@article{7512,
  abstract     = {We consider general self-adjoint polynomials in several independent random matrices whose entries are centered and have the same variance. We show that under certain conditions the local law holds up to the optimal scale, i.e., the eigenvalue density on scales just above the eigenvalue spacing follows the global density of states which is determined by free probability theory. We prove that these conditions hold for general homogeneous polynomials of degree two and for symmetrized products of independent matrices with i.i.d. entries, thus establishing the optimal bulk local law for these classes of ensembles. In particular, we generalize a similar result of Anderson for anticommutator. For more general polynomials our conditions are effectively checkable numerically.},
  author       = {Erdös, László and Krüger, Torben H and Nemish, Yuriy},
  issn         = {1096-0783},
  journal      = {Journal of Functional Analysis},
  number       = {12},
  publisher    = {Elsevier},
  title        = {{Local laws for polynomials of Wigner matrices}},
  doi          = {10.1016/j.jfa.2020.108507},
  volume       = {278},
  year         = {2020},
}

@phdthesis{7514,
  abstract     = {We study the interacting homogeneous Bose gas in two spatial dimensions in the thermodynamic limit at fixed density. We shall be concerned with some mathematical aspects of this complicated problem in many-body quantum mechanics. More specifically, we consider the dilute limit where the scattering length of the interaction potential, which is a measure for the effective range of the potential, is small compared to the average distance between the particles. We are interested in a setting with positive (i.e., non-zero) temperature. After giving a survey of the relevant literature in the field, we provide some facts and examples to set expectations for the two-dimensional system. The crucial difference to the three-dimensional system is that there is no Bose–Einstein condensate at positive temperature due to the Hohenberg–Mermin–Wagner theorem. However, it turns out that an asymptotic formula for the free energy holds similarly to the three-dimensional case.
We motivate this formula by considering a toy model with δ interaction potential. By restricting this model Hamiltonian to certain trial states with a quasi-condensate we obtain an upper bound for the free energy that still has the quasi-condensate fraction as a free parameter. When minimizing over the quasi-condensate fraction, we obtain the Berezinskii–Kosterlitz–Thouless critical temperature for superfluidity, which plays an important role in our rigorous contribution. The mathematically rigorous result that we prove concerns the specific free energy in the dilute limit. We give upper and lower bounds on the free energy in terms of the free energy of the non-interacting system and a correction term coming from the interaction. Both bounds match and thus we obtain the leading term of an asymptotic approximation in the dilute limit, provided the thermal wavelength of the particles is of the same order (or larger) than the average distance between the particles. The remarkable feature of this result is its generality: the correction term depends on the interaction potential only through its scattering length and it holds for all nonnegative interaction potentials with finite scattering length that are measurable. In particular, this allows to model an interaction of hard disks.},
  author       = {Mayer, Simon},
  issn         = {2663-337X},
  pages        = {148},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{The free energy of a dilute two-dimensional Bose gas}},
  doi          = {10.15479/AT:ISTA:7514},
  year         = {2020},
}

@article{7534,
  abstract     = {In the past two decades, our understanding of the transition to turbulence in shear flows with linearly stable laminar solutions has greatly improved. Regarding the susceptibility of the laminar flow, two concepts have been particularly useful: the edge states and the minimal seeds. In this nonlinear picture of the transition, the basin boundary of turbulence is set by the edge state's stable manifold and this manifold comes closest in energy to the laminar equilibrium at the minimal seed. We begin this paper by presenting numerical experiments in which three-dimensional perturbations are too energetic to trigger turbulence in pipe flow but they do lead to turbulence when their amplitude is reduced. We show that this seemingly counterintuitive observation is in fact consistent with the fully nonlinear description of the transition mediated by the edge state. In order to understand the physical mechanisms behind this process, we measure the turbulent kinetic energy production and dissipation rates as a function of the radial coordinate. Our main observation is that the transition to turbulence relies on the energy amplification away from the wall, as opposed to the turbulence itself, whose energy is predominantly produced near the wall. This observation is further supported by the similar analyses on the minimal seeds and the edge states. Furthermore, we show that the time evolution of production-over-dissipation curves provides a clear distinction between the different initial amplification stages of the transition to turbulence from the minimal seed.},
  author       = {Budanur, Nazmi B and Marensi, Elena and Willis, Ashley P. and Hof, Björn},
  issn         = {2469-990X},
  journal      = {Physical Review Fluids},
  number       = {2},
  publisher    = {American Physical Society},
  title        = {{Upper edge of chaos and the energetics of transition in pipe flow}},
  doi          = {10.1103/physrevfluids.5.023903},
  volume       = {5},
  year         = {2020},
}

