Olfactory searches
Infomax strategies for an optimal balance between exploration and exploitation. G. Reddy, A. Celani & Vergassola, M. J Stat Phys, 163: 1454 , 2016.
Odor landscapes in turbulent environments. A. Celani, E. Villermaux & M. Vergassola. Physical Review X, 4, 041015, 2014. (Featured in Physics)
Chasing information to search in random environment. J.-B. Masson, M. Bailly-Bechet, M. Vergassola, J. Phys. A, 42, 434009, 2009 (Special Issue on Random Searches).
Infotaxis as a strategy for searching without gradients. M. Vergassola, E. Villermaux & B.I. Shraiman Nature, 445, 406-409, 2007.
Bacterial physiology and motility
The role of adaptation in bacterial speed races. J. Wong-Ng J, A. Melbinger, A. Celani & Vergassola M, PLOS Comp Biol 12(6): e1004974, 2016
Cell-size control and homeostasis in bacteria. S. Taheri-Araghi, S. Bradde, J.T. Sauls, N.S. Hill, P.A. Levin, J. Paulsson, M. Vergassola, & S. Jun, Current Biology 25, 385-391, 2015.
Non-linearity, fluctuations and response in sensory systems. A. Celani & M. Vergassola, Phys. Rev. Lett., 108, 258102, 2012.
Non-invasive inference of the molecular chemotaxis response using b\acterial trajectories. J.-B. Masson, G. Voisinne, J. Wong-Ng, A. Celani & M. Vergassola, Proc. Nat. Acad. Sciences, 109, 1802-7, 2012.
Functional and molecular aspects of bacterial chemotaxis. A. Celani, T.S. Shimizu & M. Vergassola J. Stat. Phys., 144, 219-40, 2011.
Bacterial strategies for chemotaxis response. A. Celani & M. Vergassola Proc. Nat. Academy Sciences, 107, 1391- 1396, 2010.
Repulsion and metabolic switches in the collective behavior of bacterial colonies. A. Sekowska, J.-B. Masson, A. Celani, A. Danchin & M. Vergassola, Biophysi\cal Journal, 97, 688-98, 2009.
Biological modeling
Learning to soar in turbulent environments. G. Reddy, A. Celani, T.J. Sejnowski & M. Vergassola. Proc Natl Acad Sci U S A. published ahead of print August 1, 2016
Tissue mechanics govern the rapidly adapting and symmetrical response to touch. A.L. Eastwood, A. Sanzeni, B.C. Petzold, S.-J. Park, M. Vergassola, B.L. Pruitt & M.B. Goodman Proc Natl Acad Sci U S A. 112(50):E6955-63 , 2015 (Featured in UCSD News)
The Impact of Environmental Fluctuations on Evolutionary Fitness Functions. A. Melbinger and M. Vergassola, Scientific Reports 5, 15211, 2015.
T-cells Integrate Local and Global Cues to Discriminate Between Structurally Similar Antigens. G. Voisinne, B. Nixon, A. Melbinger, G. Gasteiger, M. Vergassola, and G. Altan-Bonnet , Cell Reports, 1208-1219, 2015.
Decisions on the fly in cellular sensory systems. E.D. Siggia & M. Vergassola. Proc. Nat. Acad. Sciences, 110, E3704-12, 2013.
Phenotypic model for early T-cell activation displaying sensitivity, specificity and antagonism. P. François, G. Voisinne, E.D. Siggia, G. Altan-Bonnet &M. Vergassola. Proc. Nat. Acad. Sciences, 110, E888-97. 2013.
Computational Biology
Theory of feedback controlled brain stimulations for Parkinson's disease. A. Sanzeni, A. Celani, G. Tiana, M. Vergassola Physica A: Statistical Mechanics and its Applications,441:121-130, 2015.
Inference in particle tracking experiments by passing messages between images. M. Chertkov, L. Kroc, F. Krzakala, M. Vergassola, L.Zdeborova Proc. Nat. Academy Sciences, 107, 7663-8, 2010.
The Listeria transcriptional landscape from saprophytism to virulence. A. Toledo-Arana et al. (19 authors), Nature, 459, 950-956, 2009.
Inferring maps of forces inside cell membrane microdomains. J.-B. Masson, D. Casanova, S. Türkcan, G. Voisinne, M.R. Popoff, M. Vergassola, A. Alexandrou Phys. Rev. Lett 102, 048103, 2009.
