snow cover. The advanced representation of processes allowed assessing the role played by avalanching for runoff for the first time for a Himalayan catchment (5% of annual water inputs to the hydrological system are due to snow redistribution) and to quantify the hydrological significance of sub-debris ice melt (9% of annual water inputs). Snowmelt is the most important contributor to total runoff during the hydrological year 2012/2013 (representing 40% of all sources), followed by rainfall (34%) and ice melt (26%). A sensitivity analysis is used to assess the efficiency of the monitoring network and identify the timing and location of field measurements that constrain model uncertainty. The methodology to set up a glacio-hydrological model in high-elevation regions presented in this study can be regarded as a benchmark for modelers in the HKH seeking to evaluate their calibration approach, their experimental setup and thus to reduce the predictive model uncertainty. AU - Ragettli, S. AU - Pellicciotti, Francesca AU - Immerzeel, W.W. AU - Miles, E.S. AU - Petersen, L. AU - Heynen, M. AU - Shea, J.M. AU - Stumm, D. AU - Joshi, S. AU - Shrestha, A. ID - 12630 IS - 4 JF - Advances in Water Resources KW - Water Science and Technology SN - 0309-1708 TI - Unraveling the hydrology of a Himalayan catchment through integration of high resolution in situ data and remote sensing with an advanced simulation model VL - 78 ER - TY - JOUR AB - Thick debris cover on glaciers can significantly reduce ice melt. However, several studies have suggested that debris-covered glaciers in the Himalaya might have lost mass at a rate similar to debris-free glaciers. We reconstruct elevation and mass changes for the debris-covered glaciers of the upper Langtang valley, Nepalese Himalaya, using a digital elevation model (DEM) from 1974 stereo Hexagon satellite data and the 2000 SRTM (Shuttle Radar Topography Mission) DEM. Uncertainties are high in the accumulation areas, due to data gaps in the SRTM and difficulties with delineation of the glacier borders. Even with these uncertainties, we obtain thinning rates comparable to those of several other studies in the Himalaya. In particular, we obtain a total mass balance for the investigated debris-covered glaciers of the basin of –0.32 ± 0.18 m w.e. a−1. However, there are major spatial differences both between glaciers and within any single glacier, exhibiting a very distinct nonlinear mass-balance profile with elevation. Through analysis of surface velocities derived from Landsat ETM+ imagery, we show that thinning occurs in areas of low velocity and low slope. These areas are prone to a general, dynamic decay of surface features and to the development of supraglacial lakes and ice cliffs, which may be responsible for a considerable increase in overall glacier ablation. AU - Pellicciotti, Francesca AU - Stephan, Christa AU - Miles, Evan AU - Herreid, Sam AU - Immerzeel, Walter W. AU - Bolch, Tobias ID - 12628 IS - 226 JF - Journal of Glaciology KW - Earth-Surface Processes SN - 0022-1430 TI - Mass-balance changes of the debris-covered glaciers in the Langtang Himal, Nepal, from 1974 to 1999 VL - 61 ER - TY - JOUR AB - Air temperature is one of the most relevant input variables for snow and ice melt calculations. However, local meteorological conditions, complex topography, and logistical concerns in glacierized regions make the measuring and modeling of air temperature a difficult task. In this study, we investigate the spatial distribution of 2 m air temperature over mountain glaciers and propose a modification to an existing model to improve its representation. Spatially distributed meteorological data from Haut Glacier d'Arolla (Switzerland), Place (Canada), and Juncal Norte (Chile) Glaciers are used to examine approximate flow line temperatures during their respective ablation seasons. During warm conditions (off-glacier temperatures well above 0°C), observed air temperatures in the upper reaches of Place Glacier and Haut Glacier d'Arolla decrease down glacier along the approximate flow line. At Juncal Norte and Haut Glacier d'Arolla, an increase in air temperature is observed over the glacier tongue. While the temperature behavior over the upper part can be explained by the cooling effect of the glacier surface, the temperature increase over the glacier tongue may be caused by several processes induced by the surrounding warm atmosphere. In order to capture the latter effect, we add an additional term to the Greuell and Böhm (GB) thermodynamic glacier wind model. For high off-glacier temperatures, the