@article{7540,
  abstract     = { In vitro propagation of the ornamentally interesting species Wikstroemia gemmata is limited by the recalcitrance to form adventitious roots. In this article, two strategies to improve the rooting capacity of in vitro microcuttings are presented. Firstly, the effect of exogenous auxin was evaluated in both light and dark cultivated stem segments and also the sucrose-content of the medium was varied in order to determine better rooting conditions. Secondly, different spectral lights were evaluated and the effect on shoot growth and root induction demonstrated that the exact spectral composition of light is important for successful in vitro growth and development of Wikstroemia gemmata. We show that exogenous auxin cannot compensate for the poor rooting under unfavorable light conditions. Adapting the culture conditions is therefore paramount for successful industrial propagation of Wikstroemia gemmata. },
  author       = {Verstraeten, Inge and Buyle, H. and Werbrouck, S. and Van Labeke, M.C. and Geelen, D.},
  issn         = {2223-8980},
  journal      = {Israel Journal of Plant Sciences},
  number       = {1-2},
  pages        = {16--26},
  publisher    = {Brill},
  title        = {{In vitro shoot growth and adventitious rooting of Wikstroemia gemmata depends on light quality}},
  doi          = {10.1163/22238980-20191110},
  volume       = {67},
  year         = {2020},
}

@article{7541,
  abstract     = {Semiconductor nanowires have been playing a crucial role in the development of nanoscale devices for the realization of spin qubits, Majorana fermions, single photon emitters, nanoprocessors, etc. The monolithic growth of site‐controlled nanowires is a prerequisite toward the next generation of devices that will require addressability and scalability. Here, combining top‐down nanofabrication and bottom‐up self‐assembly, the growth of Ge wires on prepatterned Si (001) substrates with controllable position, distance, length, and structure is reported. This is achieved by a novel growth process that uses a SiGe strain‐relaxation template and can be potentially generalized to other material combinations. Transport measurements show an electrically tunable spin–orbit coupling, with a spin–orbit length similar to that of III–V materials. Also, charge sensing between quantum dots in closely spaced wires is observed, which underlines their potential for the realization of advanced quantum devices. The reported results open a path toward scalable qubit devices using nanowires on silicon.},
  author       = {Gao, Fei and Wang, Jian-Huan and Watzinger, Hannes and Hu, Hao and Rančić, Marko J. and Zhang, Jie-Yin and Wang, Ting and Yao, Yuan and Wang, Gui-Lei and Kukucka, Josip and Vukušić, Lada and Kloeffel, Christoph and Loss, Daniel and Liu, Feng and Katsaros, Georgios and Zhang, Jian-Jun},
  issn         = {0935-9648},
  journal      = {Advanced Materials},
  number       = {16},
  publisher    = {Wiley},
  title        = {{Site-controlled uniform Ge/Si hut wires with electrically tunable spin-orbit coupling}},
  doi          = {10.1002/adma.201906523},
  volume       = {32},
  year         = {2020},
}

