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.

Esterification kinetics of phenol with phosphoryl trichloride

1989 ◽  
Vol 54 (3) ◽  
pp. 608-615 ◽  
Author(s):  
Miroslav Magura ◽  
Ján Vojtko ◽  
Eva Zemanová ◽  
Alexander Kaszonyi ◽  
Ján Ilavský
Keyword(s):  
Liquid Phase ◽  
Linear Regression ◽  
Rate Constants ◽  
Optimization Method ◽  
Activation Energies ◽  
System Of Differential Equations ◽  
Consecutive Reactions ◽  
Esterification Rate ◽  
The Given ◽  
Kinetics Of

The liquid-phase esterification kinetics of phenol with POCl3 has been studied at isothermal conditions within the temperature interval from 90 to 110 °C. The esterification rate constants of the first, second, and third esterification steps and the activation energies of these steps have been calculated. The given system of competitive consecutive reactions can be described by a system of differential equations which has been solved by the Gauss-Newton optimization method of non-linear regression in the Marquardt modification. In the sequence of the first, second, and third step the esterification rate constants have been found to gradually decrease, whereas the activation energies uncrease in the same sequence.

scholarly journals Dissecting the self-assembly kinetics of multimeric pore-forming toxins

2016 ◽  
Vol 13 (114) ◽  
pp. 20150762 ◽  
Author(s):  
A. A. Lee ◽  
M. J. Senior ◽  
M. I. Wallace ◽  
T. E. Woolley ◽  
I. M. Griffiths
Keyword(s):  
Single Molecule ◽  
Self Assembly ◽  
Quantitative Agreement ◽  
Time Resolved ◽  
Biologically Relevant ◽  
Low Concentrations ◽  
Assembly Kinetics ◽  
Quantitative Understanding ◽  
Mechanism And Kinetics ◽  
Kinetics Of

Pore-forming toxins are ubiquitous cytotoxins that are exploited by both bacteria and the immune response of eukaryotes. These toxins kill cells by assembling large multimeric pores on the cell membrane. However, a quantitative understanding of the mechanism and kinetics of this self-assembly process is lacking. We propose an analytically solvable kinetic model for stepwise, reversible oligomerization. In biologically relevant limits, we obtain simple algebraic expressions for the rate of pore formation, as well as for the concentration of pores as a function of time. Quantitative agreement is obtained between our model and time-resolved kinetic experiments of Bacillus thuringiensis Cry1Ac (tetrameric pore), aerolysin, Staphylococcus aureus α -haemolysin (heptameric pores) and Escherichia coli cytolysin A (dodecameric pore). Furthermore, our model explains how rapid self-assembly can take place with low concentrations of oligomeric intermediates, as observed in recent single-molecule fluorescence experiments of α-haemolysin self-assembly. We propose that suppressing the concentration of oligomeric intermediates may be the key to reliable, error-free, self-assembly of pores.

Triplet-State Kinetics of 2,5 Diphenyloxazole (PPO)

1988 ◽  
Vol 42 (1) ◽  
pp. 27-31
Author(s):  
A. N. Dharamsi ◽  
Shawpin Jong
Keyword(s):  
Excited State ◽  
Triplet State ◽  
Absorption Spectra ◽  
Rate Constants ◽  
Intersystem Crossing ◽  
Time Resolved ◽  
Probe Technique ◽  
Pump And Probe ◽  
Kinetics Of ◽  
Triplet Absorption

Time-resolved excited-state triplet-triplet absorption spectra were measured for solutions of 2,5 diphenyloxazole (PPO) in various solvents, with the use of a pump and probe technique. The rate constants for intersystem crossing, triplet deactivation by oxygen, and triplet-triplet self-quenching are obtained. The latter two rate constants are substantially larger than the corresponding rate constants for 2-(1 naphthyl)-5-phenyloxazole-αNPO.

IDENTIFICATION OF RATE CONSTANTS AND NONOBSERVABLE ABSORPTION SPECTRA IN NONLINEAR BIOCHEMICAL REACTION DYNAMICS

2004 ◽  
Vol 14 (06) ◽  
pp. 2081-2092 ◽  
Author(s):  
D. MARAUN ◽  
W. HORBELT ◽  
H. RUST ◽  
J. TIMMER ◽  
H. P. HAPPERSBERGER ◽  
...  
Keyword(s):  
Absorption Spectra ◽  
Rate Constants ◽  
Reaction Dynamics ◽  
Biochemical Reaction ◽  
Multiple Shooting ◽  
Specific Rate ◽  
Time Resolved ◽  
Time Courses ◽  
Kinetics Of ◽  
Shooting Algorithm

On analyzing data of biochemical reaction dynamics monitored by time-resolved spectroscopy, one faces the problem that the concentration time courses of the involved components are not directly observed, but the superposition of their absorption spectra. Furthermore the single spectra are often unknown, because the corresponding reagents cannot be isolated. We propose a method based on Bock's multiple shooting algorithm to estimate the rate constants and individual spectra simultaneously. Applying this procedure to a biochemical reaction we identify the specific rate constants characterizing the reaction dynamics as well as the nonobservable absorption spectra. The results lead to a better understanding of the kinetics of a novel modification reaction which was used as trapping reaction in disulfide bond mediated protein folding reactions.

scholarly journals Determination of thermodynamics and kinetics of RNA reactions by force

2006 ◽  
Vol 39 (4) ◽  
pp. 325-360 ◽  
Author(s):  
Ignacio Tinoco ◽  
Pan T. X. Li ◽  
Carlos Bustamante
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Rate Constants ◽  
Magnetic Tweezers ◽  
Constant Force ◽  
Thermodynamics And Kinetics ◽  
Wide Range ◽  
Kinetic Mechanisms ◽  
Kinetics Of ◽  
Force Drop

