Entropy, minimal surfaces and negatively curved manifolds - Sanders, Andy (Ergodic theory and dynamical systems, 2018)
Taubes [Minimal surfaces in germs of hyperbolic 3-manifolds. Proceedings of the Casson Fest, Geom. Topol. Monogr. 7 (2004), 69–100 (electronic)] introduced the space of minimal hyperbolic germs with elements consisting of the first and second fundamental form of an equivariant immersed minimal disk in hyperbolic 3-space. Herein, we initiate a further study of this space by studying the behavior of a dynamically defined function which records the entropy of the geodesic flow on the associated Riemannian surface. We provide a useful estimate on this function which, in particular, yields a new proof of Bowen’s theorem on the rigidity of the Hausdorff dimension of the limit set of quasi-Fuchsian groups. These follow from new lower bounds on the Hausdorff dimension of the limit set which allow us to give a quantitative version of Bowen’s rigidity theorem. To demonstrate the strength of the techniques, these results are generalized to convex-cocompact surface groups acting on n-dimensional \mathrmCAT(-1) Riemannian manifolds.

Bi-Lagrangian structures and Teichmüller theory - Loustau, Brice; Sanders, Andy (arXiv,math.DG,1708.09145, 2017)
This paper has two purposes: the first is to study several structures on manifolds in the general setting of real and complex differential geometry; the second is to apply this study to Teichmüller theory. We primarily focus on bi-Lagrangian structures, which are the data of a symplectic structure and a pair of transverse Lagrangian foliations, and are equivalent to para-Kähler structures. First we carefully study real and complex bi-Lagrangian structures and discuss other closely related structures and their interrelationships. Next we prove the existence of a canonical complex bi-Lagrangian structure in the complexification of any real-analytic Kähler manifold and showcase its properties. We later use this bi-Lagrangian structure to construct a natural almost hyper-Hermitian structure. We then specialize our study to moduli spaces of geometric structures on closed surfaces, which tend to have a rich symplectic structure. We show that some of the recognized geometric features of these moduli spaces are formal consequences of the general theory, while revealing other new geometric features. We also gain clarity on several well-known results of Teichmüller theory by deriving them from pure differential geometric machinery.

Surface groups acting on CAT (-1) spaces - DASKALOPOULOS, GEORGIOS; MESE, CHIKAKO; Sanders, Andy; VDOVINA, ALINA (Ergodic Theory Dynam. Systems, 2019)
Harmonic map theory is used to show that a convex cocompact surface group action on a \mathrmCAT(-1) metric space fixes a convex copy of the hyperbolic plane (i.e. the action is Fuchsian) if and only if the Hausdorff dimension of the limit set of the action is equal to 1. This provides another proof of a result of Bonk and Kleiner. More generally, we show that the limit set of every convex cocompact surface group action on a \mathrmCAT(-1) space has Hausdorff dimension ≥1, where the inequality is strict unless the action is Fuchsian.

The pre-symplectic geometry of opers and the holonomy map - Sanders, Andy (arXiV Preprint, 2018)
Given a connected complex semi-simple Lie group G and a Riemann surface X, a G-oper on X is a higher rank generalization of a complex projective structure on X. These objects play an important role in integrable systems and geometric representation theory, a status that was cemented by the seminal work of Beilinson-Drinfeld \citeBD91. For G a connected complex simple Lie group of adjoint type, we study the global deformation theory of G-opers on a connected, closed, oriented smooth surface Σof genus at least two. We exhibit the deformation space of G-opers on Σas a holomorphic fiber bundle over Teichmüller space, and elucidate the relationship with the deformation space of complex projective structures. Then, we show that there is a family of identifications of the deformation space of G-opers with a holomorphic vector bundle \mathcalB_G(Σ) over Teichmüller space whose typical fiber over a Riemann surface X is a sum of spaces of pluri-canonical sections. Finally, we show that the holonomy map from the deformation space of G-opers to the deformation space of flat G-bundles on Σis a holomorphic immersion. As a consequence of this result, we show that the deformation space of G-opers carries a (pre-symplectic) closed holomorphic differential 2-form of constant rank, and we prove that a sub-family of the identifications of \mathcalB_G(Σ) with the deformation space of G-opers is a holomorphic pre-symplectic map for a natural holomorphic pre-symplectic form on \mathcalB_G(Σ). These results generalize the fundamental features of the deformation space of complex projective structures on Σto the setting of G-opers.

Polyhedral Horofunction Compactification as Polyhedral Ball - Ji, Lizhen; Schilling, Anna (arXiv,math.GT,1607.00564, 2016)
In this paper we answer positively a question raised by Kapovich and Leeb in a recent paper titled "Finsler bordifications of symmetric and certain locally symmetric spaces". Specifically, we show that for a finite-dimensional vector space with polyhedral norm, its horofunction compactification is homeomorphic to the dual unit ball of the norm by an explicit map. To prove this we establish a criterion for converging sequences in the horofunction compactification, and generalize the basic notion of the moment map in the theory of toric varieties.

Noncommutative coordinates for symplectic representations - Alessandrini, Daniele; Guichard, Olivier; Rogozinnikov, Evgenii; Wienhard, Anna (arXiv,math.DG,1911.08014, 2019)
We introduce coordinates on the space of Lagrangian decorated and framed representations of the fundamental group of a surface with punctures into the symplectic group Sp(2n,R). These coordinates provide a non-commutative generalization of the parametrizations of the spaces of representations into \mathrmSL(2,R) given by Thurston, Penner, and Fock-Goncharov. With these coordinates, the space of framed symplectic representations provides a geometric realization of the non-commutative cluster algebras introduced by Berenstein-Retakh. The locus of positive coordinates maps to the space of decorated maximal representations. We use this to determine the homotopy type of the space of decorated maximal representations, and its homeomorphism type when n=2.

Anosov representations with Lipschitz limit set - Pozzetti, Beatrice; Sambarino, Andrés; Wienhard, Anna (arXiv,math.DG,1910.06627, 2019)
We study Anosov representation for which the image of the boundary map is the graph of a Lipschitz function, and show that the orbit growth rate with respect to an explicit linear function, the unstable Jacobian, is integral. Several applications to the orbit growth rate in the symmetric space are provided.

Conformality for a robust class of non-conformal attractors - Pozzetti, Beatrice; Sambarino, Andrés; Wienhard, Anna (arXiv,math.DG,1902.01303, 2019)
In this paper we investigate the Hausdorff dimension of limit sets of Anosov representations. In this context we revisit and extend the framework of hyperconvex representations and establish a convergence property for them, analogue to a differentiability property. As an application of this convergence, we prove that the Hausdorff dimension of the limit set of a hyperconvex representation is equal to a suitably chosen critical exponent. In the appendix, in collaboration with M. Bridgeman, we extend a classical result on the Hessian of the Hausdorff dimension on purely imaginary directions.

An invitation to higher Teichmüller theory - Wienhard, Anna (Proc. Int. Cong. of Math. 2018, Rio de Janeiro, 2018)
The goal of this article is to invite the reader to get to know and to get involved into higher Teichmüller theory by describing some of its many facets.

Flows on the PGL(V)-Hitchin component - Sun, Zhe; Wienhard, Anna; Zhang, Tengren (arXiv,math.DG,1709.03580, 2017)
In this article we define new flows on the Hitchin components for \mathrmPGL(V). Special examples of these flows are associated to simple closed curves on the surface and give generalized twist flows. Other examples, so called eruption flows, are associated to pair of pants in S and capture new phenomena which are not present in the case when n = 2. Using these flows, we construct a global coordinate system on the Hitchin component. In a companion paper to this article two of the authors develop new tools to compute the Goldman symplectic form on the Hitchin component, and prove that this global coordinate system is a Darboux coordinate system.

Compactification of certain Clifford-Klein forms of reductive homogeneous spaces - Guéritaud, François; Guichard, Olivier; Kassel, Fanny; Wienhard, Anna (arXiv,math.GT,1506.03742, 2015)
We describe smooth compactifications of certain families of reductive homogeneous spaces such as group manifolds for classical Lie groups, or pseudo-Riemannian analogues of real hyperbolic spaces and their complex and quaternionic counterparts. We deduce compactifications of Clifford-Klein forms of these homogeneous spaces, namely quotients by discrete groups Gamma acting properly discontinuously, in the case that Gamma is word hyperbolic and acts via an Anosov representation. In particular, these Clifford-Klein forms are topologically tame.

Representations and geometric structures - Wienhard, Anna (arXiv,math.GT,1602.03480, 2016)
This note summarizes in an informal way some geometric properties of Anosov representations into the symplectic group, which were presented in a talk at the conference What is Next. The mathematical legacy of Bill Thurston, held in June 2014 in Cornell.

Currents, Systoles, and Compactifications of Character Varieties - Burger, M.; Iozzi, A.; Parreau, A.; Pozzetti, Beatrice (arXiv,math.GT,1902.07680, 2019)
We study the Thurston–Parreau boundary both of the Hitchin and of the maximal character varieties and determine therein an open set of discontinuity for the action of the mapping class group. This result is obtained as consequence of a canonical decomposition of a geodesic current on a surface of finite type arising from a topological decomposition of the surface along special geodesics. We show that each component either is associated to a measured lamination or has positive systole. For a current with positive systole, we show that the intersection function on the set of closed curves is bi-Lipschitz equivalent to the length function with respect to a hyperbolic metric. The results of this paper on currents generalise the ones in arXiv:1710.07060v1 to the case of surfaces of finite area with geodesic boundary. Concerning the Thurston–Parreau boundary we improve on the results in arXiv:1710.07060v1 by showing that for higher rank groups, said open set of discontinuity is not empty. We give also explicit examples in the case of the \SL(3,\mathbb R)-Hitchin component.

A structure theorem for geodesic currents and length spectrum compactifications - Burger, Marc; Iozzi, Alessandra; Parreau, Anne; Pozzetti, Beatrice (arXiv,math.GT,1710.07060, 2017)
We find a canonical decomposition of a geodesic current on a surface of finite type arising from a topological decomposition of the surface along special geodesics. We show that each component either is associated to a measured lamination or has positive systole. For a current with positive systole, we show that the intersection function on the set of closed curves is bilipschitz equivalent to the length function with respect to a hyperbolic metric. We show that the subset of currents with positive systole is open and that the mapping class group acts properly discontinuously on it. As an application, we obtain in the case of compact surfaces a structure theorem on the length functions appearing in the length spectrum compactification both of the Hitchin and of the maximal character varieties and determine therein an open set of discontinuity for the action of the mapping class group.

The zero norm subspace of bounded cohomology of acylindrically hyperbolic groups - Franceschini, Federico; Pozzetti, Beatrice (Commentarii Mathematici Helvetici, 2019)
We construct combinatorial volume forms of hyperbolic three manifolds fibering over the circle. These forms define non-trivial classes in bounded cohomology. After introducing a new seminorm on exact bounded cohomology, we use these combinatorial classes to show that, in degree 3, the zero norm subspace of the bounded cohomology of an acylindrically hyperbolic group is infinite dimensional. In the appendix we use the same techniques to give a cohomological proof of a lower bound, originally due to Brock, on the volume of the mapping torus of a cobounded pseudo-Anosov homeomorphism of a closed surface in terms of its Teichmüller translation distance.

Basmajian-type inequalities for maximal representations - Fanoni, Federica; Pozzetti, Beatrice (arXiv,math.GT,1611.00286, 2016)
For suitable metrics on the locally symmetric space associated to a maximal representation, we prove inequalities between the length of the boundary and the lengths of orthogeodesics that generalize the classical Basmajian’s identity from Teichmueller theory. Any equality characterizes diagonal embeddings.

Boundary maps and maximal representations on infinite dimensional Hermitian symmetric spaces - Duchesne, Bruno; Lécureux, Jean; Pozzetti, Beatrice (arXiV preprints, 2018)
We define a Toledo number for actions of surface groups and complex hyperbolic lattices on infinite dimensional Hermitian symmetric spaces, which allows us to define maximal representations. When the target is not of tube type we show that there cannot be Zariski-dense maximal representations, and whenever the existence of a boundary map can be guaranteed, the representation preserves a finite dimensional totally geodesic subspace on which the action is maximal. In the opposite direction we construct examples of geometrically dense maximal representation in the infinite dimensional Hermitian symmetric space of tube type and finite rank. Our approach is based on the study of boundary maps, that we are able to construct in low ranks or under some suitable Zariski-density assumption, circumventing the lack of local compactness in the infinite dimensional setting.

