@article{18919,
abstract = {The integration of theory and experiment makes possible tracking the slow evolution of a photodoped Mott insulator to a distinct non-equilibrium metallic phase under the influence of electron-lattice coupling.},
author = {Baykusheva, Denitsa Rangelova},
issn = {1745-2481},
journal = {Nature Physics},
number = {5},
pages = {684--685},
publisher = {Springer Nature},
title = {{Through the slopes of a light-induced phase transition}},
doi = {10.1038/s41567-024-02401-7},
volume = {20},
year = {2024},
}
@article{18920,
abstract = {The globally distributed marine alga Emiliania huxleyi has cooling effect on the Earth’s climate. The population density of E. huxleyi is restricted by Nucleocytoviricota viruses, including E. huxleyi virus 201 (EhV-201). Despite the impact of E. huxleyi viruses on the climate, there is limited information about their structure and replication. Here, we show that the dsDNA genome inside the EhV-201 virion is protected by an inner membrane, capsid, and outer membrane. EhV-201 virions infect E. huxleyi by using fivefold vertices to bind to and fuse the virus’ inner membrane with the cell plasma membrane. Progeny virions assemble in the cytoplasm at the surface of endoplasmic reticulum–derived membrane segments. Genome packaging initiates synchronously with the capsid assembly and completes through an aperture in the forming capsid. The genome-filled capsids acquire an outer membrane by budding into intracellular vesicles. EhV-201 infection induces a loss of surface protective layers from E. huxleyi cells, which enables the continuous release of virions by exocytosis.},
author = {Homola, Miroslav and Büttner, Renate Carina and Füzik, Tibor and Křepelka, Pavel and Holbová, Radka and Nováček, Jiří and Chaillet, Marten L. and Žák, Jakub and Grybchuk, Danyil and Förster, Friedrich and Wilson, William H. and Schroeder, Declan C. and Plevka, Pavel},
issn = {2375-2548},
journal = {Science Advances},
number = {15},
publisher = {American Association for the Advancement of Science},
title = {{Structure and replication cycle of a virus infecting climate-modulating alga Emiliania huxleyi}},
doi = {10.1126/sciadv.adk1954},
volume = {10},
year = {2024},
}
@inproceedings{18922,
abstract = {Let G be a directed graph with m edges and n vertices. We present a deterministic linear-time algorithm for computing the 3-edge-connected components of G. This is a significant improvement over the previous best bound by Georgiadis et al. [SODA 2023], which is Õ(m√{m}) and randomized. Our result is based on a novel characterization of 2-edge cuts in directed graphs and on a new technique that exploits the concept of divergent spanning trees and 2-connectivity-light graphs, and requires a careful modification of the minset-poset technique of Gabow [TALG 2016]. As a side result, our new technique yields also an oracle for providing in constant time a minimum edge-cut for any two vertices that are not 3-edge-connected. The oracle uses space O(n) and can be built in O(mlog n) time: given two query vertices, it determines in constant time whether they are 3-edge-connected, or provides a k-edge cut, with k≤ 2, that separates them.},
author = {Georgiadis, Loukas and Italiano, Giuseppe F. and Kosinas, Evangelos},
booktitle = {65th Annual Symposium on Foundations of Computer Science},
isbn = {9798331516741},
location = {Chicago, IL, United States},
pages = {62--85},
publisher = {IEEE},
title = {{Computing the 3-edge-connected components of directed graphs in linear time}},
doi = {10.1109/focs61266.2024.00015},
year = {2024},
}
@article{18923,
abstract = {Combinatorial optimization is a challenging problem applicable in a wide range of fields from logistics to finance. Recently, quantum computing has been used to attempt to solve these problems using a range of algorithms, including parameterized quantum circuits, adiabatic protocols, and quantum annealing. These solutions typically have several challenges: 1) there is little to no performance gain over classical methods; 2) not all constraints and objectives may be efficiently encoded in the quantum ansatz; and 3) the solution domain of the objective function may not be the same as the bit strings of measurement outcomes. This work presents “nonnative hybrid algorithms”: a framework to overcome these challenges by integrating quantum and classical resources with a hybrid approach. By designing nonnative quantum variational anosatzes that inherit some but not all problem structure, measurement outcomes from the quantum computer can act as a resource to be used by classical routines to indirectly compute optimal solutions, partially overcoming the challenges of contemporary quantum optimization approaches. These methods are demonstrated using a publicly available neutral-atom quantum computer on two simple problems of Max k-Cut and maximum independent set. We find improvements in solution quality when comparing the hybrid algorithm to its “no quantum” version, a demonstration of a “comparative advantage.”},
