Understanding the Stabilization of a Bulk Nanobubble: A Molecular Dynamics Analysis.

Bulk nanobubbles (NBs) have received considerable attention because of their extensive potential applications, such as in ultrasound imaging and water management. Although multiple types of experimental evidence have supported the existence and stabilization of bulk NBs, the underlying mechanism remains unclear. This study numerically investigates the bulk NB stabilization with molecular dynamics (MD) methods: the all-atom (AA) MD simulation is used for NBs of several nanometers diameter; the coarse-grained (CG) MD simulation is for the NBs of about 100 nm. The NB properties are statistically obtained and analyzed, including the inner density, inner pressure, surface charge, interfacial hydrogen bond (HB), and gaseous diffusion. The results show that the gas inside an NB has ultrahigh density (tens of kilograms per cubic meter). A double-layer surface charge exists on the NB. The inner/outer layer is positively/negatively charged, and the electrostatic stress can counteract part of the surface tension. In addition, the interfacial HB is weakened by the interaction between gas and water molecules, causing less surface tension. The above features are beneficial to NB stabilization. The NB equilibrium radii solved by the interfacial mechanical equilibrium equation agree with the MD results, indicating that this equation can describe the force balance of an NB as small as several nanometers. Besides, supersaturation appears to be necessary for the NB thermodynamic equilibrium. Based on Henry's law and the ideal gas law, the theoretical analysis suggests that the stability of the NB thermodynamic equilibrium is conditional: the number of gas molecules in NBs should be more than half that dissolved in liquid. This study unravels a stabilized bulk NB's properties and discusses the NB equilibrium and stabilization mechanism, which will advance the understanding and application of bulk NBs.

Aromatic Hydrocarbon Based and Space Interactions Induced Color-tunable Single-component Organic Phosphorescence.

Construction of new system and exploration of new approach are of great importance for the improvement of their photophysical properties to meet the growing various uses of phosphorescent materials. Triphenylmethane (TPM), composed only of carbon and hydrogen, exhibits excellent color tunable phosphorescence in air, with ultralong lifetime (836 ms), and wide color-tunable range (from cyan to green, then to yellow and finally to orange, 525 nm-616 nm). Through careful comparison with the single crystal diffraction structure of tetraphenylmethane (TTPM) and theoretical calculation analysis, we believe that various clusters formed through space interactions are crucial for color-tunable phosphorescence.

Color-Tunable Ultralong Organic Phosphorescence: Commercially Available Triphenylmethylamine for UV-Light Response and Anticounterfeiting.

Due to the unclear mechanism and lack of effective design for color-tunable ultralong organic phosphorescence (UOP) in a single-component molecule, the development of new types of single-component UOP materials with color-tunable property remains challenging. Herein, commercially available triphenylmethylamine-based single-component phosphors featuring color-tunablity and ultralong lifetime (0.56 s) are reported. The changed afterglow colors from cyan to orange were observed after different wavelengths of UV excitation. Crystal structure and calculation studies show that multiple emission centers in the aggregated states may be responsible for the color-tunablity. In addition, visual probing of UV light (from 260 to 370 nm) and colorful anti-counterfeiting were conducted. More importantly, UV light ranging from 350 to 370 nm could be detected with the minimal interval of 2 nm. The findings provide a new type of single-component color-tunable UOP materials and shed new light on mechanism and design for such materials.

Phototheranostics for NIR fluorescence image guided PDT/PTT with extended conjugation and enhanced TICT.

Introducing donor and acceptor into conjugated system can facilitate the intersystem crossing (ISC) rate to increase the generation of ROS. Twisted intramolecular charge transfer (TICT) state could favor enhance the nonradiative transition and photothermal conversion efficiency (PCE). Herein, diketopyrrolopyrrole (DPP) core functionalized benzene (PDDP), thiophene (TDPP), triphenylamine-conjugated benzene (TPA-PDDP) and thiophene (TPA-TDPP) derivatives were designed and synthesized. Electrochemistry experiments revealed the heavy atom effect and the introduction of triphenylamine reduced the energy level of TPA-TDPP and improved the ability to generate 1O2 (1O2 QY = 50%). In addition, in the aggregated state, introduction of thiophene, triphenylamine, and long alkyl chains promoted the twisting effect, preventing the intermolecular π-π interaction and enhancing the PCE of TPA-TDPP (38.7%). In vivo fluorescence imaging showed that TPA-TDPP NPs can target the tumor site with the enhanced permeability and retention (EPR) effect and presented excellent synergistic photodynamic/photothermal therapy.