ADS 3-manifolds and Higgs bundles - Alessandrini, Daniele; Li, Qiongling (arXiv,math.DG,1510.07745, 2015)
In this paper we investigate the relationships between closed \mathrmAdS 3-manifolds and Higgs bundles. We have a new way to construct AdS structures that allows us to see many of their properties explicitly, for example we can recover the very recent formula by Tholozan for the volumes. We also find applications to the theory of minimal immersions into quadrics with their natural pseudo-Riemannian structure: using the geometry of the \mathrmAdS manifolds we can characterize the representations admitting equivariant minimal immersions of the Poincaré disc into the Klein quadric, the Grassmannian \mathrmGr(2,4), and understand the geometry of these minimal immersions.

Hitchin components for orbifolds - Alessandrini, Daniele; Lee, Gye-Seon; Schaffhauser, Florent (arXiV preprints, 2018)
We extend the notion of Hitchin component from surface groups to orbifold groups and prove that this gives new examples of higher Teichmüller spaces. We show that the Hitchin component of an orbifold group is homeomorphic to an open ball and we compute its dimension explicitly. We then give applications to the study of the pressure metric, cyclic Higgs bundles, and the deformation theory of real projective structures on 3-manifolds.

Higgs Bundles and Geometric Structures on Manifolds - Alessandrini, Daniele (Symmetry, Integrability and Geometry: Methods and Applications, 2019)
Geometric structures on manifolds became popular when Thurston used them in his work on the geometrization conjecture. They were studied by many people and they play an important role in higher Teichmüller theory. Geometric structures on a manifold are closely related with representations of the fundamental group and with flat bundles. Higgs bundles can be very useful in describing flat bundles explicitly, via solutions of Hitchin’s equations. Baraglia has shown in his Ph.D. Thesis that Higgs bundles can also be used to construct geometric structures in some interesting cases. In this paper, we will explain the main ideas behind this theory and we will survey some recent results in this direction, which are joint work with Qiongling Li.

Domains of discontinuity in oriented flag manifolds - Stecker, Florian; Treib, Nicolaus (arXiV preprints, 2018)
We study actions of discrete subgroups Γof semi-simple Lie groups G on associated oriented flag manifolds. These are quotients G/P, where the subgroup P lies between a parabolic subgroup and its identity component. For Anosov subgroups Γ⊂G, we identify domains in oriented flag manifolds by removing a set obtained from the limit set of Γ, and give a combinatorial description of proper discontinuity and cocompactness of these domains. This generalizes analogous results of Kapovich-Leeb-Porti to the oriented setting. We give first examples of cocompact domains of discontinuity which are not lifts of domains in unoriented flag manifolds. These include in particular domains in oriented Grassmannians for Hitchin representations, which we also show to be nonempty. As a further application of the oriented setup, we give a new lower bound on the number of connected components of B-Anosov representations of a closed surface group into \SL(n,\mathbb R).

Balanced ideals and domains of discontinuity of Anosov representations - Stecker, Florian (arXiV preprints, 2018)
We consider the action of Anosov subgroups of a semi-simple Lie group on the associated flag manifolds. A systematic approach to construct cocompact domains of discontinuity for this action was given by Kapovich, Leeb and Porti in arXiv:1306.3837. For ∆-Anosov representations, we prove that every cocompact domain of discontinuity arises from this construction, up to a few exceptions in low rank. Then we compute which flag manifolds admit these domains and, in some cases, the number of domains. We also find a new compactification for locally symmetric spaces arising from maximal representations into \mathrmSp(4n+2,\mathbb R).

Convex projective generalized Dehn filling - Choi, Suhyoung; Lee, Gye-Seon; Marquis, Ludovic (to appear in Ann. Sci. Éc. Norm. Supér., 2018)
For d = 4,5,6, we exhibit the first examples of complete finite volume hyperbolic d-manifolds M with cusps such that infinitely many d-orbifolds M_m obtained from M by generalized Dehn filling admit properly convex real projective structures. The orbifold fundamental groups of M_m are Gromov-hyperbolic relative to a collection of subgroups virtually isomorphic to \mathbbZ^d-2, hence the images of the developing maps of the projective structures on M_m are new examples of divisible properly convex domains of the projective d-space which are not strictly convex, in contrast to the previous examples of Benoist.

Anti–de Sitter strictly GHC-regular groups which are not lattices - Lee, Gye-Seon; Marquis, Ludovic (Trans. Amer. Math. Soc., 2019)
For d=4, 5, 6, 7, 8, we exhibit examples of \mathrm AdS^d,1 strictly GHC-regular groups which are not quasi-isometric to the hyperbolic space \mathbbH^d, nor to any symmetric space. This provides a negative answer to Question 5.2 in a work of Barbot et al. and disproves Conjecture 8.11 of Barbot-Mérigot [Groups Geom. Dyn. 6 (2012), pp. 441-483]. We construct those examples using the Tits representation of well-chosen Coxeter groups. On the way, we give an alternative proof of Moussong’s hyperbolicity criterion (Ph.D. Thesis) for Coxeter groups built on Danciger-Guéritaud-Kassel’s 2017 work and find examples of Coxeter groups W such that the space of strictly GHC-regular representations of W into \mathrm PO_d,2(\mathbbR) up to conjugation is disconnected.

Pappus Theorem, Schwartz Representations and Anosov Representations - Barbot, Thierry; Lee, Gye-Seon; Valério, Viviane Pardini (Ann. Inst. Fourier (Grenoble), 2018)
In the paper \textitPappus’s theorem and the modular group, R. Schwartz constructed a 2-dimensional family of faithful representations ρ_Θof the modular group \mathrmPSL(2,\mathbbZ) into the group \mathscrG of projective symmetries of the projective plane via Pappus Theorem. The image of the unique index 2 subgroup \mathrmPSL(2,\mathbbZ)_o of \mathrmPSL(2,\mathbbZ) under each representation ρ_Θis in the subgroup \mathrmPGL(3,\mathbbR) of \mathscrG and preserves a topological circle in the flag variety, but ρ_Θis \emphnot Anosov. In her PhD Thesis, V. P. Valério elucidated the Anosov-like feature of Schwartz representations: for every ρ_Θ, there exists a 1-dimensional family of Anosov representations ρ^ε_Θ of \mathrmPSL(2,\mathbbZ)_o into \mathrmPGL(3,\mathbbR) whose limit is the restriction of ρ_Θto \mathrmPSL(2,\mathbbZ)_o. In this paper, we improve her work: for each ρ_Θ, we build a 2-dimensional family of Anosov representations of \mathrmPSL(2,\mathbbZ)_o into \mathrmPGL(3,\mathbbR) containing ρ^ε_Θ and a 1-dimensional subfamily of which can extend to representations of \mathrmPSL(2,\mathbbZ) into \mathscrG. Schwartz representations are therefore, in a sense, the limits of Anosov representations of \mathrmPSL(2,\mathbbZ) into \mathscrG.

Convex projective structures on nonhyperbolic three-manifolds - Ballas, Samuel; Danciger, Jeffrey; Lee, Gye-Seon (Geom. Topol., 2018)
Y Benoist proved that if a closed three-manifold M admits an indecomposable convex real projective structure, then M is topologically the union along tori and Klein bottles of finitely many submanifolds each of which admits a complete finite volume hyperbolic structure on its interior. We describe some initial results in the direction of a potential converse to Benoist’s theorem. We show that a cusped hyperbolic three-manifold may, under certain assumptions, be deformed to convex projective structures with totally geodesic torus boundary. Such structures may be convexly glued together whenever the geometry at the boundary matches up. In particular, we prove that many doubles of cusped hyperbolic three-manifolds admit convex projective structures.

Collar lemma for Hitchin representations - Lee, Gye-Seon; Zhang, Tengren (Geom. Topol., 2017)
There is a classical result known as the collar lemma for hyperbolic surfaces. A consequence of the collar lemma is that if two closed curves A and B on a closed orientable hyperbolizable surface intersect each other, then there is an explicit lower bound for the length of A in terms of the length of B, which holds for every hyperbolic structure on the surface. In this article, we prove an analog of the classical collar lemma in the setting of Hitchin representations.

Projective deformations of weakly orderable hyperbolic Coxeter orbifolds - Choi, Suhyoung; Lee, Gye-Seon (Geom. Topol., 2015)
A Coxeter n–orbifold is an n–dimensional orbifold based on a polytope with silvered boundary facets. Each pair of adjacent facets meet on a ridge of some order m, whose neighborhood is locally modeled on \mathbbR^n modulo the dihedral group of order 2m generated by two reflections. For n ≥3, we study the deformation space of real projective structures on a compact Coxeter n–orbifold Q admitting a hyperbolic structure. Let e_+(Q) be the number of ridges of order greater than or equal to 3. A neighborhood of the hyperbolic structure in the deformation space is a cell of dimension e_+(Q)-n if n=3 and Q is weakly orderable, ie the faces of Q can be ordered so that each face contains at most 3 edges of order 2 in faces of higher indices, or Q is based on a truncation polytope.

Deformations of convex real projective manifolds and orbifolds - Choi, Suhyoung; Lee, Gye-Seon; Marquis, Ludovic (2018)
In this survey, we study representations of finitely generated groups into Lie groups, focusing on the deformation spaces of convex real projective structures on closed manifolds and orbifolds, with an excursion on projective structures on surfaces. We survey the basics of the theory of character varieties, geometric structures on orbifolds, and Hilbert geometry. The main examples of finitely generated groups for us will be Fuchsian groups, 3-manifold groups and Coxeter groups.

A complete description of the antipodal set of most symmetric spaces of compact type - Beyrer, Jonas (Osaka J. Math, 2018)
It is known that the antipodal set of a Riemannian symmetric space of compact type G/K consists of a union of K-orbits. We determine the dimensions of these K-orbits of most irreducible symmetric spaces of compact type. The symmetric spaces we are not going to deal with are those with restricted root system \mathfrak a_r and a non-trivial fundamental group, which is not isomorphic to \mathbb Z_2 or \mathbb Z_r+1. For example, we show that the antipodal sets of the Lie groups Spin(2r+1)r≥5, E_8 and G_2 consist only of one orbit which is of dimension 2r, 128 and 6, respectively; \SO(2r+1) has also an antipodal set of dimension 2r; and the Grassmannian Gr_r,r+q(R) has a rq-dimensional orbit as antipodal set if r≥5 and r≠q>0.

Cubulations and cross ratios on contracting boundaries - Beyrer, Jonas; Fioravanti, Elia (arXiV preprints, 2018)
Many geometric structures associated to surface groups can be encoded in terms of invariant cross ratios on their circle at infinity; examples include points of Teichmüller space, Hitchin representations and geodesic currents. We add to this picture by studying cubulations of arbitrary Gromov hyperbolic groups G. Under weak assumptions, we show that the space of cubulations of G naturally injects into the space of G-invariant cross ratios on the Gromov boundary \partial_∞G. A consequence of our results is that essential, hyperplane-essential cubulations of hyperbolic groups are length-spectrum rigid, i.e. they are fully determined by their length function. This is the optimal length-spectrum rigidity result for cubulations of hyperbolic groups, as we demonstrate with some examples. In the hyperbolic setting, this constitutes a strong improvement on our previous work in arXiv:1903.02447. Along the way, we describe the relationship between the Roller boundary of a \mathrmCAT(0) cube complex, its Gromov boundary and - in the non-hyperbolic case - the contracting boundary of Charney and Sultan. All our results hold for cube complexes with variable edge lengths.

Cross ratios on CAT(0) cube complexes and marked length-spectrum rigidity - Beyrer, Jonas; Fioravanti, Elia (arXiv,math.GT,1903.02447, 2019)
We show that group actions on irreducible \CAT cube complexes with no free faces are uniquely determined by their \ell^1 length function. Actions are allowed to be non-proper and non-cocompact, as long as they are minimal and have no finite orbit in the visual boundary. This is, to our knowledge, the first length-spectrum rigidity result in a setting of \emphnon-positive curvature (with the exception of some particular cases in dimension 2 and symmetric spaces). As our main tool, we develop a notion of cross ratio on Roller boundaries of \CAT cube complexes. Inspired by results in \emphnegative curvature, we give a general framework reducing length-spectrum rigidity questions to the problem of extending cross-ratio preserving maps between (subsets of) Roller boundaries. The core of our work is then to show that, when there are no free faces, these cross-ratio preserving maps always extend to cubical isomorphisms. All our results equally apply to cube complexes with variable edge lengths. As a special case of our work, we construct a compactification of the Char\-ney–Stambaugh–Vogtmann Outer Space for the group of untwisted outer automorphisms of an (irreducible) right-angled Artin group. This generalises the length function compactification of the classical Culler–Vogtmann Outer Space.

