Related papers: The protein folding network
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
We are surrounded by spatio-temporal patterns resulting from the interaction of the numerous basic units constituting natural or human-made systems. In presence of diffusive-like coupling, Turing theory has been largely applied to explain…
The overall structure of the transition state and intermediate ensembles experimentally observed for Dihydrofolate Reductase and Interleukin-1beta can be obtained utilizing simplified models which have almost no energetic frustration. The…
RNA function crucially depends on its structure. Thermodynamic models currently used for secondary structure prediction rely on computing the partition function of folding ensembles, and can thus estimate minimum free-energy structures and…
We propose an information-based model for network dynamics in which imperfect information leads to networks where the different vertices have widely different number of edges to other vertices, and where the topology has hierarchical…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
Protein folding is one of the age-old biological problems that refers to the mechanism of understanding and predicting how a protein's linear sequence of amino acids folds into its specific three dimensional structure.This structure is…
Using a generalized random recurrent neural network model, and by extending our recently developed mean-field approach [J. Aljadeff, M. Stern, T. Sharpee, Phys. Rev. Lett. 114, 088101 (2015)], we study the relationship between the network…
Physical networks are made of nodes and links that are physical objects embedded in a geometric space. Understanding how the mutual volume exclusion between these elements affects the structure and function of physical networks calls for a…
Protein folding is analyzed using a replica variational formalism to investigate some free energy landscape characteristics relevant for dynamics. A random contact interaction model that satisfies the minimum frustration principle is used…
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…
Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor…
The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…
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.…
As protein folding is a NP-complete problem, artificial intelligence tools like neural networks and genetic algorithms are used to attempt to predict the 3D shape of an amino acids sequence. Underlying these attempts, it is supposed that…
Many-body systems when continuous phase transition occurs are mainly built in the interrelationship between particles, implemented through many-body correlations. Some of them may exhibit so-called topological order hardly measured by…
In systems characterized by a rough potential energy landscape, local energetic minima and saddles define a network of metastable states whose topology strongly influences the dynamics. Changes in temperature, causing the merging and…
The statistical mechanical approach to complex networks is the dominant paradigm in describing natural and societal complex systems. The study of network properties, and their implications on dynamical processes, mostly focus on locally…
Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…