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Table of Contents

1. Stochastic thermodynamics
• Variability in growth and division in cell populations
• Thermodynamic trade-offs and efficiency
• Thermodynamics and kinetics of reversible polymerization
• Fluctuations and broken symmetries
• Thermodynamic inference
• Modified fluctuation-dissipation theorem off-equilibrium
• Fluctuation relation for molecular motors
2. Evolution of molecular systems - Origin of life
• Transient compartmentalization dynamics
• Autocatalysis
• Homochirality of life
3. Dynamics of biofilaments: actine and microtubules
• Single filament dynamics
• Filament bundle dynamics
4. Lipid membrane systems
• Lateral diffusion of a protein within a lipid membrane
• Lipid vesicle coupled to a cytoskeleton
• Lipid vesicle coupled to light-activable ionic pumps
• Planar lipid membrane containing ion channels in an electric field
5. Other soft matter systems
• Magnetic colloids
• Liquid crystals
6. Multiple light scattering
• Patterns with diffuse polarized light
• Magneto-optics with diffuse light

1. Stochastic thermodynamics

Variability in growth and divisions in cell populations

• Linking lineage and population observables in biological branching processes,
  R. Garcia-Garcia, A. Genthon and D. Lacoste, Phys. Rev. E, 042413 (2019), [PDF], [arxiv].
  
• Fluctuation relations and fitness landscape of growing cell populations,
  A. Genthon, and D. Lacoste, Sci. Rep., 10, 1038 (2020), [PDF], [arXiv].
  
• Universal constraints on selection strength in lineage trees,
  A. Genthon, D. Lacoste, Phys. Rev. Res., 3, 023181 (2021), [PDF], [arXiv].
  
  

Thermodynamic trade-offs and efficiency

• An ordered set of power-efficiency trade-offs,
  H. Vroylandt, D. Lacoste and G. Verley, [cond-mat].
  
• A case study of thermodynamic bounds for chemical kinetics,
  K. Proesmans, L. Peliti and D. Lacoste, [cond-mat].
  
• Degree of coupling and efficiency of energy converters far-from-equilibrium,
  H. Vroylandt, D. Lacoste and G. Verley,
  J. Stat. Mech, 023205 (2018), [PDF], [cond-mat].
  

Thermodynamics and kinetics of reversible polymerization

• Length and sequence relaxation of copolymers under recombination reactions,
  A. Blokhuis and D. Lacoste,
  J. Chem. Phys., 147, 094905 (2017), [PDF], [cond-mat].
  
• Glucans monomer-exchange dynamics as an open chemical network,
  R. Rao, M. Esposito and D. Lacoste,
  J. Chem. Phys., 143, 174501 (2015), [PDF], [cond-mat].
  
• Kinetics and thermodynamics of reversible polymerization in closed systems,
  S. Lahiri, Y. Wang, M. Esposito and D. Lacoste,
  New J. Phys., 17, 085008 (2015), [PDF], [cond-mat].
  

Fluctuations and broken symmetries

• Thermodynamic bounds on equilibrium fluctuations of a global or local order parameter,
  J. Guioth and D. Lacoste,
  EPL, 115, 60007 (2016), [PDF], [cond-mat].
  
• Fluctuation relations for equilibrium states with broken discrete or continuous symmetries,
  D. Lacoste and P. Gaspard,
  J. Stat. Mech., P11018 (2015), [PDF], [cond-mat].
  
• Isometric Fluctuation Relations for equilibrium states with Broken Symmetry,
  D. Lacoste and P. Gaspard,
  Phys. Rev. Lett., 113, 240602 (2014), [PDF], together with Suppl. Info. [PDF]. [cond-mat].
  

Thermodynamic inference

• Information-theoretic analysis of the directional influence between cellular processes,
  S. Lahiri, P. Nghe, S. Tans, ML. Rosinberg and D. Lacoste,
  PLOS One 12 (11), e0187431 (2017), [PDF], [cond-mat].
  
• Thermodynamic inference based on coarse-grained data or noisy measurements ,
  R. Garcia-Garcia, S. Lahiri and D. Lacoste,
  Phys. Rev. E, 93, 032103 (2016), [PDF], [cond-mat].
  
