@article{1057, abstract = {Far-field super-resolution fluorescence microscopy discerns fluorophores residing closer than the diffraction barrier by briefly transferring them in different (typically ON and OFF) states before detection. In coordinate-targeted super-resolution variants, such as stimulated emission depletion (STED) microscopy, this state difference is created by the intensity minima and maxima of an optical pattern, causing all fluorophores to assume the off state, for instance, except at the minima. Although strong spatial confinement of the on state enables high resolution, it also subjects the fluorophores to excess intensities and state cycles at the maxima. Here, we address these issues by driving the fluorophores into a second off state that is inert to the excess light. By using reversibly switchable fluorescent proteins as labels, our approach reduces bleaching and enhances resolution and contrast in live-cell STED microscopy. Using two or more transitions to off states is a useful strategy for augmenting the power of coordinate-targeted super-resolution microscopy.}, author = {Danzl, Johann G and Sidenstein, Sven and Gregor, Carola and Urban, Nicolai and Ilgen, Peter and Jakobs, Stefan and Hell, Stefan}, issn = {1749-4893}, journal = {Nature Photonics}, pages = {122 -- 128}, publisher = {Springer Nature}, title = {{Coordinate-targeted fluorescence nanoscopy with multiple off states}}, doi = {10.1038/nphoton.2015.266}, volume = {10}, year = {2016}, } @article{1059, abstract = {A range of bright and photostable rhodamines and carbopyronines with absorption maxima in the range of λ=500-630 nm were prepared, and enabled the specific labeling of cytoskeletal filaments using HaloTag technology followed by staining with 1 μm solutions of the dye-ligand conjugates. The synthesis, photophysical parameters, fluorogenic behavior, and structure-property relationships of the new dyes are discussed. Light microscopy with stimulated emission depletion (STED) provided one- and two-color images of living cells with an optical resolution of 40-60 nm.}, author = {Butkevich, Alexey and Mitronova, Gyuzel and Sidenstein, Sven and Klocke, Jessica and Kamin, Dirk and Meineke, Dirk and D'Este, Elisa and Kraemer, Philip and Danzl, Johann G and Belov, Vladimir and Hell, Stefan}, journal = {Angewandte Chemie - International Edition}, number = {10}, pages = {3290 -- 3294}, publisher = {Wiley-Blackwell}, title = {{Fluorescent rhodamines and fluorogenic carbopyronines for super-resolution STED microscopy in living cells}}, doi = {10.1002/anie.201511018}, volume = {55}, year = {2016}, } @article{1060, abstract = {Superresolution fluorescence microscopy of multiple fluorophores still requires development. Here we present simultaneous three-colour stimulated emission depletion (STED) nanoscopy relying on a single STED beam at 620 nm. Toggling the STED beam between two or more power levels ("multilevelSTEDv) optimizes resolution and contrast in all colour channels, which are intrinsically co-aligned and well separated. Three-colour recording is demonstrated by imaging the nanoscale cytoskeletal organization in cultured hippocampal neurons. The down to ∼35 nm resolution identified periodic actin/betaII spectrin lattices along dendrites and spines; however, at presynaptic and postsynaptic sites, these patterns were found to be absent. Both our multicolour scheme and the 620 nm STED line should be attractive for routine STED microscopy applications.}, author = {Sidenstein, Sven and D'Este, Elisa and Böhm, Marvin and Danzl, Johann G and Belov, Vladimir and Hell, Stefan}, journal = {Scientific Reports}, pages = {1 -- 8}, publisher = {Nature Publishing Group}, title = {{Multicolour multilevel STED nanoscopy of actin/spectrin organization at synapses}}, doi = {10.1038/srep26725}, volume = {6}, year = {2016}, } @inproceedings{1068, abstract = {Games on graphs provide the appropriate framework to study several central problems in computer science, such as verification and synthesis of reactive systems. One of the most basic objectives for games on graphs is the liveness (or Büchi) objective that given a target set of vertices requires that some vertex in the target set is visited infinitely often. We study generalized Büchi objectives (i.e., conjunction of liveness objectives), and implications between two generalized Büchi objectives (known as GR(1) objectives), that arise in numerous applications in computer-aided verification. We