modified GB model reduces root-mean-square error up to 32% and provides a new approach for distributing air temperature over mountain glaciers as a function of off-glacier temperatures and approximate glacier flow lines. AU - Ayala, A. AU - Pellicciotti, Francesca AU - Shea, J. M. ID - 12631 IS - 8 JF - Journal of Geophysical Research: Atmospheres KW - Space and Planetary Science KW - Earth and Planetary Sciences (miscellaneous) KW - Atmospheric Science KW - Geophysics SN - 2169-897X TI - Modeling 2 m air temperatures over mountain glaciers: Exploring the influence of katabatic cooling and external warming VL - 120 ER - TY - JOUR AB - Meteorological studies in high-mountain environments form the basis of our understanding of catchment hydrology and glacier accumulation and melt processes, yet high-altitude (>4000 m above sea level, asl) observatories are rare. This research presents meteorological data recorded between December 2012 and November 2013 at seven stations in Nepal, ranging in elevation from 3860 to 5360 m asl. Seasonal and diurnal cycles in air temperature, vapour pressure, incoming short-wave and long-wave radiation, atmospheric transmissivity, wind speed, and precipitation are compared between sites. Solar radiation strongly affects diurnal temperature and vapour pressure cycles, but local topography and valley-scale circulations alter wind speed and precipitation cycles. The observed diurnal variability in vertical temperature gradients in all seasons highlights the importance of in situ measurements for melt modelling. The monsoon signal (progressive onset and sharp end) is visible in all data-sets, and the passage of the remnants of Typhoon Phailin in mid-October 2013 provides an interesting case study on the possible effects of such storms on glaciers in the region. AU - Shea, J.M. AU - Wagnon, P. AU - Immerzeel, W.W. AU - Biron, R. AU - Brun, F. AU - Pellicciotti, Francesca ID - 12629 IS - 2 JF - International Journal of Water Resources Development KW - Water Science and Technology KW - Development SN - 0790-0627 TI - A comparative high-altitude meteorological analysis from three catchments in the Nepalese Himalaya VL - 31 ER - TY - JOUR AB - Ice cliffs have been identified as a reason for higher ablation rates on debris-covered glaciers than are implied by the insulation effects of the debris. This study aims to improve our understanding of cliff backwasting, and the role of radiative fluxes in particular. An energy-balance model is forced with new data gathered in May and October 2013 on Lirung Glacier, Nepalese Himalaya. Observations show substantial variability in melt between cliffs, between locations on any cliff and between seasons. Using a high-resolution digital elevation model we calculate longwave fluxes incident to the cliff from surrounding terrain and include the effect of local shading on shortwave radiation. This is an advance over previous studies, that made simplified assumptions on cliff geometry and radiative fluxes. Measured melt rates varied between 3.25 and 8.6 cm d−1 in May and 0.18 and 1.34 cm d−1 in October. Model results reproduce the strong variability in space and time, suggesting considerable differences in radiative fluxes over one cliff. In October the model fails to reproduce stake readings, probably due to the lack of a refreezing component. Disregarding local topography can lead to overestimation of melt at the point scale by up to ∼9%. AU - Steiner, Jakob F. AU - Pellicciotti, Francesca AU - Buri, Pascal AU - Miles, Evan S. AU - Immerzeel, Walter W. AU - Reid, Tim D. ID - 12626 IS - 229 JF - Journal of Glaciology SN - 0022-1430 TI - Modelling ice-cliff backwasting on a debris-covered glacier in the Nepalese Himalaya VL - 61 ER - TY - JOUR AB - Spatial evolution of supraglacial debris cover on mountain glaciers is a largely unmonitored and poorly understood phenomenon that directly affects glacier melt. Supraglacial debris cover for 93 glaciers in the Karakoram, northern Pakistan, was mapped from Landsat imagery acquired in 1977, 1998, 2009 and 2014. Surge-type glaciers occupy 41% of the study area and were considered separately. The time series of debris-covered surface area change shows a mean value of zero or near-zero change for both surging and non-surging glaciers. An increase in debris-covered area is often associated with negative regional mass balances. We extend this logic to suggest that the stable regional mass balances in the Karakoram explain the zero or near-zero change in debris-covered area. This coupling of trends combined with our 37 year time