Pinboard (Vaguery) https://pinboard.in/u:Vaguery/public/ recent bookmarks from Vaguery [2502.08188] Breakdown of Magic Numbers in Spherical Confinement 2026-04-20T15:54:44+00:00 https://arxiv.org/abs/2502.08188 Vaguery self-organization self-assembly packing molecular-design looking-to-see physics! rather-interesting colloids combinatorics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:2386898a5462/ [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/ [2203.01669] Size Exponents of Branched Polymers/ Extension of the Isaacson-Lubensky Formula and the Application to Lattice Trees 2024-07-20T15:51:44+00:00 https://arxiv.org/abs/2203.01669 Vaguery models rather-interesting combinatorics molecular-design chemistry data-structures abstraction to-write-about to-simulate https://pinboard.in/ https://pinboard.in/u:Vaguery/b:a1db5f12a14f/ [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/ [1801.06933] Heirarchical and synergistic self-assembly in composites of model Wormlike micellar-polymers and nanoparticles results in nanostructures with diverse morphologies 2022-03-15T15:49:14+00:00 https://arxiv.org/abs/1801.06933 Vaguery self-assembly molecular-design rather-interesting materials-science indistinguishable-from-magic looking-to-see experiment https://pinboard.in/ https://pinboard.in/u:Vaguery/b:1f94a24c8222/ [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/ [2003.02121] Coding for Polymer-Based Data Storage 2020-05-23T11:43:48+00:00 https://arxiv.org/abs/2003.02121 Vaguery nanotechnology molecular-design engineering-design information-theory rather-interesting robustness material-science compression representation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ff53fad9ad03/ [1903.00441] The free energy of compressed lattice knots 2020-05-14T00:52:20+00:00 https://arxiv.org/abs/1903.00441 Vaguery lattice-polymers molecular-design physics! simulation rather-interesting to-simulate looking-to-see virtual-experiments https://pinboard.in/ https://pinboard.in/u:Vaguery/b:5eba82b2292b/ [1806.03333] The rainbow-spectrum of RNA secondary structures 2020-01-10T21:01:53+00:00 https://arxiv.org/abs/1806.03333 Vaguery structural-biology RNA-folding hey-I-know-this-guy molecular-design simulation rather-interesting feature-construction to-write-about to-simulate consider:extreme-cases consider:feature-discovery https://pinboard.in/ https://pinboard.in/u:Vaguery/b:a438e8d14c51/ Commonly-used FRET fluorophores promote collapse of an otherwise disordered protein | bioRxiv 2020-01-01T13:34:02+00:00 https://www.biorxiv.org/content/10.1101/376632v1?rss=1 Vaguery molecular-dynamics molecular-design rather-interesting biophysics solvation-dynamics simulation consider:combinatorial-chemistry https://pinboard.in/ https://pinboard.in/u:Vaguery/b:b1c118d44164/ [1908.00971] Physical machine learning outperforms "human learning" in Quantum Chemistry 2019-08-07T11:21:25+00:00 https://arxiv.org/abs/1908.00971 Vaguery emergent-design machine-learning neural-networks quantums molecular-design complexology to-write-about https://pinboard.in/ https://pinboard.in/u:Vaguery/b:6d7b4ecfd102/ [1802.03548] Constructing first-principles phase diagrams of amorphous LixSi using machine-learning-assisted sampling with an evolutionary algorithm 2019-06-12T13:15:04+00:00 https://arxiv.org/abs/1802.03548 Vaguery metaheuristics materials-science engineering-design molecular-design rather-interesting simulation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:8a0bb15c5572/ Supermultiplexed optical imaging and barcoding with engineered polyynes | Nature Methods 2018-12-29T13:10:14+00:00 https://www.nature.com/articles/nmeth.4578 Vaguery materials-science nanotechnology indistinguishable-from-magic molecular-design molecular-biology to-write-about rather-interesting https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4c599851e99b/ The Effect of Compositional Context on Synthetic Gene Net- works | bioRxiv 2017-10-15T12:17:20+00:00 https://www.biorxiv.org/content/early/2016/10/25/083329?rss=1%2522 Vaguery gene-regulatory-networks biological-engineering systems-biology rather-interesting synthetic-biology molecular-design to-write-about performance-measure https://pinboard.in/ https://pinboard.in/u:Vaguery/b:453b2a22c5c2/ 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/ [1702.01994] Polyomino Models of Surface Supramolecular Assembly: Design Constraints and Structural Selectivity 2017-09-23T12:01:03+00:00 https://arxiv.org/abs/1702.01994 Vaguery tiling supramolecular-complexes biological-engineering rather-interesting to-write-about energy-landscapes self-assembly molecular-design structural-biology nanotechnology https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d7c71fe82a17/ [1502.07144] Self-assembly of Active Colloidal Molecules with Dynamic Function 2017-05-05T11:06:41+00:00 https://arxiv.org/abs/1502.07144 Vaguery