Pinboard (Vaguery) https://pinboard.in/u:Vaguery/public/ recent bookmarks from Vaguery A recursive enzymatic competition network capable of multitask molecular information processing | Nature Chemistry 2025-12-10T14:31:54+00:00 https://www.nature.com/articles/s41557-025-01981-y Vaguery reaction-networks artificial-life reservoir-computing biochemistry nonlinear-dynamics indistinguishable-from-magic to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ed6e937bb4ae/ Site-saturation mutagenesis of 500 human protein domains | Nature 2025-04-12T13:22:20+00:00 https://www.nature.com/articles/s41586-024-08370-4 Vaguery structural-biology biochemistry molecular-biology impressive looking-to-see neural-networks protein-folding to-write-about evolutionary-biology variation-as-a-source-of-innovation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:604c7c235a9a/ [2312.13944] Docking-based generative approaches in the search for new drug candidates 2024-07-03T10:48:08+00:00 https://arxiv.org/abs/2312.13944 Vaguery biochemistry pharmaceutical design-automation rather-interesting simulation molecular-design molecular-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:9f055f81cf4a/ MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics | bioRxiv 2021-03-26T20:19:28+00:00 https://www.biorxiv.org/content/10.1101/2020.07.31.230334v1?rss=1 Vaguery python systems-biology theoretical-biology rather-interesting biochemistry models visualization project-jupyter https://pinboard.in/ https://pinboard.in/u:Vaguery/b:134d6e5931f3/ Optimal information transfer in enzymatic networks: A field theoretic formulation | bioRxiv 2020-07-09T23:31:28+00:00 https://www.biorxiv.org/content/10.1101/130112v1?rss=1 Vaguery systems-biology information-theory molecular-machinery rather-interesting cell-biology biochemistry reaction-networks to-write-about to-simulate https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8b54d2690dab/ Multiplexing information flow through dynamic signalling systems | bioRxiv 2020-06-17T14:01:31+00:00 https://www.biorxiv.org/content/10.1101/863159v2 Vaguery systems-biology reaction-networks biological-engineering biological-design theoretical-biology biochemistry to-write-about to-simulate consider:search-space consider:performance-measures https://pinboard.in/ https://pinboard.in/u:Vaguery/b:36b26660a270/ [1811.05371] The strength of protein-protein interactions controls the information capacity and dynamical response of signaling networks 2020-06-14T12:00:52+00:00 https://arxiv.org/abs/1811.05371 Vaguery theoretical-biology systems-biology biochemistry reaction-networks rather-interesting to-simulate to-write-about consider:abstractions consider:interactive-visualization biological-engineering https://pinboard.in/ https://pinboard.in/u:Vaguery/b:652e1aef1dee/ DR. HERBERT H. TSANG - http://www.herberttsang.org 2020-02-09T01:14:49+00:00 http://htsang.wikidot.com/research Vaguery structural-biology polymer-folding biochemistry biophysics simulation metaheuristics energy-landscapes rather-interesting to-write-about to-simulate to-visualize https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d531cf9636cd/ [1806.10764] Biochemical Coupling Through Emergent Conservation Laws 2019-09-29T10:38:06+00:00 https://arxiv.org/abs/1806.10764 Vaguery reaction-networks thermodynamics category-theory hypergraphs emergent-design rather-interesting to-understand biochemistry thesis-like https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d417616afa87/ [1711.08988] Exponential growth for self-reproduction in a catalytic reaction network: relevance of a minority molecular species and crowdedness 2018-02-22T00:18:19+00:00 https://arxiv.org/abs/1711.08988 Vaguery autocatalysis artificial-life origin-of-life reaction-networks self-organization biochemistry simulation rather-interesting to-write-about to-simulate https://pinboard.in/ https://pinboard.in/u:Vaguery/b:58e22fb5fef7/ [1308.6619] Backward stochastic differential equation approach to modeling of gene expression 2017-03-05T21:57:27+00:00 https://arxiv.org/abs/1308.6619 Vaguery stochastic-systems biochemistry systems-biology simulation rather-interesting cheminformatics gene-regulatory-networks to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4532ddd362ef/ [1605.06149] How can the green sulfur bacteria use quantum computing for light harvesting? 