The elastic transfer model of angular rate modulation in F1-ATPase stalling and controlled rotation experiments

2017 ◽  
Vol 31 (17) ◽  
pp. 1730002
Author(s):  
S. Volkán-Kacsó
Keyword(s):  
Single Molecule ◽  
Large Scale ◽  
Driving Forces ◽  
Angular Rate ◽  
Exponential Dependence ◽  
Transfer Model ◽  
Elastic Model ◽  
Group Transfer ◽  
Molecular Group ◽  
Rotor Angle

The recent experimental, theoretical and computational advances in the field of F1-ATPase single-molecule microscopy are briefly surveyed. The role of theory is revealed in the statistical analysis, interpretation and prediction of single-molecule experimental trajectories, and in linking them with atomistic simulations. In particular, a theoretical model of elastically coupled molecular group transfer is reviewed and a detailed method for its application in stalling and controlled rotation experiments is provided. It is shown how the model can predict, using previous experiments, the rates of ligand binding/release processes (steps) and their exponential dependence on rotor angle in these experiments. The concept of Brønsted slopes is reviewed in the context of the single-molecule experiments, and the rate versus rotor angle relations are explained using the elastic model. These experimental data are treated in terms of the effect of thermodynamic driving forces on the rates assuming that the rotor shaft is elastically coupled to stator ring subunits in which the steps occur. In the application of the group transfer model on an extended angular range processes leading up to the transfer are discussed. Implications for large-scale atomistic simulation are suggested for the treatment of torque-generating steps.

scholarly journals Theory for rates, equilibrium constants, and Brønsted slopes in F1-ATPase single molecule imaging experiments

2015 ◽  
Vol 112 (46) ◽  
pp. 14230-14235 ◽  
Author(s):  
Sándor Volkán-Kacsó ◽  
Rudolph A. Marcus
Keyword(s):  
Ligand Binding ◽  
Single Molecule ◽  
Driving Forces ◽  
Equilibrium Constants ◽  
Reaction Rates ◽  
Exponential Dependence ◽  
Single Molecule Imaging ◽  
Free Energies ◽  
Coupled Reactions ◽  
Stall Angle

A theoretical model of elastically coupled reactions is proposed for single molecule imaging and rotor manipulation experiments on F1-ATPase. Stalling experiments are considered in which rates of individual ligand binding, ligand release, and chemical reaction steps have an exponential dependence on rotor angle. These data are treated in terms of the effect of thermodynamic driving forces on reaction rates, and lead to equations relating rate constants and free energies to the stalling angle. These relations, in turn, are modeled using a formalism originally developed to treat electron and other transfer reactions. During stalling the free energy profile of the enzymatic steps is altered by a work term due to elastic structural twisting. Using biochemical and single molecule data, the dependence of the rate constant and equilibrium constant on the stall angle, as well as the Børnsted slope are predicted and compared with experiment. Reasonable agreement is found with stalling experiments for ATP and GTP binding. The model can be applied to other torque-generating steps of reversible ligand binding, such as ADP and Pi release, when sufficient data become available.

scholarly journals Theory of long binding events in single-molecule–controlled rotation experiments on F1-ATPase

2017 ◽  
Vol 114 (28) ◽  
pp. 7272-7277 ◽  
Author(s):  
Sándor Volkán-Kacsó ◽  
Rudolph A. Marcus
Keyword(s):  
Single Molecule ◽  
Rate Constants ◽  
Lifetime Distribution ◽  
Rate Data ◽  
Symmetric Form ◽  
Group Transfer ◽  
F1 Atpase ◽  
Binding Rate ◽  
Rotor Angle ◽  
Synthesis Reactions

The theory of elastic group transfer for the binding and release rate constants for nucleotides in F1-ATPase as a function of the rotor angle is further extended in several respects. (i) A method is described for predicting the experimentally observed lifetime distribution of long binding events in the controlled rotation experiments by taking into account the hydrolysis and synthesis reactions occurring during these events. (ii) A method is also given for treating the long binding events in the experiments and obtaining the rate constants for the hydrolysis and synthesis reactions occurring during these events. (iii) The theory in the previous paper is given in a symmetric form, an extension that simplifies the application of the theory to experiments. It also includes a theory-based correction of the reported “on” and “off” rates by calculating the missed events. A near symmetry of the data about the angle of −40° and a “turnover” in the binding rate data vs. rotor angle for angles greater than ∼40° is also discussed.

scholarly journals Heat Transfer in Rotating Serpentine Passages With Trips Normal to the Flow

