Related papers: RNA Folding and Large N Matrix Theory
M-theory suggests the large N limit of the matrix description of a collection of N Type IA D-particles should provide a nonperturbative formulation of heterotic string theory. In this paper states in the matrix theory corresponding to…
A unitary matrix model is proposed as the large-N matrix formulation of M theory on flat space with toroidal topology. The model reproduces the motion of elementary D-particles on the compact space, and admits membrane states with nonzero…
While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains…
The topological string interpretation of homological knot invariants has led to several insights into the structure of the theory in the case of sl(N). We study possible extensions of the matrix factorization approach to knot homology for…
We study theoretically the denaturation of single RNA molecules by mechanical stretching, focusing on signatures of the (un)folding pathway in molecular fluctuations. Our model describes the interactions between nucleotides by incorporating…
Proteins are linear molecular chains that often fold to function. The topology of folding is widely believed to define its properties and function, and knot theory has been applied to study protein structure and its implications. More that…
The prediction of protein secondary and tertiary structures from the primary amino acid sequence is both an incredibly important and incredibly difficult problem. Accurate prediction of a protein's native structure can provide critical…
Elasticity property (i.e. no-particle creation) is used in the tree level scattering of scalar particles in 1+1 dimensions to construct the affine Toda field theory(ATFT) associated with root systems of groups $a_2^{(2)}$ and $c_2^{(1)}$. A…
Understanding the mechanism of protein secondary structure formation is an essential part of protein-folding puzzle. Here we describe a simple model for the formation of the $\beta$-hairpin, motivated by the fact that folding of a…
Despite great interest in solving RNA secondary structures due to their impact on function, it remains an open problem to determine structure from sequence. Among experimental approaches, a promising candidate is the "chemical modification…
We examine compactifications of heterotic string theory on manifolds with SU(3) structure. In particular, we study N = 1/2 domain wall solutions which correspond to the perturbative vacua of the 4D, N =1 supersymmetric theories associated…
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…
We discuss the determination of the parton substructure of hadrons by casting it as a peculiar form of pattern recognition problem in which the pattern is a probability distribution, and we present the way this problem has been tackled and…
In this paper, we introduce the software suite, Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure…
Construction of (colored) knot polynomials for double-fat graphs is further generalized to the case when "fingers" and "propagators" are substituting R-matrices in arbitrary closed braids with m-strands. Original version of arXiv:1504.00371…
The $N=2$ minimal superconformal model can be twisted yielding an example of topological conformal field theory. In this article we investigate a Lie theoretic extension of this process.
A transfer-matrix formalism is introduced to evaluate exactly the partition function of the Munoz-Eaton model, relating the folding kinetics of proteins of known structure to their thermodynamics and topology. This technique can be used for…
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…
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.,…
These lectures will address two questions. Is there a simple variational principle underlying the existence of secondary motifs in the native state of proteins? Is there a general approach which can qualitatively capture the salient…