RNAGCN: RNA tertiary structure assessment with a graph convolutional network

RNAs play crucial and versatile roles in cellular biochemical reactions. Since experimental approaches of determining their three-dimensional (3D) structures are costly and less efficient, it is greatly advantageous to develop computational methods to predict RNA 3D structures. For these methods, designing a model or scoring function for structure quality assessment is an essential step but this step poses challenges. In this study, we designed and trained a deep learning model to tackle this problem. The model was based on a graph convolutional network (GCN) and named RNAGCN. The model provided a natural way of representing RNA structures, avoided complex algorithms to preserve atomic rotational equivalence, and was capable of extracting features automatically out of structural patterns. Testing results on two datasets convincingly demonstrated that RNAGCN performs similarly to or better than four leading scoring functions. Our approach provides an alternative way of RNA tertiary structure assessment and may facilitate RNA structure predictions. RNAGCN can be downloaded from https://gitee.com/dcw-RNAGCN/rnagcn.     

Progress in DNA Aptamers as Recognition Components for Protein Functional Regulation

Proteins play a central role in all domains of life, and precise regulation of their activity is essential for understanding the related biological processes and therapeutic functions. Nucleic acid aptamers, the molecular recognition components derived from systematic evolution of ligands by exponential enrichment(SELEX), can specifically identify proteins with antibody-like recognition characteristics and help to regulate their activity. This minireview covers the SELEX-based selection of protein-binding aptamers, membrane protein analytical techniques based on aptamer-mediated target recognition, aptamer-mediated functional regulation of proteins, including membrane receptors and non-membrane proteins(thrombin as a model), as well as the potential challenges and prospects regarding aptamer-mediated protein manipulation, aiming to supply some useful information for researchers in this field.     

化妆品中的肽化学*

随着科技进步和产业提升,人们不断从本源上追求美、从长效上保持美、从机制上激发美。众多肽类化合物,已被证实在人体内具有独特的生物学促进或抑制作用,也因此被广泛应用于美妆产品。以化妆品中生物活性肽的不同功效为主线,对其化学结构进行分析并阐述其中的生理作用机制。     

Explicit estimates of sums related to the Nyman–Beurling criterion for the Riemann Hypothesis

We give an estimate for sums appearing in the Nyman–Beurling criterion for the Riemann Hypothesis. These sums contain the Möbius function and are related to the imaginary part of the Estermann zeta function. The estimate is remarkably sharp in comparison to other sums containing the Möbius function. The bound is smaller than the trivial bound – essentially the number of terms – by a fixed power of that number. The exponent is made explicit. The methods intensively use tools from the theory of continued fractions and from the theory of Fourier series.     

Synthesis,Crystal Structure,and Selected Properties of [Au(S2CNH2)2]SCN: A Precursor for Gold Macro-Needles Consisting of Gold Nanoparticles Glued by Graphitic Carbon Nitride

A new preparation route is developed for the synthesis of needle-like crystals of [Au(S₂CNH₂)₂]SCN, which avoids disproportionation of the Au^I salt used as a starting material. In the crystal structure, the two crystallographically independent Au^III centers are in a square-planar environment of two S₂CNH₂ ligands. The Hirshfeld surface analysis reveals the presence of noncovalent intermolecular S⋅⋅⋅S interactions, which are essential for the spatial arrangement of the molecules. Density functional theory (DFT) calculations including dispersion and damping corrections result in a unit cell volume very close to the value determined experimentally. Thermal decomposition in an inert atmosphere generates black needles with lengths of up to 500 μm. X-ray powder diffraction and pair distribution function analyses demonstrate that the needles are composed of nanosized crystals with a volume-weighted average domain size of 20(1) nm. According to results of X-ray photoemission experiments, the black needles are covered by a nitrogen-rich carbon nitride with composition near (CN)₂N. ¹³C solid-state NMR investigations indicate that two different carbon species are present, with signals corresponding well to heptazine units as in melon and triazine units as in poly(triazin imide) type compounds. Scanning transmission electron microscopy tomography evidences that the needles are composed of slightly elongated nanoparticles.     

Binary functions,degeneracy, and alternating dimaps

This paper continues the study of combinatorial properties of binary functions — that is, functions $f:2^E\to ?$ such that $f(0?)=1$, where $E$ is a finite set. Binary functions have previously been shown to admit families of transforms that generalise duality, including a trinity transform, and families of associated minor operations that generalise deletion and contraction, with both these families parameterised by the complex numbers. Binary function representations exist for graphs (via the indicator functions of their cutset spaces) and indeed arbitrary matroids (as shown by the author previously). In this paper, we characterise degenerate elements – analogues of loops and coloops – in binary functions, with respect to any set of minor operations from our complex-parameterised family. We then apply this to study the relationship between binary functions and Tutte’s alternating dimaps, which also support a trinity transform and three associated minor operations. It is shown that only the simplest alternating dimaps have binary representations of the form we consider, which seems to be the most direct type of representation. The question of whether there exist other, more sophisticated types of binary function representations for alternating dimaps is left open.     

Delay of terminal current in systems with abruptly changed Hamiltonian

The current response for the parameter change of a mesoscopic system is a practical issue for future's circuit design. Nowadays most considered cases are various types of bias modulation, while the effect of change of conductor Hamiltonian is seldom addressed. In this paper, we investigate the response of ballistic transport induced by a sudden change of the conductor Hamiltonian. We formulize the terminal current in language of non-equilibrium Green's function. Our method is applied to one-dimensional tight-binding chains and we find that the terminal current has a delay to the Hamiltonian change. The amount of delay is not determined by the velocity of incident electrons in the bias window, but depends on the tight-binding hopping energy γ. The delay of current response at the detecting point away from where the Hamiltonian changes is $C{\gamma }^{?1}$, where C is a constant independent of the system.