1992 ◽  
Vol 114 (4) ◽  
pp. 847-857 ◽  
Author(s):  
J. H. Wagner ◽  
B. V. Johnson ◽  
R. A. Graziani ◽  
F. C. Yeh
Keyword(s):  
Heat Transfer ◽  
Turbine Blade ◽  
Large Scale ◽  
Flow Direction ◽  
Operating Conditions ◽  
Transfer Model ◽  
Transfer Coefficients ◽  
Flow Equations ◽  
Turbine Blade Cooling ◽  
Heat Transfer Coefficients

Experiments were conducted to determine the effects of buoyancy and Coriolis forces on heat transfer in turbine blade internal coolant passages. The experiments were conducted with a large-scale, multipass, heat transfer model with both radially inward and outward flow. Trip strips on the leading and trailing surfaces of the radial coolant passages were used to produce the rough walls. An analysis of the governing flow equations showed that four parameters influence the heat transfer in rotating passages: coolant-to-wall temperature ratio, Rossby number, Reynolds number, and radius-to-passage hydraulic diameter ratio. The first three of these four parameters were varied over ranges that are typical of advanced gas turbine engine operating conditions. Results were correlated and compared to previous results from stationary and rotating similar models with trip strips. The heat transfer coefficients on surfaces, where the heat transfer increased with rotation and buoyancy, varied by as much as a factor of four. Maximum values of the heat transfer coefficients with high rotation were only slightly above the highest levels obtained with the smooth wall model. The heat transfer coefficients on surfaces where the heat transfer decreased with rotation, varied by as much as a factor of three due to rotation and buoyancy. It was concluded that both Coriolis and buoyancy effects must be considered in turbine blade cooling designs with trip strips and that the effects of rotation were markedly different depending upon the flow direction.

scholarly journals Land Use Transition and Driving Forces in Chinese Loess Plateau: A Case Study from Pu County, Shanxi Province

Land ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 67
Author(s):  
Han Huang ◽  
Yang Zhou ◽  
Mingjie Qian ◽  
Zhaoqi Zeng
Keyword(s):  
Land Use ◽  
Food Security ◽  
Loess Plateau ◽  
Large Scale ◽  
Driving Forces ◽  
Chinese Loess Plateau ◽  
Shanxi Province ◽  
Forest Land ◽  
Land Use Transition ◽  
Macro Scale

Land use transition is essentially one of the manifestations of land use/cover change (LUCC). Although a large number of studies have focused on land use transitions on the macro scale, there are few studies on the micro scale. Based on the data of two high-resolution land use surveys, this study used a land use transfer matrix and GeoDetector model to explore the spatial-temporal patterns and driving forces of land use transitions at the village level in Pu County over a ten-year period. Results show that Pu County has experienced a drastic process of land use transition. More than 80% of cropland and grassland have been converted to forest land, and over 90% of the expansion of built-up land came from the occupation of forest land, cropland, and grassland. The driving forces of land use transition and its magnitude depended on the type of land use. The implementation of the policy of returning farmland to forest, or grain-for-green (GFG) was the main driving force for the large-scale conversion of cultivated land to forest land in Pu County. In the context of policy of returning farmland to forests, the hilly and gully regions of China’s Loess Plateau must balance between protecting the ecology and ensuring food security. Promoting the comprehensive consolidation of gully land and developing modern agriculture may be an important way to achieve a win-win goal of ecological protection and food security.

Study on Effective Radial Thermal Conductivity of Gas Flow through a Methanol Reactor

2015 ◽  
Vol 13 (1) ◽  
pp. 103-112 ◽  
Author(s):  
Kun Lei ◽  
Hongfang Ma ◽  
Haitao Zhang ◽  
Weiyong Ying ◽  
Dingye Fang
Keyword(s):  
Heat Transfer ◽  
Thermal Conductivity ◽  
Reynolds Number ◽  
Temperature Distribution ◽  
Large Scale ◽  
Gas Flow ◽  
Fixed Bed ◽  
Heat Transfer Model ◽  
Transfer Model ◽  
Particle Reynolds Number