CAT(0) cube complexes are determined by their boundary cross ratio - Beyrer, Jonas; Fioravanti, Elia; Incerti-Medici, Merlin ((to appear in Groups, Geometry and Dynamics), 2018)
We introduce a \Z–valued cross ratio on Roller boundaries of \mathrmCAT cube complexes. We motivate its relevance by showing that every cross-ratio preserving bijection of Roller boundaries uniquely extends to a cubical isomorphism. Our results are strikingly general and even apply to infinite dimensional, locally infinite cube complexes with trivial automorphism group.

Marked length spectrum rigidity for actions on CAT(0) cube complexes - Beyrer, Jonas ((to appear in Oberwolfach reports 2019/30), 2019)
Given an action on a metric space one can associate to each element of the group its translation length. This gives a function of the group to the reals called the marked length spectrum. Adding requirements for space and action, it is a natural question if the marked length spectrum already uniquely defines space and action. In this talk we want to show that this is the case when considering CAT(0) cube complexes (under some natural assumptions). The main tool to prove this will be a boundary rigidity using cross ratios. Joint workwith Elia Fioravanti.

Schottky groups and maximal representations - Burelle, Jean-Philippe; Treib, Nicolaus (Geometriae Dedicata, 2018)
We describe a construction of Schottky type subgroups of automorphism groups of partially cyclically ordered sets. We apply this construction to the Shilov boundary of a Hermitian symmetric space and show that in this setting Schottky subgroups correspond to maximal representations of fundamental groups of surfaces with boundary. As an application, we construct explicit fundamental domains for the action of maximal representations into \mathrm Sp(2n,\mathbb R) on \mathbb RP^2n-1.

Affine Anosov representations and proper actions - Ghosh, Sourav; Treib, Nicolaus (arXiv preprints, 2017)
We define the notion of affine Anosov representations of word hyperbolic groups into the affine group \SO^0(n+1,n)⋉\bR^2n+1. We then show that a representation ρof a word hyperbolic group is affine Anosov if and only if its linear part \mathttL_ρis Anosov in \mathsfSO^0(n+1,n) with respect to the stabilizer of a maximal isotropic plane and ρ(Γ) acts properly on \mathbbR^2n+1.

Schottky presentations of positive representations - Burelle, Jean-Philippe; Treib, Nicolaus (arXiV preprints (to be published in Mathematische Annalen), 2018)
We show that the notion of 3-hyperconvexity on oriented flag manifolds defines a partial cyclic order. Using the notion of interval given by this partial cyclic order, we construct Schottky groups and show that they correspond to images of positive representations in the sense of Fock and Goncharov. We construct polyhedral fundamental domains for the domain of discontinuity that these groups admit in the projective space or the sphere, depending on the dimension.

2π–grafting and complex projective structures, I - Baba, Shinpei (Geometry & Topology, 2015)
Let S be a closed oriented surface of genus at least two. Gallo, Kapovich and Marden asked whether 2π–grafting produces all projective structures on S with arbitrarily fixed holonomy (the Grafting conjecture). In this paper, we show that the conjecture holds true “locally” in the space \mathcalGL of geodesic laminations on S via a natural projection of projective structures on S into \mathcalGL in Thurston coordinates. In a sequel paper, using this local solution, we prove the conjecture for generic holonomy.

Holonomy map fibers of ℂP1-structures in moduli space - Baba, Shinpei; Gupta, Yachee (Journal of Topology, 2015)
Let S be a closed oriented surface of genus g≥2. Fix an arbitrary non-elementary representation ρ\colπ_1(S)→ \rm SL_2(\C) and consider all marked (complex) projective structures on S with holonomy ρ. We show that their underlying conformal structures are dense in the moduli space of S.

2π-Grafting and complex projective structures with generic holonomy - Baba, Shinpei (Geometric and Functional Analysis, 2017)
Let S be an oriented closed surface of genus at least two. We show that, given a generic representation }}{\backslashrho: \backslashpi_1(S) \backslashto {\backslashrm PSL} (2, \backslashmathbb{C})}}}ρ:π1(S)\textrightarrowPSL(2,C)in the character variety, (}}{2\backslashpi}}}2π-)grafting produces all projective structures on S with holonomy }}{\backslashrho}}}ρ.

The pressure metric on the Margulis multiverse - Ghosh, Sourav (Geometriae Dedicata, 2018)
This paper defines the pressure metric on the Moduli space of Margulis spacetimes without cusps and shows that it is positive definite on the constant entropy sections. It also demonstrates an identity regarding the variation of the cross-ratios.

Generalized stretch lines for surfaces with boundary - Alessandrini, Daniele; DiSarlo, Valentina (arXiv,math.GT,1911.10431, 2019)
In 1986 William P. Thurston introduced the celebrated (asymmetric) Lipschitz distance on the Teichmueller space of a (closed or punctured) surface. In this paper we extend his work to the Teichmueller space of a surface with boundary endowed the arc distance. In this new setting we construct a large family of geodesics, which generalize Thurston’s stretch lines. We prove that the Teichmueller space of a surface with boundary, endowed with the arc distance, is a geodesic metric space. Furthermore, the arc distance is induced by a Finsler metric. As a corollary, we describe a new class of geodesics in the Teichmueller space of a closed/punctured surface that are not stretch lines in the sense of Thurston.

Rigidity of the saddle connection complex - DiSarlo, Valentina; Randecker, Anja; Tang, Robert (arXiV preprints, 2018)
For a half-translation surface (S,q), the associated \emphsaddle connection complex \A(S,q) is the simplicial complex where vertices are the saddle connections on (S,q), with simplices spanned by sets of pairwise disjoint saddle connections. This complex can be naturally regarded as an induced subcomplex of the arc complex. We prove that any simplicial isomorphism φ\colon \A(S,q) → \A(S’,q’) between saddle connection complexes is induced by an affine diffeomorphism F \colon (S,q) → (S’,q’). In particular, this shows that the saddle connection complex is a complete invariant of affine equivalence classes of half-translation surfaces. Throughout our proof, we develop several combinatorial criteria of independent interest for detecting various geometric objects on a half-translation surface.

Simultaneous ips on triangulated surfaces - DiSarlo, Valentina; Parlier, Hugo (Michigan Math. J., 2018)
We investigate a type of distance between triangulations on finite-type surfaces where one moves between triangulations by performing simultaneous flips. We consider triangulations up to homeomorphism, and our main results are upper bounds on the distance between triangulations that only depend on the topology of the surface.

Properization: Constructing proper scoring rules via Bayes acts - Brehmer, Jonas R.; Gneiting, Tilmann (Annals of the Institute of Statistical Mathematics, 2020)

Grid- versus station-based postprocessing of ensemble temperature forecasts - Feldmann, Kira; Richardson, David S.; Gneiting, Tilmann (Geophysical Research Letters, 2019)

Evaluating probabilistic forecasts with scoringRules - Jordan, Alexander I.; Krüger, Fabian; Lerch, Sebastian (Journal of Statistical Software, 2019)

Chromatosome Structure and Dynamics from Molecular Simulations - Öztürk, Mehmet Ali; De, Madhura; Cojocaru, Vlad; Wade, Rebecca C. (Annual Review of Physical Chemistry, 2020)

Enhancement of Benzothiazoles as Pteridine Reductase-1 Inhibitors for the Treatment of Trypanosomatidic Infections - Linciano, Pasquale; Pozzi, Cecilia; Iacono, Lucia dello; di Pisa, Flavio; Landi, Giacomo; Bonucci, Alessio; Gul, Sheraz; Kuzikov, Maria; Ellinger, Bernhard; Witt, Gesa; Santarem, Nuno; Baptista, Catarina; et al. (Journal of Medicinal Chemistry, 2018)

The HIV-1 ribonucleoprotein dynamically regulates its condensate behavior and drives acceleration of protease activity through membrane-less granular phase-separation - Lyonnais, Sébastien; Sadiq, Kashif; Lorca-Oró, Cristina; Dufau, Laure; Nieto-Marquez, Sara; Escriba, Tuixent; Gabrielli, Natalia; Tan, Xiao; Ouizougun-Oubari, Mohamed; Okoronkwo, Josephine; Reboud-Ravaux, Michèle; Gatell, José Maria; et al. (2019)

Computational characterisation of protein homo- and heterodimer formation - Hanke, Anton (2019)

Molecular dynamics simulation studies of gp41 cytoplasmic tail lateral embedding in phospholipid bilayer - Ullmann, Philip (2019)

Druggability Assessment in TRAPP Procedure using Machine Learning Approaches - Yuan, Jui-Hung (2019)

Computational studies of drug-binding kinetics - Ganotra, Gaurav Kumar (2019)

Perturbation Methods in Molecular Dynamics Simulations with Implicit Solvent Models - Johann, Tim I. (2005)

Entwicklung einer erweiterten Anwendung der Hauptkomponentenanalyse fuer das Protein-Protein Dockingproblem - Neumann, Gunter F. (2003)

Glycolytic Pathway Reaction Animations - Gonzalez, Aitor (2001)

Molekulardynamische Simulation zur Aufklaerung des Substratzuganges in Cytochrom P450eryF - Gauges, Ralph (1999)

Dynamische Einstellung des Parallelitaetsgrades mit reflexiven Programmen - Reimer, Niels (1996)

De-Novo Design von Liganden zur Blockierung der Substratzugaenlichkeit von Cytochrom P450cam - Degenhardt, Michael (1995)

The Protein Structure Annotation Tool ProSAT2 - Ulbrich, Stefan (2005)

Comparative analysis of Adenylyl Cyclase binding sites - Tong, Rudi (2014)

Clustering and Scoring the Druggability of Transient Protein Pockets - Horn, Max (2015)

Brownian Dynamics Simulations of Chymotrypsin Inhibitor 2 in Concentrated Protein Solutions - Waldhauer, Max (2015)

Case Study of Human Growth Hormone Interactions by Brownian Dynamics Simulation - Stubbusch, Astrid (2016)

Towards development of Random Acceleration Molecular Dynamics simulation analysis software for predicting drug residence time - Buerkel, Carl (2017)

Modelling of Neurotrophin Receptors - Dohrke, Jan-Niklas (2018)

Peptides binding to the dimer interface of thymidylate synthase for the treatment of cancer - Costi, M. Paola; Marverti, Gaetano; Cardinale, Daniela; Venturelli, Alberto; Ferrari, Stefania; Ponterini, Glauco; Henrich, Stefan; Salo-Ahen, Outi; Wade, Rebecca C. (2009)

Uso di inhibitori della Pteridina Reduttasi per la prevenzione e/o il trattamento di infezioni parassitarie - Costi, M. Paola; Luciani, Rosaria; Nerini, Erika; D., Guerrieri; Ferrari, Stefania; Venturelli, Alberto; Lazzari, Sandra; Wade, Rebecca C.; Henrich, Stefan; Motiejunas, D. (2013)

Radio Galaxy Zoo: Knowledge Transfer Using Rotationally Invariant Self-organizing Maps - Galvin, T. J.; Huynh, M.; Norris, R. P.; Wang, X. R.; Hopkins, Erica; Wong, O. I.; Shabala, S.; Rudnick, L.; Alger, M. J.; Polsterer, Kai (Publications of the Astronomical Society of the Pacific, 2019)

Sequence Tagging with Contextual and Non-Contextual Subword Representations: A Multilingual Evaluation - Heinzerling, Benjamin; Strube, Michael (2019)

HITS-SBD at the FinSBD Task: Machine Learning vs. Rule-based Sentence Boundary Detection - Fatima, Mehwish; Müller, Mark-Christoph (2019)

Off-the-shelf Semantic Author Name Disambiguation for Bibliographic Data Bases - Müller, Mark-Christoph; Bannister, Adam; Reitz, Florian (2019)

Using Automatically Extracted Minimum Spans to Disentangle Coreference Evaluation from Boundary Detection - Moosavi, Nafise Sadat; Born, Leo; Poesio, Massimo; Strube, Michael (2019)

