Enhanced spin capturing polymerization: Numerical investigation of mechanism

Simulation on the kinetic scheme of enhanced spin capturing polymerizations (ESCP) were performed to reveal the influence of different parameters, e.g., initiation rate, spin capturing and side reactions on the properties (the monomer conversion, degree of polymerization, polydispersity index, and the fraction of “living” chains) of polymer obtained. The kinetic scheme of ESCP was solved numerically as well as the method of statistical moments of molecular weight distribution was applied to get some numerical expressions for analysis. The simulations showed that fast initiation rate can lead to decrease of living fraction and broadening of molecular weight distribution. Whereas high rate of spin capturing makes the polymer chains shorter but increases living character. And side reactions always decrease livingness of the polymer obtained. Finally in the case of absence of side reaction we were able to formulate criteria for formation of polymer with target molecular weight and quota of living chains via ESCP process. © 2015 Wiley Periodicals, Inc. J. Polym. Sci., Part A: Polym. Chem. 2015 , 53, 2546–2556     

The Early Steps of Molecule-to-Material Conversion in Chemical Vapor Deposition (CVD): A Case Study

Transition metal complexes with β-diketonate and diamine ligands are valuable precursors for chemical vapor deposition (CVD) of metal oxide nanomaterials, but the metal-ligand bond dissociation mechanism on the growth surface is not yet clarified in detail. We address this question by density functional theory (DFT) and ab initio molecular dynamics (AIMD) in combination with the Blue Moon (BM) statistical sampling approach. AIMD simulations of the Zn β-diketonate-diamine complex Zn(hfa)₂TMEDA (hfa = 1,1,1,5,5,5-hexafluoro-2,4-pentanedionate; TMEDA = N,N,N′,N′-tetramethylethylenediamine), an amenable precursor for the CVD of ZnO nanosystems, show that rolling diffusion of this precursor at 500 K on a hydroxylated silica slab leads to an octahedral-to-square pyramidal rearrangement of its molecular geometry. The free energy profile of the octahedral-to-square pyramidal conversion indicates that the process barrier (5.8 kcal/mol) is of the order of magnitude of the thermal energy at the operating temperature. The formation of hydrogen bonds with surface hydroxyl groups plays a key role in aiding the dissociation of a Zn-O bond. In the square-pyramidal complex, the Zn center has a free coordination position, which might promote the interaction with incoming reagents on the deposition surface. These results provide a valuable atomistic insight on the molecule-to-material conversion process which, in perspective, might help to tailor by design the first nucleation stages of the target ZnO-based nanostructures.     

Identification of Flavonoids as Putative ROS-1 Kinase Inhibitors Using Pharmacophore Modeling for NSCLC Therapeutics

Non-small cell lung cancer (NSCLC) is a lethal non-immunogenic malignancy and proto-oncogene ROS-1 tyrosine kinase is one of its clinically relevant oncogenic markers. The ROS-1 inhibitor, crizotinib, demonstrated resistance due to the Gly2032Arg mutation. To curtail this resistance, researchers developed lorlatinib against the mutated kinase. In the present study, a receptor-ligand pharmacophore model exploiting the key features of lorlatinib binding with ROS-1 was exploited to identify inhibitors against the wild-type (WT) and the mutant (MT) kinase domain. The developed model was utilized to virtually screen the TimTec flavonoids database and the retrieved drug-like hits were subjected for docking with the WT and MT ROS-1 kinase. A total of 10 flavonoids displayed higher docking scores than lorlatinib. Subsequent molecular dynamics simulations of the acquired flavonoids with WT and MT ROS-1 revealed no steric clashes with the Arg2032 (MT ROS-1). The binding free energy calculations computed via molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) demonstrated one flavonoid (Hit) with better energy than lorlatinib in binding with WT and MT ROS-1. The Hit compound was observed to bind in the ROS-1 selectivity pocket comprised of residues from the β-3 sheet and DFG-motif. The identified Hit from this investigation could act as a potent WT and MT ROS-1 inhibitor.     

