Related papers: Universal Cold RNA Phase Transitions
We investigated frictional effects on the folding rates of a human telomerase hairpin (hTR HP) and H-type pseudoknot from the Beet Western Yellow Virus (BWYV PK) using simulations of the Three Interaction Site (TIS) model for RNA. The heat…
Two hypothesizes concerning interaction of neutrons with nanoparticles and having applications in the physics of ultracold neutron (UCN) were recently considered in ref. [Physics of Atomic Nuclei 65(3): 400 (2002)]; they were motivated by…
We report the observation of a distinct correlation between the kinetic fragility index $m$ and the reduced Arrhenius crossover temperature $\theta_A = T_A/T_g$ in various glass-forming liquids, identifying three distinguishable groups. In…
Brittle failure is ubiquitous in amorphous materials that are sufficiently cooled below their glass transition temperature, $T_g$. This catastrophic failure mode is limiting for amorphous materials in many applications, and many fundamental…
The thermodynamics of phase transitions between phases that are size-mismatched but coherent differs from conventional stress-free thermodynamics. Most notably, in open systems such phase transitions are always associated with hysteresis.…
Single-stranded RNA viruses co-assemble their capsid with the genome and variations in capsid structures can have significant functional relevance. In particular, viruses need to respond to a dehydrating environment to prevent genomic…
Heterogeneous nucleation of a new bulk phase on a flat substrate can be associated with the surface phase transition called wetting transition. When this bulk heterogeneous nucleation occurs on a completely-wettable flat substrate with a…
Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well…
Using all atom molecular dynamics simulations, we report spontaneous unzipping and strong binding of small interfering RNA (siRNA) on graphene. Our dispersion corrected density functional theory based calculations suggest that nucleosides…
DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…
We give evidence of a clear structural signature of the glass transition, in terms of a static correlation length with the same dependence on the system size which is typical of critical phenomena. Our approach is to introduce an external,…
We propose that glass-forming liquids are intrinsically under the influences of both fluctuating interactions and random fields well-known in the field of spin systems. This is due to the frustration between the isotropic and anisotropic…
Non-coding RNAs are ubiquitous, but the discovery of new RNA gene sequences far outpaces research on their structure and functional interactions. We mine the evolutionary sequence record to derive precise information about function and…
We use Ising-like models to probe the thermal nature of Euclidean spacetime backgrounds. We determine which properties of the background -- curvature, the presence of a horizon, or temperature -- play a role in phase transitions. The…
The shapes of cooperatively rearranging regions in glassy liquids change from being compact at low temperatures to fractal or ``stringy'' as the dynamical crossover temperature from activated to collisional transport is approached from…
In this paper we study the effect of energy parameters on minimum free energy (mfe) RNA secondary structures. Employing a simplified combinatorial energy model, that is only dependent on the diagram representation and that is not sequence…
Graphynes and graphdiynes are carbon 2D allotrope structures presenting both sp2 and sp hybridized atoms. These materials have been theoretically predicted but due to intrinsic difficulties in their synthesis, only recently some of these…
Random first order transition theory is used to determine the role of attractive and repulsive interactions in the dynamics of supercooled liquids. Self-consistent phonon theory, an approximate mean field treatment consistent with random…
We present a new type of phase-change behavior relevant for information storage applications, that can be observed in 2D systems with cluster-forming ability. The temperature-based control of the ordering in 2D particle systems depends on…
Considering marginally relevant and relevant deformations of the weakly coupled $(3+1)$-dimensional large $N$ conformal gauge theories introduced in arXiv:2011.13981, we study the patterns of phase transitions in these systems that lead to…