Related papers: Folding 3-noncrossing RNA pseudoknot structures
No existing algorithm can start with arbitrary RNA sequences and return the precise, three-dimensional structures that ensures their biological function. This chapter outlines current algorithms for automated RNA structure prediction…
We employ simulations of model proteins to study folding on rugged energy landscapes. We construct ``first-passage'' networks as the system transitions from unfolded to native states. The nodes and bonds in these networks correspond to…
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial-time algorithms are heuristic algorithms with no…
We consider a model of algorithmic self-assembly of geometric shapes out of square Wang tiles studied in SODA 2010, in which there are two types of tiles (e.g., constructed out of DNA and RNA material) and one operation that destroys all…
Rapid and accurate assessment of protein structural models is essential for protein structure prediction and design. Great progress has been made in this regard, especially by recent development of ``knowledge-based'' potentials. Various…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
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…
A new statistical method of alignment of two heteropolymers which can form hierarchical cloverleaf-like secondary structures is proposed. This offers a new constructive algorithm for quantitative determination of binding free energy of two…
We propose a new conceptual approach to reach unattained dissipative properties based on the friction of slender concentric sliding columns. We begin by searching for the optimal topology in the simplest telescopic system of two concentric…
RNA molecules are single-stranded analogues of DNA that can fold into various structures which influence their biological function within the cell. RNA structures can be modelled combinatorially in terms of a certain type of graph called an…
Three-dimensional shell-like structures can be obtained spontaneously at the microscale from the self-folding of 2D templates of rigid panels. At least for simple structures, the motion of each panel is consistent with a Brownian process…
Here we analyze the electron transport properties of a device formed of two crossed graphene nanoribbons with zigzag edges (ZGNRs) in a spin state with total magnetization different from zero. While the ground state of ZGNRs has been shown…
Formation energy of the $\sigma$-phase in the Fe-Cr alloy system, $\Delta E$, was computed versus the occupancy changes on each of the five possible lattice sites. Its dependence on a number of Fe-atoms per unit cell, $N_{Fe}$, was either…
A novel technique for construction of minimum storage regenerating (MSR) codes is presented. Based on this technique, three explicit constructions of MSR codes are given. The first two constructions provide access-optimal MSR codes, with…
We apply a new approach to the reverse protein folding problem. Our method uses a minimization function in the design process which is different from the energy function used for folding. For a lattice model, we show that this new approach…
Motivated by the recent discovery of superconductivity in the iron-based ladder compound BaFe$_2$S$_3$ under high pressure, we derive low-energy effective Hamiltonians from first principles. We show that the complex band structure around…
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…
We introduce a method for predicting RNA folding pathways, with an application to the most important RNA tetraloops. The method is based on the idea that ensembles of three-dimensional fragments extracted from high-resolution crystal…
RNA secondary structures of increasing complexity are probed combining single molecule stretching experiments and stochastic unfolding/refolding simulations. We find that force-induced unfolding pathways cannot usually be interpretated by…
We propose a general model of unweighted and undirected networks having the scale-free property and fractal nature. Unlike the existing models of fractal scale-free networks (FSFNs), the present model can systematically and widely change…