相关论文: Protein folding and cosmology
Eukaryote cells have a flexible shape, which dynamically changes according to the function performed by the cell. One mechanism for deforming the cell membrane into the desired shape is through the expression of curved membrane proteins.…
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…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
The geometry of centre vortices is studied in $\mathrm{SU(3)}$ gauge theory at finite temperature to capture the key structural changes that occur through the deconfinement phase transition. Visualisations of the vortex structure in…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
Perturbing a Go model towards a realistic protein Hamiltonian by adding non-native interactions, we find that the folding rate is in general enhanced as ruggedness is initially increased, as long as the protein is sufficiently large and…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
At a very rapid superfluid transition in $^3$He, follows after a reaction with single neutron, the creation of topological defects (vortices) has recently been demonstrated in accordance with the Kibble-Zurek scenario for the cosmological…
In this letter, the possible dynamic scaling properties of protein molecules in folding are investigated theoretically by assuming that the protein molecules are percolated networks. It is shown that the fractal character and the fractal…
We elucidate the mechanism of cold denaturation through constant-pressure simulations for a model of hydrophobic molecules in an explicit solvent. We find that the temperature dependence of the hydrophobic effect is the driving…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
In this work we propose a new algorithm for the computation of statistical equilibrium quantities on a cubic lattice when both an energy and a statistical temperature are involved. We demonstrate that the pivot algorithm used in situations…
A theoretical model for the folding of proteins containing disulfide bonds is introduced. The model exploits the knowledge of the native state to favour the progressive establishment of native interactions. At variance with traditional…
Novel sampling algorithms can significantly impact open questions in computational biology, most notably the in silico protein folding problem. By using computational methods, protein folding aims to find the three-dimensional structure of…
We use a three dimensional cubic lattice model of proteins to study their properties that determine folding to the native state. The protein chain is modeled as a sequence of $N$ beads. The interactions between beads are taken from a…
We present a microscopic variational theory for the free energy surface of a fast folding protein that allows folding kinetics to be resolved to the residue level using Debye-Waller factors as local order parameters. We apply the method to…
This is an analytical study of pinning and spontaneous vortex phase is a system consisting of a superconducting thin film pierced by a long ferromagnetic columnar defect of finite radius $R$. The magnetic fields, screening currents, energy…
Coarsening dynamics, the canonical theory of phase ordering following a quench across a symmetry breaking phase transition, is thought to be driven by the annihilation of topological defects. Here we show that this understanding is…
We study the spontaneous formation of vortices during the superfluid condensation in a trapped fermionic gas subjected to a rapid thermal quench via evaporative cooling. Our work is based on the numerical solution of the time dependent…
Near a continuous phase transition, systems with different microscopic origins display universal dynamics if their underlying symmetries are compatible. In a thermally quenched system, the Kibble-Zurek mechanism for the creation of…