@article{8408, abstract = {Aromatic residues are located at structurally important sites of many proteins. Probing their interactions and dynamics can provide important functional insight but is challenging in large proteins. Here, we introduce approaches to characterize dynamics of phenylalanine residues using 1H-detected fast magic-angle spinning (MAS) NMR combined with a tailored isotope-labeling scheme. Our approach yields isolated two-spin systems that are ideally suited for artefact-free dynamics measurements, and allows probing motions effectively without molecular-weight limitations. The application to the TET2 enzyme assembly of ~0.5 MDa size, the currently largest protein assigned by MAS NMR, provides insights into motions occurring on a wide range of time scales (ps-ms). We quantitatively probe ring flip motions, and show the temperature dependence by MAS NMR measurements down to 100 K. Interestingly, favorable line widths are observed down to 100 K, with potential implications for DNP NMR. Furthermore, we report the first 13C R1ρ MAS NMR relaxation-dispersion measurements and detect structural excursions occurring on a microsecond time scale in the entry pore to the catalytic chamber and at a trimer interface that was proposed as exit pore. We show that the labeling scheme with deuteration at ca. 50 kHz MAS provides superior resolution compared to 100 kHz MAS experiments with protonated, uniformly 13C-labeled samples.}, author = {Gauto, Diego F. and Macek, Pavel and Barducci, Alessandro and Fraga, Hugo and Hessel, Audrey and Terauchi, Tsutomu and Gajan, David and Miyanoiri, Yohei and Boisbouvier, Jerome and Lichtenecker, Roman and Kainosho, Masatsune and Schanda, Paul}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {28}, pages = {11183--11195}, publisher = {American Chemical Society}, title = {{Aromatic ring dynamics, thermal activation, and transient conformations of a 468 kDa enzyme by specific 1H–13C labeling and fast magic-angle spinning NMR}}, doi = {10.1021/jacs.9b04219}, volume = {141}, year = {2019}, } @article{8409, abstract = {The bacterial cell wall is composed of the peptidoglycan (PG), a large polymer that maintains the integrity of the bacterial cell. Due to its multi-gigadalton size, heterogeneity, and dynamics, atomic-resolution studies are inherently complex. Solid-state NMR is an important technique to gain insight into its structure, dynamics and interactions. Here, we explore the possibilities to study the PG with ultra-fast (100 kHz) magic-angle spinning NMR. We demonstrate that highly resolved spectra can be obtained, and show strategies to obtain site-specific resonance assignments and distance information. We also explore the use of proton-proton correlation experiments, thus opening the way for NMR studies of intact cell walls without the need for isotope labeling.}, author = {Bougault, Catherine and Ayala, Isabel and Vollmer, Waldemar and Simorre, Jean-Pierre and Schanda, Paul}, issn = {1047-8477}, journal = {Journal of Structural Biology}, keywords = {Structural Biology}, number = {1}, pages = {66--72}, publisher = {Elsevier}, title = {{Studying intact bacterial peptidoglycan by proton-detected NMR spectroscopy at 100 kHz MAS frequency}}, doi = {10.1016/j.jsb.2018.07.009}, volume = {206}, year = {2019}, } @article{8410, author = {Schanda, Paul and Chekmenev, Eduard Y.}, issn = {1439-4235}, journal = {ChemPhysChem}, number = {2}, pages = {177--177}, publisher = {Wiley}, title = {{NMR for Biological Systems}}, doi = {10.1002/cphc.201801100}, volume = {20}, year = {2019}, } @article{8411, abstract = {Studying protein dynamics on microsecond‐to‐millisecond (μs‐ms) time scales can provide important insight into protein function. In magic‐angle‐spinning (MAS) NMR, μs dynamics can be visualized by R1p rotating‐frame relaxation dispersion experiments in different regimes of radio‐frequency field strengths: at low RF field strength, isotropic‐chemical‐shift fluctuation leads to “Bloch‐McConnell‐type” relaxation dispersion, while when the RF field approaches rotary resonance conditions bond angle fluctuations manifest as increased R1p rate constants (“Near‐Rotary‐Resonance Relaxation Dispersion”, NERRD). Here we explore the joint analysis of both regimes to gain comprehensive insight into motion in terms of geometric amplitudes, chemical‐shift changes, populations and exchange kinetics. We use a numerical simulation procedure to illustrate these effects and the potential of extracting exchange parameters, and apply the methodology to the study of a previously described conformational exchange process in microcrystalline ubiquitin.