Fine-Grained Entity Typing in Hyperbolic Space - López, Federico; Heinzerling, Benjamin; Strube, Michael (2019)

Semantic Matching of Documents from Heterogeneous Collections: A Simple and Transparent Method for Practical Applications - Müller, Mark-Christoph (2019)

A large harvested corpus of location metonymy - Mathews, Kevin; Strube, Michael (2020)

On the importance of subword information for morphological tasks in truly low-resource languages - Zhu, Yi; Heinzerling, Benjamin; Vulic, Ivan; Strube, Michael; Reichart, Roi; Korhonen, Anna (2019)

Adapting deep learning methods for mental health prediction on social media - Sekulić, Ivan; Strube, Michael (2019)

Equation of state constraints from multi-messenger observations of neutron star mergers - Bauswein, Andreas (Annals of Physics, 2019)

Spectral classification of gravitational-wave emission and equation of state constraints in binary neutron star mergers - Bauswein, A; Stergioulas, N (Journal of Physics G Nuclear Physics, 2019)

Identification of strontium in the merger of two neutron stars - Watson, Darach; Hansen, Camilla J.; Selsing, Jonatan; Koch, Andreas; Malesani, Daniele B.; Andersen, Anja C.; Fynbo, Johan P. U.; Arcones, Almudena; Bauswein, Andreas; Covino, Stefano; Grado, Aniello; Heintz, Kasper E.; et al. (\nat, 2019)

r-process nucleosynthesis: connecting rare-isotope beam facilities with the cosmos - Horowitz, C J; Arcones, A; Côté, B; Dillmann, I; Nazarewicz, W; Roederer, I U; Schatz, H; Aprahamian, A; Atanasov, D; Bauswein, A; Beers, T C; Bliss, J; et al. (Journal of Physics G Nuclear Physics, 2019)

Improved leakage-equilibration-absorption scheme (ILEAS) for neutrino physics in compact object mergers - Ardevol-Pulpillo, R; Janka, H-T; Just, O; Bauswein, A (\mnras, 2019)

Exploring the sensitivity of gravitational wave detectors to neutron star physics - Martynov, Denis; Miao, Haixing; Yang, Huan; Vivanco, Francisco Hernandez; Thrane, Eric; Smith, Rory; Lasky, Paul; East, William E.; Adhikari, Rana; Bauswein, Andreas; Brooks, Aidan; Chen, Yanbei; et al. (\prd, 2019)

Identifying a First-Order Phase Transition in Neutron-Star Mergers through Gravitational Waves - Bauswein, Andreas; Bastian, Niels-Uwe F.; Blaschke, David B.; Chatziioannou, Katerina; Clark, James A.; Fischer, Tobias; Oertel, Micaela (\prl, 2019)

Observing the post-merger signal of GW170817-like events with improved gravitational-wave detectors - Torres-Rivas, Andoni; Chatziioannou, Katerina; Bauswein, Andreas; Clark, James Alexander (\prd, 2019)

Evidence for a Chandrasekhar-mass explosion in the Ca-strong 1991bg-like type Ia supernova 2016hnk - Galbany, L.; Ashall, C.; Höflich, P.; González-Gaitán, S.; Taubenberger, S.; Stritzinger, M.; Hsiao, E. Y.; Mazzali, P.; Baron, E.; Blondin, S.; Bose, S.; Bulla, M.; et al. (A&A, 2019)

Strongly lensed SNe Ia in the era of LSST: observing cadence for lens discoveries and time-delay measurements - Huber, S.; Suyu, S. H.; Noebauer, U. M.; Bonvin, V.; Rothchild, D.; Chan, J. H. H.; Awan, H.; Courbin, F.; Kromer, M.; Marshall, P.; Oguri, M.; Ribeiro, T.; et al. (\aap, 2019)

SN 2012dn from early to late times: 09dc-like supernovae reassessed - Taubenberger, S; Floers, A; Vogl, C; Kromer, M; Spyromilio, J; Aldering, G; Antilogus, P; Bailey, S; Baltay, C; Bongard, S; Boone, K; Buton, C; et al. (Monthly Notices of the Royal Astronomical Society, 2019)

Space astrometry of the very massive ∼150 M⊙ candidate runaway star VFTS682 - Renzo, M; de Mink, S E; Lennon, D J; Platais, I; van der Marel, R P; Laplace, E; Bestenlehner, J M; Evans, C J; Hénault-Brunet, V; Justham, S; de Koter, A; Langer, N; et al. (Monthly Notices of the Royal Astronomical Society, 2019)

The VLT-FLAMES Tarantula Survey. XXX. Red stragglers in the clusters Hodge 301 and SL 639 - Britavskiy, N.; Lennon, D. J.; Patrick, L. R.; Evans, C. J.; Herrero, A.; Langer, N.; van Loon, J. Th.; Clark, J. S.; Schneider, Fabian; Almeida, L. A.; Sana, H.; de Koter, A.; et al. (\aap, 2019)

The VLT-FLAMES Tarantula Survey. XXXI. Radial velocities and multiplicity constraints of red supergiant stars in 30 Doradus - Patrick, L. R.; Lennon, D. J.; Britavskiy, N.; Evans, C. J.; Sana, H.; Taylor, W. D.; Herrero, A.; Almeida, L. A.; Clark, J. S.; Gieles, M.; Langer, N.; Schneider, Fabian; et al. (\aap, 2019)

Hydrodynamical simulations and similarity relations for eruptive mass-loss from massive stars - Owocki, Stanley P; Hirai, Ryosuke; Podsiadlowski, Philipp; Schneider, Fabian (\mnras, 2019)

A census of massive stars in NGC 346. Stellar parameters and rotational velocities - Dufton, P. L.; Evans, C. J.; Hunter, I.; Lennon, D. J.; Schneider, Fabian (\aap, 2019)

The MiMeS survey of magnetism in massive stars: magnetic properties of the O-type star population - Petit, V.; Wade, G. A.; Schneider, Fabian; Foßati, L.; Kamp, K.; Neiner, C.; David-Uraz, A.; Alecian, E.; MiMeS Collaboration, (\mnras, 2019)

The interaction of core-collapse supernova ejecta with a stellar companion - Liu, Zheng-Wei; Tauris, T. M.; Röpke, Friedrich; Moriya, T. J.; Kruckow, M.; Stancliffe, R. J.; Izzard, R. G. (Proceedings of the International Astronomical Union, 2018)

Remnants and ejecta of thermonuclear electron-capture supernovae. Constraining oxygen-neon deflagrations in high-density white dwarfs - Jones, S.; Röpke, Friedrich; Fryer, C.; Ruiter, A. J.; Seitenzahl, I. R.; Nittler, L. R.; Ohlmann, S. T.; Reifarth, R.; Pignatari, M.; Belczynski, K. (A&A, 2019)

A New Model for Electron-capture Supernovae in Galactic Chemical Evolution - Jones, Samuel; Côté, Benoit; Röpke, Friedrich; Wanajo, Shinya (\apj, 2019)

From Supernova to Supernova Remnant: The Three-dimensional Imprint of a Thermonuclear Explosion - Ferrand, Gilles; Warren, Donald C.; Ono, Masaomi; Nagataki, Shigehiro; Röpke, Friedrich; Seitenzahl, Ivo R. (\apj, 2019)

Catching Element Formation In The Act ; The Case for a New MeV Gamma-Ray Mission: Radionuclide Astronomy in the 2020s - Timmes, Frank; Fryer, Chris; Timmes, Frank; Hungerford, Aimee L.; Couture, Aaron; Adams, Fred; Aoki, Wako; Arcones, Almudena; Arnett, David; Auchettl, Katie; Avila, Melina; Badenes, Carles; et al. (Bulletin of the American Astronomical Society, 2019)

Hydrodynamical moving-mesh simulations of the tidal disruption of stars by supermassive black holes - Goicovic, Felipe G; Springel, Volker; Ohlmann, Sebastian T; Pakmor, Rüdiger (\mnras, 2019)

Data Formats for Systems Biology and Quantitative Modeling - Golebiewski, Martin (Encyclopedia of Bioinformatics and Computational Biology, 2019)
Data standards support the reliable exchange of information, the interoperability of tools, and the reproducibility of scientific results. In systems biology standards are agreed ways of structuring, describing, and associating models and data, as well as their respective parts, graphical visualization, and information about applied experimental or computational methods. Such standards also assist with describing how constituent parts interact together, or are linked, and how they are embedded in their environmental and experimental context. Here the focus will be on standards for formatting models and their content, and on metadata checklists and ontologies that support modeling.

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019 - Schreiber, Falk; Sommer, Björn; Bader, Gary D.; Gleeson, Padraig; Golebiewski, Martin; Hucka, Michael; Keating, Sarah M.; König, Matthias; Myers, Chris; Nickerson, David; Waltemath, Dagmar (Journal of Integrative Bioinformatics, 2019)

Harmonizing semantic annotations for computational models in biology - Neal, Maxwell Lewis; König, Matthias; Nickerson, David; Mısırlı, Göksel; Kalbasi, Reza; Dräger, Andreas; Atalag, Koray; Chelliah, Vijayalakshmi; Cooling, Michael T; Cook, Daniel L; Crook, Sharon; de Alba, Miguel; et al. (Briefings in Bioinformatics, 2019)

The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR - Wibberg, Daniel; Batut, Bérénice; Belmann, Peter; Blom, Jochen; Glöckner, Frank Oliver; Grüning, Björn; Hoffmann, Nils; Kleinbölting, Nils; Rahn, René; Rey, Maja; Scholz, Uwe; Sharan, Malvika; et al. (F1000Research, 2019)

Accelerating Drug Discovery Efforts for Trypanosomatidic Infections Using an Integrated Transnational Academic Drug Discovery Platform - Moraes, Carolina B.; Witt, Gesa; Kuzikov, Maria; Ellinger, Bernhard; Calogeropoulou, Theodora; Prousis, Kyriakos C.; Mangani, Stefano; Di Pisa, Flavio; Landi, Giacomo; Iacono, Lucia Dello; Pozzi, Cecilia; Freitas-Junior, Lucio H.; et al. (SLAS DISCOVERY: Advancing the Science of Drug Discovery, 2019)

Ermittlung probabilistischer Abflussvorhersagen unter Berücksichtigung zensierter Daten - Hemri, Stephan; Lisniak, Dmytro; Klein, Bastian (Hydrologie und Wasserbewirtschaftung, 2014)

Druggability Assessment in TRAPP Using Machine Learning Approaches - Yuan, Jui-Hung; Han, Sungho Bosco; Richter, Stefan; Wade, Rebecca C.; Kokh, Daria (Journal of Chemical Information and Modeling, 2020)

Eleven grand challenges in single-cell data science - Lähnemann, David; Köster, Johannes; Szczurek, Ewa; McCarthy, Davis J.; Hicks, Stephanie C.; Robinson, Mark D.; Vallejos, Catalina A.; Campbell, Kieran R.; Beerenwinkel, Niko; Mahfouz, Ahmed; Pinello, Luca; Skums, Pavel; et al. (Genome Biology, 2020)
The recent boom in microfluidics and combinatorial indexing strategies, combined with low sequencing costs, has empowered single-cell sequencing technology. Thousands—or even millions—of cells analyzed in a single experiment amount to a data revolution in single-cell biology and pose unique data science problems. Here, we outline eleven challenges that will be central to bringing this emerging field of single-cell data science forward. For each challenge, we highlight motivating research questions, review prior work, and formulate open problems. This compendium is for established researchers, newcomers, and students alike, highlighting interesting and rewarding problems for the coming years.

RootDigger : a root placement program for phylogenetic trees - Bettisworth, Ben; Stamatakis, Alexandros (2020)

Advances in molecular simulations of protein mechanical properties and function - Franz, Florian; Daday, Csaba; Gräter, Frauke (Current Opinion in Structural Biology, 2020)
Single-molecule force spectroscopy and classical molecular dynamics are natural allies. Recent advances in both experiments and simulations have increasingly facilitated a direct comparison of SMFS and MD data, most importantly by closing the gap between time scales, which has been traditionally at least 5 orders of magnitudes wide. In this review, we will explore these advances chiefly on the computational side. We focus on protein dynamics under force and highlight recent studies that showcase how lower loading rates and more statistics help to better interpret previous experiments and to also motivate new ones. At the same time, steadily increasing system sizes are used to mimic more closely the mechanical environment in the biological context. We showcase some of these advances on atomistic and coarse-grained scale, from asymmetric membrane tension to larger (multidomain/multimeric) protein assemblies under force.