Selective access to dihydrophenanthridines and phenanthridinones via cyclisation of aryl amines onto N-tethered arynes.

5,6-Dihydrophenanthridines are prepared from aryl amines via intramolecular addition to N-tethered arynes under mild conditions. A new o-silylaryl triflate precursor was developed to increase reactivity and enable electron-rich and electron-poor aryl amines to undergo cyclisation. A complete switch in product selectivity occurs when the reaction is conducted in air, affording the corresponding phenanthridin-6(5H)-one as the sole product under otherwise identical reaction conditions.

Host-Genome Similarity Characterizes the Adaption of SARS-CoV-2 to Humans.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a high mutation rate and many variants have emerged in the last 2 years, including Alpha, Beta, Delta, Gamma and Omicron. Studies showed that the host-genome similarity (HGS) of SARS-CoV-2 is higher than SARS-CoV and the HGS of open reading frame (ORF) in coronavirus genome is closely related to suppression of innate immunity. Many works have shown that ORF 6 and ORF 8 of SARS-CoV-2 play an important role in suppressing IFN-ß signaling pathway in vivo. However, the relation between HGS and the adaption of SARS-CoV-2 variants is still not clear. This work investigates HGS of SARS-CoV-2 variants based on a dataset containing more than 40,000 viral genomes. The relation between HGS of viral ORFs and the suppression of antivirus response is studied. The results show that ORF 7b, ORF 6 and ORF 8 are the top 3 genes with the highest HGS. In the past 2 years, the HGS values of ORF 8 and ORF 7B of SARS-CoV-2 have increased greatly. A remarkable correlation is discovered between HGS and inhibition of antivirus response of immune system, which suggests that the similarity between coronavirus and host gnome may be an indicator of the suppression of innate immunity. Among the five variants (Alpha, Beta, Delta, Gamma and Omicron), Delta has the highest HGS and Omicron has the lowest HGS. This finding implies that the high HGS in Delta variant may indicate further suppression of host innate immunity. However, the relatively low HGS of Omicron is still a puzzle. By comparing the mutations in genomes of Alpha, Delta and Omicron variants, a commonly shared mutation ACT > ATT is identified in high-HGS strain populations. The high HGS mutations among the three variants are quite different. This finding strongly suggests that mutations in high HGS strains are different in different variants. Only a few common mutations survive, which may play important role in improving the adaptability of SARS-CoV-2. However, the mechanism for how the mutations help SARS-CoV-2 escape immunity is still unclear. HGS analysis is a new method to study virus−host interaction and may provide a way to understand the rapid mutation and adaption of SARS-CoV-2.

Numerical Studies on Cellulose Hydrolysis in Organic-Liquid-Solid Phase Systems with a Liquid Membrane Catalysis Model.

The catalytic hydrolysis of cellulose to produce 5-hydroxymethylfurfural (HMF) is a powerful means of biomass resources. The current efficient hydrolysis of cellulose to obtain HMF is dominated by multiphase reaction systems. However, there is still a lack of studies on the synergistic mechanisms and component transport between the various processes of cellulose hydrolysis in a complex multiphase system. In this paper, a liquid membrane catalytic model was developed to simulate the hydrolysis of cellulose and its further reactions, including the adsorption of the liquid membrane on cellulose particles, the consumption of cellulose solid particles, the complex chemical reactions in the liquid membrane, and the transfer of HMF at the phase interface. The simulations show the synergistic effect between cellulose hydrolysis and multiphase mass transfer. We defined an indicator () to characterize the sensitivity of HMF yield to the initial liquid membrane thickness at different reaction stages. decreased gradually when the glucose conversion increased from 0 to 80%, and increased with the thickening of the initial liquid membrane thickness. It was shown that the thickening of the initial liquid membrane thickness promoted the HMF yield under the same glucose conversion. In summary, our results reveal the mechanism of the interaction between multiple physicochemical processes of the cellulose liquid membrane reaction system.

