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is-link">Go</button> </div> </div> </form> </div> </div> <ol class="breathe-horizontal" start="1"> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2410.08938">arXiv:2410.08938</a> <span> [<a href="https://arxiv.org/pdf/2410.08938">pdf</a>, <a href="https://arxiv.org/format/2410.08938">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Quantitative Methods">q-bio.QM</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Machine Learning">cs.LG</span> </div> </div> <p class="title is-5 mathjax"> KinDEL: DNA-Encoded Library Dataset for Kinase Inhibitors </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Chen%2C+B">Benson Chen</a>, <a href="/search/q-bio?searchtype=author&query=Danel%2C+T">Tomasz Danel</a>, <a href="/search/q-bio?searchtype=author&query=McEnaney%2C+P+J">Patrick J. McEnaney</a>, <a href="/search/q-bio?searchtype=author&query=Jain%2C+N">Nikhil Jain</a>, <a href="/search/q-bio?searchtype=author&query=Novikov%2C+K">Kirill Novikov</a>, <a href="/search/q-bio?searchtype=author&query=Akki%2C+S+U">Spurti Umesh Akki</a>, <a href="/search/q-bio?searchtype=author&query=Turnbull%2C+J+L">Joshua L. Turnbull</a>, <a href="/search/q-bio?searchtype=author&query=Pandya%2C+V+A">Virja Atul Pandya</a>, <a href="/search/q-bio?searchtype=author&query=Belotserkovskii%2C+B+P">Boris P. Belotserkovskii</a>, <a href="/search/q-bio?searchtype=author&query=Weaver%2C+J+B">Jared Bryce Weaver</a>, <a href="/search/q-bio?searchtype=author&query=Biswas%2C+A">Ankita Biswas</a>, <a href="/search/q-bio?searchtype=author&query=Nguyen%2C+D">Dat Nguyen</a>, <a href="/search/q-bio?searchtype=author&query=Dreiman%2C+G+H+S">Gabriel H. S. Dreiman</a>, <a href="/search/q-bio?searchtype=author&query=Sultan%2C+M">Mohammad Sultan</a>, <a href="/search/q-bio?searchtype=author&query=Stanley%2C+N">Nathaniel Stanley</a>, <a href="/search/q-bio?searchtype=author&query=Whalen%2C+D+M">Daniel M Whalen</a>, <a href="/search/q-bio?searchtype=author&query=Kanichar%2C+D">Divya Kanichar</a>, <a href="/search/q-bio?searchtype=author&query=Klein%2C+C">Christoph Klein</a>, <a href="/search/q-bio?searchtype=author&query=Fox%2C+E">Emily Fox</a>, <a href="/search/q-bio?searchtype=author&query=Watts%2C+R+E">R. Edward Watts</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2410.08938v1-abstract-short" style="display: inline;"> DNA-Encoded Libraries (DEL) are combinatorial small molecule libraries that offer an efficient way to characterize diverse chemical spaces. Selection experiments using DELs are pivotal to drug discovery efforts, enabling high-throughput screens for hit finding. However, limited availability of public DEL datasets hinders the advancement of computational techniques designed to process such data. To… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2410.08938v1-abstract-full').style.display = 'inline'; document.getElementById('2410.08938v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2410.08938v1-abstract-full" style="display: none;"> DNA-Encoded Libraries (DEL) are combinatorial small molecule libraries that offer an efficient way to characterize diverse chemical spaces. Selection experiments using DELs are pivotal to drug discovery efforts, enabling high-throughput screens for hit finding. However, limited availability of public DEL datasets hinders the advancement of computational techniques designed to process such data. To bridge this gap, we present KinDEL, one of the first large, publicly available DEL datasets on two kinases: Mitogen-Activated Protein Kinase 14 (MAPK14) and Discoidin Domain Receptor Tyrosine Kinase 1 (DDR1). Interest in this data modality is growing due to its ability to generate extensive supervised chemical data that densely samples around select molecular structures. Demonstrating one such application of the data, we benchmark different machine learning techniques to develop predictive models for hit identification; in particular, we highlight recent structure-based probabilistic approaches. Finally, we provide biophysical assay data, both on- and off-DNA, to validate our models on a smaller subset of molecules. Data and code for our benchmarks can be found at: https://github.com/insitro/kindel. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2410.08938v1-abstract-full').style.display = 'none'; document.getElementById('2410.08938v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 11 October, 2024; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> October 2024. