arXiv subjects

F. Thalmann

Publications and source records attributed to F. Thalmann.

4 recordsLinked to original sources

arXiv2024

Non-ideal mixing of lipids: a molecular dynamics perspective

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 systems 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.

cond-mat.soft↗

arXiv2010

Enhanced shear separation for chiral magnetic colloidal aggregates

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.

cond-mat.soft↗

arXiv2006

What is in a pebble shape?

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.

cond-mat.soft↗

arXiv2003

Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA folding simulations, which follow the stochastic closing and opening of individual RNA helices. The numerical efficacy of these stochastic simulations relies on an O(n^2) clustering algorithm which computes time averages over a continously updated set of n reference structures. Applying this exact stochastic clustering approach, we typically obtain a 5- to 100-fold simulation speed-up for RNA sequences up to 400 bases, while the effective acceleration can be as high as 100,000-fold for short multistable molecules (<150 bases). We performed extensive folding statistics on random and natural RNA sequences, and found that pseudoknots are unevenly distributed amongst RNAstructures and account for up to 30% of base pairs in G+C rich RNA sequences (Online RNA folding kinetics server including pseudoknots : http://kinefold.u-strasbg.fr/ ).

physics.bio-ph↗