@article{12876, abstract = {Motivation: The problem of model inference is of fundamental importance to systems biology. Logical models (e.g. Boolean networks; BNs) represent a computationally attractive approach capable of handling large biological networks. The models are typically inferred from experimental data. However, even with a substantial amount of experimental data supported by some prior knowledge, existing inference methods often focus on a small sample of admissible candidate models only. Results: We propose Boolean network sketches as a new formal instrument for the inference of Boolean networks. A sketch integrates (typically partial) knowledge about the network’s topology and the update logic (obtained through, e.g. a biological knowledge base or a literature search), as well as further assumptions about the properties of the network’s transitions (e.g. the form of its attractor landscape), and additional restrictions on the model dynamics given by the measured experimental data. Our new BNs inference algorithm starts with an ‘initial’ sketch, which is extended by adding restrictions representing experimental data to a ‘data-informed’ sketch and subsequently computes all BNs consistent with the data-informed sketch. Our algorithm is based on a symbolic representation and coloured model-checking. Our approach is unique in its ability to cover a broad spectrum of knowledge and efficiently produce a compact representation of all inferred BNs. We evaluate the method on a non-trivial collection of real-world and simulated data.}, author = {Beneš, Nikola and Brim, Luboš and Huvar, Ondřej and Pastva, Samuel and Šafránek, David}, issn = {1367-4811}, journal = {Bioinformatics}, number = {4}, publisher = {Oxford Academic}, title = {{Boolean network sketches: A unifying framework for logical model inference}}, doi = {10.1093/bioinformatics/btad158}, volume = {39}, year = {2023}, } @article{12877, abstract = {We consider billiards obtained by removing from the plane finitely many strictly convex analytic obstacles satisfying the non-eclipse condition. The restriction of the dynamics to the set of non-escaping orbits is conjugated to a subshift, which provides a natural labeling of periodic orbits. We show that under suitable symmetry and genericity assumptions, the Marked Length Spectrum determines the geometry of the billiard table.}, author = {De Simoi, Jacopo and Kaloshin, Vadim and Leguil, Martin}, issn = {1432-1297}, journal = {Inventiones Mathematicae}, pages = {829--901}, publisher = {Springer Nature}, title = {{Marked Length Spectral determination of analytic chaotic billiards with axial symmetries}}, doi = {10.1007/s00222-023-01191-8}, volume = {233}, year = {2023}, } @article{12878, abstract = {Salicylic acid (SA) plays important roles in different aspects of plant development, including root growth, where auxin is also a major player by means of its asymmetric distribution. However, the mechanism underlying the effect of SA on the development of rice roots remains poorly understood. Here, we show that SA inhibits rice root growth by interfering with auxin transport associated with the OsPIN3t- and clathrin-mediated gene regulatory network (GRN). SA inhibits root growth as well as Brefeldin A-sensitive trafficking through a non-canonical SA signaling mechanism. Transcriptome analysis of rice seedlings treated with SA revealed that the OsPIN3t auxin transporter is at the center of a GRN involving the coat protein clathrin. The root growth and endocytic trafficking in both the pin3t and clathrin heavy chain mutants were SA insensitivity. SA inhibitory effect on the endocytosis of OsPIN3t was dependent on clathrin; however, the root growth and endocytic trafficking mediated by tyrphostin A23 (TyrA23) were independent of the pin3t mutant under SA treatment. These data reveal that SA affects rice root growth through the convergence of transcriptional and non-SA signaling mechanisms involving OsPIN3t-mediated auxin transport and clathrin-mediated trafficking as key components.