1. Introduction 3262. Instrumentation 3282.1 Instruments to study mechanical properties of RNA 3282.1.1 AFM 3282.1.2 Magnetic tweezers 3282.1.3 Optical tweezers 3302.2 Optical trap instrumentation 3302.3 Calibrations 3322.3.1 Calibration of trap stiffness 3322.3.2 Calibration of force 3332.3.3 Calibration of distance 3342.4 Types of experiments 3342.4.1 Force-ramp 3342.4.2 Force-clamp or constant-force experiments 3352.4.3 Extension-clamp or constant extension experiments 3352.4.4 Force-jump, Force-drop 3362.4.5 Passive mode 3363. Thermodynamics 3363.1 Reversibility 3363.2 Gibbs free energy 3373.2.1 Stretching free energy 3383.2.1.1 Rigid molecules 3383.2.1.2 Compliant or flexible molecules 3393.2.2 Free energy of a reversible unfolding transition 3393.2.3 Free energy of unfolding at zero force 3403.2.4 Free energy of an irreversible unfolding transition 3403.2.4.1 Jarzynski's method 3413.2.4.2 Crooks fluctuation theorem 3434. Kinetics 3454.1 Measuring rate constants 3454.1.1 Hopping 3454.1.2 Force-jump, Force-drop 3474.1.3 Force-ramp 3484.1.4 Instrumental effects 3504.2 Kinetic mechanisms 3514.2.1 Free-energy landscapes 3514.2.2 Kinetics of unfolding 3535. Relating force-measured data to other measurements 3545.1 Thermodynamics 3545.2 Kinetics 3576. Acknowledgements 3577. References 358Single-molecule methods have made it possible to apply force to an individual RNA molecule. Two beads are attached to the RNA; one is on a micropipette, the other is in a laser trap. The force on the RNA and the distance between the beads are measured. Force can change the equilibrium and the rate of any reaction in which the product has a different extension from the reactant. This review describes use of laser tweezers to measure thermodynamics and kinetics of unfolding/refolding RNA. For a reversible reaction the work directly provides the free energy; for irreversible reactions the free energy is obtained from the distribution of work values. The rate constants for the folding and unfolding reactions can be measured by several methods. The effect of pulling rate on the distribution of force-unfolding values leads to rate constants for unfolding. Hopping of the RNA between folded and unfolded states at constant force provides both unfolding and folding rates. Force-jumps and force-drops, similar to the temperature jump method, provide direct measurement of reaction rates over a wide range of forces. The advantages of applying force and using single-molecule methods are discussed. These methods, for example, allow reactions to be studied in non-denaturing solvents at physiological temperatures; they also simplify analysis of kinetic mechanisms because only one intermediate at a time is present. Unfolding of RNA in biological cells by helicases, or ribosomes, has similarities to unfolding by force.

scholarly journals Increasing the Time Resolution of Single-Molecule Experiments with Bayesian Inference

2018 ◽  
Vol 114 (2) ◽  
pp. 289-300 ◽  
Author(s):  
Colin D. Kinz-Thompson ◽  
Ruben L. Gonzalez
Keyword(s):  
Bayesian Inference ◽  
Single Molecule ◽  
Time Resolution

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.

Pump-Probe Measurements Using Silicon Nanocrystal Waveguides

2003 ◽  
Vol 770 ◽  
Author(s):  
Nathanael Smith ◽  
Max J. Lederer ◽  
Marek Samoc ◽  
Barry Luther-Davies ◽  
Robert G. Elliman
Keyword(s):  
Probe Beam ◽  
Time Resolution ◽  
Pump Beam ◽  
Silicon Nanocrystals ◽  
Continuous Wave ◽  
Optical Gain ◽  
Optical Pump ◽  
Time Resolved ◽  
Pump Probe ◽  
Probe Measurements

AbstractOptical pump-probe measurements were performed on planar slab waveguides containing silicon nanocrystals in an attempt to measure optical gain from photo-excited silicon nanocrystals. Two experiments were performed, one with a continuous-wave probe beam and a pulsed pump beam, giving a time resolution of approximately 25 ns, and the other with a pulsed pump and probe beam, giving a time resolution of approximately 10 ps. In both cases the intensity of the probe beam was found to be attenuated by the pump beam, with the attenuation increasing monotonically with increasing pump power. Time-resolved measurements using the first experimental arrangement showed that the probe signal recovered its initial intensity on a time scale of 45-70 μs, a value comparable to the exciton lifetime in Si nanocrystals. These data are shown to be consistent with an induced absorption process such as confined carrier absorption. No evidence for optical gain was observed.

In situ Time-Resolved Small-Angle X-ray Scattering Reveals the Formation Kinetics of Polyelectrolyte Complex Micelles

2019 ◽  
Author(s):  
Hao Wu ◽  
Jeffrey Ting ◽  
Siqi Meng ◽  
Matthew Tirrell
Keyword(s):  
Small Angle ◽  
Self Assembly ◽  
Electrostatic Interactions ◽  
Polyelectrolyte Complex ◽  
Time Resolved ◽  
X Ray ◽  
X Ray Scattering ◽  
Kinetics Of ◽  
Ray Scattering

We have directly observed the <i>in situ</i> self-assembly kinetics of polyelectrolyte complex (PEC) micelles by synchrotron time-resolved small-angle X-ray scattering, equipped with a stopped-flow device that provides millisecond temporal resolution. This work has elucidated one general kinetic pathway for the process of PEC micelle formation, which provides useful physical insights for increasing our fundamental understanding of complexation and self-assembly dynamics driven by electrostatic interactions that occur on ultrafast timescales.

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