Related papers: Protein Folding and Spin Glass
The prediction of the three-dimensional native structure of proteins from the knowledge of their amino acid sequence, known as the protein folding problem, is one of the most important yet unsolved issues of modern science. Since the…
A simple spin system is studied as an analog for proteins. We investigate how the introduction of randomness and frustration into the system effects the designability and stability of ground state configurations. We observe that the spin…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
We discuss recent theoretical developments in the study of simple lattice models of proteins. Such models are designed to understand general features of protein structures and mechanism of folding. Among the topics covered are (i) the use…
The protein folding problem is stated and a list of properties that do not depend upon specific molecules is compiled and analyzed. The relationship of this analysis to future simulations is emphasized. The choice of power and time as…
Existing theories explain spin glass transition in terms of a phase transition and order parameters, and assume the existence of a distinct spin glass phase. In addition to problems related to clarifying the nature of this phase, the common…
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…
We provide here a brief perspective on the glass transition field. It is an assessment, written from the point of view of theory, of where the field is and where it seems to be heading. We first give an overview of the main phenomenological…
Understanding the mechanical properties of glasses remains elusive since the glass transition itself is not fully understood, even in well studied examples of glass formers in two dimensions. In this context we demonstrate here: (i) a…
The topic of the glass transition gives rise to a a wide diversity of views. It is, accordingly, characterized by a lack of agreement on which would be the most profitable theoretical perspective. In this chapter, I provide some elements…
In an effort to understand the glass transition, the kinetics of a spin model with frustration but no quenched randomness has been analyzed. The phenomenology of the spin model is remarkably similiar to that of structural glasses. Analysis…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
The protein folding is regarded as a quantum transition between torsion states on polypeptide chain. The deduction of the folding rate formula in our previous studies is reviewed. The rate formula is generalized to the case of frequency…
Key to resolving the scientific challenge of the glass transition is to understand the origin of the massive increase in viscosity of liquids cooled below their melting temperature (avoiding crystallisation). A number of competing and often…
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.…
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…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
Glass transition where viscosity of liquids increases dramatically upon decrease of temperature without any major change in structural properties, remains one of the most challenging problems in condensed matter physics (Cavagna, 2009;…
We present a novel statistical mechanics formalism for the theoretical description of the process of protein folding$\leftrightarrow$unfolding transition in water environment. The formalism is based on the construction of the partition…