}, author = {Jiang, Lihui and Yao, Baolin and Zhang, Xiaoyan and Wu, Lixia and Fu, Qijing and Zhao, Yiting and Cao, Yuxin and Zhu, Ruomeng and Lu, Xinqi and Huang, Wuying and Zhao, Jianping and Li, Kuixiu and Zhao, Shuanglu and Han, Li and Zhou, Xuan and Luo, Chongyu and Zhu, Haiyan and Yang, Jing and Huang, Huichuan and Zhu, Zhengge and He, Xiahong and Friml, Jiří and Zhang, Zhongkai and Liu, Changning and Du, Yunlong}, issn = {1365-313X}, journal = {Plant Journal}, number = {1}, pages = {155--174}, publisher = {Wiley}, title = {{Salicylic acid inhibits rice endocytic protein trafficking mediated by OsPIN3t and clathrin to affect root growth}}, doi = {10.1111/tpj.16218}, volume = {115}, year = {2023}, } @article{12879, abstract = {Machine learning (ML) has been widely applied to chemical property prediction, most prominently for the energies and forces in molecules and materials. The strong interest in predicting energies in particular has led to a ‘local energy’-based paradigm for modern atomistic ML models, which ensures size-extensivity and a linear scaling of computational cost with system size. However, many electronic properties (such as excitation energies or ionization energies) do not necessarily scale linearly with system size and may even be spatially localized. Using size-extensive models in these cases can lead to large errors. In this work, we explore different strategies for learning intensive and localized properties, using HOMO energies in organic molecules as a representative test case. In particular, we analyze the pooling functions that atomistic neural networks use to predict molecular properties, and suggest an orbital weighted average (OWA) approach that enables the accurate prediction of orbital energies and locations.}, author = {Chen, Ke and Kunkel, Christian and Cheng, Bingqing and Reuter, Karsten and Margraf, Johannes T.}, issn = {2041-6539}, journal = {Chemical Science}, publisher = {Royal Society of Chemistry}, title = {{Physics-inspired machine learning of localized intensive properties}}, doi = {10.1039/d3sc00841j}, year = {2023}, } @article{12880, abstract = {Peripheral heterochromatin positioning depends on nuclear envelope associated proteins and repressive histone modifications. Here we show that overexpression (OE) of Lamin B1 (LmnB1) leads to the redistribution of peripheral heterochromatin into heterochromatic foci within the nucleoplasm. These changes represent a perturbation of heterochromatin binding at the nuclear periphery (NP) through a mechanism independent from altering other heterochromatin anchors or histone post-translational modifications. We further show that LmnB1 OE alters gene expression. These changes do not correlate with different levels of H3K9me3, but a significant number of the misregulated genes were likely mislocalized away from the NP upon LmnB1 OE. We also observed an enrichment of developmental processes amongst the upregulated genes. ~74% of these genes were normally repressed in our cell type, suggesting that LmnB1 OE promotes gene de-repression. This demonstrates a broader consequence of LmnB1 OE on cell fate, and highlights the importance of maintaining proper levels of LmnB1.}, author = {Kaneshiro, Jeanae M. and Capitanio, Juliana S. and Hetzer, Martin W}, issn = {1949-1042}, journal = {Nucleus}, number = {1}, publisher = {Taylor & Francis}, title = {{Lamin B1 overexpression alters chromatin organization and gene expression}}, doi = {10.1080/19491034.2023.2202548}, volume = {14}, year = {2023}, } @phdthesis{12885, abstract = {High-performance semiconductors rely upon precise control of heat and charge transport. This can be achieved by precisely engineering defects in polycrystalline solids. There are multiple approaches to preparing such polycrystalline semiconductors, and the transformation of solution-processed colloidal nanoparticles is appealing because colloidal nanoparticles combine low cost with structural and compositional tunability along with rich surface chemistry. However, the multiple processes from nanoparticle synthesis to the final bulk nanocomposites are very complex. They involve nanoparticle purification, post-synthetic modifications, and finally consolidation (thermal treatments and densification). All these properties dictate the final material’s composition and microstructure, ultimately affecting its functional properties. This thesis explores the synthesis, surface chemistry and consolidation of colloidal semiconductor nanoparticles into dense solids. In particular, the transformations that take place during these processes, and their effect on the material’s transport properties are evaluated. }, author = {Calcabrini, Mariano}, isbn = {978-3-99078-028-2}, issn = {2663-337X}, pages = {82}, publisher = {Institute of Science and Technology Austria}, title = {{Nanoparticle-based semiconductor solids: From synthesis to consolidation}}, doi = {10.15479/at:ista:12885}, year = {2023}, } @article{12890, abstract = {We introduce a stochastic cellular automaton as a model for culture and border formation. The model can be conceptualized as a game where the expansion rate of cultures is quantified in terms of their area and perimeter in such a way that approximately geometrically round cultures get a competitive advantage. We first analyze the model with periodic boundary conditions, where we study how the model can end up in a fixed state, i.e., freezes. Then we implement the model on the European geography with mountains and rivers. We see how the model reproduces some qualitative features of European culture formation, namely, that rivers and mountains are more frequently borders between cultures, mountainous regions tend to have higher cultural diversity, and the central European plain has less clear cultural borders.