}, author = {Marion, Dominique and Gauto, Diego F. and Ayala, Isabel and Giandoreggio-Barranco, Karine and Schanda, Paul}, issn = {1439-4235}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {2}, pages = {276--284}, publisher = {Wiley}, title = {{Microsecond protein dynamics from combined Bloch-McConnell and Near-Rotary-Resonance R1p relaxation-dispersion MAS NMR}}, doi = {10.1002/cphc.201800935}, volume = {20}, year = {2019}, } @article{8412, abstract = {Microsecond to millisecond timescale backbone dynamics of the amyloid core residues in Y145Stop human prion protein (PrP) fibrils were investigated by using 15N rotating frame (R1ρ) relaxation dispersion solid‐state nuclear magnetic resonance spectroscopy over a wide range of spin‐lock fields. Numerical simulations enabled the experimental relaxation dispersion profiles for most of the fibril core residues to be modelled by using a two‐state exchange process with a common exchange rate of 1000 s−1, corresponding to protein backbone motion on the timescale of 1 ms, and an excited‐state population of 2 %. We also found that the relaxation dispersion profiles for several amino acids positioned near the edges of the most structured regions of the amyloid core were better modelled by assuming somewhat higher excited‐state populations (∼5–15 %) and faster exchange rate constants, corresponding to protein backbone motions on the timescale of ∼100–300 μs. The slow backbone dynamics of the core residues were evaluated in the context of the structural model of human Y145Stop PrP amyloid.}, author = {Shannon, Matthew D. and Theint, Theint and Mukhopadhyay, Dwaipayan and Surewicz, Krystyna and Surewicz, Witold K. and Marion, Dominique and Schanda, Paul and Jaroniec, Christopher P.}, issn = {1439-4235}, journal = {ChemPhysChem}, keywords = {Physical and Theoretical Chemistry, Atomic and Molecular Physics, and Optics}, number = {2}, pages = {311--317}, publisher = {Wiley}, title = {{Conformational dynamics in the core of human Y145Stop prion protein amyloid probed by relaxation dispersion NMR}}, doi = {10.1002/cphc.201800779}, volume = {20}, year = {2019}, } @article{8413, abstract = {NMR relaxation dispersion methods provide a holistic way to observe microsecond time-scale protein backbone motion both in solution and in the solid state. Different nuclei (1H and 15N) and different relaxation dispersion techniques (Bloch–McConnell and near-rotary-resonance) give complementary information about the amplitudes and time scales of the conformational dynamics and provide comprehensive insights into the mechanistic details of the structural rearrangements. In this paper, we exemplify the benefits of the combination of various solution- and solid-state relaxation dispersion methods on a microcrystalline protein (α-spectrin SH3 domain), for which we are able to identify and model the functionally relevant conformational rearrangements around the ligand recognition loop occurring on multiple microsecond time scales. The observed loop motions suggest that the SH3 domain exists in a binding-competent conformation in dynamic equilibrium with a sterically impaired ground-state conformation both in solution and in crystalline form. This inherent plasticity between the interconverting macrostates is compatible with a conformational-preselection model and provides new insights into the recognition mechanisms of SH3 domains.