@article{2126, abstract = {Let K be an irreducible and reversible Markov kernel on a finite set X. We construct a metric W on the set of probability measures on X and show that with respect to this metric, the law of the continuous time Markov chain evolves as the gradient flow of the entropy. This result is a discrete counterpart of the Wasserstein gradient flow interpretation of the heat flow in Rn by Jordan, Kinderlehrer and Otto (1998). The metric W is similar to, but different from, the L2-Wasserstein metric, and is defined via a discrete variant of the Benamou–Brenier formula. }, author = {Jan Maas}, journal = {Journal of Functional Analysis}, number = {8}, pages = {2250 -- 2292}, publisher = {Academic Press}, title = {{Gradient flows of the entropy for finite Markov chains}}, doi = {10.1016/j.jfa.2011.06.009 }, volume = {261}, year = {2011}, } @unpublished{2138, abstract = {A (diatomic) shape resonance is a metastable state of a pair of colliding atoms quasi-bound by the centrifugal barrier imposed by the angular momentum involved in the collision. The temporary trapping of the atoms' scattering wavefunction corresponds to an enhanced atom pair density at low interatomic separations. This leads to larger overlap of the wavefunctions involved in a molecule formation process such as photoassociation, rendering the process more efficient. However, for an ensemble of atoms, the atom pair density will only be enhanced if the energy of the resonance comes close to the temperature of the atomic ensemble. Herein we explore the possibility of controlling the energy of a shape resonance by shifting it toward the temperature of atoms confined in a trap. The shifts are imparted by the interaction of non-resonant light with the anisotropic polarizability of the atom pair, which affects both the centrifugal barrier and the pair's rotational and vibrational levels. We find that at laser intensities of up to 5×109 W/cm2 the pair density is increased by one order of magnitude for 87Rb atoms at 100μK and by two orders of magnitude for 88Sr atoms at 20μK.}, author = {Ağanoğlu, Ruzin and Mikhail Lemeshko and Friedrich, Břetislav and González-Férez, Rosario and Koch, Christiane P}, booktitle = {Unknown}, publisher = {ArXiv}, title = {{Controlling a diatomic shape resonance with non-resonant light}}, year = {2011}, } @article{2198, abstract = {We show that dressing polar molecules with a far-off-resonant optical field leads to new types of intermolecular potentials, which undergo a crossover from the inverse power to oscillating behavior depending on the intermolecular distance, and whose parameters can be tuned by varying the laser intensity and wavelength. We present analytic expressions for the potential energy surfaces, thereby providing direct access to the parameters of an optical field required to design intermolecular interactions experimentally.}, author = {Mikhail Lemeshko}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {5}, publisher = {American Physical Society}, title = {{Shaping interactions between polar molecules with far-off-resonant light}}, doi = {10.1103/PhysRevA.83.051402}, volume = {83}, year = {2011}, } @article{2199, abstract = {By invoking supersymmetry, we found a condition under which the Stark-effect problem for a polar and polarizable molecule subject to nonresonant electric fields becomes exactly solvable for the family of stretched states. The analytic expressions for the wave function and eigenenergy and other expectation values allow one to readily reverse-engineer the problem of finding the values of the interaction parameters required for creating quantum states with preordained characteristics. The method also allows the construction of families of isospectral potentials, realizable with combined fields.}, author = {Mikhail Lemeshko and Mustafa, Mustafa K and Kais, Sabre and Friedrich, Břetislav}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {4}, publisher = {American Physical Society}, title = {{Supersymmetric factorization yields exact solutions to the molecular Stark-effect problem for "stretched" states}}, doi = {10.1103/PhysRevA.83.043415}, volume = {83}, year = {2011}, } @article{2200, abstract = {We made use of supersymmetric (SUSY) quantum mechanics to find the condition under which the Stark effect problem for a polar and polarizable closed-shell diatomic molecule subjected to collinear electrostatic and nonresonant radiative fields becomes exactly solvable. The condition Δω = ω2/4(m+1)2 connects values of the dimensionless parameters