TY - JOUR
AB - The Pauli operator describes the energy of a nonrelativistic quantum particle with spin 1/2 in a magnetic field and an external potential. A new Lieb-Thirring type inequality on the sum of the negative eigenvalues is presented. The main feature compared to earlier results is that in the large field regime the present estimate grows with the optimal (first) power of the strength of the magnetic field. As a byproduct of the method, we also obtain an optimal upper bound on the pointwise density of zero energy eigenfunctions of the Dirac operator. The main technical tools are: (i) a new localization scheme for the square of the resolvent of a general class of second order elliptic operators; (ii) a geometric construction of a Dirac operator with a constant magnetic field that approximates the original Dirac operator in a tubular neighborhood of a fixed field line. The errors may depend on the regularity of the magnetic field but they are uniform in the field strength.
AU - László Erdös
AU - Solovej, Jan P
ID - 2741
IS - 4
JF - Annales Henri Poincare
TI - Uniform Lieb-Thirring inequality for the three-dimensional Pauli operator with a strong non-homogeneous magnetic field
VL - 5
ER -
TY - JOUR
AB - We consider a system of N weakly interacting fermions with a real analytic pair interaction. We prove that for a general class of initial data there exists a fixed time T such that the difference between the one particle density matrix of this system and the solution of the nonlinear Hartree equation is of order N−1 for any time t⩽T.
AU - Elgart, Alexander
AU - László Erdös
AU - Schlein, Benjamin
AU - Yau, Horng-Tzer
ID - 2742
IS - 10
JF - Journal de Mathématiques Pures et Appliquées
TI - Nonlinear Hartree equation as the mean field limit of weakly coupled fermions
VL - 83
ER -
TY - JOUR
AB - The Pauli operator describes the energy of a nonrelativistic quantum particle with spin in a magnetic field and an external potential. Bounds on the sum of the negative eigenvalues are called magnetic Lieb-Thirring (MLT) inequalities. The purpose of this paper is twofold. First, we prove a new MLT inequality in a simple way. Second, we give a short summary of our recent proof of a more refined MLT inequality(8) and we explain the differences between the two results and methods. The main feature of both estimates, compared to earlier results, is that in the large field regime they grow with the optimal (first) power of the strength of the magnetic field. As a byproduct of the method, we also obtain optimal upper bounds on the pointwise density of zero energy eigenfunctions of the Dirac operator.
AU - László Erdös
AU - Solovej, Jan P
ID - 2706
IS - 1-4
JF - Journal of Statistical Physics
TI - Magnetic Lieb-Thirring inequalities with optimal dependence on the field strength
VL - 116
ER -
TY - JOUR
AB - We give a nonrigorous derivation of the nonlinear Boltzmann equation from the Schrödinger evolution of interacting fermions. The argument is based mainly on the assumption that a quasifree initial state satisfies a property called restricted quasifreeness in the weak coupling limit at any later time. By definition, a state is called restricted quasifree if the four-point and the eight-point functions of the state factorize in the same manner as in a quasifree state.
AU - László Erdös
AU - Salmhofer, Manfred
AU - Yau, Horng-Tzer
ID - 2707
IS - 1-4
JF - Journal of Statistical Physics
TI - On the quantum Boltzmann equation
VL - 116
ER -
TY - JOUR
AB - Transition to turbulence in pipe flow is one of the most fundamental and longest- standing problems in fluid dynamics. Stability theory suggests that the flow remains laminar for all flow rates, but in practice pipe flow becomes turbulent even at moderate speeds. This transition drastically affects the transport efficiency of mass, momentum, and heat. On the basis of the recent discovery of unstable traveling waves in computational studies of the Navier-Stokes equations and ideas from dynamical systems theory, a model for the transition process has been suggested. We report experimental observation of these traveling waves in pipe flow, confirming the proposed transition scenario and suggesting that the dynamics associated with these unstable states may indeed capture the nature of fluid turbulence.
