Limits on the computational expressivity of non-equilibrium biophysical processes
Abstract Many biological decision-making tasks require classifying high-dimensional chemical states. The biophysical and computational mechanisms that enable classification remain enigmatic. In this work, using Markov jump processes as an abstraction of general biochemical networks, we reveal severa...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2025-08-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-025-61873-0 |
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| _version_ | 1849342878496587776 |
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| author | Carlos Floyd Aaron R. Dinner Arvind Murugan Suriyanarayanan Vaikuntanathan |
| author_facet | Carlos Floyd Aaron R. Dinner Arvind Murugan Suriyanarayanan Vaikuntanathan |
| author_sort | Carlos Floyd |
| collection | DOAJ |
| description | Abstract Many biological decision-making tasks require classifying high-dimensional chemical states. The biophysical and computational mechanisms that enable classification remain enigmatic. In this work, using Markov jump processes as an abstraction of general biochemical networks, we reveal several unanticipated and universal limitations on the classification ability of generic biophysical processes. These limits arise from a fundamental non-equilibrium thermodynamic constraint that we have derived. Importantly, we show that these limitations can be overcome using common biochemical mechanisms that we term input multiplicity, examples of which include enzymes acting on multiple targets. Analogous to how increasing depth enhances the expressivity and classification ability of neural networks, our work demonstrates how tuning input multiplicity can potentially enable an exponential increase in a biological system’s ability to classify and process information. |
| format | Article |
| id | doaj-art-df6c8efca1a4415f81b7e0b230bd63ac |
| institution | Kabale University |
| issn | 2041-1723 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj-art-df6c8efca1a4415f81b7e0b230bd63ac2025-08-20T03:43:14ZengNature PortfolioNature Communications2041-17232025-08-0116111210.1038/s41467-025-61873-0Limits on the computational expressivity of non-equilibrium biophysical processesCarlos Floyd0Aaron R. Dinner1Arvind Murugan2Suriyanarayanan Vaikuntanathan3The Chicago Center for Theoretical Chemistry, The University of ChicagoThe Chicago Center for Theoretical Chemistry, The University of ChicagoThe James Franck Institute, The University of ChicagoThe Chicago Center for Theoretical Chemistry, The University of ChicagoAbstract Many biological decision-making tasks require classifying high-dimensional chemical states. The biophysical and computational mechanisms that enable classification remain enigmatic. In this work, using Markov jump processes as an abstraction of general biochemical networks, we reveal several unanticipated and universal limitations on the classification ability of generic biophysical processes. These limits arise from a fundamental non-equilibrium thermodynamic constraint that we have derived. Importantly, we show that these limitations can be overcome using common biochemical mechanisms that we term input multiplicity, examples of which include enzymes acting on multiple targets. Analogous to how increasing depth enhances the expressivity and classification ability of neural networks, our work demonstrates how tuning input multiplicity can potentially enable an exponential increase in a biological system’s ability to classify and process information.https://doi.org/10.1038/s41467-025-61873-0 |
| spellingShingle | Carlos Floyd Aaron R. Dinner Arvind Murugan Suriyanarayanan Vaikuntanathan Limits on the computational expressivity of non-equilibrium biophysical processes Nature Communications |
| title | Limits on the computational expressivity of non-equilibrium biophysical processes |
| title_full | Limits on the computational expressivity of non-equilibrium biophysical processes |
| title_fullStr | Limits on the computational expressivity of non-equilibrium biophysical processes |
| title_full_unstemmed | Limits on the computational expressivity of non-equilibrium biophysical processes |
| title_short | Limits on the computational expressivity of non-equilibrium biophysical processes |
| title_sort | limits on the computational expressivity of non equilibrium biophysical processes |
| url | https://doi.org/10.1038/s41467-025-61873-0 |
| work_keys_str_mv | AT carlosfloyd limitsonthecomputationalexpressivityofnonequilibriumbiophysicalprocesses AT aaronrdinner limitsonthecomputationalexpressivityofnonequilibriumbiophysicalprocesses AT arvindmurugan limitsonthecomputationalexpressivityofnonequilibriumbiophysicalprocesses AT suriyanarayananvaikuntanathan limitsonthecomputationalexpressivityofnonequilibriumbiophysicalprocesses |