Hybrid Kinetic Monte Carlo/Molecular Dynamics Simulations of Bond Scissions in Proteins. - Rennekamp, B.; Kutzki, F.; Obarska-Kosinska, A.; Zapp, C.; Grater, F. (J Chem Theory Comput, 2020)
Proteins are exposed to various mechanical loads that can lead to covalent bond scissions even before macroscopic failure occurs. Knowledge of these molecular breakages is important to understand mechanical properties of the protein. In regular molecular dynamics (MD) simulations, covalent bonds are predefined, and reactions cannot occur. Furthermore, such events rarely take place on MD time scales. Existing approaches that tackle this limitation either rely on computationally expensive quantum calculations (e.g., QM/MM) or complex bond order formalisms in force fields (e.g., ReaxFF). To circumvent these limitations, we present a new reactive kinetic Monte Carlo/molecular dynamics (KIMMDY) scheme. Here, bond rupture rates are calculated based on the interatomic distances in the MD simulation and then serve as an input for a kinetic Monte Carlo step. This easily scalable hybrid approach drastically increases the accessible time scales. Using this new technique, we investigate bond ruptures in a multimillion atom system of tensed collagen, a structural protein found in skin, bones, and tendons. Our findings show a clear concentration of bond scissions near chemical cross-links in collagen. We also examine subsequent dynamic relaxation steps. Our method exhibits only a minor slowdown compared to classical MD and is straightforwardly applicable to other complex (bio)materials under load and related chemistries.
Keywords: Animals; Collagen/chemistry; Dipeptides/chemistry; Humans; Kinetics; Molecular Dynamics Simulation; Monte Carlo Method; Protein Conformation; Proteins/*chemistry; Quantum Theory; Stress, Mechanical

The plakin domain of C. elegans VAB-10/plectin acts as a hub in a mechanotransduction pathway to promote morphogenesis - Suman, Shashi Kumar; Daday, Csaba; Ferraro, Teresa; Vuong-Brender, Thanh; Tak, Saurabh; Quintin, Sophie; Robin, François; Gräter, Frauke; Labouesse, Michel (Development, 2019)

Structure and dynamics of the platelet integrin-binding C4 domain of von Willebrand factor - Xu, Emma-Ruoqi; von Bülow, Sören; Chen, Po-Chia; Lenting, Peter J.; Kolšek, Katra; Aponte-Santamaría, Camilo; Simon, Bernd; Foot, Jaelle; Obser, Tobias; Schneppenheim, Reinhard; Gräter, Frauke; Denis, Cécile V.; et al. (Blood, 2019)
Von Willebrand factor (VWF) is a key player in the regulation of hemostasis by promoting recruitment of platelets to sites of vascular injury. An array of 6 C domains forms the dimeric C-terminal VWF stem. Upon shear force activation, the stem adopts an open conformation allowing the adhesion of VWF to platelets and the vessel wall. To understand the underlying molecular mechanism and associated functional perturbations in disease-related variants, knowledge of high-resolution structures and dynamics of C domains is of paramount interest. Here, we present the solution structure of the VWF C4 domain, which binds to the platelet integrin and is therefore crucial for the VWF function. In the structure, we observed 5 intra- and inter-subdomain disulfide bridges, of which 1 is unique in the C4 domain. The structure further revealed an unusually hinged 2-subdomain arrangement. The hinge is confined to a very short segment around V2547 connecting the 2 subdomains. Together with 2 nearby inter-subdomain disulfide bridges, this hinge induces slow conformational changes and positional alternations of both subdomains with respect to each other. Furthermore, the structure demonstrates that a clinical gain-of-function VWF variant (Y2561) is more likely to have an effect on the arrangement of the C4 domain with neighboring domains rather than impairing platelet integrin binding.

Inositol hexakisphosphate increases the size of platelet aggregates - Brehm, Maria A.; Klemm, Ulrike; Rehbach, Christoph; Erdmann, Nina; Kolšek, Katra; Lin, Hongying; Aponte-Santamaría, Camilo; Gräter, Frauke; Rauch, Bernhard H.; Riley, Andrew M.; Mayr, Georg W.; Potter, Barry V.L.; et al. (Biochemical Pharmacology, 2019)
The inositol phosphates, InsP5 and InsP6, have recently been identified as binding partners of fibrinogen, which is critically involved in hemostasis by crosslinking activated platelets at sites of vascular injury. Here, we investigated the putative physiological role of this interaction and found that platelets increase their InsP6 concentration upon stimulation with the PLC-activating agonists thrombin, collagen I and ADP and present a fraction of it at the outer plasma membrane. Cone and plate analysis in whole blood revealed that InsP6 specifically increases platelet aggregate size. This effect is fibrinogen-dependent, since it is inhibited by an antibody that blocks fibrinogen binding to platelets. Furthermore, InsP6 has only an effect on aggregate size of washed platelets when fibrinogen is present, while it has no influence in presence of von Willebrand factor or collagen. By employing blind docking studies we predicted the binding site for InsP6 at the bundle between the γand βhelical subunit of fibrinogen. Since InsP6 is unable to directly activate platelets and it did not exhibit an effect on thrombin formation or fibrin structure, our data indicate that InsP6 might be a hemostatic agent that is produced by platelets upon stimulation with PLC-activating agonists to promote platelet aggregation by supporting crosslinking of fibrinogen and activated platelets.

How ARVC-Related Mutations Destabilize Desmoplakin: An MD Study - Daday, Csaba; Mateyka, Laura Marlene; Gräter, Frauke (Biophysical Journal, 2019)
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is a familial heart disease linked to mutations in several desmosomal proteins, but the specific effects of these mutations on the molecular level are poorly understood. Among the many documented ARVC-related genetic variants, a striking hotspot of nine mutations has been identified in the plakin domain of desmoplakin. This hotspot can be found at the meeting point of three different subdomains of desmoplakin: two spectrin repeats and a Src homology 3 domain. We set out to understand the effect of these mutations. We determine, using molecular dynamics simulations, how these mutations affect the mechanics of this interface, performing two different classes of simulations. First, we sample the dynamics of the plakin domain, in particular the tendency of the interdomain hinge to buckle, and then we apply an external force onto the constructs and determine the force necessary to break them. We find that surface-exposed mutations are not affecting the dynamics to a very large degree but that most buried mutations make the junction more flexible and decrease the rupture forces observed. Our data suggest that buried ARVC mutations destabilize desmoplakin and thereby impair desmosome integrity under tension.

Structural and mechanistic insights into mechanoactivation of focal adhesion kinase - Bauer, Magnus Sebastian; Baumann, Fabian; Daday, Csaba; Redondo, Pilar; Durner, Ellis; Jobst, Markus Andreas; Milles, Lukas Frederik; Mercadante, Davide; Pippig, Diana Angela; Gaub, Hermann Eduard; Gräter, Frauke; Lietha, Daniel (Proceedings of the National Academy of Sciences, 2019)

How Fast Is Too Fast in Force-Probe Molecular Dynamics Simulations? - Sheridan, Steven; Gräter, Frauke; Daday, Csaba (The Journal of Physical Chemistry B, 2019)

Molecular Dynamics Simulations of Molecules in Uniform Flow - Herrera-Rodríguez, Ana M.; Miletić, Vedran; Aponte-Santamaría, Camilo; Gräter, Frauke (Biophysical Journal, 2019)
Flow at the molecular level induces shear-induced unfolding of single proteins and can drive their assembly, the mechanisms of which are not completely understood. To be able to analyze the role of flow on molecules, we present uniform-flow molecular dynamics simulations at atomic level. The pull module of the GRoningen MAchine for Chemical Simulations package was extended to be able to force-group atoms within a defined layer of the simulation box. Application of this external enforcement to explicit water molecules, together with the coupling to a thermostat, led to a uniform terminal velocity of the solvent water molecules. We monitored the density of the whole system to establish the conditions under which the simulated flow is well-behaved. A maximal velocity of 1.3 m/s can be generated if a pull slice of 8 nm is used, and high velocities would require larger pull slices to still maintain a stable density. As expected, the target velocity increases linearly with the total external force applied. Finally, we suggest an appropriate setup to stretch a protein by uniform flow, in which protein extensions depend on the flow conditions. Our implementation provides an efficient computational tool to investigate the effect of the flow at the molecular level.

A new method for the construction of coarse-grained models of large biomolecules from low-resolution cryo-electron microscopy data - Zhang, Yuwei; Xia, Kelin; Cao, Zexing; Gräter, Frauke; Xia, Fei (Physical Chemistry Chemical Physics, 2019)

Studying Functional Disulphide Bonds by Computer Simulations - Gräter, Frauke; Li, Wenjin (Functional Disulphide Bonds, 2019)
Biochemical and structural data reveal important aspects of the properties and function of a protein disulphide bond. Molecular dynamics simulations can complement this experimental data and can yield valuable insights into the dynamical behavior of the disulphide bond within the protein environment. Due to the increasing accuracy of the underlying energetic description and the increasing computational power at hand, such simulations have now reached a level, at which they can also make quantitative and experimentally testable predictions. We here give an overview of the computational methods used to predict functional aspects of protein disulphides, including the prestress, protein allosteric effects upon thiol/disulphide exchange, and disulphide redox potentials. We then outline in detail the use of free-energy perturbation methods to calculate the redox potential of a protein disulphide bond of interest. In a step-by-step protocol, we describe the workflow within the MD suite Gromacs, including practical advice on the simulation setup and choice of parameters. For other disulphide-related simulation methods, we refer to resources available online.

BRAF mutation testing of MSI CRCs in Lynch syndrome diagnostics: performance and efficiency according to patient‘s age - Bläker, Hendrik; Haupt, Saskia; Morak, Monika; Holinski-Feder, Elke; Arnold, Alexander; Horst, David; Sieber-Frank, Julia; Seidler, Florian; von Winterfeld, Moritz; Alwers, Elizabeth; Chang-Claude, Jenny; Brenner, Hermann; et al. (medRxiv, 2019)

The shared neoantigen landscape of MSI cancers reflects immunoediting during tumor evolution - Ballhausen, Alexej; Przybilla, Moritz Jakob; Jendrusch, Michael; Haupt, Saskia; Pfaffendorf, Elisabeth; Draxlbauer, Markus; Seidler, Florian; Krausert, Sonja; Ahadova, Aysel; Kalteis, Martin Simon; Heid, Daniel; Gebert, Johannes; et al. (bioRxiv, 2019)

Analysis of the Stationary Thermal-ElectroHydrodynamic Boussinesq Equations - Gerstner, Philipp; Baumann, Martin; Heuveline, Vincent (EMCL PrePrint Series, No 2019-01, 2019)

A time step reduction method for Multi-Period Optimal Power Flow problems - Schween, Nils; Meyer-Hübner, Nico; Gerstner, Philipp; Heuveline, Vincent (EMCL PrePrint Series, No 2019-02, 2019)

Dielectrophoretic force driven convection in annular geometry under Earth’s gravity - Seelig, Torsten; Meyer, Antoine; Gerstner, Philipp; Meier, Martin; Jongmanns, Marcel; Baumann, Martin; Heuveline, Vincent; Egbers, Christoph (International Journal of Heat and Mass Transfer, 2019)
Context A radial temperature difference together with an inhomogeneous radial electric field gradient is applied to a dielectric fluid confined in a vertical cylindrical annulus inducing thermal electro-hydrodynamic convection. Aims Identification of the stability of the flow and hence of the line of marginal stability separating stable laminar free (natural) convection from thermal electro-hydrodynamic convection, its flow structures, pattern formation and critical parameters. Methods Combination of different measurement techniques, namely the shadowgraph method and particle image velocimetry, as well as numerical simulation are used to qualify/quantify the flow. Results We identify the transition from stable laminar free convection to thermal electro-hydrodynamic convective flow in a wide range of Rayleigh number and electric potential. The line of marginal stability found confirms results from linear stability analysis. The flow after first transition forms a structure of axially aligned stationary columnar modes. We experimentally confirm critical parameters resulting from linear stability analysis and we show numerically an enhancement of heat transfer.