author = {Wurtz, Jonathan and Sack, Stefan and Wang, Sheng-Tao},
issn = {2689-1808},
journal = {IEEE Transactions on Quantum Engineering},
pages = {1--14},
publisher = {Institute of Electrical and Electronics Engineers },
title = {{Solving nonnative combinatorial optimization problems using hybrid quantum–classical algorithms}},
doi = {10.1109/tqe.2024.3443660},
volume = {5},
year = {2024},
}
@inproceedings{18925,
abstract = {Given the increasingly stringent requirements on the performance and efficiency of communication networks, over the last years, great efforts have been made to render networks more flexible and programmable. In particular, modern networks support a flexible rerouting of flows, e.g., depending on the dynamically changing traffic or network conditions. However, the underlying algorithmic problems are still not well-understood today.In this paper, we revisit the k-Network Flow Update problem that asks for a schedule to reroute k unsplittable flows from their current paths to the given new paths, in a congestion-free manner in a capacitated network. We show that the problem is already NP-hard for three acyclic flows on simple directed graphs. Our main contribution is an efficient algorithm for sparse networks; specifically the algorithm is fixed parameter tractable in the number of flows and the treewidth of a graph that is the union of all flows. Our results also settle the open complexity question in the literature.},
author = {Ceylan, Esra and Chatterjee, Krishnendu and Schmid, Stefan and Svoboda, Jakub},
booktitle = {NOMS 2024-2024 IEEE Network Operations and Management Symposium},
isbn = {9798350327946},
issn = {2374-9709},
location = {Seoul, Republic of Korea},
publisher = {IEEE},
title = {{Congestion-free rerouting of network flows: Hardness and an FPT algorithm}},
doi = {10.1109/noms59830.2024.10575579},
year = {2024},
}
@article{18926,
abstract = {We study weak solutions to mean curvature flow satisfying Young’s angle condition for general contact angles α ∈ (0, π). First, we construct BV solutions by using the Allen-Cahn approximation with boundary contact energy as proposed by Owen and Sternberg. Second, we prove the weak-strong uniqueness and stability for this solution concept. The main ingredient for both results is a relative energy, which can also be interpreted as a tilt excess. },
author = {Hensel, Sebastian and Laux, Tim},
issn = {0022-2518},
journal = {Indiana University Mathematics Journal},
number = {1},
pages = {111--148},
publisher = {Indiana University Mathematics Journal},
title = {{BV solutions for mean curvature flow with constant angle: Allen-Cahn approximation and weak-strong uniqueness}},
doi = {10.1512/iumj.2024.73.9701},
volume = {73},
year = {2024},
}
@inproceedings{18928,
abstract = {Algorithms with predictions is a new research direction that leverages machine learned predictions for algorithm design. So far a plethora of recent works have incorporated predictions to improve on worst-case bounds for online problems. In this paper, we initiate the study of complexity of dynamic data structures with predictions, including dynamic graph algorithms. Unlike online algorithms, the goal in dynamic data structures is to maintain the solution efficiently with every update.
We investigate three natural models of prediction: (1) δ-accurate predictions where each predicted request matches the true request with probability δ, (2) list-accurate predictions where a true request comes from a list of possible requests, and (3) bounded delay predictions where the true requests are a permutation of the predicted requests. We give general reductions among the prediction models, showing that bounded delay is the strongest prediction model, followed by list-accurate, and δ-accurate.
Further, we identify two broad problem classes based on lower bounds due to the Online Matrix Vector (OMv) conjecture. Specifically, we show that locally correctable dynamic problems have strong conditional lower bounds for list-accurate predictions that are equivalent to the non-prediction setting, unless list-accurate predictions are perfect. Moreover, we show that locally reducible dynamic problems have time complexity that degrades gracefully with the quality of bounded delay predictions. We categorize problems with known OMv lower bounds accordingly and give several upper bounds in the delay model that show that our lower bounds are almost tight.
