David Holcman - Publications

Affiliations: 
MAT Mathematics Weizmann Institute of Science, Rehovot, Israel 
Area:
Mathematics

94 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Basnayake K, Holcman D. Extreme escape from a cusp: When does geometry matter for the fastest Brownian particles moving in crowded cellular environments? Journal of Chemical Physics. 152: 134104. PMID 32268749 DOI: 10.1063/5.0002030  0.323
2020 Heine M, Holcman D. Asymmetry Between Pre- and Postsynaptic Transient Nanodomains Shapes Neuronal Communication. Trends in Neurosciences. 43: 182-196. PMID 32101710 DOI: 10.1016/J.Tins.2020.01.005  0.326
2019 Parutto P, Heck J, Heine M, Holcman D. Biophysics of high density nanometer regions extracted from super-resolution single particle trajectories: application to voltage-gated calcium channels and phospholipids. Scientific Reports. 9: 18818. PMID 31827157 DOI: 10.1038/S41598-019-55124-8  0.314
2019 Basnayake K, Mazaud D, Bemelmans A, Rouach N, Korkotian E, Holcman D. Fast calcium transients in dendritic spines driven by extreme statistics. Plos Biology. 17: e2006202. PMID 31163024 DOI: 10.1371/Journal.Pbio.2006202  0.308
2019 Cartailler J, Holcman D. Steady-state voltage distribution in three-dimensional cusp-shaped funnels modeled by PNP. Journal of Mathematical Biology. 79: 155-185. PMID 30968199 DOI: 10.1007/S00285-019-01353-4  0.318
2019 Schuss Z, Basnayake K, Holcman D. Redundancy principle and the role of extreme statistics in molecular and cellular biology. Physics of Life Reviews. PMID 30691960 DOI: 10.1016/J.Plrev.2019.01.001  0.337
2019 Dobramysl U, Holcman D. Mixed analytical-stochastic simulation method for the recovery of a Brownian gradient source from probability fluxes to small windows. Journal of Computational Physics. 355: 22-36. PMID 29456262 DOI: 10.1016/J.Jcp.2017.10.058  0.353
2019 Basnayake K, Schuss Z, Holcman D. Asymptotic Formulas for Extreme Statistics of Escape Times in 1, 2 and 3-Dimensions Journal of Nonlinear Science. 29: 461-499. DOI: 10.1007/S00332-018-9493-7  0.329
2018 Holcman D, Parutto P, Chambers JE, Fantham M, Young LJ, Marciniak SJ, Kaminski CF, Ron D, Avezov E. Single particle trajectories reveal active endoplasmic reticulum luminal flow. Nature Cell Biology. PMID 30224760 DOI: 10.1016/J.Bpj.2018.11.964  0.311
2018 Guerrier C, Holcman D. The First 100 nm Inside the Pre-synaptic Terminal Where Calcium Diffusion Triggers Vesicular Release. Frontiers in Synaptic Neuroscience. 10: 23. PMID 30083101 DOI: 10.3389/Fnsyn.2018.00023  0.317
2018 Cartailler J, Holcman D. Electrical transient laws in neuronal microdomains based on electro-diffusion. Physical Chemistry Chemical Physics. 20: 21062-21067. PMID 30074044 DOI: 10.1039/C8Cp02593B  0.311
2018 Amitai A, Holcman D. Encounter times of chromatin loci influenced by polymer decondensation. Physical Review E. 97: 32417. PMID 29776075 DOI: 10.1103/Physreve.97.032417  0.305
2018 Schuss Z, Tor K, Holcman D. Do cells sense time by number of divisions? Journal of Theoretical Biology. PMID 29752953 DOI: 10.1016/J.Jtbi.2018.05.001  0.316
2018 Cartailler J, Kwon T, Yuste R, Holcman D. Deconvolution of Voltage Sensor Time Series and Electro-diffusion Modeling Reveal the Role of Spine Geometry in Controlling Synaptic Strength. Neuron. PMID 29429935 DOI: 10.1016/J.Neuron.2018.01.034  0.311