@article{7546,
  abstract     = {The extent to which behavior is shaped by experience varies between individuals. Genetic differences contribute to this variation, but the neural mechanisms are not understood. Here, we dissect natural variation in the behavioral flexibility of two Caenorhabditis elegans wild strains. In one strain, a memory of exposure to 21% O2 suppresses CO2-evoked locomotory arousal; in the other, CO2 evokes arousal regardless of previous O2 experience. We map that variation to a polymorphic dendritic scaffold protein, ARCP-1, expressed in sensory neurons. ARCP-1 binds the Ca2+-dependent phosphodiesterase PDE-1 and co-localizes PDE-1 with molecular sensors for CO2 at dendritic ends. Reducing ARCP-1 or PDE-1 activity promotes CO2 escape by altering neuropeptide expression in the BAG CO2 sensors. Variation in ARCP-1 alters behavioral plasticity in multiple paradigms. Our findings are reminiscent of genetic accommodation, an evolutionary process by which phenotypic flexibility in response to environmental variation is reset by genetic change.},
  author       = {Beets, Isabel and Zhang, Gaotian and Fenk, Lorenz A. and Chen, Changchun and Nelson, Geoffrey M. and Félix, Marie-Anne and de Bono, Mario},
  issn         = {0896-6273},
  journal      = {Neuron},
  number       = {1},
  pages        = {106--121.e10},
  publisher    = {Cell Press},
  title        = {{Natural variation in a dendritic scaffold protein remodels experience-dependent plasticity by altering neuropeptide expression}},
  doi          = {10.1016/j.neuron.2019.10.001},
  volume       = {105},
  year         = {2020},
}

@article{7554,
  abstract     = {Slicing a Voronoi tessellation in ${R}^n$ with a $k$-plane gives a $k$-dimensional weighted Voronoi tessellation, also known as a power diagram or Laguerre tessellation. Mapping every simplex of the dual weighted Delaunay mosaic to the radius of the smallest empty circumscribed sphere whose center lies in the $k$-plane gives a generalized discrete Morse function. Assuming the Voronoi tessellation is generated by a Poisson point process in ${R}^n$, we study the expected number of simplices in the $k$-dimensional weighted Delaunay mosaic as well as the expected number of intervals of the Morse function, both as functions of a radius threshold. As a by-product, we obtain a new proof for the expected number of connected components (clumps) in a line section of a circular Boolean model in ${R}^n$.},
  author       = {Edelsbrunner, Herbert and Nikitenko, Anton},
  issn         = {1095-7219},
  journal      = {Theory of Probability and its Applications},
  number       = {4},
  pages        = {595--614},
  publisher    = {SIAM},
  title        = {{Weighted Poisson–Delaunay mosaics}},
  doi          = {10.1137/S0040585X97T989726},
  volume       = {64},
  year         = {2020},
}

@misc{9878,
  author       = {Gupta, Chitrak and Khaniya, Umesh and Chan, Chun Kit and Dehez, Francois and Shekhar, Mrinal and Gunner, M.R. and Sazanov, Leonid A and Chipot, Christophe and Singharoy, Abhishek},
  publisher    = {American Chemical Society},
  title        = {{Movies}},
  doi          = {10.1021/jacs.9b13450.s002},
  year         = {2020},
}

@misc{17444,
  abstract     = {The first wafer-scale growth of site-controlled Ge/Si nanowires is reported by Georgios Katsaros, Jian-Jun Zhang, and co-workers in article number 1906523. They are highly uniform and their position, distance, length, and even square- or L-shaped structures can all be precisely controlled. The electrically tunable spin-orbit coupling demonstrated by transport measurements and the charge sensing between quantum dots in closely spaced wires open a path toward scalable qubit devices using nanowires on silicon.},
  author       = {Gao, Fei and Wang, Jian‐Huan and Watzinger, Hannes and Hu, Hao and Rančić, Marko J. and Zhang, Jie‐Yin and Wang, Ting and Yao, Yuan and Wang, Gui‐Lei and Kukucka, Josip and Vukušić, Lada and Kloeffel, Christoph and Loss, Daniel and Liu, Feng and Katsaros, Georgios and Zhang, Jian‐Jun},
  booktitle    = {Advanced Materials},
  issn         = {1521-4095},
  number       = {16},
  publisher    = {Wiley},
  title        = {{Nanowires: Site‐controlled uniform Ge/Si Hut wires with electrically tunable spin–orbit coupling (Adv. Mater. 16/2020)}},
  doi          = {10.1002/adma.202070122},
  volume       = {32},
  year         = {2020},
}