We note that concurrent work by v.d.Brand et al. [SODA '24] and Liu and Srinivas [arXiv:2307.08890] independently study dynamic graph algorithms with predictions, but their work is mostly focused on showing upper bounds.},
author = {Henzinger, Monika H and Saha, Barna and Seybold, Martin P. and Ye, Christopher},
booktitle = {15th Innovations in Theoretical Computer Science Conference},
isbn = {9783959773096},
issn = {1868-8969},
location = {Berkeley, CA, United States},
pages = {62:1--62:25},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{On the complexity of algorithms with predictions for dynamic graph problems}},
doi = {10.4230/LIPIcs.ITCS.2024.62},
volume = {287},
year = {2024},
}
@article{18930,
abstract = {We study sumsets 𝒜 + ℬ in the set of squares 𝒮 (and, more generally, in the set of kth powers 𝒮k, where k ≥2 is an integer). It is known by a result of Gyarmati that 𝒜 + ℬ ⊂ 𝒮k ∩[1,N] implies that min(|𝒜|,|ℬ|) =Ok(logN). Here, we study how the upper bound on |ℬ| decreases, when the size of |𝒜| increases (or vice versa). In particular, if |𝒜| ≥ Ck1m m(logN)1m , then |ℬ| = Ok(m2logN), for sufficiently large N, a positive integer m and an explicit constant C > 0. For example, with m ∼ loglogN this gives: If |𝒜| ≥ CkloglogN,then |ℬ| = Ok(logN(loglogN)2).},
author = {Elsholtz, Christian and Wurzinger, Lena},
issn = {1464-3847},
journal = {The Quarterly Journal of Mathematics},
number = {4},
pages = {1243--1254},
publisher = {Oxford University Press},
title = {{Sumsets in the set of squares}},
doi = {10.1093/qmath/haae044},
volume = {75},
year = {2024},
}
@article{18934,
abstract = {The assembly of biomolecular condensate in eukaryotic cells and the accumulation of amyloid deposits in neurons are processes involving the nucleation and growth (NAG) of new protein phases. To therapeutically target protein phase separation, drug candidates are tested in in vitro assays that monitor the increase in the mass or size of the new phase. Limited mechanistic insight is, however, provided if empirical or untestable kinetic models are fitted to these progress curves. Here we present the web server NAGPKin that quantifies NAG rates using mass-based or size-based progress curves as the input data. A report is generated containing the fitted NAG parameters and elucidating the phase separation mechanisms at play. The NAG parameters can be used to predict particle size distributions of, for example, protein droplets formed by liquid-liquid phase separation (LLPS) or amyloid fibrils formed by protein aggregation. Because minimal intervention is required from the user, NAGPKin is a good platform for standardized reporting of LLPS and protein self-assembly data. NAGPKin is useful for drug discovery as well as for fundamental studies on protein phase separation. NAGPKin is freely available (no login required) at https://nagpkin.i3s.up.pt .},
author = {Sárkány, Zsuzsa and Figueiredo, Francisco and Macedo-Ribeiro, Sandra and Martins, Pedro M.},
issn = {1939-4586},
journal = {Molecular Biology of the Cell},
number = {3},
publisher = {American Society for Cell Biology},
title = {{NAGPKin: Nucleation-and-growth parameters from the kinetics of protein phase separation}},
doi = {10.1091/mbc.e23-07-0289},
volume = {35},
year = {2024},
}
@article{18937,
abstract = {A detailed structural, magnetic as well as dielectric dynamics study is carried out to investigate the influence of Bi3+ on YCrO3. All the samples crystalize in orthorhombic structure with Pnma symmetry and the grains are mostly stretched with Bi. A coexisting tunable fraction of both antiferromagnetic (AFM) and weak ferromagnetic (WFM) phases is acquired by the system down to Low-T. An abnormal negative magnetization in zero field is correlated to the competition among AFM and WFM phases. Maximum magnetization decreases while the coercivity first increases and then decreases with Bi is correlated to the competing effect between the local deformation and Cr–O–Cr exchange interaction. The magnetodielectric coupling with improved permittivity might be associated with the 6s2 lone pair electron of Bi3+. Furthermore, ac-conductivity increases with a decrease in activation energy (0.27–0.11 eV), is explained in the framework of structural model and charge carrier hopping between Cr3+ and Cr4+ ions.},
