23 research outputs found
Cold denaturation of RNA secondary structures with loop entropy and quenched disorder
The critical behavior of ribonucleic acid (RNA) secondary structures with quenched sequence randomness is studied by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In addition to the expected melting at high temperature, a cold-melting transition appears when the disorder strength induces competition between favorable and unfavorable base pairs. Our results suggest that the cold denaturation of RNA found experimentally might be triggered by quenched sequence disorder. We calculate hot- and cold-melting critical temperatures for competing favorable and unfavorable base-pair energies and present a folding phase diagram as a function of the loop exponent and temperature
Osmotic pressure induced coupling between cooperativity and stability of a helix-coil transition
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 the helical state formation; and geometric, indicating how many
repeating units are affected by the formation of one helical state. Depending
on their effect on the helix-coil transition, solvents or co-solutes can be
classified with respect to their action on these parameters. Solvent
interactions that alter the entropic cost of helix formation by their osmotic
action can affect both the stability (transition temperature) and the
cooperativity (transition interval) of the helix-coil transition. A consistent
inclusion of osmotic pressure effects in a description of helix-coil transition
for poly(L-glutamic acid) in solution with polyethylene glycol can offer an
explanation of the experimentally observed linear dependence of transition
temperature on osmotic pressure as well as the concurrent changes in the
cooperativity of the transition.Comment: 5 pages, 3 figures. To be submitted to Phys.Rev.Let
Partially Annealed Disorder and Collapse of Like-Charged Macroions
Charged systems with partially annealed charge disorder are investigated
using field-theoretic and replica methods. Charge disorder is assumed to be
confined to macroion surfaces surrounded by a cloud of mobile neutralizing
counterions in an aqueous solvent. A general formalism is developed by assuming
that the disorder is partially annealed (with purely annealed and purely
quenched disorder included as special cases), i.e., we assume in general that
the disorder undergoes a slow dynamics relative to fast-relaxing counterions
making it possible thus to study the stationary-state properties of the system
using methods similar to those available in equilibrium statistical mechanics.
By focusing on the specific case of two planar surfaces of equal mean surface
charge and disorder variance, it is shown that partial annealing of the
quenched disorder leads to renormalization of the mean surface charge density
and thus a reduction of the inter-plate repulsion on the mean-field or
weak-coupling level. In the strong-coupling limit, charge disorder induces a
long-range attraction resulting in a continuous disorder-driven collapse
transition for the two surfaces as the disorder variance exceeds a threshold
value. Disorder annealing further enhances the attraction and, in the limit of
low screening, leads to a global attractive instability in the system.Comment: 21 pages, 2 figure
Modelling DNA adsorption on CNT
Due to the attraction between the polycyclic aromatic surface elements of carbon nanotubes (CNT)
and the aromatic nucleotides of deoxyribonucleic acid (DNA) a reversible adsorption (physisorption)
between them takes place. A large number of technologies are based on DNA-CNT hybrids [1], and
thus require the theoretical support. Modelling this phenomenon in terms of Statistical Mechanics
became recently possible, thanks to the Hamiltonian formulation of the zipper model [2]
Kinetics of the long ssRNA: Steady state
The steady state in the kinetic pathways of the long single-strand RNA (ssRNA) in the approximation of a coarse-grained model is studied with analytic calculations. It is assumed that the characteristic time of the secondary-structure rearrangement is much longer than that for the formation of the tertiary structure. The entropy and the specific heat of the system as functions of the temperature are calculated and plotted. A non-equilibrium phase transition of the 2nd order has been observed. The possible biological implication of the obtained results is discussed