Related papers: A Continuum Poisson-Boltzmann Model for Membrane C…
Macromolecular complexation leading to coupling of two or more cellular membranes is a crucial step in a number of biological functions of the cell. While other mechanisms may also play a role, adhesion always involves the fluctuations of…
Central to understanding membrane bound cell signaling is to quantify how the membrane ultra-structure consisting of transient spatial domains modulates signaling and how the signaling influences this ultra-structure. Yet, measuring the…
For many membrane proteins the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as…
We developed a multiscale approach (MultiSCAAL) that integrates the potential of mean force (PMF) obtained from all-atomistic molecular dynamics simulations with a knowledge-based energy function for coarse-grained molecular simulations in…
Three coarse-grained molecular dynamics (MD) models are investigated with the aim of developing and analyzing multiscale methods which use MD simulations in parts of the computational domain and (less detailed) Brownian dynamics (BD)…
A continuum electromechanical model is proposed to describe the membrane curvature induced by electrostatic interactions in a solvated protein-membrane system. The model couples the macroscopic strain energy of membrane and the…
The self-organization of proteins into enriched compartments and the formation of complex patterns are crucial processes for life on the cellular level. Liquid-liquid phase separation is one mechanism for forming such enriched compartments.…
Membrane proteins are crucial in regulating biomembrane shapes and controlling the dynamic changes in membrane morphology during essential cellular processes. These proteins can localize to regions with their preferred curvatures (curvature…
Understanding protein solubility is essential for their functional applications. Computational methods for predicting protein solubility are crucial for reducing experimental costs and enhancing the efficiency and success rates of protein…
Curvature-sensing and curvature-remodeling proteins are known to reshape cell membranes, and this remodeling event is essential for key biophysical processes such as tubulation, exocytosis, and endocytosis. Curvature-inducing proteins can…
Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We…
Computational elucidation of membrane protein (MP) structures is challenging partially due to lack of sufficient solved structures for homology modeling. Here we describe a high-throughput deep transfer learning method that first predicts…
Membranes are ubiquitous in nature with primary functions that include adaptive filtering and selective transport of chemical and molecular species. Being critical to cellular functions, they are also fundamental in many areas of science…
Biological membranes are self-assembled complex fluid interfaces that host proteins, molecular motors and other macromolecules essential for cellular function. These membranes have a distinct in-plane fluid response with a surface viscosity…
Lipid membranes and membrane deformations are a long-standing area of research in soft matter and biophysics. Computer simulations have complemented analytical and experimental approaches as one of the pillars in the field. However, setting…
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…
Lattice-Boltzmann (LB) simulations are a common tool to numerically estimate the permeability of porous media. For valuable results, the porous structure has to be well resolved resulting in a large computational effort as well as high…
The shapes of cell membranes are largely regulated by membrane associated, curvature active, proteins. We use a numerical model of the membrane with elongated membrane inclusions, recently developed by us, which posses spontaneous…
Membrane proteins serve a wide range of vital roles in the functioning of living organisms. Compared to other classes of proteins, determining membrane protein structures remains a challenge, in large part due to the difficulty in…
This work introduces a novel application for predicting the macroscopic intrinsic permeability tensor in deformable porous media, using a limited set of micro-CT images of real microgeometries. The primary goal is to develop an efficient,…