A cationic near infrared fluorescent agent and ethyl-cinnamate tissue clearing protocol for vascular staining and imaging - Huang, Jiaguo; Brenna, Cinzia; Khan, Arif ul Maula; Daniele, Cristina; Rudolf, Rüdiger; Heuveline, Vincent; Gretz, Norbert (Nature Scientific Reports, 2019)

GOODE: A Gaussian Off-The-Shelf Ordinary Differential Equation Solver - John, David; Heuveline, Vincent; Schober, Michael (2019)

Emergence of Hierarchical Modularity in Evolving Networks Uncovered by Phylogenomic Analysis. - Caetano-Anolles, G.; Aziz, M. F.; Mughal, F.; Grater, F.; Koc, I.; Caetano-Anolles, K.; Caetano-Anolles, D. (Evol Bioinform Online, 2019)
Networks describe how parts associate with each other to form integrated systems which often have modular and hierarchical structure. In biology, network growth involves two processes, one that unifies and the other that diversifies. Here, we propose a biphasic (bow-tie) theory of module emergence. In the first phase, parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are often selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In the second phase, variants of the modules diversify and become new parts for a new generative cycle of higher level organization. The paradigm predicts the rise of hierarchical modularity in evolving networks at different timescales and complexity levels. Remarkably, phylogenomic analyses uncover this emergence in the rewiring of metabolomic and transcriptome-informed metabolic networks, the nanosecond dynamics of proteins, and evolving networks of metabolism, elementary functionomes, and protein domain organization.

Single molecule force spectroscopy data and BD- and MD simulations on the blood protein von Willebrand factor. - Posch, S.; Aponte-Santamaria, C.; Schwarzl, R.; Karner, A.; Radtke, M.; Grater, F.; Obser, T.; Konig, G.; Brehm, M. A.; Gruber, H. J.; Netz, R. R.; Baldauf, C.; et al. (Data Brief, 2016)
We here give information for a deeper understanding of single molecule force spectroscopy (SMFS) data through the example of the blood protein von Willebrand factor (VWF). It is also shown, how fitting of rupture forces versus loading rate profiles in the molecular dynamics (MD) loading-rate range can be used to demonstrate the qualitative agreement between SMFS and MD simulations. The recently developed model by Bullerjahn, Sturm, and Kroy (BSK) was used for this demonstration. Further, Brownian dynamics (BD) simulations, which can be utilized to estimate the lifetimes of intramolecular VWF interactions under physiological shear, are described. For interpretation and discussion of the methods and data presented here, we would like to directly point the reader to the related research paper, "Mutual A domain interactions in the force sensing protein von Willebrand Factor" (Posch et al., 2016) [1].

Protein S-Bacillithiolation Functions in Thiol Protection and Redox Regulation of the Glyceraldehyde-3-Phosphate Dehydrogenase Gap in Staphylococcus aureus Under Hypochlorite Stress. - Imber, M.; Huyen, N. T. T.; Pietrzyk-Brzezinska, A. J.; Loi, V. V.; Hillion, M.; Bernhardt, J.; Tharichen, L.; Kolsek, K.; Saleh, M.; Hamilton, C. J.; Adrian, L.; Grater, F.; et al. (Antioxid Redox Signal, 2018)
AIMS: Bacillithiol (BSH) is the major low-molecular-weight thiol of the human pathogen Staphylococcus aureus. In this study, we used OxICAT and Voronoi redox treemaps to quantify hypochlorite-sensitive protein thiols in S. aureus USA300 and analyzed the role of BSH in protein S-bacillithiolation. RESULTS: The OxICAT analyses enabled the quantification of 228 Cys residues in the redox proteome of S. aureus USA300. Hypochlorite stress resulted in >10% increased oxidation of 58 Cys residues (25.4%) in the thiol redox proteome. Among the highly oxidized sodium hypochlorite (NaOCl)-sensitive proteins are five S-bacillithiolated proteins (Gap, AldA, GuaB, RpmJ, and PpaC). The glyceraldehyde-3-phosphate (G3P) dehydrogenase Gap represents the most abundant S-bacillithiolated protein contributing 4% to the total Cys proteome. The active site Cys151 of Gap was very sensitive to overoxidation and irreversible inactivation by hydrogen peroxide (H(2)O(2)) or NaOCl in vitro. Treatment with H(2)O(2) or NaOCl in the presence of BSH resulted in reversible Gap inactivation due to S-bacillithiolation, which could be regenerated by the bacilliredoxin Brx (SAUSA300_1321) in vitro. Molecular docking was used to model the S-bacillithiolated Gap active site, suggesting that formation of the BSH mixed disulfide does not require major structural changes. Conclusion and Innovation: Using OxICAT analyses, we identified 58 novel NaOCl-sensitive proteins in the pathogen S. aureus that could play protective roles against the host immune defense and include the glycolytic Gap as major target for S-bacillithiolation. S-bacillithiolation of Gap did not require structural changes, but efficiently functions in redox regulation and protection of the active site against irreversible overoxidation in S. aureus. Antioxid. Redox Signal. 28, 410-430.
Keywords: Bacterial Proteins/genetics/*metabolism; Cysteine/*analogs & derivatives/metabolism; GTPase-Activating Proteins/chemistry/metabolism; Glucosamine/*analogs & derivatives/metabolism; Glyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)/chemistry/*metabolism; Humans; Hydrogen Peroxide/metabolism; Hypochlorous Acid/toxicity; Protein Conformation/drug effects; Staphylococcus aureus/genetics/*metabolism/pathogenicity; Stress, Physiological/drug effects/genetics

Uncertainty Assessment of the Blood Damage in a FDA Blood Pump - Song, Chen; Heuveline, Vincent (Proceedings of the 3rd International Conference on Uncertainty Quantification in Computational Sciences and Engineering (UNCECOMP 2019), 2019)

Discovery of an Exceptionally Strong - Kirsebom, O. S.; Jones, S.; Strömberg, D. F.; Martínez-Pinedo, G.; Langanke, K.; Röpke, Friedrich; Brown, B. A.; Eronen, T.; Fynbo, H. O. U.; Hukkanen, M.; Idini, A.; Jokinen, A.; et al. (2019)

Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative - Hucka, Michael; Nickerson, David Phillip; Bader, Gary; Bergmann, Frank T; Cooper, Jonathan; Demir, Emek; Garny, Alan; Golebiewski, Martin; Myers, Chris John; Schreiber, Falk; Waltemath, Dagmar; Novère, Nicolas Le (Frontiers in Bioengineering and Biotechnology, 2015)
The Computational Modeling in Biology Network (COMBINE) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE’s aim is to act as a coordinator, facilitator, and resource for different standardization efforts whose domains of use cover related areas of the computational biology space. In this perspective article, we summarize COMBINE, its general organization, and the community standards and other efforts involved in it. Our goals are to help guide readers toward standards that may be suitable for their research activities, as well as to direct interested readers to relevant communities where they can best expect to receive assistance in how to develop interoperable computational models.

Radical orbital switching - Gryn'ova, Ganna; Coote, M. L. (2014)

Structural, Energetic, and Dynamic Aspects of Ligand–Receptor Interactions - Motiejunas, D.; Wade, Rebecca C. (Comprehensive Medicinal Chemistry II, 2007)

Molecular Recognition: Computational Analysis and Modelling - Feldman-Salit, Anna; Wade, Rebecca C. (2007)
Abstract Molecular recognition is critical to many fundamental processes in biology, including enzymatic reactions, signal transduction, genetic information processing, as well as molecular and cellular transport. The question of how proteins selectively recognize and correctly associate with their partners is an active research problem. For many proteins, experimental information about the structures of their molecular complexes and the details of their interactions are lacking. Macromolecular, structure-based computational techniques provide a means to predict the interactions of proteins and to investigate their recognition mechanisms. Here, we first discuss the general mechanism of molecular recognition as a multistep process from diffusion of one molecule toward the second to tight complex formation. We then describe the main forces and the physical properties that govern biomolecular interactions and introduce the principles of modeling them. Finally, simulation methods and computational approaches for molecular docking are briefly presented.

Protein–surface interactions: challenging experiments and computations - Cohavi, Ori; Corni, Stefano; Rienzo, Francesca De; Felice, Rosa Di; Gottschalk, Kay E.; Hoefling, Martin; Kokh, Daria; Molinari, Elisa; Schreiber, Gideon; Vaskevich, Alexander; Wade, Rebecca C. (Journal of Molecular Recognition, 2009)
Abstract Protein–surface interactions are fundamental in natural processes, and have great potential for applications ranging from nanotechnology to medicine. A recent workshop highlighted the current achievements and the main challenges in the field. Copyright © 2009 John Wiley & Sons, Ltd.

Computational approaches to identifying and characterizing protein binding sites for ligand design - Henrich, Stefan; Salo-Ahen, Outi M. H.; Huang, Bingding; Rippmann, Friedrich F.; Cruciani, Gabriele; Wade, Rebecca C. (Journal of Molecular Recognition, 2009)
Abstract Given the three-dimensional structure of a protein, how can one find the sites where other molecules might bind to it? Do these sites have the properties necessary for high affinity binding? Is this protein a suitable target for drug design? Here, we discuss recent developments in computational methods to address these and related questions. Geometric methods to identify pockets on protein surfaces have been developed over many years but, with new algorithms, their performance is still improving. Simulation methods show promise in accounting for protein conformational variability to identify transient pockets but lack the ease of use of many of the (rigid) shape-based tools. Sequence and structure comparison approaches are benefiting from the constantly increasing size of sequence and structure databases. Energetic methods can aid identification and characterization of binding pockets, and have undergone recent improvements in the treatment of solvation and hydrophobicity. The “druggability” of a binding site is still difficult to predict with an automated procedure. The methodologies available for this purpose range from simple shape and hydrophobicity scores to computationally demanding free energy simulations. Copyright © 2009 John Wiley & Sons, Ltd.

The Effect of Force-Field Parameters on Cytochrome P450-Membrane Interactions: Structure and Dynamics - Mustafa, Ghulam; Nandekar, Prajwal P.; Mukherjee, Goutam; Bruce, Neil J.; Wade, Rebecca C. (Scientific Reports, 2020)

Uncertain photometric redshifts via combining deep convolutional and mixture density networks - D'Isanto, Antonio; Polsterer, Kai (2017)

Structural characterization of an Arf dimer interface: molecular mechanism of Arf‐dependent membrane scission - Diestelkoetter‐Bachert, Petra; Beck, Rainer; Reckmann, Inge; Hellwig, Andrea; Garcia‐Saez, Ana; Zelman‐Hopf, Monika; Hanke, Anton; Nunes Alves, Ariane; Wade, Rebecca C.; Mayer, Matthias P.; Wieland, Felix (FEBS Letters, 2020)

Computation of FRAP recovery times for linker histone – chromatin binding on the basis of Brownian dynamics simulations - Öztürk, Mehmet Ali; Wade, Rebecca C. (Biochimica et Biophysica Acta (BBA) - General Subjects, 2020)

SNe Ia from double detonations: Impact of core-shell mixing on the carbon ignition mechanism - Gronow, Sabrina; Collins, Christine; Ohlmann, Sebastian T.; Pakmor, Rüdiger; Kromer, Markus; Seitenzahl, Ivo R.; Sim, Stuart A.; Röpke, Friedrich (Astronomy & Astrophysics, 2020)
Sub-Chandrasekhar mass white dwarfs accreting a helium shell on a carbon-oxygen core are potential progenitors of normal Type Ia supernovae. This work focuses on the details of the onset of the carbon detonation in the double detonation sub-Chandrasekhar model. In order to simulate the influence of core-shell mixing on the carbon ignition mechanism, the helium shell and its detonation are followed with an increased resolution compared to the rest of the star treating the propagation of the detonation wave more accurately. This significantly improves the predictions of the nucleosynthetic yields from the helium burning. The simulations were carried out with the AREPO code. A carbon-oxygen core with a helium shell was set up in one dimension and mapped to three dimensions. We ensured the stability of the white dwarf with a relaxation step before the hydrodynamic detonation simulation started. Synthetic observables were calculated with the radiative transfer code ARTIS. An ignition mechanism of the carbon detonation was observed, which received little attention before. In this "scissors mechanism", the impact the helium detonation wave has on unburnt material when converging opposite to its ignition spot is strong enough to ignite a carbon detonation. This is possible in a carbon enriched transition region between the core and shell. The detonation mechanism is found to be sensitive to details of the core-shell transition and our models illustrate the need to consider core-shell mixing taking place during the accretion process. Even though the detonation ignition mechanism differs form the converging shock mechanism, the differences in the synthetic observables are not significant. Though they do not fit observations better than previous simulations, they illustrate the need for multi-dimensional simulations.