2016-07-04T00:32:17+00:00 http://arxiv.org/abs/1605.06149# Vaguery rather-interesting quantums quantum-computing systems-biology biochemistry to-understand to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:644d88941f31/ [1605.01624] Complete integrability of information processing by biochemical reactions 2016-05-09T11:47:58+00:00 http://arxiv.org/abs/1605.01624 Vaguery biochemistry systems-biology S-systems nonlinear-dynamics biological-engineering nudge-targets consider:feature-discovery consider:robustness https://pinboard.in/ https://pinboard.in/u:Vaguery/b:bbe015942a29/ A universal mathematical model of non-photochemical quenching to study short-term light memory in plants | bioRxiv 2016-03-26T22:10:31+00:00 http://biorxiv.org/content/early/2016/03/18/044628?rss=1%2522 Vaguery systems-biology biochemistry photobiology theoretical-biology dynamical-systems biological-engineering rather-interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:62bf291251d4/ [1501.03971] Bayesian protein structure alignment 2016-02-27T21:43:28+00:00 http://arxiv.org/abs/1501.03971 Vaguery biochemistry structural-biology protein-folding bioinformatics algorithms machine-learning statistics metrics nudge-targets consider:distance-measure https://pinboard.in/ https://pinboard.in/u:Vaguery/b:eefeff02cf1a/ [1501.04040] Nonlinearity arising from noncooperative transcription factor binding enhances negative feedback and promotes genetic oscillations 2015-12-15T15:08:37+00:00 http://arxiv.org/abs/1501.04040 Vaguery systems-biology biophysics biochemistry reaction-networks engineering-design biological-engineering nudge-targets nonlinear-dynamics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:1d64e177a2d7/ [1405.5621] A Theory of Decomposition of Complex Chemical Networks using the Hill Functions 2015-12-11T22:27:32+00:00 http://arxiv.org/abs/1405.5621 Vaguery theoretical-biology systems-biology simulation generative-models rather-interesting biochemistry reaction-networks nudge-targets consider:representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:2e0c3fd40f36/ [1508.01737] Comparison of moment-closure approximations for stochastic chemical kinetics 2015-09-04T19:11:06+00:00 http://arxiv.org/abs/1508.01737 Vaguery reaction-networks systems-biology biochemistry numerical-methods robustness approximation stochastic-systems models horse-races performance-measure nudge-targets consider:representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:200bf1fc5411/ [1412.3138] Computational Protein Design Using AND/OR Branch-and-Bound Search 2015-07-25T11:29:08+00:00 http://arxiv.org/abs/1412.3138 Vaguery structural-biology biochemistry constraint-satisfaction biological-engineering engineering-design nudge-targets consider:rediscovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:fcb821ffbd3e/ [1410.4465] On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment 2015-03-15T20:39:42+00:00 http://arxiv.org/abs/1410.4465 Vaguery bioinformatics biochemistry structural-biology protein-folding Thom-LaBean's-thesis it's-more-complicated-than-you-think Oh Science. https://pinboard.in/ https://pinboard.in/u:Vaguery/b:e941d1fa5934/ [1403.0336] States with identical steady dissipation rate: Role of kinetic constants in enzyme catalysis 2014-12-24T12:40:22+00:00 http://arxiv.org/abs/1403.0336 Vaguery reaction-networks thermodynamics biochemistry modeling nudge-targets consider:structure:elaboration performance-measure constraints https://pinboard.in/ https://pinboard.in/u:Vaguery/b:3531b0026c7b/ [1410.4530] Fatigueless response of spider draglines in cyclic torsion facilitated by reversible molecular deformation 2014-12-06T17:13:09+00:00 http://arxiv.org/abs/1410.4530 Vaguery materials-science biological-engineering spiders-rock biochemistry structural-biology mechanical-engineering https://pinboard.in/ https://pinboard.in/u:Vaguery/b:87ddee18247e/ [1410.0652] Using Simulations and kinetic network models to reveal the dynamics and functions of Riboswitches 2014-10-08T20:32:11+00:00 http://arxiv.org/abs/1410.0652 Vaguery molecular-machinery molecular-biology biochemistry macromolecules biological-engineering nanotechnology experiment simulation nudge-targets consider:rule-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:c6444c89d292/ [1309.0765] A Model of Gene Expression Based on Random Dynamical Systems Reveals Modularity Properties of Gene Regulatory Networks 2014-08-22T12:38:33+00:00 http://arxiv.org/abs/1309.0765 Vaguery biochemistry network-theory dynamical-systems biological-engineering complexology simulation analytics nudge-targets Kauffmania engineering-design https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4c8bbe60ba1e/ COPASI : COPASI 