series of data suggests the Karakoram anomaly extends further back in time than previously known. AU - Herreid, Sam AU - Pellicciotti, Francesca AU - Ayala, Alvaro AU - Chesnokova, Anna AU - Kienholz, Christian AU - Shea, Joseph AU - Shrestha, Arun ID - 12627 IS - 227 JF - Journal of Glaciology SN - 0022-1430 TI - Satellite observations show no net change in the percentage of supraglacial debris-covered area in northern Pakistan from 1977 to 2014 VL - 61 ER - TY - JOUR AB - CCL19 and CCL21 are chemokines involved in the trafficking of immune cells, particularly within the lymphatic system, through activation of CCR7. Concurrent expression of PSGL-1 and CCR7 in naive T-cells enhances recruitment of these cells to secondary lymphoid organs by CCL19 and CCL21. Here the solution structure of CCL19 is reported. It contains a canonical chemokine domain. Chemical shift mapping shows the N-termini of PSGL-1 and CCR7 have overlapping binding sites for CCL19 and binding is competitive. Implications for the mechanism of PSGL-1's enhancement of resting T-cell recruitment are discussed. AU - Veldkamp, Christopher AU - Kiermaier, Eva AU - Gabel Eissens, Skylar AU - Gillitzer, Miranda AU - Lippner, David AU - Disilvio, Frank AU - Mueller, Casey AU - Wantuch, Paeton AU - Chaffee, Gary AU - Famiglietti, Michael AU - Zgoba, Danielle AU - Bailey, Asha AU - Bah, Yaya AU - Engebretson, Samantha AU - Graupner, David AU - Lackner, Emily AU - Larosa, Vincent AU - Medeiros, Tysha AU - Olson, Michael AU - Phillips, Andrew AU - Pyles, Harley AU - Richard, Amanda AU - Schoeller, Scott AU - Touzeau, Boris AU - Williams, Larry AU - Sixt, Michael K AU - Peterson, Francis ID - 1618 IS - 27 JF - Biochemistry TI - Solution structure of CCL19 and identification of overlapping CCR7 and PSGL-1 binding sites VL - 54 ER - TY - CONF AU - Martius, Georg S AU - Olbrich, Eckehard ID - 12881 SN - 9780262330275 T2 - Proceedings of the 13th European Conference on Artificial Life TI - Quantifying self-organizing behavior of autonomous robots ER - TY - JOUR AB - SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in the induction of defense responses. However, the molecular mechanisms underlying NLR activation and the subsequent provocation of immune responses are only partially characterized. To identify negative regulators of NLR-mediated immunity, a forward genetic screen was undertaken to search for enhancers of the dwarf, autoimmune gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism, the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display wild-type-like morphology and resistance. M2 progeny were screened for mutant, snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes. The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated expression of the pPR2-GUS defense marker reporter gene and enhanced resistance to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning and Illumina sequencing, it was determined that the muse9 mutation is in the gene encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10. The syd-10 single mutant has no observable alteration from wild-type-like resistance, although the syd-4 T-DNA insertion allele displays enhanced resistance to the bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated immunity. SYD may work with other proteins at the chromatin level to repress SNC1 transcription; such regulation is important for fine-tuning the expression of NLR-encoding genes to prevent unpropitious autoimmunity. AU - Johnson, Kaeli C.M. AU - Xia, Shitou AU - Feng, Xiaoqi AU - Li, Xin ID - 12196 IS - 8 JF - Plant and Cell Physiology KW - Cell Biology KW - Plant Science KW - Physiology KW - General Medicine SN - 0032-0781 TI - The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity VL - 56 ER - TY - JOUR AB - The chemical behaviour of molecules can be significantly modified by confinement to volumes comparable to the dimensions of the molecules. Although such confined spaces can be found in various nanostructured materials, such as zeolites, nanoporous organic frameworks and colloidal nanocrystal assemblies, the slow diffusion of molecules in and out of these materials has greatly hampered studying the effect of confinement on their physicochemical properties. Here, we show that this diffusion limitation can be overcome by reversibly creating and destroying confined environments by means of ultraviolet and visible light irradiation. We use colloidal nanocrystals functionalized with light-responsive ligands that readily self-assemble and trap various molecules from the surrounding bulk solution. Once trapped, these