• Stochastic thermodynamics of a tagged particle within an harmonic chain,
  D. Lacoste and M. A. Lomholt,
  Phys. Rev. E, 91, 022114 (2015), [PDF], [cond-mat].
  
• Energy versus information based estimations of dissipation using a pair of magnetic colloidal particles,
  S. Tush, A. Kundu, G. Verley, T. Blondel, V. Miralles, D. Lacoste and J. Baudry,
  Phys. Rev. Lett., 112, 180604 (2014), [PDF], together with Suppl. Info. [PDF].
  
• Non-invasive estimation of dissipation from non-equilibrium fluctuations in chemical reactions,
  S. Muy, A. Kundu and D. Lacoste,
  J. Chem. Phys., 139, 124109 (2013), [PDF]. [cond-mat].
  

Modified fluctuation-dissipation theorem off-equilibrium and generalization of the second law of thermodynamics

• Fluctuation theorems and inequalities generalizing the second law of thermodynamics out of equilibrium,
  G. Verley and D. Lacoste,
  Phys. Rev. E, 86, 051127 (2012), [PDF]. [cond-mat].
  
• Fluctuations and response from a Hatano-Sasa approach,
  G. Verley and D. Lacoste,
  Phys. Scr., 86, 058505 (2012), [PDF].
  
• Inequalities generalizing the second law of thermodynamics for transitions between non-stationary states,
  G. Verley, R. Chétrite and D. Lacoste,
  Phys. Rev. Lett., 108 120601 (2012), [PDF], [cond-mat].
  
• Modified fluctuation-dissipation theorem for general non-stationary states and application to the Glauber Ising chain,
  G. Verley, R. Chétrite and D. Lacoste,
  J. Stat. Mech. P10025 (2011), [PDF], [cond-mat].
  
• Modified fluctuation-dissipation theorem for non-equilibrium steady states and applications to molecular motors,
  G. Verley, K. Mallick and D. Lacoste,
  Europhys. Lett., 93, 10002 (2011), [PDF], [cond-mat].
  

Fluctuation theorems for molecular motors

• Fluctuation relation for molecular motors,
  D. Lacoste and K. Mallick, in B. Duplantier and V. Rivasseau (eds), 2010. "Biological Physics. Poincaré Seminar 2009",
  Progress in Mathematical Physics Vol 60, Birkhäuser [PDF], [cond-mat],
• Fluctuation Theorem for the flashing ratchet model of molecular motors,
  D. Lacoste and K. Mallick,
  Phys. Rev. E, 80, 021923 (2009), [PDF], [cond-mat].
  
• Stochastic model for nucleosome sliding in the presence of DNA ligands,
  L. Mollazadeh-Beidokhi, J. Deseigne, D. Lacoste, F. Mohammad-Raffie and H. Schiessel,
  Phys. Rev. E, 79, 031922 (2009), [PDF], [cond-mat].
  
• Fluctuation Theorem and large deviation function for a solvable model of a molecular motor,
  D. Lacoste, A. W. C. Lau, and K. Mallick,
  Phys. Rev. E, 78, 011915 (2008), [PDF], [cond-mat].
  
• Non-equilibrium fluctuations and mechanochemical couplings of a molecular motor,
  A. W. C. Lau, D. Lacoste, and K. Mallick,
  Phys. Rev. Lett., 99, 158102 (2007), [PDF], [cond-mat].
  
  

2. Evolution of molecular systems - Origin of life

Transient compartmentalization dynamics

• Selection dynamics in transient compartmentalization,
  A. Blokhuis, D. Lacoste, P. Nghe and L. Peliti,
  Phys. Rev. Lett., 120, 158101 (2018), [PDF], [arxiv].
  
• The generality of transient compartmentalization and its associated error threshold,
  A. Blokhuis, P. Nghe, L. Peliti and D. Lacoste, J. Theor. Bio, 487, 110110 (2020), [PDF], [arxiv].
  
• Survival of self-replicating molecules under transient compartmentalization with natural selection,
  G. Laurent, L. Peliti and D. Lacoste, Life,9,78 (2019), [PDF], [arxiv].
  
• Reaction kinetics in open reactors and serial transfers between closed reactors,
  A. Blokhuis, D. Lacoste, P. Gaspard
  J. Chem. Phys., 148, 144902 (2018), [PDF], [arxiv].
  