}, author = {Klausen, Frederik Ravn and Lauritsen, Asbjørn Bækgaard}, issn = {2470-0053}, journal = {Physical Review E}, number = {5}, publisher = {American Physical Society}, title = {{Stochastic cellular automaton model of culture formation}}, doi = {10.1103/PhysRevE.108.054307}, volume = {108}, year = {2023}, } @phdthesis{12891, abstract = {The tight spatiotemporal coordination of signaling activity determining embryo patterning and the physical processes driving embryo morphogenesis renders embryonic development robust, such that key developmental processes can unfold relatively normally even outside of the full embryonic context. For instance, embryonic stem cell cultures can recapitulate the hallmarks of gastrulation, i.e. break symmetry leading to germ layer formation and morphogenesis, in a very reduced environment. This leads to questions on specific contributions of embryo-specific features, such as the presence of extraembryonic tissues, which are inherently involved in gastrulation in the full embryonic context. To address this, we established zebrafish embryonic explants without the extraembryonic yolk cell, an important player as a signaling source and for morphogenesis during gastrulation, as a model of ex vivo development. We found that dorsal-marginal determinants are required and sufficient in these explants to form and pattern all three germ layers. However, formation of tissues, which require the highest Nodal-signaling levels, is variable, demonstrating a contribution of extraembryonic tissues for reaching peak Nodal signaling levels. Blastoderm explants also undergo gastrulation-like axis elongation. We found that this elongation movement shows hallmarks of oriented mesendoderm cell intercalations typically associated with dorsal tissues in the intact embryo. These are disrupted by uniform upregulation of BMP signaling activity and concomitant explant ventralization, suggesting that tight spatial control of BMP signaling is a prerequisite for explant morphogenesis. This control is achieved by Nodal signaling, which is critical for effectively downregulating BMP signaling in the mesendoderm, highlighting that Nodal signaling is not only directly required for mesendoderm cell fate specification and morphogenesis, but also by maintaining low levels of BMP signaling at the dorsal side. Collectively, we provide insights into the capacity and organization of signaling and morphogenetic domains to recapitulate features of zebrafish gastrulation outside of the full embryonic context.}, author = {Schauer, Alexandra}, issn = {2663 - 337X}, pages = {190}, publisher = {Institute of Science and Technology Austria}, title = {{Mesendoderm formation in zebrafish gastrulation: The role of extraembryonic tissues}}, doi = {10.15479/at:ista:12891}, year = {2023}, } @phdthesis{12897, abstract = {Inverse design problems in fabrication-aware shape optimization are typically solved on discrete representations such as polygonal meshes. This thesis argues that there are benefits to treating these problems in the same domain as human designers, namely, the parametric one. One reason is that discretizing a parametric model usually removes the capability of making further manual changes to the design, because the human intent is captured by the shape parameters. Beyond this, knowledge about a design problem can sometimes reveal a structure that is present in a smooth representation, but is fundamentally altered by discretizing. In this case, working in the parametric domain may even simplify the optimization task. We present two lines of research that explore both of these aspects of fabrication-aware shape optimization on parametric representations. The first project studies the design of plane elastic curves and Kirchhoff rods, which are common mathematical models for describing the deformation of thin elastic rods such as beams, ribbons, cables, and hair. Our main contribution is a characterization of all curved shapes that can be attained by bending and twisting