2018 Dobramysl U, Holcman D. Reconstructing the gradient source position from steady-state fluxes to small receptors. Scientific Reports. 8: 941. PMID 29343770 DOI: 10.1038/S41598-018-19355-5  0.319
2018 Basnayake K, Hubl A, Schuss Z, Holcman D. Extreme Narrow Escape: Shortest paths for the first particles among n to reach a target window Physics Letters A. 382: 3449-3454. DOI: 10.1016/J.Physleta.2018.09.040  0.338
2017 Shukron O, Holcman D. Statistics of randomly cross-linked polymer models to interpret chromatin conformation capture data. Physical Review E. 96: 12503. PMID 29347098 DOI: 10.1103/Physreve.96.012503  0.303
2017 Cartailler J, Schuss Z, Holcman D. Electrostatics of non-neutral biological microdomains Scientific Reports. 7: 11269-11269. PMID 28900187 DOI: 10.1038/S41598-017-11590-6  0.322
2017 Shukron O, Hauer M, Holcman D. Two loci single particle trajectories analysis: constructing a first passage time statistics of local chromatin exploration. Scientific Reports. 7: 10346. PMID 28871173 DOI: 10.1038/S41598-017-10842-9  0.343
2017 Shukron O, Holcman D. Transient chromatin properties revealed by polymer models and stochastic simulations constructed from Chromosomal Capture data. Plos Computational Biology. 13: e1005469. PMID 28369076 DOI: 10.1371/Journal.Pcbi.1005469  0.308
2017 Amitai A, Seeber A, Gasser SM, Holcman D. Visualization of Chromatin Decompaction and Break Site Extrusion as Predicted by Statistical Polymer Modeling of Single-Locus Trajectories. Cell Reports. 18: 1200-1214. PMID 28147275 DOI: 10.1016/J.Celrep.2017.01.018  0.315
2017 Holcman D, Schuss Z. 100 years after Smoluchowski: stochastic processes in cell biology Journal of Physics A. 50: 93002. DOI: 10.1088/1751-8121/50/9/093002  0.358
2017 Amitai A, Holcman D. Polymer physics of nuclear organization and function Physics Reports. 678: 1-83. DOI: 10.1016/J.Physrep.2017.02.002  0.343
2017 Cartailler J, Schuss Z, Holcman D. Analysis of the Poisson–Nernst–Planck equation in a ball for modeling the Voltage–Current relation in neurobiological microdomains Physica D: Nonlinear Phenomena. 339: 39-48. DOI: 10.1016/J.Physd.2016.09.001  0.315
2017 Guerrier C, Holcman D. Multiscale models and stochastic simulation methods for computing rare but key binding events in cell biology Journal of Computational Physics. 340: 617-638. DOI: 10.1016/J.Jcp.2017.03.058  0.384
2017 Lagache T, Holcman D. Extended Narrow Escape with Many Windows for Analyzing Viral Entry into the Cell Nucleus Journal of Statistical Physics. 166: 244-266. DOI: 10.1007/S10955-016-1691-9  0.339
2016 Guerrier C, Holcman D. Hybrid Markov-mass action law model for cell activation by rare binding events: Application to calcium induced vesicular release at neuronal synapses. Scientific Reports. 6: 35506. PMID 27752087 DOI: 10.1038/Srep35506  0.355
2016 Duc KD, Schuss Z, Holcman D. Oscillatory survival probability: Analytical and numerical study of a non-poissonian exit time Multiscale Modeling and Simulation. 14: 772-798. DOI: 10.1137/151004100  0.347
2015 Yang J, Kupka I, Schuss Z, Holcman D. Search for a small egg by spermatozoa in restricted geometries. Journal of Mathematical Biology. PMID 26707857 DOI: 10.1007/S00285-015-0955-3  0.315
2015 Dao Duc K, Parutto P, Chen X, Epsztein J, Konnerth A, Holcman D. Synaptic dynamics and neuronal network connectivity are reflected in the distribution of times in Up states. Frontiers in Computational Neuroscience. 9: 96. PMID 26283956 DOI: 10.3389/Fncom.2015.00096  0.325
