scholarly journals Exploring biomolecular machines: energy landscape control of biological reactions

2006 ◽  
Vol 361 (1472) ◽  
pp. 1439-1443 ◽  
Author(s):  
José N Onuchic ◽  
Chigusa Kobayashi ◽  
Osamu Miyashita ◽  
Patricia Jennings ◽  
Kim K Baldridge
Keyword(s):  
Large Scale ◽  
Thermal Fluctuations ◽  
Destructive Interference ◽  
Electron Tunnelling ◽  
Protein Functions ◽  
Partial Unfolding ◽  
Pathway Models ◽  
Scale Motion ◽  
Landscape Control ◽  
Franck Condon

For almost 15 years, our Pathway model has been the most powerful model in terms of predicting the tunnelling mechanism for electron transfer (ET) in biological systems, particularly proteins. Going beyond the conventional Pathway models, we have generalized our method to understand how protein dynamics modulate not only the Franck–Condon factor, but also the tunnelling matrix element. We have demonstrated that when interference among pathways modulates the electron tunnelling interactions in proteins (particularly destructive interference), dynamical effects are of critical importance. Tunnelling can be controlled by protein conformations that lie far from equilibrium—those that minimize the effect of destructive interference during tunnelling, for example. In the opposite regime, electron tunnelling is mediated by one (or a few) constructively interfering pathway tubes and dynamical effects are modest. This new mechanism for dynamical modulation of the ET rate has been able to explain and/or predict several rates that were later confirmed by experiment. However, thermal fluctuations can also affect these molecular machines in many other ways. For example, we show how global transformations, which control protein functions such as allostery, may involve large-scale motion and possibly partial unfolding during the reaction event.

Large-scale Motion of Solar Filaments

2000 ◽  
Vol 179 ◽  
pp. 205-208
Author(s):  
Pavel Ambrož ◽  
Alfred Schroll
Keyword(s):  
Magnetic Flux ◽  
Proper Motion ◽  
Time Scale ◽  
Large Scale ◽  
Accuracy Of Measurements ◽  
Solar Filaments ◽  
General Movement ◽  
Scale Motion ◽  
Velocity Scatter

AbstractPrecise measurements of heliographic position of solar filaments were used for determination of the proper motion of solar filaments on the time-scale of days. The filaments have a tendency to make a shaking or waving of the external structure and to make a general movement of whole filament body, coinciding with the transport of the magnetic flux in the photosphere. The velocity scatter of individual measured points is about one order higher than the accuracy of measurements.

scholarly journals Interaction of Very Large Scale Motion of Coherent Structures with Sediment Particle Exposure

Water ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 248
Author(s):  
Sencer Yücesan ◽  
Daniel Wildt ◽  
Philipp Gmeiner ◽  
Johannes Schobesberger ◽  
Christoph Hauer ◽  
...  
Keyword(s):  
Coherent Structures ◽  
Large Scale ◽  
Numerical Study ◽  
Local Maximum ◽  
Wave Number ◽  
Exposure Level ◽  
Sediment Particle ◽  
High Wave Number ◽  
Large Scale Motion ◽  
Scale Motion

A systematic variation of the exposure level of a spherical particle in an array of multiple spheres in a high Reynolds number turbulent open-channel flow regime was investigated while using the Large Eddy Simulation method. Our numerical study analysed hydrodynamic conditions of a sediment particle based on three different channel configurations, from full exposure to zero exposure level. Premultiplied spectrum analysis revealed that the effect of very-large-scale motion of coherent structures on the lift force on a fully exposed particle resulted in a bi-modal distribution with a weak low wave number and a local maximum of a high wave number. Lower exposure levels were found to exhibit a uni-modal distribution.

Squidball: An Experiment in Large-Scale Motion Capture and Game Design

2005 ◽  
pp. 23-33 ◽  
Author(s):  
Christoph Bregler ◽  
Clothilde Castiglia ◽  
Jessica DeVincezo ◽  
Roger Luke DuBois ◽  
Kevin Feeley ◽  
...  
Keyword(s):  
Motion Capture ◽  
Game Design ◽  
Large Scale ◽  
Large Scale Motion ◽  
Scale Motion

Large-scale motion in the intermittent region of a turbulent boundary layer

1970 ◽  
Vol 41 (2) ◽  
pp. 283-325 ◽  
Author(s):  
Leslie S. G. Kovasznay ◽  
Valdis Kibens ◽  
Ron F. Blackwelder
Keyword(s):  
Boundary Layer ◽  
Turbulent Boundary Layer ◽  
Large Scale ◽  
Cross Correlation ◽  
Turbulent Regime ◽  
Conditional Sampling ◽  
Correlation Data ◽  
Measuring Techniques ◽  
Conditional Averaging ◽  
Scale Motion

