Engineering topics
Chen, Yu
Publications and source records attributed to Chen, Yu.
Obesity is associated with biliary tract cancer mortality and incidence: A pooled analysis of 21 cohort studies in the Asia Cohort Consortium
Abstract Body fatness is considered a probable risk factor for biliary tract cancer (BTC), whereas cholelithiasis is an established factor. Nevertheless, although obesity is an established risk factor for cholelithiasis, previous studies of the association of body mass index (BMI) and BTC did not take the effect of cholelithiasis fully into account. To better understand the effect of BMI on BTC, we conducted a pooled analysis using population‐based cohort studies in Asians. In total, 905 530 subjects from 21 cohort studies participating in the Asia Cohort Consortium were included. BMI was categorized into four groups: underweight (<18.5 kg/m 2 ); normal (18.5‐22.9 kg/m 2 ); overweight (23‐24.9 kg/m 2 ); and obese (25+ kg/m 2 ). The association between BMI and BTC incidence and mortality was assessed using hazard ratios (HR) and 95% confidence intervals (CIs) by Cox regression models with shared frailty. Mediation analysis was used to decompose the association into a direct and an indirect (mediated) effect. Compared to normal BMI, high BMI was associated with BTC mortality (HR 1.19 [CI 1.02‐1.38] for males, HR 1.30 [1.14‐1.49] for females). Cholelithiasis had significant interaction with BMI on BTC risk. BMI was associated with BTC risk directly and through cholelithiasis in females, whereas the association was unclear in males. When cholelithiasis was present, BMI was not associated with BTC death in either males or females. BMI was associated with BTC death among females without cholelithiasis. This study suggests BMI is associated with BTC mortality in Asians. Cholelithiasis appears to contribute to the association; and moreover, obesity appears to increase BTC risk without cholelithiasis.
Exploring diverse reactive warheads for the design of SARS-CoV-2 main protease inhibitors
Not provided.
Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures
Abstract DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.
Mechanical properties of heterogeneous metallic glasses: Insights from brick-and-mortar designs
The brick-and-mortar architectural paradigm is commonly applied in structural design to achieve an exceptional combination of strength and plasticity due to its highly tunable mechanical attributes. This study applies molecular dynamics simulations of tensile loading to investigate the mechanical properties and failure mechanisms of brick-and-mortar metallic glasses (BMMGs). The focus is primarily on the implications of the aspect ratio of the bricks and interlayer thickness on the strength, plasticity, and deformation mechanisms. Results indicate that the failure mode is typified by multiple shear bands localized within the softer mortar regions, creating a staggered network under smaller aspect ratios that significantly enhances plastic deformation. However, a transition to a single dominant SB occurs when the aspect ratio exceeds 4.1. In addition, results indicate that a concurrent improvement in strength and plasticity can be achieved by modulating the distance between brick layers in BMMGs. This enhancement originates from the extensive generation and interaction of shear transformation zones. Furthermore, this study highlights that a desirable balance between strength and plasticity can be obtained in BMMGs with appropriate brick aspect ratios and interlayer thicknesses, providing a potential design strategy for the advancement of novel metallic glasses with superior properties.
Assessing Thermodynamic Selectivity of Solid-State Reactions for the Predictive Synthesis of Inorganic Materials
Not Available
Activation of human STING by a molecular glue-like compound
Stimulator of interferon genes (STING) is a dimeric transmembrane adapter protein that plays a key role in the human innate immune response to infection and has been therapeutically exploited for its antitumor activity. The activation of STING requires its high-order oligomerization, which could be induced by binding of the endogenous ligand, cGAMP, to the cytosolic ligand-binding domain. Here we report the discovery through functional screens of a class of compounds, named NVS-STGs, that activate human STING. Our cryo-EM structures show that NVS-STG2 induces the high-order oligomerization of human STING by binding to a pocket between the transmembrane domains of the neighboring STING dimers, effectively acting as a molecular glue. Our functional assays showed that NVS-STG2 could elicit potent STING-mediated immune responses in cells and antitumor activities in animal models.
Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures
DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, in this study, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.
Structure-based design of nanobodies that inhibit seeding of Alzheimer’s patient–extracted tau fibrils
Despite much effort, antibody therapies for Alzheimer’s disease (AD) have shown limited efficacy. Challenges to the rational design of effective antibodies include the difficulty of achieving specific affinity to critical targets, poor expression, and antibody aggregation caused by buried charges and unstructured loops. To overcome these challenges, we grafted previously determined sequences of fibril-capping amyloid inhibitors onto a camel heavy chain antibody scaffold. These sequences were designed to cap fibrils of tau, known to form the neurofibrillary tangles of AD, thereby preventing fibril elongation. The nanobodies grafted with capping inhibitors blocked tau aggregation in biosensor cells seeded with postmortem brain extracts from AD and progressive supranuclear palsy (PSP) patients. The tau capping nanobody inhibitors also blocked seeding by recombinant tau oligomers. Another challenge to the design of effective antibodies is their poor blood–brain barrier (BBB) penetration. In this study, we also designed a bispecific nanobody composed of a nanobody that targets a receptor on the BBB and a tau capping nanobody inhibitor, conjoined by a flexible linker. We provide evidence that the bispecific nanobody improved BBB penetration over the tau capping inhibitor alone after intravenous administration in mice. Our results suggest that the design of synthetic antibodies that target sequences that drive protein aggregation may be a promising approach to inhibit the prion-like seeding of tau and other proteins involved in AD and related proteinopathies.
