Faraday Discussions最新文献

{"title":"Molecular sandwich-based DNAzyme catalytic reaction towards transducing efficient nanopore electrical detection for antigen proteins","authors":"Lebing Wang, Shou Zhou, Yunjiao Wang, Yan Wang, Jing Li, Xiaohan Chen, Daming Zhou, Liyuan Liang, Bohua Yin, Youwen Zhang, Liang Wang","doi":"10.1039/d4fd00146j","DOIUrl":"https://doi.org/10.1039/d4fd00146j","url":null,"abstract":"Despite significant advances in nanopore nucleic acids sequencing and sensing, proteins detection remains challenging due to the complexity of inherent protein molecular properties (i.e., net charges, polarity, molecular conformation & dimension) and sophisticated environmental parameters (i.e., biofluids), resulting in unsatisfied electrical signal resolution for proteins detection such as poor accessibility, selectivity and sensitivity. The selection of an appropriate electroanalytical approach is strongly desired which should be capable of offering easily detectable and readable signals regarding proteins particularly depending on the practical application. Herein, a molecular sandwich-based DNAzyme catalytic reaction cooperated nanopore detecting approach was designed. Especially, this approach is given the easy use of Mg2+ catalyzed DNAzyme (10-23) toward nucleic acids digestion for efficient antigen protein examination. Its applicability within the proposed strategy operates by initial formation of a molecular sandwich containing capture antibody-antigen-detection antibody for efficiently entrapment of target proteins (herein taking HIV p24 antigen for example) and immobilized on magnetic beads surface. After that, the DNAzyme was linked to the detection antibody via biotin−streptavidin interaction. In the presence of Mg2+, DNAzyme catalytic reaction was triggered to digest nucleic acids substrates and release unique cleavage fragments as reporters capable of transducing easier detectable nucleic acids as substitute of complicated and difficulty-yielded protein signals, in a nanopore. Notably, experimental validation confirms the detecting stability and sensitivity for target antigen referenced with other antigen proteins, meanwhile demonstrates the detection efficacy in human serum environment at very low concentration (LoD ~1.24 pM). This DNAzyme cooperated nanopore electroanalytical approach denotes an advancement in protein examination, may benefit in vitro test of proteinic biomarkers for disease diagnosis and prognosis assessment.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141884833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Electrochemiluminescence microscopy for the investigation of peptides interactions within planar lipid membranes","authors":"Kaoru Hiramoto, Kosuke Ino, Ibuki Takahashi, Ayumi Hirano-Iwata, Hitoshi Shiku","doi":"10.1039/d4fd00137k","DOIUrl":"https://doi.org/10.1039/d4fd00137k","url":null,"abstract":"Understanding the interactions between lipid membranes and peptides is crucial for controlling bacterial and viral infections, and developing effective drugs. In this study, we proposed the use of electrochemiluminescence (ECL) microscopy in a solution of [Ru(bpy)<small>₃</small>]<small>²⁺</small> and tri-n-propylamine to monitor alterations in the lipid membranes due to peptide action. A planar artificial lipid membrane served as a model platform, and its surface was observed using ECL microscopy during exposure to melittin, a representative membrane lytic peptide. Upon exposure to melittin, the light-emitting process of the [Ru(bpy)<small>₃</small>]<small>²⁺</small>/tri-n-propylamine system through the lipid membrane exhibited complex changes, suggesting that stepwise peptide actions can be monitored through the system. Furthermore, wide-field imaging with ECL microscopy provided an effective means of elucidating the membrane surface at the submicron level and revealing heterogeneous changes upon exposure to melittin. This complemented the spatiotemporal information that could not be obtained using conventional electrochemical measurements","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141864346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Restoring translational symmetry in periodic all-orbital dynamical mean-field theory simulations.","authors":"Jiachen Li, Tianyu Zhu","doi":"10.1039/d4fd00068d","DOIUrl":"https://doi.org/10.1039/d4fd00068d","url":null,"abstract":"<p><p>Dynamical mean-field theory (DMFT) and its cluster extensions provide an efficient Green's function formalism to simulate spectral properties of periodic systems at the quantum many-body level. However, traditional cluster DMFT breaks translational invariance in solid-state