scholarly journals Organic molecule fluorescence as an experimental test-bed for quantum jumps in thermodynamics

2017 ◽  
Vol 473 (2204) ◽  
pp. 20170099
Author(s):  
Cormac Browne ◽  
Tristan Farrow ◽  
Oscar C. O. Dahlsten ◽  
Robert A. Taylor ◽  
Vedral Vlatko
Keyword(s):  
Single Molecule ◽  
Energy Difference ◽  
Transformative Change ◽  
Test Bed ◽  
Final State ◽  
Time Resolved ◽  
Quantum Jumps ◽  
Jarzynski Equality ◽  
Set Up ◽  
Natural Test

We demonstrate with an experiment how molecules are a natural test bed for probing fundamental quantum thermodynamics. Single-molecule spectroscopy has undergone transformative change in the past decade with the advent of techniques permitting individual molecules to be distinguished and probed. We demonstrate that the quantum Jarzynski equality for heat is satisfied in this set-up by considering the time-resolved emission spectrum of organic molecules as arising from quantum jumps between states. This relates the heat dissipated into the environment to the free energy difference between the initial and final state. We demonstrate also how utilizing the quantum Jarzynski equality allows for the detection of energy shifts within a molecule, beyond the relative shift.

Structural dynamics of P-type ATPase ion pumps

2019 ◽  
Vol 47 (5) ◽  
pp. 1247-1257 ◽  
Author(s):  
Mateusz Dyla ◽  
Sara Basse Hansen ◽  
Poul Nissen ◽  
Magnus Kjaergaard
Keyword(s):  
Structural Dynamics ◽  
Single Molecule ◽  
New Technologies ◽  
Atp Hydrolysis ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Time Resolved ◽  
Dynamics Simulations ◽  
Types Of Information ◽  
P Type

Abstract P-type ATPases transport ions across biological membranes against concentration gradients and are essential for all cells. They use the energy from ATP hydrolysis to propel large intramolecular movements, which drive vectorial transport of ions. Tight coordination of the motions of the pump is required to couple the two spatially distant processes of ion binding and ATP hydrolysis. Here, we review our current understanding of the structural dynamics of P-type ATPases, focusing primarily on Ca2+ pumps. We integrate different types of information that report on structural dynamics, primarily time-resolved fluorescence experiments including single-molecule Förster resonance energy transfer and molecular dynamics simulations, and interpret them in the framework provided by the numerous crystal structures of sarco/endoplasmic reticulum Ca2+-ATPase. We discuss the challenges in characterizing the dynamics of membrane pumps, and the likely impact of new technologies on the field.

scholarly journals Attosecond intra-valence band dynamics and resonant-photoemission delays in W(110)

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
S. Heinrich ◽  
T. Saule ◽  
M. Högner ◽  
Y. Cui ◽  
V. S. Yakovlev ◽  
...  
Keyword(s):  
Valence Band ◽  
Photoelectron Spectroscopy ◽  
Electronic Band Structure ◽  
Photoelectric Effect ◽  
Final State ◽  
Electronic Band ◽  
Time Resolved ◽  
Resonant Photoemission ◽  
Pulse Trains ◽  
Electron Correlation Effects

AbstractTime-resolved photoelectron spectroscopy with attosecond precision provides new insights into the photoelectric effect and gives information about the timing of photoemission from different electronic states within the electronic band structure of solids. Electron transport, scattering phenomena and electron-electron correlation effects can be observed on attosecond time scales by timing photoemission from valence band states against that from core states. However, accessing intraband effects was so far particularly challenging due to the simultaneous requirements on energy, momentum and time resolution. Here we report on an experiment utilizing intracavity generated attosecond pulse trains to meet these demands at high flux and high photon energies to measure intraband delays between sp- and d-band states in the valence band photoemission from tungsten and investigate final-state effects in resonant photoemission.

