@article{175,
abstract = {An upper bound sieve for rational points on suitable varieties isdeveloped, together with applications tocounting rational points in thin sets,to local solubility in families, and to the notion of “friable” rational pointswith respect to divisors. In the special case of quadrics, sharper estimates areobtained by developing a version of the Selberg sieve for rational points.},
author = {Browning, Timothy D and Loughran, Daniel},
issn = {10886850},
journal = {Transactions of the American Mathematical Society},
number = {8},
pages = {5757--5785},
publisher = {American Mathematical Society},
title = {{Sieving rational points on varieties}},
doi = {10.1090/tran/7514},
volume = {371},
year = {2019},
}
@article{196,
abstract = {The abelian sandpile serves as a model to study self-organized criticality, a phenomenon occurring in biological, physical and social processes. The identity of the abelian group is a fractal composed of self-similar patches, and its limit is subject of extensive collaborative research. Here, we analyze the evolution of the sandpile identity under harmonic fields of different orders. We show that this evolution corresponds to periodic cycles through the abelian group characterized by the smooth transformation and apparent conservation of the patches constituting the identity. The dynamics induced by second and third order harmonics resemble smooth stretchings, respectively translations, of the identity, while the ones induced by fourth order harmonics resemble magnifications and rotations. Starting with order three, the dynamics pass through extended regions of seemingly random configurations which spontaneously reassemble into accentuated patterns. We show that the space of harmonic functions projects to the extended analogue of the sandpile group, thus providing a set of universal coordinates identifying configurations between different domains. Since the original sandpile group is a subgroup of the extended one, this directly implies that it admits a natural renormalization. Furthermore, we show that the harmonic fields can be induced by simple Markov processes, and that the corresponding stochastic dynamics show remarkable robustness over hundreds of periods. Finally, we encode information into seemingly random configurations, and decode this information with an algorithm requiring minimal prior knowledge. Our results suggest that harmonic fields might split the sandpile group into sub-sets showing different critical coefficients, and that it might be possible to extend the fractal structure of the identity beyond the boundaries of its domain. },
author = {Lang, Moritz and Shkolnikov, Mikhail},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences},
number = {8},
pages = {2821--2830},
publisher = {National Academy of Sciences},
title = {{Harmonic dynamics of the Abelian sandpile}},
doi = {10.1073/pnas.1812015116},
volume = {116},
year = {2019},
}
@article{7146,
abstract = {Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity.},
author = {Vicoso, Beatriz},
issn = {2397-334X},
journal = {Nature Ecology & Evolution},
number = {12},
pages = {1632--1641},
publisher = {Springer Nature},
title = {{Molecular and evolutionary dynamics of animal sex-chromosome turnover}},
doi = {10.1038/s41559-019-1050-8},
volume = {3},
year = {2019},
}
@inproceedings{7147,
abstract = {The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.
In this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.
The behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions.},
author = {Guet, Calin C and Henzinger, Thomas A and Igler, Claudia and Petrov, Tatjana and Sezgin, Ali},
booktitle = {17th International Conference on Computational Methods in Systems Biology},
isbn = {9783030313036},
issn = {1611-3349},
location = {Trieste, Italy},
pages = {155--187},
publisher = {Springer Nature},
title = {{Transient memory in gene regulation}},
doi = {10.1007/978-3-030-31304-3_9},
volume = {11773},
year = {2019},
}
@article{7150,
abstract = {In this work, we use algebraic methods for studying distance computation and subgraph detection tasks in the congested clique model. Specifically, we adapt parallel matrix multiplication implementations to the congested clique, obtaining an O(n1−2/ω) round matrix multiplication algorithm, where ω<2.3728639 is the exponent of matrix multiplication. In conjunction with known techniques from centralised algorithmics, this gives significant improvements over previous best upper bounds in the congested clique model. The highlight results include:
1. triangle and 4-cycle counting in O(n0.158) rounds, improving upon the O(n1/3) algorithm of Dolev et al. [DISC 2012],
2. a (1+o(1))-approximation of all-pairs shortest paths in O(n0.158) rounds, improving upon the O~(n1/2)-round (2+o(1))-approximation algorithm given by Nanongkai [STOC 2014], and
3. computing the girth in O(n0.158) rounds, which is the first non-trivial solution in this model.
In addition, we present a novel constant-round combinatorial algorithm for detecting 4-cycles.},
author = {Censor-Hillel, Keren and Kaski, Petteri and Korhonen, Janne and Lenzen, Christoph and Paz, Ami and Suomela, Jukka},
issn = {0178-2770},
journal = {Distributed Computing},
number = {6},
pages = {461--478},
publisher = {Springer Nature},
title = {{Algebraic methods in the congested clique}},
doi = {10.1007/s00446-016-0270-2},
volume = {32},
year = {2019},
}