Fabrice Thalmann’s research while affiliated with University of Strasbourg and other places

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Publications (61)


FIG. 1. Snapshot of a pure DPPC bilayer in fluid state containing 256 lipid molecules per leaflet. The water solvent molecules are not explicitly shown and correspond to the blue shaded regions.
FIG. 2. SPICA coarse-grained mapping and chemical formula of DPPC (left) and DLiPC (right).
FIG. 3. This picture illustrates the idea of replication of the bilayer fluid. Each leaflet contains two types of molecules (square, circles). Molecules from the upper leaflet (open symbols) interact weakly with molecules from the second leaflet (full symbols) (a). The projection of the system onto a single plane is equivalent to a quaternary lipid mixture, each species possessing a chemical index (square, circle) and a replica, or leaflet index (empty, full) (b).
FIG. 4. The simplest membrane model is the infinitely thin flat surface (a). Thermal fluctuations distorts the plane which becomes a curved surface described by the Helfrich elastic energy (b). The next level distinguishes the two leaflets introducing new elastic terms such as the area difference elasticity 35 . A bilayer can finally be described with fluid elastonematic model 36 .
FIG. 7. Radial distribution function within a single leaflet of DPPC. Bead names refer to the SPICA decomposition of Fig. 2.

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Non-ideal mixing of lipids: a molecular dynamics perspective
  • Preprint
  • File available

August 2024

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38 Reads

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R. Kosciurzinski

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F. Thalmann

Lipid membranes have complex compositions and modeling the thermodynamic properties of multi-component lipid systems remains a remote goal. In this work we attempt to describe the thermodynamics of binary lipid mixtures by mapping coarse-grained molecular dynamics simulations to two-dimensional simple fluid mixtures. By computing and analysing the density fluctuations of this model lipid bilayer we determine the numerical value of the quadratic coupling term appearing in a model of regular solutions for the DPPC-DLiPC pair of lipids at three different compositions. Our methodology is general and discussed in detail.

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Coarse-Grained MD snapshot superimposed with the two solid blocks (1, 2) and water solvent (3). Each of the 3 components is uniquely located by a single center of mass coordinate along the x direction. The solvent flow is linear-parabolic in the z direction, L z is the thickness of the (periodic) box, L b the bilayer thickness, L w = L z − L b the water thickness.
Average displacements correlation matrix ΔXi(t)ΔXj(t) for 0 < t < 4 ns. Diffusion coefficients D 1, …D 6 can be estimated from a linear fit of the second half of the curves (2–4 ns). The total simulation time was 10 μs.
Internal lipid bilayer friction coefficient from equilibrium canonical simulations

January 2023

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40 Reads

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1 Citation

A fundamental result in the theory of Brownian motion is the Einstein-Sutherland relation between mobility and diffusion constant. Any classical linear response transport coefficient obeys a similar Einstein-Helfand relation. We show in this work how to derive the interleaflet friction coefficient of lipid bilayer by means of an adequate generalisation of the Einstein relation. Special attention must be paid in practical cases to the constraints on the system center of mass position that must be enforced when coupling the system to thermostat.


Stress overshoot, hysteresis, and the Bauschinger effect in sheared dense colloidal suspensions

September 2022

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24 Reads

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4 Citations

PHYSICAL REVIEW E

The mechanical nonlinear response of dense Brownian suspensions of polymer gel particles is studied experimentally and by means of numerical simulations. It is shown that the response to the application of a constant shear rate depends on the previous history of the suspension. When the flow starts from a suspension at rest, it exhibits an elastic response followed by a stress overshoot and then a plastic flow regime. Conversely, after flow reversal, the stress overshoot does not occur, and the apparent elastic modulus is reduced while numerical simulations reveal that the anisotropy of the local microstructure is delayed relative to the macroscopic stress.


Coarse-grained description of monounsaturated peroxidized phospholipidbilayers

August 2022

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46 Reads

Lipid peroxides result from a reaction between cis-unsaturated lipid chains and singlet oxygen molecules leading to the addition of a peroxide OOH side group next to the acyl-chain double bond. It is now established that HP-POPC (hydroperoxidized POPC) molecules form stable, thin and laterally expanded bilayers. The difference in structural organisation arises from the hydrophilic character of the OOH side group that has strong affinity with the water interface region, leading to significant reorganisation of the bilayer. In this Article we describe a coarse-grained (CG) model of POPC and DOPC lipid peroxides within the framework of the Martini CG force-field (v2.2), derived from experimental data. We then discuss extensively the predicted structure and the influence of hydration and show how shifting the position of the unsaturated bonds along the chain changes the structure. Finally, we provide electron and neutron scattering length density profiles of the simulated bilayers.