2015 Guerrier C, Hayes JA, Fortin G, Holcman D. Robust network oscillations during mammalian respiratory rhythm generation driven by synaptic dynamics. Proceedings of the National Academy of Sciences of the United States of America. 112: 9728-33. PMID 26195782 DOI: 10.1073/Pnas.1421997112  0.304
2015 Dao Duc K, Lee CY, Parutto P, Cohen D, Segal M, Rouach N, Holcman D. Bursting reverberation as a multiscale neuronal network process driven by synaptic depression-facilitation. Plos One. 10: e0124694. PMID 26017681 DOI: 10.1371/Journal.Pone.0124694  0.305
2015 Hoze N, Holcman D. Kinetics of aggregation with a finite number of particles and application to viral capsid assembly. Journal of Mathematical Biology. 70: 1685-705. PMID 25103220 DOI: 10.1007/S00285-014-0819-2  0.303
2015 Guerrier C, Holcman D. Search time for a small ribbon and application to vesicular release at neuronal synapses Multiscale Modeling and Simulation. 13: 1173-1193. DOI: 10.1137/15M1009512  0.355
2015 Hoze N, Holcman D. Recovering a stochastic process from super-resolution noisy ensembles of single-particle trajectories Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 92. DOI: 10.1103/Physreve.92.052109  0.345
2015 Holcman D, Hoze N, Schuss Z. Analysis and Interpretation of Superresolution Single-Particle Trajectories Biophysical Journal. 109: 1761-1771. DOI: 10.1016/J.Bpj.2015.09.003  0.351
2014 Hoze N, Holcman D. Residence times of receptors in dendritic spines analyzed by stochastic simulations in empirical domains. Biophysical Journal. 107: 3008-17. PMID 25517165 DOI: 10.1016/J.Bpj.2014.10.018  0.314
2014 Guerrier C, Holcman D. Brownian search for targets hidden in cusp-like pockets: Progress and Applications European Physical Journal: Special Topics. 223: 3273-3285. DOI: 10.1140/Epjst/E2014-02332-6  0.374
2014 Holcman D, Schuss Z. Oscillatory survival probability and eigenvalues of the non-self-adjoint Fokker-Planck operator Multiscale Modeling and Simulation. 12: 1294-1308. DOI: 10.1137/130925414  0.318
2014 Duc KD, Schuss Z, Holcman D. Oscillatory decay of the survival probability of activated diffusion across a limit cycle Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 89. DOI: 10.1103/Physreve.89.030101  0.314
2014 Holcman D, Schuss Z. Time scale of diffusion in molecular and cellular biology Journal of Physics a: Mathematical and Theoretical. DOI: 10.1088/1751-8113/47/17/173001  0.366
2014 Holcman D. Multiscale Modeling, Stochastic And Asymptotic Approaches For Analyzing Neural Networks Based On Synaptic Dynamics Esaim: Proceedings. 47: 36-54. DOI: 10.1051/Proc/201447003  0.333
2014 Hozé N, Holcman D. Modeling capsid kinetics assembly from the steady state distribution of multi-sizes aggregates Physics Letters, Section a: General, Atomic and Solid State Physics. 378: 531-534. DOI: 10.1016/J.Physleta.2013.12.019  0.308
2014 Holcman D, Amitai A. Dynamics of dsDNA Break, Organization of the Nucleus Based on Polymer Dynamics Biophysical Journal. 106: 2-2. DOI: 10.1016/J.Bpj.2013.11.1596  0.313
2013 Duc KD, Holcman D. Computing the length of the shortest telomere in the nucleus Physical Review Letters. 111: 228104. PMID 24329474 DOI: 10.1103/Physrevlett.111.228104  0.322