Structure prediction for the helical skeletons detected from the low resolution protein density map.

BACKGROUND: The current advances in electron cryo-microscopy technique have made it possible to obtain protein density maps at about 6-10 A resolution. Although it is hard to derive the protein chain directly from such a low resolution map, the location of the secondary structures such as helices and strands can be computationally detected. It has been demonstrated that such low-resolution map can be used during the protein structure prediction process to enhance the structure prediction. RESULTS: We have developed an approach to predict the 3-dimensional structure for the helical skeletons that can be detected from the low resolution protein density map. This approach does not require the construction of the entire chain and distinguishes the structures based on the conformation of the helices. A test with 35 low resolution density maps shows that the highest ranked structure with the correct topology can be found within the top 1% of the list ranked by the effective energy formed by the helices. CONCLUSION: The results in this paper suggest that it is possible to eliminate the great majority of the bad conformations of the helices even without the construction of the entire chain of the protein. For many proteins, the effective contact energy formed by the secondary structures alone can distinguish a small set of likely structures from the pool.

Reduction of the secondary structure topological space through direct estimation of the contact energy formed by the secondary structures.

BACKGROUND: Electron cryomicroscopy is a fast developing technique aiming at the determination of the 3-dimensional structures of large protein complexes. Using this technique, protein density maps can be generated with 6 to 10 A resolution. At such resolutions, the secondary structure elements such as helices and beta-strands appear to be skeletons and can be computationally detected. However, it is not known which segment of the protein sequence corresponds to which of the skeletons. The topology in this paper refers to the linear order and the directionality of the secondary structures. For a protein with N helices and M strands, there are (N!2N)(M!2M) different topologies, each of which maps N helix segments and M strand segments on the protein sequence to N helix and M strand skeletons. Since the backbone position is not available in the skeleton, each topology of the skeletons corresponds to additional freedom to position the atoms in the skeletons. RESULTS: We have developed a method to construct the possible atomic structures for the helix skeletons by sampling the solution space of all the possible topologies of the skeletons. Our method also ranks the possible structures based on the contact energy formed by the secondary structures, rather than the entire chain. If we assume that the backbone atomic positions are known for the skeletons, then the native topology of the secondary structures can be found in the top 30% of the ranked list of all possible topologies for all the 30 proteins tested, and within the top 5% for most of the 30 proteins. Without assuming the backbone location of the skeletons, the possible atomic structures of the skeletons can be constructed using the axis of the skeleton and the sequence segments. The best constructed structure for the skeletons has RMSD to native between 4 and 5 A for the four tested alpha-proteins. These best constructed structures were ranked the 17th, 31st, 16th and 5th respectively for the four proteins out of 32066, 391833, 98755 and 192935 possible assignments in the pool. CONCLUSION: Our work suggested that the direct estimation of the contact energy formed by the secondary structures is quite effective in reducing the topological space to a small subset that includes a near native structure for the skeletons.

Native secondary structure topology has near minimum contact energy among all possible geometrically constrained topologies.

Secondary structure topology in this article refers to the order and the direction of the secondary structures, such as helices and strands, with respect to the protein sequence. Even when the locations of the secondary structure Calpha atoms are known, there are still (N!2(N))(M!2(M)) different possible topologies for a protein with N helices and M strands. This work explored the question if the native topology is likely to be identified among a large set of all possible geometrically constrained topologies through an evaluation of the residue contact energy formed by the secondary structures, instead of the entire chain. We developed a contact pair specific and distance specific multiwell function based on the statistical characterization of the side chain distances of 413 proteins in the Protein Data Bank. The multiwell function has specific parameters to each of the 210 pairs of residue contacts. We illustrated a general mathematical method to extend a single well function to a multiwell function to represent the statistical data. We have performed a mutation analysis using 50 proteins to generate all the possible geometrically constrained topologies of the secondary structures. The result shows that the native topology is within the top 25% of the list ranked by the effective contact energies of the secondary structures for all the 50 proteins, and is within the top 5% for 34 proteins. As an application, the method was used to derive the structure of the skeletons from a low resolution density map that can be obtained through electron cryomicroscopy.