molecules can undergo chemical reactions with increased rates and with stereoselectivities significantly different from those in bulk solution. Illumination with visible light disassembles these nanoflasks, releasing the product in solution and thereby establishes a catalytic cycle. These dynamic nanoflasks can be useful for studying chemical reactivities in confined environments and for synthesizing molecules that are otherwise hard to achieve in bulk solution. AU - Zhao, Hui AU - Sen, Soumyo AU - Udayabhaskararao, T. AU - Sawczyk, Michał AU - Kučanda, Kristina AU - Manna, Debasish AU - Kundu, Pintu K. AU - Lee, Ji-Woong AU - Král, Petr AU - Klajn, Rafal ID - 13392 JF - Nature Nanotechnology KW - Electrical and Electronic Engineering KW - Condensed Matter Physics KW - General Materials Science KW - Biomedical Engineering KW - Atomic and Molecular Physics KW - and Optics KW - Bioengineering SN - 1748-3387 TI - Reversible trapping and reaction acceleration within dynamically self-assembling nanoflasks VL - 11 ER - TY - JOUR AB - The ability to guide the assembly of nanosized objects reversibly with external stimuli, in particular light, is of fundamental importance, and it contributes to the development of applications as diverse as nanofabrication and controlled drug delivery. However, all the systems described to date are based on nanoparticles (NPs) that are inherently photoresponsive, which makes their preparation cumbersome and can markedly hamper their performance. Here we describe a conceptually new methodology to assemble NPs reversibly using light that does not require the particles to be functionalized with light-responsive ligands. Our strategy is based on the use of a photoswitchable medium that responds to light in such a way that it modulates the interparticle interactions. NP assembly proceeds quantitatively and without apparent fatigue, both in solution and in gels. Exposing the gels to light in a spatially controlled manner allowed us to draw images that spontaneously disappeared after a specific period of time. AU - Kundu, Pintu K. AU - Samanta, Dipak AU - Leizrowice, Ron AU - Margulis, Baruch AU - Zhao, Hui AU - Börner, Martin AU - Udayabhaskararao, T. AU - Manna, Debasish AU - Klajn, Rafal ID - 13394 JF - Nature Chemistry KW - General Chemical Engineering KW - General Chemistry SN - 1755-4330 TI - Light-controlled self-assembly of non-photoresponsive nanoparticles VL - 7 ER - TY - JOUR AB - Precise control of the self-assembly of selected components within complex mixtures is a challenging goal whose realization is important for fabricating novel nanomaterials. Herein we show that by decorating the surfaces of metallic nanoparticles with differently substituted azobenzenes, it is possible to modulate the wavelength of light at which the self-assembly of these nanoparticles is induced. Exposing a mixture of two types of nanoparticles, each functionalized with a different azobenzene, to UV or blue light induces the selective self-assembly of only one type of nanoparticles. Irradiation with the other wavelength triggers the disassembly of the aggregates, and the simultaneous self-assembly of nanoparticles of the other type. By placing both types of azobenzenes on the same nanoparticles, we created unique materials (“frustrated” nanoparticles) whose self-assembly is induced irrespective of the wavelength of the incident light. AU - Manna, Debasish AU - Udayabhaskararao, Thumu AU - Zhao, Hui AU - Klajn, Rafal ID - 13393 IS - 42 JF - Angewandte Chemie International Edition KW - General Chemistry KW - Catalysis SN - 1433-7851 TI - Orthogonal light-induced self-assembly of nanoparticles using differently substituted azobenzenes VL - 54 ER - TY - JOUR AB - Metallic nanoparticles co-functionalised with monolayers of UV- and CO2-sensitive ligands were prepared and shown to respond to these two types of stimuli reversibly and in an orthogonal fashion. The composition of the coating could be tailored to yield nanoparticles capable of aggregating exclusively when both UV and CO2 were applied at the same time, analogously to the behaviour of an AND logic gate. AU - Lee, Ji-Woong AU - Klajn, Rafal ID - 13395 IS - 11 JF - Chemical Communications KW - Materials Chemistry KW - Metals and Alloys KW - Surfaces KW - Coatings and Films KW - General Chemistry KW - Ceramics and Composites KW - Electronic KW - Optical and Magnetic Materials KW - Catalysis SN - 1359-7345 TI - Dual-responsive nanoparticles that aggregate under the simultaneous action of light and CO2 VL - 51 ER - TY - JOUR AB - Photoswitching in densely packed azobenzene