#### 2016 |

Guo, Y., Baulin, V. A., & Thalmann, F. (2016). Peroxidised phospholipid bilayers: insight from coarse-grained molecular dynamics simulations. *Soft Matter*, *12*(1), 263–271.**Abstract:** An original coarse-grained model for peroxidised phospholipids is presented, based on the MARTINI lipid force field. This model results from a combination of thermodynamic modelling and structural information on the area per lipid, which have been made available recently. The resulting coarse-grained lipid molecules form stable bilayers, and a set of elastic coefficients (compressibility and bending moduli) is obtained. We compare the compressibility coefficient to the experimental values [Weber et al., Soft Matter, 2014, 10, 4241]. Predictions for the mechanical properties, membrane thickness and lateral distribution of hydroperoxide groups in the phospholipid bilayer are presented.
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#### 2015 |

Gromer, A., Nassar, M., Thalmann, F., Hebraud, P., & Holl, Y. (2015). Simulation of Latex Film Formation Using a Cell Model in Real Space: Vertical Drying. *Langmuir*, *31*(40), 10983–10994. **Abstract:** This paper presents a simulation tool applied to latex film formation by drying, a hybrid between a classical numerical resolution method using finite differences and cellular automata, and making use of object-oriented programming. It consists of dividing real space into cells and applying local physical laws to simulate the exchange of matter between neighboring cells. In a first step, the simulation was applied to the simple case of vertical drying of a latex containing only one population of monodisperse particles and water. Our results show how the distribution of latex particles evolves through the different drying stages due to a combination of diffusion, convection, and particle deformation. While repulsive interactions between the particles tend to favor homogeneous distributions in the first drying stage, concentration gradients that develop in opposite ways can be observed depending on the drying regime. The distributions, calculated in various cases, reproduce and extend several theoretical results and are in qualitative agreement with some experimental findings.
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#### 2014 |

Johner, A., Thalmann, F., Baschnagel, J., Meyer, H., Obukhov, S., & Wittmer, J. P. (2014). Two-dimensional polymeric liquids and polymer stars: learning from conflicting theories. *Journal of Statistical Mechanics-Theory and Experiment*, *2014*.**Abstract:** We discuss systems for which two carefully derived, yet conflicting, theories coexisted. Dense polymers in two dimensions and star-shaped polymers in the theta-regime are considered. In both cases the two proposed theories are in a sense exact, but turn out to satisfy different crossing rules (for the 2d polymer) or to correspond to different orders of limits. Finally, both theories prove very useful, albeit for different subclasses of physical systems.
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Mertins, O., Bacellar, I. O. L., Thalmann, F., Marques, C. M., Baptista, M. S., & Itri, R. (2014). Physical Damage on Giant Vesicles Membrane as a Result of Methylene Blue Photoirradiation. *Biophysical Journal*, *106*(1), 162–171. **Abstract:** In this study we pursue a closer analysis of the photodamage promoted on giant unilamellar vesicles membranes made of dioleoyl-sn-glycero-3-phosphocholine (DOPC) or 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), by irradiating methylene blue present in the giant unilamellar vesicles solution. By means of optical microscopy and electro-deformation experiments, the physical damage on the vesicle membrane was followed and the phospholipids oxidation was evaluated in terms of changes in the membrane surface area and permeability. As expected, oxidation modifies structural characteristics of the phospholipids that lead to remarkable membrane alterations. By comparing DOPC- with POPC-made membranes, we observed that the rate of pore formation and vesicle degradation as a function of methylene blue concentration follows a diffusion law in the case of DOPC and a linear variation in the case of POPC. We attributed this scenario to the nucleation process of oxidized species following a diffusion-limited growth regime for DOPC and in the case of POPC a homogeneous nucleation process. On the basis of these premises, we constructed models based on reaction-diffusion equations that fit well with the experimental data. This information shows that the outcome of the photosensitization reactions is critically dependent on the type of lipid present in the membrane.
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#### 2011 |

Thalmann, F., Billot, V., & Marques, C. M. (2011). Lipid bilayer adhesion on sparse DNA carpets: Theoretical analysis of membrane deformations induced by single-end-grafted polymers. *Physical Review E*, *83*(6).**Abstract:** We consider a single-end-grafted polymer chain covered by a membrane in contact with a flat and rigid surface in the context of supported membrane adhesion on surfaces carrying dilute polymer brushes. The fluid membrane adheres to the surface due to attractive interactions; the presence of a macromolecule locally hinders the membrane-surface contact and creates a protuberant membrane bulge. We study both the size and elevation of such membrane deformations as a function of curvature modulus, surface tension, adhesion energy, and chain size. Scaling results are derived, valid for both ideal and nonideal chain statistics, leading to complex diagrams of states depending on curvature modulus, tension, and adhesion values. We also compute quantitatively the membrane deformation profile for shallow bulges and make predictions for realistic systems involving DNA grafted chains covered by lipid membranes.
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Wolff, J., Marques, C. M., & Thalmann, F. (2011). Thermodynamic Approach to Phase Coexistence in Ternary Phospholipid-Cholesterol Mixtures. *Physical Review Letters*, *106*(12).**Abstract:** We introduce a simple and predictive model for determining the phase stability of ternary phospholipid-cholesterol mixtures. Assuming that competition between the liquid and gel order of the phospholipids is the main driving force behind lipid segregation, we derive a Gibbs free energy of mixing, based on the thermodynamic properties of the lipids main transition. A numerical approach was devised that enables the fast and efficient determination of the ternary diagrams associated with our Gibbs free energy. The computed phase coexistence diagram of DOPC/DPPC/cholesterol reproduces well-known features for this system at 10 degrees C, as well as its evolution with temperature.
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#### 2010 |

