Transition state theory demonstrated at the micron scale with out-of-equilibrium transport in a confined environment
Christian L. Vestergaard,Morten Bo Lindholm Mikkelsen,Walter Reisner,Walter Reisner,Anders Kristensen,Henrik Flyvbjerg +5 more
TLDR
This work applies transition state theory to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field.Abstract:
Transition state theory (TST) provides a simple interpretation of many thermally activated processes. It applies successfully on timescales and length scales that differ several orders of magnitude: to chemical reactions, breaking of chemical bonds, unfolding of proteins and RNA structures and polymers crossing entropic barriers. Here we apply TST to out-of-equilibrium transport through confined environments: the thermally activated translocation of single DNA molecules over an entropic barrier helped by an external force field. Reaction pathways are effectively one dimensional and so long that they are observable in a microscope. Reaction rates are so slow that transitions are recorded on video. We find sharp transition states that are independent of the applied force, similar to chemical bond rupture, as well as transition states that change location on the reaction pathway with the strength of the applied force. The states of equilibrium and transition are separated by micrometres as compared with angstroms/nanometres for chemical bonds.read more
Citations
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Probing the organization and dynamics of two DNA chains trapped in a nanofluidic cavity
TL;DR: A pneumatically-actuated nanofluidic platform that has the capability of dynamically controlling the confinement environment of macromolecules in solution is presented, using pneumatic pressure to deflect a thin nitride lid into a nanoslit, confining molecules in an array of cavities embedded in the slit.
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Evolution of Nested Folding States in Compression of a Strongly Confined Semiflexible Chain
TL;DR: In this article, a gasket translating at a fixed sliding speed impinges on a nanochannel extended chain and a unique folding kinetics driven by repeated double-fold nucleation events and growth of nested folds is investigated.
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Waves of DNA: Propagating excitations in extended nanoconfined polymers.
TL;DR: In this article, a single DNA molecule is confined in a nanofluidic slit etched with arrays of embedded nanocavities; the cavity lattice is designed so that a single chain occupies multiple cavities.
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Modeling in food across the scales: towards a universal mass transfer simulator of small molecules in food
Olivier Vitrac,M. Hayert +1 more
TL;DR: In this paper, a special implementation of Langevin dynamics is proposed to describe mass transfer in structured food, where the concepts of random walks over discrete times and physicochemical interactions are connected via an exact solution of the Fokker-Planck equation across interfaces.
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Concentrating and labeling genomic DNA in a nanofluidic array
TL;DR: A device and a protocol for the enzymatic labeling of genomic DNA arranged in a dense array of single molecules without attaching the enzyme or the DNA to a surface is demonstrated and may be an important preparative module for carrying out enzymatics processing on DNA extracted from single-cells in a microfluidic chip.
References
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