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2308.08708">arXiv:2308.08708</a> <span> [<a href="https://arxiv.org/pdf/2308.08708">pdf</a>, <a href="https://arxiv.org/format/2308.08708">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Artificial Intelligence">cs.AI</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Computers and Society">cs.CY</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Machine Learning">cs.LG</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Neurons and Cognition">q-bio.NC</span> </div> </div> <p class="title is-5 mathjax"> Consciousness in Artificial Intelligence: Insights from the Science of Consciousness </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Butlin%2C+P">Patrick Butlin</a>, <a href="/search/q-bio?searchtype=author&query=Long%2C+R">Robert Long</a>, <a href="/search/q-bio?searchtype=author&query=Elmoznino%2C+E">Eric Elmoznino</a>, <a href="/search/q-bio?searchtype=author&query=Bengio%2C+Y">Yoshua Bengio</a>, <a href="/search/q-bio?searchtype=author&query=Birch%2C+J">Jonathan Birch</a>, <a href="/search/q-bio?searchtype=author&query=Constant%2C+A">Axel Constant</a>, <a href="/search/q-bio?searchtype=author&query=Deane%2C+G">George Deane</a>, <a href="/search/q-bio?searchtype=author&query=Fleming%2C+S+M">Stephen M. Fleming</a>, <a href="/search/q-bio?searchtype=author&query=Frith%2C+C">Chris Frith</a>, <a href="/search/q-bio?searchtype=author&query=Ji%2C+X">Xu Ji</a>, <a href="/search/q-bio?searchtype=author&query=Kanai%2C+R">Ryota Kanai</a>, <a href="/search/q-bio?searchtype=author&query=Klein%2C+C">Colin Klein</a>, <a href="/search/q-bio?searchtype=author&query=Lindsay%2C+G">Grace Lindsay</a>, <a href="/search/q-bio?searchtype=author&query=Michel%2C+M">Matthias Michel</a>, <a href="/search/q-bio?searchtype=author&query=Mudrik%2C+L">Liad Mudrik</a>, <a href="/search/q-bio?searchtype=author&query=Peters%2C+M+A+K">Megan A. K. Peters</a>, <a href="/search/q-bio?searchtype=author&query=Schwitzgebel%2C+E">Eric Schwitzgebel</a>, <a href="/search/q-bio?searchtype=author&query=Simon%2C+J">Jonathan Simon</a>, <a href="/search/q-bio?searchtype=author&query=VanRullen%2C+R">Rufin VanRullen</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2308.08708v3-abstract-short" style="display: inline;"> Whether current or near-term AI systems could be conscious is a topic of scientific interest and increasing public concern. This report argues for, and exemplifies, a rigorous and empirically grounded approach to AI consciousness: assessing existing AI systems in detail, in light of our best-supported neuroscientific theories of consciousness. We survey several prominent scientific theories of con… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2308.08708v3-abstract-full').style.display = 'inline'; document.getElementById('2308.08708v3-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2308.08708v3-abstract-full" style="display: none;"> Whether current or near-term AI systems could be conscious is a topic of scientific interest and increasing public concern. This report argues for, and exemplifies, a rigorous and empirically grounded approach to AI consciousness: assessing existing AI systems in detail, in light of our best-supported neuroscientific theories of consciousness. We survey several prominent scientific theories of consciousness, including recurrent processing theory, global workspace theory, higher-order theories, predictive processing, and attention schema theory. From these theories we derive "indicator properties" of consciousness, elucidated in computational terms that allow us to assess AI systems for these properties. We use these indicator properties to assess several recent AI systems, and we discuss how future systems might implement them. Our analysis suggests that no current AI systems are conscious, but also suggests that there are no obvious technical barriers to building AI systems which satisfy these indicators. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2308.08708v3-abstract-full').style.display = 'none'; document.getElementById('2308.08708v3-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 22 August, 2023; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 16 August, 2023; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> August 2023. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2212.13543">arXiv:2212.13543</a> <span> [<a href="https://arxiv.org/pdf/2212.13543">pdf</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Molecular Networks">q-bio.MN</span> </div> </div> <p class="title is-5 mathjax"> Democratising Knowledge Representation with BioCypher </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Lobentanzer%2C+S">Sebastian Lobentanzer</a>, <a href="/search/q-bio?searchtype=author&query=Aloy%2C+P">Patrick Aloy</a>, <a href="/search/q-bio?searchtype=author&query=Baumbach%2C+J">Jan Baumbach</a>, <a href="/search/q-bio?searchtype=author&query=Bohar%2C+B">Balazs Bohar</a>, <a href="/search/q-bio?searchtype=author&query=Charoentong%2C+P">Pornpimol Charoentong</a>, <a href="/search/q-bio?searchtype=author&query=Danhauser%2C+K">Katharina Danhauser</a>, <a href="/search/q-bio?searchtype=author&query=Do%C4%9Fan%2C+T">Tunca Do臒an</a>, <a href="/search/q-bio?searchtype=author&query=Dreo%2C+J">Johann Dreo</a>, <a href="/search/q-bio?searchtype=author&query=Dunham%2C+I">Ian Dunham</a>, <a href="/search/q-bio?searchtype=author&query=Fernandez-Torras%2C+A">Adri脿 Fernandez-Torras</a>, <a href="/search/q-bio?searchtype=author&query=Gyori%2C+B+M">Benjamin M. Gyori</a>, <a href="/search/q-bio?searchtype=author&query=Hartung%2C+M">Michael Hartung</a>, <a href="/search/q-bio?searchtype=author&query=Hoyt%2C+C+T">Charles Tapley Hoyt</a>, <a href="/search/q-bio?searchtype=author&query=Klein%2C+C">Christoph Klein</a>, <a href="/search/q-bio?searchtype=author&query=Korcsmaros%2C+T">Tamas Korcsmaros</a>, <a href="/search/q-bio?searchtype=author&query=Maier%2C+A">Andreas Maier</a>, <a href="/search/q-bio?searchtype=author&query=Mann%2C+M">Matthias Mann</a>, <a href="/search/q-bio?searchtype=author&query=Ochoa%2C+D">David Ochoa</a>, <a href="/search/q-bio?searchtype=author&query=Pareja-Lorente%2C+E">Elena Pareja-Lorente</a>, <a href="/search/q-bio?searchtype=author&query=Popp%2C+F">Ferdinand Popp</a>, <a href="/search/q-bio?searchtype=author&query=Preusse%2C+M">Martin Preusse</a>, <a href="/search/q-bio?searchtype=author&query=Probul%2C+N">Niklas Probul</a>, <a href="/search/q-bio?searchtype=author&query=Schwikowski%2C+B">Benno Schwikowski</a>, <a href="/search/q-bio?searchtype=author&query=Sen%2C+B">B眉nyamin Sen</a>, <a href="/search/q-bio?searchtype=author&query=Strauss%2C+M+T">Maximilian T. Strauss</a> , et al. (4 additional authors not shown) </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2212.13543v3-abstract-short" style="display: inline;"> Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessi… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2212.13543v3-abstract-full').style.display = 'inline'; document.getElementById('2212.13543v3-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2212.13543v3-abstract-full" style="display: none;"> Standardising the representation of biomedical knowledge among all researchers is an insurmountable task, hindering the effectiveness of many computational methods. To facilitate harmonisation and interoperability despite this fundamental challenge, we propose to standardise the framework of knowledge graph creation instead. We implement this standardisation in BioCypher, a FAIR (findable, accessible, interoperable, reusable) framework to transparently build biomedical knowledge graphs while preserving provenances of the source data. Mapping the knowledge onto biomedical ontologies helps to balance the needs for harmonisation, human and machine readability, and ease of use and accessibility to non-specialist researchers. We demonstrate the usefulness of this framework on a variety of use cases, from maintenance of task-specific knowledge stores, to interoperability between biomedical domains, to on-demand building of task-specific knowledge graphs for federated learning. BioCypher (https://biocypher.org) frees up valuable developer time; we encourage further development and usage by the community. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2212.13543v3-abstract-full').style.display = 'none'; document.getElementById('2212.13543v3-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 17 January, 2023; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 27 December, 2022; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> December 2022. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">34 pages, 6 figures; submitted to Nature Biotechnology</span> </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/2111.11880">arXiv:2111.11880</a> <span> [<a href="https://arxiv.org/pdf/2111.11880">pdf</a>, <a href="https://arxiv.org/format/2111.11880">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Genomics">q-bio.GN</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1038/s41467-022-30843-1">10.1038/s41467-022-30843-1 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> CRISPR SWAPnDROP -- A multifunctional system for genome editing and large-scale interspecies gene transfer </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Teufel%2C+M">Marc Teufel</a>, <a