相关论文: Thermodynamics of a model for RNA folding

The computer-aided folding of biomolecules, particularly RNAs, is one of the most difficult challenges in computational structural biology. RNA tetraloops are fundamental RNA motifs playing key roles in RNA folding and RNA-RNA and…

This contribution focuses on the fascinating RNA molecule, its sequence-dependent folding driven by base-pairing interactions, the interplay between these interactions and natural evolution, and its multiple regulatory roles. The four of us…

DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…

We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…

RNAs are negatively charged molecules residing in macromolecular crowding cellular environments. Macromolecular confinement can influence the ion effects in RNA folding. In this work, using the recently developed tightly bound ion model for…

In this work we apply entropic sampling simulations to a three-state model which has exact solutions in the microcanonical and grand-canonical ensembles. We consider $N$ chains placed on an unidimensional lattice, such that each site may…

RNA function is deeply intertwined with its conformational dynamics. In this review, we survey recent advances in the use of atomistic molecular dynamics simulations to characterize RNA dynamics in diverse contexts, including isolated…

The radiative thermal neutron capture cross sections over the range of thermal energies from 1 keV to 1 MeV are studied in statistical Hauser-Feshbach formalism. The optical model potential is constructed by folding the density dependent…

We consider an arbitrary translationally invariant chain model with nearest neighbors interaction and satisfying periodic boundary condition. The approach developed here allows a thermodynamic description of the chain model directly in…

The field of chemical computation attempts to model computational behavior that arises when molecules, typically nucleic acids, are mixed together. Thermodynamic binding networks (TBNs) is a highly abstracted model that focuses on which…

RNA duplex stability depends strongly on ionic conditions, and inside cells RNAs are exposed to both monovalent and multivalent ions. Despite recent advances, we do not have general methods to quantitatively account for the effects of…

Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…

We consider a new model which consists of a DNA together with a RNA. Here we assume that DNA is from a mammal or bird but RNA comes from a virus. To study thermodynamic properties of this model we use methods of statistical mechanics,…

The thermodynamic properties for three different types of off-lattice four-strand beta-sheet protein models interacting via a hybrid Go-type potential have been investigated. Discontinuous molecular dynamic simulations have been performed…

We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…

We investigate the sequence-dependent properties of proteins that determine the dual requirements of stability of the native state and its kinetic accessibility using simple cubic lattice models. Three interaction schemes are used to…

Determination of sizes and flexibilities of RNA molecules is important in understanding the nature of packing in folded structures and in elucidating interactions between RNA and DNA or proteins. Using the coordinates of the structures of…

We refine a protein model that reproduces fundamental aspects of protein thermodynamics. The model exhibits two transitions, hot and cold unfolding. The number of relevant parameters is reduced to three: 1) binding energy of folding…

We consider a system of $N$ particles living on the noncommutative plane in the presence of a confining potential and study its thermodynamics properties. Indeed, after calculating the partition function, we determine the corresponding…

Existing state-of-the-art methods that take a single RNA sequence and predict the corresponding RNA secondary-structure are thermodynamic methods. These predict the most stable RNA structure, but do not consider the process of structure…