}, author = {Rovó, Petra and Smith, Colin A. and Gauto, Diego and de Groot, Bert L. and Schanda, Paul and Linser, Rasmus}, issn = {0002-7863}, journal = {Journal of the American Chemical Society}, keywords = {Colloid and Surface Chemistry, Biochemistry, General Chemistry, Catalysis}, number = {2}, pages = {858--869}, publisher = {American Chemical Society}, title = {{Mechanistic insights into microsecond time-scale motion of solid proteins using complementary 15N and 1H relaxation dispersion techniques}}, doi = {10.1021/jacs.8b09258}, volume = {141}, year = {2019}, } @article{8415, abstract = {We consider billiards obtained by removing three strictly convex obstacles satisfying the non-eclipse condition on the plane. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift on three symbols that provides a natural labeling of all periodic orbits. We study the following inverse problem: does the Marked Length Spectrum (i.e., the set of lengths of periodic orbits together with their labeling), determine the geometry of the billiard table? We show that from the Marked Length Spectrum it is possible to recover the curvature at periodic points of period two, as well as the Lyapunov exponent of each periodic orbit.}, author = {Bálint, Péter and De Simoi, Jacopo and Kaloshin, Vadim and Leguil, Martin}, issn = {0010-3616}, journal = {Communications in Mathematical Physics}, keywords = {Mathematical Physics, Statistical and Nonlinear Physics}, number = {3}, pages = {1531--1575}, publisher = {Springer Nature}, title = {{Marked length spectrum, homoclinic orbits and the geometry of open dispersing billiards}}, doi = {10.1007/s00220-019-03448-x}, volume = {374}, year = {2019}, } @article{8416, abstract = {In this paper, we show that any smooth one-parameter deformations of a strictly convex integrable billiard table Ω0 preserving the integrability near the boundary have to be tangent to a finite dimensional space passing through Ω0.}, author = {Huang, Guan and Kaloshin, Vadim}, issn = {1609-4514}, journal = {Moscow Mathematical Journal}, number = {2}, pages = {307--327}, publisher = {American Mathematical Society}, title = {{On the finite dimensionality of integrable deformations of strictly convex integrable billiard tables}}, doi = {10.17323/1609-4514-2019-19-2-307-327}, volume = {19}, year = {2019}, } @article{8418, abstract = {For the Restricted Circular Planar 3 Body Problem, we show that there exists an open set U in phase space of fixed measure, where the set of initial points which lead to collision is O(μ120) dense as μ→0.}, author = {Guardia, Marcel and Kaloshin, Vadim and Zhang, Jianlu}, issn = {0003-9527}, journal = {Archive for Rational Mechanics and Analysis}, keywords = {Mechanical Engineering, Mathematics (miscellaneous), Analysis}, number = {2}, pages = {799--836}, publisher = {Springer Nature}, title = {{Asymptotic density of collision orbits in the Restricted Circular Planar 3 Body Problem}}, doi = {10.1007/s00205-019-01368-7}, volume = {233}, year = {2019}, } @inproceedings{8570, abstract = {This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with linear continuous dynamics. The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2019. In its third edition, seven tools have been applied to solve six different benchmark problems in the category for linear continuous dynamics (in alphabetical order): CORA, CORA/SX, HyDRA, Hylaa, JuliaReach, SpaceEx, and XSpeed. This report is a snapshot of the current landscape of tools and the types of benchmarks they are particularly suited for. Due to the diversity of problems, we are not ranking tools, yet the presented results provide one of the most complete assessments of tools for the safety verification of continuous and hybrid systems with linear continuous dynamics up to this date.}, author = {Althoff, Matthias and Bak, Stanley and Forets, Marcelo and Frehse, Goran and Kochdumper, Niklas and Ray, Rajarshi and Schilling, Christian and Schupp, Stefan}, booktitle = {EPiC Series in Computing}, issn = {23987340}, location = {Montreal, Canada}, pages = {14--40}, publisher = {EasyChair}, title = {{ARCH-COMP19 Category Report: Continuous and hybrid systems with linear continuous dynamics}}, doi = {10.29007/bj1w}, volume = {61}, year = {2019}, } @article{8693, abstract = {We review V. I. Arnold’s 1963 celebrated paper [1] Proof of A. N. Kolmogorov’s Theorem on the Conservation of Conditionally Periodic Motions with a Small Variation in the Hamiltonian, and prove that, optimising Arnold’s scheme, one can get “sharp” asymptotic quantitative conditions (as ε → 0, ε being the strength of the perturbation). All constants involved are explicitly computed.