ω and Δω that characterize the strengths of the permanent and induced dipole interactions of the molecule with the respective fields. The exact solutions are obtained for the \J̃ = m, m; ω, Δω) family of 'stretched' states. The field-free and strong-field limits of the combined-fields problem were found to exhibit supersymmetry and shape invariance, which is indeed the reason why they are analytically solvable. By making use of the analytic form of the \J̃ = m,m; ω, Δω) wavefunctions, we obtained simple formulae for the expectation values of the space-fixed electric dipole moment, the alignment cosine and the angular momentum squared, and derived a 'sum rule' that combines the above expectation values into a formula for the eigenenergy. The analytic expressions for the characteristics of the strongly oriented and aligned states provide direct access to the values of the interaction parameters required for creating such states in the laboratory.}, author = {Mikhail Lemeshko and Mustafa, Mustafa K and Kais, Sabre and Friedrich, Břetislav}, journal = {New Journal of Physics}, publisher = {IOP Publishing Ltd.}, title = {{Supersymmetry identifies molecular Stark states whose eigenproperties can be obtained analytically}}, doi = {10.1088/1367-2630/13/6/063036}, volume = {13}, year = {2011}, } @inproceedings{2320, abstract = {The binding of polarons, or its absence, is an old and subtle topic. After defining the model we state some recent theorems of ours. First, the transition from many-body collapse to the existence of a thermodynamic limit for N polarons occurs precisely at U = 2α, where U is the electronic Coulomb repulsion and α is the polaron coupling constant. Second, if U is large enough, there is no multi-polaron binding of any kind. We also discuss the Pekar-Tomasevich approximation to the ground state energy, which is valid for large α. Finally, we derive exact results, not reported before, about the one-dimensional toy model introduced by E. P. Gross.}, author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer and Thomas, Lawrence E}, pages = {21 -- 32}, publisher = {World Scientific Publishing}, title = {{Binding, stability, and non-binding of multi-polaron systems}}, doi = {10.1142/9789814350365_0002}, year = {2011}, } @inproceedings{2321, abstract = {We derive a sharp bound on the location of non-positive eigenvalues of Schrödinger operators on the half-line with complex-valued potentials.}, author = {Frank, Rupert L and Laptev, Ari and Robert Seiringer}, pages = {39 -- 44}, publisher = {Springer}, title = {{ A sharp bound on eigenvalues of Schrödinger operators on the halfline with complex-valued potentials}}, doi = {10.1007/978-3-7643-9994-8_3}, volume = {214}, year = {2011}, } @article{2390, abstract = {We resolve several longstanding problems concerning the stability and the absence of multi-particle binding for N≥2 polarons. Fröhlich's 1937 polaron model describes non-relativistic particles interacting with a scalar quantized field with coupling √α, and with each other by Coulomb repulsion of strength U. We prove the following: (i) While there is a known thermodynamic instability for U<2α, stability of matter does hold for U>2α, that is, the ground state energy per particle has a finite limit as N→∞. (ii) There is no binding of any kind if U exceeds a critical value that depends on α but not on N. The same results are shown to hold for the Pekar-Tomasevich model.}, author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer and Thomas, Lawrence E}, journal = {Publications Mathematiques de l Institut des Hautes Etudes Scientifiques}, number = {1}, pages = {39 -- 67}, publisher = {Springer}, title = {{Stability and absence of binding for multi-polaron systems}}, doi = {10.1007/s10240-011-0031-5}, volume = {113}, year = {2011}, } @article{2391, abstract = {The change in energy of an ideal Fermi gas when a local one-body potential is inserted into the system, or when the density is changed locally, are important quantities in condensed matter physics. We show that they can be rigorously bounded from below by a universal constant times the value given by the semiclassical approximation.}, author = {Frank, Rupert L and Lewin, Mathieu and Lieb, Élliott H and Robert Seiringer}, journal = {Physical Review Letters}, number = {15}, publisher = {American Physical Society}, title = {{Energy cost to make a hole in the fermi sea}}, doi = {10.1103/PhysRevLett.106.150402}, volume = {106}, year = {2011}, } @article{2393, abstract = {We investigate the low energy excitation spectrum of a Bose gas with weak, long range repulsive interactions. In particular, we prove that the Bogoliubov spectrum of elementary excitations with linear dispersion relation for small momentum becomes exact in the mean-field limit.