author = {Ray, Sujata Kumari and Pati, Anupama and Sahoo, Payala and Sahoo, A.K. and Singh, Saurabh and Takeuchi, Tsunehiro and Dash, S.},
issn = {0921-4526},
journal = {Physica B: Condensed Matter},
publisher = {Elsevier},
title = {{Tunable magnetoelectronic properties in Bi3+ substituted YCrO3}},
doi = {10.1016/j.physb.2024.416018},
volume = {685},
year = {2024},
}
@article{18938,
abstract = {The synthesis of proteins as encoded in the genome depends critically on translational fidelity. Nevertheless, errors inevitably occur, and those that result in reading frame shifts are particularly consequential because the resulting polypeptides are typically nonfunctional. Despite the generally maladaptive impact of such errors, the proper decoding of certain mRNAs, including many viral mRNAs, depends on a process known as programmed ribosomal frameshifting. The fact that these programmed events, commonly involving a shift to the –1 frame, occur at specific evolutionarily optimized “slippery” sites has facilitated mechanistic investigation. By contrast, less is known about the scope and nature of error (i.e., nonprogrammed) frameshifting. Here, we examine error frameshifting by monitoring spontaneous frameshift events that suppress the effects of single base pair deletions affecting two unrelated test proteins. To map the precise sites of frameshifting, we developed a targeted mass spectrometry–based method called “translational tiling proteomics” for interrogating the full set of possible –1 slippage events that could produce the observed frameshift suppression. Surprisingly, such events occur at many sites along the transcripts, involving up to one half of the available codons. Only a subset of these resembled canonical “slippery” sites, implicating alternative mechanisms potentially involving noncognate mispairing events. Additionally, the aggregate frequency of these events (ranging from 1 to 10% in our test cases) was higher than we might have anticipated. Our findings point to an unexpected degree of mechanistic diversity among ribosomal frameshifting events and suggest that frameshifted products may contribute more significantly to the proteome than generally assumed.},
author = {Springstein, Benjamin L and Paulo, Joao A. and Park, Hankum and Henry, Kemardo and Fleming, Eleanor and Feder, Zoë and Harper, J. Wade and Hochschild, Ann},
issn = {1091-6490},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
number = {6},
publisher = {National Academy of Sciences},
title = {{Systematic analysis of nonprogrammed frameshift suppression in E.coli via translational tiling proteomics}},
doi = {10.1073/pnas.2317453121},
volume = {121},
year = {2024},
}
@article{18940,
abstract = {BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. We identified several so far uncharacterized BMP-dependent transcription factors and signaling molecules, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules is zswim4-6, which encodes a novel nuclear protein that can modulate the pSMAD1/5 gradient and potentially promote BMP-dependent gene repression.},
author = {Knabl, Paul and Schauer, Alexandra and Pomreinke, Autumn P and Zimmermann, Bob and Rogers, Katherine W and Čapek, Daniel and Müller, Patrick and Genikhovich, Grigory},
issn = {2050-084X},
journal = {eLife},
publisher = {eLife Sciences Publications},
title = {{Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator}},
doi = {10.7554/elife.80803},
volume = {13},
year = {2024},
}
@article{18944,
