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Membrane phase-separation is a mechanism that biological membranes often use to locally concentrate specific lipid species in order to organize diverse membrane processes. Phase separation has also been explored as a tool for the design of…
Molecular communication (MC) is a new communication engineering paradigm where molecules are employed as information carriers. MC systems are expected to enable new revolutionary applications such as sensing of target substances in…
Most organic and inorganic surfaces (e.g., glass, nucleic acids or lipid membranes) become charged in aqueous solutions. The resulting ionic distribution induces effective interactions between the charged surfaces. Stacks of like-charged…
A variety of models for the membrane-mediated interaction of particles in lipid membranes, mostly well-established in theoretical physics, is reviewed from a mathematical perspective. We provide mathematically consistent formulations in a…
Membrane tubulation is a ubiquitous process that occurs both at the plasma membrane and on the membranes of intracellular organelles. These tubulation events are known to be mediated by forces applied on the membrane either due to motor…
Proteins are miniature machines whose function depends on their three-dimensional (3D) structure. Determining this structure computationally remains an unsolved grand challenge. A major bottleneck involves selecting the most accurate…
Structural biology has made significant progress in determining membrane proteins, leading to a remarkable increase in the number of available structures in dedicated databases. The inherent complexity of membrane protein structures,…
Molecular dynamics (MD) simulations give access to equilibrium structures and dynamic properties given an ergodic sampling and an accurate force-field. The force-field parameters are calibrated to reproduce properties measured by…
Many proteins and peptides have an intrinsic capacity to sense and induce membrane curvature, and play crucial roles for organizing and remodelling cell membranes. However, the molecular driving forces behind these processes are not well…
The assembly of banana-shaped rodlike proteins on membranes, and the associated membrane shape transformations, are investigated by analytical theory and coarse-grained simulations. The membrane-mediated interactions between two…
Proteins constitute a large group of macromolecules with a multitude of functions for all living organisms. Proteins achieve this by adopting distinct three-dimensional structures encoded by the sequence of their constituent amino acids in…
Understanding the behavior of biomolecules such as proteins requires understanding the critical influence of the surrounding fluid (solvent) environment--water with mobile salt ions such as sodium. Unfortunately, for many studies, fully…
Protein representation learning plays a crucial role in understanding the structure and function of proteins, which are essential biomolecules involved in various biological processes. In recent years, deep learning has emerged as a…
Non-particulate continuum descriptions allow for computationally efficient modeling of suspension flows at scales that are inaccessible to more detailed particulate approaches. It is well known that the presence of particles influences the…
The MolMod database is presented, which is openly accessible at http://molmod.boltzmann-zuse.de/ and contains presently intermolecular force fields for over 150 pure fluids. It was developed and is maintained by the Boltzmann-Zuse Society…
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress has been made in predicting static folded structures, modeling protein motions on microsecond to…
We describe simulations of Proteins and artificial pseudo-molecules interacting and shaping lipid bilayer membranes. We extract protein diffusion Parameters, membrane deformation profiles and the elastic properties of the used membrane…
Human blood flow is a multi-scale problem: in first approximation, blood is a dense suspension of plasma and deformable red cells. Physiological vessel diameters range from about one to thousands of cell radii. Current computational models…
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar…
Hydrophobic patches on protein surfaces play important functional roles in protein-protein and protein-ligand interactions. Large hydrophobic surfaces are also involved in the progression of aggregation diseases. Predicting exposed…