}, author = {Robert Seiringer}, journal = {Communications in Mathematical Physics}, number = {2}, pages = {565 -- 578}, publisher = {Springer}, title = {{The excitation spectrum for weakly interacting Bosons}}, doi = {10.1007/s00220-011-1261-6}, volume = {306}, year = {2011}, } @article{2454, abstract = {Within a multicellular tissue cells may coordinately form a singular or multiple polar axes, but it is unclear whether a common mechanism governs different types of polar axis formation. The phosphorylation status of PIN proteins, which is directly affected by the PINOID (PID) protein kinase and the PP2A protein phosphatase, is known to regulate the apical-basal polarity of PIN localization in bipolar cells of roots and shoot apices. Here, we provide evidence that the phosphorylation status-mediated PIN polarity switch is widely used to modulate cellular processes in Arabidopsis including multipolar pavement cells (PC) with interdigitated lobes and indentations. The degree of PC interdigitation was greatly reduced either when the FYPP1 gene, which encodes a PP2A called phytochrome-associated serine/threonine protein phosphatase, was knocked out or when the PID gene was overexpressed (35S:PID). These genetic modifications caused PIN1 localization to switch from lobe to indentation regions. The PP2A and PID mediated switching of PIN1 localization is strikingly similar to their regulation of the apical-basal polarity switch of PIN proteins in other cells. Our findings suggest a common mechanism for the regulation of PIN1 polarity formation, a fundamental cellular process that is crucial for pattern formation both at the tissue/organ and cellular levels.}, author = {Hongjiang Li and Lin, Deshu and Dhonukshe, Pankaj B and Nagawa, Shingo and Chen, Dandan and Jirí Friml and Scheres, Ben and Guo, Hongwei and Yang, Zhenbiao}, journal = {Cell Research}, number = {6}, pages = {970 -- 978}, publisher = {Nature Publishing Group}, title = {{Phosphorylation switch modulates the interdigitated pattern of PIN1 localization and cell expansion in Arabidopsis leaf epidermis}}, doi = {10.1038/cr.2011.49}, volume = {21}, year = {2011}, } @article{2961, abstract = {Rapid research progress in genotyping techniques have allowed large genome-wide association studies. Existing methods often focus on determining associations between single loci and a specic phenotype. However, a particular phenotype is usually the result of complex relationships between multiple loci and the environment. In this paper, we describe a two-stage method for detecting epistasis by combining the traditionally used single-locus search with a search for multiway interactions. Our method is based on an extended version of Fisher's exact test. To perform this test, a Markov chain is constructed on the space of multidimensional contingency tables using the elements of a Markov basis as moves. We test our method on simulated data and compare it to a two-stage logistic regression method and to a fully Bayesian method, showing that we are able to detect the interacting loci when other methods fail to do so. Finally, we apply our method to a genome-wide data set consisting of 685 dogs and identify epistasis associated with canine hair length for four pairs of single nucleotide polymorphisms (SNPs).}, author = {Malaspinas, Anna-Sapfo and Caroline Uhler}, journal = {Journal of Algebraic Statistics}, number = {1}, pages = {36 -- 53}, publisher = {Public Knowledge Project}, title = {{Detecting epistasis via Markov bases}}, doi = {http://dx.doi.org/10.18409/jas.v2i1.27}, volume = {2}, year = {2011}, } @article{3091, author = {Sauer, Michael and Friml, Jirí}, journal = {Molecular Systems Biology}, publisher = {Nature Publishing Group}, title = {{Fleeting hormone cues get stabilized for plant organogenesis}}, doi = {10.1038/msb.2011.45}, volume = {7}, year = {2011}, } @article{3092, abstract = {The phytohormone auxin is vital to plant growth and development. A unique property of auxin among all other plant hormones is its cell-to-cell polar transport that requires activity of polarly localized PIN-FORMED (PIN) auxin efflux transporters. Despite the substantial molecular insight into the cellular PIN polarization, the mechanistic understanding for developmentally and environmentally regulated PIN polarization