相关论文: Kinetics of the helix-coil transition
A microscopic spin model is proposed for the phenomenological Zimm-Bragg model for the helix-coil transition in biopolymers. This model is shown to provide the same thermophysical properties of the original Zimm-Bragg model and it allows a…
Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to…
We study the stress response to a step strain of covalently bonded gelatin gels in the temperature range where triple helix reversible crosslink formation is prohibited. We observe slow stress relaxation towards a $T$-dependent finite…
The quasi-equilibrium evolution of the helical fraction occurring in a biopolymer network (gelatin gel) under an applied stress has been investigated by observing modulation in its optical activity. Its variation with the imposed chain…
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…
In this paper we investigate, both analytically and numerically, the emergence of a kinetic glass transition in two different model systems: a uniformly heated granular gas and a molecular fluid with nonlinear drag. Despite the profound…
In this work, the nonequilibrium pathways of the collapse of the helix-forming biopolymer polyalanine are investigated. To this end, the full time evolution of the helix-coil transition is simulated using molecular dynamics simulations. At…
The transport properties of the planar rotator model on a square lattice are analyzed by means of microcanonical and non--equilibrium simulations. Well below the Kosterlitz--Thouless--Berezinskii transition temperature, both approaches…
The glass transition refers to the non-equilibrium process by which an equilibrium liquid is transformed to a non-equilibrium disordered solid, or vice versa. Associated response functions, such as heat capacities, are markedly different on…
Biological molecules can form hydrogen bonds between nearby residues, leading to helical secondary structures. The associated reduction of configurational entropy leads to a temperature dependence of this effect: the "helix-coil…
The theory of transition between $\alpha$-helix, $\beta$-sheet and random coil conformation of a protein is discussed through a simple model, that includes both short and long-range interactions. Besides the bonding parameter and helical…
Thermodynamics of helix-coil transitions in amino-acid homo-oligomers are studied by the recently proposed multicanonical algorithms. Homo-oligomers of length 10 are considered for three characteristic amino acids, alanine (helix former),…
We study the kinetics of helix-coil transition in water solutions of gelatin (collagen protein) by optical rotation techniques combined with thermal characterization. By examining the rates of secondary helix folding, and covering a very…
We calculate the Yang-Lee zeros for characteristic temperatures of the helix-coil transition in a continuum model of polyalanine. The distribution of these zeros differs from predictions of the Zimm-Bragg theory and supports recent claims…
In this paper we summarize some results of our theoretical investigations of helix-coil transition both in single-strand (polypeptides) and two-strand (polynucleotides) macromolecules. The Hamiltonian does not contain any parameter designed…
The overall solid-to-solid phase transformation kinetics under non-isothermal conditions has been modeled by means of a differential equation method. The method requires provisions for expressions of the fraction of the transformed phase in…
We study the nonequilibrium kinetics during the coil-globule transition of a flexible polymer chain with active beads after a quench from good to poor solvent condition using molecular dynamics simulation. Activity for each bead is…
In a nematic gel, the appearance of nematic order is accompanied by a spontaneous elongation of the gel parallel to the nematic director. If such a gel is made chiral, it has a tendency to form a cholesteric helical texture, in which local…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
The basic models of helix-coil transitions in biomolecules are introduced. These include phenomenological, zipper (Bragg-Zimm) models of polypeptides, loop-entropy (Poland-Scheraga) and Hamiltonian (Peyrard-Bishop) models of homogeneous DNA…