Related papers: Statistical Analysis of Structural Transitions in …
In any valid Monte Carlo sampling that realizes microcanonical property we can collect statistics for a transition matrix in energy. This matrix is used to determine the density of states, from which most of the thermodynamical averages can…
A great many observables seen in intermediate energy heavy ion collisions can be explained on the basis of statistical equilibrium. Calculations based on statistical equilibrium can be implemented in microcanonical ensemble (energy and…
Thermodynamical properties of the helix-coil transition were successfully described in the past by the model of Lifson, Poland and Sheraga. Here we compute the corresponding structure factor and show that it possesses a universal scaling…
In the theoretical modelling of a physical system a crucial step consists in the identification of those degrees of freedom that enable a synthetic, yet informative representation of it. While in some cases this selection can be carried out…
For the estimation of transition points of finite elastic, flexible polymers with chain lengths from $13$ to $309$ monomers, we compare systematically transition temperatures obtained by the Fisher partition function zeros approach with…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
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…
Phase transitions of first and second order can easily be distinguished in small systems in the microcanonical ensemble. Configurations of phase coexistence, which are suppressed in the canonical formulation, carry important information…
Detecting conformational transitions in molecular systems is key to understanding biological processes. Here, we investigate the force variance in single-molecule pulling experiments as an indicator of molecular folding transitions. We…
The development of reliable methods for estimating microcanonical averages constitutes an important issue in statistical mechanics. One possibility consists of calculating a given microcanonical quantity by means of typical relations in the…
Phase transitions are ubiquitous across life, yet hard to quantify and describe accurately. In this work, we develop an approach for characterizing generic attributes of phase transitions from very limited observations made deep within…
The microscopic model in which nodes interacting with each other are statistical systems is introduced. The nodes conditions are connected with a string of distinct microscopic configurations and depend on external parameters (pressure and…
Systems with long-range interactions when quenced into a metastable state near the pseudo-spinodal exhibit nucleation processes that are quite different from the classical nucleation seen near the coexistence curve. In systems with…
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…
Two-dimensional (2D) particulate aggregates formed due to competing interactions exhibit a range of non-equilibrium steady state morphologies from finite-size compact crystalline structures to non-compact string-like conformations. We…
In recent experiments on sodium chloride clusters structural transitions between nanocrystals with different cuboidal shapes were detected. Here we presents results for the thermodynamics and dynamics of one of these clusters, (NaCl)35Cl-.…
We have developed a simple model for the study of a cubic to tetragonal martensitic transition, under athermal conditions, in systems with a certain amount of disorder. We have performed numerical simulations that allow for a statistical…
By observing trends in the folding kinetics of experimental 2-state proteins at their transition midpoints, and by observing trends in the barrier heights of numerous simulations of coarse grained, C-alpha model, Go proteins, we show that…
The past two decades have seen a revolution in statistical physics, generalizing it to apply to systems of arbitrary size, evolving while arbitrarily far from equilibrium. Many of these new results are based on analyzing the dynamics of the…
In this study, we experimentally investigated the time dependence of the statistical properties of two-dimensional drying crack patterns to determine the functional form of fragment size distribution. Experiments using a thin layer of a…