Themes of research (Selected Publications)

Modeling and Analysis of molecular and cellular biology: the function of microdomains

Modeling synapses

* A. Taflia, D. Holcman, Estimating the synaptic current in a multi-conductance AMPA receptor model, Biophysical Journal. 101(4):781-92, (2011).

*D. Fresche, U. Panache N. Rouach D Holcman, Synapse geometry and receptor dynamics modulate synaptic strength PloS One;6(10):e25122, (2011).

*N. Hoze N Deepack JB. Sibarita D. Choquet D. Holcman, Stochatic modeling to analysis AMPAR trajectories 2011.

*U. Pannasch, L.Vargova, J. Reingruber, P. Ezan, C. Giaume, D. Holcman, E. Sykova Nathalie Rouach, Astroglial networks scale synaptic activity and plasticity, PNAS 2011 A108: 8467-8472

*D. Fresche, C.Y. Lee N. Rouach, D. Holcman, Synaptic transmission in neurological disorders dissected by a quantitative approach, 5:5, 1-5; Communicative & Integrative Biology (2012).

Analysis of Molecular Trafficking and chemical reactions

*D. Holcman, Schuss Z: Escape through a small opening: receptor trafficking in a synaptic membrane. J. Statist. Phys. 117 (2004), 5-6, 975—1014.

* D. Holcman, Z. Schuss. A theory of stochastic chemical reactions in confined microstructures, Journal of Chemical Physics 122, 114710, 2005.

* D. Holcman, A. Singer Z, Schuss, Narrow Escape: Theory and Applications to Cellular Microdomains, PNAS, 2007.

*C. Ribrault, J. Reingruber, N. E. Ziv, D. Holcman, A.Triller, Syntaxin1A diffusion reveals transient and local SNARE interactions, J. Neuroscience 31(48):17590-17602. 2011.

* N.Hoze, N. Deepak, E. Hosy, C. Sieben, S. Manley, A. Herrmann, JB Sibarita, D. Choquet, D. Holcman, Stochastic analysis of receptor trajectories from superresolution data, PNAS doi:10.1073/pnas.1204589109 2012

Theory of diffusion for Dendritic spines

*D. Holcman Z. Schuss, Diffusion laws in dendritic spines, J. Math. Neuroscience 1:10 2011, doi:10.1186/2190-8567-1-10.

*D. Holcman, E. Korkotian, M. Segal, Calcium dynamic in dendritic spine, modeling and experiments, (review 2005) .

* E. Korkotian, D. Holcman, M. Segal, Dynamic Regulation of Spine-Dendrite Coupling in Cultured Hippocampal Neurons, Euro J. of Neuroscience, 2004 (10):2649-63.

* D. Holcman, Z. Schuss, E. Korkotian, Calcium dynamic in dendritic spines and spine motility, Biophysical Journal 87:81-91 (2004).

* D. Holcman, Z. Schuss, Modeling Calcium Dynamics in Dendritic Spines, SIAM of Applied Math (2004).

Modeling the nuclear organization and function

*J. Reingruber D. Holcman, Transcription factor search for a DNA promoter in a three-state model.

*N. Hoze A., D. Holcman, Coagulation–fragmentation for a finite number of particles and application to telomere clustering in the yeast nucleus, Physics Letters A,376, 6–7, 845–849, 2012.

*N.Hoze, C. Amuroso, M. Ruault, A Taddei, D. Holcman, Dynamics of telomere clustering in the nucleus, Molecular Biology of the Cell, 24(11):1791-800 (2013)

* A. Amitai, D. Holcman, Diffusing polymers in confined microdomains and estimation of chromosomal territory sizes from chromosome capture data, Phys. Rev. Lett. 110, 248105 (2013)

Physical modeling the early steps of viral infection, viral trafficking

* T. Lagache, O. Danos, D. Holcman, Modeling endosomal escape of non enveloped viruses, case of the AAV Biophysical J. 102(5):980-9. 2012

* T. Lagache, D. Holcman, Effective drift for a virus trafficking inside a biological cell, in SIAM of App. Math., 68, 4 2008, 1146-1167.

* D. Holcman, Modeling viral DNA trafficking in a biological cell. JSP, 2007

* T. Lagache, D. Holcman, Quantifying intermittent transport in cell cytoplasm, Phys. Rev. E-Short Com. 77, 030901® (2008)

*T. Lagache, C Sieben, A Hermann, D. Holcman, Endosomal escape for enveloped viruses.

Analysis of Phototransduction

* D. Holcman, J. Korenbrot, Longitudinal diffusion in retinal rod and cone outer segment cytoplasm: the consequence of cell structure , Biophysical Journal 86:2566-2582 (2004).

*D. Holcman J. Korenbrot, The limit of photoreceptor sensitivity; molecular mechanisms of dark current noise in retinal, J Gen Physiol.,125(6):641-60, 2005.

*J. Reingruber D. Holcman, The dynamics of phosphodiesterase activation in rods and cones, 15;94(6):1954-70 Biophys. J. 2008.

* . Reingruber D. Holcman, Estimating the rate constant of cyclic GMP hydrolysis by activated phosphodiesterase in photoreceptors, J. Chem. Physics. 129,14.145102 2008.

*J. Reingruber J. Pahlberg M. Woodroof A. Sampath G. Fain D. Holcman, Detection of of a single photon response in mouse and toad rods, PNAS 110(48):19378-83 (2013).

Early Development and Morphogenetic Gradients

* V. Kasatkin, A. Prochiantz, D. Holcman, Morphogenetic gradients and the stability of boundaries between neighboring morphogenetic regions;70(1):156-78. Bull. Math Biology 2007.

* K. Tsaneva, A. Burgo, T. Galli, D. Holcman, Modeling neurite growth Biophysical Journal 2009.

