Related papers: Universal Cold RNA Phase Transitions
We consider a simple model for the unfolding of RNA tertiary structure under dynamic loading. The opening of such a structure is regarded as a two step process, each corresponding to the overcoming of a single energy barrier. The resulting…
Four on-lattice and six off-lattice models for active matter are studied numerically, showing that in contact with a wall, they display universal wetting transitions between three distinctive phases. The particles, which interact via…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
Phases with distinct thermodynamic properties must differ in their underlying distributions of microscopic structures. While ordered phases are readily distinguished by unit cells and space groups, the local structural basis differentiating…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
Lipid structures exhibit complex and highly dynamic lateral structure; and changes in lipid density and fluidity are believed to play an essential role in membrane targeting and function. The dynamic structure of liquids on the molecular…
We study the temperature crossovers seen in the magnetic and transport properties of cuprates using a nearly antiferromagnetic Fermi liquid model (NAFLM). For the overdoped cuprates, we find, in agreement with earlier work, mean-field $z=2$…
Recent experimental and computational studies have demonstrated that nanoconfinement profoundly alters the phase behavior of water, facilitating complex phase transitions at pressures and temperatures far lower than typically observed in…
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…
Understanding how proteins fold into their native structure is a fundamental problem in biophysics, crucial for protein design. It has been hypothesized that the formation of a molten globule intermediate precedes folding to the native…
We argue that hadron multiplicities in central high energy nucleus-nucleus collisions are established very close to the phase boundary between hadronic and quark matter. In the hadronic picture this can be described by multi-particle…
The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific…
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by softening of the vibrational force constant by electrostatic and van der Waals forces…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
We describe quantitatively a RNA molecule under the influence of an external force exerted at its two ends as in a typical single-molecule experiment. Our calculation incorporates the interactions between nucleotides by using the…
Two dimensional crystalline membranes in isotropic embedding space exhibit a flat phase with anomalous elasticity, relevant e.g., for graphene. Here we study their thermal fluctuations in the absence of exact rotational invariance in the…
Molecular dynamics simulations are carried out to explore the dynamical crossover phenomenon in strongly confined and mildly supercooled water in graphene oxide nanopores. In contrast to studies where confinement is used to study the…
The correlations of the free-energy landscape of mean-field spin glasses at different temperatures are investigated, concentrating on models with a first order freezing transition. Using a ``potential function'' we follow the metastable…
Quantum critical systems derive their finite temperature properties from the influence of a zero temperature quantum phase transition. The paradigm is essential for understanding unconventional high-Tc superconductors and the non-Fermi…
The processes by which protein sidechains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of sidechain relaxation exhibit a distribution over the protein…