present improved algorithms and conditional super-linear lower bounds based on widely believed assumptions about the complexity of (A1) combinatorial Boolean matrix multiplication and (A2) CNF-SAT. We consider graph games with n vertices, m edges, and generalized Büchi objectives with k conjunctions. First, we present an algorithm with running time O(k*n^2), improving the previously known O(k*n*m) and O(k^2*n^2) worst-case bounds. Our algorithm is optimal for dense graphs under (A1). Second, we show that the basic algorithm for the problem is optimal for sparse graphs when the target sets have constant size under (A2). Finally, we consider GR(1) objectives, with k_1 conjunctions in the antecedent and k_2 conjunctions in the consequent, and present an O(k_1 k_2 n^{2.5})-time algorithm, improving the previously known O(k_1*k_2*n*m)-time algorithm for m > n^{1.5}. }, author = {Chatterjee, Krishnendu and Dvorák, Wolfgang and Henzinger, Monika H and Loitzenbauer, Veronika}, location = {Krakow, Poland}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Conditionally optimal algorithms for generalized Büchi Games}}, doi = {10.4230/LIPIcs.MFCS.2016.25}, volume = {58}, year = {2016}, } @inproceedings{1069, abstract = {The Continuous Skolem Problem asks whether a real-valued function satisfying a linear differen- tial equation has a zero in a given interval of real numbers. This is a fundamental reachability problem for continuous linear dynamical systems, such as linear hybrid automata and continuous- time Markov chains. Decidability of the problem is currently open – indeed decidability is open even for the sub-problem in which a zero is sought in a bounded interval. In this paper we show decidability of the bounded problem subject to Schanuel’s Conjecture, a unifying conjecture in transcendental number theory. We furthermore analyse the unbounded problem in terms of the frequencies of the differential equation, that is, the imaginary parts of the characteristic roots. We show that the unbounded problem can be reduced to the bounded problem if there is at most one rationally linearly independent frequency, or if there are two rationally linearly independent frequencies and all characteristic roots are simple. We complete the picture by showing that de- cidability of the unbounded problem in the case of two (or more) rationally linearly independent frequencies would entail a major new effectiveness result in Diophantine approximation, namely computability of the Diophantine-approximation types of all real algebraic numbers.}, author = {Chonev, Ventsislav K and Ouaknine, Joël and Worrell, James}, location = {Rome, Italy}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{On the skolem problem for continuous linear dynamical systems}}, doi = {10.4230/LIPIcs.ICALP.2016.100}, volume = {55}, year = {2016}, } @inproceedings{1070, abstract = {We present a logic that extends CTL (Computation Tree Logic) with operators that express synchronization properties. A property is synchronized in a system if it holds in all paths of a certain length. The new logic is obtained by using the same path quantifiers and temporal operators as in CTL, but allowing a different order of the quantifiers. This small syntactic variation induces a logic that can express non-regular properties for which known extensions of MSO with equality of path length are undecidable. We show that our variant of CTL is decidable and that the model-checking problem is in Delta_3^P = P^{NP^NP}, and is DP-hard. We analogously consider quantifier exchange in extensions of CTL, and we present operators defined using basic operators of CTL* that express the occurrence of infinitely many synchronization points. We show that the model-checking problem remains in Delta_3^P. The distinguishing power of CTL and of our new logic coincide if the Next operator is allowed in the logics, thus the classical bisimulation quotient can be used for state-space reduction before model checking. }, author = {Chatterjee, Krishnendu and Doyen, Laurent}, location = {Rome, Italy}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Computation tree logic for synchronization properties}}, doi = {10.4230/LIPIcs.ICALP.2016.98}, volume = {55}, year = {2016}, } @inproceedings{1071, abstract = {We consider data-structures for answering reachability and distance queries on constant-treewidth graphs with n nodes, on the standard RAM computational model with wordsize W=Theta(log n). Our first contribution is a data-structure that after O(n) preprocessing time, allows (1) pair reachability queries in O(1) time; and (2) single-source reachability queries in O(n/log n) time. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries. The data-structure uses at all times O(n) space. Our second contribution is a space-time tradeoff data-structure for distance queries. For any epsilon in [1/2,1], we provide a data-structure with polynomial preprocessing time that allows pair queries in O(n^{1-\epsilon} alpha(n)) time, where alpha is the inverse of the Ackermann function, and at all times uses O(n^epsilon) space. The input graph G is not considered in the space complexity. }, author = {Chatterjee, Krishnendu and Ibsen-Jensen, Rasmus and Pavlogiannis, Andreas}, location = {Aarhus, Denmark}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Optimal reachability and a space time tradeoff for distance queries in constant treewidth graphs}}, doi = {10.4230/LIPIcs.ESA.2016.28}, volume = {57}, year = {2016}, } @inproceedings{10746, abstract = {Vortex states in superconducting (SC) structures, their dynamics and ways to manipulate them are topics of great interest. We report a new method of magnetic force microscopy (MFM) that allows the study of vortex states in mesoscopic SC samples. For the case of a SC ring, which is biased to a half-integer flux quantum, the flux modulation through the ring caused by the motion of the magnetic tip drives the ring between two consecutive fluxoid states. The corresponding current switching in the ring produces strong position-dependent forces on the cantilever. In the regime where the frequency of the thermally activated jumps between fluxoid states is close to the frequency of the cantilever, large changes in the cantilever frequency and dissipation are observed. This effect may be understood as a stochastic resonance (SR) process. These changes in the cantilever’s mechanical properties are used to “image” the barrier energies between fluxoid states. Additionally, SR imaging of the barrier energies are used to study the effect of the locally applied magnetic field from the MFM tip on the barrier heights. We report the results of measurements for Al rings. Further, the same imaging technique can be applied to more sophisticated SC structures such as arrays of Josephson junctions.}, author = {Polshyn, Hryhoriy and Naibert, Tyler and Chua, Victor and Budakian, Raffi}, booktitle = {APS March Meeting 2016}, issn = {0003-0503}, location = {Baltimore, MD, United States}, number = {2}, publisher = {American Physical Society}, title = {{Study of vortex states and dynamics in mesoscopic superconducting samples with MFM}}, volume = {61}, year = {2016}, } @inproceedings{10747, abstract = {Vortex interactions are key to explaining the behavior of many two dimensional superconducting systems. We report on the development of a technique to locally probe vortex interactions in a 2D array of Josephson junctions. Scanning a magnetic tip attached to an ultra-soft cantilever over the array produces changes in the frequency of the cantilever along certain lines, forming geometric patterns in the scans. Different tip-surface separations and external magnetic fields produce a number of different patterns. These patterns correspond to tip locations in which two configurations of vortices in the lattice have degenerate energies. By imaging the locations of these degeneracies, information on the local vortex interactions may be obtained.}, author = {Naibert, Tyler and Polshyn, Hryhoriy and Wolin, Brian and Durkin, Malcolm and Garrido Menacho, Rita and Shem, Ian Mondragon and Chua, Victor and Hughes, Taylor and Mason, Nadya and Budakian, Raffi}, booktitle = {APS March Meeting 2016}, issn = {0003-0503}, location = {Baltimore, MD, United States}, number = {2}, publisher = {American Physical Society}, title = {{Stochastic resonance magnetic force microscopy imaging of Josephson arrays}}, volume = {61}, year = {2016}, } @article{1081, abstract = {The asymmetric localization of proteins in the plasma membrane domains of eukaryotic cells is a fundamental manifestation of cell polarity that is central to multicellular organization and developmental patterning. In plants, the mechanisms underlying the polar localization of cargo proteins are still largely unknown and appear to be fundamentally distinct from those operating in mammals. Here, we present a systematic, quantitative comparative analysis of the