Insertion-deletion systems with substitutions I

In this paper, we discuss the addition of substitutions as a further type of operations to (in particular, context-free) insertion-deletion systems, i.e., in addition to insertions and deletions we allow single letter replacements to occur. We investigate the effect of the addition of substitution rules on the context dependency of such systems, thereby also obtaining new characterizations of and even normal forms for context-sensitive (CS) and recursively enumerable (RE) languages and their phrase-structure grammars. More specifically, we prove that for each RE language, there is a system generating this language that only inserts and deletes strings of length two without considering the context of the insertion or deletion site, but which may change symbols (by a substitution operation) by checking a single symbol to the left of the substitution site. When we allow checking left and right single-letter context in substitutions, even context-free insertions and deletions of single letters suffice to reach computational completeness. When allowing context-free insertions only, checking left and right single-letter context in substitutions gives a new characterization of CS. This clearly shows the power of this new type of rules.

Genetic Characteristics of Human Parainfluenza Virus Types 1–4 From Patients With Clinical Respiratory Tract Infection in China

Human parainfluenza viruses (HPIV1–4) cause acute respiratory tract infections, thereby impacting human health worldwide. However, there are no current effective antivirals or licensed vaccines for infection prevention. Moreover, sequence information for human parainfluenza viruses (HPIVs) circulating in China is inadequate. Therefore, to shed light on viral genetic diversity and evolution, we collected samples from patients infected with HPIV1–4 in China from 2012 to 2018 to sequence the viruses. We obtained 24 consensus sequences, comprising 1 for HPIV1, 2 for HPIV2, 19 for HPIV3, and 2 for HPIV4A. Phylogenetic analyses classified the 1 HPIV1 into clade 2, and the 2 HPIV4 sequences into cluster 4A. Based on the hemagglutinin-neuraminidase (HN) gene, a new sub-cluster was identified in one of the HPIV2, namely G1c, and the 19 HPIV3 sequences were classified into the genetic lineages of C3f and C3a. The results indicated that HPIV1–4 were co-circulated in China. Further, the lineages of sub-cluster C3 of HPIV3 were co-circulated in China. A recombination analysis indicated that a putative recombination event may have occurred in the HN gene of HPIV3. In the obtained sequences of HPIV3, we found that two amino acid substitution sites (R73K in the F protein of PUMCH14028/2014 and A281V in the HN protein of PUMCH13961/2014) and a negative selection site (amino acid position 398 in the F protein) corresponded to the previously reported neutralization-related sites. Moreover, amino acid substitution site (K108E) corresponded to the negative selection site (amino acid position 108) in the 10 F proteins of HPIV3. However, no amino acid substitution site corresponded to the glycosylation site in the obtained HPIV3 sequences. These results might help in studying virus evolution, developing vaccines, and monitoring HPIV-related respiratory diseases.

The Structure of the “Vibration Hole” around an Isotopic Substitution—Implications for the Calculation of Nuclear Magnetic Resonance (NMR) Isotopic Shifts

Calculations of nuclear magnetic resonance (NMR) isotopic shifts often rest on the unverified assumption that the “vibration hole”, that is, the change of the vibration motif upon an isotopic substitution, is strongly localized around the substitution site. Using our recently developed difference-dedicated (DD) second-order vibrational perturbation theory (VPT2) method, we test this assumption for a variety of molecules. The vibration hole turns out to be well localized in many cases but not in the interesting case where the H/D substitution site is involved in an intra-molecular hydrogen bond. For a series of salicylaldehyde derivatives recently studied by Hansen and co-workers (Molecules 2019, 24, 4533), the vibrational hole was found to stretch over the whole hydrogen-bond moiety, including the bonds to the neighbouring C atoms, and to be sensitive to substituent effects. We discuss consequences of this finding for the accurate calculation of NMR isotopic shifts and point out directions for the further improvement of our DD-VPT2 method.

Substitution site effect of naphthyl substituted anthracene derivatives and their applications in organic optoelectronics

Two different naphthyl substituted anthracene derivatives were synthesized. A tiny change of the substitution site of the naphthyl group leads to a significant difference of the molecular packing and exerts great impact on optoelectronic properties.

Electronic and luminescence characteristics of Bi/Al co-doped silica optical fiber

Electronic and luminescence characteristics of Bi/Al co-doped silica optical fiber model were investigated by using first-principle methods. Our results show that the preference Al substitution site is the adjacent Si site rather than O site. The doping of Al can contribute to the dispersion of Bi[Formula: see text] luminescence center and generate new luminescence center at [Formula: see text]1100 nm by affecting [Formula: see text] orbital of the O atom near Bi atom. Our results give a possible explanation of the near-infrared (NIR) luminescence in Bi/Al co-doped silica optical fibers.