@article{13271, abstract = {In this paper, we prove the convexity of trace functionals (A,B,C)↦Tr|BpACq|s, for parameters (p, q, s) that are best possible, where B and C are any n-by-n positive-definite matrices, and A is any n-by-n matrix. We also obtain the monotonicity versions of trace functionals of this type. As applications, we extend some results in Carlen et al. (Linear Algebra Appl 490:174–185, 2016), Hiai and Petz (Publ Res Inst Math Sci 48(3):525-542, 2012) and resolve a conjecture in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) in the matrix setting. Other conjectures in Al-Rashed and Zegarliński (Infin Dimens Anal Quantum Probab Relat Top 17(4):1450029, 2014) will also be discussed. We also show that some related trace functionals are not concave in general. Such concavity results were expected to hold in different problems.}, author = {Zhang, Haonan}, issn = {1424-0637}, journal = {Annales Henri Poincare}, publisher = {Springer Nature}, title = {{Some convexity and monotonicity results of trace functionals}}, doi = {10.1007/s00023-023-01345-7}, year = {2023}, } @article{13258, abstract = {Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation.}, author = {Kleshnina, Maria and Hilbe, Christian and Simsa, Stepan and Chatterjee, Krishnendu and Nowak, Martin A.}, issn = {2041-1723}, journal = {Nature Communications}, publisher = {Springer Nature}, title = {{The effect of environmental information on evolution of cooperation in stochastic games}}, doi = {10.1038/s41467-023-39625-9}, volume = {14}, year = {2023}, } @article{13263, abstract = {Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date. Results: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models.}, author = {Trinh, Van Giang and Benhamou, Belaid and Henzinger, Thomas A and Pastva, Samuel}, issn = {1367-4811}, journal = {Bioinformatics}, number = {Supplement_1}, pages = {i513--i522}, publisher = {Oxford Academic}, title = {{Trap spaces of multi-valued networks: Definition, computation, and applications}}, doi = {10.1093/bioinformatics/btad262}, volume = {39}, year = {2023}, } @article{13316, abstract = {Although budding yeast has been extensively used as a model organism for studying organelle functions and intracellular vesicle trafficking, whether it possesses an independent endocytic early/sorting compartment that sorts endocytic cargos to the endo-lysosomal pathway or the recycling pathway has long been unclear. The structure and properties of the endocytic early/sorting compartment differ significantly between organisms; in plant cells, the trans-Golgi network (TGN) serves this role, whereas in mammalian cells a separate intracellular structure performs this function. The yeast syntaxin homolog Tlg2p, widely localizing to the TGN and endosomal compartments, is presumed to act as a Q-SNARE for endocytic vesicles, but which compartment is the direct target for endocytic vesicles remained unanswered. Here we demonstrate by high-speed and high-resolution 4D imaging of fluorescently labeled endocytic cargos that the Tlg2p-residing compartment within the TGN functions as the early/sorting compartment. After arriving here, endocytic cargos are recycled to the plasma membrane or transported to the yeast Rab5-residing endosomal compartment through the pathway requiring the clathrin adaptors GGAs. Interestingly, Gga2p predominantly localizes at the Tlg2p-residing compartment, and the deletion of GGAs has little effect on another TGN region where Sec7p is present but suppresses dynamics of the Tlg2-residing early/sorting compartment, indicating that the Tlg2p- and Sec7p-residing regions are discrete entities in the mutant. Thus, the Tlg2p-residing region seems to serve as an early/sorting compartment and function independently of the Sec7p-residing region within the TGN.}, author = {Toshima, Junko Y. and Tsukahara, Ayana and Nagano, Makoto and Tojima, Takuro and Siekhaus, Daria E and Nakano, Akihiko and Toshima, Jiro}, issn = {2050-084X}, journal = {eLife}, publisher = {eLife Sciences Publications}, title = {{The yeast endocytic early/sorting compartment exists as an independent sub-compartment within the trans-Golgi network}}, doi = {10.7554/eLife.84850}, volume = {12}, year = {2023}, } @article{13317, abstract = {We prove the Eigenstate Thermalisation Hypothesis (ETH) for local observables in a typical translation invariant system of quantum spins with L-body interactions, where L is the number of spins. This mathematically verifies the observation first made by Santos and Rigol (Phys Rev E 82(3):031130, 2010, https://doi.org/10.1103/PhysRevE.82.031130) that the ETH may hold for systems with additional translational symmetries for a naturally restricted class of observables. We also present numerical support for the same phenomenon for Hamiltonians with local interaction.