### Recent Submissions

• #### Molecular engineering of intrinsically microporous polybenzimidazole for energy-efficient gas separation

(Applied Materials Today, Elsevier BV, 2021-12-04) [Article]
Polybenzimidazole (PBI) is a high-performance polymer that exhibits high thermal and chemical stability. However, it suffers from low porosity and low fractional free volume, which hinder its application as separation material. Herein, we demonstrate the molecular engineering of gas separation materials by manipulating a PBI backbone possessing kinked moieties. PBI was selected as it contains NH groups which increase the affinity towards CO$_2$, increase sorption capacity, and favors CO$_2$ over other gasses. We have designed and synthesized an intrinsically microporous polybenzimidazole (iPBI) featuring a spirobisindane structure. Introducing a kinked moiety in conjunction with crosslinking enhanced the polymer properties, markedly increasing the gas separation performance. In particular, the BET surface area of PBI increased 30-fold by replacing a flat benzene ring with a kinked structure. iPBI displayed a good CO$_2$ uptake of 1.4 mmol g$^{−1}$ at 1 bar and 3.6 mmol g$^{−1}$ at 10 bar. Gas sorption uptake and breakthrough experiments were conducted using mixtures of CO$_2$/CH$_4$ (50%/50%) and CO$_2$/N$_2$ (50%/50%), which revealed the high selectivity of CO$_2$ over both CH$_4$ and N$_2$. The obtained CO$_2$/N$_2$ selectivity is attractive for power plant flue gas application requiring CO$_2$ capturing materials. Energy and process simulations of biogas CO$_2$ removal demonstrated that up to 70% of the capture energy could be saved when iPBI was used rather than the current amine technology (methyl diethanolamine [MDEA]). Similarly, the combination of iPBI and MDEA in a hybrid system exhibited the highest CO$_2$ capture yield (99%), resulting in nearly 50% energy saving. The concept of enhancing the porosity of PBI using kinked moieties provides new scope for designing highly porous polybenzimidazoles for various separation processes.
• #### Room-temperature multiple ligands-tailored SnO2 quantum dots endow in situ dual-interface binding for upscaling efficient perovskite photovoltaics with high VOC.

(Light, science & applications, Springer Science and Business Media LLC, 2021-12-03) [Article]
The benchmark tin oxide (SnO2) electron transporting layers (ETLs) have enabled remarkable progress in planar perovskite solar cell (PSCs). However, the energy loss is still a challenge due to the lack of "hidden interface" control. We report a novel ligand-tailored ultrafine SnO2 quantum dots (QDs) via a facile rapid room temperature synthesis. Importantly, the ligand-tailored SnO2 QDs ETL with multi-functional terminal groups in situ refines the buried interfaces with both the perovskite and transparent electrode via enhanced interface binding and perovskite passivation. These novel ETLs induce synergistic effects of physical and chemical interfacial modulation and preferred perovskite crystallization-directing, delivering reduced interface defects, suppressed non-radiative recombination and elongated charge carrier lifetime. Power conversion efficiency (PCE) of 23.02% (0.04 cm2) and 21.6% (0.98 cm2, VOC loss: 0.336 V) have been achieved for the blade-coated PSCs (1.54 eV Eg) with our new ETLs, representing a record for SnO2 based blade-coated PSCs. Moreover, a substantially enhanced PCE (VOC) from 20.4% (1.15 V) to 22.8% (1.24 V, 90 mV higher VOC, 0.04 cm2 device) in the blade-coated 1.61 eV PSCs system, via replacing the benchmark commercial colloidal SnO2 with our new ETLs.
• #### BC6P Monolayer: Isostructural and Isoelectronic Analogues of Graphene with Desirable Properties for K-Ion Batteries

(Chemistry of Materials, American Chemical Society (ACS), 2021-12-03) [Article]
K-ion batteries are interesting alternatives to Li-ion batteries because of the earth-abundance of K and the similar chemistry between K and Li. However, a lack of high-performance anode materials is a major obstacle to the development of K-ion batteries. We show that the BC6P monolayer, which is isostructural and isoelectronic to graphene due to charge compensation between the constituent elements, can fill this gap. The capacity is found to be 1410 mAh/g (BC6PK6), i.e., about four times that of graphite. The diffusion barrier is as low as 0.13 eV and the average open-circuit voltage is as low as 0.35 V, ensuring high rate performance and high safety, respectively. Metallic states induced by K adsorption provide electrical conductivity during the battery cycle.
• #### Growth of Two-Dimensional Materials at the Wafer Scale