elastic rods having a stiffness that is allowed to vary across the length. Elements like these can be manufactured using digital fabrication devices such as 3d printers and digital cutters, and have applications in free-form architecture and soft robotics. We show that the family of curved shapes that can be produced this way admits geometric description that is concise and computationally convenient. In the case of plane curves, the geometric description is intuitive enough to allow a designer to determine whether a curved shape is physically achievable by visual inspection alone. We also present shape optimization algorithms that convert a user-defined curve in the plane or in three dimensions into the geometry of an elastic rod that will naturally deform to follow this curve when its endpoints are attached to a support structure. Implemented in an interactive software design tool, the rod geometry is generated in real time as the user edits a curve and enables fast prototyping. The second project tackles the problem of general-purpose shape optimization on CAD models using a novel variant of the extended finite element method (XFEM). Our goal is the decoupling between the simulation mesh and the CAD model, so no geometry-dependent meshing or remeshing needs to be performed when the CAD parameters change during optimization. This is achieved by discretizing the embedding space of the CAD model, and using a new high-accuracy numerical integration method to enable XFEM on free-form elements bounded by the parametric surface patches of the model. Our simulation is differentiable from the CAD parameters to the simulation output, which enables us to use off-the-shelf gradient-based optimization procedures. The result is a method that fits seamlessly into the CAD workflow because it works on the same representation as the designer, enabling the alternation of manual editing and fabrication-aware optimization at will.}, author = {Hafner, Christian}, isbn = {978-3-99078-031-2}, issn = {2663-337X}, pages = {180}, publisher = {Institute of Science and Technology Austria}, title = {{Inverse shape design with parametric representations: Kirchhoff Rods and parametric surface models}}, doi = {10.15479/at:ista:12897}, year = {2023}, } @phdthesis{12900, abstract = {About a 100 years ago, we discovered that our universe is inherently noisy, that is, measuring any physical quantity with a precision beyond a certain point is not possible because of an omnipresent inherent noise. We call this - the quantum noise. Certain physical processes allow this quantum noise to get correlated in conjugate physical variables. These quantum correlations can be used to go beyond the potential of our inherently noisy universe and obtain a quantum advantage over the classical applications. Quantum noise being inherent also means that, at the fundamental level, the physical quantities are not well defined and therefore, objects can stay in multiple states at the same time. For example, the position of a particle not being well defined means that the particle is in multiple positions at the same time. About 4 decades ago, we started exploring the possibility of using objects which can be in multiple states at the same time to increase the dimensionality in computation. Thus, the field of quantum computing was born. We discovered that using quantum entanglement, a property closely related to quantum correlations, can be used to speed up computation of certain problems, such as factorisation of large numbers, faster than any known classical algorithm. Thus began the pursuit to make quantum computers a reality. Till date, we have explored quantum control over many physical systems including photons, spins, atoms, ions and even simple circuits made up of superconducting material. However, there persists one ubiquitous theme. The more readily a system interacts with an external field or matter, the more easily we can control it. But this also means that such a system can easily interact with a noisy environment and quickly lose its coherence. Consequently, such systems like electron spins need to be protected from the environment to ensure the longevity of their coherence. Other systems like nuclear spins are naturally protected as they do not interact easily with the environment. But, due to the same reason, it is harder to interact with such systems. After decades of experimentation with various systems, we are convinced that no one type of quantum system would be the best for all the quantum applications. We would need hybrid systems which are all interconnected - much like the current