The outer intermittent region of a fully developed turbulent boundary layer with zero pressure gradient was extensively explored in the hope of shedding some light on the shape and motion of the interface separating the turbulent and non-turbulent regions as well as on the nature of the related large-scale eddies within the turbulent regime. Novel measuring techniques were devised, such as conditional sampling and conditional averaging, and others were turned to new uses, such as reorganizing in map form the space-time auto- and cross-correlation data involving both the U and V velocity components as well as I, the intermittency function. On the basis of the new experimental results, a conceptual model for the development of the interface and for the entrainment of new fluid is proposed.

scholarly journals Deciphering and engineering chromodomain-methyllysine peptide recognition

2018 ◽  
Vol 4 (11) ◽  
pp. eaau1447 ◽  
Author(s):  
Ryan Hard ◽  
Nan Li ◽  
Wei He ◽  
Brian Ross ◽  
Gary C. H. Mo ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Posttranslational Modifications ◽  
Large Scale ◽  
Regulation Of Gene Expression ◽  
Live Cells ◽  
Lysine Methylation ◽  
Dynamic Regulation ◽  
Peptide Recognition ◽  
Protein Functions ◽  
Domain Peptide

Posttranslational modifications (PTMs) play critical roles in regulating protein functions and mediating protein-protein interactions. An important PTM is lysine methylation that orchestrates chromatin modifications and regulates functions of non-histone proteins. Methyllysine peptides are bound by modular domains, of which chromodomains are representative. Here, we conducted the first large-scale study of chromodomains in the human proteome interacting with both histone and non-histone methyllysine peptides. We observed significant degenerate binding between chromodomains and histone peptides, i.e., different histone sites can be recognized by the same set of chromodomains, and different chromodomains can share similar binding profiles to individual histone sites. Such degenerate binding is not dictated by amino acid sequence or PTM motif but rather rooted in the physiochemical properties defined by the PTMs on the histone peptides. This molecular mechanism is confirmed by the accurate prediction of the binding specificity using a computational model that captures the structural and energetic patterns of the domain-peptide interaction. To further illustrate the power and accuracy of our model, we used it to effectively engineer an exceptionally strong H3K9me3-binding chromodomain and to label H3K9me3 in live cells. This study presents a systematic approach to deciphering domain-peptide recognition and reveals a general principle by which histone modifications are interpreted by reader proteins, leading to dynamic regulation of gene expression and other biological processes.

The Fully Developed Wake of a Circular Cylinder

1949 ◽  
Vol 2 (4) ◽  
pp. 451 ◽  
Author(s):  
AA Townsend
Keyword(s):  
Circular Cylinder ◽  
Diffusion Coefficients ◽  
Large Scale ◽  
Turbulent Transport ◽  
Turbulent Energy ◽  
Small Scale ◽  
Mean Velocity ◽  
Turbulent Fluid ◽  
Air Stream ◽  
Scale Motion

Extending previous work on turbulent diffusion in the wake of a circular-cylinder, a series of measurements have been made of the turbulent transport of mean stream momentum, turbulent energy, and heat in the wake of a cylinder of 0.169 cm. diameter, placed in an air-stream of velocity 1280 cm. sec.-1. It has been possible to extend the measurements to 960 diameters down-stream from the cylinder, and it 1s found that, at distances in excess of 600 diameters, the requirements of dynamical similarity are very nearly satisfied. To account for the observed rates of transport of turbulent energy and heat, it is necessary that only part of this transport be due to bulk convection by the slow large-scale motion of the jets of turbulent fluid emitted by the central, fully turbulent core of the wake, which had been supposed previously to perform most of the transport. The remainder of the transport is carried out by the small-scale diffusive motion of the turbulent eddies within the jets, and may be described by assigning diffusion coefficients to the turbulent fluid. It is found that the diffusion coefficients for momentum and heat are approximately equal, but that for turbulent energy is considerably smaller. On the basis of these hypotheses, it is possible to calculate $he form of the mean velocity distribution in good agreement with experiment, and to give a qualitative explanation of the apparently more rapid diffusion of heat.

Large-scale motion between Pacific and Atlantic hotspots

Nature ◽  
1995 ◽  
Vol 378 (6556) ◽  
pp. 477-480 ◽  
Author(s):  
John A. Tarduno ◽  
Jeff Gee
Keyword(s):  
Large Scale ◽  
Large Scale Motion ◽  
Scale Motion
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