Abstract The heat conduction performance of the methanol synthesis reactor is significant for the development of large-scale methanol production. The present work has measured the temperature distribution in the fixed bed at air volumetric flow rate 2.4–7 m3 · h−1, inlet air temperature 160–200°C and heating tube temperature 210–270°C. The effective radial thermal conductivity and effective wall heat transfer coefficient were derived based on the steady-state measurements and the two-dimensional heat transfer model. A correlation was proposed based on the experimental data, which related well the Nusselt number and the effective radial thermal conductivity to the particle Reynolds number ranging from 59.2 to 175.8. The heat transfer model combined with the correlation was used to calculate the temperature profiles. A comparison with the predicated temperature and the measurements was illustrated and the results showed that the predication agreed very well with the experimental results. All the absolute values of the relative errors were less than 10%, and the model was verified by experiments. Comparing the correlations of both this work with previously published showed that there are considerable discrepancies among them due to different experimental conditions. The influence of the particle Reynolds number on the temperature distribution inside the bed was also discussed and it was shown that improving particle Reynolds number contributed to enhance heat transfer in the fixed bed.

scholarly journals 3D DNA structural barcode copying and random access

2020 ◽  
Author(s):  
Filip Bošković ◽  
Alexander Ohmann ◽  
Ulrich F. Keyser ◽  
Kaikai Chen
Keyword(s):  
Data Storage ◽  
Single Molecule ◽  
Self Assembly ◽  
Large Scale ◽  
Three Dimensional ◽  
Random Access ◽  
Scale Production ◽  
Digital Information ◽  
Dna Nanostructures ◽  
Large Scale Production

AbstractThree-dimensional (3D) DNA nanostructures built via DNA self-assembly have established recent applications in multiplexed biosensing and storing digital information. However, a key challenge is that 3D DNA structures are not easily copied which is of vital importance for their large-scale production and for access to desired molecules by target-specific amplification. Here, we build 3D DNA structural barcodes and demonstrate the copying and random access of the barcodes from a library of molecules using a modified polymerase chain reaction (PCR). The 3D barcodes were assembled by annealing a single-stranded DNA scaffold with complementary short oligonucleotides containing 3D protrusions at defined locations. DNA nicks in these structures are ligated to facilitate barcode copying using PCR. To randomly access a target from a library of barcodes, we employ a non-complementary end in the DNA construct that serves as a barcode-specific primer template. Readout of the 3D DNA structural barcodes was performed with nanopore measurements. Our study provides a roadmap for convenient production of large quantities of self-assembled 3D DNA nanostructures. In addition, this strategy offers access to specific targets, a crucial capability for multiplexed single-molecule sensing and for DNA data storage.

scholarly journals Large-scale validation of SCIAMACHY reflectance in the ultraviolet

2005 ◽  
Vol 5 (2) ◽  
pp. 1771-1796 ◽  
Author(s):  
G. van Soest ◽  
L. G. Tilstra ◽  
P. Stammes
Keyword(s):  
Radiative Transfer ◽  
Validation Study ◽  
Large Scale ◽  
Scale Validation ◽  
Radiative Transfer Model ◽  
Transfer Model ◽  
Time Level ◽  
Standard Calibration ◽  
Level 1 ◽  
Reflectance Data

Abstract. In this paper we present an extensive validation of calibrated SCIAMACHY nadir reflectance in the UV (240–400 nm) by comparison with spectra calculated with a fast radiative transfer model. We use operationally delivered near-real-time level 1 data, processed with 5 standard calibration tools. A total of 9 months of data has been analysed. This is the first reflectance validation study incorporating such a large amount of data. It is shown that this method is a valuable tool for spotting spatial and temporal anomalies. We conclude that SCIAMACHY reflectance data in this wavelength range are stable over the investigated period. In addition, we show an example of an 10 anomaly in the data due to an error in the processing chain that could be detected by our comparison. This validation method could be extremely useful too for validation of other satellite spectrometers, such as OMI and GOME-2.

Increased frequency of Eurasian double jets linked to summer heat extremes in Europe

2021 ◽  
Author(s):  
Efi Rousi ◽  
Kai Kornhuber ◽  
Goratz Beobide Arsuaga ◽  
Fei Luo ◽  
Dim Coumou
Keyword(s):  
Zonal Wind ◽  
Large Scale ◽  
Driving Forces ◽  
Linear Regression Analysis ◽  
Reanalysis Data ◽  
Self Organizing Maps ◽  
Upper Troposphere ◽  
The North ◽  
Heat Extremes ◽  
Different Levels