internet where all sorts of devices can all talk to each other - but now for quantum devices. A quantum internet. Optical photons are the best contenders to carry information for the quantum internet. They can carry quantum information cheaply and without much loss - the same reasons which has made them the backbone of our current internet. Following this direction, many systems, like trapped ions, have already demonstrated successful quantum links over a large distances using optical photons. However, some of the most promising contenders for quantum computing which are based on microwave frequencies have been left behind. This is because high energy optical photons can adversely affect fragile low-energy microwave systems. In this thesis, we present substantial progress on this missing quantum link between microwave and optics using electrooptical nonlinearities in lithium niobate. The nonlinearities are enhanced by using resonant cavities for all the involved modes leading to observation of strong direct coupling between optical and microwave frequencies. With this strong coupling we are not only able to achieve almost 100\% internal conversion efficiency with low added noise, thus presenting a quantum-enabled transducer, but also we are able to observe novel effects such as cooling of a microwave mode using optics. The strong coupling regime also leads to direct observation of dynamical backaction effect between microwave and optical frequencies which are studied in detail here. Finally, we also report first observation of microwave-optics entanglement in form of two-mode squeezed vacuum squeezed 0.7dB below vacuum level. With this new bridge between microwave and optics, the microwave-based quantum technologies can finally be a part of a quantum network which is based on optical photons - putting us one step closer to a future with quantum internet. }, author = {Sahu, Rishabh}, isbn = {978-3-99078-030-5}, issn = {2663 - 337X}, keywords = {quantum optics, electrooptics, quantum networks, quantum communication, transduction}, pages = {190}, publisher = {Institute of Science and Technology Austria}, title = {{Cavity quantum electrooptics}}, doi = {10.15479/at:ista:12900}, year = {2023}, } @article{12911, abstract = {This paper establishes new connections between many-body quantum systems, One-body Reduced Density Matrices Functional Theory (1RDMFT) and Optimal Transport (OT), by interpreting the problem of computing the ground-state energy of a finite-dimensional composite quantum system at positive temperature as a non-commutative entropy regularized Optimal Transport problem. We develop a new approach to fully characterize the dual-primal solutions in such non-commutative setting. The mathematical formalism is particularly relevant in quantum chemistry: numerical realizations of the many-electron ground-state energy can be computed via a non-commutative version of Sinkhorn algorithm. Our approach allows to prove convergence and robustness of this algorithm, which, to our best knowledge, were unknown even in the two marginal case. Our methods are based on a priori estimates in the dual problem, which we believe to be of independent interest. Finally, the above results are extended in 1RDMFT setting, where bosonic or fermionic symmetry conditions are enforced on the problem.}, author = {Feliciangeli, Dario and Gerolin, Augusto and Portinale, Lorenzo}, issn = {1096-0783}, journal = {Journal of Functional Analysis}, number = {4}, publisher = {Elsevier}, title = {{A non-commutative entropic optimal transport approach to quantum composite systems at positive temperature}}, doi = {10.1016/j.jfa.2023.109963}, volume = {285}, year = {2023}, } @article{12912, abstract = {The chemical potential of adsorbed or confined fluids provides insight into their unique thermodynamic properties and determines adsorption isotherms. However, it is often difficult to compute this quantity from atomistic simulations using existing statistical mechanical methods. We introduce a computational framework that utilizes static structure factors, thermodynamic integration, and free energy perturbation for calculating the absolute chemical potential of fluids. For demonstration, we apply the method to compute the adsorption isotherms of carbon dioxide in a metal-organic framework and water in carbon nanotubes.