polar delivery and subcellular localization of proteins that characterize distinct polar plasma membrane domains in plant cells. The combination of microscopic analyses and computational modeling revealed a mechanistic framework common to diverse polar cargos and underlying the establishment and maintenance of apical, basal, and lateral polar domains in plant cells. This mechanism depends on the polar secretion, constitutive endocytic recycling, and restricted lateral diffusion of cargos within the plasma membrane. Moreover, our observations suggest that polar cargo distribution involves the individual protein potential to form clusters within the plasma membrane and interact with the extracellular matrix. Our observations provide insights into the shared cellular mechanisms of polar cargo delivery and polarity maintenance in plant cells.}, author = {Łangowski, Łukasz and Wabnik, Krzysztof T and Li, Hongjiang and Vanneste, Steffen and Naramoto, Satoshi and Tanaka, Hirokazu and Friml, Jirí}, journal = {Cell Discovery}, publisher = {Nature Publishing Group}, title = {{Cellular mechanisms for cargo delivery and polarity maintenance at different polar domains in plant cells}}, doi = {10.1038/celldisc.2016.18}, volume = {2}, year = {2016}, } @inproceedings{10810, abstract = {The main goal of the SCP-ECG standard is to address ECG data and related metadata structuring, semantics and syntax, with the objective of facilitating interoperability and thus supporting and promoting the exchange of the relevant information for unary and serial ECG diagnosis. Starting with version V3.0, the standard now also provides support for the storage of continuous, long-term ECG recordings and affords a repository for selected ECG sequences and the related metadata to accommodate stress tests, drug trials and protocol-based ECG recordings. The global and per-lead measurements sections have been extended and three new sections have been introduced for storing beat-by-beat and/or spike-by-spike measurements and annotations. The used terminology and the provided measurements and annotations have been harmonized with the ISO/IEEE 11073-10102 Annotated ECG standard. Emphasis has also been put on harmonizing the Universal Statement Codes with the CDISC and the categorized AHA statement codes and similarly the drug and implanted devices codes with the ATC and NASPE/BPEG codes. }, author = {Rubel, Paul and Pani, Danilo and Schlögl, Alois and Fayn, Jocelyne and Badilini, Fabio and Macfarlane, Peter and Varri, Alpo}, booktitle = {2016 Computing in Cardiology Conference}, issn = {2325-887X}, location = {Vancouver, Canada}, pages = {309--312}, publisher = {Computing in Cardiology}, title = {{SCP-ECG V3.0: An enhanced standard communication protocol for computer-assisted electrocardiography}}, doi = {10.22489/cinc.2016.090-500}, volume = {43}, year = {2016}, } @article{7599, abstract = {Normal leaf margin development is important for leaf morphogenesis and contributes to diverse leaf shapes in higher plants. We here show the crucial roles of an atypical type II phosphatidylinositol 4-kinase, PI4Kγ5, in Arabidopsis leaf margin development. PI4Kγ5 presents a dynamics expression pattern along with leaf development and a T-DNA mutant lacking PI4Kγ5, pi4kγ5–1, presents serrated leaves, which is resulted from the accelerated cell division and increased auxin concentration at serration tips. Studies revealed that PI4Kγ5 interacts with and phosphorylates a membrane-bound NAC transcription factor, ANAC078. Previous studies demonstrated that membrane-bound transcription factors regulate gene transcription by undergoing proteolytic process to translocate into nucleus, and ANAC078 undergoes proteolysis by cleaving off the transmembrane region and carboxyl terminal. Western blot analysis indeed showed that ANAC078 deleting of carboxyl terminal is significantly reduced in pi4kγ5–1, indicating that PI4Kγ5 is important for the cleavage of ANAC078. This is consistent with the subcellular localization observation showing that fluorescence by GFP-ANAC078 is detected at plasma membrane but not nucleus in pi4kγ5–1 mutant and that expression of ANAC078 deleting of carboxyl terminal, driven by PI4Kγ5 promoter, could rescue the leaf serration defects of pi4kγ5–1. Further analysis showed that ANAC078 suppresses the auxin synthesis by directly binding and regulating the expression of auxin synthesis-related genes. These results indicate that PI4Kγ5 interacts with ANAC078 to negatively regulate auxin synthesis and hence influences cell proliferation and leaf development, providing informative clues for the regulation of in situ auxin synthesis and cell division, as well as the cleavage and functional mechanism of membrane-bound transcription factors.