abstract = {Understanding connectivity patterns exhibited by endangered species living in fragmented habitats is fundamental to improving management and conservation actions. Such improvements can be particularly pressing at the trailing edges of these habitats, where populations are facing the greatest challenges from climate change, and appear even more crucial if the species is commercially harvested. Seascape genetics have been increasingly used to meet these needs. In this study, we examined connectivity patterns among 32 populations of the oarweed kelp Laminaria digitata located at the species’ southern range limit. The distance (or sampling gap) between neighboring populations ranged from a few km to a few 100s of km. By genotyping 11 microsatellite markers, we aimed to (1) refine analyses of population structure; (2) test whether on-shelf islands are genetically more differentiated than mainland populations; (3) evaluate the relative importance of various abiotic conditions in shaping the genetic structure; and (4) evaluate if the relative importance of each environmental factor varied according to sampling schemes. Our analyses revealed a positive relationship between connectivity links and genetic diversity: populations with high levels of connectivity were genetically enriched while isolated populations showed signs of genetic erosion. The genetically impoverished populations corresponded to the southernmost populations as well as populations along the northern coast of Brittany (Locquirec, Saint-Malo Bay) and the northernmost population in Pas-de-Calais. By performing distance-based redundancy analysis on various sampling schemes, geographic distance appeared as the dominant factor influencing connectivity between populations separated by great distances, while hydrodynamic processes were the main factor when analyzing at a final spatial resolution.},
author = {Fouqueau, Louise and Reynes, L and Tempera, F and Bajjouk, T and Blanfuné, A and Chevalier, C and Laurans, M and Mauger, S and Sourisseau, M and Assis, J and Lévêque, L and Valero, M},
issn = {1616-1599},
journal = {Marine Ecology Progress Series},
pages = {23--42},
publisher = {Inter-Research Science Center},
title = {{Seascape genetic study on Laminaria digitata underscores the critical role of sampling schemes}},
doi = {10.3354/meps14640},
volume = {740},
year = {2024},
}
@article{18945,
abstract = {Vaccinia-related kinase 1 (VRK1) and the δ and ε isoforms of casein kinase 1 (CK1) are linked to various disease-relevant pathways. However, the lack of tool compounds for these kinases has significantly hampered our understanding of their cellular functions and therapeutic potential. Here, we describe the structure-based development of potent inhibitors of VRK1, a kinase highly expressed in various tumor types and crucial for cell proliferation and genome integrity. Kinome-wide profiling revealed that our compounds also inhibit CK1δ and CK1ε. We demonstrate that dihydropteridinones 35 and 36 mimic the cellular outcomes of VRK1 depletion. Complementary studies with existing CK1δ and CK1ε inhibitors suggest that these kinases may play overlapping roles in cell proliferation and genome instability. Together, our findings highlight the potential of VRK1 inhibition in treating p53-deficient tumors and possibly enhancing the efficacy of existing cancer therapies that target DNA stability or cell division.},
author = {de Souza Gama, Fernando H. and Dutra, Luiz A. and Hawgood, Michael and dos Reis, Caio Vinícius and Serafim, Ricardo A. M. and Ferreira, Marcos A. and Teodoro, Bruno V. M. and Takarada, Jéssica Emi and Santiago, André S. and Balourdas, Dimitrios-Ilias and Nilsson, Ann-Sofie and Urien, Bruno and Almeida, Vitor M. and Gileadi, Carina and Ramos, Priscila Z. and Testa Salmazo, Anita P and Vasconcelos, Stanley N. S. and Cunha, Micael R. and Mueller, Susanne and Knapp, Stefan and Massirer, Katlin B. and Elkins, Jonathan M. and Gileadi, Opher and Mascarello, Alessandra and Lemmens, Bennie B. L. G. and Guimarães, Cristiano R. W. and Azevedo, Hatylas and Couñago, Rafael M.},
issn = {1520-4804},
journal = {Journal of Medicinal Chemistry},
number = {11},
pages = {8609--8629},
publisher = {American Chemical Society},
title = {{Novel dihydropteridinone derivatives as potent inhibitors of the understudied human kinases vaccinia-related kinase 1 and casein kinase 1δ/ε}},
doi = {10.1021/acs.jmedchem.3c02250},
volume = {67},
year = {2024},
}
@inbook{18948,
abstract = {We consider a gas of N bosons with interactions in the mean-field scaling regime. We review a recent proof of the asymptotic expansion of its spectrum and eigenstates and two applications of this result, namely the derivation of an Edgeworth expansion for fluctuations of one-body operators and the computation of the binding energy of an inhomogeneous Bose gas to any order. Finally, we collect related results for the dynamics of the weakly interacting Bose gas and for the regularized Nelson model.},
