相关论文: On the structure of RNA branching polytopes
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
The dual graph $\Gamma(h)$ of a regular triangulation $\Sigma(h)$ carries a natural metric structure. The minimum spanning trees of $\Gamma(h)$ recently proved to be conclusive for detecting significant data signal in the context of…
It is a common practice to describe branching random walks in terms of birth, death and walk of particles, which makes it easier to use them in different applications. The main results obtained for the models of symmetric continuous-time…
Possible crystalline modifications of chemical compounds at low temperatures correspond to local minima of the energy landscape. Determining these minima via simulated annealing is one method for the prediction of crystal structures, where…
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…
Models with nonlinear architectures/parameterizations such as deep neural networks (DNNs) are well known for their mysteriously good generalization performance at overparameterization. In this work, we tackle this mystery from a novel…
We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large…
By decomposing the random walk path, we construct a multitype branching process with immigration in random environment for corresponding random walk with bounded jumps in random environment. Then we give two applications of the branching…
The origin of allometric scaling patterns that are multiples of 1/4 has long fascinated biologists. While not universal, scaling relationships with exponents that are close to multiples of 1/4 are common and have been described in all major…
Motivation: Non-coding RNAs (ncRNAs) express their functions by adopting molecular structures. Specifically, RNA secondary structures serve as a relatively stable intermediate step before tertiary structures, offering a reliable signature…
The primary structure of a ribonucleic acid (RNA) molecule can be represented as a sequence of nucleotides (bases) over the alphabet {A, C, G, U}. The secondary or tertiary structure of an RNA is a set of base pairs which form bonds between…
The design of multi-stable RNA molecules has important applications in biology, medicine, and biotechnology. Synthetic design approaches profit strongly from effective in-silico methods, which can tremendously impact their cost and…
Understanding the base pairing of an RNA sequence provides insight into its molecular structure.By mining suboptimal sampling data, RNAprofiling 1.0 identifies the dominant helices in low-energy secondary structures as features, organizes…
Assumption of certain hierarchy of soft ferromagnet energy terms, realized in small enough flat nano-elements, allows to obtain explicit expressions for their magnetization distributions. By minimising the energy terms sequentially, from…
The approximation capability of ANNs and their RNN instantiations, is strongly correlated with the number of parameters packed into these networks. However, the complexity barrier for human understanding, is arguably related to the number…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
The Click-though Rate (CTR) prediction task is a basic task in recommendation system. Most of the previous researches of CTR models built based on Wide \& deep structure and gradually evolved into parallel structures with different modules.…
Nonlinear normal modes (NNMs) are widely used as a tool for developing mathematical models of nonlinear structures and understanding their dynamics. NNMs can be identified experimentally through a phase quadrature condition between the…
Over the last 10-15 years a general understanding of the chemical reaction of protein folding has emerged from statistical mechanics. The lessons learned from protein folding kinetics based on energy landscape ideas have benefited protein…
Nucleic acid sequence design via codon optimization is a fundamental task with applications across synthetic biology, mRNA therapeutics, and vaccine design. Given a target protein, it is a major open challenge to navigate the…