self-assembled monolayers (SAMs) is strongly affected by steric constraints and excitonic coupling between neighboring chromophores. Therefore, control of the chromophore density is essential for enhancing and manipulating the photoisomerization yield. We systematically compare two methods to achieve this goal: First, we assemble monocomponent azobenzene–alkanethiolate SAMs on gold nanoparticles of varying size. Second, we form mixed SAMs of azobenzene–alkanethiolates and “dummy” alkanethiolates on planar substrates. Both methods lead to a gradual decrease of the chromophore density and enable efficient photoswitching with low-power light sources. X-ray spectroscopy reveals that coadsorption from solution yields mixtures with tunable composition. The orientation of the chromophores with respect to the surface normal changes from a tilted to an upright position with increasing azobenzene density. For both systems, optical spectroscopy reveals a pronounced excitonic shift that increases with the chromophore density. In spite of exciting the optical transition of the monomer, the main spectral change in mixed SAMs occurs in the excitonic band. In addition, the photoisomerization yield decreases only slightly by increasing the azobenzene–alkanethiolate density, and we observed photoswitching even with minor dilutions. Unlike in solution, azobenzene in the planar SAM can be switched back almost completely by optical excitation from the cis to the original trans state within a short time scale. These observations indicate cooperativity in the photoswitching process of mixed SAMs. AU - Moldt, Thomas AU - Brete, Daniel AU - Przyrembel, Daniel AU - Das, Sanjib AU - Goldman, Joel R. AU - Kundu, Pintu K. AU - Gahl, Cornelius AU - Klajn, Rafal AU - Weinelt, Martin ID - 13396 IS - 3 JF - Langmuir KW - Electrochemistry KW - Spectroscopy KW - Surfaces and Interfaces KW - Condensed Matter Physics KW - General Materials Science SN - 0743-7463 TI - Tailoring the properties of surface-immobilized azobenzenes by monolayer dilution and surface curvature VL - 31 ER - TY - JOUR AB - Self-assembly of inorganic nanoparticles has been studied extensively for particles having different sizes and compositions. However, relatively little attention has been devoted to how the shape and surface chemistry of magnetic nanoparticles affects their self-assembly properties. Here, we undertook a combined experiment–theory study aimed at better understanding of the self-assembly of cubic magnetite (Fe3O4) particles. We demonstrated that, depending on the experimental parameters, such as the direction of the magnetic field and nanoparticle density, a variety of superstructures can be obtained, including one-dimensional filaments and helices, as well as C-shaped assemblies described here for the first time. Furthermore, we functionalized the surfaces of the magnetic nanocubes with light-sensitive ligands. Using these modified nanoparticles, we were able to achieve orthogonal control of self-assembly using a magnetic field and light. AU - Singh, Gurvinder AU - Chan, Henry AU - Udayabhaskararao, T. AU - Gelman, Elijah AU - Peddis, Davide AU - Baskin, Artem AU - Leitus, Gregory AU - Král, Petr AU - Klajn, Rafal ID - 13397 JF - Faraday Discussions KW - Physical and Theoretical Chemistry SN - 1359-6640 TI - Magnetic field-induced self-assembly of iron oxide nanocubes VL - 181 ER - TY - JOUR AU - Sun, Yugang AU - Scarabelli, Leonardo AU - Kotov, Nicholas AU - Tebbe, Moritz AU - Lin, Xiao-Min AU - Brullot, Ward AU - Isa, Lucio AU - Schurtenberger, Peter AU - Moehwald, Helmuth AU - Fedin, Igor AU - Velev, Orlin AU - Faivre, Damien AU - Sorensen, Christopher AU - Perzynski, Régine AU - Chanana, Munish AU - Li, Zhihai AU - Bresme, Fernando AU - Král, Petr AU - Firlar, Emre AU - Schiffrin, David AU - Souza Junior, Joao Batista AU - Fery, Andreas AU - Shevchenko, Elena AU - Tarhan, Ozgur AU - Alivisatos, Armand Paul AU - Disch, Sabrina AU - Klajn, Rafal AU - Ghosh, Suvojit ID - 13398 JF - Faraday Discussions KW - Physical and Theoretical Chemistry SN - 1359-6640 TI - Field-assisted self-assembly process: General discussion VL - 181 ER - TY - JOUR AB - The detection of electron motion and electronic wave-packet dynamics is one of the core goals of attosecond science. Recently, choosing the nitric oxide molecule as an example, we have introduced and demonstrated an experimental approach to measure coupled valence electronic and rotational wave packets using high-order-harmonic-generation (HHG) spectroscopy [Kraus et al., Phys. Rev. Lett. 111, 243005 (2013)]. A short outline of the theory to describe the combination of the pump and HHG probe process was published together with an extensive discussion of experimental results [Baykusheva et al., Faraday Discuss. 