author = {Bossmann, Lea and Leopold, Nikolai and Mitrouskas, David Johannes and Petrat, Sören},
booktitle = {Physics and the Nature of Reality},
editor = {Bassi, Angelo and Goldstein, Sheldon and Tumulka, Roderich and Zanghi, Nino},
isbn = {9783031454332},
issn = {2365-6425},
pages = {307--321},
publisher = {Springer Nature},
title = {{Asymptotic Analysis of the Weakly Interacting Bose Gas: A Collection of Recent Results and Applications}},
doi = {10.1007/978-3-031-45434-9_22},
volume = {215},
year = {2024},
}
@article{18949,
abstract = {Speciation research—the scientific field focused on understanding the origin and diversity of species—has a long and complex history. While relevant to one another, the specific goals and activities of speciation researchers are highly diverse, and scattered across a collection of different perspectives. Thus, our understanding of speciation will benefit from efforts to bridge scientific findings and the diverse people who do the work. In this paper, we outline two ways of integrating speciation research: (i) scientific integration, through the bringing together of ideas, data, and approaches; and (ii) social integration, by creating ways for a diversity of researchers to participate in the scientific process. We then discuss five challenges to integration: (i) the multidisciplinary nature of speciation research, (ii) the complex language of speciation; (iii) a bias toward certain study systems; (iv) the challenges of working across scales; and (v) inconsistent measures and reporting standards. We provide practical steps that individuals and groups can take to help overcome these challenges, and argue that integration is a team effort in which we all have a role to play.},
author = {Stankowski, Sean and Cutter, Asher D and Satokangas, Ina and Lerch, Brian A and Rolland, Jonathan and Smadja, Carole M and Segami Marzal, J Carolina and Cooney, Christopher R and Feulner, Philine G D and Domingos, Fabricius Maia Chaves Bicalho and North, Henry L and Yamaguchi, Ryo and Butlin, Roger K and Wolf, Jochen B W and Coughlan, Jenn and Heidbreder, Patrick and Hernández-Gutiérrez, Rebeca and Barnard-Kubow, Karen B and Peede, David and Rancilhac, Loïs and Salvador, Rodrigo Brincalepe and Thompson, Ken A and Stacy, Elizabeth A and Moyle, Leonie C and Garlovsky, Martin D and Maulana, Arif and Kantelinen, Annina and Cacho, N Ivalú and Schneemann, Hilde and Domínguez, Marisol and Dopman, Erik B and Lohse, Konrad and Rometsch, Sina J and Comeault, Aaron A and Merrill, Richard M and Scordato, Elizabeth S C and Singhal, Sonal and Pärssinen, Varpu and Lackey, Alycia C R and Kumar, Sanghamitra and Meier, Joana I and Barton, Nicholas H and Fraisse, Christelle and Ravinet, Mark and Kulmuni, Jonna},
issn = {2752-938X},
journal = {Evolutionary Journal of the Linnean Society},
number = {1},
publisher = {Oxford University Press},
title = {{Toward the integration of speciation research}},
doi = {10.1093/evolinnean/kzae001},
volume = {3},
year = {2024},
}
@article{18951,
abstract = {We consider local dynamics of the dimer model (perfect matchings) on hypercubic boxes [n]
d . These consist of successively switching the dimers along alternating cycles of prescribed (small) lengths. We study the connectivity properties of the dimer configuration space equipped with these transitions. Answering a question of Freire, Klivans, Milet, and Saldanha, we show that in three dimensions any configuration admits an alternating cycle of length at most 6. We further establish that any configuration on [n] d features order n d−2 alternating cycles of length at most 4d−2. We also prove that the dynamics of dimer configurations on the unit hypercube of dimension d is ergodic when switching alternating cycles of length at most 4d−4. Finally, in the planar but non-bipartite case, we show that parallelogram-shaped boxes in the triangular lattice are ergodic for switching alternating cycles of lengths 4 and 6 only, thus improving a result of Kenyon and Rémila, which also uses 8-cycles. None of our proofs make reference to height functions.},
