scholarly journals Communication: Transition-path velocity as an experimental measure of barrier crossing dynamics

2018 ◽  
Vol 148 (20) ◽  
pp. 201102 ◽  
Author(s):  
Alexander M. Berezhkovskii ◽  
Dmitrii E. Makarov
Keyword(s):  
Transition Path ◽  
Barrier Crossing ◽  
Experimental Measure

scholarly journals Slow Transition Path Times Reveal a Complex Folding Barrier in a Designed Protein

2020 ◽  
Vol 8 ◽  
Author(s):  
Alexander Mehlich ◽  
Jie Fang ◽  
Benjamin Pelz ◽  
Hongbin Li ◽  
Johannes Stigler
Keyword(s):  
Optical Tweezers ◽  
Single Molecule ◽  
De Novo ◽  
High Energy ◽  
Transition Path ◽  
Barrier Crossing ◽  
Designed Proteins ◽  
Transition Barrier ◽  
Millisecond Range ◽  
Transition Times

De-novo designed proteins have received wide interest as potential platforms for nano-engineering and biomedicine. While much work is being done in the design of thermodynamically stable proteins, the folding process of artificially designed proteins is not well-studied. Here we used single-molecule force spectroscopy by optical tweezers to study the folding of ROSS, a de-novo designed 2x2 Rossmann fold. We measured a barrier crossing time in the millisecond range, much slower than what has been reported for other systems. While long transition times can be explained by barrier roughness or slow diffusion, we show that isotropic roughness cannot explain the measured transition path time distribution. Instead, this study shows that the slow barrier crossing of ROSS is caused by the population of three short-lived high-energy intermediates. In addition, we identify incomplete and off-pathway folding events with different barrier crossing dynamics. Our results hint at the presence of a complex transition barrier that may be a common feature of many artificially designed proteins.

Rare event simulation

2017 ◽  
Author(s):  
Michael P. Allen ◽  
Dominic J. Tildesley
Keyword(s):  
Rare Event ◽  
Path Sampling ◽  
Rapid Progress ◽  
Computationally Efficient ◽  
Transition Path ◽  
Transition Path Sampling ◽  
Event Simulation ◽  
Reaction Coordinates ◽  
Simulation Techniques ◽  
Transition Interface

The development of techniques to simulate infrequent events has been an area of rapid progress in recent years. In this chapter, we shall discuss some of the simulation techniques developed to study the dynamics of rare events. A basic summary of the statistical mechanics of barrier crossing is followed by a discussion of approaches based on the identification of reaction coordinates, and those which seek to avoid prior assumptions about the transition path. The demanding technique of transition path sampling is introduced and forward flux sampling and transition interface sampling are considered as rigorous but computationally efficient approaches.

scholarly journals Catalytic Mechanism of Processive GlfT2: Transition Path Sampling Investigation of Substrate Translocation

ACS Omega ◽  
2020 ◽  
Vol 5 (34) ◽  
pp. 21374-21384
Author(s):  
Pavel Janoš ◽  
Igor Tvaroška ◽  
Christoph Dellago ◽  
Jaroslav Koča
Keyword(s):  
Catalytic Mechanism ◽  
Path Sampling ◽  
Transition Path ◽  
Transition Path Sampling

scholarly journals The use of nocturnal flights for barrier crossing in a diurnally migrating songbird

2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Christie D. Lavallée ◽  
Saeedeh Bani Assadi ◽  
Alicia M. Korpach ◽  
James D. Ray ◽  
Jason D. Fischer ◽  
...  
Keyword(s):  
Energy Savings ◽  
Open Water ◽  
Gps Tracking ◽  
Future Research ◽  
Barrier Crossing ◽  
Migration Patterns ◽  
Migration Strategies ◽  
Diurnal Migrant ◽  
Time And Energy ◽  
High Degree

Abstract Background The migration patterns of land birds can generally be divided into those species that migrate principally during the day and those that migrate during the night. Some species may show individual plasticity in the use of day or night flight, particularly when crossing large, open-water or desert barriers. However, individual plasticity in circadian patterns of migratory flights in diurnally migrating songbirds has never been investigated. Methods We used high precision GPS tracking of a diurnal, migratory swallow, the purple martin (Progne subis), to determine whether individuals were flexible in their spring migration strategies to include some night flight, particularly at barrier crossing. Results Most (91%) of individuals made large (sometimes > 1000 km), open-water crossings of the Caribbean Sea and the Gulf of Mexico that included the use of night flight. 32% of all water crossings were initiated at night, demonstrating that night flight is not only used to complete large crossings but may confer other advantages for diurnal birds. Birds were not more likely to initiate crossings with supportive winds, however crossings were more likely when they reduced travel distances. Our results are consistent with diurnal birds using night flight to help achieve time- and energy-savings through ‘short cuts’ at barrier crossings, at times and locations when foraging opportunities are not available. Conclusions Overall, our results demonstrate the use of nocturnal flight and a high degree of individual plasticity in migration strategies on a circadian scale in a species generally considered to be a diurnal migrant. Nocturnal flights at barrier crossing may provide time and energy savings where foraging opportunities are low in an otherwise diurnal strategy. Future research should target how diel foraging and refueling strategies support nocturnal flights and barrier crossing in this and other diurnal species.

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