scholarly journals Tracking interfacial single-molecule pH and binding dynamics via vibrational spectroscopy

2021 ◽  
Vol 7 (23) ◽  
pp. eabg1790
Author(s):  
Junyang Huang ◽  
David-Benjamin Grys ◽  
Jack Griffiths ◽  
Bart de Nijs ◽  
Marlous Kamp ◽  
...  
Keyword(s):  
Vibrational Spectroscopy ◽  
Single Molecule ◽  
High Speed ◽  
Reaction Pathways ◽  
Optical Manipulation ◽  
Critical Importance ◽  
Ambient Conditions ◽  
Protonation State ◽  
Discrete States ◽  
Direct Tracking

Understanding single-molecule chemical dynamics of surface ligands is of critical importance to reveal their individual pathways and, hence, roles in catalysis, which ensemble measurements cannot see. Here, we use a cascaded nano-optics approach that provides sufficient enhancement to enable direct tracking of chemical trajectories of single surface-bound molecules via vibrational spectroscopy. Atomic protrusions are laser-induced within plasmonic nanojunctions to concentrate light to atomic length scales, optically isolating individual molecules. By stabilizing these atomic sites, we unveil single-molecule deprotonation and binding dynamics under ambient conditions. High-speed field-enhanced spectroscopy allows us to monitor chemical switching of a single carboxylic group between three discrete states. Combining this with theoretical calculation identifies reversible proton transfer dynamics (yielding effective single-molecule pH) and switching between molecule-metal coordination states, where the exact chemical pathway depends on the intitial protonation state. These findings open new domains to explore interfacial single-molecule mechanisms and optical manipulation of their reaction pathways.

scholarly journals Exploring Reaction Pathways of Single-Molecule Interactions through the Manipulation and Tracking of a Potential-Confined Microsphere in Three Dimensions

2003 ◽  
Vol 790 ◽  
Author(s):  
Wesley P. Wong ◽  
Volkmar Heinrich ◽  
Evan Evans
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Molecular Motors ◽  
High Speed ◽  
Three Dimensions ◽  
Dynamics Simulation ◽  
Reaction Pathways ◽  
Dynamic Force ◽  
Brownian Dynamics Simulation ◽  
3D Motion

ABSTRACTWeak non-covalent interactions between single molecules govern many aspects of microscopic biological structure and function, e.g. cell adhesion, protein folding, molecular motors and mechanical enzymes. The dynamics of a weak biomolecular bond are suitably characterized by the kinetic transport of molecular states over an effective energy landscape defined along one or more optimal reaction pathways. Motivated by earlier developments [1,2], we present a novel method to quantify subtle features of weak chemical transitions by analyzing the 3D Brownian fluctuations of a functionalized microsphere held near a reactive substrate. A weak optical-trapping potential is used to confine motion of the bead to a nanoscale domain, and to apply a controlled bias field to the interaction. Stochastic interruptions in the monitored bead dynamics report formation and release of single molecular bonds. In addition, variations in the motion of a bead linked to the substrate via a biomolecule (a protein or nucleic acid) signal conformational changes in the molecule, such as the folding/unfolding of protein domains or the unzipping of DNA. Thus, energy landscapes of complex biomolecular interactions are mapped by identifying distinct fluctuation regimes in the 3D motion of a test microsphere, and by quantifying the rates of transition between these regimes as mediated by the applied confining potential.The 3D motion of the bead is tracked using a reflection interference technique combined with high-speed video microscopy. The position of the bead is measured over 100 times per second with a lateral resolution of ∼3–5 nm and a vertical resolution of ∼1–2 nm. Crucial to the interpretation of results, a Brownian Dynamics simulation has been developed to relate the statistics of bead displacements to molecular-scale kinetics of chemical interactions and structural transitions. The experimental approach is designed to enlarge the scope of current techniques (e.g. dynamic force spectroscopy [3]) to encompass near-equilibrium forward/reverse transitions of weak-complex interactions with multiple binding configurations and more than one transition pathway.

scholarly journals Single-molecule imaging of DNA gyrase activity in livingEscherichia coli

2018 ◽  
Author(s):  
Mathew Stracy ◽  
Adam J.M. Wollman ◽  
Elzbieta Kaja ◽  
Jacek Gapinski ◽  
Ji-Eun Lee ◽  
...  
Keyword(s):  
Single Molecule ◽  
High Speed ◽  
Replication Fork ◽  
Dna Gyrase ◽  
Chromosomal Dna ◽  
Replication Fork Progression ◽  
Dna Strands ◽  
Steady State Levels ◽  
Negative Supercoiling ◽  
Supercoil Relaxation

ABSTRACTBacterial DNA gyrase introduces negative supercoils into chromosomal DNA and relaxes positive supercoils introduced by replication and transiently by transcription. Removal of these positive supercoils is essential for replication fork progression and for the overall unlinking of the two duplex DNA strands, as well as for ongoing transcription. To address how gyrase copes with these topological challenges, we used high-speed single-molecule fluorescence imaging in liveEscherichia colicells. We demonstrate that at least 300 gyrase molecules are stably bound to the chromosome at any time, with ∼12 enzymes enriched near each replication fork. Trapping of reaction intermediates with ciprofloxacin revealed complexes undergoing catalysis. Dwell times of ∼2 s were observed for the dispersed gyrase molecules, which we propose maintain steady-state levels of negative supercoiling of the chromosome. In contrast, the dwell time of replisome-proximal molecules was ∼8 s, consistent with these catalyzing processive positive supercoil relaxation in front of the progressing replisome.