Wafer-scale growth has become a critical bottleneck for scaling up applications of van der Waal (vdW) layered two-dimensional (2D) materials in high-end electronics and optoelectronics. Most vdW 2D materials were initially obtained through top-down synthesis methods, such as exfoliation, which can only prepare small flakes on a micrometer scale. Bottom-up growth can enable 2D flake growth over a large area. However, seamless merging of these flakes to form large-area continuous films with well-controlled layer thickness and lattice orientation is still a significant challenge. In this review, we briefly introduce several vdW layered 2D materials covering their lattice structures, representative physical properties, and potential roles in large-scale applications. Then, several methods used to grow vdW layered 2D materials at the wafer-scale are reviewed in depth. In particular, we summarize three strategies that enable 2D film growth with a single-crystalline structure over the whole wafer: growth of an isolated domain, growth of unidirectional domains, and conversion of oriented precursors. After that, we review the progress in using wafer-scale 2D materials in integrated devices and advanced epitaxy. Finally, future directions in the growth and scaling of vdW layered 2D materials are discussed.
• #### Temporal and spatial earthquake clustering revealed through comparison of millennial strain-rates from 36Cl cosmogenic exposure dating and decadal GPS strain-rate

(Scientific Reports, Springer Science and Business Media LLC, 2021-12-02) [Article]
To assess whether continental extension and seismic hazard are spatially-localized on single faults or spread over wide regions containing multiple active faults, we investigated temporal and spatial slip-rate variability over many millennia using in-situ $^{36}$Cl cosmogenic exposure dating for active normal faults near Athens, Greece. We study a ~ NNE-SSW transect, sub-parallel to the extensional strain direction, constrained by two permanent GPS stations located at each end of the transect and arranged normal to the fault strikes. We sampled 3 of the 7 seven normal faults that exist between the GPS sites for $^{36}$Cl analyses. Results from Bayesian inference of the measured $^{36}$Cl data implies that some faults slip relatively-rapidly for a few millennia accompanied by relative quiescence on faults across strike, defining out-of-phase fault activity. Assuming that the decadal strain-rate derived from GPS applies over many millennia, slip on a single fault can accommodate ~ 30–75% of the regional strain-rate for a few millennia. Our results imply that only a fraction of the total number of Holocene active faults slip over timescales of a few millennia, so continental deformation and seismic hazard are localized on specific faults and over a length-scale shorter than the spacing of the present GPS network over this time-scale. Thus, (1) the identification of clustered fault activity is vital for probabilistic seismic hazard assessments, and (2) a combination of dense geodetic observations and palaeoseismology is needed to identify the precise location and width of actively deforming zones over specific time periods.
• #### Factors Limiting the Range Extension of Corals into High-Latitude Reef Regions

(Diversity, MDPI AG, 2021-12-01) [Article]
Reef-building corals show a marked decrease in total species richness from the tropics to high latitude regions. Several hypotheses have been proposed to account for this pattern in the context of abiotic and biotic factors, including temperature thresholds, light limitation, aragonite saturation, nutrient or sediment loads, larval dispersal constraints, competition with macro-algae or other invertebrates, and availability of suitable settlement cues or micro-algal symbionts. Surprisingly, there is a paucity of data supporting several of these hypotheses. Given the immense pressures faced by corals in the Anthropocene, it is critical to understand the factors limiting their distribution in order to predict potential range expansions and the role that high latitude reefs can play as refuges from climate change. This review examines these factors and outlines critical research areas to address knowledge gaps in our understanding of light/temperature interactions, coral-Symbiodiniaceae associations, settlement cues, and competition in high latitude reefs.
• #### Differential susceptibility of reef-building corals to deoxygenation reveals remarkable hypoxia tolerance.

