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The design of hybrid peptide-solid interfaces for nanotechnological applications such as biomolecular nanoarrays requires a deep understanding of the basic mechanisms of peptide binding and assembly at solid substrates. Here we show by…
The molecular simulations solve the equation of motion of molecular systems, making 3D shapes of molecules four-dimensional by adding the time coordinate. These methods have a great potential in drug discovery because they can realistically…
The physical approach of a small particle (virus, medical drug) to the cell membrane represents the crucial first step before active internalization and is governed by thermal diffusion. Using a fully analytical theory we show that the…
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently…
Above a critical concentration a wide variety of peptides and proteins self-assemble into amyloid fibrils which entangle to form percolating networks called hydrogels. Such hydrogels have important applications as biomaterials and in…
Particle-wall interactions play a crucially important role in various applications such as microfluidic devices for cell sorting, particle separation, entire class of hydrodynamic filtration and its derivatives, etc. Yet, accurate…
Membrane organization is essential for cellular functions such as signal transduction and membrane trafficking. A major challenge is to understand the lateral heterogeneous structures in membranes and membrane fluidity in the presence of…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
The gut microbiome plays a crucial role in human health, yet the mechanisms underlying host-microbiome interactions remain unclear, limiting its translational potential. Recent microbiome multiomics studies, particularly paired…
The activity of cell membrane inclusions (such as ion channels) is influenced by the host lipid membrane, to which they are elastically coupled. This coupling concerns the hydrophobic thickness of the bilayer (imposed by the length of the…
Hypothesis: A broad range of phenomena, such as emulsification and emulsion stability, foam formation or liquid evaporation, are closely related to the dynamics of adsorbing colloidal particles. Elucidation of the mechanisms implied is key…
Inspired by recent suggestions that the Alzheimer's amyloid beta peptide (A beta) can insert into cell membranes and form harmful ion channels, we model insertion of the 40 and 42 residue forms of the peptide into cell membranes using a…
In this work we want to simulate with the Lattice-Boltzmann method in 2D the capillary infiltration into porous structures obtained from the packing of particles. The experimental problem motivating our work is the densification of carbon…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
Understanding and manipulating the interactions between foreign bodies and cell membranes during endo- and phagocytosis is of paramount importance, not only for the fate of living cells but also for numerous biomedical applications. This…
Rigid bodies, made of smaller composite beads, are commonly used to simulate anisotropic particles with molecular dynamics or Monte Carlo methods. To accurately represent the particle shape and to obtain smooth and realistic effective pair…
Peptide-based drugs can bind to protein interaction sites that small molecules often cannot, and are easier to produce than large protein drugs. However, designing effective peptide binders is difficult. A typical peptide has an enormous…
Understanding molecular structure, dynamics, and reactivity requires bridging processes that occur across widely separated time scales. Conventional molecular dynamics simulations provide atomistic resolution, but their femtosecond time…
Lipid membranes are abundant in living organisms, where they constitute a surrounding shell for cells and their organelles. There are many circumstances in which the deformations of lipid membranes are involved in living cells: fusion and…
The collective motion of membrane lipids over hundred of nanometers and nanoseconds is essential for the formation of submicron complexes of lipids and proteins in the cell membrane. These dynamics are difficult to access experimentally and…