author = {Hartarsky, Ivailo and Lichev, Lyuben and Toninelli, Fabio Lucio},
issn = {2308-5835},
journal = {Annales de l’Institut Henri Poincaré D, Combinatorics, Physics and their Interactions},
publisher = {EMS Press},
title = {{Local dimer dynamics in higher dimensions}},
doi = {10.4171/aihpd/200},
year = {2024},
}
@article{18952,
abstract = {A seventh blind test of crystal structure prediction was organized by the Cambridge Crystallographic Data Centre featuring seven target systems of varying complexity: a silicon and iodine-containing molecule, a copper coordination complex, a near-rigid molecule, a cocrystal, a polymorphic small agrochemical, a highly flexible polymorphic drug candidate, and a polymorphic morpholine salt. In this first of two parts focusing on structure generation methods, many crystal structure prediction (CSP) methods performed well for the small but flexible agrochemical compound, successfully reproducing the experimentally observed crystal structures, while few groups were successful for the systems of higher complexity. A powder X-ray diffraction (PXRD) assisted exercise demonstrated the use of CSP in successfully determining a crystal structure from a low-quality PXRD pattern. The use of CSP in the prediction of likely cocrystal stoichiometry was also explored, demonstrating multiple possible approaches. Crystallographic disorder emerged as an important theme throughout the test as both a challenge for analysis and a major achievement where two groups blindly predicted the existence of disorder for the first time. Additionally, large-scale comparisons of the sets of predicted crystal structures also showed that some methods yield sets that largely contain the same crystal structures.},
author = {Hunnisett, Lily M. and Nyman, Jonas and Francia, Nicholas and Abraham, Nathan S. and Adjiman, Claire S. and Aitipamula, Srinivasulu and Alkhidir, Tamador and Almehairbi, Mubarak and Anelli, Andrea and Anstine, Dylan M. and Anthony, John E. and Arnold, Joseph E. and Bahrami, Faezeh and Bellucci, Michael A. and Bhardwaj, Rajni M. and Bier, Imanuel and Bis, Joanna A. and Boese, A. Daniel and Bowskill, David H. and Bramley, James and Brandenburg, Jan Gerit and Braun, Doris E. and Butler, Patrick W. V. and Cadden, Joseph and Carino, Stephen and Chan, Eric J. and Chang, Chao and Cheng, Bingqing and Clarke, Sarah M. and Coles, Simon J. and Cooper, Richard I. and Couch, Ricky and Cuadrado, Ramon and Darden, Tom and Day, Graeme M. and Dietrich, Hanno and Ding, Yiming and DiPasquale, Antonio and Dhokale, Bhausaheb and van Eijck, Bouke P. and Elsegood, Mark R. J. and Firaha, Dzmitry and Fu, Wenbo and Fukuzawa, Kaori and Glover, Joseph and Goto, Hitoshi and Greenwell, Chandler and Guo, Rui and Harter, Jürgen and Helfferich, Julian and Hofmann, Detlef W. M. and Hoja, Johannes and Hone, John and Hong, Richard and Hutchison, Geoffrey and Ikabata, Yasuhiro and Isayev, Olexandr and Ishaque, Ommair and Jain, Varsha and Jin, Yingdi and Jing, Aling and Johnson, Erin R. and Jones, Ian and Jose, K. V. Jovan and Kabova, Elena A. and Keates, Adam and Kelly, Paul F. and Khakimov, Dmitry and Konstantinopoulos, Stefanos and Kuleshova, Liudmila N. and Li, He and Lin, Xiaolu and List, Alexander and Liu, Congcong and Liu, Yifei Michelle and Liu, Zenghui and Liu, Zhi-Pan and Lubach, Joseph W. and Marom, Noa and Maryewski, Alexander A. and Matsui, Hiroyuki and Mattei, Alessandra and Mayo, R. Alex and Melkumov, John W. and Mohamed, Sharmarke and Momenzadeh Abardeh, Zahrasadat and Muddana, Hari S. and Nakayama, Naofumi and Nayal, Kamal Singh and Neumann, Marcus A. and Nikhar, Rahul and Obata, Shigeaki and O'Connor, Dana and Oganov, Artem R. and Okuwaki, Koji and Otero-de-la-Roza, Alberto and Pantelides, Constantinos C. and Parkin, Sean and Pickard, Chris J. and Pilia, Luca and Pivina, Tatyana and Podeszwa, Rafał and Price, Alastair J. A. and Price, Louise S. and Price, Sarah L. and Probert, Michael R. and Pulido, Angeles and Ramteke, Gunjan Rajendra and Rehman, Atta Ur and Reutzel-Edens, Susan