Perturbing the catenoid: Stability and mechanical properties of nonaxisymmetric minimal surfaces

July 2022

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49 Reads

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3 Citations

PHYSICAL REVIEW E

Minimal surface problems arise naturally in many soft matter systems whose free energies are dominated by surface or interface energies. Of particular interest are the shapes, stability, and mechanical stresses of minimal surfaces spanning specific geometric boundaries. The "catenoid" is the best-known example where an analytical solution is known which describes the form and stability of a minimal surface held between two parallel, concentric circular frames. Here we extend this problem to nonaxisymmetric, parallel frame shapes of different orientations by developing a perturbation approach around the known catenoid solution. We show that the predictions of the perturbation theory are in good agreement with experiments on soap films and finite element simulations (Surface Evolver). Combining theory, experiment, and simulation, we analyze in depth how the shapes, stability, and mechanical properties of the minimal surfaces depend on the type and orientation of elliptic and three-leaf clover shaped frames. In the limit of perfectly aligned nonaxisymmetric frames, our predictions show excellent agreement with a recent theory established by Alimov et al. [Phys. Fluids 33, 052104 (2021)1070-663110.1063/5.0047461]. Moreover, we put in evidence the intriguing capacity of minimal surfaces between nonaxisymmetric frames to transmit a mechanical torque despite being completely liquid. These forces could be interesting to exploit for mechanical self-assembly of soft matter systems or as highly sensitive force captors.


FIG. 1. Coarse-Grained MD snapshot superimposed with the two solid blocks (1,2) and water solvent (3). Each of the 3 components is uniquely located by a single center of mass coordinate along the x direction. The solvent flow is linear-parabolic in the z direction, Lz is the thickness of the (periodic) box, Lb the bilayer thickness, Lw = Lz − Lb the water thickness.
FIG. 2. Illustration of the projection procedure. Velocities are constrained to an hyperplane m T v = 0, momenta are constrained to the hyperplane U T p = 0. To satisfy the conservation of the center of mass position, the linear force Kx must be projected onto the momenta hyperplane. In simulations, the constraint on the system center of mass position acts by removing the out-of-plane component of the force.
Figure 2: Average displacements correlation matrix ∆X i (t)∆X j (t), averaged over 10 µs. Diffusion coefficients D 1 , . . . D 6 can be estimated from a linear fit of the second half of the curves.
Interbilayer lipid friction coefficient from equilibrium canonical simulations

April 2022

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22 Reads

A fundamental result in the theory of Brownian motion is the Einstein-Sutherland relation between mobility and diffusion constant. Any classical linear response transport coefficient obeys a similar Einstein-Helfand relation. We show in this work how to derive the interleaflet friction coefficient of lipid bilayer by means of an adequate generalisation of the Einstein relation. Special attention must be paid in practical cases to the constraints on the system center of mass position that must be enforced when coupling the system to thermostat.


FIG. 4. Pair distribution of terminal subgroups. The vertical dashed line indicates the horizontal separation r = 0.5.
Excimer formation of pyrene labeled lipids interpreted by means of coarse-grained molecular dynamics simulations

April 2022

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40 Reads

The excimer formation dynamics of pyrene-labeled molecules in lipid bilayers depends on molecular motion over distances of the order of 1-2 nm. From the concentration dependence of the excimer photoemission curve, it is possible to derive a value for the lipid self-diffusion coefficient. This technique has been intensively used in the past twenty years, leading to rather large numerical values for self-diffusion compared with other approaches based on fluorescent probes tracking. In most cases, the interpretation of the experimental data rely on models for diffusion limited 2d reaction rates, or comparison with 2d lattice random walks. Our approach uses realistic molecular dynamics trajectories to reinterpret these experiments. Based on a well established coarse-grained model for lipid MD simulations (Martini), we show how to relate simulation results to experimental data on excimer formation. Our procedure is quite general and is applicable to all diffusion-limited kinetic processes. Key to our approach is the determination of the acceleration factor of lipid coarse-grained numerical models compared to reality. We find a significant reduction of the diffusion coefficient values, in particular when interleaflet association is taken into account. Our work does not point to deviation from a diffusion-limited mechanism but indicates that the excimer formation across bilayer leaflets could be hindered.