}, author = {Tang, Yong and Zhao, Chun-Yan and Tan, Shutang and Xue, Hong-Wei}, issn = {1553-7404}, journal = {PLOS Genetics}, number = {8}, publisher = {Public Library of Science}, title = {{Arabidopsis type II phosphatidylinositol 4-kinase PI4Kγ5 regulates auxin biosynthesis and leaf margin development through interacting with membrane-bound transcription factor ANAC078}}, doi = {10.1371/journal.pgen.1006252}, volume = {12}, year = {2016}, } @article{7734, abstract = {Importance: Considerable partner resemblances have been found for a wide range of psychiatric disorders, meaning that partners of affected individuals have an increased risk of being affected compared with partners of unaffected individuals. If this resemblance is reflected in genetic similarity between partners, genetic risk is anticipated to accumulate in offspring, but these potential consequences have not been quantified and have been left implicit. Observations: The anticipated consequences of partner resemblance on prevalence and heritability of psychiatric traits in the offspring generation were modeled for disorders with varying heritabilities, population prevalence (lifetime risk), and magnitudes of partner resemblance. These models facilitate interpretation for a wide range of psychiatric disorders, such as autism, schizophrenia, and depression. The genetic consequences of partner resemblance are most pronounced when attributable to phenotypic assortment (driven by the psychiatric trait). Phenotypic assortment results in increased genetic variance in the offspring generation, which may result in increased heritability and population prevalence. These consequences add generation after generation to a limit, but assortative mating is unlikely to balance the impact of reduced fecundity of patients with psychiatric disorders in the long term. This modeling suggests that the heritabilities of psychiatric disorders are unlikely to increase by more than 5% from 1 generation of assortative mating (maximally 13% across multiple generations). The population prevalence will increase most for less common disorders with high heritability; for example, the prevalence of autism might increase by 1.5-fold after 1 generation of assortative mating (≥2.4-fold in the long term) depending on several assumptions. Conclusions and Relevance: The considerable partner resemblances found for psychiatric disorders deserve more detailed interpretation than has been provided thus far. Although the limitations of modeling are emphasized, the anticipated consequences are at most modest for the heritability but may be considerable for the population prevalence of rare disorders with a high heritability.}, author = {Peyrot, Wouter J. and Robinson, Matthew Richard and Penninx, Brenda W. J. H. and Wray, Naomi R.}, issn = {2168-622X}, journal = {JAMA Psychiatry}, number = {11}, pages = {1189--1195}, publisher = {American Medical Association}, title = {{Exploring boundaries for the genetic consequences of assortative mating for psychiatric traits}}, doi = {10.1001/jamapsychiatry.2016.2566}, volume = {73}, year = {2016}, } @article{7736, abstract = {We develop a novel approach to identify regions of the genome underlying population genetic differentiation in any genetic data where the underlying population structure is unknown, or where the interest is assessing divergence along a gradient. By combining the statistical framework for genome-wide association studies (GWASs) with eigenvector decomposition (EigenGWAS), which is commonly used in population genetics to characterize the structure of genetic data, loci under selection can be identified without a requirement for discrete populations. We show through theory and simulation that our approach can identify regions under selection along gradients of ancestry, and in real data we confirm this by demonstrating LCT to be under selection between HapMap CEU–TSI cohorts, and we then validate this selection signal across European countries in the POPRES samples. HERC2 was also found to be differentiated between both the CEU–TSI cohort and within the POPRES sample, reflecting the likely anthropological differences in skin and hair colour between northern and southern European populations. Controlling for population stratification is of great importance in any quantitative genetic study and our approach also provides a simple, fast and accurate way of predicting principal components in independent samples. With ever increasing sample sizes across many fields, this approach is likely to be greatly utilized to gain individual-level eigenvectors avoiding the computational challenges associated with conducting singular value decomposition in large data sets. We have developed freely available software, Genetic Analysis Repository (GEAR), to facilitate the application of the methods.