Message-passing algorithms for the prediction of protein domain interactions from protein–protein interaction data. M. Iqbal, A.A. Freitas, C.G. Johnson & M. Vergassola Bioinformatics 24, 2064-2070, 2008.
Causes for the intriguing presence of tRNAs in phages. M. Bailly-Bechet, M. Vergassola & EPC Rocha Genome Research, 17, 1486-1495, 2007.
Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae. E. Aurell, A. Fouquier d’Herouel, C. Malmnas & M. Vergassola Physical Biology, 4: 134-143, 2007.
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. P. Mandin*, F. Repoila*, M. Vergassola*, T. Geissmann & P. Cossart Nucleic Acids Research, 35: 962-74 2007 (*Equal contributions).
Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages. G. Fischer, EPC Rocha, F. Brunet, M. Vergassola & B. Dujon PLoS Genetics 2 (3): 253-261, 2006.
Codon usage domains over bacterial chromosomes. M. Bailly-Bechet, A. Danchin, M. Iqbal, M. Marsili & M. Vergassola PLoS Computational Biology 2 (4): 263-275, 2006.
Cooperative evolution in protein complexes of yeast from comparative analyses of its interaction network. M. Vergassola, A. Vespignani & B. Dujon Proteomics 5 (12): 3116-3119, 2005.
VirR, a response regulator critical for Listeria monocytogenes virulence. P. Mandin, H. Fsihi, O. Dussurget, M. Vergassola, E. Milohanic, A. Toledo-Arana, I. Lasa, J. Johansson & P. Cossart Molecular Microbiology 57 (5): 1367- 1380, 2005.
An evolutionary and functional assessment of regulatory network motifs in yeast. A. Mazurie, S. Bottani & M. Vergassola, BMC Genome Biology, 6(4), R35, 2005.
CovR/CovS of group B Streptococcus: a two-component regulatory system involved in virulence. M.-C. Lamy, M. Zouine, J. Fert, M. Vergassola, E. Couvé, E. Pellegrini, P. Glaser, F. Kunst, T. Msadek, P. Trieu-Cuot & C. Poyart, Molecular Microbiology, 54, 1250-1268, 2004.
DNA macroarray for identification and typing of Staphylococcus aureus isolates. S. Trad, J. Allignet, L. Frangeuil, M. Davi, M. Vergassola, E. Couvé, A. Morvan, A. Kechrid, C. Buchrieser, P. Glaser & N. El Solh; J. Clinical Microbiology, 42, 2054-2064, 2004.
Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. N. Rajewsky, M. Vergassola, U. Gaul & E.D. Siggia; BMC Bioinformatics, 3:Art. 30, 2002.
Random Matrices
Statistical distribution of quantum entanglement for a random bipartite state. C. Nadal, S.N. Majumdar & M. Vergassola, J. Stat. Phys. 142, 403-438, 2011.
Phase transitions in the distribution of bipartite entanglement of a random pure state. C. Nadal, S.N. Majumdar & M. Vergassola, Phys. Rev. Lett. 104, 110501, 2010.
Large deviations of the maximum eigenvalue for Wishart and Gaussian random matrices. S.N. Majumdar & M. Vergassola Phys. Rev. Lett 102, 060601, 2009.
Complex Fluids
Nonlinear dynamics of the viscoelastic Kolmogorov flow. A. Bistagnino, G. Boffetta, A. Celani, A. Mazzino, A. Puliafito, M. Vergassola, J. Fluid Mechanics, 590, 61-80, 2007.
The viscoelastic Kolmogorov flow: eddy viscosity and linear stability. G. Boffetta, A Celani, A. Mazzino, A. Puliafito & M. Vergassola; J. Fluid Mechanics, 523, 99-108, 2005.
Partial screening in dense lattice-configuration suspensions. P.J. Mucha, I. Goldhirsch, S.A. Orszag & M. Vergassola; Phys. Rev. Lett., 83, 3414-3417, 1999.
Anomalous Scaling in Statistical Fluid Dynamics
Shear effects on passive scalar spectra. A. Celani, M. Cencini, M. Vergassola, E. Villermaux & D. Vincenzi; J. Fluid Mechanics Letters, 523, 99-108, 2005.
Active and passive fields face to face. A. Celani, M. Cencini, A. Mazzino & M. Vergassola, New Journal of Physics, 6, Art. 72, 2004.