materials, and the best strategy to capture non-local correlation effects within cluster DMFT remains elusive. In this work, we investigate the use of overlapping atom-centered impurity fragments in recently-developed <i>ab initio</i> all-orbital DMFT, where all local orbitals within the impurity are treated with high-level quantum chemistry impurity solvers. We demonstrate how the translational symmetry of the lattice self-energy can be restored by designing symmetry-adapted embedding problems, which results in an improved description of spectral functions in two-dimensional boron nitride monolayers and graphene at the levels of many-body perturbation theory (GW) and coupled-cluster theory. Furthermore, we study the convergence of self-energy and density of states as the embedding size is systematically expanded in one-shot and self-consistent DMFT calculations.</p>","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141791345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enzyme-modified Pt nanoelectrodes for glutamate detection","authors":"Peibo Xu, Henry David Jetmore, Ran Chen, Mei Shen","doi":"10.1039/d4fd00138a","DOIUrl":"https://doi.org/10.1039/d4fd00138a","url":null,"abstract":"We present here a glutamate oxidase (GluOx)-modified platinum (Pt) nanoelectrode with a planar geometry for glutamate detection. The Pt nanoelectrode was characterized using electrochemistry and scanning electron microscopy (SEM). The radius of the Pt nanoelectrode measured using SEM is ~210 nm. GluOx-modified Pt nanoelectrodes were generated by dip coating GluOx on the Pt nanoelectrode in a solution of 0.9% (wt%) bovine serum albumin (BSA), 0.126% (wt%) glutaraldehyde, and 100 U/mL GluOx. An increase in current was observed at +0.7 V vs. Ag/AgCl/1M KCl with adding increasing concentrations of glutamate. A two-sample t-test results showed that there is a significant difference for current at +0.7 V between the blank and the added lowest glutamate concentration, as well as between adjacent glutamate concentrations, confirming that the increase in current is related to the increased glutamate concentration. The experimental current-concentration curve of glutamate detection fitted well to the theoretical Michaelis-Menten curve. At the low concentration range (50 μM to 200 μM), a linear relationship between the current and glutamate concentration was observed. The Michaelis-Menten constants of Imax and Km were calculated to be 1.093 pA and 0.227 mM, respectively. Biosensor efficiency (the ratio of glutamate sensitivity to H2O2 sensitivity) is calculated to be 57.9%. Enzact (Imax /H2O2 sensitivity, an indicator of the amount of enzyme loaded on the electrode) of the GluOx-modified Pt nanoelectrode is 0.243 mM. We further compared the sensitivity of a GluOx-modified Pt nanoelectrode with a GluOx-modified carbon fiber microelectrode (7-μm diameter and a sensing length of ~350 μm). Glutamate detection on the GluOx-modified carbon fiber microelectrode fitted well to a Michaelis-Menten like response. Based on the fitting, the GluOx-modified carbon fiber microelectrode exhibited an Imax of 0.689 nA and a Km of 301.2 μM towards glutamate detection. The best linear range of glutamate detection on the GluOx-modified carbon fiber microelectrode is from 50 μM to 150 μM Glutamate. GluOx-modified carbon fiber microelectrode exhibited a higher potential requirement for glutamate detection comparing to the GluOx-modified Pt nanoelectrode.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141864348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Web-BO: Towards increased accessibility of Bayesian optimisation (BO) for chemistry","authors":"Austin Mroz, Piotr N Toka, Antonio Del Rio Chanona, Kim E. Jelfs","doi":"10.1039/d4fd00109e","DOIUrl":"https://doi.org/10.1039/d4fd00109e","url":null,"abstract":"Historically, the chemical discovery process has predominantly been a matter of trial-and-improvement, where small modifications are made to a chemical system, guided by chemical knowledge, with the aim of optimising towards a target property or combination of properties. While a trial-and-improvement approach is frequently successful, especially when assisted by the help of serendipity, the approach is incredibly time- and resource-intensive. Complicating this further, the available chemical space that could, in theory, be explored is remarkably vast. As we are faced with near infinite possibilities and limited resources, we require improved search methods to effectively move towards desired optima, e.g. chemical systems exhibiting a target property, or several desired properties. Bayesian optimisation (BO) has recently gained