href="/search/q-bio?searchtype=author&query=Klein%2C+C+A">Carlo A. Klein</a>, <a href="/search/q-bio?searchtype=author&query=Mager%2C+M">Maurice Mager</a>, <a href="/search/q-bio?searchtype=author&query=Sobetzko%2C+P">Patrick Sobetzko</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="2111.11880v1-abstract-short" style="display: inline;"> The need for diverse chromosomal modifications in biotechnology, synthetic biology and basic research requires the development of new technologies. With CRISPR SWAPnDROP, we extend the limits of genome editing to large-scale in-vivo DNA transfer between bacterial species. Its modular platform approach facilitates species specific adaptation to confer genome editing in various species. In this stud… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2111.11880v1-abstract-full').style.display = 'inline'; document.getElementById('2111.11880v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="2111.11880v1-abstract-full" style="display: none;"> The need for diverse chromosomal modifications in biotechnology, synthetic biology and basic research requires the development of new technologies. With CRISPR SWAPnDROP, we extend the limits of genome editing to large-scale in-vivo DNA transfer between bacterial species. Its modular platform approach facilitates species specific adaptation to confer genome editing in various species. In this study, we show the implementation of the CRISPR SWAPnDROP concept for the model organism Escherichia coli and the currently fastest growing and biotechnologically relevant organism Vibrio natriegens. We demonstrate the excision, transfer and integration of 151kb chromosomal DNA between E. coli strains and from E. coli to V. natriegens without size-limiting intermediate DNA extraction. With the transfer of the E. coli MG1655 wild type lac operon, we establish a functional lactose and galactose degradation pathway in V. natriegens to extend its biotechnological spectrum. We also transfer the E. coli DH5alpha lac operon and make V. natriegens capable of alpha-complementation - a step towards an ultra-fast cloning strain. Furthermore, CRISPR SWAPnDROP is designed to be the swiss army knife of genome engineering. Its spectrum of application comprises scarless, marker-free, iterative and parallel insertions and deletions, genome rearrangements, as well as gene transfer between strains and across species. The modular character facilitates DNA library applications and the recycling of standardized parts. Its novel multi-color scarless co-selection system significantly improves editing efficiency to 92% for single edits and 83% for quadruple edits and provides visual quality controls throughout the assembly and editing process. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('2111.11880v1-abstract-full').style.display = 'none'; document.getElementById('2111.11880v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 23 November, 2021; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> November 2021. </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/1502.00156">arXiv:1502.00156</a> <span> [<a href="https://arxiv.org/pdf/1502.00156">pdf</a>, <a href="https://arxiv.org/ps/1502.00156">ps</a>, <a href="https://arxiv.org/format/1502.00156">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Subcellular Processes">q-bio.SC</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1186/2046-1682-5-22">10.1186/2046-1682-5-22 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Baschek%2C+J+E">Johanna E. Baschek</a>, <a href="/search/q-bio?searchtype=author&query=Klein%2C+H+C+R">Heinrich C. R. Klein</a>, <a href="/search/q-bio?searchtype=author&query=Schwarz%2C+U+S">Ulrich S. Schwarz</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="1502.00156v1-abstract-short" style="display: inline;"> In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the time course of assembly (direct assembly). In some cases, however, binding site… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1502.00156v1-abstract-full').style.display = 'inline'; document.getElementById('1502.00156v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="1502.00156v1-abstract-full" style="display: none;"> In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually assume that the bonds leading to cluster formation have constant reactivity over the time course of assembly (direct assembly). In some cases, however, binding sites between the capsomers have been reported to be activated during the self-assembly process (hierarchical assembly). In order to study possible advantages of such hierarchical schemes for icosahedral