AU - Björn Hof
AU - van Doorne, Casimir W
AU - Westerweel, Jerry
AU - Nieuwstadt, Frans T
AU - Faisst, Holger
AU - Eckhardt, Bruno
AU - Wedin, Håkan
AU - Kersweli, Richard R
AU - Waleffe, Fabian
ID - 2786
IS - 5690
JF - Science
TI - Experimental observation of nonlinear traveling waves in turbulent pipe flow
VL - 305
ER -
TY - JOUR
AB - The results of experimental and numerical investigations of the onset of oscillatory convection in a sidewall heated rectangular cavity of molten gallium are reported. Detailed comparisons are made between experimental observations and calculations from numerical simulations of a three-dimensional Boussinesq model. The onset of time-dependence takes place through supercritical Hopf bifurcations and the loci of critical points in the (Gr, Pr)-plane are qualitatively similar with excellent agreement between the frequencies of the oscillatory motion. This provides a severe test of the control of the experiment since the mode of oscillation is extremely sensitive to imperfections. Detailed numerical investigations reveal that there are a pair of Hopf bifurcations which exist on two asymmetric states which themselves arise at a subcritical pitchfork from the symmetric state. There is no evidence for this in the experiment and this qualitative difference is attributed to non-Boussinesq perturbations which increase with Gr. However, the antisymmetric spatial structure of the oscillatory state is robust and is present in both the experiment and the numerical model. Moreover, the detailed analysis of the numerical results reveals the origins of the oscillatory instability.
AU - Björn Hof
AU - Juel, Anne
AU - Zhao, Li
AU - Henry, Daniel
AU - Ben Hadid, Hamda
AU - Mullin, Tom P
ID - 2787
JF - Journal of Fluid Mechanics
TI - On the onset of oscillatory convection in molten gallium
VL - 515
ER -
TY - JOUR
AB - Polar transport-dependent local accumulation of auxin provides positional cues for multiple plant patterning processes. This directional auxin flow depends on the polar subcellular localization of the PIN auxin efflux regulators. Overexpression of the PINOID protein kinase induces a basal-to-apical shift in PIN localization, resulting in the loss of auxin gradients and strong defects in embryo and seedling roots. Conversely, pid loss of function induces an apical-to-basal shift in PIN1 polar targeting at the inflorescence apex, accompanied by defective organogenesis. Our results show that a PINOID-dependent binary switch controls PIN polarity and mediates changes in auxin flow to create local gradients for patterning processes.
AU - Jirí Friml
AU - Yang, Xiong
AU - Michniewicz, Marta
AU - Weijers, Dolf
AU - Quint, Ab
AU - Tietz, Olaf
AU - Benjamins, René
AU - Ouwerkerk, Pieter B
AU - Ljung, Karin
AU - Sandberg, Göran
AU - Hooykaas, Paul J
AU - Palme, Klaus
AU - Offringa, Remko
ID - 2997
IS - 5697
JF - Science
TI - A PINOID-dependent binary switch in apical-basal PIN polar targeting directs auxin efflux
VL - 306
ER -
TY - JOUR
AB - The packaging of the genomic DNA into chromatin in the cell nucleus requires machineries that facilitate DNA-dependent processes such as transcription in the presence of repressive chromatin structures. Using co-immunoprecipitation we have identified in Arabidopsis thaliana cells the FAcilitates Chromatin Transcription (FACT) complex, consisting of the 120-kDa Spt16 and the 71-kDa SSRP1 proteins. Indirect immunofluorecence analyses revealed that both FACT subunits co-localize to nuclei of the majority of cell types in embryos, shoots and roots, whereas FACT is not present in terminally differentiated cells such as mature trichoblasts or cells of the root cap. In the nucleus, Spt16 and SSRP1 are found in the cytologically defined euchromatin of interphase cells independent of the status of DNA replication, but the proteins are not associated with heterochromatic chromocentres and condensed mitotic chromosomes. FACT can be detected by chromatin immunoprecipitation over the entire transcribed region (5′-UTR, coding sequence, 3′-UTR) of actively transcribed genes, whereas it does not occur at transcriptionally inactive heterochromatic regions and intergenic regions. FACT localizes to inducible genes only after induction of transcription, and the association of the complex with the genes correlates with the level of transcription. Collectively, these results indicate that FACT assists transcription elongation through plant chromatin.