Effects of spray inoculation equipment on the viability of Rhizobium spp. in liquid inoculants for legumes

1982 ◽  
Vol 22 (117) ◽  
pp. 299 ◽  
Author(s):  
RR Gault ◽  
DL Chase ◽  
J Brockwell
Keyword(s):  
Soybean Seed ◽  
Strain Differences ◽  
Significant Loss ◽  
Operating Pressure ◽  
Test Bed ◽  
Spray Inoculation ◽  
Rhizobium Spp ◽  
Set Up ◽  
Pumping Equipment ◽  
Liquid Inoculant

Pumping equipment designed for seedbed inoculation of legumes with liquid inoculants was set up on a test bed in the laboratory. Experiments, in which liquid inoculant was circulated through the equipment, were conducted to determine the effect on inoculant viability of variables likely to be encountered when farmers used the equipment in the field. Provided that peat cultures of Rhizobium spp. were used to make liquid inoculant, neither pump type, operating pressure up to 173 kPa, water temperature up to 35�C, nor water impurity up to a level equivalent to 170 �S/cm conductivity seriously reduced inoculant populations during the first hour of treatment, although a significant decline in numbers occurred in three out of 16 experiments. When inoculant was exposed to the various treatments for long periods, a significant loss of viability occurred, in 7 out of 13 experiments, between 4-8 h. R. meliloti was least affected by treatment and R. leguminosarum most affected, but this may have been due to strain differences as much as to species differences. Liquid inoculants which were made from broth cultures lost viability very quickly. R.. meliloti liquid inoculant, prepared from a peat culture and introduced by spraying into a dry soil of neutral pH in the absence of any host plant, did not lose viability during a period of four weeks. The spray inoculation equipment was also used successfully in a field experiment to add water to the seedbed to aid in the germination of soybean seed sown into drying soil.

Tetrapeptide unfolding dynamics followed by core-level spectroscopy: a first-principles approach

2015 ◽  
Vol 17 (17) ◽  
pp. 11269-11276 ◽  
Author(s):  
Simone Taioli ◽  
Stefano Simonucci ◽  
Silvio a Beccara ◽  
Marco Garavelli
Keyword(s):  
First Principles ◽  
Core Level ◽  
Time Resolved ◽  
Level Shifts ◽  
Set Up

An apparatus set-up for performing time-resolved synchrotron measurements of core level shifts in a model bio-molecule.

scholarly journals Increasing the time resolution of single-molecule experiments with Bayesian inference

2017 ◽  
Author(s):  
Colin D. Kinz-Thompson ◽  
Ruben L. Gonzalez
Keyword(s):  
Bayesian Inference ◽  
Single Molecule ◽  
Time Resolution ◽  
Rate Constants ◽  
Computational Approach ◽  
Biomolecular Systems ◽  
Time Resolved ◽  
The Given ◽  
Kinetics Of ◽  
Resolution Data

AbstractMany time-resolved, single-molecule biophysics experiments seek to characterize the kinetics of biomolecular systems exhibiting dynamics that challenge the time resolution of the given technique. Here we present a general, computational approach to this problem that employs Bayesian inference to learn the underlying dynamics of such systems, even when they are much faster than the time resolution of the experimental technique being used. By accurately and precisely inferring rate constants, our Bayesian Inference for the Analysis of Sub-temporal-resolution Data (BIASD) approach effectively enables the experimenter to super-resolve the poorly resolved dynamics that are present in their data.

scholarly journals Hierarchical coupling between ATP hydrolysis and Hsp90’s client binding site

2020 ◽  
Author(s):  
Steffen Wolf ◽  
Benedikt Sohmen ◽  
Björn Hellenkamp ◽  
Johann Thurn ◽  
Gerhard Stock ◽  
...  
Keyword(s):  
Binding Site ◽  
Single Molecule ◽  
Information Transfer ◽  
Atp Hydrolysis ◽  
Structural Information ◽  
Substrate Binding ◽  
Signal Propagation ◽  
Nonequilibrium Molecular Dynamics ◽  
Time Resolved ◽  
Substrate Binding Site