scholarly journals Plasma Catalytic Conversion of CH4 to Alkanes, Olefins and H2 in a Packed Bed DBD Reactor

Processes ◽  
2020 ◽  
Vol 8 (7) ◽  
pp. 774
Author(s):  
Mohammadreza Taheraslani ◽  
Han Gardeniers
Keyword(s):  
Barrier Discharge ◽  
Plasma Reactor ◽  
Packed Bed ◽  
Reaction Pathways ◽  
Ambient Conditions ◽  
Alumina Catalyst ◽  
Dbd Plasma ◽  
Hydrogenation Reactions ◽  
Notable Increase

Methane is activated at ambient conditions in a dielectric barrier discharge (DBD) plasma reactor packed with Pd/γ-alumina catalyst containing different loadings of Pd (0.5, 1, 5 wt%). Results indicate that the presence of Pd on γ-alumina substantially abates the formation of deposits, leads to a notable increase in the production of alkanes and olefins and additionally improves the energy efficiency compared to those obtained for the non-packed reactor and the bare γ-alumina packed reactor. A low amount of Pd (0.5 and 1 wt%) favors achieving a higher production of olefins (mainly C2H4 and C3H6) and a higher yield of H2. Increasing Pd loading to 5 wt% promotes the interaction of H2 and olefins, which consequently intensifies the successive hydrogenation of unsaturated compounds, thus incurring a higher production of alkanes (mainly C2H6 and C3H8). The substantial abatement of the deposits is ascribed to the role of Palladium in moderating the strength of the electric and shifting the reaction pathways, in the way that hydrogenation reactions of deposits’ precursors become faster than their deposition on the catalyst.

scholarly journals Experimental and Mathematical Tools to Predict Droplet Size and Velocity Distribution for a Two-Fluid Nozzle

Fluids ◽  
2020 ◽  
Vol 5 (4) ◽  
pp. 231
Author(s):  
Sadegh Poozesh ◽  
Nelson K. Akafuah ◽  
Heather R. Campbell ◽  
Faezeh Bashiri ◽  
Kozo Saito
Keyword(s):  
Droplet Size ◽  
High Speed ◽  
Droplet Size Distribution ◽  
Integral Form ◽  
Accurate Estimation ◽  
Ambient Conditions ◽  
Computational Tools ◽  
Model Predictions ◽  
Model Fluids ◽  
Two Fluid

Despite progress in laser-based and computational tools, an accessible model that relies on fundamentals and offers a reasonably accurate estimation of droplet size and velocity is lacking, primarily due to entangled complex breakup mechanisms. Therefore, this study aims at using the integral form of the conservation equations to create a system of equations by solving which, the far-field secondary atomization can be analyzed through predicting droplet size and velocity distributions of the involved phases. To validate the model predictions, experiments are conducted at ambient conditions using water, methanol, and acetone as model fluids with varying formulation properties, such as density, viscosity, and surface tension. Droplet size distribution and velocity are measured with laser diffraction and a high-speed camera, respectively. Finally, an attempt is made to utilize non-scaled parameters to characterize the atomization process, useful for extrapolating the sensitivity analysis to other scales. The merit of this model lies in its simplicity for use in process control and optimization.

Assessment of engine combustion network recommendations for measurement of ignition and lift-off length

2020 ◽  
pp. 146808742092264
Author(s):  
Boni F Yraguen ◽  
Farzad Poursadegh ◽  
Caroline L Genzale
Keyword(s):  
Ignition Delay ◽  
High Speed ◽  
Operating Conditions ◽  
Bias Error ◽  
Ambient Conditions ◽  
Intensity Histogram ◽  
Wide Range ◽  
Engine Combustion ◽  
Length Measurements ◽  
Lift Off

The engine combustion network recommends two different imaging-based diagnostics for the measurement of diesel spray ignition delay and lift-off length, respectively. To measure ignition delay, high-speed imaging of broadband luminosity, spectrally filtered to limit collected wavelengths below 600 nm, is recommended. This diagnostic is often referred to as broadband natural luminosity. For lift-off length measurements, the engine combustion network recommends imaging of OH* chemiluminescence. This diagnostic requires using an image-intensified camera to detect narrowly filtered light around 310 nm. Alternatively, it has been shown that the lift-off length can be measured using broadband natural luminosity, avoiding the need for an intensifier and ultraviolet-transmitting optics. However, care is needed in the collection and processing of this diagnostic to accurately isolate the chemiluminescence signal. Particularly, standard intensity thresholding techniques are not sufficient for isolating the chemiluminescence signal in broadband natural luminosity images. Thus, an intensity-histogram-based thresholding method is introduced. This article assesses the feasibility and practicality of measuring lift-off length using broadband natural luminosity using a detailed comparison to OH* chemiluminescence measurements. It is shown that lift-off length measurements using broadband natural luminosity are prone to user bias error in the optical setup and data processing, especially under moderate- to high-sooting conditions. We conclude that while OH* imaging provides the most reliable and accurate measurement of lift-off length at a wide range of ambient conditions, an intensity-histogram analysis can help discriminate the high-temperature chemiluminescence signal from others in a broadband natural luminosity image at higher-sooting operating conditions than demonstrated in current literature.

scholarly journals High-Speed Single-Molecule Tracking of CXCL13 in the B-Follicle

2018 ◽  
Vol 9 ◽  
Author(s):  
Helen Miller ◽  
Jason Cosgrove ◽  
Adam J. M. Wollman ◽  
Emily Taylor ◽  
Zhaokun Zhou ◽  
...  
Keyword(s):  
Single Molecule ◽  
High Speed ◽  
Single Molecule Tracking
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