virus capsid assembly, we use Brownian dynamics simulations of a patchy particle model that allows us to switch binding sites on and off during assembly. For T1 viruses, we implement a hierarchical assembly scheme where inter-capsomer bonds become active only if a complete pentamer has been assembled. We find direct assembly to be favorable for reversible bonds allowing for repeated structural reorganizations, while hierarchical assembly is favorable for strong bonds with small dissociation rate, as this situation is less prone to kinetic trapping. However, at the same time it is more vulnerable to monomer starvation during the final phase. Increasing the number of initial monomers does have only a weak effect on these general features. The differences between the two assembly schemes become more pronounced for more complex virus geometries, as shown here for T3 viruses, which assemble through homogeneous pentamers and heterogeneous hexamers in the hierarchical scheme. In order to complement the simulations for this more complicated case, we introduce a master equation approach that agrees well with the simulation results. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1502.00156v1-abstract-full').style.display = 'none'; document.getElementById('1502.00156v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 31 January, 2015; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> February 2015. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">Revtex, 31 pages, 9 EPS figures</span> </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> BMC Biophysics 5:22 (2012) </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/1502.00155">arXiv:1502.00155</a> <span> [<a href="https://arxiv.org/pdf/1502.00155">pdf</a>, <a href="https://arxiv.org/ps/1502.00155">ps</a>, <a href="https://arxiv.org/format/1502.00155">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Subcellular Processes">q-bio.SC</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Biological Physics">physics.bio-ph</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Biomolecules">q-bio.BM</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1088/1478-3975/12/1/016014">10.1088/1478-3975/12/1/016014 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> Role of dynamic capsomere supply for viral capsid self-assembly </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Boettcher%2C+M+A">Marvin A. Boettcher</a>, <a href="/search/q-bio?searchtype=author&query=Klein%2C+H+C+R">Heinrich C. R. Klein</a>, <a href="/search/q-bio?searchtype=author&query=Schwarz%2C+U+S">Ulrich S. Schwarz</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="1502.00155v1-abstract-short" style="display: inline;"> Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to persistent infections, capsomeres are continuously produced in the cytoplasm of the host cell while completed capsids exit the cell for a new round of infection. Here we… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1502.00155v1-abstract-full').style.display = 'inline'; document.getElementById('1502.00155v1-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="1502.00155v1-abstract-full" style="display: none;"> Many viruses rely on the self-assembly of their capsids to protect and transport their genomic material. For many viral systems, in particular for human viruses like hepatitis B, adeno or human immunodeficiency virus, that lead to persistent infections, capsomeres are continuously produced in the cytoplasm of the host cell while completed capsids exit the cell for a new round of infection. Here we use coarse-grained Brownian dynamics simulations of a generic patchy particle model to elucidate the role of the dynamic supply of capsomeres for the reversible self-assembly of empty T1 icosahedral virus capsids. We find that for high rates of capsomere influx only a narrow range of bond strengths exists for which a steady state of continuous capsid production is possible. For bond strengths smaller and larger than this optimal value, the reaction volume becomes crowded by small and large intermediates, respectively. For lower rates of capsomere influx a broader range of bond strengths exists for which a steady state of continuous capsid production is established, although now the production rate of capsids is smaller. Thus our simulations suggest that the importance of an optimal bond strength for viral capsid assembly typical for in vitro conditions can be reduced by the dynamic influx of capsomeres in a cellular environment. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1502.00155v1-abstract-full').style.display = 'none'; document.getElementById('1502.00155v1-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 31 January, 2015; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> February 2015. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">Revtex, 26 pages, 7 EPS figures</span> </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> Phys. Biol. 12:016014 (2015) </p> </li> <li class="arxiv-result"> <div class="is-marginless"> <p class="list-title is-inline-block"><a href="https://arxiv.org/abs/1404.5827">arXiv:1404.5827</a> <span> [<a href="https://arxiv.org/pdf/1404.5827">pdf</a>, <a href="https://arxiv.org/format/1404.5827">other</a>] </span> </p> <div class="tags is-inline-block"> <span class="tag is-small is-link tooltip is-tooltip-top" data-tooltip="Subcellular Processes">q-bio.SC</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Soft Condensed Matter">cond-mat.soft</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Statistical Mechanics">cond-mat.stat-mech</span> <span class="tag is-small is-grey tooltip is-tooltip-top" data-tooltip="Biomolecules">q-bio.BM</span> </div> <div class="is-inline-block" style="margin-left: 0.5rem"> <div class="tags has-addons"> <span class="tag is-dark is-size-7">doi</span> <span class="tag is-light is-size-7"><a class="" href="https://doi.org/10.1063/1.4873708">10.1063/1.4873708 <i class="fa fa-external-link" aria-hidden="true"></i></a></span> </div> </div> </div> <p class="title is-5 mathjax"> Studying protein assembly with reversible Brownian dynamics of patchy particles </p> <p class="authors"> <span class="search-hit">Authors:</span> <a href="/search/q-bio?searchtype=author&query=Klein%2C+H+C+R">Heinrich C. R. Klein</a>, <a href="/search/q-bio?searchtype=author&query=Schwarz%2C+U+S">Ulrich S. Schwarz</a> </p> <p class="abstract mathjax"> <span class="has-text-black-bis has-text-weight-semibold">Abstract</span>: <span class="abstract-short has-text-grey-dark mathjax" id="1404.5827v2-abstract-short" style="display: inline;"> Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy parti… <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1404.5827v2-abstract-full').style.display = 'inline'; document.getElementById('1404.5827v2-abstract-short').style.display = 'none';">▽ More</a> </span> <span class="abstract-full has-text-grey-dark mathjax" id="1404.5827v2-abstract-full" style="display: none;"> Assembly of protein complexes like virus shells, the centriole, the nuclear pore complex or the actin cytoskeleton is strongly determined by their spatial structure. Moreover it is becoming increasingly clear that the reversible nature of protein assembly is also an essential element for their biological function. Here we introduce a computational approach for the Brownian dynamics of patchy particles with anisotropic assemblies and fully reversible reactions. Different particles stochastically associate and dissociate with microscopic reaction rates depending on their relative spatial positions. The translational and rotational diffusive properties of all protein complexes are evaluated on-the-fly. Because we focus on reversible assembly, we introduce a scheme which ensures detailed balance for patchy particles. We then show how the macroscopic rates follow from the microscopic ones. As an instructive example, we study the assembly of a pentameric ring structure, for which we find excellent agreement between simulation results and a macroscopic kinetic description without any adjustable parameters. This demonstrates that our approach correctly accounts for both the diffusive and reactive processes involved in protein assembly. <a class="is-size-7" style="white-space: nowrap;" onclick="document.getElementById('1404.5827v2-abstract-full').style.display = 'none'; document.getElementById('1404.5827v2-abstract-short').style.display = 'inline';">△ Less</a> </span> </p> <p class="is-size-7"><span class="has-text-black-bis has-text-weight-semibold">Submitted</span> 12 May, 2014; <span class="has-text-black-bis has-text-weight-semibold">v1</span> submitted 23 April, 2014; <span class="has-text-black-bis has-text-weight-semibold">originally announced</span> April 2014. </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Comments:</span> <span class="has-text-grey-dark mathjax">Revtex, 41 pages, 9 figures, includes some small corrections compared to first version</span> </p> <p class="comments is-size-7"> <span class="has-text-black-bis has-text-weight-semibold">Journal ref:</span> J. Chem. Phys. 140, 184112 (2014) </p> </li> </ol> <div class="is-hidden-tablet">  <span class="help" style="display: inline-block;"><a