Perturbing the catenoid: stability and mechanical properties of non-axisymmetric minimal surfaces

March 2022

·

40 Reads

Minimal surface problems arise naturally in many soft matter systems whose free energies are dominated by surface or interface energies. Of particular interest are the shapes, stability and mechanical stresses of minimal surfaces spanning specific geometric boundaries. The "catenoid" is the best-known example where an analytical solution is known which describes the form and stability of a minimal surface held between two parallel, concentric circular frames. Here we extend this problem to non-axisymmetric, parallel frame shapes of different orientations, by developing a perturbation approach around the known catenoid solution. We show that the predictions of the perturbation theory are in good agreement with experiments on soap films and finite element simulations (Surface Evolver). Combining theory, experiment and simulation, we analyse in depth how the shapes, stability and mechanical properties of the minimal surfaces depend on the type and orientation of elliptical and three-leaf clover shaped frames. In the limit of perfectly aligned non-axisymmetric frames, our predictions show excellent agreement with a recent theory established by Alimov et al (M. M. Alimov, A. V. Bazilevsky and K. G. Kornev, Physics of Fluids, 2021, 33, 052104). Moreover, we put in evidence the intriguing capacity of minimal surfaces between non-axisymmetric frames to transmit a mechanical torque despite being completely liquid. These forces could be interesting to exploit for mechanical self-assembly of soft matter systems or as highly sensitive force captors.


Stress overshoot, hysteresis and Bauschinger effect in sheared dense colloidal suspensions

February 2022

·

45 Reads

The mechanical non-linear response of dense Brownian suspensions of polymer gel particles is studied experimentally and by means of numerical simulations. It is shown that the response to the application of a constant shear rate depends on the previous history of the suspension. When the flow starts from a suspension at rest, it exhibits an elastic response followed by a stress overshoot and then a plastic flow regime. Conversely, after flow reversal, the stress overshoot does not occur, and the apparent elastic modulus is reduced while numerical simulations reveal that the anisotropy of the local microstructure is delayed relative to the macroscopic stress.


Citations (34)


... One immediate phenomenon corresponding to this shape deformation is the appearance of a normal force or flow component perpendicular to a flexible wall. 10 Recently, there has been a renewed interest in exploring hydrodynamic-induced effects near walls, [11][12][13][14][15] their potential applications, 16,17 and possible relevance in biofluid mechanics. 18,19 Although downscaling from macroscopic to microscopic experiments faced significant practical challenges due to the smallness of the induced deformations in the results compared to macro-scale experiments and the existence of thermal fluctuations of the membrane boundary at this scale, 11 studying this phenomenon at the micrometer-scale realm is important due to its relevance to numerous vital processes of flow patterns near biological membranes. ...

Reference:

Normal deformation of a soft lipid-based microtube in response to the flow generated by a tangential motion of a nearby microbead
Rotational and translational drags of a Janus particle close to a wall and a lipid membrane

Journal of Colloid and Interface Science

... While the first systematic studies comparing the lateral diffusion coefficients from MD simulations and experiments have emerged, 32,35,37,38 no such comparison of diffusion in monolayers has been performed to our knowledge. Regarding interleaflet friction, there are multiple strategies available for extracting it from non-equilibrium [39][40][41][42] or equilibrium 43 simulations. Most of the studies are performed at a coarse-grained resolution for which the potential energy surface is smoother than at atomistic resolution and the extracted b values are an order of magnitude smaller than those from state-of-the-art tank-treading experiments. ...

Internal lipid bilayer friction coefficient from equilibrium canonical simulations

... More generally, the Bauschinger effect is used to describe the lowering of the yield stress under the reverse loading following the previous forward loading [3]. The Bauschinger effect has been evidenced in most materials [8][9][10][11][12][13][14][15], such as single-crystal metals [8], polycrystalline metals [9], polymers [10], and amorphous materials [11]. When the deformation * Contact author: fengyan@suda.edu.cn is loading history dependent, the Bauschinger effect plays an important role in the failure of materials, which has several important practical implications [8]. ...