@article{15079,
  abstract     = {Large complex systems tend to develop universal patterns that often represent their essential characteristics. For example, the cumulative effects of independent or weakly dependent random variables often yield the Gaussian universality class via the central limit theorem. For non-commutative random variables, e.g. matrices, the Gaussian behavior is often replaced by another universality class, commonly called random matrix statistics. Nearby eigenvalues are strongly correlated, and, remarkably, their correlation structure is universal, depending only on the symmetry type of the matrix. Even more surprisingly, this feature is not restricted to matrices; in fact Eugene Wigner, the pioneer of the field, discovered in the 1950s that distributions of the gaps between energy levels of complicated quantum systems universally follow the same random matrix statistics. This claim has never been rigorously proved for any realistic physical system but experimental data and extensive numerics leave no doubt as to its correctness. Since then random matrices have proved to be extremely useful phenomenological models in a wide range of applications beyond quantum physics that include number theory, statistics, neuroscience, population dynamics, wireless communication and mathematical finance. The ubiquity of random matrices in natural sciences is still a mystery, but recent years have witnessed a breakthrough in the mathematical description of the statistical structure of their spectrum. Random matrices and closely related areas such as log-gases have become an extremely active research area in probability theory.
This workshop brought together outstanding researchers from a variety of mathematical backgrounds whose areas of research are linked to random matrices. While there are strong links between their motivations, the techniques used by these researchers span a large swath of mathematics, ranging from purely algebraic techniques to stochastic analysis, classical probability theory, operator algebra, supersymmetry, orthogonal polynomials, etc.},
  author       = {Erdös, László and Götze, Friedrich and Guionnet, Alice},
  issn         = {1660-8933},
  journal      = {Oberwolfach Reports},
  number       = {4},
  pages        = {3459--3527},
  publisher    = {EMS Press},
  title        = {{Random matrices}},
  doi          = {10.4171/owr/2019/56},
  volume       = {16},
  year         = {2020},
}

@article{8042,
  abstract     = {We consider systems of N bosons in a box of volume one, interacting through a repulsive two-body potential of the form κN3β−1V(Nβx). For all 0<β<1, and for sufficiently small coupling constant κ>0, we establish the validity of Bogolyubov theory, identifying the ground state energy and the low-lying excitation spectrum up to errors that vanish in the limit of large N.},
  author       = {Boccato, Chiara and Brennecke, Christian and Cenatiempo, Serena and Schlein, Benjamin},
  issn         = {1435-9855},
  journal      = {Journal of the European Mathematical Society},
  number       = {7},
  pages        = {2331--2403},
  publisher    = {EMS Press},
  title        = {{The excitation spectrum of Bose gases interacting through singular potentials}},
  doi          = {10.4171/JEMS/966},
  volume       = {22},
  year         = {2020},
}

@article{9007,
  abstract     = {Motivated by a recent question of Peyre, we apply the Hardy–Littlewood circle method to count “sufficiently free” rational points of bounded height on arbitrary smooth projective hypersurfaces of low degree that are defined over the rationals.},
  author       = {Browning, Timothy D and Sawin, Will},
  issn         = {1420-8946},
  journal      = {Commentarii Mathematici Helvetici},
  number       = {4},
  pages        = {635--659},
  publisher    = {EMS Press},
  title        = {{Free rational points on smooth hypersurfaces}},
  doi          = {10.4171/CMH/499},
  volume       = {95},
  year         = {2020},
}