I.ABSTRACTSeveral indicators for a signal propagation from a binding site to a distant functional site have been found in the Hsp90 dimer. Here we determined a time-resolved pathway from ATP hydrolysis to changes in a distant folding substrate binding site. This was possible by combining single-molecule fluorescence-based methods with extensive atomistic nonequilibrium molecular dynamics simulations. We find that hydrolysis of one ATP effects a structural asymmetry in the full Hsp90 dimer that leads to the collapse of a central folding substrate binding site. Arg380 is the major mediator in transferring structural information from the nucleotide to the substrate binding site. This allosteric process occurs via hierarchical dynamics that involve timescales from picoto milliseconds and length scales from Ångstroms to several nanometers. We presume that similar hierarchical mechanisms are fundamental for information transfer through many other proteins.

scholarly journals Visual Biochemistry: modular microfluidics enables kinetic insight from time-resolved cryo-EM

2020 ◽  
Author(s):  
Märt-Erik Mäeots ◽  
Byungjin Lee ◽  
Andrea Nans ◽  
Seung-Geun Jeong ◽  
Mohammad M. N. Esfahani ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Reaction Intermediates ◽  
Protein Distribution ◽  
Time Resolved ◽  
Biochemical Processes ◽  
Molecular Events ◽  
Biophysical Analysis ◽  
Common Strategy ◽  
Set Up

AbstractMechanistic understanding of biochemical reactions requires structural and kinetic characterization of the underlying chemical processes. However, no single experimental technique can provide this information in a broadly applicable manner and thus structural studies of static macromolecules are often complemented by biophysical analysis. Moreover, the common strategy of utilizing mutants or crosslinking probes to stabilize otherwise short-lived reaction intermediates is prone to trapping off-pathway artefacts and precludes determining the order of molecular events. To overcome these limitations and allow visualisation of biochemical processes at near-atomic spatial resolution and millisecond time scales, we developed a time-resolved sample preparation method for cryo-electron microscopy (trEM). We integrated a modular microfluidic device, featuring a 3D-mixing unit and a delay line of variable length, with a gas-assisted nozzle and motorised plunge-freeze set-up that enables automated, fast, and blot-free sample vitrification. This sample preparation not only preserves high-resolution structural detail but also substantially improves protein distribution across the vitreous ice. We validated the method by examining the formation of RecA filaments on single-stranded DNA. We could reliably visualise reaction intermediates of early filament growth across three orders of magnitude on sub-second timescales. Quantification of the trEM data allowed us to characterize the kinetics of RecA filament growth. The trEM method reported here is versatile, easy to reproduce and thus readily adaptable to a broad spectrum of fundamental questions in biology.

scholarly journals Tropospheric eddy feedback to different stratospheric conditions in idealised baroclinic life cycles

2021 ◽  
Vol 2 (1) ◽  
pp. 111-128
Author(s):  
Philip Rupp ◽  
Thomas Birner
Keyword(s):  
Lower Stratosphere ◽  
Polar Vortex ◽  
Surface Friction ◽  
Life Cycles ◽  
Synoptic Scale ◽  
Final State ◽  
Northern Annular Mode ◽  
Wind Structure ◽  
Basic Set ◽  
Set Up

Abstract. A pronounced signature of stratosphere–troposphere coupling is a robust negative anomaly in the surface northern annular mode (NAM) following sudden stratospheric warming (SSW) events, consistent with an equatorward shift in the tropospheric jet. It has previously been pointed out that tropospheric synoptic-scale eddy feedbacks, mainly induced by anomalies in the lowermost extratropical stratosphere, play an important role in creating this surface NAM signal. Here, we use the basic set-up of idealised baroclinic life cycles to investigate the influence of stratospheric conditions on the behaviour of tropospheric synoptic-scale eddies. Particular attention is given to the enhancement of the tropospheric eddy response by surface friction and the sensitivity to wind anomalies in the lower stratosphere. We find systems that include a tropospheric jet only (modelling post-SSW conditions) to be characterised by an equatorward shift in the tropospheric jet in the final state of the life cycle, relative to systems that include a representation of the polar vortex (mimicking more undisturbed stratospheric wintertime conditions), consistent with the observed NAM response after SSWs. The corresponding relative surface NAM signal is increased if the system includes surface friction, presumably due to a direct coupling of the eddy field at tropopause level to the surface winds. We further show that the jet shift signal observed in our experiments is mainly caused by changes in the zonal wind structure of the lowermost stratosphere, while changes in the wind structure of the middle and upper stratosphere have almost no influence.

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