Improved Temporal Resolution and Linked Hidden Markov Modeling for Switchable Single‐Molecule FRET

ChemPhysChem ◽  
2011 ◽  
Vol 12 (3) ◽  
pp. 571-579 ◽  
Author(s):  
Stephan Uphoff ◽  
Kristofer Gryte ◽  
Geraint Evans ◽  
Achillefs N. Kapanidis
2021 ◽  
Author(s):  
Paul David Harris ◽  
Shimon Weiss ◽  
Eitan Lerner

AbstractSingle molecule FRET (smFRET) is a useful tool for studying biomolecular sub-populations and their dynamics. Advanced smFRET-based techniques often track multiple parameters simultaneously, increasing the information content of the measurement. Photon-by-photon hidden Markov modelling (H2MM) is a smFRET analysis tool that quantifies FRET dynamics of single biomolecules, even if they occur in sub-milliseconds. However, sub-populations can be characterized by additional experimentally-derived parameters other than the FRET efficiency. We introduce multi-parameter H2MM (mpH2MM) that identifies sub-populations and their transition dynamics based on multiple experimentally-derived parameters, simultaneously. We show the use of this tool in deciphering the number of underlying sub-populations, their mean characteristics and the rate constants of their transitions for a DNA hairpin exhibiting milliseconds FRET dynamics, and for the RNA polymerase promoter open complex exhibiting sub-millisecond FRET dynamics of the transcription bubble. Overall, we show that using mpH2MM facilitates the identification and quantification of biomolecular sub-populations in smFRET measurements that are otherwise difficult to identify. Finally we provide the means to use mpH2MM in analyzing FRET dynamics in advanced multi-color smFRET-based measurements.


2006 ◽  
Vol 91 (5) ◽  
pp. 1941-1951 ◽  
Author(s):  
Sean A. McKinney ◽  
Chirlmin Joo ◽  
Taekjip Ha

Author(s):  
Mario R. Blanco ◽  
Alexander E. Johnson-Buck ◽  
Nils G. Walter

2013 ◽  
pp. 971-975 ◽  
Author(s):  
Mario R. Blanco ◽  
Alexander E. Johnson-Buck ◽  
Nils G. Walter

2012 ◽  
Vol 102 (3) ◽  
pp. 595a-596a
Author(s):  
Kristofer Gryte ◽  
Alistair Wardrope ◽  
Geraint Evans ◽  
Stephan Uphoff ◽  
Ludovic Le Reste ◽  
...  

Author(s):  
Pratima Saravanan ◽  
Jessica Menold

Objective This research focuses on studying the clinical decision-making strategies of expert and novice prosthetists for different case complexities. Background With an increasing global amputee population, there is an urgent need for improved amputee care. However, current prosthetic prescription standards are based on subjective expertise, making the process challenging for novices, specifically during complex patient cases. Hence, there is a need for studying the decision-making strategies of prosthetists. Method An interactive web-based survey was developed with two case studies of varying complexities. Navigation between survey pages and time spent were recorded for 28 participants including experts ( n = 20) and novices ( n = 8). Using these data, decision-making strategies, or patterns of decisions, during prosthetic prescription were derived using hidden Markov modeling. A qualitative analysis of participants’ rationale regarding decisions was used to add a deep contextualized understanding of decision-making strategies derived from the quantitative analysis. Results Unique decision-making strategies were observed across expert and novice participants. Experts tended to focus on the personal details, activity level, and state of the residual limb prior to prescription, and this strategy was independent of case complexity. Novices tended to change strategies dependent upon case complexity, fixating on certain factors when case complexity was high. Conclusion The decision-making strategies of experts stayed the same across the two cases, whereas the novices exhibited mixed strategies. Application By modeling the decision-making strategies of experts and novices, this study builds a foundation for development of an automated decision-support tool for prosthetic prescription, advancing novice training, and amputee care.


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