M. and Rogal, Jutta and Ross, Marta J. and Rumson, Adrian F. and Sadiq, Ghazala and Saeed, Zeinab M. and Salimi, Alireza and Salvalaglio, Matteo and Sanders de Almada, Leticia and Sasikumar, Kiran and Sekharan, Sivakumar and Shang, Cheng and Shankland, Kenneth and Shinohara, Kotaro and Shi, Baimei and Shi, Xuekun and Skillman, A. Geoffrey and Song, Hongxing and Strasser, Nina and van de Streek, Jacco and Sugden, Isaac J. and Sun, Guangxu and Szalewicz, Krzysztof and Tan, Benjamin I. and Tan, Lu and Tarczynski, Frank and Taylor, Christopher R. and Tkatchenko, Alexandre and Tom, Rithwik and Tuckerman, Mark E. and Utsumi, Yohei and Vogt-Maranto, Leslie and Weatherston, Jake and Wilkinson, Luke J. and Willacy, Robert D. and Wojtas, Lukasz and Woollam, Grahame R. and Yang, Zhuocen and Yonemochi, Etsuo and Yue, Xin and Zeng, Qun and Zhang, Yizu and Zhou, Tian and Zhou, Yunfei and Zubatyuk, Roman and Cole, Jason C.},
issn = {2052-5206},
journal = {Acta Crystallographica Section B Structural Science, Crystal Engineering and Materials},
number = {6},
pages = {517--547},
publisher = {International Union of Crystallography},
title = {{The seventh blind test of crystal structure prediction: Structure generation methods}},
doi = {10.1107/s2052520624007492},
volume = {80},
year = {2024},
}
@inproceedings{18955,
abstract = {We give a simple proof that assuming the Exponential Time Hypothesis (ETH), determining the winner of a Rabin game cannot be done in time 2o(k log k) · nO(1), where k is the number of pairs of vertex subsets involved in the winning condition and n is the vertex count of the game graph. While this result follows from the lower bounds provided by Calude et al [SIAM J. Comp. 2022], our reduction is considerably simpler and arguably provides more insight into the complexity of the problem. In fact, the analogous lower bounds discussed by Calude et al, for solving Muller games and multidimensional parity games, follow as simple corollaries of our approach. Our reduction also highlights the usefulness of a certain pivot problem — Permutation SAT — which may be of independent interest.},
author = {Casares, Antonio and Pilipczuk, Marcin and Pilipczuk, Michał and Souza, Uéverton S. and Thejaswini, K. S.},
booktitle = {2024 Symposium on Simplicity in Algorithms},
isbn = {9781611977936},
location = {Alexandria, VA, United States},
pages = {160--167},
publisher = {Society for Industrial and Applied Mathematics},
title = {{Simple and tight complexity lower bounds for solving Rabin games}},
doi = {10.1137/1.9781611977936.16},
year = {2024},
}
@inproceedings{18956,
abstract = {Group Activity Recognition (GAR) aims to detect the activity performed by multiple actors in a scene. Prior works model the spatio-temporal features based on the RGB, optical flow or keypoint data types. On the contrary, our hypothesis is that by only using the RGB data without temporality, the performance can be maintained with a negligible loss in accuracy. To that end, we propose a novel GAR technique for volleyball videos, DECOMPL, which consists of two complementary branches. In the visual branch, it extracts the features using attention pooling. In the coordinate branch, it considers the configuration of the players and extracts the spatial information from the box coordinates. Moreover, we analyzed the Volleyball dataset that the recent literature is mostly based on, and systematically reannotated it to emphasize the group concept. Experimental results demonstrated the effectiveness of the proposed model DECOMPL, which delivered the best/second best GAR performance with the reannotations/original annotations among the comparable state-of-the-art methods. Code and new annotations are available at GitHub: https://github.com/berkerdemirel/decompl},
author = {Demirel, Berker and Ozkan, Huseyin},
booktitle = {2024 IEEE International Conference on Image Processing},
issn = {2381-8549},
location = {Abu Dhabi, United Arab Emirates},
pages = {977--983},
publisher = {IEEE},
title = {{Decompl: Decompositional learning with attention pooling for group activity recognition from a single volleyball image}},
doi = {10.1109/icip51287.2024.10647499},
year = {2024},
}