}, author = {Chierchia, Luigi and Koudjinan, Edmond}, journal = {Regular and Chaotic Dynamics}, pages = {583–606}, publisher = {Springer}, title = {{V. I. Arnold’s “pointwise” KAM theorem}}, doi = {10.1134/S1560354719060017}, volume = {24}, year = {2019}, } @article{170, abstract = {Upper and lower bounds, of the expected order of magnitude, are obtained for the number of rational points of bounded height on any quartic del Pezzo surface over ℚ that contains a conic defined over ℚ .}, author = {Browning, Timothy D and Sofos, Efthymios}, journal = {Mathematische Annalen}, number = {3-4}, pages = {977--1016}, publisher = {Springer Nature}, title = {{Counting rational points on quartic del Pezzo surfaces with a rational conic}}, doi = {10.1007/s00208-018-1716-6}, volume = {373}, year = {2019}, } @article{175, abstract = {An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.}, author = {Browning, Timothy D and Loughran, Daniel}, issn = {10886850}, journal = {Transactions of the American Mathematical Society}, number = {8}, pages = {5757--5785}, publisher = {American Mathematical Society}, title = {{Sieving rational points on varieties}}, doi = {10.1090/tran/7514}, volume = {371}, year = {2019}, } @article{196, abstract = {The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain. }, author = {Lang, Moritz and Shkolnikov, Mikhail}, issn = {1091-6490}, journal = {Proceedings of the National Academy of Sciences}, number = {8}, pages = {2821--2830}, publisher = {National Academy of Sciences}, title = {{Harmonic dynamics of the Abelian sandpile}}, doi = {10.1073/pnas.1812015116}, volume = {116}, year = {2019}, } @article{6611, abstract = {Cell polarity is crucial for the coordinated development of all multicellular organisms. In plants, this is exemplified by the PIN-FORMED (PIN) efflux carriers of the phytohormone auxin: The polar subcellular localization of the PINs is instructive to the directional intercellular auxin transport, and thus to a plethora of auxin-regulated growth and developmental processes. Despite its importance, the regulation of PIN polar subcellular localization remains poorly understood. Here, we have employed advanced live-cell imaging techniques to study the roles of microtubules and actin microfilaments in the establishment of apical polar localization of PIN2 in the epidermis of the Arabidopsis root meristem. We report that apical PIN2 polarity requires neither intact actin microfilaments nor microtubules, suggesting that the primary spatial cue for polar PIN distribution is likely independent of cytoskeleton-guided endomembrane trafficking.}, author = {Glanc, Matous and Fendrych, Matyas and Friml, Jiří}, journal = {Biomolecules}, number = {6}, publisher = {MDPI}, title = {{PIN2 polarity establishment in arabidopsis in the absence of an intact cytoskeleton}}, doi = {10.3390/biom9060222}, volume = {9}, year = {2019}, } @article{6617, abstract = {The effective large-scale properties of materials with random heterogeneities on a small scale are typically determined by the method of representative volumes: a sample of the random material is chosen—the representative volume—and its effective properties are computed by the cell formula. Intuitively, for a fixed sample size it should be possible to increase the accuracy of the method by choosing a material sample which captures the statistical properties of the material particularly well; for example, for a composite material consisting of two constituents, one would select a representative volume in which the volume fraction of the constituents matches closely with their volume fraction in the overall material. Inspired by similar attempts in materials science, Le Bris, Legoll and Minvielle have designed a selection approach for representative volumes which performs remarkably well in numerical examples of linear materials with moderate contrast. In the present work, we provide a rigorous analysis of this selection approach for representative volumes in the context of stochastic homogenization of linear elliptic equations. In particular, we prove that the method essentially never performs worse than a random selection of the material sample and may perform much better if the selection criterion for the material samples is chosen suitably.