significant traction in chemistry, where within the BO framework, prior knowledge is used to inform and guide the search process to optimise towards desired chemical targets, e.g. optimal reaction conditions to maximise yield, or optimal catalyst exhibiting improved catalytic activity. While powerful, implementing BO algorithms in practice is largely limited to interfacing via various APIs – requiring advanced coding experience and bespoke scripts for each optimisation task. Further, it is challenging to seamlessly link these with electronic lab notebooks via a graphical user interface (GUI). Ultimately, this limits the accessibility of BO algorithms. Here, we present Web-BO, a GUI to support BO for chemical optimisation tasks. We demonstrate its performance using an open source dataset and associated emulator, and link the platform with an existing electronic lab notebook, datalab. By providing a GUI-based BO service, we hope to improve the accessibility of data-driven optimisation tools in chemistry; https://suprashare.rcs.ic.ac.uk/web-bo/.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141864347","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Micropore Nanoband Electrode Array for Enhanced Electrochemical Generation/Analysis in Flow Systems","authors":"Fiona Moore, Ilka Schmueser, Jonathan G Terry, Andrew R Mount","doi":"10.1039/d4fd00125g","DOIUrl":"https://doi.org/10.1039/d4fd00125g","url":null,"abstract":"Our previous work has established that micron resolution photolithography can be employed to make microsquare nanoband edge electrode (MNEE) arrays. The MNEE configuration enables systematic control of the parameters (electrode number, cavity array spacing, and nanoelectrode dimensions and placement) which control geometry, conferring consistent high-fidelity electrode response across the array (e.g. high signal, high signal-to-noise, low limits of detection and fast, steady-state, reproducible and quantitative response) and allowing the tuning of individual and combined electrode interactions. Building on this, in this paper we now produce and characterise a Micropore Nanoband Electrode (MNE) Array designed for flow-through detection, where an MNEE edge electrode configuration is used to form a nanotube electrode embedded in the wall of each micropore, formed as an array of pores of controlled pore size and placement through an insulating membrane of sub-micrometer thickness. The success of this approach is established by the close correspondence between experiment and simulation and the enhanced and quantitative detection of redox species flowing through the micropores over the very wide range of flow rates relevant e.g. to (bio)sensing and chromatography. Quantitative electrochemical reaction with low conversion, suitable for analysis, is demonstrated at high flow, whilst quantitative electrochemical reaction with high conversion, suitable for electrochemical product generation, is enabled at lower flow. The fundamental array response is analysed in terms of established flow theories, demonstrating the additive contributions of within pore enhanced diffusional (nanoband edge) and advective (Levich-type) currents, the control of the degree of diffusional overlap between pores through pore spacing and flow rate, the control by design across length scales ranging from nanometer through micrometer to a centimetre array and the ready determination of physicochemical parameters, enabling discussion of the potential of this breakthrough technology to addresses unmet needs in generation and analysis.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774438","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Tiled unitary product states for strongly correlated Hamiltonians.","authors":"Hugh G A Burton","doi":"10.1039/d4fd00064a","DOIUrl":"https://doi.org/10.1039/d4fd00064a","url":null,"abstract":"<p><p>Approximating the electronic wave function for strongly correlated systems remains a major theoretical challenge. Emerging quantum computers can enable new types of wave-function ansatz to be considered, with the potential to overcome the exponential memory storage for strong correlation. I have recently introduced the tiled Unitary Product States (tUPS) ansatz, which successfully combines the preservation of particle-number and spin symmetry with shallow quantum circuits and local qubit connectivity [H. G. A. Burton, <i>Phys. Rev. Res.