Related papers: Backbone and Sidechain Ordering in a small Protein
This work relaxes the assumption of point particles prevalent in the study of thermal transport characteristics in $\Phi^4$ chains. The particles of the modified chain, henceforth termed as the $\Phi^{4C}$ chain, can collide with each…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
A coarse-grained molecular dynamics model of linear polyethylene-like polymer chain system was built to investigate the responds of structure and mechanical properties during uniaxial deformation. The influence of chain length, temperature,…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
We study the classical 120-degree and related orbital models. These are the classical limits of quantum models which describe the interactions among orbitals of transition-metal compounds. We demonstrate that at low temperatures these…
We present the results of a quantitative study of the phase behavior of a model polymer chain with side spheres using two independent computer simulation techniques. We find that the mere addition of side spheres results in key…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
In the framework of an extended phenomenological approach to phase transitions, it is shown that existing nonlinear relation between local critical atomic parameters and phenomenological order parameter induces the corresponding nonlinear…
We study the statistical mechanics of double-stranded semi-flexible polymers using both analytical techniques and simulation. We find a transition at some finite temperature, from a type of short range order to a fundamentally different…
Self-organization of proteins in space and time is of crucial importance for the functioning of cellular processes. Often, this organization takes place in the presence of strong random fluctuations due to the small number of molecules…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
The paper considers heat transport in diatomic one-dimensional lattices, containing equal amounts of particles with different masses. Ordering of the particles in the chain is governed by single correlation parameter -- the probability for…
We introduce a lattice model of protein conformations which is able to reproduce second structures of proteins (alpha--helices and beta--sheets). This model is based on the following two main ideas. First, we model backbone parts of amino…
Because the constant extension ensemble of single chain molecule is not always equivalent with constant force ensemble, a model of double-stranded conformations, as in RNA molecules and $\beta$-sheets in proteins, with fixed extension…
In view of the important role helix-sheet transitions play in protein aggregation, we introduce a simple model to study secondary structural transitions of helix-coil-sheet systems using a Potts model starting with an effective Hamiltonian.…
Exploring the protein-folding problem has been a long-standing challenge in molecular biology. Protein folding is highly dependent on folding of secondary structures as the way to pave a native folding pathway. Here, we demonstrate that a…
Methods of local topology are introduced to the field of protein physics. This is achieved by explaining how the folding and unfolding processes of a globular protein alter the local topology of the protein's C-alpha backbone through…
The study of protein interactions has generated great interest in the food industry. Therefore, research on new supramolecular structures shows promise. Supramolecular structures of the whey proteins {\alpha}-lactalbumin and…
Mimicking vascular systems in living beings, designers have realized microvascular composites to achieve thermal regulation and other functionalities, such as electromagnetic modulation, sensing, and healing. Such material systems avail…
The statistics of the heat exchanged between two quantum XX spin chains prepared at different temperatures is studied within the assumption of weak coupling. This provides simple formulas for the average heat and its corresponding…