(Scientific reports, Springer Science and Business Media LLC, 2021-12-01) [Article]
Ocean deoxygenation threatens the persistence of coastal ecosystems worldwide. Despite an increasing awareness that coastal deoxygenation impacts tropical habitats, there remains a paucity of empirical data on the effects of oxygen limitation on reef-building corals. To address this knowledge gap, we conducted laboratory experiments with ecologically important Caribbean corals Acropora cervicornis and Orbicella faveolata. We tested the effects of continuous exposure to conditions ranging from extreme deoxygenation to normoxia (~ 1.0 to 6.25 mg L$^{-1}$ dissolved oxygen) on coral bleaching, photophysiology, and survival. Coral species demonstrated markedly different temporal resistance to deoxygenation, and within a species there were minimal genotype-specific treatment effects. Acropora cervicornis suffered tissue loss and mortality within a day of exposure to severe deoxygenation (~ 1.0 mg L$^{-1}$), whereas O. faveolata remained unaffected after 11 days of continuous exposure to 1.0 mg L$^{-1}$. Intermediate deoxygenation treatments (~ 2.25 mg L$^{-1}$, ~ 4.25 mg L$^{-1}$) elicited minimal responses in both species, indicating a low oxygen threshold for coral mortality and coral resilience to oxygen concentrations that are lethal for other marine organisms. These findings demonstrate the potential for variability in species-specific hypoxia thresholds, which has important implications for our ability to predict how coral reefs may be affected as ocean deoxygenation intensifies. With deoxygenation emerging as a critical threat to tropical habitats, there is an urgent need to incorporate deoxygenation into coral reef research, management, and action plans to facilitate better stewardship of coral reefs in an era of rapid environmental change.
• #### Stable near-to-ideal performance of a solution-grown single-crystal perovskite X-ray detector

(Research Square Platform LLC, 2021-12-01) [Preprint]
Abstract The ideal photodetector is the one able to detect every single incoming photon. In particular, in X-ray medical imaging, the radiation dose for patients can then approach its fundamentally lowest limit set by the Poisson photon statistics. Such near-to-ideal X-ray detection characteristics have been demonstrated with only a few semiconductor materials such as Si1 and CdTe2; however, their industrial deployment in medical diagnostics is still impeded by elaborate and costly fabrication processes. Hybrid metal halide perovskites – newcomer semiconductors -– make for a viable alternative3,4,5 owing to their scalable, inexpensive, robust, and versatile solution growth and recent demonstrations of single gamma-photon counting under high applied bias voltages6,7. The major hurdle with perovskites as mixed electronic-ionic conductors, however, arises from the rapid material's degradation under high electric field8,9,10,11, thus far used in perovskite X-ray detectors12,13. Here we show that both near-to-ideal and long-term stable performance of perovskite X-ray detectors can be attained in the photovoltaic mode of operation at zero-voltage bias, employing thick and uniform methylammonium lead iodide (MAPbI3) single crystal (SC) films (up to 300 µm), solution-grown directly on hole-transporting electrodes. The operational device stability is equivalent to the intrinsic chemical shelf lifetime of MAPbI3, being at least one year in the studied case. Detection efficiency of 88% and noise equivalent dose of 90 pGyair (lower than the dose of a single incident photon) are obtained with 18 keV X-rays, allowing for single-photon counting, as well as low-dose and energy-resolved X-ray imaging. These findings benchmark hybrid perovskites as practically suited materials for developing low-cost commercial detector arrays for X-ray imaging technologies.
• #### msRepDB: a comprehensive repetitive sequence database of over 80 000 species.

(Nucleic acids research, Oxford University Press (OUP), 2021-12-01) [Article]
Repeats are prevalent in the genomes of all bacteria, plants and animals, and they cover nearly half of the Human genome, which play indispensable roles in the evolution, inheritance, variation and genomic instability, and serve as substrates for chromosomal rearrangements that include disease-causing deletions, inversions, and translocations. Comprehensive identification, classification and annotation of repeats in genomes can provide accurate and targeted solutions towards understanding and diagnosis of complex diseases, optimization of plant properties and development of new drugs. RepBase and Dfam are two most frequently used repeat databases, but they are not sufficiently complete. Due to the lack of a comprehensive repeat database of multiple species, the current research in this field is far from being satisfactory. LongRepMarker is a new framework developed recently by our group for comprehensive identification of genomic repeats. We here propose msRepDB based on LongRepMarker, which is currently the most comprehensive multi-species repeat database, covering >80 000 species. Comprehensive evaluations show that msRepDB contains more species, and more complete repeats and families than RepBase and Dfam databases. (https://msrepdb.cbrc.kaust.edu.sa/pages/msRepDB/index.html).
• #### Tailored Pore Size and Microporosity of Covalent Organic Framework (COF) Membranes for Improved Molecular Separation