}, author = {Schmid, Rochus and Cheng, Bingqing}, issn = {1089-7690}, journal = {The Journal of Chemical Physics}, number = {16}, publisher = {AIP Publishing}, title = {{Computing chemical potentials of adsorbed or confined fluids}}, doi = {10.1063/5.0146711}, volume = {158}, year = {2023}, } @article{12913, abstract = {The coexistence of gate-tunable superconducting, magnetic and topological orders in magic-angle twisted bilayer graphene provides opportunities for the creation of hybrid Josephson junctions. Here we report the fabrication of gate-defined symmetry-broken Josephson junctions in magic-angle twisted bilayer graphene, where the weak link is gate-tuned close to the correlated insulator state with a moiré filling factor of υ = −2. We observe a phase-shifted and asymmetric Fraunhofer pattern with a pronounced magnetic hysteresis. Our theoretical calculations of the junction weak link—with valley polarization and orbital magnetization—explain most of these unconventional features. The effects persist up to the critical temperature of 3.5 K, with magnetic hysteresis observed below 800 mK. We show how the combination of magnetization and its current-induced magnetization switching allows us to realise a programmable zero-field superconducting diode. Our results represent a major advance towards the creation of future superconducting quantum electronic devices.}, author = {Díez-Mérida, J. and Díez-Carlón, A. and Yang, S. Y. and Xie, Y. M. and Gao, X. J. and Senior, Jorden L and Watanabe, K. and Taniguchi, T. and Lu, X. and Higginbotham, Andrew P and Law, K. T. and Efetov, Dmitri K.}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{Symmetry-broken Josephson junctions and superconducting diodes in magic-angle twisted bilayer graphene}}, doi = {10.1038/s41467-023-38005-7}, volume = {14}, year = {2023}, } @article{12914, abstract = {We numerically study two methods of measuring tunneling times using a quantum clock. In the conventional method using the Larmor clock, we show that the Larmor tunneling time can be shorter for higher tunneling barriers. In the second method, we study the probability of a spin-flip of a particle when it is transmitted through a potential barrier including a spatially rotating field interacting with its spin. According to the adiabatic theorem, the probability depends on the velocity of the particle inside the barrier. It is numerically observed that the probability increases for higher barriers, which is consistent with the result obtained by the Larmor clock. By comparing outcomes for different initial spin states, we suggest that one of the main causes of the apparent decrease in the tunneling time can be the filtering effect occurring at the end of the barrier.}, author = {Suzuki, Fumika and Unruh, William G.}, issn = {2469-9934}, journal = {Physical Review A}, number = {4}, publisher = {American Physical Society}, title = {{Numerical quantum clock simulations for measuring tunneling times}}, doi = {10.1103/PhysRevA.107.042216}, volume = {107}, year = {2023}, } @article{12915, abstract = {Cu2–xS and Cu2–xSe have recently been reported as promising thermoelectric (TE) materials for medium-temperature applications. In contrast, Cu2–xTe, another member of the copper chalcogenide family, typically exhibits low Seebeck coefficients that limit its potential to achieve a superior thermoelectric figure of merit, zT, particularly in the low-temperature range where this material could be effective. To address this, we investigated the TE performance of Cu1.5–xTe–Cu2Se nanocomposites by consolidating surface-engineered Cu1.5Te nanocrystals. This surface engineering strategy allows for precise adjustment of Cu/Te ratios and results in a reversible phase transition at around 600 K in Cu1.5–xTe–Cu2Se nanocomposites, as systematically confirmed by in situ high-temperature X-ray diffraction combined with differential scanning calorimetry analysis. The phase transition leads to a conversion from metallic-like to semiconducting-like TE properties. Additionally, a layer of Cu2Se generated around Cu1.5–xTe nanoparticles effectively inhibits Cu1.5–xTe grain growth, minimizing thermal conductivity and decreasing hole concentration. These properties indicate that copper telluride based compounds have a promising thermoelectric potential, translated into a high dimensionless zT of 1.3 at 560 K.