Related papers: Membrane-mediated protein-protein interaction: A M…
We examine the interactions between actively rotating proteins moving in a membrane. Experimental evidence suggests that such rotor proteins, like the ATP synthases of the inner mitochondrial membrane, can arrange themselves into lattices.…
Some aspects of a recent paper about protein-membrane interaction are inadequate due to lack of structural information.
It has recently been proposed that proteins embedded in lipidic bio-membranes can spontaneously self-organize into stable small clusters, or membrane nano-domains, due to the competition between short-range attractive and longer-range…
Biological membranes are shaped by various proteins that either generate inward or outward membrane curvature. In this article, we investigate the membrane morphologies induced by mixtures of arc-shaped particles with coarse-grained…
The question of whether proteins originate from random sequences of amino acids is addressed. A statistical analysis is performed in terms of blocked and random walk values formed by binary hydrophobic assignments of the amino acids along…
Realistic physical systems are characterised by emergent interactions across multiple length and time scales, posing a significant challenge for predictive machine learning (ML) models. Most scientific ML models focus on a narrow range of…
Transport of molecules across membrane channels is investigated theoretically using exactly solvable discrete stochastic site-binding models. It is shown that the interaction potential between molecules and the channel has a strong effect…
How internal forces are transduced into motion through soft, fluid membranes remains a fundamental question in the study of active systems. To investigate this coupling, we develop a minimal system consisting of a single ferromagnetic…
We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model when proteins fold under…
Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…
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…
Mean field models (MFMs) of cortical tissue incorporate salient features of neural masses to model activity at the population level. One of the common aspects of MFM descriptions is the presence of a high dimensional parameter space…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Binary mixtures of hard-spheres with different diameters and square-well attraction between different particles are studied by theory and Monte Carlo simulations. In our mesoscopic theory, local fluctuations of the volume fraction of the…
The last decade has witnessed a swiftly increasing interest in the design and production of novel multivalent molecules as powerful alternatives for conventional antibodies in the fight against cancer and infectious diseases. However, while…
The fluctuation-induced interaction between two rod-like, rigid inclusions in a fluid vesicle is studied by means of canonical ensemble Monte Carlo simulations. The vesicle membrane is represented by a triangulated network of hard spheres.…
The use of beta-solenoid proteins as functionalizable, nanoscale, self-assembling molecular building blocks may have many applications, including templating the growth of wires or higher-dimensional structures. By understanding their…
Living cells respond to mechanical changes in the matrix surrounding them by applying contractile forces that are in turn transmitted to distant cells. We calculate the mechanical work that each cell performs in order to deform the matrix,…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
We discuss the hydrodynamic collective effects due to active protein molecules that are immersed in lipid bilayer membranes and modeled as stochastic force dipoles. We specifically take into account the presence of the bulk solvent which…