Impact of the Journal of Chemical Information and Modeling Special Issue on Women in Computational Chemistry - Mazzolari, Angelica; Nunes Alves, Ariane; Wahab, Habibah A.; Amaro, Rommie E.; Cournia, Zoe; Merz, Kenneth M. (Journal of Chemical Information and Modeling, 2020)

Recent progress in molecular simulation methods for drug binding kinetics - Nunes Alves, Ariane; Kokh, Daria; Wade, Rebecca C. (Current Opinion in Structural Biology, 2020)

Mechanoradicals in tensed tendon collagen as a source of oxidative stress. - Zapp, C.; Obarska-Kosinska, A.; Rennekamp, B.; Kurth, M.; Hudson, D. M.; Mercadante, D.; Barayeu, U.; Dick, T. P.; Denysenkov, V.; Prisner, T.; Bennati, M.; Daday, C.; et al. (Nat Commun, 2020)
As established nearly a century ago, mechanoradicals originate from homolytic bond scission in polymers. The existence, nature and biological relevance of mechanoradicals in proteins, instead, are unknown. We here show that mechanical stress on collagen produces radicals and subsequently reactive oxygen species, essential biological signaling molecules. Electron-paramagnetic resonance (EPR) spectroscopy of stretched rat tail tendon, atomistic molecular dynamics simulations and quantum-chemical calculations show that the radicals form by bond scission in the direct vicinity of crosslinks in collagen. Radicals migrate to adjacent clusters of aromatic residues and stabilize on oxidized tyrosyl radicals, giving rise to a distinct EPR spectrum consistent with a stable dihydroxyphenylalanine (DOPA) radical. The protein mechanoradicals, as a yet undiscovered source of oxidative stress, finally convert into hydrogen peroxide. Our study suggests collagen I to have evolved as a radical sponge against mechano-oxidative damage and proposes a mechanism for exercise-induced oxidative stress and redox-mediated pathophysiological processes.
Keywords: Animals; Biocompatible Materials/chemistry; Biopolymers/chemistry; Collagen/*chemistry; Dihydroxyphenylalanine/chemistry; Electron Spin Resonance Spectroscopy; Free Radicals/chemistry; Oxidation-Reduction; Oxidative Stress; Rats; Reactive Oxygen Species/chemistry; Tendons/*chemistry

Fully compressible simulations of waves and core convection in main-sequence stars - Horst, Leonhard; Edelmann, P. V. F.; Andrássy, Róbert; Röpke, Friedrich; Bowman, D. M.; Aerts, C.; Ratnasingam, R. P. (Astronomy & Astrophysics, 2020)
Context. Recent, nonlinear simulations of wave generation and propagation in full-star models have been carried out in the anelastic approximation using spectral methods. Although it makes long time steps possible, this approach excludes the physics of sound waves completely and requires rather high artificial viscosity and thermal diffusivity for numerical stability. A direct comparison with observations is thus limited.

Photometric detection of internal gravity waves in upper main-sequence stars - Bowman, D. M.; Burssens, S.; Simón-Díaz, S.; Edelmann, P. V. F.; Rogers, T. M.; Horst, Leonhard; Röpke, Friedrich; Aerts, C. (Astronomy & Astrophysics, 2020)
Context. Massive stars are predicted to excite internal gravity waves (IGWs) by turbulent core convection and from turbulent pressure fluctuations in their near-surface layers. These IGWs are extremely efficient at transporting angular momentum and chemical species within stellar interiors, but they remain largely unconstrained observationally.

A workflow for exploring ligand dissociation from a macromolecule: Efficient random acceleration molecular dynamics simulation and interaction fingerprint analysis of ligand trajectories - Kokh, Daria; Doser, Bernd; Richter, Stefan; Ormersbach, Fabian; Cheng, Xingyi; Wade, Rebecca C. (The Journal of Chemical Physics, 2020)

Myotubularin-related protein 7 activates peroxisome proliferator-activated receptor-gamma - Weidner, Philip; Söhn, Michaela; Schroeder, Torsten; Helm, Laura; Hauber, Veronika; Gutting, Tobias; Betge, Johannes; Röcken, Christoph; Rohrbacher, Florian N.; Pattabiraman, Vijaya R.; Bode, Jeffrey W.; Seger, Rony; et al. (Oncogenesis, 2020)

Centering-based Neural Coherence Modeling with Hierarchical Discourse Segments - Jeon, Sungho; Strube, Michael (2020)

A Fully Hyperbolic Neural Model for Hierarchical Multi-class Classification - López, Federico; Strube, Michael (2020)

pyMMAX2: Deep Access to MMAX2 Projects from Python - Müller, Mark-Christoph (2020)

Reconstructing Manual Information Extraction with DB-to-Document Backprojection: Experiments in the Life Science Domain - Müller, Mark-Christoph; Ghosh, Sucheta; Rey, Maja; Wittig, Ulrike; Müller, Wolfgang; Strube, Michael (2020)

Evaluation of Coreference Resolution Systems Under Adversarial Attacks - Chai, Haixia; Zhao, Wei; Eger, Steffen; Strube, Michael (2020)

SCRAPP : A tool to assess the diversity of microbial samples from phylogenetic placements - Barbera, Pierre; Czech, Lucas; Lutteropp, Sarah; Stamatakis, Alexandros (Molecular Ecology Resources, 2020)

CellPhy: accurate and fast probabilistic inference of single-cell phylogenies from scDNA-seq data - Kozlov, Alexey; Alves, Joao; Stamatakis, Alexandros; Posada, David (2020)

The windblown: possible explanations for dinophyte DNA in forest soils - Gottschling, Marc; Czech, Lucas; Mahé, Frédéric; Adl, Sina; Dunthorn, Micah (2020)

Petabase-scale sequence alignment catalyses viral discovery - Edgar, Robert C.; Taylor, Jeff; Altman, Tomer; Barbera, Pierre; Meleshko, Dmitry; Lin, Victor; Lohr, Dan; Novakovsky, Gherman; Al-Shayeb, Basem; Banfield, Jillian F.; Korobeynikov, Anton; Chikhi, Rayan; et al. (2020)

SoftWipe – a tool and benchmark to assess scientific software quality - Zapletal, Adrian; Höhler, Dimitri; Sinz, Carsten; Stamatakis, Alexandros (2020)

Asteroseismic inference of subgiant evolutionary parameters with deep learning - Hon, Marc; Bellinger, Earl P; Hekker, Saskia; Stello, Dennis; Kuszlewicz, James S (Monthly Notices of the Royal Astronomical Society, 2020)
With the observations of an unprecedented number of oscillating subgiant stars expected from NASA's TESS mission, the asteroseismic characterization of subgiant stars will be a vital task for stellar population studies and for testing our theories of stellar evolution. To determine the fundamental properties of a large sample of subgiant stars efficiently, we developed a deep learning method that estimates distributions of fundamental parameters like age and mass over a wide range of input physics by learning from a grid of stellar models varied in eight physical parameters. We applied our method to four Kepler subgiant stars and compare our results with previously determined estimates. Our results show good agreement with previous estimates for three of them (KIC 11026764, KIC 10920273, KIC 11395018). With the ability to explore a vast range of stellar parameters, we determine that the remaining star, KIC 10005473, is likely to have an age 1 Gyr younger than its previously determined estimate. Our method also estimates the efficiency of overshooting, undershooting, and microscopic diffusion processes, from which we determined that the parameters governing such processes are generally poorly constrained in subgiant models. We further demonstrate our method's utility for ensemble asteroseismology by characterizing a sample of 30 Kepler subgiant stars, where we find a majority of our age, mass, and radius estimates agree within uncertainties from more computationally expensive grid-based modelling techniques.

A Layered Approach to Robust Determination of Asteroseismic Parameters - Elsworth, Yvonne; Themeßl, Nathalie; Hekker, Saskia; Chaplin, William (Research Notes of the AAS, 2020)
We describe here a layered approach to the robust determination of the broad characteristics of the asteroseismic signal from red-giant stars. No single stringent test can exclude all false results. The use of multiple, weak tests not only provides robust results but also avoids over-constraining the parameter space.

Incremental Neural Lexical Coherence Modeling - Jeon, Sungho; Strube, Michael (2020)
Pretrained language models, neural models pretrained on massive amounts of data, have established the state of the art in a range of NLP tasks. They are based on a modern machine-learning technique, the Transformer which relates all items simultaneously to capture semantic relations in sequences. However, it differs from what humans do. Humans read sentences one-by-one, incrementally. Can neural models benefit by interpreting texts incrementally as humans do? We investigate this question in coherence modeling. We propose a coherence model which interprets sentences incrementally to capture lexical relations between them. We compare the state of the art in each task, simple neural models relying on a pretrained language model, and our model in two downstream tasks. Our findings suggest that interpreting texts incrementally as humans could be useful to design more advanced models.

Phylogenetic analysis of SARS-CoV-2 data is difficult - Morel, Benoit; Barbera, Pierre; Czech, Lucas; Bettisworth, Ben; Hübner, Lukas; Lutteropp, Sarah; Serdari, Dora; Kostaki, Evangelia-Georgia; Mamais, Ioannis; Kozlov, Alexey; Pavlidis, Pavlos; Paraskevis, Dimitrios; et al. (Molecular Biology and Evolution, 2020)

Photoreceptor diversification accompanies the evolution of Anthozoa - Gornik, Sebastian G; Bergheim, B Gideon; Morel, Benoit; Stamatakis, Alexandros; Foulkes, Nicholas S; Guse, Annika (Molecular Biology and Evolution, 2020)

RASPD+: Fast Protein-Ligand Binding Free Energy Prediction Using Simplified Physicochemical Features - Holderbach, Stefan; Adam, Lukas; Jayaram, B.; Wade, Rebecca C.; Mukherjee, Goutam (Frontiers in Molecular Biosciences, 2020)
The virtual screening of large numbers of compounds against target protein binding sites has become an integral component of drug discovery workflows. This screening is often done by computationally docking ligands into a protein binding site of interest, but this has the drawback of a large number of poses that must be evaluated to obtain accurate estimates of protein-ligand binding affinity. We here introduce a fast pre-filtering method for ligand prioritization that is based on a set of machine learning models and uses simple pose-invariant physicochemical descriptors of the ligands and the protein binding pocket. Our method, Rapid Screening with Physicochemical Descriptors + machine learning (RASPD+), is trained on PDBbind data and achieves a regression performance that is better than that of the original RASPD method and traditional scoring functions on a range of different test sets without the need for generating ligand poses. Additionally, we use RASPD+ to identify molecular features important for binding affinity and assess the ability of RASPD+ to enrich active molecules from decoys.

A fast and memory-efficient implementation of the transfer bootstrap - Lutteropp, Sarah; Kozlov, Alexey; Stamatakis, Alexandros (Bioinformatics, 2020)
Motivation

What Makes a Paper Be Highly Cited? 60 Years of the Journal of Chemical Information and Modeling - Nunes Alves, Ariane; Mazzolari, Angelica; Merz, Kenneth M. (Journal of Chemical Information and Modeling, 2020)

Molecular Dynamics Simulations in Drug Discovery and Pharmaceutical Development - Salo-Ahen, Outi M. H.; Alanko, Ida; Bhadane, Rajendra; Bonvin, Alexandre M. J. J.; Honorato, Rodrigo Vargas; Hossain, Shakhawath; Juffer, André H.; Kabedev, Aleksei; Lahtela-Kakkonen, Maija; Larsen, Anders Støttrup; Lescrinier, Eveline; Marimuthu, Parthiban; et al. (Processes, 2021)

Stellar mergers as the origin of magnetic massive stars - Schneider, Fabian; Ohlmann, Sebastian T.; Podsiadlowski, Philipp; Röpke, Friedrich; Balbus, Steven A.; Pakmor, Rüdiger; Springel, Volker (Nature, 2019)

Cataloguing the radio-sky with unsupervised machine learning: a new approach for the SKA era - Galvin, T J; Huynh, M T; Norris, R P; Wang, X R; Hopkins, Erica; Polsterer, Kai; Ralph, N O; O’Brien, A N; Heald, G H (Monthly Notices of the Royal Astronomical Society, 2020)

An electron transfer competent structural ensemble of membrane-bound cytochrome P450 1A1 and cytochrome P450 oxidoreductase - Mukherjee, Goutam; Nandekar, Prajwal P.; Wade, Rebecca C. (Communications Biology, 2021)
Abstract Cytochrome P450 (CYP) heme monooxygenases require two electrons for their catalytic cycle. For mammalian microsomal CYPs, key enzymes for xenobiotic metabolism and steroidogenesis and important drug targets and biocatalysts, the electrons are transferred by NADPH-cytochrome P450 oxidoreductase (CPR). No structure of a mammalian CYP–CPR complex has been solved experimentally, hindering understanding of the determinants of electron transfer (ET), which is often rate-limiting for CYP reactions. Here, we investigated the interactions between membrane-bound CYP 1A1, an antitumor drug target, and CPR by a multiresolution computational approach. We find that upon binding to CPR, the CYP 1A1 catalytic domain becomes less embedded in the membrane and reorients, indicating that CPR may affect ligand passage to the CYP active site. Despite the constraints imposed by membrane binding, we identify several arrangements of CPR around CYP 1A1 that are compatible with ET. In the complexes, the interactions of the CPR FMN domain with the proximal side of CYP 1A1 are supplemented by more transient interactions of the CPR NADP domain with the distal side of CYP 1A1. Computed ET rates and pathways agree well with available experimental data and suggest why the CYP–CPR ET rates are low compared to those of soluble bacterial CYPs.