active-matter self-organization physics! emergence rather-interesting to-understand molecular-design https://pinboard.in/ https://pinboard.in/u:Vaguery/b:eb94098aa55e/ Chromatin structure shapes the search process of transcription factors | bioRxiv 2016-05-01T11:57:47+00:00 http://biorxiv.org/content/early/2016/04/25/050146?rss=1%2522 Vaguery structural-biology molecular-design molecular-biology systems-biology bioinformatics it's-more-complicated-than-you-think https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f151d98280fe/ [1505.01215] Binding of transcription factors adapts to resolve information-energy trade-off 2016-03-26T22:16:17+00:00 http://arxiv.org/abs/1505.01215 Vaguery molecular-design molecular-biology information-theory theoretical-biology adaptationism robustness https://pinboard.in/ https://pinboard.in/u:Vaguery/b:7bc9dd13806d/ [1505.01023] Classical Liquids in Fractal Dimension 2015-09-05T17:24:28+00:00 http://arxiv.org/abs/1505.01023 Vaguery fluid-dynamics but-different fractals physics simulation percolation molecular-design rather-interesting nonlinear-dynamics condensed-matter https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ab7a548b3cdb/ [1506.08611] Energy landscapes for the self-assembly of supramolecular polyhedra 2015-08-01T11:54:07+00:00 http://arxiv.org/abs/1506.08611 Vaguery statistical-mechanics energy-landscapes molecular-design engineering-design rather-interesting models-and-modes nudge-targets nonlinear-dynamics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:afedfebcfece/ [1401.1491] Gradient-Driven Molecule Construction: An Inverse Approach Applied to the Design of Small-Molecule Fixating Catalysts 2015-02-08T15:47:14+00:00 http://arxiv.org/abs/1401.1491 Vaguery engineering-design chemistry cheminformatics molecular-design algorithms generative-methods nudge-targets consider:performance-measures https://pinboard.in/ https://pinboard.in/u:Vaguery/b:0ced88d759c5/ [1310.5091] Synchronization as a unifying mechanism for protein folding 2014-11-09T12:21:24+00:00 http://arxiv.org/abs/1310.5091 Vaguery protein-folding molecular-design coupled-oscillators simulation coordination rather-interesting nudge-targets consider:detectors https://pinboard.in/ https://pinboard.in/u:Vaguery/b:32a42af2d6c6/ Systematic Imaging Reveals Features of Localized mRNAs and Their Changing Subcellular Destinations in Development | bioRxiv 2014-11-05T12:33:06+00:00 http://biorxiv.org/content/early/2014/11/04/008938 Vaguery evo-devo developmental-biology experiment molecular-biology visualization dynamical-systems rather-interesting molecular-design biological-engineering self-organization design-patterns https://pinboard.in/ https://pinboard.in/u:Vaguery/b:d43c9ecf0818/ Scaling properties of evolutionary paths in a biophysical model of protein adaptation | bioRxiv 2014-10-16T12:07:32+00:00 http://biorxiv.org/content/early/2014/10/06/010082 Vaguery fitness-landscapes Kauffmania theoretical-biology molecular-design complexology nudge-targets multiscale-representations? approximation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4d9ffafb9afd/ [1401.4475] Controlled self-assembly of periodic and aperiodic cluster crystals 2014-09-28T11:43:49+00:00 http://arxiv.org/abs/1401.4475 Vaguery molecular-design self-organization self-assembly nanotechnology simulation condensed-matter pattern-formation nudge-targets consider:diversity-of-particles https://pinboard.in/ https://pinboard.in/u:Vaguery/b:a9917f955e14/ [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/ [1311.0684] Uniform generation of RNA-RNA interaction structures of fixed topological genus 2014-04-19T08:20:41+00:00 http://arxiv.org/abs/1311.0684 Vaguery bioinformatics molecular-design RNA macromolecular-dynamics nudge-targets algorithms https://pinboard.in/ https://pinboard.in/u:Vaguery/b:cfb6d37f447a/ [1401.6866] Unconventional ordering behavior of semi-flexible polymers in dense brushes under compression 2014-04-07T11:30:08+00:00 http://arxiv.org/abs/1401.6866 Vaguery simulation molecular-design nanotechnology condensed-matter phase-transitions emergence nudge-targets consider:heterogeneity https://pinboard.in/ https://pinboard.in/u:Vaguery/b:60808dad545c/ [1311.1178] When are rough surfaces sticky? 