Related papers: Protein Folding and Spin Glass
The emergence of biochemical activities in a protein seem to commence with the onset of atomic mean-square displacements along the protein lattice. The ensuing protein dynamical transition has been discussed extensively in the literature,…
We study a colloidal suspension confined between two quasi-parallel walls as a model system for glass transitions in confined geometries. The suspension is a mixture of two particle sizes to prevent wall-induced crystallization. We use…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
Enormous enhancement in the viscosity of a liquid near its glass transition is generally connected to the growing many-body static correlations near the transition, often coined as `amorphous ordering'. Estimating the length scales of such…
While many good textbooks are available on Protein Structure, Molecular Simulations, Thermodynamics and Bioinformatics methods in general, there is no good introductory level book for the field of Structural Bioinformatics. This book aims…
The importance of torsion vibration in the transmission of life information is indicated. The localization of quantum torsion state is proved. Following these analyses a formalism on the quantum theory of conformation-electron system is…
Glass formation is one of the most interesting phenomena in the condensed matter field. Considerable effort has gone into understanding and predicting the glass formability. However, the previous prediction requires the glass first made…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
We present a detailed analysis of glass transitions induced by pinning particles at random from an equilibrium configuration. We first develop a mean-field analysis based on the study of p-spin spherical disordered models and then obtain…
This is a commentary on two recent experimental papers in PNAS by Vivek et al. and Illing et al. that convincingly address an issue at the junction of two fundamental questions in glass physics: the role of the dimensionality of space on…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
The glass-forming ability is an important material property for manufacturing glasses and understanding the long-standing glass transition problem. Because of the nonequilibrium nature, it is difficult to develop the theory for it. Here we…
Proteins are a matter of dual nature. As a physical object, a protein molecule is a folded chain of amino acids with multifarious biochemistry. But it is also an instantiation along an evolutionary trajectory determined by the function…
The purpose of this manuscript is to review my recent activity on three main research topics. The first concerns the nature of low temperature amorphous solids and their relation with the spin glass transition in a magnetic field. This is…
Simple statistical agglomeration models can provide a universal link between the local structure and the glass transition temperature in network glasses. We first stress the physical features of the models and the hypothesis made, and then…
As well as several different kinds of periodically ordered ferroic phases, there are now recognized several different examples of ferroic glassiness, although not always described as such and in material fields of study that have mostly…
Reaching a ground state of a spin system is analogous to a protein evolving into its native state. We study the ``folding'' times for various random Ising spin systems and determine characteristic temperatures that relate to the…
Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
We study a physical system which, while devoid of the complexity one usually associates with proteins, nevertheless displays a remarkable array of protein-like properties. The constructive hypothesis that this striking resemblance is not…