Stress overshoot, hysteresis, and the Bauschinger effect in sheared dense colloidal suspensions
  • Citing Article
  • September 2022

PHYSICAL REVIEW E

... The numerical model was constructed in Surface Evolver (SE) to simulate the wetting state of the capillary bridge based on energy minimization. Various stabilization capillary bridge systems have been investigated using the energy minimization method [37][38][39]. The model was constructed by setting parameters, building the initial skeleton, defining the boundary conditions and performing the surface evolution. ...

Perturbing the catenoid: Stability and mechanical properties of nonaxisymmetric minimal surfaces
  • Citing Article
  • July 2022

PHYSICAL REVIEW E

... While the first systematic studies comparing the lateral diffusion coefficients from MD simulations and experiments have emerged, 32,35,37,38 no such comparison of diffusion in monolayers has been performed to our knowledge. Regarding interleaflet friction, there are multiple strategies available for extracting it from non-equilibrium [39][40][41][42] or equilibrium 43 simulations. Most of the studies are performed at a coarse-grained resolution for which the potential energy surface is smoother than at atomistic resolution and the extracted b values are an order of magnitude smaller than those from state-of-the-art tank-treading experiments. ...

Rheology of sliding leaflets in coarse-grained DSPC lipid bilayers
  • Citing Article
  • November 2021

PHYSICAL REVIEW E

... Their behavior is mainly determined by order-disorder transitions, which are associated with melting phenomena of the lipid hydrocarbon chains [1]. For membranes consisting of 1,2-dipalmitoylphosphatidylcholine (DPPC), the liquid crystal phase (L c ) is found below 280K, the gel or L β' phase manifests between 290K and 305K, a so-called ripple phase (P β' ) that is the most prominent at 310K, while at higher temperatures (above 315K), the liquid disordered or L α phase can be seen [2,3]. At the latter temperatures, a strong increase in permeability is observed, which is well exploited to deliver, e.g., anticancer drugs to solid tumors in hyperthermia therapy [4,5]. ...

Ripple-like instability in the simulated gel phase of finite size phosphocholine bilayers

Biochimica et Biophysica Acta (BBA) - Biomembranes

... The observed increase is thus better interpreted as due to a lowering of the membrane barrier potential, U m = −1.4 k B T , at least with respect to anion Cl − that dominates transport here, consistently with the known increase of polarity of the inner membrane region (20). ...

Molecular organization in hydroperoxidized POPC bilayers
  • Citing Article
  • May 2021

Biochimica et Biophysica Acta (BBA) - Biomembranes

... In addition, MPs/NPs with different numbers and shapes have been detected in edible salt and seafood in many countries, demonstrating contaminant entry into the food chain and may pose unknown threat to human health [7,8]. It has been reported that MPs/NPs with specific size and shape characteristics can be ingested by aquatic animal species, and that the residual MPs/NPs may induce toxicity, such as oxidative stress, immune injury, lipid membrane damage, and reproductive toxicity [9][10][11]. Teng et al. exposed zebrafish to 1, 10, and 100 μg/L polystyrene nanoplastics (PS-NPs) (44 nm) for 30 days and found that PS-NPs inhibited growth and adversely impacted inflammatory response and intestinal permeability [12]. ...

Accumulation of styrene oligomers alters lipid membrane phase order and miscibility
  • Citing Article
  • January 2021

Proceedings of the National Academy of Sciences

... interactions, which are difficult to accurately parameterize (132)(133)(134). Modern computer software and recent multiscale models combined with machine learning present new opportunities for further development (126,135,136). There are many opportunities to use vibrational techniques for characterizing interactions in heterogeneous samples, and provide useful molecular-level information for benchmarking simulations (43,121,137,138). ...

A machine learning study of the two states model for lipid bilayer phase transitions

Physical Chemistry Chemical Physics

... Previous efforts to study lipid−surface interactions at varying hydration levels have focused on hydrophilic surfaces with constant solvent molecules of varying surface thicknesses that change the thickness of the lubricating water layer. 25,29 To the best of our knowledge, this work represents the first to use MD to study the effect of surface polarity at variable solvent concentrations under spatial confinement. Additionally, we evaluate the impact of evaporation rate by comparing assemblies with and without glycerol to investigate the role glycerol plays in addition to simply slowing down evaporation. ...

Coarse-Grain Simulations of Solid Supported Lipid Bilayers with Varying Hydration Level
  • Citing Article
  • August 2020

The Journal of Physical Chemistry B