Related papers: Response to Halatek and Frey: Effective two-dimens…
We study the dynamic structure of lipid domain inclusions embedded within a phase-separated reconstituted lipid bilayer in contact with a swarming flow of gliding filamentous actin. Passive circular domains transition into highly-deformed…
A mesoscopic coarse-grain model for computationally-efficient simulations of biomembranes is presented. It combines molecular dynamics simulations for the lipids, modeled as elastic chains of beads, with multiparticle collision dynamics for…
The electric structure of twisted bilayer GeSe, which shows a rectangular moir\'{e} pattern, is analyzed using a $\bm{k}\cdot\bm{p}$ type effective continuum model. The effective model is constructed on the basis of the the local…
Motivated by the unique physical properties of {\em biological active matter}, e.g., cytoskeletal dynamics in eukaryotic cells, we set up {\em effective} two-dimensional (2d) coarse-grained hydrodynamic equations for the dynamics of thin…
The mechanism by which a patterned state accommodates the breaking of translational symmetry by a phase boundary or a sample wall has been addressed in the context of Landau branching in type-I superconductors, refinement of magnetic…
This article presents a novel computational model to study the selective filtering of biological hydrogels due to the surface charge and size of diffusing particles. It is the first model that includes the random 3D fiber orientation and…
In this paper, we present numerical and experimental evidence of directional wave behavior, i.e. beaming and diffraction, along high-order rotational symmetries of quasicrystalline elastic metamaterial plates. These structures are obtained…
Collective guidance of out-of-equilibrium systems without using external fields is a challenge of paramount importance in active matter, ranging from bacterial colonies to swarms of self-propelled particles. Designing strategies to guide…
According to the lipid raft hypothesis, biological lipid membranes are laterally heterogeneous and filled with nanoscale ordered "raft" domains, which are believed to play an important role for the organization of proteins in membranes.…
Ever since the raft model for biomembranes has been proposed, the traditional view of biomembranes based on the fluid-mosaic model has been altered. In the raft model, dynamical heterogeneities in multi-component lipid bilayers play an…
This paper deepens into the analysis of the protein secondary structure using Frenet frame to describe the curvature and torsion of the discrete curve formed by the protein $\alpha$-carbons. We show how a simple criterion based on the…
Although coherent light is usually required for the self-organization of regular spatial patterns from optical beams, we show that peculiar light matter interaction can break this evidence. In the traditional method to record laser-induced…
The viscosity of lipid bilayer membranes plays an important role in determining the diffusion constant of embedded proteins and the dynamics of membrane deformations, yet it has historically proven very difficult to measure. Here we…
The mechanical properties of tissues play an essential role for all tissue properties such as cell division, and differentiation or morphogenesis. Here, we study theoretically the rheology of 2-dimensional epithelial tissues described by a…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the…
In this work lipid ordering phase changes arising in planar membrane bilayers is investigated both accounting for elas- ticity alone and for effective viscoelastic response of such assemblies. The mechanical response of such membranes is…
Membrane proteins deform the surrounding lipid bilayer, which can lead to membrane-mediated interactions between neighboring proteins. Using the mechanosensitive channel of large conductance (MscL) as a model system, we demonstrate how the…
We consider the problem of elastic diffraction tomography, which consists in reconstructing elastic properties (i.e. mass density and elastic Lam\'e parameters) of a weakly scattering medium from full-field data of scattered waves outside…
In his 1952 paper "The chemical basis of morphogenesis", Alan M. Turing presented a model for the formation of skin patterns. While it took several decades, the model has been validated by finding corresponding natural phenomena, e.g. in…