}, author = {Xing, Congcong and Zhang, Yu and Xiao, Ke and Han, Xu and Liu, Yu and Nan, Bingfei and Ramon, Maria Garcia and Lim, Khak Ho and Li, Junshan and Arbiol, Jordi and Poudel, Bed and Nozariasbmarz, Amin and Li, Wenjie and Ibáñez, Maria and Cabot, Andreu}, issn = {1936-086X}, journal = {ACS Nano}, number = {9}, pages = {8442--8452}, publisher = {American Chemical Society}, title = {{Thermoelectric performance of surface-engineered Cu1.5–xTe–Cu2Se nanocomposites}}, doi = {10.1021/acsnano.3c00495}, volume = {17}, year = {2023}, } @article{12916, abstract = {We apply a variant of the square-sieve to produce an upper bound for the number of rational points of bounded height on a family of surfaces that admit a fibration over P1 whose general fibre is a hyperelliptic curve. The implied constant does not depend on the coefficients of the polynomial defining the surface. }, author = {Bonolis, Dante and Browning, Timothy D}, issn = {2036-2145}, journal = {Annali della Scuola Normale Superiore di Pisa - Classe di Scienze}, number = {1}, pages = {173--204}, publisher = {Scuola Normale Superiore - Edizioni della Normale}, title = {{Uniform bounds for rational points on hyperelliptic fibrations}}, doi = {10.2422/2036-2145.202010_018}, volume = {24}, year = {2023}, } @misc{12933, abstract = {Datasets of the publication "Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster".}, author = {Puixeu Sala, Gemma}, publisher = {Institute of Science and Technology Austria}, title = {{Data from: Sex-specific estimation of cis and trans regulation of gene expression in heads and gonads of Drosophila melanogaster}}, doi = {10.15479/AT:ISTA:12933}, year = {2023}, } @misc{12945, abstract = {basic data for use in code for experimental data analysis for manuscript under revision: Dynamic pathogen detection and social feedback shape collective hygiene in ants Casillas-Pérez B, Boďová K, Grasse AV, Tkačik G, Cremer S}, author = {Cremer, Sylvia}, keywords = {collective behavior, host-pathogen interactions, social immunity, epidemiology, social insects, probabilistic modeling}, publisher = {Institute of Science and Technology Austria}, title = {{Data from: "Dynamic pathogen detection and social feedback shape collective hygiene in ants" }}, doi = {10.15479/AT:ISTA:12945}, year = {2023}, } @misc{12949, abstract = {The classical infinitesimal model is a simple and robust model for the inheritance of quantitative traits. In this model, a quantitative trait is expressed as the sum of a genetic and a non-genetic (environmental) component and the genetic component of offspring traits within a family follows a normal distribution around the average of the parents’ trait values, and has a variance that is independent of the trait values of the parents. Although the trait distribution across the whole population can be far from normal, the trait distributions within families are normally distributed with a variance-covariance matrix that is determined entirely by that in the ancestral population and the probabilities of identity determined by the pedigree. Moreover, conditioning on some of the trait values within the pedigree has predictable effects on the mean and variance within and between families. In previous work, Barton et al. (2017), we showed that when trait values are determined by the sum of a large number of Mendelian factors, each of small effect, one can justify the infinitesimal model as limit of Mendelian inheritance. It was also shown that under some forms of epistasis, trait values within a family are still normally distributed.}, author = {Barton, Nicholas H}, keywords = {Quantitative genetics, infinitesimal model}, publisher = {Institute of Science and Technology Austria}, title = {{The infinitesimal model with dominance}}, doi = {10.15479/AT:ISTA:12949}, year = {2023}, } @article{12959, abstract = {This paper deals with the large-scale behaviour of dynamical optimal transport on Zd -periodic graphs with general lower semicontinuous and convex energy densities. Our main contribution is a homogenisation result that describes the effective behaviour of the discrete problems in terms of a continuous optimal transport problem. The effective energy density can be explicitly expressed in terms of a cell formula, which is a finite-dimensional convex programming problem that depends non-trivially on the local geometry of the discrete graph and the discrete energy density. Our homogenisation result is derived from a Γ -convergence result for action functionals on curves of measures, which we prove under very mild growth conditions on the energy density. We investigate the cell formula in several cases of interest, including finite-volume discretisations of the Wasserstein distance, where non-trivial limiting behaviour occurs.}, author = {Gladbach, Peter and Kopfer, Eva and Maas, Jan and Portinale, Lorenzo}, issn = {1432-0835}, journal = {Calculus of Variations and Partial Differential Equations}, number = {5}, publisher = {Springer Nature}, title = {{Homogenisation of dynamical optimal transport on periodic graphs}}, doi = {10.1007/s00526-023-02472-z}, volume = {62}, year = {2023}, }