4.12 (Build 81) Released 2014-04-18T20:17:52+00:00 http://www.copasi.org/tiki-read_article.php?articleId=55 Vaguerysimulation biochemistry reaction-networks nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:60fa6513164e/ [1312.6209] What makes the lac-pathway switch: identifying the fluctuations that trigger phenotype switching in gene regulatory systems 2014-04-07T11:27:01+00:00 http://arxiv.org/abs/1312.6209 Vaguery systems-biology gene-regulatory-networks experiment biochemistry physiology simulation interesting stochastic-systems molecular-machinery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:46baae3d4e15/ [1312.0688] Biophysical Fitness Landscapes for Transcription Factor Binding Sites 2014-03-30T11:24:11+00:00 http://arxiv.org/abs/1312.0688 Vaguery fitness-landscapes bioinformatics biochemistry biological-engineering experiment simulation interesting theoretical-biology of-course-it's-physics-now https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f78e8bd6839a/ [1312.4146] Unfolding kinetics of periodic DNA hairpins 2014-01-17T14:57:29+00:00 http://arxiv.org/abs/1312.4146 Vaguery structural-biology molecular-machinery experiment modeling DNA biochemistry https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cd0bd3a00371/ [1310.7899] Evolution of autocatalytic sets in a competitive percolation model 2013-12-16T22:42:57+00:00 http://arxiv.org/abs/1310.7899 Vaguery origin-of-life chemical-reaction-networks artificial-life theoretical-biology self-organization nudge-targets simulation biochemistry consider:spatial-percolation-too https://pinboard.in/ https://pinboard.in/u:Vaguery/b:665f61e4cdda/ [1310.8267] Realization of Morphing Logic Gates in a Repressilator with Quorum Sensing Feedback 2013-11-11T23:48:44+00:00 http://arxiv.org/abs/1310.8267 Vaguery theoretical-biology systems-biology biochemistry regulation algorithms nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:0eb2c858fe3b/ [1305.3007] Probing water structures in nanopores using tunneling currents 2013-09-17T12:13:19+00:00 http://arxiv.org/abs/1305.3007 Vaguery molecular-machinery simulation biochemistry nanotechnology nudge-targets consider:design-substrate https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d347927f9ed2/ [1306.0069] Statistical Methods for Estimating Complexity from Competition Experiments between Two Populations 2013-06-07T11:30:45+00:00 http://arxiv.org/abs/1306.0069 Vaguery bioinformatics statistics complexity SELEX performance-measure biochemistry https://pinboard.in/ https://pinboard.in/u:Vaguery/b:baf65a514f5a/ [1207.6431] Optimal reconstruction of the folding landscape using differential energy surface analysis 2013-05-25T11:10:38+00:00 http://arxiv.org/abs/1207.6431 Vaguery biochemistry protein-folding fitness-landscapes nudge-targets algorithms performance-measure https://pinboard.in/ https://pinboard.in/u:Vaguery/b:33b681fa8b38/ [1304.7241] pH-dependent Response of Coiled Coils: A Coarse-Grained Molecular Simulation Study 2013-04-30T21:56:20+00:00 http://arxiv.org/abs/1304.7241 Vaguery biochemistry protein-folding structural-biology engineering-design biological-engineering nudge-targets simulation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8e7ba4a2acc9/ [1212.4312] pH-dependent coarse-grained model of peptides 2013-04-30T21:55:33+00:00 http://arxiv.org/abs/1212.4312 Vaguery structural-biology protein-folding biochemistry models simulation interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8d8919003693/ [1211.0662] Hidden Complexity in the Isomerization Dynamics of Holliday Junctions 2013-03-06T19:06:36+00:00 http://arxiv.org/abs/1211.0662 Vaguery molecular-design molecular-machinery biochemistry experiment protein-folding structural-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:95b009c64a0f/ [1207.3453] Complex-linear invariants of biochemical networks 2012-08-29T11:11:19+00:00 http://arxiv.org/abs/1207.3453 Vaguery reaction-networks systems-biology biochemistry simulation heuristics nudge-targets be-wise-linearize https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8bd61f1bab7a/ [1206.1571] Steady-state fluctuations of a genetic feedback loop: an exact solution 2012-06-09T11:41:00+00:00 http://arxiv.org/abs/1206.1571 Vaguery unphysical biochemistry models analytical-models-of-messy-old-life https://pinboard.in/ https://pinboard.in/u:Vaguery/b:7bc6cbf9484d/ [1105.2204] A Bayesian Model of NMR Spectra for the Deconvolution and Quantification of Metabolites in Complex Biological Mixtures 2012-06-08T15:21:20+00:00 