<p>Persistent summer extremes, such as heatwaves and droughts, can have considerable impacts on nature and societies. There is evidence that weather persistence has increased in Europe over the past decades, in association to changes in atmosphere dynamics, but uncertainties remain and the driving forces are not yet well understood. </p><p>Particularly for Europe, the jet stream may affect surface weather significantly by modulating the North Atlantic storm tracks. Here, we examine the hypothesis that high-latitude warming and decreased westerlies in summer result in more double jets, consisting of two distinct maxima of the zonal wind in the upper troposphere, over the Eurasian sector. Previous work has shown that such double jet states are related to persistent blocking-like circulation in the mid-latitudes. </p><p>We adapt a dynamical perspective of heat extreme trends by looking at large scale circulation and in particular, changes in the zonal mean zonal wind in different levels of the upper troposphere. We define clusters of jet states with the use of Self-Organizing Maps and analyze their characteristics. We find an increase in frequency and persistence of a cluster of double jet states for the period 1979-2019 during July-August (in ERA5 reanalysis data). Those states are linked to increased surface temperature and more frequent heatwaves compared to climatology over western, central, and northern Europe. Significant positive double jet anomalies are found to be dominant in the days preceding and/or coinciding with some of the most intense historical heatwaves in Europe, such as those of 2003 and 2018. A linear regression analysis shows that the increase in frequency and persistence of double jet states may explain part of the strong upward trend in heat extremes over these European regions.</p>

Quantifying Intrinsic and Extrinsic Contributions to Elastic Anisotropy Observed in Seismic Tomography Models

2021 ◽  
Author(s):  
John Keith Magali ◽  
Thomas Bodin ◽  
Navid Hedjazian ◽  
Yanick Ricard ◽  
Yann Capdeville
Keyword(s):  
Seismic Tomography ◽  
Large Scale ◽  
Seismic Anisotropy ◽  
Texture Evolution ◽  
Scaling Law ◽  
Preferred Orientation ◽  
Elastic Model ◽  
Effective Anisotropy ◽  
Crystallographic Preferred Orientation ◽  
Radial Anisotropy

<p>Large-scale seismic anisotropy inferred from seismic observations has been loosely interpreted either in terms of intrinsic anisotropy due to Crystallographic Preferred Orientation (CPO) development of mantle minerals or extrinsic anisotropy due to rock-scale Shape Preferred Orientation (SPO). The coexistence of both contributions misconstrues the origins of seismic anisotropy observed in seismic tomography models. It is thus essential to discriminate CPO from SPO in the effective anisotropy of an upscaled/homogenized medium, that is, the best possible elastic model recovered using finite-frequency seismic data assuming perfect data coverage. In this work, we investigate the effects of upscaling an intrinsically-anisotropic and highly-heterogeneous Earth's mantle. The problem is applied to a 2-D marble cake model of the mantle with a binary composition in the presence of CPO obtained from a micro-mechanical model. We compute the long-wavelength effective equivalent of this mantle model using the 3D non-periodic elastic homogenization technique. Our numerical findings predict that overall, upscaling purely intrinsically anisotropic medium amounts to the convection-scale averaging of CPO. As a result, it always underestimates the anisotropy, and may only be overestimated due to the additive extrinsic anisotropy from SPO. Finally, we show analytically (in 1D) and numerically (in 2D) that the full effective radial anisotropy ξ<sup>*</sup> is approximately just the product of the effective intrinsic radial anisotropy ξ<sup>*</sup><sub>CPO</sub> and the extrinsic radial anisotropy ξ<sub>SPO</sub>:</p><p>ξ<sup>* </sup>= ξ<sup>*</sup><sub>CPO </sub>× ξ<sub>SPO</sub></p><p>Based on the above relation, it is imperative to homogenize a texture evolution model first before drawing interpretations from existing anisotropic tomography models. Such a scaling law can therefore be used as a constraint to better estimate the separate contributions of CPO and SPO from the effective anisotropy observed in tomographic models.</p>

Wavelength Division Multiplexed Passive Optical Networks

2010 ◽  
pp. 68-101
Author(s):  
Calvin C.K. Chan
Keyword(s):  
Optical Networks ◽  
Large Scale ◽  
Driving Forces ◽  
Optical Network ◽  
Access Network ◽  
High Capacity ◽  
Next Generation ◽  
Wavelength Division ◽  
Wavelength Division Multiplexed ◽  
Capacity Data

Wavelength division multiplexed passive optical network has emerged as a promising solution to support a robust and large-scale next generation optical access network. It offers high-capacity data delivery and flexible bandwidth provisioning to all subscribers, so as to meet the ever-increasing bandwidth requirements as well as the quality of service requirements of the next generation broadband access networks. The maturity and reduced cost of the WDM components available in the market are also among the major driving forces to enhance the feasibility and practicality of commercial deployment. In this chapter, the author will provide a comprehensive discussion on the basic principles and network architectures for WDM-PONs, as well as their various enabling technologies. Different feasible approaches to support the two-way transmission will be discussed. It is believed that WDM-PON is an attractive solution to realize fiber-to-the-home (FTTH) applications.

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