Autocatalysis

• Universal motifs and the diversity of autocatalytic systems,
  A. Blokhuis, D. Lacoste, and P. Nghe, Proc. Natl. Acad. Sci. U.S.A., 117, 25230 (2020), [PDF], [ChemRxiv].
  
  

Homochirality of life

• Emergence of homochirality in large molecular systems,
  G. Laurent, D. Lacoste, and P. Gaspard, Proc. Natl. Acad. Sci. U.S.A. , 118, (2021), [PDF], [Hal].
  
  

3. Dynamics of biofilaments: actine and microtubules

Single filament dynamics

• History-dependent depolymerization of actin filaments,
  I. Jain, D. Lacoste, D. Panda and R. Padinhateeri,
  Biochemistry, 51, 7580 (2012), [PDF], [Suppl. Mat.]
  
• Random hydrolysis controls the dynamic instability of microtubules,
  R. Padinhateeri, A. Kolomeisky and D. Lacoste,
  Biophys. J, 102, 1274 (2012), [PDF], [cond-mat].
  
• Role of ATP-hydrolysis in the dynamics of a single actin filament,
  P. Ranjith, K. Mallick, JF. Joanny, and D. Lacoste,
  Biophys. J, 98, 1418 (2010), [PDF], [cond-mat].
  
• Non-equilibrum self-assembly of a filament coupled to ATP/GTP hydrolysis,
  P. Ranjith, D. Lacoste, K. Mallick and JF. Joanny,
  Biophys. J., 96, 2146 (2009), [PDF], [cond-mat].
  

Filament bundle dynamics

• Condensation of actin filaments pushing against a barrier,
  K. Tsekouras, D. Lacoste, K. Mallick and J.F. Joanny,
  New J. Phys., 13, 103032 (2011), [PDF], [cond-mat].
  

3. Biomimetic systems based on lipid membranes

Lateral diffusion of a protein within a lipid membrane

• Mechanical factors affecting the mobility of membrane proteins,
  V. Demery and D. Lacoste, in "Physics of biological membranes", Springer (2019), [cond-mat].
  
• Shape matters in protein mobility within membranes,
  F. Quemeneur, J. K. Sigurdsson, M. Renner, P. J. Atzberger, P. Bassereau and D. Lacoste,
  Proc. Nat. Acad. Science USA, 111, 5083 (2014), [PDF], together with Suppl. Info. [PDF].
  

Lipid vesicle coupled to a cytoskeleton

• Fluctuation spectrum of fluid membranes coupled to an elastic meshwork:
  jump of the effective surface tension at the mesh size,
  J.-B. Fournier, D. Lacoste, E. Raphaël,
  Phys. Rev. Lett. 92, 018102 (2004), [PDF], [cond-mat].
  

Lipid vesicle coupled to light-activable ionic pumps

• An update on active membranes,
  D. Lacoste and P. Bassereau,
  CRC Press, Taylor and Francis group, Abington, UK, 271, (2014), [PDF].
  
• Membrane tension lowering induced by protein activity,
  M. D. El Alaoui, D. Lacoste, J. Pécréaux, JF. Joanny, J. Prost, and P. Bassereau,
  Phys. Rev. Lett., 102, 038102 (2009), [PDF], [cond-mat].
  
• Dynamics of active membrane with internal noise,
  D. Lacoste and A. Lau,
  Europhys. Lett., 70 (3), 418 (2005), [PDF], [cond-mat].
  

Planar lipid membrane containing ion channels in an electric field

• A planar lipid bilayer in an electric field: membrane instability, flow field and electrical impedance,
  F. Ziebert and D. Lacoste,
  Advances in Planar Lipid Bilayers and Liposomes, 14, 63 (2011), [PDF], [cond-mat].
  
• A Poisson-Boltzmann approach for a lipid membrane in an electric field,
  F. Ziebert and D. Lacoste,
  New J. Phys., 12, 095002 (2010), [PDF], [cond-mat].
  
• Effective zero-thickness model for a conductive membrane driven by an electric field,
  F. Ziebert, M. Z. Bazant, and D. Lacoste,
  Phys. Rev. E, 81, 031912 (2010), [PDF], [cond-mat].
  