Predictive scale-bridging simulations through active learning
Throughout computational science, there is a growing need to utilize the continual improvements in raw computational horsepower to achieve greater physical fidelity through scale-bridging over brute-force increases in the number of mesh elements. For instance, quantitative predictions of transport in nanoporous media, critical to hydrocarbon extraction from tight shale formations, are impossible without accounting for molecular-level interactions. Similarly, inertial confinement fusion simulations rely on numerical diffusion to simulate molecular effects such as non-local transport and mixing without truly accounting for molecular interactions. With these two disparate applications in mind, we develop a novel capability which uses an active learning approach to optimize the use of local fine-scale simulations for informing coarse-scale hydrodynamics. Our approach addresses three challenges: forecasting continuum coarse-scale trajectory to speculatively execute new fine-scale molecular dynamics calculations, dynamically updating coarse-scale from fine-scale calculations, and quantifying uncertainty in neural network models.
Tuning of the magnetotransport properties of a spin-polarized 2D electron system using visible light
We report on the effects of visible light on the low temperature electronic properties of the spin-polarized two dimensional electron system (2DES) formed at the interfaces between LaAlO 3 , EuTiO 3 and (001) SrTiO 3 . A strong, persistent modulation of both longitudinal and transverse conductivity was obtained using light emitting diodes (LEDs) with emissions at different wavelengths in the visible spectrum range. In particular, Hall effect data show that visible light induces a non-volatile electron filling of bands with mainly 3 dxz,yz character, and at the same time an enhancement of the anomalous Hall effect associated to the magnetic properties of the system. Accordingly, a suppression of the weak-anti localization corrections to the magneto-conductance is found, which correlates with an enhancement of the spin-polarization and of the ferromagnetic character of 2DES. The results establish the LED-induced photo-doping as a viable route for the control of the ground state properties of artificial spin-polarized oxide 2DES.
Learning noise via dynamical decoupling of entangled qubits
Understanding noise in entangled systems is a prerequisite for developing scalable quantum computers. Here, we propose and apply multiqubit dynamical decoupling sequences that characterize noise during two-qubit gates. Furthermore, this noise is qualitatively different from the well-studied noise that leads to single-qubit dephasing; it simultaneously affects the two qubits, inducing fluctuations in their entangling parameter. In our superconducting system, the experimentally observed noise comes from coupler flux fluctuations and is observed to be non-Gaussian, leading to the stepwise decay of signals.
Development of the Safe and Broad‐Spectrum Aldehyde and Ketoamide Mpro inhibitors Derived from the Constrained α, γ‐AA Peptide Scaffold
Abstract SARS‐CoV‐2 is still wreaking havoc all over the world with surging morbidity and high mortality. The main protease (M pro ) is essential in the replication of SARS‐CoV‐2, enabling itself an active target for antiviral development. Herein, we reported the design and synthesis of a new class of peptidomimetics‐constrained α, γ‐AA peptides, based on which a series of aldehyde and ketoamide inhibitors of the M pro of SARS‐CoV‐2 were prepared. The lead compounds showed excellent inhibitory activity in the FRET‐based M pro enzymatic assay not only for the M pro of SARS‐CoV‐2 but also for SARS‐CoV and MERS‐CoV, along with HCoVs like HCoV‐OC43, HCoV‐229E, HCoV‐NL63 and HKU1. The X‐ray crystallographic results demonstrated that our compounds form a covalent bond with the catalytic Cys145. They also demonstrated effective antiviral activity against live SARS‐CoV‐2. Overall, the results suggest that α, γ‐AA peptide could be a promising molecular scaffold in designing novel M pro inhibitors of SARS‐CoV‐2 and other coronaviruses.
A reversible perovskite air electrode for active and durable oxygen reduction and evolution reactions via the A-site entropy engineering
The performance of reversible solid oxide electrochemical cells (R-SOECs) is largely hindered by the insufficient electroactivity and poor durability of the bifunctional air electrodes, where the oxygen reduction and evolution reactions (ORR and OER) occur. Here, we report our findings in boosting the electrochemical activity and durability of an air electrode with Pr 0.2 Ba 0.2 Sr 0.2 La 0.2 Ca 0.2 CoO 3-δ (PBSLCC) via an A-site entropy engineering. The PBSLCC electrode shows enhanced oxygen reaction activity and excellent durability compared to binary and ternary double perovskites (PrBaCo 2 O 5+δ and Pr 0.8 Ba 0.8 Ca 0.4 Co 2 O 5+δ , respectively). A low and nearly unchanged area-specific resistance of 0.042Ωcm 2 is achieved at 750 °C during the 225-h stability test. La 0.9 Sr 0.1 Ga 0.8 Mg 0.2 O 3-δ electrolyte-supported cells with the PBSLCC air electrode show remarkable performance at 800 °C, demonstrating a peak power density of 1.2Wcm -2 in the fuel cell mode, and a current density of -1.1 Acm -2 at 1.3 V in the electrolysis mode while maintaining the excellent cycling durability of 228 h at ±0.5 Acm -2 under humidified H 2 (10% H 2 O). A bulk oxygen p-band center model is applied to verify that tailoring of the A-site entropy strongly influences the surface exchange coefficients (k* chem ), leading to higher oxygen reaction activity of PBSLCC than the binary and ternary perovskites. Finally, this study opens a new class of high-entropy perovskites for the rational design of air electrodes for R-SOECs with high activity and durability.