Arnold, C., Thalmann, F., Marques, C., Marie, P., & Holl, Y. (2010). Surfactant Distribution in Waterborne Acrylic Films. 1. Bulk Investigation. *J. Phys. Chem. B*, *114*(28), 9135–9147. **Abstract:** The distribution of an anionic surfactant, sodium dodecyl sulfate (SDS), in waterborne acrylic films was investigated, focusing on the effects of particle composition and size, and pH of the latex. The observed surfactant distributions could be classified in two categories: homogeneous and heterogeneous, the latter showing SDS aggregates. The shape of the profiles was related to the stability of the latex during drying, at short interparticular distances. The stability of the latex was determined by the presence or not of fixed charges at the surface of the particles. The latices with particles carrying neutralized acrylic acid at high pH (COO-) led to homogeneous distributions, whereas the latices with acrylic acid at low pH (COOH) or without acrylic acid led to heterogeneous distributions. Our interpretation is that the stable latices present a narrow network of paths between particles at high polymer volume fraction, limiting the mobility of the surfactant, whereas in the less stable latices wider routes between flocs allow enough mobility for large aggregate formation. Thermal treatments of the dry films confirmed the strong confinement of the surfactant in the dense film structure obtained at high pH and the more open structure, allowing easier surfactant transport and oxygen penetration, observed at low pH. In order to account for the shapes of the profiles more quantitatively, a model was developed based on the diffusion of the surfactant and its transport by the drying front. It was found that the apparent diffusion coefficient of SDS micelles had to be lowered to a great extent (D = 10(-13)-10(-14) m(2)/s) during drying in order to explain aggregate formation. It should be even lower (D = 10(-15) m(2)/s) to interpret homogeneous surfactant profiles. These results are consistent with our hypothesis of the key importance of the surfactant mobility during drying.
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Mendoza, C. I., Marques, C. M., & Thalmann, F. (2010). Enhanced shear separation for chiral magnetic colloidal aggregates. *Phys. Rev. E*, *82*(6), 4 pp.**Abstract:** We study the designing principles of the simplest colloidal propeller, an architecture built from four identical spheres that can couple translation with rotation to produce controlled drift motion. By considering superparamagnetic beads, we show that the simultaneous action of a magnetic field and a shear flow leads to the migration of the cluster in the vorticity direction. We investigate the dependence of the migration velocity on the geometrical parameters of the cluster and find that significant cluster separation can be achieved under the typical operation conditions of microfluidic devices.
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Nam, G., Hisette, M. L., Sun, Y. L., Gisler, T., Johner, A., Thalmann, F., et al. (2010). Scraping and Stapling of End-Grafted DNA Chains by a Bioadhesive Spreading Vesicle to Reveal Chain Internal Friction and Topological Complexity. *Prl*, *105*(8), 088101.**Abstract:** Stained end-grafted DNA molecules about 20  μm long are scraped away and stretched out by the spreading front of a bioadhesive vesicle. Tethered biotin ligands bind the vesicle bilayer to a streptavidin substrate, stapling the DNAs into frozen confinement paths. Image analysis of the stapled DNA gives access, within optical resolution, to the local stretching values of individual DNA molecules swept by the spreading front, and provides evidence of self-entanglements.
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Thalmann, F. (2010). A schematic model for molecular affinity and binding with Ising variables. *Eur. Phys. J. E*, *31*(4), 441–454.**Abstract:** After discussing the relevance of statistical physics in molecular recognition processes, we present a schematic model for ligand-receptor association based on an Ising chain. We discuss the possible behaviors of the affinity when the stiffness of the ligand increases. We also consider the case of flexible receptors. A variety of interesting behaviors is obtained, including some affinity modulation upon bond hardening or softening. The affinity of a ligand for its receptor is shown to depend on the details of its rigidity profile, and we question the possibility of encoding information in the rigidities as well as in the shape. An exhaustive study of the selectivity of patterns with length n < 8 is carried out. Connection with other spin models, in particular spin glasses is mentioned in the conclusion.
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#### 2009 |