@article{15070,
  abstract     = {This workshop focused on interactions between the various perspectives on the moduli space of Higgs bundles over a Riemann surface. This subject draws on algebraic geometry, geometric topology, geometric analysis and mathematical physics, and the goal was to promote interactions between these various branches of the subject. The main current directions of research were well represented by the participants, and the talks included many from both senior and junior participants.},
  author       = {Anderson, Lara and Hausel, Tamás and Mazzeo, Rafe and Schaposnik, Laura},
  issn         = {1660-8933},
  journal      = {Oberwolfach Reports},
  keywords     = {Organic Chemistry, Biochemistry},
  number       = {2},
  pages        = {1357--1417},
  publisher    = {EMS Press},
  title        = {{Geometry and physics of Higgs bundles}},
  doi          = {10.4171/owr/2019/23},
  volume       = {16},
  year         = {2020},
}

@article{15072,
  abstract     = {The interaction among fundamental particles in nature leads to many interesting effects in quantum statistical mechanics; examples include superconductivity for charged systems and superfluidity in cold gases. It is a huge challenge for mathematical physics to understand the collective behavior of systems containing a large number of particles, emerging from known microscopic interactions. In this workshop we brought together researchers working on different aspects of many-body quantum mechanics to discuss recent developments, exchange ideas and propose new challenges and research directions.},
  author       = {Hainzl, Christian and Schlein, Benjamin and Seiringer, Robert and Warzel, Simone},
  issn         = {1660-8933},
  journal      = {Oberwolfach Reports},
  number       = {3},
  pages        = {2541--2603},
  publisher    = {EMS Press},
  title        = {{Many-body quantum systems}},
  doi          = {10.4171/owr/2019/41},
  volume       = {16},
  year         = {2020},
}

@article{8973,
  abstract     = {We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity.},
  author       = {Redig, Frank and Saada, Ellen and Sau, Federico},
  issn         = {1083-6489},
  journal      = {Electronic Journal of Probability},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Symmetric simple exclusion process in dynamic environment: Hydrodynamics}},
  doi          = {10.1214/20-EJP536},
  volume       = {25},
  year         = {2020},
}

@article{8040,
  abstract     = {The mitochondrial respiratory chain, formed by five protein complexes, utilizes energy from catabolic processes to synthesize ATP. Complex I, the first and the largest protein complex of the chain, harvests electrons from NADH to reduce quinone, while pumping protons across the mitochondrial membrane. Detailed knowledge of the working principle of such coupled charge-transfer processes remains, however, fragmentary due to bottlenecks in understanding redox-driven conformational transitions and their interplay with the hydrated proton pathways. Complex I from Thermus thermophilus encases 16 subunits with nine iron–sulfur clusters, reduced by electrons from NADH. Here, employing the latest crystal structure of T. thermophilus complex I, we have used microsecond-scale molecular dynamics simulations to study the chemo-mechanical coupling between redox changes of the iron–sulfur clusters and conformational transitions across complex I. First, we identify the redox switches within complex I, which allosterically couple the dynamics of the quinone binding pocket to the site of NADH reduction. Second, our free-energy calculations reveal that the affinity of the quinone, specifically menaquinone, for the binding-site is higher than that of its reduced, menaquinol form—a design essential for menaquinol release. Remarkably, the barriers to diffusive menaquinone dynamics are lesser than that of the more ubiquitous ubiquinone, and the naphthoquinone headgroup of the former furnishes stronger binding interactions with the pocket, favoring menaquinone for charge transport in T. thermophilus. Our computations are consistent with experimentally validated mutations and hierarchize the key residues into three functional classes, identifying new mutation targets. Third, long-range hydrogen-bond networks connecting the quinone-binding site to the transmembrane subunits are found to be responsible for proton pumping. Put together, the simulations reveal the molecular design principles linking redox reactions to quinone turnover to proton translocation in complex I.},
  author       = {Gupta, Chitrak and Khaniya, Umesh and Chan, Chun Kit and Dehez, Francois and Shekhar, Mrinal and Gunner, M. R. and Sazanov, Leonid A and Chipot, Christophe and Singharoy, Abhishek},
  issn         = {1520-5126},
  journal      = {Journal of the American Chemical Society},
  number       = {20},
  pages        = {9220--9230},
  publisher    = {American Chemical Society},
  title        = {{Charge transfer and chemo-mechanical coupling in respiratory complex I}},
  doi          = {10.1021/jacs.9b13450},
  volume       = {142},
  year         = {2020},
}