is scarce. The long-standing belief that auxin modulates its own transport by means of a positive feedback mechanism has inspired both experimentalists and theoreticians for more than two decades. Recently, theoretical models for auxin-dependent patterning in plants include the feedback between auxin transport and the PIN protein localization. These computer models aid to assess the complexity of plant development by testing and predicting plausible scenarios for various developmental processes that occur in planta. Although the majority of these models rely on purely heuristic principles, the most recent mechanistic models tentatively integrate biologically testable components into known cellular processes that underlie the PIN polarity regulation. The existing and emerging computational approaches to describe PIN polarization are presented and discussed in the light of recent experimental data on the PIN polar targeting.}, author = {Wabnik, Krzysztof T and Govaerts, Willy and Friml, Jirí and Kleine Vehn, Jürgen}, journal = {Molecular BioSystems}, number = {8}, pages = {2352 -- 2359}, publisher = {Royal Society of Chemistry}, title = {{Feedback models for polarized auxin transport: An emerging trend}}, doi = {10.1039/c1mb05109a}, volume = {7}, year = {2011}, } @article{3100, abstract = {In multicellular organisms, morphogenesis relies on a strict coordination in time and space of cell proliferation and differentiation. In contrast to animals, plant development displays continuous organ formation and adaptive growth responses during their lifespan relying on a tight coordination of cell proliferation. How developmental signals interact with the plant cell-cycle machinery is largely unknown. Here, we characterize plant A2-type cyclins, a small gene family of mitotic cyclins, and show how they contribute to the fine-tuning of local proliferation during plant development. Moreover, the timely repression of CYCA2;3 expression in newly formed guard cells is shown to require the stomatal transcription factors FOUR LIPS/MYB124 and MYB88, providing a direct link between developmental programming and cell-cycle exit in plants. Thus, transcriptional downregulation of CYCA2s represents a critical mechanism to coordinate proliferation during plant development.}, author = {Vanneste, Steffen and Coppens, Frederik and Lee, EunKyoung and Donner, Tyler J and Xie, Zidian and Van Isterdael, Gert and Dhondt, Stijn and De Winter, Freya and De Rybel, Bert and Vuylsteke, Marnik and De Veylder, Lieven and Jirí Friml and Inzé, Dirk and Grotewold, Erich and Scarpella, Enrico and Sack, Fred and Beemster, Gerrit T and Beeckman, Tom}, journal = {EMBO Journal}, number = {16}, pages = {3430 -- 3441}, publisher = {Wiley-Blackwell}, title = {{Developmental regulation of CYCA2s contributes to tissue-specific proliferation in Arabidopsis }}, doi = {10.1038/emboj.2011.240}, volume = {30}, year = {2011}, } @article{3101, abstract = {Subcellular trafficking is required for a multitude of functions in eukaryotic cells. It involves regulation of cargo sorting, vesicle formation, trafficking and fusion processes at multiple levels. Adaptor protein (AP) complexes are key regulators of cargo sorting into vesicles in yeast and mammals but their existence and function in plants have not been demonstrated. Here we report the identification of the protein-affected trafficking 4 (pat4) mutant defective in the putative δ subunit of the AP-3 complex. pat4 and pat2, a mutant isolated from the same GFP imaging-based forward genetic screen that lacks a functional putative AP-3 β, as well as dominant negative AP-3 μ transgenic lines display undistinguishable phenotypes characterized by largely normal morphology and development, but strong intracellular accumulation of membrane proteins in aberrant vacuolar structures. All mutants are defective in morphology and function of lytic and protein storage vacuoles (PSVs) but show normal sorting of reserve proteins to PSVs. Immunoprecipitation experiments and genetic studies revealed tight functional and physical associations of putative AP-3 β and AP-3 δ subunits. Furthermore, both proteins are closely linked with putative AP-3 μ and σ subunits and several components of the clathrin and dynamin machineries. Taken together, these results demonstrate that AP complexes, similar to those in other eukaryotes, exist in plants, and that AP-3 plays a specific role in the regulation of biogenesis and function of vacuoles in plant cells. © 2011 IBCB, SIBS, CAS All rights reserved}, author = {Zwiewka, Marta and Feraru, Elena and Möller, Barbara and Hwang, Inhwan and Feraru, Mugurel I and Kleine-Vehn, Jürgen and Weijers, Dolf and Jirí Friml}, journal = {Cell Research}, number = {12}, pages = {1711 -- 1722}, publisher = {Nature Publishing Group}, title = {{The AP 3 adaptor complex is required for vacuolar function in Arabidopsis}}, doi = {10.1038/cr.2011.99}, volume = {21}, year = {2011}, } @article{3269, abstract = {The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss-Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi-resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi-projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods.}, author = {Sheng, Yu and Cutler, Barbara and Chen, Chao and Nasman, Joshua}, journal = {Computer Graphics Forum}, number = {4}, pages = {1261 -- 1268}, publisher = {Wiley-Blackwell}, title = {{Perceptual global illumination cancellation in complex projection environments}}, doi = {10.1111/j.1467-8659.2011.01985.x}, volume = {30}, year = {2011}, } @phdthesis{3275, abstract = {Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. }, author = {Schumann, Kathrin}, issn = {2663-337X}, pages = {141}, publisher = {Institute of Science and Technology Austria}, title = {{The role of chemotactic gradients in dendritic cell migration}}, year = {2011}, } @article{3276, abstract = {We present an algorithm to identify individual neural spikes observed on high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers of distinct neural units, even when spikes overlap, and accounts for intrinsic variability of spikes from each unit. As MEAs grow larger, it is important to find spike-identification methods that are scalable, that is, the computational cost of spike fitting should scale well with the number of units observed. Our algorithm accomplishes this goal, and is fast, because it exploits the spatial locality of each unit and the basic biophysics of extracellular signal propagation. Human interaction plays a key role in our method; but effort is minimized and streamlined via a graphical interface. We illustrate our method on data from guinea pig retinal ganglion cells and document its performance on simulated data consisting of spikes added to experimentally measured background noise. We present several tests demonstrating that the algorithm is highly accurate: it exhibits low error rates on fits to synthetic data, low refractory violation rates, good receptive field coverage, and consistency across users.}, author = {Prentice, Jason S and Homann, Jan and Simmons, Kristina D and Gasper Tkacik and Balasubramanian, Vijay and Nelson, Philip C}, journal = {PLoS One}, number = {7}, publisher = {Public Library of Science}, title = {{Fast, scalable, Bayesian spike identification for multi-electrode arrays}}, doi = {10.1371/journal.pone.0019884}, volume = {6}, year = {2011}, } @article{3288, abstract = {The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion where cellular forces are exerted and resisted. Increasing evidence indicates that E-cadherin adhesion molecules at the ZA serve to sense force applied on the junctions and coordinate cytoskeletal responses to those forces. Efforts to understand the role that cadherins play in mechanotransduction have been limited by the lack of assays to measure the impact of forces on the ZA. In this study we used 4D imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions in confluent epithelial monolayers displayed prominent movements oriented orthogonal (perpendicular) to the ZA itself. Two components were identified in these movements: a relatively slow unidirectional (translational) component that could be readily fitted by least-squares regression analysis, upon which were superimposed more rapid oscillatory movements. Myosin IIB was a dominant factor responsible for driving the unilateral translational movements. In contrast, frequency spectrum analysis revealed that depletion of Myosin IIA increased the power of the oscillatory movements. This implies that Myosin IIA may serve to dampen oscillatory movements of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate that Myosin IIA and Myosin IIB make distinct contributions to junctional movement at the ZA.}, author = {Smutny, Michael and Wu, Selwin and Gomez, Guillermo and Mangold, Sabine and Yap, Alpha and Hamilton, Nicholas}, journal = {PLoS One}, number = {7}, publisher = {Public Library of Science}, title = {{Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens}}, doi = {10.1371/journal.pone.0022458}, volume = {6}, year = {2011}, }