Thalmann, F., & Lee, N. - K. (2009). Fast algorithms for classical X->0 diffusion-reaction processes. *Journal of Chemical Physics*, *130*(7), 074102.**Abstract:** The Doi formalism treats a reaction-diffusion process as a quantum many-body problem. We use this second-quantized formulation as a starting point to derive a numerical scheme for simulating X-->0 reaction-diffusion processes, following a well-established time discretization procedure. In the case of a reaction zone localized in the configuration space, this formulation provides also a systematic way of designing an optimized, multiple time step algorithm, spending most of the computation time to sample the configurations where the reaction is likely to occur.
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#### 2008 |

Cohen-Tannoudji, L., Bertrand, E., Baudry, J., Robic, C., Goubault, C., Pellissier, M., et al. (2008). Measuring the kinetics of biomolecular recognition with magnetic colloids. *Physical Review Letters*, *100*(10), 108301.**Abstract:** We introduce a general methodology based on magnetic colloids to study the recognition kinetics of tethered biomolecules. Access to the full kinetics of the reaction is provided by an explicit measure of the time evolution of the reactant densities. Binding between a single ligand and its complementary receptor is here limited by the colloidal rotational diffusion. It occurs within a binding distance that can be extracted by a reaction-diffusion theory that properly accounts for the rotational Brownian dynamics. Our reaction geometry allows us to probe a large diversity of bioadhesive molecules and tethers, thus providing a quantitative guidance for designing more efficient reactive biomimetic surfaces, as required for diagnostic, therapeutic, and tissue engineering techniques.
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Lee, N. K., Johner, A., Thalmann, F., Cohen-Tannoudji, L., Bertrand, E., Baudry, J., et al. (2008). Ligand-receptor interactions in chains of colloids: When reactions are limited by rotational diffusion. *Langmuir*, *24*(4), 1296–1307. **Abstract:** We discuss the theory of ligand receptor reactions between two freely rotating colloids in close proximity to one other. Such reactions, limited by rotational diffusion, arise in magnetic bead suspensions where the beads are driven into close contact by an applied magnetic field as they align in chainlike structures. By a combination of reaction-diffusion theory, numerical simulations, and heuristic arguments, we compute the time required for a reaction to occur in a number of experimentally relevant situations. We find in all cases that the time required for a reaction to occur is larger than the characteristic rotation time of the diffusion motion tau(rot). When the colloids carry one ligand only and a number n of receptors, we find that the reaction time is, in units of tau(rot), a function simply of n and of the relative surface alpha occupied by one reaction patch alpha = pi rc(2)/(4 pi r(2)), where r(c) is the ligand receptor capture radius and r is the radius of the colloid.
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#### 2007 |

Baulin, V. A., Marques, C. M., & Thalmann, F. (2007). Collision induced spatial organization of microtubules. *Biophysical Chemistry*, *128*(2-3), 231–244.**Abstract:** The dynamic behavior of microtubules in solution can be strongly modified by interactions with walls or other structures. We examine here a microtubule growth mode I where the increase in size of the plus-end is perturbed by collisions with other microtubules. We show that such a simple mechanism of constrained growth can induce ordered structures and patterns from an initially isotropic and homogeneous suspension. We find that microtubules self-organize locally in randomly oriented domains that grow and compete with each other. A weak orientation bias, similar to the one induced by gravity or cellular boundaries is enough to influence the domain growth direction, eventually leading to a macroscopic sample orientation. (c) 2007 Elsevier B.V. All rights reserved.
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Thalmann, F., & Farago, J. (2007). Trotter derivation of algorithms for Brownian and dissipative particle dynamics. *Journal of Chemical Physics*, *127*(12), 124109.**Abstract:** This paper focuses on the temporal discretization of the Langevin dynamics, and on different resulting numerical integration schemes. Using a method based on the exponentiation of time dependent operators, we carefully derive a numerical scheme for the Langevin dynamics, which we found equivalent to the proposal of Ermak and Buckholtz [J. Comput. Phys. 35, 169 (1980)] and not simply to the stochastic version of the velocity-Verlet algorithm. However, we checked on numerical simulations that both algorithms give similar results, and share the same “weak order two” accuracy. We then apply the same strategy to derive and test two numerical schemes for the dissipative particle dynamics. The first one of them was found to compare well, in terms of speed and accuracy, with the best currently available algorithms.
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#### 2006 |

Durian, D. J., Bideaud, H., Duringer, P., Schroder, A., Thalmann, F., & Marques, C. M. (2006). What is in a pebble shape? *Phys. Rev. Lett.*, *97*(2), 4 pp.**Abstract:** We propose to characterize the shapes of flat pebbles in terms of the statistical distribution of curvatures measured along the pebble contour. This is demonstrated for the erosion of clay pebbles in a controlled laboratory apparatus. Photographs at various stages of erosion are analyzed, and compared with two models. We find that the curvature distribution complements the usual measurement of aspect ratio, and connects naturally to erosion processes that are typically faster at protruding regions of high curvature.
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