2013 Reingruber J, Pahlberg J, Woodruff ML, Sampath AP, Fain GL, Holcman D. Detection of single photons by toad and mouse rods. Proceedings of the National Academy of Sciences of the United States of America. 110: 19378-83. PMID 24214653 DOI: 10.1073/Pnas.1314030110  0.31
2013 Bouchoucha YX, Reingruber J, Labalette C, Wassef MA, Thierion E, Desmarquet-Trin Dinh C, Holcman D, Gilardi-Hebenstreit P, Charnay P. Dissection of a Krox20 positive feedback loop driving cell fate choices in hindbrain patterning. Molecular Systems Biology. 9: 690. PMID 24061538 DOI: 10.1038/Msb.2013.46  0.304
2013 Holcman D, Schuss Z. Control of flux by narrow passages and hidden targets in cellular biology Reports On Progress in Physics. 76. PMID 23787818 DOI: 10.1088/0034-4885/76/7/074601  0.35
2013 Amitai A, Kupka I, Holcman D. Kinetics of Diffusing Polymer Encounter in Confined Cellular Microdomains Journal of Statistical Physics. 153: 1107-1131. DOI: 10.1007/S10955-013-0876-8  0.313
2012 Freche D, Lee CY, Rouach N, Holcman D. Synaptic transmission in neurological disorders dissected by a quantitative approach. Communicative & Integrative Biology. 5: 448-52. PMID 23181158 DOI: 10.4161/Cib.20818  0.3
2012 Hoze N, Nair D, Hosy E, Sieben C, Manley S, Herrmann A, Sibarita JB, Choquet D, Holcman D. Heterogeneity of AMPA receptor trafficking and molecular interactions revealed by superresolution analysis of live cell imaging. Proceedings of the National Academy of Sciences of the United States of America. 109: 17052-7. PMID 23035245 DOI: 10.1073/Pnas.1204589109  0.33
2012 Lagache T, Danos O, Holcman D. Modeling the step of endosomal escape during cell infection by a nonenveloped virus. Biophysical Journal. 102: 980-9. PMID 22404920 DOI: 10.1016/J.Bpj.2011.12.037  0.316
2012 Amitai A, Kupka I, Holcman D. Analysis of the mean first looping time of a rod-polymer Multiscale Modeling and Simulation. 10: 612-632. DOI: 10.1137/110842624  0.308
2012 Amitai A, Kupka I, Holcman D. Computation of the mean first-encounter time between the ends of a polymer chain Physical Review Letters. 109. DOI: 10.1103/Physrevlett.109.108302  0.353
2012 Holcman D, Schuss Z. Brownian needle in dire straits: Stochastic motion of a rod in very confined narrow domains Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 85. DOI: 10.1103/Physreve.85.010103  0.31
2011 Holcman D, Schuss Z. Diffusion laws in dendritic spines. Journal of Mathematical Neuroscience. 1: 10. PMID 22655862 DOI: 10.1186/2190-8567-1-10  0.343
2011 Ribrault C, Reingruber J, Petković M, Galli T, Ziv NE, Holcman D, Triller A. Syntaxin1A lateral diffusion reveals transient and local SNARE interactions. The Journal of Neuroscience : the Official Journal of the Society For Neuroscience. 31: 17590-602. PMID 22131420 DOI: 10.1523/Jneurosci.4065-11.2011  0.328
2011 Biess A, Korkotian E, Holcman D. Barriers to diffusion in dendrites and estimation of calcium spread following synaptic inputs. Plos Computational Biology. 7: e1002182. PMID 22022241 DOI: 10.1371/Journal.Pcbi.1002182  0.349
2011 Taflia A, Holcman D. Estimating the synaptic current in a multiconductance AMPA receptor model. Biophysical Journal. 101: 781-92. PMID 21843468 DOI: 10.1016/J.Bpj.2011.05.032  0.311
2011 Malherbe G, Holcman D. Stochastic modeling of gene activation and applications to cell regulation. Journal of Theoretical Biology. 271: 51-63. PMID 21129382 DOI: 10.1016/J.Jtbi.2010.11.032  0.319