171, 113 (2014)]. The comparison of theory and experiment showed good agreement on a quantitative level. Here, we present the theory in detail, which is based on a generalized density-matrix approach that describes the pump process and the subsequent probing of the wave packets by a semiclassical quantitative rescattering approach. An in-depth analysis of the different Raman scattering contributions to the creation of the coupled rotational and electronic spin-orbit wave packets is made. We present results for parallel and perpendicular linear polarizations of the pump and probe laser pulses. Furthermore, an analysis of the combined rotational-electronic density matrix in terms of irreducible components is presented that facilitates interpretation of the results. AU - Zhang, Song Bin AU - Baykusheva, Denitsa Rangelova AU - Kraus, Peter M. AU - Wörner, Hans Jakob AU - Rohringer, Nina ID - 14017 IS - 2 JF - Physical Review A KW - Atomic and Molecular Physics KW - and Optics SN - 1050-2947 TI - Theoretical study of molecular electronic and rotational coherences by high-order-harmonic generation VL - 91 ER - TY - JOUR AB - All attosecond time-resolved measurements have so far relied on the use of intense near-infrared laser pulses. In particular, attosecond streaking, laser-induced electron diffraction and high-harmonic generation all make use of non-perturbative light–matter interactions. Remarkably, the effect of the strong laser field on the studied sample has often been neglected in previous studies. Here we use high-harmonic spectroscopy to measure laser-induced modifications of the electronic structure of molecules. We study high-harmonic spectra of spatially oriented CH3F and CH3Br as generic examples of polar polyatomic molecules. We accurately measure intensity ratios of even and odd-harmonic orders, and of the emission from aligned and unaligned molecules. We show that these robust observables reveal a substantial modification of the molecular electronic structure by the external laser field. Our insights offer new challenges and opportunities for a range of emerging strong-field attosecond spectroscopies. AU - Kraus, P. M. AU - Tolstikhin, O. I. AU - Baykusheva, Denitsa Rangelova AU - Rupenyan, A. AU - Schneider, J. AU - Bisgaard, C. Z. AU - Morishita, T. AU - Jensen, F. AU - Madsen, L. B. AU - Wörner, H. J. ID - 14016 JF - Nature Communications KW - General Physics and Astronomy KW - General Biochemistry KW - Genetics and Molecular Biology KW - General Chemistry KW - Multidisciplinary TI - Observation of laser-induced electronic structure in oriented polyatomic molecules VL - 6 ER - TY - JOUR AB - The ultrafast motion of electrons and holes after light-matter interaction is fundamental to a broad range of chemical and biophysical processes. We advanced high-harmonic spectroscopy to resolve spatially and temporally the migration of an electron hole immediately after ionization of iodoacetylene while simultaneously demonstrating extensive control over the process. A multidimensional approach, based on the measurement and accurate theoretical description of both even and odd harmonic orders, enabled us to reconstruct both quantum amplitudes and phases of the electronic states with a resolution of ~100 attoseconds. We separately reconstructed quasi-field-free and laser-controlled charge migration as a function of the spatial orientation of the molecule and determined the shape of the hole created by ionization. Our technique opens the prospect of laser control over electronic primary processes. AU - Kraus, P. M. AU - Mignolet, B. AU - Baykusheva, Denitsa Rangelova AU - Rupenyan, A. AU - Horný, L. AU - Penka, E. F. AU - Grassi, G. AU - Tolstikhin, O. I. AU - Schneider, J. AU - Jensen, F. AU - Madsen, L. B. AU - Bandrauk, A. D. AU - Remacle, F. AU - Wörner, H. J. ID - 14013 IS - 6262 JF - Science KW - Multidisciplinary SN - 0036-8075 TI - Measurement and laser control of attosecond charge migration in ionized iodoacetylene VL - 350 ER - TY - JOUR AB - We advance high-harmonic spectroscopy to resolve molecular charge migration in time and space and simultaneously demonstrate extensive control over the process. A multidimensional approach enables us to reconstruct both quantum amplitudes and phases with a resolution of better than 100 attoseconds and to separately reconstruct field-free and laser- driven charge migration. Our techniques