Pinboard (Vaguery) https://pinboard.in/u:Vaguery/public/ recent bookmarks from Vaguery [2408.05395] The evolution of systems biology and systems medicine: From mechanistic models to uncertainty quantification 2026-05-24T10:49:45+00:00 https://arxiv.org/abs/2408.05395 Vaguery systems-biology molecular-machinery medicine medical-technology network-theory pharmaceutical machine-learning rather-interesting models-and-modes reaction-networks systems-thinking https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d028f0a81a52/ [2101.12258] Microswimmers learning chemotaxis with genetic algorithms 2024-08-14T20:20:29+00:00 https://arxiv.org/abs/2101.12258 Vaguery molecular-design molecular-machinery evolutionary-algorithms rather-interesting biophysics to-write-about to-simulate consider:topology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:475b291f07dc/ [2009.00090] A Survey of Molecular Communication in Cell Biology: Establishing a New Hierarchy for Interdisciplinary Applications 2021-06-27T12:05:15+00:00 https://arxiv.org/abs/2009.00090 Vaguery systems-biology signal-transduction molecular-design molecular-biology molecular-machinery design-patterns rather-interesting consider:simulation to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:a3998b4b2f25/ [1703.03398] Identifying feasible operating regimes for early T-cell recognition: The speed, energy, accuracy trade-off in kinetic proofreading and adaptive sorting 2020-07-15T13:43:54+00:00 https://arxiv.org/abs/1703.03398 Vaguery immunology molecular-machinery rather-interesting reaction-networks systems-biology to-understand consider:simulation to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:05bbf84038a2/ 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/ Towards experimental P-systems using multivesicular liposomes | SpringerLink 2019-02-14T02:08:54+00:00 https://link.springer.com/article/10.1007/s41965-018-00006-7 Vaguery unconventional-computing molecular-machinery rather-interesting vesicular-computing experiment nanotechnology to-write-about to-simulate https://pinboard.in/ https://pinboard.in/u:Vaguery/b:1a04f7554a0c/ Foldamer hypothesis for the growth and sequence differentiation of prebiotic polymers 2017-09-23T12:05:58+00:00 http://www.pnas.org/content/114/36/E7460.abstract Vaguery lattice-polymers biophysics self-organization origin-of-life simulation rather-interesting to-write-about molecular-design molecular-machinery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:996a1862cead/ [1509.04145] The physics of epigenetics 2016-02-25T11:54:51+00:00 http://arxiv.org/abs/1509.04145 Vaguery epigenetic review biophysics supramolecular-complexes it's-more-complicated-than-you-think molecular-machinery complexology theory-and-practice-sitting-in-a-tree https://pinboard.in/ https://pinboard.in/u:Vaguery/b:e502aa78093a/ [1512.00268] Chromatin assortativity: integrating epigenomic data and 3D genomic structure 2016-02-25T11:23:58+00:00 http://arxiv.org/abs/1512.00268 Vaguery bioinformatics structural-biology it's-more-complicated-than-you-think supramolecular-complex cell-biology molecular-machinery experiment https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d7eadedfcdd2/ [1505.01980] Evolving Boolean Networks with RNA Editing 2015-06-12T10:55:21+00:00 http://arxiv.org/abs/1505.01980 Vaguery Kauffmania boolean-networks molecular-machinery engineering-design biological-engineering nudge-targets consider:stress-testing https://pinboard.in/ https://pinboard.in/u:Vaguery/b:824633090d20/ [1412.8634] Transcriptional bursting in gene expression: analytical results for general stochastic models 2015-06-01T11:24:47+00:00 http://arxiv.org/abs/1412.8634 Vaguery biophysics molecular-machinery molecular-biology queueing-theory planning inference rather-interesting models nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f01ea27716bc/ Layering genetic circuits to build a single cell, bacterial half adder | bioRxiv 2015-05-29T10:54:29+00:00 http://biorxiv.org/content/early/2015/05/12/019257 Vaguery boolean-networks molecular-machinery biological-engineering Kauffmania rather-interesting experiment https://pinboard.in/ https://pinboard.in/u:Vaguery/b:53ae4976d405/ A mechanistic link between cellular trade-offs, gene expression and growth | bioRxiv 2015-05-28T11:05:55+00:00 http://biorxiv.org/content/early/2015/02/03/014787 Vaguery cell-biology simulation theoretical-biology crowding molecular-machinery systems-biology nonlinear-dynamics rather-interesting towards-a-more-realistic-theoretical-biology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ed2eb15cf6dc/ Predicting genetic interactions from Boolean models of biological networks | bioRxiv 2015-05-26T11:01:10+00:00 http://biorxiv.org/content/early/2015/04/24/018507 Vaguery bioinformatics molecular-machinery inference boolean-networks gene-regulatory-networks data-fusion prediction algorithms nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f54447946d81/ [1405.1242] Swimming of an assembly of rigid spheres at low Reynolds number 2014-11-27T11:32:30+00:00 http://arxiv.org/abs/1405.1242 Vaguery engineering-design nanotechnology molecular-machinery physics fluid-dynamics analytical-approach nudge-targets simulation-would-be-good-about-now https://pinboard.in/ https://pinboard.in/u:Vaguery/b:0c7773581d0d/ [1410.4258] A Comprehensive Survey of Recent Advancements in Molecular Communication 2014-10-19T12:24:54+00:00 http://arxiv.org/abs/1410.4258 Vaguery molecular-machinery biological-engineering communication systems-biology engineering-design design-patterns ontology review interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4b8177d27e7c/ [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/ [1304.3675] Self-assembly of colloidal polymers via depletion-mediated lock and key binding 2014-08-31T12:27:29+00:00 http://arxiv.org/abs/1304.3675 Vaguery self-assembly molecular-machinery physical-chemistry simulation experiment molecular-crowding rather-interesting nanohistory nudge-targets consider:strategies consider:rule-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:db5fc3f5ace7/ [1403.2269] Virus Assembly on a Membrane is Facilitated by Membrane Microdomains 2014-04-20T10:28:46+00:00 http://arxiv.org/abs/1403.2269 Vaguery structural-biology simulation membrane-biochemistry self-assembly molecular-design molecular-machinery well-duh it's-crowded-inside-a-cell https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f4c5e15ddc07/ [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/ [1312.5565] What Transcription Factors Can't Do: On the Combinatorial Limits of Gene Regulatory Networks 2014-03-31T20:25:50+00:00 http://arxiv.org/abs/1312.5565 Vaguery gene-regulatory-networks systems-biology Kauffmania theoretical-biology molecular-machinery combinatorics bioinformatics the-mangle-in-practice https://pinboard.in/ https://pinboard.in/u:Vaguery/b:75a62a9f1db7/ [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/ [1310.4309] Optimizing water permeability through the hourglass shape of aquaporins 2013-12-04T23:11:35+00:00 http://arxiv.org/abs/1310.4309 Vaguery molecular-design molecular-machinery biological-engineering structural-biology engineering-design https://pinboard.in/ https://pinboard.in/u:Vaguery/b:b530f83e2d6e/ [1311.4514] The importance of crowding in signaling, genetic, and metabolic networks 2013-12-04T21:31:10+00:00 http://arxiv.org/abs/1311.4514 Vaguery systems-biology structural-biology molecular-machinery dynamical-systems space-matters simulation departures-from-the-ideal interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f5cfd1d5738f/ [1309.6449] Exploring Programmable Self-Assembly in Non-DNA based Molecular Computing 2013-11-28T12:34:50+00:00 http://arxiv.org/abs/1309.6449 Vaguery self-assembly nanotechnology molecular-design molecular-machinery stamp-collecting classification emergent-design https://pinboard.in/ https://pinboard.in/u:Vaguery/b:45dc27288a65/ [1310.5778] Interplay between single-stranded binding proteins on RNA secondary structure 2013-11-03T13:23:36+00:00 http://arxiv.org/abs/1310.5778 Vaguery RNA structural-biology molecular-biology molecular-machinery bioinformatics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4857b22685c7/ [1310.1579] Distribution of lifetimes of kinetochore-microtubule attachments:interplay of energy landscape, molecular motors and microtubule (de-)polymerization 2013-10-18T12:27:35+00:00 http://arxiv.org/abs/1310.1579 Vaguery structural-biology cellular-biology simulation molecular-machinery cell-physiology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d7548cf5d108/ [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/ [1302.1853] Cooperative effects enhance the transport properties of molecular spider teams 2013-04-16T22:59:48+00:00 http://arxiv.org/abs/1302.1853 Vaguery nanotechnology molecular-design molecular-machinery molecular-spider-team-ACTIVATE https://pinboard.in/ https://pinboard.in/u:Vaguery/b:eaf0ce79bd59/ [1209.6379] Crowding induced entropy-enthalpy compensation in protein association equilibria 2013-04-14T12:00:09+00:00 http://arxiv.org/abs/1209.6379 Vaguery simulation molecular-machinery structural-biology biophysics macromolecules nudge-targets experiment https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d095d98ce5d0/ [1303.3898] Crumpled globule possesses the properties of molecular machines 2013-03-30T14:09:53+00:00 http://arxiv.org/abs/1303.3898 Vaguery molecular-design molecular-machinery structural-biology energy-landscapes protein-folding nudge-targets https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d43fda22c6ea/ [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/ [1102.2359] A Phyllotactic Approach to the Structure of Collagen Fibrils 2011-04-02T12:48:50+00:00 http://arxiv.org/abs/1102.2359 Vaguery self-assembly nanotechnology molecular-design molecular-machinery theoretical-biology structural-biology crystallography condensed-matter https://pinboard.in/u:Vaguery/b:4e0746d267c7/ [1008.1101] Control of pathways and yields of protein crystallization through the interplay of nonspecific and specific attractions 2010-08-12T19:04:35+00:00 http://arxiv.org/abs/1008.1101 Vaguery molecular-design molecular-machinery simulation self-assembly emergent-design nudge-targets physics-is-fun https://pinboard.in/u:Vaguery/b:0019f59e075d/ [1003.1324] Passive swimming in low Reynolds number flows 2010-08-03T01:02:27+00:00 http://arxiv.org/abs/1003.1324 Vaguery molecular-design molecular-machinery biomechanics nudge-targets emergent-design https://pinboard.in/u:Vaguery/b:2fa67b55c8df/ [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/ [1007.4583] A population-based microbial oscillator 2010-07-28T11:29:25+00:00 http://arxiv.org/abs/1007.4583 Vaguery biological-engineering microbiology complexology oscillator-networks molecular-machinery quorum-sensing nudge-targets https://pinboard.in/u:Vaguery/b:9805a2ad1ce6/ [1007.3712] Formal Verification of Self-Assembling Systems 2010-07-26T13:04:58+00:00 http://arxiv.org/abs/1007.3712 Vaguery self-assembly nanotechnology emergent-design molecular-design molecular-machinery engineering-design testing https://pinboard.in/u:Vaguery/b:1487dcb6313c/