Related papers: The self-assembly and evolution of homomeric prote…
We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in…
Phase separation has emerged as an essential concept for the spatial organization inside biological cells. However, despite the clear relevance to virtually all physiological functions, we understand surprisingly little about what phases…
We present a model for the joint self-assembly of amphiphilic polymers and small amphiphilic molecules (surfactants) in a dilute aqueous solution. The polymer is assumed to consist of a hydrophilic backbone and a large number of hydrophobic…
We study analytically the emergence of spontaneous collective motion within large bidimensional groups of self-propelled particles with noisy local interactions, a schematic model for assemblies of biological organisms. As a central result,…
We systematically study the design of simple patchy sphere models that reversibly self-assemble into monodisperse icosahedral clusters. We find that the optimal patch width is a compromise between structural specificity (the patches must be…
Protein assembly plays an important role in the regulation of biological systems. The cytoskeleton assembly activity is provided by the binding cofactors GTP (guanidine triphosphate) or ATP(adenosine triphosphate) to monomeric protein, and…
The dynamic of complex ordering systems with active rotational degrees of freedom exemplified by protein self-assembly is explored using a machine learning workflow that combines deep learning-based semantic segmentation and rotationally…
We use computer simulation to investigate the self-assembly of Janus-like amphiphilic peanut-shaped nanoparticles, finding phases of clusters, bilayers and micelles in accord with ideas of packing familiar from the study of molecular…
Mesoscopic structure of the periodically alternating layers of stretched homopolymer chains surrounded by perpendicularly oriented oligomeric tails is studied for the systems with both strong (ionic) and weak (hydrogen) interactions. We…
Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…
The sequence of a protein is not only constrained by its physical and biochemical properties under current selection, but also by features of its past evolutionary history. Understanding the extent and the form that these evolutionary…
We present a simple physical model which demonstrates that the native state folds of proteins can emerge on the basis of considerations of geometry and symmetry. We show that the inherent anisotropy of a chain molecule, the geometrical and…
In this letter we present a theorem on the dynamics of the generalized Hubbard models. This theorem shows that the symmetry of the single particle Hamiltonian can protect a kind of dynamical symmetry driven by the interactions. Here the…
By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic bead-stick model, where nonbonded monomers interact via Lennard-Jones…
Here we investigate how local properties of particles in a thermal bath influence the thermodynamics of the bath. We utilize nanothermodynamics, based on two postulates: that small systems can be treated self-consistently by coupling to an…
We present an analytically solvable model for self-assembly of a molecular complex on a filament. The process is driven by a seed molecule that undergoes facilitated diffusion, which is a search strategy that combines diffusion in…
In this work, we discovered a fundamental connection between selection for protein stability and emergence of preferred structures of proteins. Using standard exact 3-dimensional lattice model we evolve sequences starting from random ones…
The fluid phase diagram of trimer particles composed of one central attractive bead and two repulsive beads was determined as a function of simple geometric parameters using flat-histogram Monte Carlo methods. A variety of self-assembled…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
The molecular self-assembly of various structures such as micelles and vesicles has been the subject of comprehensive studies. Recently, a new approach to design these structures, the frame-guided assembly, has been developed to progress…