}, author = {Fischer, Julian L}, issn = {1432-0673}, journal = {Archive for Rational Mechanics and Analysis}, number = {2}, pages = {635–726}, publisher = {Springer}, title = {{The choice of representative volumes in the approximation of effective properties of random materials}}, doi = {10.1007/s00205-019-01400-w}, volume = {234}, year = {2019}, } @article{6620, abstract = {This paper establishes an asymptotic formula with a power-saving error term for the number of rational points of bounded height on the singular cubic surface of ℙ3ℚ given by the following equation 𝑥0(𝑥21+𝑥22)−𝑥33=0 in agreement with the Manin-Peyre conjectures. }, author = {De La Bretèche, Régis and Destagnol, Kevin N and Liu, Jianya and Wu, Jie and Zhao, Yongqiang}, issn = {16747283}, journal = {Science China Mathematics}, number = {12}, pages = {2435–2446}, publisher = {Springer}, title = {{On a certain non-split cubic surface}}, doi = {10.1007/s11425-018-9543-8}, volume = {62}, year = {2019}, } @article{6621, abstract = {We read with great interest the recent work in PNAS by Bergero et al. (1) describing differences in male and female recombination patterns on the guppy (Poecilia reticulata) sex chromosome. We fully agree that recombination in males is largely confined to the ends of the sex chromosome. Bergero et al. interpret these results to suggest that our previous findings of population-level variation in the degree of sex chromosome differentiation in this species (2) are incorrect. However, we suggest that their results are entirely consistent with our previous report, and that their interpretation presents a false controversy.}, author = {Wright, Alison E. and Darolti, Iulia and Bloch, Natasha I. and Oostra, Vicencio and Sandkam, Benjamin A. and Buechel, Séverine D. and Kolm, Niclas and Breden, Felix and Vicoso, Beatriz and Mank, Judith E.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {26}, pages = {12607--12608}, publisher = {Proceedings of the National Academy of Sciences}, title = {{On the power to detect rare recombination events}}, doi = {10.1073/pnas.1905555116}, volume = {116}, year = {2019}, } @article{6627, abstract = {Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation.}, author = {Adamowski, Maciek and Li, Lanxin and Friml, Jiří}, issn = {1422-0067}, journal = {International Journal of Molecular Sciences}, number = {13}, publisher = {MDPI}, title = {{Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling}}, doi = {10.3390/ijms20133337}, volume = {20}, year = {2019}, } @inproceedings{6628, abstract = {Fejes Tóth [5] and Schneider [9] studied approximations of smooth convex hypersurfaces in Euclidean space by piecewise flat triangular meshes with a given number of vertices on the hypersurface that are optimal with respect to Hausdorff distance. They proved that this Hausdorff distance decreases inversely proportional with m 2/(d−1), where m is the number of vertices and d is the dimension of Euclidean space. Moreover the pro-portionality constant can be expressed in terms of the Gaussian curvature, an intrinsic quantity. In this short note, we prove the extrinsic nature of this constant for manifolds of sufficiently high codimension. We do so by constructing an family of isometric embeddings of the flat torus in Euclidean space.}, author = {Vegter, Gert and Wintraecken, Mathijs}, booktitle = {The 31st Canadian Conference in Computational Geometry}, location = {Edmonton, Canada}, pages = {275--279}, title = {{The extrinsic nature of the Hausdorff distance of optimal triangulations of manifolds}}, year = {2019}, }