Related papers: Universal Cold RNA Phase Transitions
Clarification of the detailed mechanisms involved in the DNA polymorphism is an important challenge for computational molecular biophysics. This paper reports about reversible A/B transitions in DNA observed in silico in a simulated…
By performing a comprehensive study on 1832 segments of 1212 complete genomes of viruses, we show that in viral genomes the hairpin structures of thermodynamically predicted RNA secondary structures are more abundant than expected under a…
We report that protein confinement within nanoscopic vesicular compartments corresponds to a liquid-liquid phase transition with the protein/water within vesicle lumen interacting very differently than in bulk. We show this effect leads to…
If a binary liquid mixture, composed of two alternative species with equal amounts, is quenched from a high temperature to a low temperature, below the critical point of demixing, then the mixture will phase separate through a process known…
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected…
We propose a lattice model for RNA based on a self-interacting two-tolerant trail. Self-avoidance and elements of tertiary structure are taken into account. We investigate a simple version of the model in which the native state of RNA…
We analyze the thermodynamic properties of a simplified model for folded RNA molecules recently studied by G. Vernizzi, H. Orland, A. Zee (in {\it Phys. Rev. Lett.} {\bf 94} (2005) 168103). The model consists of a chain of one-flavor base…
We introduce a new quantity to probe the glass transition. This quantity is a linear generalized compressibility which depends solely on the positions of the particles. We have performed a molecular dynamics simulation on a glass forming…
Strong changes in bulk properties, such as modulus and viscosity, are observed near the glass transition temperature, T_{g}, of amorphous materials. For more than a century, intense efforts have been made to define a microscopic origin for…
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…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
The use of micro-Raman spectroscopy, through chemical bond nano-scale probes, allows the changes in conformations (alpha helix -> beta sheet), chain orientation, disconnection of disulfide bonds (-20%) and the increase of intra and…
Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped…
Conformational dynamics is crucial for ribonucleic acid (RNA) function. Techniques such as nuclear magnetic resonance, cryo-electron microscopy, small- and wide-angle X-ray scattering, chemical probing, single-molecule F\"orster resonance…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
Across many scientific and engineering disciplines, it is important to consider how much the output of a given system changes due to perturbations of the input. Here, we investigate the glassy phase of $\pm J$ spin glasses at zero…
To characterize the pairing-specificity of RNA secondary structures as a function of temperature, we analyse the statistics of the pairing weights as follows : for each base $(i)$ of the sequence of length N, we consider the $(N-1)$ pairing…
We analyze the ways in which the random first order phase transition (RFOT) of the glass transition differs from the well-studied regular first order and second order (or continuous) phase transitions. Just as is the case in the latter two…
We summarize the recent simulation progress of micromanipulation experiments on RNAs. Our work mainly consults with two important small RNAs unfolding experiments carried out by Bustamante group. Our results show that, in contrast to…
We have simulated structure and dynamics of water in the grooves of a DNA duplex using moleculear dynamics simulations. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both…