Related papers: Statistical Physics of RNA-folding
We introduce a coarse-grained model of DNA with bases modeled as rigid-body ellipsoids to capture their anisotropic stereochemistry. Interaction potentials are all physicochemical and generated from all-atom simulation/parameterization with…
HiRE-RNA is a simplified, coarse-grained RNA model for the prediction of equilibrium configurations, dynamics and thermodynamics. Using a reduced set of particles and detailed interactions accounting for base-pairing and stacking we show…
We present a study on the role of defects on the stability of short DNA molecules. We consider short DNA molecules (16 base pairs) and investigate the thermal as well as mechanical denaturation of these molecules in the presence of defects…
The Poland-Scheraga model is a celebrated model for the denaturation transition of DNA, which has been widely used in the bio-physical literature to study, and investigated by mathematicians. In the original model, only opposite bases of…
We apply Kramers theory to investigate the dissociation of multiple bonds under mechanical force and interpret experimental results for the unfolding/refolding force distributions of an RNA hairpin pulled at different loading rates using…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
A quadratic extension of REM has been treated. Discussed here is the origin of relation of REM to strings and other complex physical phenomena. Two basic features of the REM class of complex phenomena were identified: the double…
Accurate prediction of RNA secondary structure underpins transcriptome annotation, mechanistic analysis of non-coding RNAs, and RNA therapeutic design. Recent gains from deep learning and RNA foundation models are difficult to interpret…
Second order phase transitions are universally driven by an order parameter which becomes trivial at the critical point. At the same time, collective excitations which involve the amplitude of the order parameter develop a gap which…
A detailed description of the conformational plasticity of double stranded DNA (ds) is a necessary framework for understanding protein-DNA interactions. Until now, however structure and kinetics of the transition from the basic conformation…
We study theoretically the mechanical failure of a simple model of double stranded DNA under an applied shear. Starting from a more microscopic Hamiltonian that describes a sheared DNA, we arrive at a nonlinear generalization of a ladder…
We recently proposed a dynamical mesoscopic model for DNA, which is based, like statistical ones, on site-dependent finite stacking and pairing enthalpies. In the present article, we first describe how the parameters of this model are…
In this paper, we use the biological domain knowledge incorporated into stochastic models for ab initio RNA secondary-structure prediction to improve the state of the art in joint compression of RNA sequence and structure data (Liu et al.,…
The thermally induced denaturation of DNA in the presence of attractive solid surface is studied. The two strands of DNA are modeled via two coupled flexible chains without volume interactions. If the two strands are adsorbed on the…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
The prevalent method for RNA secondary structure prediction for a single sequence is free energy minimization based on the nearest neighbor thermodynamic model (NNTM). One of the least well-developed parts of the model is the energy…
We model unzipping of DNA/RNA molecules subject to an external force by a spin-oscillator system. The system comprises a macroscopic degree of freedom, represented by a one-dimensional oscillator, and internal degrees of freedom,…
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…
Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…