(Journal of Membrane Science Letters, Elsevier BV, 2021-12) [Article]
Three highly crystalline truxene-based β-ketoenamine COF membranes (TFP-HETTA, TFP-HBTTA and TFP-HHTTA) are fabricated via a de novo monomer design approach to understand the fundamental correlations between pore structure and molecular separation performance. By introducing bulky alkyl groups into the truxene framework, the pore size of TFP-HETTA, TFP-HBTTA, and TFP-HHTTA are systematically tuned from 1.08 to 0.72 nm. Accordingly, the TFP-HETTA showed good water permeance of 47 L m−2 h−1 bar−1 along with a prominent rejection rate of Reactive Blue (RB, 800 Da) but less than 10% rejection rate of inorganic salts. In contrast, the TFP-HHTTA membrane with pore size of 0.72 nm can reject small dye molecules (SO, 350 Da) and trivalent salts but with a moderate water permeance of 19 L m−2 h−1 bar−1. The pore-flow model rooted from the viscous flow could well fit the observed organic solvent nanofiltration results of all three COF membranes.
• #### A decoupled scheme to solve the mass and momentum conservation equations of the improved Darcy–Brinkman–Forchheimer framework in matrix acidization

(AIP Advances, AIP Publishing, 2021-12-01) [Article]
Matrix acidization simulation is a challenging task in the study of flows in porous media due to the changing porosity in the procedure. The improved Darcy–Brinkman–Forchheimer framework is one model to do this simulation. In this framework, the mass and momentum conservation equations are discretized to form a pressure–velocity linear system. However, the coefficient matrix of the linear system has a large condition number, and solving the linear system belongs to the saddle point problem. As a result of that, convergence is hard to achieve when solving it with iterative solvers. It is well known that the scale of the linear systems in matrix acidization simulation is large, and therefore, the usage of iterative solvers is required. Thus, a decoupled scheme is proposed in this work to decouple the pressure–velocity linear system into two independent linear systems: one is to solve for pressure, and the other one is to solve for velocity. It is emphasized that both of the linear systems are discretized from the elliptical partial differential equations, which guarantees fast convergence can be achieved by iterative solvers. A numerical experiment is carried out to demonstrate the correctness of the decoupled scheme and its higher computing efficiency. After that, the decoupled scheme is applied in investigating the factors that cannot change the optimal injected velocity and the dissolution pattern in matrix acidization.
• #### MAD: A Scalable Dataset for Language Grounding in Videos from Movie Audio Descriptions

(arXiv, 2021-12-01) [Preprint]
The recent and increasing interest in video-language research has driven the development of large-scale datasets that enable data-intensive machine learning techniques. In comparison, limited effort has been made at assessing the fitness of these datasets for the video-language grounding task. Recent works have begun to discover significant limitations in these datasets, suggesting that state-of-the-art techniques commonly overfit to hidden dataset biases. In this work, we present MAD (Movie Audio Descriptions), a novel benchmark that departs from the paradigm of augmenting existing video datasets with text annotations and focuses on crawling and aligning available audio descriptions of mainstream movies. MAD contains over 384,000 natural language sentences grounded in over 1,200 hours of video and exhibits a significant reduction in the currently diagnosed biases for video-language grounding datasets. MAD's collection strategy enables a novel and more challenging version of video-language grounding, where short temporal moments (typically seconds long) must be accurately grounded in diverse long-form videos that can last up to three hours.
• #### Critical role of backbone coordination in the mRNA recognition by RNA induced silencing complex

(Communications Biology, Springer Science and Business Media LLC, 2021-11-30) [Article]
AbstractDespite its functional importance, the molecular mechanism underlying target mRNA recognition by Argonaute (Ago) remains largely elusive. Based on extensive all-atom molecular dynamics simulations, we constructed quasi-Markov State Model (qMSM) to reveal the dynamics during recognition at position 6-7 in the seed region of human Argonaute 2 (hAgo2). Interestingly, we found that the slowest mode of motion therein is not the gRNA-target base-pairing, but the coordination of the target phosphate groups with a set of positively charged residues of hAgo2. Moreover, the ability of Helix-7 to approach the PIWI and MID domains was found to reduce the effective volume accessible to the target mRNA and therefore facilitate both the backbone coordination and base-pair formation. Further mutant simulations revealed that alanine mutation of the D358 residue on Helix-7 enhanced a trap state to slow down the loading of target mRNA. Similar trap state was also observed when wobble pairs were introduced in g6 and g7, indicating the role of Helix-7 in suppressing non-canonical base-paring. Our study pointed to a general mechanism for mRNA recognition by eukaryotic Agos and demonstrated the promise of qMSM in investigating complex conformational changes of biomolecular systems.
• #### The large time profile for Hamilton–Jacobi–Bellman equations

