相关论文: A new formalism for calculation of the partition f…

Loops are essential secondary structure elements in folded DNA and RNA molecules and proliferate close to the melting transition. Using a theory for nucleic acid secondary structures that accounts for the logarithmic entropy c ln m for a…

Two-state cooperativity is an important characteristic in protein folding. It is defined by a depletion of states lying energetically between folded and unfolded conformations. While there are different ways to test for two-state…

We modify and extend the recently developed statistical mechanical model for predicting the thermodynamic properties of chain molecules having noncovalent double-stranded conformations, as in RNA or ssDNA, and $\beta-$sheets in protein, by…

The conformational dynamics of single-stranded nucleic acids are fundamental for nucleic acid folding and function. However, their elementary chain dynamics have been difficult to resolve experimentally. Here we employ a combination of…

Protein folding cooperativity is defined by the nature of the finite-size thermodynamic transition exhibited upon folding: two-state transitions show a free energy barrier between the folded and unfolded ensembles, while downhill folding is…

The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…

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…

RNA secondary structure prediction is widely used to understand RNA function. Recently, there has been a shift away from the classical minimum free energy (MFE) methods to partition function-based methods that account for folding ensembles…

RNAs self-interact through hydrogen-bond base-pairing between nucleotides and fold into specific, stable structures that substantially govern their biochemical behaviour. Experimental characterization of these structures remains difficult,…

A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…

Ab initio RNA secondary structure predictions have long dismissed helices interior to loops, so-called pseudoknots, despite their structural importance. Here, we report that many pseudoknots can be predicted through long time scales RNA…

We formulate the RNA folding problem as an $N\times N$ matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is…

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a novel…

The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…

The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…

One-neutron halo nuclei, composed by a weakly-bound particle coupled to a core nucleus, are studied within a particle-plus-core model. A semi-microscopic method to generate the two-body Hamiltonian of such a system, including core…

The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer…

Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…