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1579 Publications visible to you, out of a total of 1579
Expansion of Accreting Main-sequence Stars during Rapid Mass Transfer

Abstract (Expand)

Accreting main-sequence stars expand significantly when the mass accretion timescale is much shorter than their thermal timescales. This occurs during mass transfer from an evolved giant star onto a … main-sequence companion in a binary system and is an important phase in the formation of compact binaries including X-ray binaries, cataclysmic variables, and gravitational-wave sources. In this study, we compute 1D stellar models of main-sequence accretors with different initial masses and accretion rates. The calculations are used to derive semianalytical approximations to the maximum expansion radius. We assume that mass transfer remains fully conservative as long as the inflated accretor fits within its Roche lobe, leading stars to behave like hamsters, stuffing excess material behind their expanding cheeks. We suggest a physically motivated prescription for the mass growth of such "hamstars," which can be used to determine mass-transfer efficiency in rapid binary population synthesis models. With this prescription, we estimate that progenitors of high-mass X-ray binaries and gravitational-wave sources may have experienced highly nonconservative mass transfer. In contrast, for low-mass accretors, the accretion timescale can exceed the thermal timescale by a larger factor without causing significant radial expansion.

Authors: Mike Lau, Ryosuke Hirai, Ilya Mandel, Christopher A. Tout

Date Published: 24th Apr 2024

Publication Type: Journal

Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome 2B4

Abstract (Expand)

Cytochrome P450 2B4 (CYP 2B4) is one of the best characterized CYPs and serves as a key model system for understanding the mechanisms of microsomal class II CYPs, which metabolize most known drugs. The …n drugs. The highly flexible nature of CYP 2B4 is apparent from crystal structures that show the active site with either a wide open or a closed heme binding cavity. Here, we investigated the conformational ensemble of the full-length CYP 2B4 in a phospholipid bilayer, using multiresolution molecular dynamics (MD) simulations. Coarse-grained MD simulations revealed two predominant orientations of CYP 2B4's globular domain with respect to the bilayer. Their refinement by atomistic resolution MD showed adaptation of the enzyme's interaction with the lipid bilayer, leading to open configurations that facilitate ligand access to the heme binding cavity. CAVER analysis of enzyme tunnels, AquaDuct analysis of water routes, and Random Acceleration Molecular Dynamics simulations of ligand dissociation support the conformation-dependent passage of molecules between the active site and the protein surroundings. Furthermore, simulation of the re-entry of the inhibitor bifonazole into the open conformation of CYP 2B4 resulted in binding at a transient hydrophobic pocket within the active site cavity that may play a role in substrate binding or allosteric regulation. Together, these results show how the open conformation of CYP 2B4 facilitates binding of substrates from and release of products to the membrane, whereas the closed conformation prolongs the residence time of substrates or inhibitors and selectively allows the passage of smaller reactants via the solvent and water channels.

Authors: Sungho Bosco Han, Jonathan Teuffel, Goutam Mukherjee, Rebecca C. Wade

Date Published: 18th Apr 2024

Publication Type: Journal

Attention or convolution: Transformer encoders in audio language models for inference efficiency

Abstract

Not specified

Authors: Sungho Jeon, Ching-Feng Yeh, Hakan Inan, Wei-Ning Hsu, Rashi Rungta, Yashar Mehdad, Daniel Bikel

Date Published: 14th Apr 2024

Publication Type: InProceedings

Complexity of avian evolution revealed by family-level genomes

Abstract (Expand)

Despite tremendous efforts in the past decades, relationships among main avian lineages remain heavily debated without a clear resolution. Discrepancies have been attributed to diversity of species … sampled, phylogenetic method, and the choice of genomic regions 1–3. Here, we address these issues by analyzing genomes of 363 bird species 4 (218 taxonomic families, 92% of total). Using intergenic regions and coalescent methods, we present a well-supported tree but also a remarkable degree of discordance. The tree confirms that Neoaves experienced rapid radiation at or near the Cretaceous–Paleogene (K–Pg) boundary. Sufficient loci rather than extensive taxon sampling were more effective in resolving difficult nodes. Remaining recalcitrant nodes involve species that challenge modeling due to extreme GC content, variable substitution rates, incomplete lineage sorting, or complex evolutionary events such as ancient hybridization. Assessment of the impacts of different genomic partitions showed high heterogeneity across the genome. We discovered sharp increases in effective population size, substitution rates, and relative brain size following the K–Pg extinction event, supporting the hypothesis that emerging ecological opportunities catalyzed the diversification of modern birds. The resulting phylogenetic estimate offers novel insights into the rapid radiation of modern birds and provides a taxon-rich backbone tree for future comparative studies.

Authors: Josefin Stiller, Shaohong Feng, Al-Aabid Chowdhury, Iker Rivas-González, David A. Duchêne, Qi Fang, Yuan Deng, Alexey Kozlov, Alexandros Stamatakis, Santiago Claramunt, Jacqueline M. T. Nguyen, Simon Y. W. Ho, Brant C. Faircloth, Julia Haag, Peter Houde, Joel Cracraft, Metin Balaban, Uyen Mai, Guangji Chen, Rongsheng Gao, Chengran Zhou, Yulong Xie, Zijian Huang, Zhen Cao, Zhi Yan, Huw A. Ogilvie, Luay Nakhleh, Bent Lindow, Benoit Morel, Jon Fjeldså, Peter A. Hosner, Rute R. da Fonseca, Bent Petersen, Joseph A. Tobias, Tamás Székely, Jonathan David Kennedy, Andrew Hart Reeve, Andras Liker, Martin Stervander, Agostinho Antunes, Dieter Thomas Tietze, Mads Bertelsen, Fumin Lei, Carsten Rahbek, Gary R. Graves, Mikkel H. Schierup, Tandy Warnow, Edward L. Braun, M. Thomas P. Gilbert, Erich D. Jarvis, Siavash Mirarab, Guojie Zhang

Date Published: 1st Apr 2024

Publication Type: Journal

Myotubularin-related-protein-7 inhibits mutant (G12V) K-RAS by direct interaction

Abstract

Not specified

Authors: Philip Weidner, Daniel Saar, Michaela Söhn, Torsten Schroeder, Yanxiong Yu, Frank G. Zöllner, Norbert Ponelies, Xiaobo Zhou, André Zwicky, Florian N. Rohrbacher, Vijaya R. Pattabiraman, Matthias Tanriver, Alexander Bauer, Hazem Ahmed, Simon M. Ametamey, Philipp Riffel, Rony Seger, Jeffrey W. Bode, Rebecca C. Wade, Matthias P.A. Ebert, Birthe B. Kragelund, Elke Burgermeister

Date Published: 1st Apr 2024

Publication Type: Journal

Thermonuclear explosions as Type II supernovae

Abstract

Not specified

Authors: Alexandra Kozyreva, Javier Morán-Fraile, Alexander Holas, Vincent A. Bronner, Friedrich K. Röpke, Nikolay Pavlyuk, Alexey Mironov, Dmitry Tsvetkov

Date Published: 1st Apr 2024

Publication Type: Journal

Grappa – A Machine Learned Molecular Mechanics Force Field

Abstract

Not specified

Authors: Leif Seute, Eric Hartmann, Jan Stühmer, Frauke Gräter

Date Published: 25th Mar 2024

Publication Type: Journal

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