Fabrication of three-component hydrogen-bonded covalent-organic polymers for ciprofloxacin decontamination from water: adsorption mechanism and modeling

A three-component hydrogen-bonded covalent organic polymer, namely JLUE-H_COP-66, was fabricated via a facile multiple-linking-site solvothermal approach to overcome the weakness of poor function complexity and limited structure diversity of the pure covalent skeletons. The as-prepared JLUE-H_COP-66 polymers were employed to decontaminate ciprofloxacin (CIP), a popular F-quinolones (FQNs) antibiotic, from water and exhibited satisfactory adsorption performance. Specifically, JLUE-H_COP-66 polymers have high adsorption capacity with the maximum contribution of 111.1 mg/g according to the Langmuir model, good antiinterference to NaCl salts, and excellent regeneration property. The pH-dependent experiment results signified the probably dominated mechanism of electrostatic interaction. In addition, adsorption studies and structural characterization in combination illustrated that the pore-filling effect, hydrogen bonding formation might also govern the whole process, accompanied by electrostatic interaction, dipole-dipole complexation, π-π EDA interaction, and hydrophobic-hydrophobic interaction besides. Moreover, electrostatic potentials, as well as the frontier molecular orbital distributions (HOMO and LUMO) of CIP and JLUE-H_COP-66 fragment, were calculated using density functional theory to theoretically support the research. Furthermore, the response surface methodology (RSM) according to the CCD matrix was used to not only study the interactive and cooperative effects of initial CIP concentration, initial pH, ionic strength along with JLUE-H_COP-66 dosage on CIP removal using JLUE-H_COP-66 but also optimize the operation conditions. Given the peculiar structure and functional feature, this work could hopefully bring H_COPs into the practical applications of such challenging and persistent ciprofloxacin potent removal with further large-scale efficiency.     

Melting thermodynamics of oligonucleic acids conjugated with relatively solvophobic linear polymers: A coarse‐grained molecular simulation study

Oligonucleic acids (ONAs), such as DNA and RNA, are used in various biotechnology and nanotechnology applications due to their ability to form a double helix that is stable at low temperature and melts at high temperatures. The melting temperature (T_m) of ONA duplexes can be tuned by the ONA composition, sequence, length and concentration, solvent quality, and salt concentration and by conjugation to other macromolecules. In this article, we use coarse‐grained (CG) molecular simulations to study ONAs conjugated with linear homopolymers that are relatively more solvophobic than the ONA. We study charged and stiff 8‐mer ONAs (e.g., DNA) and neutral and flexible 8‐mer ONAs (e.g., peptide nucleic acids or PNA), and vary the composition (or G‐C content) and sequence of ONA, conjugated homopolymer lengths and solvent quality for the polymer. For neutral and flexible ONAs, as the solvent quality worsens for the polymer, the ONA melting temperature increases from that of unconjugated ONA. The melting curves broaden with polymer length and worsening solvent quality, especially for ONAs with higher G‐C content. For charged and stiff ONAs, as the solvent quality worsens, the ONA melting temperature decreases compared to unconjugated ONA while the width of the melting curve remains the same. © 2019 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2019 , 57, 1196–1208     

Object and Mathematical Simulation of Ammonium Hexafluorosilicate Sublimation

An integration of different modelling methods including object and mathematical simulation are suggested for sublimation processes of inorganic fluorides to optimally simulate the real technological conditions. The paper presents the results of testing this methodology on ammonium hexafluorosilicate sublimation.     

Good match exploration for thermal infrared face recognition based on YWF-SIFT with multi-scale fusion

Stable local feature detection is a critical prerequisite in the problem of infrared (IR) face recognition. Recently, Scale Invariant Feature Transform (SIFT) is introduced for feature detection in an infrared face frame, which is achieved by applying a simple and effective averaging window with SIFT termed as Y-styled Window Filter (YWF). However, the thermal IR face frame has an intrinsic characteristic such as lack of feature points (keypoints); therefore, the performance of the YWF-SIFT method will be inevitably influenced when it was used for IR face recognition. In this paper, we propose a novel method combining multi-scale fusion with YWF-SIFT to explore more good feature matches. The multi-scale fusion is performed on a thermal IR frame and a corresponding auxiliary visual frame generated from an off-the-shelf low-cost visual camera. The fused image is more informative, and typically contains much more stable features. Besides, the use of YWF-SIFT method enables us to establish feature correspondences more accurately. Quantitative experimental results demonstrate that our algorithm is able to significantly improve the quantity of feature points by approximately 38%. As a result, the performance of YWF-SIFT with multi-scale fusion is enhanced about 12% in infrared human face recognition.     

Optimising the Termofluids CFD code for petascale simulations

ABSTRACT

This paper presents some recent efforts carried out on the expansion of the scalability of TermoFluids multi-physics Computational Fluid Dynamics (CFD) code, aiming to achieve petascale capacity for a single simulation. We describe different aspects that we have improved in our code in order to efficiently run it on 131,072 CPU-cores. This work has been developed using the BlueGene/Q Mira supercomputer of the Argonne Leadership Computing Facility, where we have obtained feedback at the targeted scale. In summary, this is a practical paper showing our experience at reaching the petascale paradigm for a single simulation with TermoFluids.