Related papers: Statistical Physics of RNA-folding
The thermodynamics of the $q$-state Potts model with arbitrary $q$ on a class of hierarchical lattices is considered. Contrary to the case of the crystal lattices, it has always the second-order phase transitions. The analytical expressions…
A quantitative characterization of the relationship between molecular sequence and structure is essential to improve our understanding of how function emerges. This particular genotype-phenotype map has been often studied in the context of…
We discern hydration geometries around the sugar-phosphate-backbone of an RNA double helix at the molecular level. RNA disordering upon melting is connected with a transition from ordered water structures towards local phosphate group…
We study quenched disorder in strongly correlated systems via holography, focusing on the thermodynamic effects of mild electric disorder. Disorder is introduced through a random potential which is assumed to self-average on macroscopic…
A formal analogy of fluctuating diffusivity to thermodynamics is discussed for messenger RNA molecules fluorescently fused to a protein in living cells. Regarding the average value of the fluctuating diffusivity of such RNA-protein…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…
Literature data on the properties of DNA open states are reviewed and analyzed. These states are formed as a result of strong DNA fluctuations and have a great impact on a number of biochemical processes; among them is charge transfer in…
RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…
We introduce a three-state model for a single DNA chain under tension that distinguishes between B-DNA, S-DNA and M (molten or denatured) segments and at the same time correctly accounts for the entropy of molten loops, characterized by the…
A double stranded DNA molecule under the stress of a pulling force acting on the strand terminals exhibits a partially denatured structure or can be completely unzipped depending the magnitude of the pulling force. A scaling argument for…
We construct and study an extended random matrix model of RNA (polymer) folding. A perturbation which acts on all the nucleotides in the chain is added to the action of the RNA partition function. The effect of this perturbation on the…
Mechanical unfolding trajectories, generated by applying constant force in optical tweezer experiments, show that RNA hairpins and the P5abc subdomain of the group I intron unfold reversibly. We use coarse-grained Go-like models for RNA…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
The physics and morphology of biomolecular condensates formed through liquid-liquid phase separation underpin diverse biological processes, exemplified by the nested organization of nucleoli that facilitates ribosome biogenesis. Here, we…