@article{7166,
  abstract     = {In the living cell, we encounter a large variety of motile processes such as organelle transport and cytoskeleton remodeling. These processes are driven by motor proteins that generate force by transducing chemical free energy into mechanical work. In many cases, the molecular motors work in teams to collectively generate larger forces. Recent optical trapping experiments on small teams of cytoskeletal motors indicated that the collectively generated force increases with the size of the motor team but that this increase depends on the motor type and on whether the motors are studied in vitro or in vivo. Here, we use the theory of stochastic processes to describe the motion of N motors in a stationary optical trap and to compute the N-dependence of the collectively generated forces. We consider six distinct motor types, two kinesins, two dyneins, and two myosins. We show that the force increases always linearly with N but with a prefactor that depends on the performance of the single motor. Surprisingly, this prefactor increases for weaker motors with a lower stall force. This counter-intuitive behavior reflects the increased probability with which stronger motors detach from the filament during strain generation. Our theoretical results are in quantitative agreement with experimental data on small teams of kinesin-1 motors.},
  author       = {Ucar, Mehmet C and Lipowsky, Reinhard},
  issn         = {1530-6992},
  journal      = {Nano Letters},
  number       = {1},
  pages        = {669--676},
  publisher    = {American Chemical Society},
  title        = {{Collective force generation by molecular motors is determined by strain-induced unbinding}},
  doi          = {10.1021/acs.nanolett.9b04445},
  volume       = {20},
  year         = {2020},
}

@misc{9713,
  abstract     = {Additional analyses of the trajectories},
  author       = {Gupta, Chitrak and Khaniya, Umesh and Chan, Chun Kit and Dehez, Francois and Shekhar, Mrinal and Gunner, M.R. and Sazanov, Leonid A and Chipot, Christophe and Singharoy, Abhishek},
  publisher    = {American Chemical Society},
  title        = {{Supporting information}},
  doi          = {10.1021/jacs.9b13450.s001},
  year         = {2020},
}

@misc{9885,
  abstract     = {Data obtained from the fine-grained simulations used in Figures 2-5, data obtained from the coarse-grained numerical calculations used in Figure 6, and a sample script for the fine-grained simulation as a Jupyter notebook (ZIP)},
  author       = {Ucar, Mehmet C and Lipowsky, Reinhard},
  publisher    = {American Chemical Society},
  title        = {{MURL_Dataz}},
  doi          = {10.1021/acs.nanolett.9b04445.s002},
  year         = {2020},
}

@phdthesis{8155,
  abstract     = {In the thesis we focus on the interplay of the biophysics and evolution of gene regulation. We start by addressing how the type of prokaryotic gene regulation – activation and repression – affects spurious binding to DNA, also known as
transcriptional crosstalk. We propose that regulatory interference caused by excess regulatory proteins in the dense cellular medium – global crosstalk – could be a factor in determining which type of gene regulatory network is evolutionarily preferred. Next,we use a normative approach in eukaryotic gene regulation to describe minimal
non-equilibrium enhancer models that optimize so-called regulatory phenotypes. We find a class of models that differ from standard thermodynamic equilibrium models by a single parameter that notably increases the regulatory performance. Next chapter addresses the question of genotype-phenotype-fitness maps of higher dimensional phenotypes. We show that our biophysically realistic approach allows us to understand how the mechanisms of promoter function constrain genotypephenotype maps, and how they affect the evolutionary trajectories of promoters.
In the last chapter we ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using mathematical modeling, we show that amplifications can tune gene expression in many environments, including those where transcription factor-based schemes are
hard to evolve or maintain. },
  author       = {Grah, Rok},
  issn         = {2663-337X},
  pages        = {310},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Gene regulation across scales – how biophysical constraints shape evolution}},
  doi          = {10.15479/AT:ISTA:8155},
  year         = {2020},
}