(Mathematische Annalen, Springer Science and Business Media LLC, 2021-11-30) [Article]
Here, we study the large-time limit of viscosity solutions of the Cauchy problem for second-order Hamilton–Jacobi–Bellman equations with convex Hamiltonians in the torus. This large-time limit solves the corresponding stationary problem, sometimes called the ergodic problem. This problem, however, has multiple viscosity solutions and, thus, a key question is which of these solutions is selected by the limit. Here, we provide a representation for the viscosity solution to the Cauchy problem in terms of generalized holonomic measures. Then, we use this representation to characterize the large-time limit in terms of the initial data and generalized Mather measures. In addition, we establish various results on generalized Mather measures and duality theorems that are of independent interest.
• #### Micro/Nanopatterned Superhydrophobic Surfaces Fabrication for Biomolecules and Biomaterials Manipulation and Analysis

(Micromachines, MDPI AG, 2021-11-30) [Article]
Superhydrophobic surfaces display an extraordinary repulsion to water and water-based solutions. This effect emerges from the interplay of intrinsic hydrophobicity of the surface and its morphology. These surfaces have been established for a long time and have been studied for decades. The increasing interest in recent years has been focused towards applications in many different fields and, in particular, biomedical applications. In this paper, we review the progress achieved in the last years in the fabrication of regularly patterned superhydrophobic surfaces in many different materials and their exploitation for the manipulation and characterization of biomaterial, with particular emphasis on the issues affecting the yields of the fabrication processes and the quality of the manufactured devices.
• #### Ultrafast Aggregation-Induced Tunable Emission Enhancement in a Benzothiadiazole-Based Fluorescent Metal–Organic Framework Linker

(The Journal of Physical Chemistry B, American Chemical Society (ACS), 2021-11-30) [Article]
Aggregation-induced emission enhancement (AIEE) is a process recently exploited in solid-state materials and organic luminophores, and it is explained by tight-molecular packaging. However, solution-phase AIEE and its formation mechanism have not been widely explored. This work investigated AIEE phenomena in two donor–acceptor–donor-type benzodiazole-based molecules (the organic building block in metal–organic frameworks) with an acetylene and phenyl π-conjugated backbone tapered with a carboxylic acid group at either end. This was done using time-resolved electronic and vibrational spectroscopy in conjunction with time-dependent density functional theory (TD-DFT) calculations. Fluorescence up-conversion spectroscopy and time-correlated single-photon counting conclusively showed an intramolecular charge transfer-driven aggregate emission enhancement. This is shown by a red spectral shift of the emission spectra as well as an increase in the fluorescence lifetime from 746 ps at 1.0 × 10–11 to 2.48 ns at 2.0 × 10–3 M. The TD-DFT calculations showed that a restricted intramolecular rotation mechanism is responsible for the enhanced emission. The femtosecond infrared (IR) transient absorption results directly revealed the structural dynamics of aggregate formation, as evident from the evolution of the C≡C vibrational marker mode of the acetylene unit upon photoexcitation. Moreover, the IR data clearly indicated that the aggregation process occurred over a time scale of 10 ps, which is consistent with the fluorescence up-conversion results. Interestingly, time-resolved results and DFT calculations clearly demonstrated that both acetylene bonds and the sulfur atom are the key requirements to achieve such a controllable aggregation-induced fluorescence enhancement. The finding of the work not only shows how slight changes in the chemical structure of fluorescent chromophores could make a tremendous change in their optical behavior but also prompts a surge of research into a profound understanding of the mechanistic origins of this phenomenon. This may lead to the discovery of new chemical strategies that aim to synthesize novel chromophores with excellent optical properties for light-harvesting applications.
• #### Noncatalytic Oxidative Coupling of Methane (OCM): Gas-Phase Reactions in a Jet Stirred Reactor (JSR)

(ACS Omega, American Chemical Society (ACS), 2021-11-30) [Article]
Oxidative coupling of methane (OCM) is a promising technique for converting methane to higher hydrocarbons in a single reactor. Catalytic OCM is known to proceed via both gas-phase and surface chemical reactions. It is essential to first implement an accurate gas-phase model and then to further develop comprehensive homogeneous–heterogeneous OCM reaction networks. In this work, OCM gas-phase kinetics using a jet-stirred reactor are studied in the absence of a catalyst and simulated using a 0-D reactor model. Experiments were conducted in OCM-relevant operating conditions under various temperatures, residence times, and inlet CH4/O2 ratios. Simulations of different gas-phase models related to methane oxidation were implemented and compared against the experimental data. Quantities of interest (QoI) and rate of production analyses on hydrocarbon products were also performed to evaluate the models. The gas-phase models taken from catalytic reaction networks could not adequately describe the experimental gas-phase performances. NUIGMech1.1 was selected as the most comprehensive model to describe the OCM gas-phase kinetics; it is recommended for further use as the gas-phase model for constructing homogeneous–heterogeneous reaction networks.