Related papers: Multi-scale approach for self-Assembly and protein…
Theories of protein crystallization based on spheres that form close-packed crystals predict optimal assembly within a `slot' of second virial coefficients and enhanced assembly near the metastable liquid-vapor critical point. However, most…
Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh…
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…
Liquid water is not only of obvious importance but also extremely intriguing, displaying many anomalies that still challenge our understanding of such an a priori simple system. The same is true when looking at nanoconfined water: The…
Unstructured proteins can modulate cellular responses to environmental conditions by undergoing coil-globule transitions and phase separation. However, the molecular mechanisms of these phenomena still need to be fully understood. Here, we…
Protein structure is key to understanding protein function and is essential for progress in bioengineering, drug discovery, and molecular biology. Recently, with the incorporation of generative AI, the power and accuracy of computational…
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and…
Building structures with hierarchical order through the self-assembly of smaller blocks is not only a prerogative of nature, but also a strategy to design artificial materials with tailored functions. We explore in simulation the…
Self-assembly is traditionally described as the process through which an initially disordered system relaxes towards an equilibrium ordered phase only driven by local interactions between its building blocks. However, This definition is too…
In this work we describe a set of Coarse-grained (CG) tools that allow to simulate the uptake of the nanoparticles (NPs) coated with proteins by a lipid bilayer. We describe a CG model to calculate the adsorption energies and the most…
Designing protein sequences that fold into a target 3-D structure, termed as the inverse folding problem, is central to protein engineering. However, it remains challenging due to the vast sequence space and the importance of local…
Treating realistically the ambient water is one of the main difficulties in applying Monte Carlo methods to protein folding. The solvent-accessible area method, a popular method for treating water implicitly, is investigated by means of…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Fine-tuned ion transport across nanoscale pores is key to many biological processes such as neurotransmission. Recent advances have enabled the confinement of water and ions to two dimensions, unveiling transport properties unreachable at…
The mechanism of cold- and pressure-denaturation are matter of debate. Some models propose that when denaturation occurs more hydrogen bonds between the molecules of hydration water are formed. Other models identify the cause in the density…
Extensive Monte Carlo folding simulations for four proteins of various structural classes are carried out, using a single atomistic potential. In all cases, collapse occurs at a very early stage, and proteins fold into their native-like…
De novo protein structure prediction from amino acid sequence is one of the most challenging problems in computational biology. As one of the extensively explored mathematical models for protein folding, Hydrophobic-Polar (HP) model enables…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…