Lagrangian dispersion in Gaussian self-similar velocity ensembles. M. Chaves, K. Gawedzki, P. Horvai, A. Kupiainen & M. Vergassola; J. Statistical Physics 113, 643-692, 2004.
Scaling and universality in turbulent convection. A. Celani, T. Matsumoto, A. Mazzino & M. Vergassola; Phys. Rev. Lett., 88, Art. No. 054503, 2002.
Particles and fields in fluid turbulence. G. Falkovich, K. Gawedzki & M. Vergassola; Rev. Mod. Physics, 73, 913- 975, 2001.
Statistical conservation laws in turbulent transport. I. Arad, L. Biferale, A. Celani, I. Procaccia & M. Vergassola; Phys. Rev. Lett., 87, Art. No. 164502, 2001.
Thermal plume turbulence. A. Celani, A. Mazzino & M. Vergassola; Physics of Fluids, 13, 2133-2135, 2001. Fronts in passive scalar turbulence. A. Celani, A. Lanotte, A. Mazzino & M. Vergassola; Physics of Fluids, 13, 1768-1783, 2001.
Universal decay of passive scalar turbulence. M. Chaves, G. Eyink, U. Frisch & M. Vergassola; Phys. Rev. Lett., 86, 2305-2308, 2001.
Statistical geometry in scalar turbulence. A. Celani & M. Vergassola; Phys. Rev. Lett., 86, 424-427, 2001.
Universality and saturation of intermittency in passive scalar turbulence. A. Celani, A. Lanotte, A. Mazzino & M. Vergassola; Phys. Rev. Lett., 84, 2385-2388, 2000.
Lagrangian method for multiple correlations in passive scalar advection. U. Frisch, A. Mazzino, A. Noullez & M. Vergassola; Physics of Fluids, 11, 2178-2186, 1999.
Intermittency in passive scalar advection. U. Frisch, A. Mazzino & M. Vergassola; Phys. Rev. Lett., 80, 5532- 5535, 1998.
Structures and intermittency in a passive scalar model. M. Vergassola & A. Mazzino; Phys. Rev. Lett., 78, 1849-1852, 1997.
Inverse Cascades and Large-Scale Patterning
Inverse cascade in two-dimensional turbulence: deviations from Gaussian behavior. G. Boffetta, A. Celani & M. Vergassola; Phys. Rev. E, 61, R29-32, 2000.
Phase transition in passive scalar advection. K. Gawedzki & M. Vergassola; Physica D, 138, 63-90, 2000.
Inverse versus direct cascades in turbulent advection. M. Chertkov, I. Kolokolov & M. Vergassola; Phys. Rev. Lett. 80, 512-515, 1998.
Inverse cascade and intermittency of passive scalar in 1d smooth flow. M. Chertkov, I. Kolokolov & M. Vergassola; Phys. Rev. E 56, 5483-5499, 1997.
Magnetic Fields, Dynamo
Active vs passive scalar turbulence. A. Celani, M. Cencini, A. Mazzino & M. Vergassola; Phys. Rev. Lett., 89, Art. No. 234502-1, 2002.
Small-scale turbulent dynamo. M. Chertkov, G. Falkovich, I. Kolokolov, & M. Vergassola; Phys. Rev. Lett., 83, 4065-4068, 1999.
Large scale dynamo by negative eddy diffusivities. A. Lanotte, A. Noullez, M. Vergassola & A. Wirth; Geophysical & Astrophysical Fluid Dynamics, 91, 131-146, 1999.
Anomalous scaling for passively advected magnetic fields. M. Vergassola; Phys. Rev. E R53, 3021-3024, 1996.
Formation of Cosmological Large-Scale Structures
Burgers equation, devil's staircases and mass-distribution for large-scale structures. M. Vergassola, B. Dubrulle, U. Frisch & A. Noullez; Astronomy and Astrophysics. 289, 325-356, 1994.
A fast Legendre transform algorithm and applications to the adhesion model. A. Noullez & M. Vergassola; J. Scientific Computing 9, 259-281, 1994.
Turbulent Diffusion and Homogenization Methods
Resonant enhanced diffusion in time-dependent flow. P. Castiglione, A. Crisanti, A. Mazzino, M. Vergassola & A. Vulpiani; J. Phys. A 31, 7197-7210, 1998.
Scalar transport in compressible flow. M. Vergassola & M. Avellaneda; Physica D 106, 148-166, 1997.