2011 Reingruber J, Holcman D. The narrow escape problem in a flat cylindrical microdomain with application to diffusion in the synaptic cleft Multiscale Modeling and Simulation. 9: 793-816. DOI: 10.1137/100807612  0.371
2011 Holcman D, Hoze N, Schuss Z. Narrow escape through a funnel and effective diffusion on a crowded membrane Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 84. DOI: 10.1103/Physreve.84.021906  0.332
2011 Amitai A, Kupka I, Holcman D. The Mean Looping Time of DNA Biophysical Journal. 100. DOI: 10.1016/J.Bpj.2010.12.623  0.334
2011 Vakeroudis S, Yor M, Holcman D. The Mean First Rotation Time of a Planar Polymer Journal of Statistical Physics. 143: 1074-1095. DOI: 10.1007/S10955-011-0227-6  0.31
2010 Reingruber J, Holcman D. Narrow escape for a stochastically gated Brownian ligand. Journal of Physics. Condensed Matter : An Institute of Physics Journal. 22: 065103. PMID 21389363 DOI: 10.1088/0953-8984/22/6/065103  0.304
2010 Bouzigues C, Holcman D, Dahan M. A mechanism for the polarity formation of chemoreceptors at the growth cone membrane for gradient amplification during directional sensing. Plos One. 5: e9243. PMID 20179770 DOI: 10.1371/Journal.Pone.0009243  0.305
2010 Dao Duc K, Holcman D. Threshold activation for stochastic chemical reactions in microdomains Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 81. DOI: 10.1103/Physreve.81.041107  0.335
2010 Reingruber J, Bosanac L, Darzacq X, Holcman D. Transcription Factor Switching Dynamics Regulates Gene Activation Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.398  0.317
2010 Lagache T, Holcman D. Mean Time and Probability to Reach a Structured Target Biophysical Journal. 98. DOI: 10.1016/J.Bpj.2009.12.3958  0.338
2009 Reingruber J, Holcman D. Gated narrow escape time for molecular signaling. Physical Review Letters. 103: 148102. PMID 19905605 DOI: 10.1103/Physrevlett.103.148102  0.319
2009 Lagache T, Dauty E, Holcman D. Physical principles and models describing intracellular virus particle dynamics Current Opinion in Microbiology. 12: 439-445. PMID 19608455 DOI: 10.1016/J.Mib.2009.06.015  0.345
2009 Reingruber J, Holcman D. Diffusion in narrow domains and application to phototransduction. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 030904. PMID 19391893 DOI: 10.1103/Physreve.79.030904  0.347
2009 Reingruber J, Abad E, Holcman D. Narrow escape time to a structured target located on the boundary of a microdomain. The Journal of Chemical Physics. 130: 094909. PMID 19275426 DOI: 10.1063/1.3081633  0.323
2009 Lagache T, Dauty E, Holcman D. Quantitative analysis of virus and plasmid trafficking in cells. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 79: 011921. PMID 19257083 DOI: 10.1103/Physreve.79.011921  0.367
2009 Tsaneva-Atanasova K, Burgo A, Galli T, Holcman D. Quantifying neurite growth mediated by interactions among secretory vesicles, microtubules, and actin networks. Biophysical Journal. 96: 840-57. PMID 19186125 DOI: 10.1016/J.Bpj.2008.10.036  0.313
2008 Lagache T, Holcman D. Quantifying intermittent transport in cell cytoplasm. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 77: 030901. PMID 18517320 DOI: 10.1103/Physreve.77.030901  0.325
2008 Lagache T, Holcman D. Effective motion of a virus trafficking inside a biological cell Siam Journal On Applied Mathematics. 68: 1146-1167. DOI: 10.1137/060672820  0.312