AU - Duroux, Meg
AU - Houben, Andreas
AU - Růžička, Kamil
AU - Jirí Friml
AU - Grasser, Klaus D
ID - 2998
IS - 5
JF - Plant Journal
TI - The chromatin remodelling complex FACT associates with actively transcribed regions of the Arabidopsis genome
VL - 40
ER -
TY - JOUR
AB - Embryogenesis of flowering plants establishes a basic body plan with apical-basal, radial and bilateral patterns from the single-celled zygote. Arabidopsis embryogenesis exhibits a nearly invariant cell division pattern and therefore is an ideal system for studies of early plant development. However, plant embryos are difficult to access for experimental manipulation, as they develop deeply inside maternal tissues. Here we present a method for the culture of zygotic Arabidopsis embryos in vitro. The technique omits excision of the embryo by culturing the entire ovule, thus greatly facilitating the time and effort involved. It enables external manipulation of embryo development and culture from the earliest developmental stages up to maturity. Administration of various chemical treatments as well as the use of different molecular markers is demonstrated together with standard techniques for visualizing gene expression and protein localization in in vitro cultivated embryos. The presented set of techniques allows for so far unavailable molecular physiology approaches in the study of early plant development.
AU - Sauer, Michael
AU - Jirí Friml
ID - 2999
IS - 5
JF - Plant Journal
TI - In vitro culture of Arabidopsis embryos within their ovules
VL - 40
ER -
TY - GEN
AB - Assembly of neuronal circuits is controlled by the sequential acquisition of neuronal subpopulation-specific identities at progressive developmental steps. Whereas neuronal features involved in initial phases of differentiation are already established at cell-cycle exit, recent findings, based mainly on work in the peripheral nervous system, suggest that the timely integration of signals encountered en route to targets and from the target region itself is essential to control late steps in connectivity. As neurons project towards their targets they require target-derived signals to establish mature axonal projections and acquire neuronal traits such as the expression of distinct combinations of neurotransmitters. Recent evidence presented in this review shows that this principle, of a signaling interplay between target-derived signals and neuronal cell bodies, is often mediated through transcriptional events and is evolutionarily conserved.
AU - Simon Hippenmeyer
AU - Kramer, Ina
AU - Arber, Silvia
ID - 3142
IS - 8
T2 - Trends in Neurosciences
TI - Control of neuronal phenotype: What targets tell the cell bodies
VL - 27
ER -
TY - JOUR
AB - The simultaneous multiple volume (SMV) approach in navigator-gated MRI allows the use of the whole motion range or the entire scan time for the reconstruction of final images by simultaneously acquiring different image volumes at different motion states. The motion tolerance range for each volume is kept small, thus SMV substantially increases the scan efficiency of navigator methods while maintaining the effectiveness of motion suppression. This article reports a general implementation of the SMV approach using a multiprocessor scheduling algorithm. Each motion state is regarded as a processor and each volume is regarded as a job. An efficient scheduling that completes all jobs in minimal time is maintained even when the motion pattern changes. Initial experiments demonstrated that SMV significantly increased the scan efficiency of navigatorgated MRI.
AU - Vladimir Kolmogorov
AU - Nguyen, Thành D
AU - Nuval, Anthony
AU - Spincemaille, Pascal
AU - Prince, Martin R
AU - Zabih, Ramin
AU - Wang, Yusu
ID - 3172
IS - 2
JF - Magnetic Resonance in Medicine
TI - Multiprocessor scheduling implementation of the simultaneous multiple volume SMV navigator method
VL - 52
ER -
TY - JOUR
AB - In the last few years, several new algorithms based on graph cuts have been developed to solve energy minimization problems in computer vision. Each of these techniques constructs a graph such that the minimum cut on the graph also minimizes the energy. Yet, because these graph constructions are complex and highly specific to a particular energy function, graph cuts have seen limited application to date. In this paper, we give a characterization of the energy functions that can be minimized by graph cuts. Our results are restricted to functions of binary variables. However, our work generalizes many previous constructions and is easily applicable to vision problems that involve large numbers of labels, such as stereo, motion, image restoration, and scene reconstruction. We give a precise characterization of what energy functions can be minimized using graph cuts, among the energy functions that can be written as a sum of terms containing three or fewer binary variables. We also provide a general-purpose construction to minimize such an energy function. Finally, we give a necessary condition for any energy function of binary variables to be minimized by graph cuts. Researchers who are considering the use of graph cuts to optimize a particular energy function can use our results to determine if this is possible and then follow our construction to create the appropriate graph. A software implementation is freely available.
