Related papers: Protein folding and cosmology
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…
A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for…
Phase transitions are ubiquitous in nature, ranging from protein folding and denaturisation, to the superconductor-insulator quantum phase transition, to the decoupling of forces in the early universe. Remarkably, phase transitions can be…
Over the years, advances in experimental and computational methods have helped us to understand the role of thermodynamic, kinetic and active (chaperone-aided) effects in coordinating the folding steps required to achieving a knotted native…
The mechanical unfolding of proteins is investigated by extending the Wako-Saito-Munoz-Eaton model, a simplified protein model with binary degrees of freedom, which has proved successful in describing the kinetics of protein folding. Such a…
Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…
Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…
Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…
It is argued that the Universe reheating in bouncing cosmologies could be explained via gravitational particle production, as due to a sudden phase transition in the contracting regime. To this end, it is shown that gravitational production…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
Self-assembling novel ordered structures with nanoparticles has recently received much attention. Here we use computer simulations to study a two-dimensional model system characterized by a simple isotropic interaction that could be…
A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G.…
The formation of topological defects in a second order phase transition in the early universe is an out-of-equilibrium process. Condensed matter experiments seem to support Zurek's mechanism, in which the freezing of thermal fluctuations…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein…
We have studied the effects of an external sinusoidal force in protein folding kinetics. The externally applied force field acts on the each amino acid residues of polypeptide chains. Our simulation results show that mean protein folding…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…
Melting is often understood in purely equilibrium terms, where crystalline order disappears once the free energy of the solid equals that of the liquid. Yet at the microscopic level, the initiating events for melting can often be traced to…
We investigate the cosmological consequences of particle physics theories that admit stable loops of superconducting cosmic string - {\it vortons}. General symmetry breaking schemes are considered, in which strings are formed at one energy…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…