Related papers: Universal Cold RNA Phase Transitions
Water is essential for the activity of proteins. However, the effect of the properties of water on the behavior of proteins is only partially understood. Recently, several experiments have investigated the relation between the dynamics of…
Native membranes of biological cells display melting transitions of their lipids at a temperature of 10-20 degrees below body temperature. Such transitions can be observed in various bacterial cells, in nerves, in cancer cells, but also in…
The glass transition plays a central role in nature as well as in industry, ranging from biological systems such as proteins and DNA to polymers and metals. Yet the fundamental understanding of the glass transition which is a prerequisite…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
We investigate superfluid phase transitions of asymmetric nuclear matter at finite temperature ($T$) and density ($\rho$) with a low proton fraction ($Y_{\rm p} \le 0.2$) which is relevant to the inner crust and outer core of neutron stars.…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
The mechanical unfolding of a simple RNA hairpin and of a 236--bases portion of the Tetrahymena thermophila ribozyme is studied by means of an Ising--like model. Phase diagrams and free energy landscapes are computed exactly and suggest a…
Water has many anomalous properties compared to "simple" liquids, and these anomalies are typically enhanced in supercooled water. While numerous models have been proposed, including the liquid-liquid critical point, the singularity-free…
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the…
Since the Hadean era of Earth's history, peptides/proteins and RNA have undergone a complex evolutionary trajectory. Originating from simple monomeric units, these molecules evolved abiotically under various biochemical and biophysical…
When liquids are classified using Tg -scaled Arrhenius plots of relaxation times (or relative rates of entropy increase above Tg) across a "strong-fragile" spectrum of behaviors, the "strong" liquids have always appeared rather…
We report experimental evidence of a Gardner-like transition from variable to persistent force contacts in a two-dimensional, bidisperse granular crystal by analyzing the variability of both particle positions and force networks formed…
We introduce a polymer model where the transition from swollen to compact configurations is due to interactions between the monomers and the solvent. These interactions are the origin of the effective attractive interactions between…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
Hydrogen bond patterns, proton ordering, and phase transitions of monolayer ice in two-dimensional hydrophobic confinement are fundamentally different from those found for bulk ice. To investigate the behavior of quasi-2D ice, we perform…
Using molecular dynamics simulations, we investigate the relation between the dynamic transitions of biomolecules (lysozyme and DNA) and the dynamic and thermodynamic properties of hydration water. We find that the dynamic transition of the…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
Proteins work only if folded in their native state, but changes in temperature T and pressure P induce their unfolding. Therefore for each protein there is a stability region (SR) in the T-P thermodynamic plane outside which the biomolecule…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…