}, author = {Sugimoto, Shoki and Henheik, Sven Joscha and Riabov, Volodymyr and Erdös, László}, issn = {1572-9613}, journal = {Journal of Statistical Physics}, number = {7}, publisher = {Springer Nature}, title = {{Eigenstate thermalisation hypothesis for translation invariant spin systems}}, doi = {10.1007/s10955-023-03132-4}, volume = {190}, year = {2023}, } @article{13278, abstract = {We present a numerical analysis of spin-1/2 fermions in a one-dimensional harmonic potential in the presence of a magnetic point-like impurity at the center of the trap. The model represents a few-body analogue of a magnetic impurity in the vicinity of an s-wave superconductor. Already for a few particles we find a ground-state level crossing between sectors with different fermion parities. We interpret this crossing as a few-body precursor of a quantum phase transition, which occurs when the impurity "breaks" a Cooper pair. This picture is further corroborated by analyzing density-density correlations in momentum space. Finally, we discuss how the system may be realized with existing cold-atoms platforms.}, author = {Rammelmüller, Lukas and Huber, David and Čufar, Matija and Brand, Joachim and Hammer, Hans-Werner and Volosniev, Artem}, issn = {2542-4653}, journal = {SciPost Physics}, keywords = {General Physics and Astronomy}, number = {1}, publisher = {SciPost Foundation}, title = {{Magnetic impurity in a one-dimensional few-fermion system}}, doi = {10.21468/scipostphys.14.1.006}, volume = {14}, year = {2023}, } @article{13274, abstract = {Viscous flows through pipes and channels are steady and ordered until, with increasing velocity, the laminar motion catastrophically breaks down and gives way to turbulence. How this apparently discontinuous change from low- to high-dimensional motion can be rationalized within the framework of the Navier-Stokes equations is not well understood. Exploiting geometrical properties of transitional channel flow we trace turbulence to far lower Reynolds numbers (Re) than previously possible and identify the complete path that reversibly links fully turbulent motion to an invariant solution. This precursor of turbulence destabilizes rapidly with Re, and the accompanying explosive increase in attractor dimension effectively marks the transition between deterministic and de facto stochastic dynamics.}, author = {Paranjape, Chaitanya S and Yalniz, Gökhan and Duguet, Yohann and Budanur, Nazmi B and Hof, Björn}, issn = {1079-7114}, journal = {Physical Review Letters}, keywords = {General Physics and Astronomy}, number = {3}, publisher = {American Physical Society}, title = {{Direct path from turbulence to time-periodic solutions}}, doi = {10.1103/physrevlett.131.034002}, volume = {131}, year = {2023}, } @article{13261, abstract = {Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.}, author = {Brückner, David and Chen, Hongtao and Barinov, Lev and Zoller, Benjamin and Gregor, Thomas}, issn = {1095-9203}, journal = {Science}, number = {6652}, pages = {1357--1362}, publisher = {American Association for the Advancement of Science}, title = {{Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome}}, doi = {10.1126/science.adf5568}, volume = {380}, year = {2023}, } @misc{13336, author = {Kleshnina, Maria}, publisher = {Zenodo}, title = {{kleshnina/stochgames_info: The effect of environmental information on evolution of cooperation in stochastic games}}, doi = {10.5281/ZENODO.8059564}, year = {2023}, } @article{13443, abstract = {The ages of solar-like stars have been at the center of many studies such as exoplanet characterization or Galactic-archeology. While ages are usually computed from stellar evolution models, relations linking ages to other stellar properties, such as rotation and magnetic activity, have been investigated. With the large catalog of 55,232 rotation periods, Prot, and photometric magnetic activity index, Sph from Kepler data, we have the opportunity to look for such magneto-gyro-chronology relations. Stellar ages are obtained with two stellar evolution codes that include treatment of angular momentum evolution, hence using Prot as input in addition to classical atmospheric parameters. We explore two different ways of predicting stellar ages on three subsamples with spectroscopic observations: solar analogs, late-F and G dwarfs, and K dwarfs. We first perform a Bayesian analysis to derive relations between Sph and ages between 1 and 5 Gyr, and other stellar properties. For late-F and G dwarfs, and K dwarfs, the multivariate regression favors the model with Prot and Sph with median differences of 0.1% and 0.2%, respectively. We also apply Machine Learning techniques with a Random Forest algorithm to predict ages up to 14 Gyr with the same set of input parameters. For late-F, G and K dwarfs together, predicted ages are on average within 5.3% of the model ages and improve to 3.1% when including Prot. These are very promising results for a quick age estimation for solar-like stars with photometric observations, especially with current and future space missions.}, author = {Mathur, Savita and Claytor, Zachary R. and Santos, Ângela R. G. and García, Rafael A. and Amard, Louis and Bugnet, Lisa Annabelle and Corsaro, Enrico and Bonanno, Alfio and Breton, Sylvain N. and Godoy-Rivera, Diego and Pinsonneault, Marc H. and van Saders, Jennifer}, issn = {1538-4357}, journal = {The Astrophysical Journal}, keywords = {Space and Planetary Science, Astronomy and Astrophysics}, number = {2}, publisher = {American Astronomical Society}, title = {{Magnetic activity evolution of solar-like stars. I. Sph–age relation derived from Kepler observations}}, doi = {10.3847/1538-4357/acd118}, volume = {952}, year = {2023}, }