AU - Vladimir Kolmogorov
AU - Zabih, Ramin
ID - 3173
IS - 2
JF - IEEE Transactions on Pattern Analysis and Machine Intelligence
TI - What energy functions can be minimized via graph cuts?
VL - 26
ER -
TY - CONF
AB - Feature space clustering is a popular approach to image segmentation, in which a feature vector of local properties (such as intensity, texture or motion) is computed at each pixel. The feature space is then clustered, and each pixel is labeled with the cluster that contains its feature vector. A major limitation of this approach is that feature space clusters generally lack spatial coherence (i.e., they do not correspond to a compact grouping of pixels). In this paper, we propose a segmentation algorithm that operates simultaneously in feature space and in image space. We define an energy function over both a set of clusters and a labeling of pixels with clusters. In our framework, a pixel is labeled with a single cluster (rather than, for example, a distribution over clusters). Our energy function penalizes clusters that are a poor fit to the data in feature space, and also penalizes clusters whose pixels lack spatial coherence. The energy function can be efficiently minimized using graph cuts. Our algorithm can incorporate both parametric and non-parametric clustering methods. It can be applied to many optimization-based clustering methods, including k-means and k-medians, and can handle models which are very close in feature space. Preliminary results are presented on segmenting real and synthetic images, using both parametric and non-parametric clustering.
AU - Zabih, Ramin
AU - Vladimir Kolmogorov
ID - 3177
TI - Spatially coherent clustering using graph cuts
VL - 2
ER -
TY - JOUR
AB - Minimum cut/maximum flow algorithms on graphs have emerged as an increasingly useful tool for exactor approximate energy minimization in low-level vision. The combinatorial optimization literature provides many min-cut/max-flow algorithms with different polynomial time complexity. Their practical efficiency, however, has to date been studied mainly outside the scope of computer vision. The goal of this paper is to provide an experimental comparison of the efficiency of min-cut/max flow algorithms for applications in vision. We compare the running times of several standard algorithms, as well as a new algorithm that we have recently developed. The algorithms we study include both Goldberg-Tarjan style "push -relabel" methods and algorithms based on Ford-Fulkerson style "augmenting paths." We benchmark these algorithms on a number of typical graphs in the contexts of image restoration, stereo, and segmentation. In many cases, our new algorithm works several times faster than any of the other methods, making near real-time performance possible. An implementation of our max-flow/min-cut algorithm is available upon request for research purposes.
AU - Boykov, Yuri
AU - Vladimir Kolmogorov
ID - 3178
IS - 9
JF - IEEE Transactions on Pattern Analysis and Machine Intelligence
TI - An experimental comparison of min-cut/max-flow algorithms for energy minimization in vision
VL - 26
ER -
TY - CONF
AB - The problem of efficient, interactive foreground/background segmentation in still images is of great practical importance in image editing. Classical image segmentation tools use either texture (colour) information, e.g. Magic Wand, or edge (contrast) information, e.g. Intelligent Scissors. Recently, an approach based on optimization by graph-cut has been developed which successfully combines both types of information. In this paper we extend the graph-cut approach in three respects. First, we have developed a more powerful, iterative version of the optimisation. Secondly, the power of the iterative algorithm is used to simplify substantially the user interaction needed for a given quality of result. Thirdly, a robust algorithm for "border matting" has been developed to estimate simultaneously the alpha-matte around an object boundary and the colours of foreground pixels. We show that for moderately difficult examples the proposed method outperforms competitive tools.
AU - Rother, Carsten
AU - Vladimir Kolmogorov
AU - Blake, Andrew
ID - 3179
IS - 3
TI - "GrabCut" - Interactive foreground extraction using iterated graph cuts
VL - 23
ER -
TY - CONF
AB - A new technique for proving the adaptive indistinguishability of two systems, each composed of some component systems, is presented, using only the fact that corresponding component systems are non-adaptively indistinguishable. The main tool is the definition of a special monotone condition for a random system F, relative to another random system G, whose probability of occurring for a given distinguisher D is closely related to the distinguishing advantage ε of D for F and G, namely it is lower and upper bounded by ε and (1+ln1), respectively.