*D. Holcman V. Kasatkin A. Prochiantz Modeling homeoprotein intercellular transfer unveils a parsimonious mechanism for gradient and boundary formation in early brain J. Theor. Biology 249(3):503-17, 2007.

*G. Malherbe D. Holcman, Stochastic modeling of gene activation and application to cell regulation, J. Th.Bio 271, 1 p51-63 (2010).

*O Stettler, RL. Joshi, A.Wizenmann, J. Reingruber, D. Holcman, C.Bouillot, F. Castagner, A. Prochiantz, and KL. Moya, Engrailed homeoprotein recruits the adenosine A1 receptor to potentiate Ephrin A5 function in retinal growth cones, Development;139(1):215-24. (2012).

*, Y Reingruber*, J. Le Men, J Gilardi-Hebenstreit, P, D. Holcman* Charnay*, P Stochastic switching in a feedback loop controls vertebrate hindbrain patterning revision, Mol. Sys. Biol. *: equally.;9:690. doi: 10.1038/msb.2013.46. (2013)

System Neuroscience, Neuron-gli interactions, cortical plasticity and cortex dynamics

*K. Dao Duc, J Sibille, N. Rouach, D. Holcman, Potassium regulation through the Kir4.1 channel in astrocyte, consequence for the neural activity.

* C. Giaume, A. Koulakoff, L. Roux, D. Holcman and N. Rouach, Astroglial connexin-mediated networks:a step further in neuroglial interactions, Nat. Rev. Neuroscience (2009).

* Barrie J.M., Holcman D., Freeman W.J., Statistical evaluation of clusters derived by nonlinear mapping of EEG spatial patterns, J. of Neuro. Methods (90) 1999 p87-9

* E. Bart S. Bao D. Holcman, Modeling the spontaneous activity of the auditory cortex, 2005.

* D. Holcman M.Tsodyks, Emergence of Up and Down states in cortical neurons, PloS Comp. 2006.

* K. Dao Duc, D. Cohen M. Segal, N.Rouach D. Holcman, Facilitation-depression synapses underlie neuronal network reverberation.

Stochastic processes, Brownian motion and the Narrow escape theory

*D. Holcman Z. Schuss, the narrow escape problem, SIAM Rev 56 no. 2, 213–257 2014.

*Z. Schuss D. Holcman, Time scales of Diffusion for Molecular and Cellular processes, J.Phys A. 2014.

* D. Holcman, Z. Schuss, Escape through a small opening: receptor trafficking in a synaptic membrane, J. of Statistical Physics 117, 5/6 Dec. (2004)p 191-230.

* A. Singer Z, Schuss, D. Holcman,B. Eisenberg Narrow Escape I, 2006.

* A. Singer Z, Schuss, D. Holcman, Narrow Escape II, 2006.

* A. Singer Z, Schuss, D. Holcman, Narrow Escape III, 2006.

* Reinbruber D. Holcman, Narrow escape for a stochastically gated Brownian ligand, J. Cond. Matt, 22 2010

Modeling polymers in confined microdomains

* A. Amitai, D. Holcman, beta-model application to DNA modeling in the nucleus, Phys. Rev E. 88, 052604 (2013)

* A. Amitai, I. Kupka D. Holcman, Kinetics of diffusing polymer encounter in confined cellular microdomains, J. Stat. Phys. 153 (2013), no. 6, 1107–1131. (2013)

*S. Vakeroudis M. Yor D. Holcman, The Mean First Rotation Time of a planar Polymer J. Stat. Phys. DOI: 10.1007/s10955-011-0227-6 (2011).

Partial differential equations and Asymptotics

K. Dao duc, Z. Schuss D. Holcman, Oscillatory decay of the survival probability of activated diffusion across a limit cycle, Phys. Rev E 2014.

Singular perturbations

* D. Holcman, Nonlinear PDE with vector fields, J. Anal. Math. 81 (2000), 111—137.

* D. Holcman, EDP non lineaires avec champ de vecteurs, Compt. Rend. Acad. Sci. Paris, 1999

* D. Holcman I. Kupka, Singular perturbation for the first eigenfunction and blow up analysis, Forum Math. 2006

* D. Holcman I. Kupka, Semi-classical limit of the first eigenfunction and concentration on the recurrent sets of a dynamical system.

Nonlinear Analysis on Manifolds.

* D. Holcman, Solutions nodales sur les varietes Riemanniennes, J. of Funct. Analys., 1999,Vol. 26 p219-245.

* D. Holcman E. Humbert, Poincare-Sobolev inequality on manifolds with boundary, Math. Z. 237 (2001), no. 4, 669—695

* D. Holcman, Influence de la masse sur les solutions nodales d’EDP non lineaires, Bull. Sci. Math. 124 (2000), no. 5, 385—414

* D. Holcman, On the mass of manifolds with boundary, C. R. Acad. Sci. Paris Sér. I Math. 328 (1999), no. 12, 1191—1196

* D. Holcman, Prescribed Scalar Curvature problem on Complete manifolds, J. Math. Pures Appl. (9) 80 (2001), no. 2, 223— Appl. 2001.

* D. Holcman I. Kupka, Perturbation Methods and First Order Differential Equations, Quarterly Journal of Mathematics (2004).

* D. Holcman, C. Pugh,The Boundary between Compact and Noncompact Complete Riemann Manifolds.

Subriemannian Geometry and Control theory

* D.Holcman M.Margaliot, Stability Analysis of Switched Homogeneous Systems in the plane, SIAM J. of Control, Jan 2003, vol. 41, 5 pp. 1609-1625

* P. Greiner D. Holcman Y. Kannai, Wave Kernel related to second order operators, Duke Mathematical Journal, 114 (2002), no. 2, 329–386