相关论文: On the structure of RNA branching polytopes

We present analysis of a novel tool for protein secondary structure prediction using the recently-investigated Neural Machine Translation framework. The tool provides a fast and accurate folding prediction based on primary structure with…

We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…

Probabilistic models can be defined by an energy function, where the probability of each state is proportional to the exponential of the state's negative energy. This paper considers a generalization of energy-based models in which the…

Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop…

Recently, it became possible to experimentally generate and characterize a very thin silica system on a substrate which can be basically described as a 2D random network. The key structural properties, in particular related to the ring…

Requirements on subsystems have been made clear in this paper for a linear time invariant (LTI) networked dynamic system (NDS), under which subsystem interconnections can be estimated from external output measurements. In this NDS,…

Multitype branching processes with immigration in one type are used to model the dynamics of stage-structured plant populations. Parametric inference is first carried out when count data of all types are observed. Statistical…

Background: Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences i.e.~sequences that satisfy the base pairing constraints of a given RNA…

Populations of heterogeneous cells play an important role in many biological systems. In this paper we consider systems where each cell can be modelled by an ordinary differential equation. To account for heterogeneity, parameter values are…

An introduction to the minimal supersymmetric Standard Model (MSSM) is given. The motivation for ``low-energy'' supersymmetry is reviewed, and the structure of the MSSM is outlined. In its most general form, the MSSM can be viewed as a…

A study of parameter sensitivity of nuclear energy density functionals, initiated in the first part of this work \cite{NV.16}, is extended by the inclusion of data on ground-state properties of finite nuclei in the application of the…

In cond-mat/9907125 the low-temperature behavior of a model for RNA secondary structure was studied. It is claimed that the model exhibits a breaking of the replica symmetry, since the width of the distribution P(q) of overlaps may converge…

RNA's diverse biological functions stem from its structural versatility, yet accurately predicting and designing RNA sequences given a 3D conformation (inverse folding) remains a challenge. Here, I introduce a deep learning framework that…

The objective of the present paper is to develop a two-step methodology integrating system identification and numerical continuation for the experimental extraction of nonlinear normal modes (NNMs) under broadband forcing. The first step…

The reconstruction of the neutrino energy is crucial in oscillation experiments that use interactions with nuclei to detect the neutrino. The common reconstruction procedure is based on the kinematics of the final-state lepton. The…

In functional linear regression, the parameters estimation involves solving a non necessarily well-posed problem and it has points of contact with a range of methodologies, including statistical smoothing, deconvolution and projection on…

Training over sparse multipath channels is explored. The energy allocation and the optimal shape of training signals that enable error free communications over unknown channels are characterized as a function of the channels' statistics.…

The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…

Given a random RNA secondary structure, $S$, we study RNA sequences having fixed ratios of nuclotides that are compatible with $S$. We perform this analysis for RNA secondary structures subject to various base pairing rules and minimum arc-…

This work examines a field theory for RNA-like molecules in a good solvent. The field theory is based on a lattice model for single- and double-strand RNA with a periodic base sequence, and otherwise contains all known relevant details…