2014-04-03T11:40:46+00:00 http://arxiv.org/abs/1311.1178 Vaguery physics molecular-design simulation nudge-targets consider:surface-geometry https://pinboard.in/ https://pinboard.in/u:Vaguery/b:7bf81873d14b/ [1310.7019] Simulations of imaging of the local density of states by charged probe technique for resonant cavities 2014-03-30T11:44:18+00:00 http://arxiv.org/abs/1310.7019 Vaguery nanotechnology molecular-design simulation electromagnetism nudge-targets consider:inverse-problem consider:robustness https://pinboard.in/ https://pinboard.in/u:Vaguery/b:e29ed849ba68/ [1312.0075] Sequence-dependent folding landscapes of adenine riboswitch aptamers 2014-03-30T11:36:24+00:00 http://arxiv.org/abs/1312.0075 Vaguery RNA-folding biophysics simulation contingency energy-landscapes molecular-design interesting nudge-targets consider:explanatory-model-refinement note:self-organizing-polymer-model https://pinboard.in/ https://pinboard.in/u:Vaguery/b:ae78b47ddc94/ [1310.3000] Fractionalization of Interstitials in Curved Colloidal Crystals 2014-01-18T13:33:03+00:00 http://arxiv.org/abs/1310.3000 Vaguery nanotechnology materials-science experiment molecular-design interesting outside-the-box https://pinboard.in/ https://pinboard.in/u:Vaguery/b:bec4e363a71b/ [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/ [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/ [1309.0294] Bottom-up Engineering of Diamond Nanostructures 2013-09-05T11:38:39+00:00 http://arxiv.org/abs/1309.0294 Vaguery nanotechnology engineering-design emergent-design molecular-design https://pinboard.in/ https://pinboard.in/u:Vaguery/b:5400f2c4f259/ [1304.1740] Contact processes in crowded environments 2013-04-16T23:03:21+00:00 http://arxiv.org/abs/1304.1740 Vaguery simulation molecular-design nudge-targets fluid-dynamics diffusion biophysics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:f0b47e36000b/ [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/ [1304.2054] Monte-Carlo Simulation of a Multi-Dimensional Switch-Like Model of Stem Cell Differentiation 2013-04-10T11:23:28+00:00 http://arxiv.org/abs/1304.2054 Vaguery theoretical-biology systems-biology developmental-biology engineering-design control-theory molecular-design nudge-targets simulation https://pinboard.in/ https://pinboard.in/u:Vaguery/b:4b8e765ed450/ [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/ [1302.1385] Graphene as a Prototype Crystalline Membrane 2013-03-08T04:55:11+00:00 http://arxiv.org/abs/1302.1385 Vaguery chemistry molecular-design grapheme dynamical-systems structure-function-relationships biophysics https://pinboard.in/ https://pinboard.in/u:Vaguery/b:012d3c155d2a/ [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/ [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/ [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/ [0901.1849] Randomized Self-Assembly for Exact Shapes 2010-08-03T11:11:30+00:00 http://arxiv.org/abs/0901.1849 Vaguery molecular-design nanotechnology DNA-computing nudge-targets emergent-design https://pinboard.in/u:Vaguery/b:b8a0522a8aa9/ [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/ [1007.3554] Designer disordered materials with large complete photonic band gaps 2010-07-29T13:00:18+00:00 http://arxiv.org/abs/1007.3554 Vaguery engineering-design molecular-design simulation nudge-targets photonics materials-science https://pinboard.in/u:Vaguery/b:4fc7f9cb6dd2/ [0902.3631] Distributed Agreement in Tile Self-Assembly 2010-07-28T11:35:04+00:00 http://arxiv.org/abs/0902.3631 Vaguery nanotechnology self-assembly molecular-design distributed-processing complexology emergent-design nudge-targets https://pinboard.in/u:Vaguery/b:bf383da051cc/ [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/ PLoS ONE: Is Thermosensing Property of RNA Thermometers Unique? 2010-07-03T12:09:33+00:00 http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011308 Vaguery molecular-design simulation computational-methods RNA-folding biomolecules nudge-targets via:twitter https://pinboard.in/u:Vaguery/b:a8902a834691/ [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/ [1006.3736] Force-detected nuclear magnetic resonance: Recent advances and future challenges 2010-06-28T14:52:37+00:00 http://arxiv.org/abs/1006.3736 Vaguery nanotechnology atomic-force-microscopy physics molecular-design https://pinboard.in/u:Vaguery/b:62ee966f8d97/ [1006.3518] Graphene: A sub-nanometer trans-electrode membrane 2010-06-28T14:45:53+00:00 http://arxiv.org/abs/1006.3518 Vaguery nanotechnology molecular-design graphene engineering https://pinboard.in/u:Vaguery/b:33ad8f317c13/ [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/ [0912.0027] Temperature 1 Self-Assembly: Deterministic Assembly in 3D and Probabilistic Assembly in 2D 2010-05-16T10:25:35+00:00 http://arxiv.org/abs/0912.0027 Vaguery molecular-design DNA-computing Wang-tiles emergent-design LaBean nudge-targets https://pinboard.in/u:Vaguery/b:8c2e0e5974db/ 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/ [1004.4383] Self-Assembly of Arbitrary Shapes with RNA and DNA tiles (extended abstract) 2010-04-29T21:49:49+00:00 http://arxiv.org/abs/1004.4383 Vaguery molecular-design nanotechnology DNA biological-engineering https://pinboard.in/u:Vaguery/b:f00ac480f5de/ Sequenomics 2007-07-15T19:34:42+00:00 http://sequenomics.com/ Vaguery startups Thom-LaBean Erik-Schultes sequenomics science molecular-design combinatorial-libraries biopolymers bioinformatics irrational-design https://pinboard.in/u:Vaguery/b:d5bb015fdf94/