</i>, 2024, <b>6</b>, 023300]. In this contribution, I investigate the accuracy of this tUPS hierarchy for strongly-correlated Hamiltonians. I consider the picket-fence pairing Hamiltonian and the two-dimensional Hubbard lattice, which collectively describe a range of strong correlation mechanisms found in molecules. Numerical results demonstrate that highly accurate energies can be achieved with a compact approximation for both weak and strong correlation in the Hubbard model, and the repulsive pairing regime. These data provide valuable insights into the applicability of the tUPS hierarchy for strong electron correlation.</p>","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.3,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141755712","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Discovery of highly anisotropic dielectric crystals with equivariant graph neural networks","authors":"Yuchen Lou, Alex M Ganose","doi":"10.1039/d4fd00096j","DOIUrl":"https://doi.org/10.1039/d4fd00096j","url":null,"abstract":"Anisotropy in crystals plays a pivotal role in many technological applications. For example, anisotropic electronic and thermal transport are thought to be beneficial for thermoelectric applications, while anisotropic mechanical properties are of interest for emerging metamaterials, and anisotropic dielectric materials have been suggested as a novel platform for dark matter detection. Understanding and tailoring anisotropy in crystals is therefore essential for the design of next-generation functional materials. To date, however, most data-driven approaches have focused on the prediction of scalar crystal properties, such as the spherically averaged dielectric tensor or the bulk and shear elastic moduli. Here, we adopt the latest approaches in equivariant graph neural networks to develop a model that can predict the full dielectric tensor of crystals. Our model, trained on the Materials Project dataset of c.a.~6,700 dielectric tensors, achieves state-of-the-art accuracy in scalar dielectric prediction in addition to capturing the directional response. We showcase the performance of the model by discovering crystals with almost isotropic connectivity but highly anisotropic dielectric tensors, thereby broadening our knowledge of the structure-property relationships in dielectric crystals.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774441","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ion Current Oscillation with Polyelectrolyte Modified Micropipettes","authors":"Tianyi Xiong, Wenjie Ma, Ping Yu","doi":"10.1039/d4fd00135d","DOIUrl":"https://doi.org/10.1039/d4fd00135d","url":null,"abstract":"Here, we report for the first time that ion current oscillation (ICO) with periodic amplitude and frequency can autonomously occur at polyimidazole brush (PvimB) modified pipettes in an asymmetric solution with pH gradient (e.g. pH 6.0/pH 8.0). Experimental results demonstrated that under a strong bias voltage, the proton responsible PvimB modified pipettes exhibited significant current switching behavior under negative bias voltages, which contributed to periodic oscillating ion current under constant biases. Based on this dynamic, the frequency and amplitude of the ICO phenomenon were regulated by adjusting the pH gradient in the asymmetric solution. ICO under different bias voltages were further explored to show the voltage-dependent nature of this phenomenon. This observation of ICO phenomena offers a new strategy that designing iontronic devices with dynamic conductivity changes induced by surface chemical interactions in spatial confinements.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141774440","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Accurate predictions of Chemical Shifts with the rSCAN and r2SCAN mGGA exchange-correlation functionals","authors":"Jonathan Robert Yates, Albert P. Bartók","doi":"10.1039/d4fd00142g","DOIUrl":"https://doi.org/10.1039/d4fd00142g","url":null,"abstract":"We benchmark the rSCAN and r2SCAN exchange-correlation functionals by comparing the Nuclear Magnetic Resonance magnetic shieldings predicted by Density Functional Theory to experimentally observed chemical shifts of halide and oxide inorganic compounds. Significant improvement in accuracy is achieved compared to the Generalised Gradient Approximation at a marginally higher computational cost. When using rSCAN or r2SCAN, the correlation coefficient between computationally predicted and experimental values approaches the theoretically expected value of -1 while reducing the deviation, allowing more accurate and reliable spectrum assignments of complex compounds in experimental investigations.","PeriodicalId":76,"journal":{"name":"Faraday Discussions","volume":null,"pages":null},"PeriodicalIF":3.4,"publicationDate":"2024-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141785205","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}