href="https://github.com/arXiv/arxiv-search/releases">Search v0.5.6 released 2020-02-24</a>  </span> </div> </div> </main> <footer> <div class="columns is-desktop" role="navigation" aria-label="Secondary">  <div class="column"> <div class="columns"> <div class="column"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/about">About</a></li> <li><a href="https://info.arxiv.org/help">Help</a></li> </ul> </div> <div class="column"> <ul class="nav-spaced"> <li> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><title>contact arXiv</title><desc>Click here to contact arXiv</desc><path d="M502.3 190.8c3.9-3.1 9.7-.2 9.7 4.7V400c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V195.6c0-5 5.7-7.8 9.7-4.7 22.4 17.4 52.1 39.5 154.1 113.6 21.1 15.4 56.7 47.8 92.2 47.6 35.7.3 72-32.8 92.3-47.6 102-74.1 131.6-96.3 154-113.7zM256 320c23.2.4 56.6-29.2 73.4-41.4 132.7-96.3 142.8-104.7 173.4-128.7 5.8-4.5 9.2-11.5 9.2-18.9v-19c0-26.5-21.5-48-48-48H48C21.5 64 0 85.5 0 112v19c0 7.4 3.4 14.3 9.2 18.9 30.6 23.9 40.7 32.4 173.4 128.7 16.8 12.2 50.2 41.8 73.4 41.4z"/></svg> <a href="https://info.arxiv.org/help/contact.html"> Contact</a> </li> <li> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><title>subscribe to arXiv mailings</title><desc>Click here to subscribe</desc><path d="M476 3.2L12.5 270.6c-18.1 10.4-15.8 35.6 2.2 43.2L121 358.4l287.3-253.2c5.5-4.9 13.3 2.6 8.6 8.3L176 407v80.5c0 23.6 28.5 32.9 42.5 15.8L282 426l124.6 52.2c14.2 6 30.4-2.9 33-18.2l72-432C515 7.8 493.3-6.8 476 3.2z"/></svg> <a href="https://info.arxiv.org/help/subscribe"> Subscribe</a> </li> </ul> </div> </div> </div>   <div class="column"> <div class="columns"> <div class="column"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/help/license/index.html">Copyright</a></li> <li><a href="https://info.arxiv.org/help/policies/privacy_policy.html">Privacy Policy</a></li> </ul> </div> <div class="column sorry-app-links"> <ul class="nav-spaced"> <li><a href="https://info.arxiv.org/help/web_accessibility.html">Web Accessibility Assistance</a></li> <li> <p class="help"> <a class="a11y-main-link" href="https://status.arxiv.org" target="_blank">arXiv Operational Status <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 256 512" class="icon filter-dark_grey" role="presentation"><path d="M224.3 273l-136 136c-9.4 9.4-24.6 9.4-33.9 0l-22.6-22.6c-9.4-9.4-9.4-24.6 0-33.9l96.4-96.4-96.4-96.4c-9.4-9.4-9.4-24.6 0-33.9L54.3 103c9.4-9.4 24.6-9.4 33.9 0l136 136c9.5 9.4 9.5 24.6.1 34z"/></svg></a><br> Get status notifications via <a class="is-link" href="https://subscribe.sorryapp.com/24846f03/email/new" target="_blank"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 512 512" class="icon filter-black" role="presentation"><path d="M502.3 190.8c3.9-3.1 9.7-.2 9.7 4.7V400c0 26.5-21.5 48-48 48H48c-26.5 0-48-21.5-48-48V195.6c0-5 5.7-7.8 9.7-4.7 22.4 17.4 52.1 39.5 154.1 113.6 21.1 15.4 56.7 47.8 92.2 47.6 35.7.3 72-32.8 92.3-47.6 102-74.1 131.6-96.3 154-113.7zM256 320c23.2.4 56.6-29.2 73.4-41.4 132.7-96.3 142.8-104.7 173.4-128.7 5.8-4.5 9.2-11.5 9.2-18.9v-19c0-26.5-21.5-48-48-48H48C21.5 64 0 85.5 0 112v19c0 7.4 3.4 14.3 9.2 18.9 30.6 23.9 40.7 32.4 173.4 128.7 16.8 12.2 50.2 41.8 73.4 41.4z"/></svg>email</a> or <a class="is-link" href="https://subscribe.sorryapp.com/24846f03/slack/new" target="_blank"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 448 512" class="icon filter-black" role="presentation"><path d="M94.12 315.1c0 25.9-21.16 47.06-47.06 47.06S0 341 0 315.1c0-25.9 21.16-47.06 47.06-47.06h47.06v47.06zm23.72 0c0-25.9 21.16-47.06 47.06-47.06s47.06 21.16 47.06 47.06v117.84c0 25.9-21.16 47.06-47.06 47.06s-47.06-21.16-47.06-47.06V315.1zm47.06-188.98c-25.9 0-47.06-21.16-47.06-47.06S139 32 164.9 32s47.06 21.16 47.06 47.06v47.06H164.9zm0 23.72c25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06H47.06C21.16 243.96 0 222.8 0 196.9s21.16-47.06 47.06-47.06H164.9zm188.98 47.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06s-21.16 47.06-47.06 47.06h-47.06V196.9zm-23.72 0c0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06V79.06c0-25.9 21.16-47.06 47.06-47.06 25.9 0 47.06 21.16 47.06 47.06V196.9zM283.1 385.88c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06-25.9 0-47.06-21.16-47.06-47.06v-47.06h47.06zm0-23.72c-25.9 0-47.06-21.16-47.06-47.06 0-25.9 21.16-47.06 47.06-47.06h117.84c25.9 0 47.06 21.16 47.06 47.06 0 25.9-21.16 47.06-47.06 47.06H283.1z"/></svg>slack</a> </p> </li> </ul> </div> </div> </div>  </div> </footer> <script src="https://static.arxiv.org/static/base/1.0.0a5/js/member_acknowledgement.js"></script> </body> </html>

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