A concrete instantiation of this result shows that the cascade of two random permutations (with the second one inverted) is indistinguishable from a uniform random permutation by adaptive distinguishers which may query the system from both sides, assuming the components’ security only against non-adaptive one-sided distinguishers.
As applications we provide some results in various fields as almost k-wise independent probability spaces, decorrelation theory and computational indistinguishability (i.e., pseudo-randomness).
AU - Maurer, Ueli M
AU - Krzysztof Pietrzak
ID - 3208
TI - Composition of random systems: When two weak make one strong
VL - 2951
ER -
TY - JOUR
AB - The folding and stability of transmembrane proteins is a fundamental and unsolved biological problem. Here, single bacteriorhodopsin molecules were mechanically unfolded from native purple membranes using atomic force microscopy and force spectroscopy. The energy landscape of individual transmembrane α helices and polypeptide loops was mapped by monitoring the pulling speed dependence of the unfolding forces and applying Monte Carlo simulations. Single helices formed independently stable units stabilized by a single potential barrier. Mechanical unfolding of the helices was triggered by 3.9–7.7 Å extension, while natural unfolding rates were of the order of 10−3 s−1. Besides acting as individually stable units, helices associated pairwise, establishing a collective potential barrier. The unfolding pathways of individual proteins reflect distinct pulling speed-dependent unfolding routes in their energy landscapes. These observations support the two-stage model of membrane protein folding in which α helices insert into the membrane as stable units and then assemble into the functional protein.
AU - Harald Janovjak
AU - Struckmeier, Jens
AU - Hubain, Maurice
AU - Kessler, Max
AU - Kedrov, Alexej
AU - Mueller, Daniel J
ID - 3419
IS - 5
JF - Structure
TI - Probing the energy landscape of the membrane protein bacteriorhodopsin
VL - 12
ER -
TY - JOUR
AB - Single-molecule force-spectroscopy was employed to unfold and refold single sodium-proton antiporters (NhaA) of Escherichia coli from membrane patches. Although transmembrane α-helices and extracellular polypeptide loops exhibited sufficient stability to individually establish potential barriers against unfolding, two helices predominantly unfolded pairwise, thereby acting as one structural unit. Many of the potential barriers were detected unfolding NhaA either from the C-terminal or the N-terminal end. It was found that some molecular interactions stabilizing secondary structural elements were directional, while others were not. Additionally, some interactions appeared to occur between the secondary structural elements. After unfolding ten of the 12 helices, the extracted polypeptide was allowed to refold back into the membrane. After five seconds, the refolded polypeptide established all secondary structure elements of the native protein. One helical pair showed a characteristic spring like “snap in” into its folded conformation, while the refolding process of other helices was not detected in particular. Additionally, individual helices required characteristic periods of time to fold. Correlating these results with the primary structure of NhaA allowed us to obtain the first insights into how potential barriers establish and determine the folding kinetics of the secondary structure elements.
AU - Kedrov, Alexej
AU - Ziegler, Christine
AU - Harald Janovjak
AU - Kühlbrandt, Werner
AU - Mueller, Daniel J
ID - 3420
IS - 5
JF - Journal of Molecular Biology
TI - Controlled unfolding and refolding of a single sodium/proton antiporter using atomic force microscopy
VL - 340
ER -
TY - CHAP
AU - Herbert Edelsbrunner
ID - 3574
T2 - Handbook of Discrete and Computational Geometry
TI - Biological applications of computational topology
ER -
TY - CHAP
AB - The Jacobi set of two Morse functions defined on a common - manifold is the set of critical points of the restrictions of one func- tion to the level sets of the other function. Equivalently, it is the set of points where the gradients of the functions are parallel. For a generic pair of Morse functions, the Jacobi set is a smoothly embed- ded 1-manifold. We give a polynomial-time algorithm that com- putes the piecewise linear analog of the Jacobi set for functions specified at the vertices of a triangulation, and we generalize all results to more than two but at most Morse functions.
AU - Herbert Edelsbrunner
AU - Harer, John
ID - 3575
T2 - Foundations of Computational Mathematics
TI - Jacobi sets of multiple Morse functions
VL - 312
ER -