}, author = {Chen, G-B and Lee, S H and Zhu, Z-X and Benyamin, B and Robinson, Matthew Richard}, issn = {0018-067X}, journal = {Heredity}, pages = {51--61}, publisher = {Springer Nature}, title = {{EigenGWAS: Finding loci under selection through genome-wide association studies of eigenvectors in structured populations}}, doi = {10.1038/hdy.2016.25}, volume = {117}, year = {2016}, } @article{7737, abstract = {Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with human complex traits. However, the genes or functional DNA elements through which these variants exert their effects on the traits are often unknown. We propose a method (called SMR) that integrates summary-level data from GWAS with data from expression quantitative trait locus (eQTL) studies to identify genes whose expression levels are associated with a complex trait because of pleiotropy. We apply the method to five human complex traits using GWAS data on up to 339,224 individuals and eQTL data on 5,311 individuals, and we prioritize 126 genes (for example, TRAF1 and ANKRD55 for rheumatoid arthritis and SNX19 and NMRAL1 for schizophrenia), of which 25 genes are new candidates; 77 genes are not the nearest annotated gene to the top associated GWAS SNP. These genes provide important leads to design future functional studies to understand the mechanism whereby DNA variation leads to complex trait variation.}, author = {Zhu, Zhihong and Zhang, Futao and Hu, Han and Bakshi, Andrew and Robinson, Matthew Richard and Powell, Joseph E and Montgomery, Grant W and Goddard, Michael E and Wray, Naomi R and Visscher, Peter M and Yang, Jian}, issn = {1061-4036}, journal = {Nature Genetics}, number = {5}, pages = {481--487}, publisher = {Springer Nature}, title = {{Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets}}, doi = {10.1038/ng.3538}, volume = {48}, year = {2016}, } @article{7760, abstract = {We propose a Widom-like scaling ansatz for the critical jamming transition. Our ansatz for the elastic energy shows that the scaling of the energy, compressive strain, shear strain, system size, pressure, shear stress, bulk modulus, and shear modulus are all related to each other via scaling relations, with only three independent scaling exponents. We extract the values of these exponents from already known numerical or theoretical results, and we numerically verify the resulting predictions of the scaling theory for the energy and residual shear stress. We also derive a scaling relation between pressure and residual shear stress that yields insight into why the shear and bulk moduli scale differently. Our theory shows that the jamming transition exhibits an emergent scale invariance, setting the stage for the potential development of a renormalization group theory for jamming.}, author = {Goodrich, Carl Peter and Liu, Andrea J. and Sethna, James P.}, issn = {0027-8424}, journal = {Proceedings of the National Academy of Sciences}, number = {35}, pages = {9745--9750}, publisher = {Proceedings of the National Academy of Sciences}, title = {{Scaling ansatz for the jamming transition}}, doi = {10.1073/pnas.1601858113}, volume = {113}, year = {2016}, } @article{7761, abstract = {We study the effect of dilute pinning on the jamming transition. Pinning reduces the average contact number needed to jam unpinned particles and shifts the jamming threshold to lower densities, leading to a pinning susceptibility, χp. Our main results are that this susceptibility obeys scaling form and diverges in the thermodynamic limit as χp∝|ϕ−ϕ∞c|−γp where ϕ∞c is the jamming threshold in the absence of pins. Finite-size scaling arguments yield these values with associated statistical (systematic) errors γp=1.018±0.026(0.291) in d=2 and γp=1.534±0.120(0.822) in d=3. Logarithmic corrections raise the exponent in d=2 to close to the d=3 value, although the systematic errors are very large.