http://arxiv.org/abs/1105.2204 Vaguery statistics inverse-problems biochemistry signal-processing algorithms machine-learning nudge-targets inference-of-things-that-aren't-toys https://pinboard.in/ https://pinboard.in/u:Vaguery/b:41e4d3ff67b8/ [1206.1098] The interplay of intrinsic and extrinsic bounded noises in genetic networks 2012-06-08T15:09:03+00:00 http://arxiv.org/abs/1206.1098 Vaguery biochemistry structural-biology reaction-networks biological-engineering noise its-complicated-inside-a-cell simulation nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:5b5907dd51b0/ [1010.4735] Exploring the Energy Landscapes of Protein Folding Simulations with Bayesian Computation 2012-01-05T13:38:06+00:00 http://arxiv.org/abs/1010.4735 Vaguery structural-biology biochemistry modeling algorithms statistics metamodeling https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cc962a18eda9/ [1109.2618] Fast and Accurate Modeling of Molecular Atomization Energies with Machine Learning 2012-01-05T13:34:06+00:00 http://arxiv.org/abs/1109.2618 Vaguery machine-learning learning-from-data biochemistry computational-science nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4990c6d3af52/ [1112.5794] BATMAN-an R package for the automated quantification of metabolites from NMR spectra using a Bayesian Model 2012-01-02T15:16:22+00:00 http://arxiv.org/abs/1112.5794 Vaguery learning-from-data statistics modeling biochemistry nudge-targets image-segmentation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:1a3062560e0a/ [1109.5389] Water drives peptide conformational transitions 2011-10-10T11:31:39+00:00 http://arxiv.org/abs/1109.5389 Vaguery molecular-design systems-biology simulation intracellular-dynamics kinda-knew-this-a-long-time-ago biochemistry https://pinboard.in/ https://pinboard.in/u:Vaguery/b:96f0382ba1af/ [1105.4335] Physical approaches to the dynamics of genetic circuits: A tutorial 2011-10-04T14:05:03+00:00 http://arxiv.org/abs/1105.4335 Vaguery systems-biology biological-engineering genetic-regulatory-networks emergent-design biochemistry overview https://pinboard.in/ https://pinboard.in/u:Vaguery/b:734a5a06dd70/ [1007.2668] Protein abundances and interactions coevolve to promote functional complexes while suppressing non-specific binding 2010-07-30T11:57:49+00:00 http://arxiv.org/abs/1007.2668 Vaguery systems-biology biochemistry emergent-design systems-engineering molecular-machinery nudge-targets https://pinboard.in/u:Vaguery/b:343ad9444251/ [1003.2791] Adaptive response and enlargement of dynamic range 2010-07-30T01:46:55+00:00 http://arxiv.org/abs/1003.2791 Vaguery biochemistry molecular-machinery systems-biology dynamical-systems dynamic-control-prospects https://pinboard.in/u:Vaguery/b:1f106a9453aa/ [1006.4265] Modeling capsid self-assembly: Design and analysis 2010-06-29T00:12:59+00:00 http://arxiv.org/abs/1006.4265 Vaguery molecular-design virus biochemistry self-assembly simulation nudge-targets theoretical-biology biological-engineering https://pinboard.in/u:Vaguery/b:737c72315493/ [1002.4273] Mutual information in time-varying biochemical systems 2010-06-28T14:00:13+00:00 http://arxiv.org/abs/1002.4273 Vaguery biochemistry theoretical-biology molecular-design biological-engineering network-theory complexology nudge-targets https://pinboard.in/u:Vaguery/b:654e1ededccc/ [1005.1142] Reproduction of a Protocell by Replication of Minority Molecule in Catalytic Reaction Network 2010-05-12T12:17:36+00:00 http://arxiv.org/abs/1005.1142 Vaguery origin-of-life artificial-life self-organization biochemistry autopoiesis abiogenesis simulation individuation https://pinboard.in/u:Vaguery/b:743d2e661e5b/ [1005.1191] Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics 2010-05-12T12:00:04+00:00 http://arxiv.org/abs/1005.1191 Vaguery origin-of-life autocatalysis biochemistry theoretical-biology models nudge-targets https://pinboard.in/u:Vaguery/b:94deb5efcf5f/ Untangling the Quantum Entanglement Behind Photosynthesis: Berkeley scientists shine new light on green plant secrets « Berkeley Lab News Center 2010-05-11T13:40:39+00:00 http://newscenter.lbl.gov/feature-stories/2010/05/10/untangling-quantum-entanglement/ Vaguery photosynthesis biochemistry biophysics molecular-design quantum-computing nanotechnology entanglement https://pinboard.in/u:Vaguery/b:1b7bf18a64b6/ [0712.4248] Computer algebra in systems biology 2008-01-06T13:13:19+00:00 http://arxiv.org/abs/0712.4248 Vaguery bioinformatics systems-biology dynamics biochemistry https://pinboard.in/u:Vaguery/b:319aedac9d4d/