Improving RNA secondary structure prediction using direct coupling analysis

Secondary structures of RNAs are the basis of understanding their tertiary structures and functions and so their predictions are widely needed due to increasing discovery of noncoding RNAs.In the last decades,a lot of methods have been proposed to predict RNA secondary structures but their accuracies encountered bottleneck.Here we present a method for RNA secondary structure prediction using direct coupling analysis and a remove-and-expand algorithm that shows better performance than four existing popular multiple-sequence methods.We further show that the results can also be used to improve the prediction accuracy of the single-sequence methods.

A direct coupling analysis method and its application to the Scientific Research and Demonstration Platform

Design of a very large floating structure(VLFS)deployed near islands and reefs,different from those in the open sea,inevitably faces new technical challenges including numerical analysis methods.In this paper,a direct coupling analysis method(DCAM)has been established based on the Boussinesq equations and the three-dimensional hydroelasisity theory with Rankine source method to analyze the responses of a VLFS in shallow sea with complicated geographical environment.Model tests have been carried out to validate the DCAM.To further verify the numerical methods and investigate the performance of such a VLFS,a“Scientific Research and Demonstration Platform(SRDP)”was built and deployed in 2019 at the site about 1000 m off an island with water depth around 40m in South China Sea.It is a simplified small model of a two-module semi-submersible-type VLFS.The numerical simulation of its responses on severe waves with focus on motions and connector forces is conduct by DCAM,and compared with the on-site measurements.Good agreement has been achieved.This approves the DCAM as a feasible tool for design and safety assessment of a VLFS deployed near islands and reefs.

ANALYSIS OF COUPLING INFLUENCES OF LABYRINTH SEAL PARAMETERS ON CROSS COUPLED STIFFNESS AND DIRECT DAMPING COEFFICIENT

Labyrinth seal can cause steam-exciting, the structural and operating parameters of labyrinth seal have effect on stability of rotor-system. For investigating the coupling influences of the structure and operating parameters of labyrinth seals on dynamic coefficients, a model of calculating dynamic coefficients of labyrinth seals is presented using a two control volume model. The coupling influences of parameters on cross-coupled stiffness and direct damping of labyrinth seal are discussed. In the conclusion, a reference of preventing steam-exciting vibration and optimum determination of design parameters of labyrinth seals are provided.

Effects of Tensor Couplings on Nucleonic Direct URCA Processes in Neutron Star Matter

The relativistic neutrino emissivity of the nucleonic direct URCA processes in neutron star matter is investigated within the relativistic Hartree-Fock approximation. We particularly study the influences of the tensor couplings of vector mesons ω and ρ on the nucleonic direct URCA processes. It is found that the inclusion of the tensor couplings of vector mesons w and p can slightly increase the maximum mass of neutron stars. In addition, the results indicate that the tensor couplings of vector mesons ω and ρ lead to obvious enhancement of the total neutrino emissivity for the nucleonic direct URCA processes, which must accelerate the cooling rate of the non- superfluid neutron star matter. However, when considering only the tensor coupling of vector meson ρ, the neutrino emissivity for the nucleonic direct URCA processes slightly declines at low densities and significantly increases at high densities. That is, the tensor coupling of vector meson ρ leads to the slow cooling rate of a low-mass neutron star and rapid cooling rate of a massive neutron star.

Facile and Cost-Efficient Synthesis of Photovoltaic Polymers via Direct Arylation Coupling

As the high calibre candidate of lightweight and flexible solar cells,polymer solar cells(PSCs)have made tremendous progress in recent years.However,the active photovoltaic materials in PSCs are mainly synthesized by metal-mediated coupling reaction requiring harsh reaction conditions,multiple-step synthesis,and cumbersome purification,which is not cost-efficient and may bring toxicity concerns.It is not favorable to the production of photovoltaic polymers and PSC devices on a large scale,and therefore unsuitable for the PSCs industrialization.Direct arylation coupling reaction via aromatic C―H bonds activation enables the synthesis of conjugated polymers under mild conditions and simultaneously reduces synthetic steps,difficulty,and toxic reaction byproducts.This review provides an overview of the history of preparing representative photovoltaic polymers utilized in PSCs through direct arylation reactions and discusses the activity and selectivity of C―H bonds in typical building blocks under different reaction conditions.Especially,the impact of direct arylation condition on defect formation and photovoltaic performance of the photovoltaic polymers is addressed and compared with conventional Stille coupling methods.