}, author = {Graves, Amy L. and Nashed, Samer and Padgett, Elliot and Goodrich, Carl Peter and Liu, Andrea J. and Sethna, James P.}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {23}, publisher = {American Physical Society}, title = {{Pinning susceptibility: The effect of dilute, quenched disorder on jamming}}, doi = {10.1103/physrevlett.116.235501}, volume = {116}, year = {2016}, } @article{7762, abstract = {Characterizing structural inhomogeneity is an essential step in understanding the mechanical response of amorphous materials. We introduce a threshold-free measure based on the field of vectors pointing from the center of each particle to the centroid of the Voronoi cell in which the particle resides. These vectors tend to point in toward regions of high free volume and away from regions of low free volume, reminiscent of sinks and sources in a vector field. We compute the local divergence of these vectors, where positive values correspond to overpacked regions and negative values identify underpacked regions within the material. Distributions of this divergence are nearly Gaussian with zero mean, allowing for structural characterization using only the moments of the distribution. We explore how the standard deviation and skewness vary with the packing fraction for simulations of bidisperse systems and find a kink in these moments that coincides with the jamming transition.}, author = {Rieser, Jennifer M. and Goodrich, Carl Peter and Liu, Andrea J. and Durian, Douglas J.}, issn = {0031-9007}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society}, title = {{Divergence of Voronoi cell anisotropy vector: A threshold-free characterization of local structure in amorphous materials}}, doi = {10.1103/physrevlett.116.088001}, volume = {116}, year = {2016}, } @article{7763, abstract = {An orthogonal wavelet basis is characterized by its approximation order, which relates to the ability of the basis to represent general smooth functions on a given scale. It is known, though perhaps not widely known, that there are ways of exceeding the approximation order, i.e., achieving higher-order error in the discretized wavelet transform and its inverse. The focus here is on the development of a practical formulation to accomplish this first for 1D smooth functions, then for 1D functions with discontinuities and then for multidimensional (here 2D) functions with discontinuities. It is shown how to transcend both the wavelet approximation order and the 2D Gibbs phenomenon in representing electromagnetic fields at discontinuous dielectric interfaces that do not simply follow the wavelet-basis grid.}, author = {Lombardini, Richard and Acevedo, Ramiro and Kuczala, Alexander and Keys, Kerry P. and Goodrich, Carl Peter and Johnson, Bruce R.}, issn = {0021-9991}, journal = {Journal of Computational Physics}, pages = {244--262}, publisher = {Elsevier}, title = {{Higher-order wavelet reconstruction/differentiation filters and Gibbs phenomena}}, doi = {10.1016/j.jcp.2015.10.035}, volume = {305}, year = {2016}, } @article{7764, abstract = {States of self stress, organizations of internal forces in many-body systems that are in equilibrium with an absence of external forces, can be thought of as the constitutive building blocks of the elastic response of a material. In overconstrained disordered packings they have a natural mathematical correspondence with the zero-energy vibrational modes in underconstrained systems. While substantial attention in the literature has been paid to diverging length scales associated with zero- and finite-energy vibrational modes in jammed systems, less is known about the spatial structure of the states of self stress. In this work we define a natural way in which a unique state of self stress can be associated with each bond in a disordered spring network derived from a jammed packing, and then investigate the spatial structure of these bond-localized states of self stress. This allows for an understanding of how the elastic properties of a system would change upon changing the strength or even existence of any bond in the system.}, author = {Sussman, Daniel M. and Goodrich, Carl Peter and Liu, Andrea J.}, issn = {1744-683X}, journal = {Soft Matter}, number = {17}, pages = {3982--3990}, publisher = {Royal Society of Chemistry}, title = {{Spatial structure of states of self stress in jammed systems}}, doi = {10.1039/c6sm00094k}, volume = {12}, year = {2016}, }