Liquid membrane catalytic model of hydrolyzing cellulose into 5-hydroxymethylfurfural based on the lattice Boltzmann method.

Conversion of cellulose to 5-hydroxymethylfurfural (HMF) is an important means of biomass utilization. However, simulation of hydrolysis of cellulose and species transport in multiphase systems is still missing. In this paper, a multiphase lattice Boltzmann method of the Shan-Chen model has been applied for simulating the complex chemical reactions and interphase mass transfer in a liquid membrane catalytic reactor. For the sake of simplification, a single particle liquid membrane catalytic model is developed to simulate the hydrolysis of cellulose into HMF and its side reactions, which include the adsorption of cellulose particles on the liquid membrane, the complex chemical reactions inside the liquid membrane and the interphase transfer of HMF. This simulation presents the results of hydrolysis of cellulose and the HMF transport process. Additionally, the results show that the thinner liquid membrane thickness is beneficial for increasing the yield of HMF.

The Relationship Between Low-Frequency Motions and Community Structure of Residue Network in Protein Molecules.

The global shape of a protein molecule is believed to be dominant in determining low-frequency deformational motions. However, how structure dynamics relies on residue interactions remains largely unknown. The global residue community structure and the local residue interactions are two important coexisting factors imposing significant effects on low-frequency normal modes. In this work, an algorithm for community structure partition is proposed by integrating Miyazawa-Jernigan empirical potential energy as edge weight. A sensitivity parameter is defined to measure the effect of local residue interaction on low-frequency movement. We show that community structure is a more fundamental feature of residue contact networks. Moreover, we surprisingly find that low-frequency normal mode eigenvectors are sensitive to some local critical residue interaction pairs (CRIPs). A fair amount of CRIPs act as bridges and hold distributed structure components into a unified tertiary structure by bonding nearby communities. Community structure analysis and CRIP detection of 116 catalytic proteins reveal that breaking up of a CRIP can cause low-frequency allosteric movement of a residue at the far side of protein structure. The results imply that community structure and CRIP may be the structural basis for low-frequency motions.

[Study on the accuracy of oxygen concentration of modified oxygen treatment with Venturi and humidity system].

OBJECTIVE: To verify the accuracy of oxygen concentration (FiO2) of modified oxygen treatment with Venturi and humidity system. METHODS: Patients just after ventilator weaning and before the removal of tracheal intubation/tracheotomy tube, who admitted to the intensive care unit (ICU) of Henan Provincial People's Hospital from May 1st to December 15th in 2017, were enrolled. All patients were given a modified oxygen treatment with Venturi and humidity system, and the oxygen flow rate (Flow) of the Venturi device and the oretical value of FiO2 were adjusted according to the patient's condition. Patients were divided into five groups based on doctor's orders: Flow 3 L/min FiO2 0.24, Flow 3 L/min FiO2 0.26, Flow 6 L/min FiO2 0.28, Flow 6 L/min FiO2 0.30, Flow 9 L/min FiO2 0.35. The value of FiO2 at the inhalation end of patients of each group was measured by TSI airflow analyzer, and the consistency between the measured value of FiO2 at the inhalation end and the FiO2 marked value of Venturi was compared and analyzed. RESULTS: When the FiO2 theoretical value of Venturi were adjusted to 0.24, 0.26, 0.28, 0.30, and 0.35, the measured values of FiO2 at the inhalation end of patients were 0.38±0.05, 0.38±0.05, 0.40±0.04, 0.41±0.04, and 0.77±0.11, respectively, which were all significantly higher than the theoretical value of FiO2 (all P < 0.01). The difference between the measured value of FiO2 at the inhalation side and the FiO2 value of the Venturi annotated and the difference rate were both "V"-shaped, both of which decreased with the increase in theoretical value of FiO2 to a Flow of 9 L/min and a theoretical value of FiO2 0.35, the accuracy was the worst, with the FiO2 difference of 0.42±0.11, and the FiO2 difference rate of (121.6±36.5)%. CONCLUSIONS: There is a difference between the measured value and the theoretical value of FiO2 at the inhalation end of the modified Venturi oxygen therapy humidification system, which needs to be paid attention to during clinical oxygen therapy.