Methods and applications of RNA contact prediction

The RNA tertiary structure is essential to understanding the function and biological processes. Unfortunately, it is still challenging to determine the large RNA structure from direct experimentation or computational modeling. One promising approach is first to predict the tertiary contacts and then use the contacts as constraints to model the structure. The RNA structure modeling depends on the contact prediction accuracy. Although many contact prediction methods have been developed in the protein field, there are only several contact prediction methods in the RNA field at present. Here, we first review the theoretical basis and test the performances of recent RNA contact prediction methods for tertiary structure and complex modeling problems. Then, we summarize the advantages and limitations of these RNA contact prediction methods. We suggest some future directions for this rapidly expanding field in the last.

Catalyst-Dependent Direct and Deoxygenative Coupling of Alcohols by Convergent Paired Electrolysis

Developing a general and mild approach to upgrade alcohols into high value products is a hot topic in synthetic chemistry because alcohol is one of the most abundant raw chemicals.Specifically,direct coupling and deoxygenative coupling of alcohols are the two main approaches for the functionalization of alcohols to afford structurally diverse products,and it receives considerable attention.Despite significant advances in the field,there still remains a great challenge to develop a general approach accommodating both coupling reactions,as they commonly involve distinct pathways.Herein,we report an electrochemical approach for the direct coupling and deoxygenative coupling of alcohols with fluorenones.Under paired electrolysis,this catalyst-dependent protocol gives divergent access to diols and tertiary alcohols.Moreover,the synthetic utility of 9H-fluoren-9-ol products has been demonstrated in the synthesis of organic luminophores,phenanthrol,phenanthridine,and amino alcohol.The present approach exhibits some impressive features:(a)catalystdependent selectivity;(b)excellentfunctional-group tolerance(156 examples);(c)mild conditions;and(d)good scalability(∼20 gram scale).

DecPDEVS: New Simulation Algorithms to Improve Message Handling in PDEVS

This work proposes a new simulation algorithm to improve message handling in discrete event formalism. We present an approach to minimize simulation execution time. To do this, we propose to reduce the number of exchanged messages between Parallel DEVS (PDEVS) components (simulators and coordinators). We propose three changes from PDEVS: direct coupling, flat structure and local schedule. The goal is the decentralisation of a number of tasks to make the simulators more autonomous and simplify the coordinators to achieve a greater speedup. We propose to compare the simulation results of several models to demonstrate the benefits of our approach.

DOA estimation and mutual coupling calibration with the SAGE algorithm

In this paper, a novel algorithm is presented for direction of arrival（DOA） estimation and array self-calibration in the presence of unknown mutual coupling. In order to highlight the relationship between the array output and mutual coupling coefficients, we present a novel model of the array output with the unknown mutual coupling coefficients. Based on this model, we use the space alternating generalized expectation-maximization（SAGE） algorithm to jointly estimate the DOA parameters and the mutual coupling coefficients. Unlike many existing counterparts, our method requires neither calibration sources nor initial calibration information. At the same time,our proposed method inherits the characteristics of good convergence and high estimation precision of the SAGE algorithm. By numerical experiments we demonstrate that our proposed method outperforms the existing method for DOA estimation and mutual coupling calibration.

Loss-induced control of light propagation direction in passive linear coupled optical cavities

Redirecting the flow of light on the basis of the absorption/gain properties of optical systems is of great interest in many research fields, ranging from optical routing to optical cloaking. In this paper we investigate the control of the direction of the light propagation through loss-induced absorption in passive linear coupled optical systems. The considered optical system consists of a mode-splitting resonant cavity formed by coupling a Fabry–Perot(FP) cavity with a ring resonator. The coalescence of the asymmetric resonances, generated through mode-splitting dynamics, is the spectral result of the parity time symmetry breaking at FP resonance wavelengths.For specific values of the FP overall loss, a predominant backward propagation in the FP ring resonator occurs.In fiber optics technology, this device shows an ability to invert the sense of propagation of the light, quantified through the contrast ratio, in the order of 20 dB. This value can be obtained by externally varying the FP loss coefficient for a fixed set of the other physical parameters of the FP ring resonator. Our results can open a new way toward novel high-performance optical modulation and routing schemes.

High Sensitive Methane Sensor With Temperature Compensation Based on Selectively Liquid-Infiltrated Photonic Crystal Fibers

A highly sensitive and temperature-compensated methane sensor based on a liquid-infiltrated photonic crystal fiber (PCF) is proposed. Two bigger holes near the core area are coated with a methane-sensitive compound film, and specific cladding air holes are infiltrated into the liquid material to form new defective channels. The proposed sensor can achieve accurate measurement of methane concentration through temperature compensation. The sensitivity can reach to 20.07nm/% with a high linearity as the methane concentration is within the range of 0%-3.5% by volume. The proposed methane sensor can not only improve the measurement accuracy, but also reduce the metrical difficulty and simplify the process.