2008 Singer A, Schuss Z, Holcman D. Narrow escape and leakage of Brownian particles Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 78. DOI: 10.1103/Physreve.78.051111  0.33
2007 Holcman D, Kasatkin V, Prochiantz A. Modeling homeoprotein intercellular transfer unveils a parsimonious mechanism for gradient and boundary formation in early brain development Journal of Theoretical Biology. 249: 503-517. PMID 17904161 DOI: 10.1016/J.Jtbi.2007.07.026  0.325
2007 Schuss Z, Singer A, Holcman D. The narrow escape problem for diffusion in cellular microdomains Proceedings of the National Academy of Sciences of the United States of America. 104: 16098-16103. PMID 17901203 DOI: 10.1073/Pnas.0706599104  0.387
2007 Taflia A, Holcman D. Dwell time of a Brownian molecule in a microdomain with traps and a small hole on the boundary. The Journal of Chemical Physics. 126: 234107. PMID 17600404 DOI: 10.1063/1.2746840  0.357
2007 Singer A, Schuss Z, Osipov A, Holcman D. Partially reflected diffusion Siam Journal On Applied Mathematics. 68: 844-868. DOI: 10.1137/060663258  0.3
2007 Biess A, Korkotian E, Holcman D. Diffusion in a dendritic spine: The role of geometry Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 76. DOI: 10.1103/Physreve.76.021922  0.349
2007 Holcman D. Modeling DNA and virus trafficking in the cell cytoplasm Journal of Statistical Physics. 127: 471-494. DOI: 10.1007/S10955-007-9282-4  0.333
2006 Holcman D, Triller A. Modeling synaptic dynamics driven by receptor lateral diffusion. Biophysical Journal. 91: 2405-15. PMID 16844759 DOI: 10.1529/Biophysj.106.081935  0.316
2006 Holcman D, Tsodyks M. The emergence of Up and Down states in cortical networks. Plos Computational Biology. 2: e23. PMID 16557293 DOI: 10.1371/Journal.Pcbi.0020023  0.31
2006 Singer A, Schuss Z, Holcman D. Narrow escape, part II: The circular disk Journal of Statistical Physics. 122: 465-489. DOI: 10.1007/S10955-005-8027-5  0.326
2005 Holcman D, Marchewka A, Schuss Z. Survival probability of diffusion with trapping in cellular neurobiology. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 72: 031910. PMID 16241485 DOI: 10.1103/Physreve.72.031910  0.346
2005 Holcman D, Korkotian E, Segal M. Calcium dynamics in dendritic spines, modeling and experiments. Cell Calcium. 37: 467-75. PMID 15820395 DOI: 10.1016/J.Ceca.2005.01.015  0.311
2005 Holcman D, Schuss Z. Modeling calcium dynamics in dendritic spines Siam Journal On Applied Mathematics. 65: 1006-1026. DOI: 10.1137/S003613990342894X  0.325
2005 Holcman D, Schuss Z. Stochastic chemical reactions in microdomains Journal of Chemical Physics. 122. DOI: 10.1063/1.1849155  0.329
2004 Holcman D, Schuss Z, Korkotian E. Calcium dynamics in dendritic spines and spine motility Biophysical Journal. 87: 81-91. PMID 15240447 DOI: 10.1529/Biophysj.103.035972  0.311
2004 Holcman D, Korenbrot JI. Longitudinal diffusion in retinal rod and cone outer segment cytoplasm: the consequence of cell structure. Biophysical Journal. 86: 2566-82. PMID 15041693 DOI: 10.1016/S0006-3495(04)74312-X  0.303
2004 Holcman D, Schuss Z. Escape through a small opening: Receptor trafficking in a synaptic membrane Journal of Statistical Physics. 117: 975-1014. DOI: 10.1007/S10955-004-5712-8  0.354
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