• Electrostatic and electrokinetic contributions to the elastic moduli of a driven membrane,
  D. Lacoste, G. I. Menon, M. Z. Bazant and J.-F. Joanny,
  Eur. Phys. J. E, 28, 243-264 (2009), [PDF], [cond-mat].
  
• Fluctuations of a driven membrane in an electrolyte,
  D. Lacoste, M. Cosentino Lagomarsino, and JF. Joanny,
  Europhys. Lett. , 77, 18006 (2007), [PDF], [cond-mat].
  

4. Soft matter systems

Magnetic colloids

• Thermal expansion within a chain of magnetic colloidal particles,
  D. Lacoste, C. Brangbour, J. Bibette and J. Baudry,
  Phys. Rev. E, 80, 011401 (2009), [PDF], [cond-mat].
  
• Measuring colloidal forces with the magnetic chaining technique,
  R. Dreyfus, D. Lacoste, J. Bibette, and J. Baudry,
  Eur. Phys. J. E, 28, 113 (2009), [PDF], [cond-mat].
  
• Field-induced structures in miscible ferrofluid suspensions with and without latex spheres,
  M. Islam, K. Lin, D. Lacoste, T. Lubensky and A. Yodh,
  Phys. Rev. E, 67, 021402 (2003), [PDF]
  
• Phase transitions in a ferrofluid at magnetic field induced microphase separation,
  D. Lacoste and T. Lubensky,
  Phys. Rev. E , 64, 041506 (2001), [PDF],[cond-mat].
  

Liquid crystals

• Phase transitions in lyotropic nematic gels,
  D. Lacoste, A. Lau and T. Lubensky
  Eur. Phys. J. E 8, 403 (2002),[PDF], [cond-mat].
  
• Effective index of refraction, optical rotation, and circular dichroism in isotropic liquid crystals,
  D. Lacoste, P. Collings and T. Lubensky,
  Phys. Rev. E, 65, 031717 (2002), [PDF], [cond-mat].
  

5. Multiple light scattering

Light scattering in magneto-optical or chiral media

• PhD thesis of D. Lacoste from J. Fourier University (in french), (1999), [PDF],
  

Patterns with diffuse polarized light

• Geometric depolarization in patterns formed by backscattered light,
  D. Lacoste, V. Rossetto, F. Jaillon and H. Saint-Jalmes,
  Optics Letters, 29(17), 2040-2 (2004), [PDF], [cond-mat].
  
• Depolarization of backscattered linearly polarized light,
  L-F. Rochas Ochoa, D. Lacoste, R. Lenke, P. Schurtenberger and F. Scheffold,
  J. Opt. Soc. Am. A, 21(9), 1799-1804 (2004), [PDF], [cond-mat].
  

Magneto-optics with diffuse light

• Coherent Backscattering of light in a magnetic field,
  D. Lacoste and B. van Tiggelen,
  Phys. Rev. E, 61(4), 4556-65 (2000), [PDF], [cond-mat].
  
• Transport mean free path for magneto-transverse light diffusion: an alternative approach,
  D. Lacoste,
  Waves in Random Media, 10(3), 367-372 (2000), [PDF], [cond-mat].
  
• Magneto-Optics with diffuse light,
  D. Lacoste and B. van Tiggelen and G. Rikken,
  Physica B, 279 13-16, (2000), [PDF].
  
• Photonic Hall effect in ferrofluids: theory and experiments,
  D. Lacoste, F. Donatini, S. Neveu, S. Serughettti and B. van Tiggelen,
  Phys. Rev. E, 62(3), 3934-43 (2000), [PDF], [cond-mat].
  
• The Photonic Hall Effect in absorbing media,
  S. Wiebel, A. Sparenberg, G. Rikken, D. Lacoste and B. van Tiggelen,
  Phys. Rev. E, 62(6), 8636-9 (2000) [PDF].
  
• Transport Mean Free Path for Magneto-Transverse Light Diffusion,
  D. Lacoste and B. van Tiggelen,
  Europhys. Lett., 45(6), 721-725 (1999), [PDF], [cond-mat].
  
• Optics of a Faraday Mie sphere,
  D. Lacoste, B. van Tiggelen, G. Rikken and A. Sparenberg,
  J. Opt. Soc. Am. A, 15(6), 1632-42 (1998). [PDF], [cond-mat].
  

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