Interference between turbulent and molecular diffusion. A. Mazzino & M. Vergassola; Europhysics Letters 37, 535-540, 1997.
Escape rates in Hamiltonian systems. A. Morbidelli & M. Vergassola; J. Statistical Physics 89, 549-560, 1997.
Vorticity selection in large-scale two dimensional flow. R. Benzi, A.J. Manfroi & M. Vergassola; Europhysics Letters 36, 367-371, 1996.
Large-scale dynamics in Burgers equation. M. Vergassola & A. Wirth; J. Phys. II France 6, 1841-1849, 1996.
Eddy diffusivities in scalar transport. L. Biferale, A. Crisanti, M. Vergassola & A. Vulpiani; Physics of Fluids 7, 2725-2734, 1995.
Stieltjes integral representation of effective diffusivities in time-dependent flows. M. Avellaneda & M. Vergassola; Phys. Rev. E52, 3249-3251, 1995.
Slow-down of nonlinearity in the large-scale dynamics of Navier-Stokes flows. S. Gama & M. Vergassola; Physica D 76, 291-296, 1994.
Negative eddy-viscosity in isotropically forced two-dimensional flow: linear and nonlinear dynamics. S. Gama, M. Vergassola & U. Frisch; J. Fluid Mechanics 260, 95-126, 1994.
Chiral nonlinearities in forced 2-D Navier-Stokes flows. M. Vergassola; Europhysics Letters 24, 41-45,1993.
Phenomenology and Simulations of Fully Developed Turbulent Flows
The decay of homogeneous anisotropic turbulence. L. Biferale, G. Boffetta, A. Celani, A. Lanotte, F. Toschi & M. Vergassola; Physics of Fluids, 15, 2105-12, 2003.
Intermittency in two-dimensional Ekman-Navier-Stokes turbulence. G. Boffetta, A. Celani, S. Musacchio & M. Vergassola; Phys. Rev. E, 66, Art. No. 026304, 2002.
Isotropy vs anisotropy in small-scale turbulence. L. Biferale & M. Vergassola; Physics of Fluids, 13, 2139-2141, 2001.
Further results on multifractality in shell models. D. Pisarenko, L. Biferale, D. Courvoisier, U. Frisch & M. Vergassola; Physics of Fluids A, 5, 2533-2538, 1993.
Wavelet analysis of a Gaussian Kolmogorov signal. M. Vergassola, R. Benzi, L. Biferale & D. Pisarenko; J. Physics A 26, 6093-6099, 1993.
A random process for the construction of multiaffine fields. R. Benzi, L. Biferale, A. Crisanti, G. Paladin, M. Vergassola & A. Vulpiani; Physica D 65, 352-358, 1993.
On the multifractal properties of the energy dissipation from turbulence data. E. Aurell, U. Frisch, J. Lutsko & M. Vergassola; J. Fluid Mechanics 238, 467-486, 1992.
Wavelet transforms of self-similar processes. M. Vergassola & U. Frisch; Physica D 54, 58-64, 1991.
Optimal wavelet analysis and its application to two dimensional turbulence. R. Benzi & M. Vergassola; Fluid Dynamics Research 8, 117-126, 1991.
Multifractality in the statistics of the velocity gradients. R. Benzi, L. Biferale, G. Paladin, A. Vulpiani & M. Vergassola; Phys. Rev. Lett 67, 2299-2302, 1991.
Non-conservative character of the intersection of self-similar cascades. M. Vergassola & A. Vespignani; Physica A 174, 425-437, 1991.
A prediction of the multifractal model: the intermediate dissipation range. U. Frisch & M. Vergassola; Europhysics Letters 14, 439-444, 1991.
Cellular Automata and Lattice Gas
The lattice Boltzmann equation: theory and applications. R. Benzi, S. Succi & M. Vergassola; Physics Reports 222, 145-197, 1992.
Lattice Boltzmann scheme for two-dimensional magnetohydrodynamics. S. Succi, M. Vergassola & R. Benzi; Phys. Rev. A 43, 4521-4524, 1991.
Turbulence modelling by non-hydrodynamic variables. R. Benzi, S. Succi & M. Vergassola; Europhysics Letters 13, 727-732, 1990.
On the hydrodynamic behaviour of the lattice Boltzmann equation. M. Vergassola, R. Benzi & S. Succi; Europhysics Letters 13, 411-416, 1990.