Computerwissenschaften und The Circle -- The Circle und Computerwissenschaften - Strube, Michael (2021)

Structure-Kinetic-Relationship Reveals the Mechanism of Selectivity of FAK Inhibitors Over PYK2 - Berger, Benedict-Tilman; Amaral, Marta; Kokh, Daria; Nunes Alves, Ariane; Musil, Djordje; Heinrich, Timo; Schröder, Martin; Neil, Rebecca; Wang, Jing; Navratilova, Iva; Bomke, Joerg; Elkins, Jonathan M.; et al. (SSRN Electronic Journal, 2020)

Use of a quantitative data report in a hypothetical decision scenario for health policymaking: a computer-assisted laboratory study - Wronski, Pamela; Wensing, Michel; Ghosh, Sucheta; Gärttner, Lukas; Müller, Wolfgang; Koetsenruijter, Jan (BMC Medical Informatics and Decision Making, 2021)
Background: Quantitative data reports are widely produced to inform health policy decisions. Policymakers are expected to critically assess provided information in order to incorporate the best available evidence into the decision-making process. Many other factors are known to influence this process, but little is known about how quantitative data reports are actually read. We explored the reading behavior of (future) health policy decision-makers, using innovative methods. Methods: We conducted a computer-assisted laboratory study, involving starting and advanced students in medicine and health sciences, and professionals as participants. They read a quantitative data report to inform a decision on the use of resources for long-term care in dementia in a hypothetical decision scenario. Data were collected through eye-tracking, questionnaires, and a brief interview. Eye-tracking data were used to generate ‘heatmaps’ and five measures of reading behavior. The questionnaires provided participants’ perceptions of understandability and helpfulness as well as individual characteristics. Interviews documented reasons for attention to specific report sections. The quantitative analysis was largely descriptive, complemented by Pearson correlations. Interviews were analyzed by qualitative content analysis. Results: In total, 46 individuals participated [students (85%), professionals (15%)]. Eye-tracking observations showed that the participants spent equal time and attention for most parts of the presented report, but were less focused when reading the methods section. The qualitative content analysis identified 29 reasons for attention to a report section related to four topics. Eye-tracking measures were largely unrelated to participants’ perceptions of understandability and helpfulness of the report. Conclusions: Eye-tracking data added information on reading behaviors that were not captured by questionnaires or interviews with health decision-makers.

Polluting the Pair-instability Mass Gap for Binary Black Holes through Super-Eddington Accretion in Isolated Binaries - van Son, L. A. C.; De Mink, S. E.; Broekgaarden, F. S.; Renzo, M.; Justham, S.; Laplace, E.; Moran Fraile, Javier; Hendriks, D. D.; Farmer, R. (The Astrophysical Journal, 2020)
The theory for single stellar evolution predicts a gap in the mass distribution of black holes (BHs) between approximately 45 and 130 $\,M_{\odot }$, the so-called "pair-instability mass gap." We examine whether BHs can pollute the gap after accreting from a stellar companion. To this end, we simulate the evolution of isolated binaries using a population synthesis code, where we allow for super-Eddington accretion. Under our most extreme assumptions, we find that at most about 2% of all merging binary BH systems contains a BH with a mass in the pair-instability mass gap, and we find that less than 0.5% of the merging systems has a total mass larger than 90 $\,M_{\odot }$. We find no merging binary BH systems with a total mass exceeding 100 $\,M_{\odot }$. We compare our results to predictions from several dynamical pathways to pair-instability mass gap events and discuss the distinguishable features. We conclude that the classical isolated binary formation scenario will not significantly contribute to the pollution of the pair-instability mass gap. The robustness of the predicted mass gap for the isolated binary channel is promising for the prospective of placing constraints on (i) the relative contribution of different formation channels, (ii) the physics of the progenitors including nuclear reaction rates, and, tentatively, (iii) the Hubble parameter.

Constraining the onset density of the hadron-quark phase transition with gravitational-wave observations - Blacker, Sebastian; Bastian, Niels-Uwe F.; Bauswein, Andreas; Blaschke, David B.; Fischer, Tobias; Oertel, Micaela; Soultanis, Theodoros; Typel, Stefan (Phys. Rev. D, 2020)

The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE) - Waltemath, Dagmar; Golebiewski, Martin; Blinov, Michael L; Gleeson, Padraig; Hermjakob, Henning; Hucka, Michael; Inau, Esther Thea; Keating, Sarah M; König, Matthias; Krebs, Olga; Malik-Sheriff, Rahuman S; Nickerson, David; et al. (Journal of Integrative Bioinformatics, 2020)
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

Data management and data enrichment for systems biology projects - Wittig, Ulrike; Rey, Maja; Weidemann, Andreas; Müller, Wolfgang (Journal of Biotechnology, 2017)

SBML Level 3: an extensible format for the exchange and reuse of biological models - Keating, Sarah M; Waltemath, Dagmar; König, Matthias; Zhang, Fengkai; Dräger, Andreas; Chaouiya, Claudine; Bergmann, Frank T; Finney, Andrew; Gillespie, Colin S; Helikar, Tomáš; Hoops, Stefan; Malik‐Sheriff, Rahuman S; et al. (Molecular Systems Biology, 2020)

Pre-supernova evolution, compact-object masses, and explosion properties of stripped binary stars - Schneider, Fabian; Podsiadlowski, Ph.; Müller, B. (Astronomy and Astrophysics, 2021)

The R136 star cluster dissected with Hubble Space Telescope/STIS - II. Physical properties of the most massive stars in R136 - Bestenlehner, Joachim M.; Crowther, Paul A.; Caballero-Nieves, Saida M.; Schneider, Fabian; Simón-Dı́az, Sergio; Brands, Sarah A.; de Koter, Alex; Gräfener, Götz; Herrero, Artemio; Langer, Norbert; Lennon, Daniel J.; Maı́z Apellániz, Jesus; et al. (Monthly Notices of the Royal Astronomical Society, 2020)

Common-envelope evolution with an asymptotic giant branch star - Sand, Christian; Ohlmann, Sebastian T.; Schneider, Fabian; Pakmor, Rüdiger; Röpke, Friedrich (Astronomy and Astrophysics, 2020)

Formation of sdB-stars via common envelope ejection by substellar companions - Kramer, Manuel; Schneider, Fabian; Ohlmann, S. T.; Geier, S.; Schaffenroth, V.; Pakmor, R.; Röpke, Friedrich (Astronomy and Astrophysics, 2020)

The VLT-FLAMES Tarantula Survey - Evans, C.; Lennon, D.; Langer, N.; Almeida, L.; Bartlett, E.; Bastian, N.; Bestenlehner, J.; Britavskiy, N.; Castro, N.; Clark, S.; Crowther, P.; de Koter, A.; et al. (The Messenger, 2020)

The Art of Modeling Stellar Mergers and the Case of the B[e] Supergiant R4 in the Small Magellanic Cloud - Wu, Samantha; Everson, Rosa Wallace; Schneider, Fabian; Podsiadlowski, Philipp; Ramirez-Ruiz, Enrico (The Astrophysical Journal, 2020)

Long-term evolution of a magnetic massive merger product - Schneider, Fabian; Ohlmann, S. T.; Podsiadlowski, Ph; Röpke, Friedrich; Balbus, S. A.; Pakmor, R. (Monthly Notices of the Royal Astronomical Society, 2020)

Properties of OB star-black hole systems derived from detailed binary evolution models - Langer, N.; Schürmann, C.; Stoll, K.; Marchant, P.; Lennon, D. J.; Mahy, L.; de Mink, S. E.; Quast, M.; Riedel, W.; Sana, H.; Schneider, P.; Schootemeijer, A.; et al. (Astronomy and Astrophysics, 2020)

The Tarantula Massive Binary Monitoring. IV. Double-lined photometric binaries - Mahy, L.; Almeida, L. A.; Sana, H.; Clark, J. S.; de Koter, A.; de Mink, S. E.; Evans, C. J.; Grin, N. J.; Langer, N.; Moffat, A. F. J.; Schneider, Fabian; Shenar, T.; et al. (Astronomy and Astrophysics, 2020)

The Tarantula Massive Binary Monitoring. III. Atmosphere analysis of double-lined spectroscopic systems - Mahy, L.; Sana, H.; Abdul-Masih, M.; Almeida, L. A.; Langer, N.; Shenar, T.; de Koter, A.; de Mink, S. E.; de Wit, S.; Grin, N. J.; Evans, C. J.; Moffat, A. F. J.; et al. (Astronomy and Astrophysics, 2020)

The young massive SMC cluster NGC 330 seen by MUSE. I. Observations and stellar content - Bodensteiner, J.; Sana, H.; Mahy, L.; Patrick, L. R.; de Koter, A.; de Mink, S. E.; Evans, C. J.; Götberg, Y.; Langer, N.; Lennon, D. J.; Schneider, Fabian; Tramper, F. (Astronomy and Astrophysics, 2020)

How Do Stars Form? Open Questions on the Stellar Initial Mass Function - Calzetti, Daniela; Bastian, Nate; Conroy, Charlie; Elmegreen, Bruce G.; Gallagher, John S.; Krumholz, Mark; de Mink, Selma E.; Offner, Stella S.; Sabbi, Elena; Schneider, Fabian; Wofford, Aida; Wyse, Rosemary F. G. (Bulletin of the American Astronomical Society, 2019)

The shared frameshift mutation landscape of microsatellite-unstable cancers suggests immunoediting during tumor evolution - Ballhausen, Alexej; Przybilla, Moritz Jakob; Jendrusch, Michael; Haupt, Saskia; Pfaffendorf, Elisabeth; Seidler, Florian; Witt, Johannes; Hernandez Sanchez, Alejandro; Urban, Katharina; Draxlbauer, Markus; Krausert, Sonja; Ahadova, Aysel; et al. (Nature Communications, 2020)

Age‐dependent performance of - Bläker, Hendrik; Haupt, Saskia; Morak, Monika; Holinski‐Feder, Elke; Arnold, Alexander; Horst, David; Sieber‐Frank, Julia; Seidler, Florian; Winterfeld, Moritz; Alwers, Elizabeth; Chang‐Claude, Jenny; Brenner, Hermann; et al. (2020)

New technical approaches for 3D morphological imaging and quantification of measurements - Brenna, Cinzia; Khan, Arif ul Maula; Picascia, Tiziana; Sun, Quanchao; Heuveline, Vincent; Gretz, Norbert (The Anatomical Record, 2020)

SYCL-Bench: A Versatile Cross-Platform Benchmark Suite for Heterogeneous Computing - Lal, Sohan; Alpay, Aksel; Salzmann, Philip; Cosenza, Biagio; Hirsch, Alexander; Stawinoga, Nicolai; Thoman, Peter; Fahringer, Thomas; Heuveline, Vincent (Euro-Par 2020: Parallel Processing, 2020)

Analysis and Numerical Approximation of Dielectrophoretic Force Driven Flow Problems - Gerstner, Philipp (2020)

New Time Step Strategy for Multi-period Optimal Power Flow Problems - Schween, Nils; Gerstner, Philipp; Meyer-Hübner, Nico; Heuveline, Vincent (Mathematical Modeling, Simulation and Optimization for Power Engineering and Management, 2021)