Related papers: Protein folding and cosmology
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
It is proposed that a rearrangement of single-particle degrees of freedom may occur in a portion of the quantum fluid interior of a neutron star. Such a rearrangement is associated with the pronounced softening of the spin-isospin…
Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…
Studying the properties of the solvent around proteins, we propose a much more sophisticated model of solvation than temperature-independent pairwise interactions between monomers, as is used commonly in lattice representations. We applied…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
Protein collapse can be viewed as a dynamical phase transition, during which new scales and collective variables become excited while the old ones recede and fade away. This causes formidable computational bottle-necks in approaches that…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
We present a model for quark matter with a density dependent quark-quark (confining) potential, which allows to describe a deconfinement phase transition as the system evolves from a low density assembly of bound structures to a high…
In cellular environment, confinement and macromulecular crowding play an important role on thermal stability and folding kinetics of a protein. We have resorted to a generalized version of the Wako-Saito-Munoz-Eaton model for protein…
Using a simple three-dimensional lattice copolymer model and Monte Carlo dynamics, we study the collapse and folding of protein-like heteropolymers. The polymers are 27 monomers long and consist of two monomer types. Although these chains…
The de-confinement phase transition in SU(2) Yang-Mills theory is revisited in the vortex picture. Defining the world sheets of the confining vortices by maximal center projection, the percolation properties of the vortex lines in the…
We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…
In the cell, proteins fold and perform complex functions through global structural rearrangements. Function requires a protein to be at the brink of stability to be susceptible to small environmental fluctuations, yet stable enough to…
We present a study of the 3d O(2) non-linear $\sigma$-model on the lattice, which exhibits topological defects in the form of vortices. They tend to organize into vortex lines that bear close analogies with global cosmic strings. Therefore,…
The energy landscapes of proteins have evolved to be different from most random heteropolymers. Many studies have concluded that evolutionary selection for rapid and reliable folding to a given structure that is stable at biological…
Single molecule force spectroscopy methods can be used to generate folding trajectories of biopolymers from arbitrary regions of the folding landscape. We illustrate the complexity of the folding kinetics and generic aspects of the collapse…
We provide evidence that the energy landscapes of folded proteins do not shift with temperature, but the onset of functional dynamics is associated with its effective sampling. The motion of the backbone is described by three distinct…
We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can…