OPUS-DOSP: A Distance- and Orientation-Dependent All-Atom Potential Derived from Side-Chain Packing.

We report a new distance- and orientation-dependent, all-atom statistical potential derived from side-chain packing, named OPUS-DOSP, for protein structure modeling. The framework of OPUS-DOSP is based on OPUS-PSP, previously developed by us [JMB (2008), 376, 288-301], with refinement and new features. In particular, distance or orientation contribution is considered depending on the range of contact distance. A new auxiliary function in energy function is also introduced, in addition to the traditional Boltzmann term, in order to adjust the contributions of extreme cases. OPUS-DOSP was tested on 11 decoy sets commonly used for statistical potential benchmarking. Among 278 native structures, 239 and 249 native structures were recognized by OPUS-DOSP without and with the auxiliary function, respectively. The results show that OPUS-DOSP has an increased decoy recognition capability comparing with those of other relevant potentials to date.

Intermolecular Aryne Ene Reaction of Hantzsch Esters: Stable Covalent Ene Adducts from a 1,4-Dihydropyridine Reaction.

The reaction of arynes with 1,4-dihydropyridines affords 2-aryl-1,2-dihydropyridines or 2-methylene-3-aryl-1,2,3,4-tetrahydropyridines via a regioselective C-2 or C-3 arylation. These compounds are the first series of isolable and bench-stable covalent ene adducts formed between dihydropyridines and unsaturated substrates. Experimental studies and DFT calculations provide mechanistic support for a concerted intermolecular aryne ene process, which may have implications for NAD(P)H model reactions.

Lineage-specific expression of polypyrimidine tract binding protein (PTB) in Drosophila embryos.

Polypyrimidine tract binding protein (PTB) is a member of the hnRNP family of RNA binding proteins (Nucleic Acids Res., 20 (1992) 3671) that functions in a number of processes important for the regulation of mRNA metabolism and gene expression (reviewed in Curr. Biol., 7 (1997) R705). Specifically, PTB binds polypyrimidine-rich intronic elements upstream of alternatively spliced exons to antagonize the binding of the essential U2AF splicing factor and repress the use of the regulated exons in specific tissues (RNA, 1 (1995) 234). Additionally, PTB interacts with elements that mediate 3-prime end processing of nascent transcripts (Mol. Cell. Biol., 19 (1999) 78) and is required for the expression of viral mRNAs that contain an internal ribosome binding site (RNA, 5 (1999) 344; RNA, 1 (1995) 924). Tissue-specific or alternatively spliced isoforms of PTB are thought to have different gene regulatory properties (Proc. Natl Acad. Sci. USA, 97 (2000) 6350; RNA, 7 (2001) 819), but little is known about the function and activity of PTB isoforms during development. Here, we investigate the expression of PTB during Drosophila embryogenesis using in situ hybridization assays. We show that PTB expression is patterned in the early embryo and occurs in specific mesodermal and neuronal lineages as well as in the imaginal discs and adult germline. These data indicate that PTB regulates gene expression in specific tissue lineages during development.

From isotropic to anisotropic side chain representations: comparison of three models for residue contact estimation.

The criterion to determine residue contact is a fundamental problem in deriving knowledge-based mean-force potential energy calculations for protein structures. A frequently used criterion is to require the side chain center-to-center distance or the -to- atom distance to be within a pre-determined cutoff distance. However, the spatially anisotropic nature of the side chain determines that it is challenging to identify the contact pairs. This study compares three side chain contact models: the Atom Distance criteria (ADC) model, the Isotropic Sphere Side chain (ISS) model and the Anisotropic Ellipsoid Side chain (AES) model using 424 high resolution protein structures in the Protein Data Bank. The results indicate that the ADC model is the most accurate and ISS is the worst. The AES model eliminates about 95% of the incorrectly counted contact-pairs in the ISS model. Algorithm analysis shows that AES model is the most computational intensive while ADC model has moderate computational cost. We derived a dataset of the mis-estimated contact pairs by AES model. The most misjudged pairs are Arg-Glu, Arg-Asp and Arg-Tyr. Such a dataset can be useful for developing the improved AES model by incorporating the pair-specific information for the cutoff distance.