Nonequilibrium thermodynamics of single DNA hairpins in a dual-trap optical tweezers setup

2011 ◽  
Author(s):  
M. Ribezzi Crivellari ◽  
J. M. Huguet ◽  
F. Ritort
Keyword(s):  
Optical Tweezers ◽  
Nonequilibrium Thermodynamics ◽  
Dna Hairpins

scholarly journals Measuring the average shape of transition paths during the folding of a single biological molecule

2019 ◽  
Vol 116 (17) ◽  
pp. 8125-8130 ◽  
Author(s):  
Noel Q. Hoffer ◽  
Krishna Neupane ◽  
Andrew G. T. Pyo ◽  
Michael T. Woodside
Keyword(s):  
Optical Tweezers ◽  
Transition Path ◽  
Dna Hairpins ◽  
Extension Domain ◽  
Average Shape ◽  
Rich Information ◽  
Reliable Representation ◽  
Transition Paths ◽  
The Rich ◽  
The Time Domain

Transition paths represent the parts of a reaction where the energy barrier separating products and reactants is crossed. They are essential to understanding reaction mechanisms, yet many of their properties remain unstudied. Here, we report measurements of the average shape of transition paths, studying the folding of DNA hairpins as a model system for folding reactions. Individual transition paths were detected in the folding trajectories of hairpins with different sequences held under tension in optical tweezers, and path shapes were computed by averaging all transitions in the time domain, 〈t(x)〉, or by averaging transitions of a given duration in the extension domain, 〈x(t|τ)〉τ. Whereas 〈t(x)〉 was close to straight, with only a subtle curvature, 〈x(t|τ)〉τhad more pronounced curvature that fit well to theoretical expectations for the dominant transition path, returning diffusion coefficients similar to values obtained previously from independent methods. Simulations suggested that 〈t(x)〉 provided a less reliable representation of the path shape than 〈x(t|τ)〉τ, because it was far more sensitive to the effects of coupling the molecule to the experimental force probe. Intriguingly, the path shape variance was larger for some hairpins than others, indicating sequence-dependent changes in the diversity of transition paths reflective of differences in the character of the energy barriers, such as the width of the barrier saddle-point or the presence of parallel paths through multiple barriers between the folded and unfolded states. These studies of average path shapes point the way forward for probing the rich information contained in path shape fluctuations.

Defining the trapping limits of holographical optical tweezers

2004 ◽  
Vol 51 (3) ◽  
pp. 409-414 ◽  
Author(s):  
P. Jordan ◽  
J. Leach ◽  
M. J. Padgett ◽  
J. Cooper ◽  
G. Sinclair
Keyword(s):  
Optical Tweezers

Electromagnetic-matter interactions and devices

2017 ◽  
Author(s):  
Sandip Tiwari
Keyword(s):  
Optical Tweezers ◽  
Quantum Cascade Lasers ◽  
Accelerator Physics ◽  
X Ray ◽  
Quantum Cascade ◽  
Inorganic Systems ◽  
Charge Cloud ◽  
Atomic Distance ◽  
Extinction Length ◽  
Cascade Lasers

This chapter explores electromagnetic-matter interactions from photon to extinction length scales, i.e., nanometer of X-ray and above. Starting with Casimir-Polder effect to understand interactions of metals and dielectrics at near-atomic distance scale, it stretches to larger wavelengths to explore optomechanics and its ability for energy exchange and signal transduction between PHz and GHz. This range is explored with near-quantum sensitivity limits. The chapter also develops the understanding phononic bandgaps, and for photons, it explores the use of energetic coupling for useful devices such as optical tweezers, confocal microscopes and atomic clocks. It also explores miniature accelerators as a frontier area in accelerator physics. Plasmonics—the electromagnetic interaction with electron charge cloud—is explored for propagating and confined conditions together with the approaches’ possible uses. Optoelectronic energy conversion is analyzed in organic and inorganic systems, with their underlying interaction physics through solar cells and its thermodynamic limit, and quantum cascade lasers.

scholarly journals Protocol to measure the membrane tension and bending modulus of cells using optical tweezers and scanning electron microscopy

2021 ◽  
Vol 2 (1) ◽  
pp. 100283
Author(s):  
Pedro Pompeu ◽  
Pedro S. Lourenço ◽  
Diney S. Ether ◽  
Juliana Soares ◽  
Jefte Farias ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Optical Tweezers ◽  
Membrane Tension ◽  
Bending Modulus ◽  
Scanning Electron

scholarly journals Nonequilibrium thermodynamics of acoustic phonons in suspended graphene

2020 ◽  
Vol 2 (1) ◽  
Author(s):  
Robin J. Dolleman ◽  
Gerard J. Verbiest ◽  
Yaroslav M. Blanter ◽  
Herre S. J. van der Zant ◽  
Peter G. Steeneken
Keyword(s):  
Nonequilibrium Thermodynamics ◽  
Acoustic Phonons ◽  
Suspended Graphene

Optimizing Optical Tweezers Experiments for Magnetic Resonance Sensing with Nanodiamonds

ACS Photonics ◽  
2021 ◽  
Author(s):  
Lachlan W. Russell ◽  
Eloise C. Dossetor ◽  
Alexander A. Wood ◽  
David A. Simpson ◽  
Peter J. Reece
Keyword(s):  
Magnetic Resonance ◽  
Optical Tweezers

scholarly journals Nano‐Optical Tweezers: Methods and Applications for Trapping Single Molecules and Nanoparticles

ChemPhysChem ◽  
2021 ◽  
Vol 22 (14) ◽  
pp. 1408-1408
Author(s):  
Joshua D. Kolbow ◽  
Nathan C. Lindquist ◽  
Christopher T. Ertsgaard ◽  
Daehan Yoo ◽  
Sang‐Hyun Oh
Keyword(s):  
Optical Tweezers ◽  
Single Molecules
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