make charge migration in molecules measurable on the attosecond time scale and open new avenues for laser control of electronic primary processes. AU - Kraus, P M AU - Mignolet, B AU - Baykusheva, Denitsa Rangelova AU - Rupenyan, A AU - Horný, L AU - Penka, E F AU - Tolstikhin, O I AU - Schneider, J AU - Jensen, F AU - Madsen, L B AU - Bandrauk, A D AU - Remacle, F AU - Wörner, H J ID - 14015 IS - 11 JF - Journal of Physics: Conference Series KW - General Physics and Astronomy SN - 1742-6588 TI - Attosecond charge migration and its laser control VL - 635 ER - TY - JOUR AB - We have studied a coupled electronic-nuclear wave packet in nitric oxide using time-resolved strong-field photoelectron holography and rescattering. We show that the electronic dynamics mainly appears in the holographic structures whereas nuclear motion strongly modulates the angular distribution of the rescattered photoelectrons. AU - Walt, Samuel G AU - Ram, N Bhargava AU - von Conta, Aaron AU - Baykusheva, Denitsa Rangelova AU - Atala, Marcos AU - Wörner, Hans Jakob ID - 14014 IS - 11 JF - Journal of Physics: Conference Series KW - General Physics and Astronomy SN - 1742-6588 TI - Resolving the dynamics of valence-shell electrons and nuclei through laser-induced diffraction and holography VL - 635 ER - TY - GEN AB - Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance. AU - Wielgoss, Sébastien AU - Bergmiller, Tobias AU - Bischofberger, Anna M. AU - Hall, Alex R. ID - 9719 TI - Data from: Adaptation to parasites and costs of parasite resistance in mutator and non-mutator bacteria ER - TY - THES AB - The human ability to recognize objects in complex scenes has driven research in the computer vision field over couple of decades. This thesis focuses on the object recognition task in images. That is, given the image, we want the computer system to be able to predict the class of the object that appears in the image. A recent successful attempt to bridge semantic understanding of the image perceived by humans and by computers uses attribute-based models. Attributes are semantic properties of the objects shared across different categories, which humans and computers can decide on. To explore the attribute-based models we take a statistical machine learning approach, and address two key learning challenges in view of object recognition task: learning augmented attributes as mid-level discriminative feature representation, and learning with attributes as privileged information. Our main contributions are parametric and non-parametric models and algorithms to solve these frameworks. In the parametric approach, we explore an autoencoder model combined with the large margin nearest neighbor principle for mid-level feature learning, and linear support vector machines for learning with privileged information. In the non-parametric approach, we propose a supervised Indian Buffet Process for automatic augmentation of semantic attributes, and explore the Gaussian Processes classification framework for learning with privileged information. A thorough experimental analysis shows the effectiveness of the proposed models in both parametric and non-parametric views. AU - Sharmanska, Viktoriia ID - 1401 SN - 2663-337X TI - Learning with attributes for object recognition: Parametric and non-parametrics views ER - TY - JOUR AB - The competition for resources among cells, individuals or species is a fundamental characteristic of evolution. Biological all-pay auctions have been used to model situations where multiple individuals compete for a single resource. However, in many situations multiple resources with various values exist and single reward auctions are not applicable. We generalize the model to multiple rewards and study the evolution of strategies. In biological all-pay auctions the bid of an individual corresponds to its strategy and is equivalent to its payment in the auction. The decreasingly ordered rewards are distributed according to the decreasingly ordered bids of the participating individuals. The reproductive success of an individual is proportional to its fitness given by the sum of the rewards won minus its payments. Hence, successful bidding strategies spread in the population. We find that the results for the multiple reward case are very different from the single reward case. While the mixed strategy equilibrium in the single reward case with more than two players consists of mostly low-bidding individuals, we show that the equilibrium can convert to many high-bidding individuals and a few low-bidding individuals in the multiple reward case. Some