Phase transitions and configuration space topology

M Kastner - Reviews of Modern Physics, 2008 - APS
Equilibrium phase transitions may be defined as nonanalytic points of thermodynamic
functions, eg, of the canonical free energy. Given a certain physical system, it is of interest to …

[图书][B] Geometry and topology in Hamiltonian dynamics and statistical mechanics

M Pettini - 2007 - Springer
Phase transitions are among the most impressive phenomena occurring in nature. They are
an example of emergent behavior, ie, of collective properties having no direct counterpart in …

Hydrophobic core formation and dehydration in protein folding studied by generalized-ensemble simulations

T Yoda, Y Sugita, Y Okamoto - Biophysical journal, 2010 - cell.com
Despite its small size, chicken villin headpiece subdomain HP36 folds into the native
structure with a stable hydrophobic core within several microseconds. How such a small …

Microcanonical versus canonical analysis of protein folding

J Hernández-Rojas, JM Gomez Llorente - Physical review letters, 2008 - APS
The microcanonical analysis is shown to be a powerful tool to characterize the protein
folding transition and to neatly distinguish between good and bad folders. An off-lattice …

Topological origin of the protein folding transition

L Di Cairano, R Capelli, G Bel-Hadj-Aissa, M Pettini - Physical Review E, 2022 - APS
In this paper, a geometrical and thermodynamical analysis of the global properties of the
potential energy landscape of a minimalistic model of a polypeptide is presented. The global …

Topology, symmetry, phase transitions, and noncollinear spin structures

FAN Santos, MD Coutinho-Filho - … Review E—Statistical, Nonlinear, and Soft …, 2009 - APS
We use a topological approach to describe the frustration-and field-induced phase
transitions exhibited by the infinite-range XY model on the AB 2 chain, including …

[HTML][HTML] Multifractal analysis of polyalanines time series

PH Figueiredo, E Nogueira Jr, MA Moret… - Physica A: Statistical …, 2010 - Elsevier
Multifractal properties of the energy time series of short α-helix structures, specifically from a
polyalanine family, are investigated through the MF-DFA technique (multifractal detrended …

Classifying proteinlike sequences in arbitrary lattice protein models using LatPack

M Mann, D Maticzka, R Saunders, R Backofen - HFSP journal, 2008 - Taylor & Francis
Knowledge of a protein's three‐dimensional native structure is vital in determining its
chemical properties and functionality. However, experimental methods to determine …

Relationship between protein folding thermodynamics and the energy landscape

J Kim, T Keyes, JE Straub - Physical Review E—Statistical, Nonlinear, and Soft …, 2009 - APS
The origin of protein folding thermodynamics is examined in terms of the energy landscape,
employing an off-lattice protein model with scaled non-native attractions, which is …

Graph theoretical analysis of the energy landscape of model polymers

M Baiesi, L Bongini, L Casetti, L Tattini - Physical Review E—Statistical …, 2009 - APS
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 …