reward values lead to a specialization among the individuals where one subpopulation competes for the rewards and the other subpopulation largely avoids costly competitions. Whether the mixed strategy equilibrium is an evolutionarily stable strategy (ESS) depends on the specific values of the rewards. AU - Reiter, Johannes AU - Kanodia, Ayush AU - Gupta, Raghav AU - Nowak, Martin AU - Chatterjee, Krishnendu ID - 1709 IS - 1812 JF - Proceedings of the Royal Society of London Series B Biological Sciences TI - Biological auctions with multiple rewards VL - 282 ER - TY - THES AB - Cancer results from an uncontrolled growth of abnormal cells. Sequentially accumulated genetic and epigenetic alterations decrease cell death and increase cell replication. We used mathematical models to quantify the effect of driver gene mutations. The recently developed targeted therapies can lead to dramatic regressions. However, in solid cancers, clinical responses are often short-lived because resistant cancer cells evolve. We estimated that approximately 50 different mutations can confer resistance to a typical targeted therapeutic agent. We find that resistant cells are likely to be present in expanded subclones before the start of the treatment. The dominant strategy to prevent the evolution of resistance is combination therapy. Our analytical results suggest that in most patients, dual therapy, but not monotherapy, can result in long-term disease control. However, long-term control can only occur if there are no possible mutations in the genome that can cause cross-resistance to both drugs. Furthermore, we showed that simultaneous therapy with two drugs is much more likely to result in long-term disease control than sequential therapy with the same drugs. To improve our understanding of the underlying subclonal evolution we reconstruct the evolutionary history of a patient's cancer from next-generation sequencing data of spatially-distinct DNA samples. Using a quantitative measure of genetic relatedness, we found that pancreatic cancers and their metastases demonstrated a higher level of relatedness than that expected for any two cells randomly taken from a normal tissue. This minimal amount of genetic divergence among advanced lesions indicates that genetic heterogeneity, when quantitatively defined, is not a fundamental feature of the natural history of untreated pancreatic cancers. Our newly developed, phylogenomic tool Treeomics finds evidence for seeding patterns of metastases and can directly be used to discover rules governing the evolution of solid malignancies to transform cancer into a more predictable disease. AU - Reiter, Johannes ID - 1400 SN - 2663-337X TI - The subclonal evolution of cancer ER - TY - JOUR AB - Motivated by recent ideas of Harman (Unif. Distrib. Theory, 2010) we develop a new concept of variation of multivariate functions on a compact Hausdorff space with respect to a collection D of subsets. We prove a general version of the Koksma-Hlawka theorem that holds for this notion of variation and discrepancy with respect to D. As special cases, we obtain Koksma-Hlawka inequalities for classical notions, such as extreme or isotropic discrepancy. For extreme discrepancy, our result coincides with the usual Koksma-Hlawka theorem. We show that the space of functions of bounded D-variation contains important discontinuous functions and is closed under natural algebraic operations. Finally, we illustrate the results on concrete integration problems from integral geometry and stereology. AU - Pausinger, Florian AU - Svane, Anne ID - 1792 IS - 6 JF - Journal of Complexity TI - A Koksma-Hlawka inequality for general discrepancy systems VL - 31 ER - TY - THES AB - This thesis is concerned with the computation and approximation of intrinsic volumes. Given a smooth body M and a certain digital approximation of it, we develop algorithms to approximate various intrinsic volumes of M using only measurements taken from its digital approximations. The crucial idea behind our novel algorithms is to link the recent theory of persistent homology to the theory of intrinsic volumes via the Crofton formula from integral geometry and, in particular, via Euler characteristic computations. Our main contributions are a multigrid convergent digital algorithm to compute the first intrinsic volume of a solid body in R^n as well as an appropriate integration pipeline to approximate integral-geometric integrals defined over the Grassmannian manifold. AU - Pausinger, Florian ID - 1399 SN - 2663-337X TI - On the approximation of intrinsic volumes ER -