Modeling and analysis of single-molecule experiments by Witkoskie, James B

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Polymers through pores: single-molecule experiments with nucleic acids, polypeptides and polysaccharides by Bayley, H

A framework to validate fluorescently labeled DNA-binding proteins for single-molecule experiments by Miranda Molina, Lindsey E. Way, Zhongqing Ren, Qin Liao, Bianca Guerra, Brandon Shields, Xindan Wang, HyeongJun Kim

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Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning by Yasuhiro Matsunaga, Yuji Sugita

Subjects: “…single-molecule experiment…”
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Beta-Barrel Channel Response to High Electric Fields: Functional Gating or Reversible Denaturation? by Ekaterina M. Nestorovich, Sergey M. Bezrukov

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Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding by Xu, Xinliang, Ge, Hao, Gu, Chan, Gao, Yi Qin, Wang, Siyuan S., Thio, Beng Joo Reginald, Hynes, James T., Xie, X. Sunney, Cao, Jianshu

“…This length scale is in agreement with that reported from the single-molecule experiment. Our model can be reduced to the worm-like chain form at length scales larger than lP but is able to explain DNA’s mechanical properties on shorter length scales, in particular, the DNA allostery of protein–DNA interactions.…”
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Single-molecule chemistry studied using the protein pore -α-hemolysin by Choi, LS

“…However, due to the ‘slow’ reaction rate of the Diels-Alder reaction (rate constant ~10⁻¹ M⁻¹s⁻) relative to the time-scale of the single-molecule experiment, we failed to observed chemical conversion at the single-molecule level. …”

Overcoming chromatin barriers by Babette E de Jong, John van Noort

“…Single-molecule experiments reveal the dynamics of transcription through a nucleosome with single-base-pair accuracy.…”
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On the move by Robert A Forties, Jie Ma, Michelle D Wang

“…Single-molecule experiments have shed new light on the mechanisms responsible for the movement of RNA polymerase along DNA during transcription.…”
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High-throughput single-molecule quantification of individual base stacking energies in nucleic acids by Jibin Abraham Punnoose, Kevin J. Thomas, Arun Richard Chandrasekaran, Javier Vilcapoma, Andrew Hayden, Kacey Kilpatrick, Sweta Vangaveti, Alan Chen, Thomas Banco, Ken Halvorsen

“…In this work, the authors use a centrifuge force microscope for high-throughput single-molecule experiments to elucidate stacking energies between individual bases of DNA.…”
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Single-molecule biophysics experiments in silico: Toward a physical model of a replisome by Christopher Maffeo, Han-Yi Chou, Aleksei Aksimentiev

“…Summary: The interpretation of single-molecule experiments is frequently aided by computational modeling of biomolecular dynamics. …”
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Shining the spotlight on functional molecular complexes: The new science of single-molecule cell biology. by Leake, M

“…What has emerged recently is the technical ability to now perform key single-molecule experiments whilst retaining the native biological context-namely to do single-molecule experiments on functional living cells. …”

Mechanical Constraint Effect on DNA Persistence Length by Cheng-Yin Zhang, Neng-Hui Zhang

“…The mechanical constraints applied on DNA chains in new single-molecule experiments play a complex role in measuring DNA persistence length; however, there is a difficulty in quantitatively characterizing the mechanical constraint effects due to their complex interactions with electrostatic repulsions and thermal fluctuations. …”
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Coarse-Grained Models for Protein-Cell Membrane Interactions by Ryan Bradley, Ravi Radhakrishnan

“…This paper reviews continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes.…”
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Heterogeneous Ultrafast Energy Transfer in Photosynthetic Proteins by Moya III, Raymundo

“…Lastly, in Chapter 4 I present the first single-molecule experiments on light-harvesting complexes from cryptophyte algae. …”
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Noise Reduction Method of Nanopore Based on Wavelet and Kalman Filter by Zhouchang Huang, Xiaoqing Zeng, Deqiang Wang, Shaoxi Fang

“…Nanopore detection technology has now developed into an indispensable tool for single molecule experiments, in which useful information on molecular properties can be obtained from the ion current flow induced by individual molecules, but the relatively high background noise affects the data analysis. …”
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Coarse-grained modelling of supercoiled RNA by Matek, C, Šulc, P, Randisi, F, Doye, J, Louis, A

“…Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. …”

Deformation Response of Catenated DNA Networks in a Planar Elongational Field by Soh, Beatrice W, Doyle, Patrick S

“…In this work, we use single-molecule experiments to study the transient and steady-state deformation of kinetoplasts in a planar elongational field. …”
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Mechanistic insights into bacterial AAA+ proteases and protein-remodelling machines by Olivares, Adrian O., Baker, Tania, Sauer, Robert T.

“…Recent structural and biochemical studies, in combination with direct visualization of unfolding and translocation in single-molecule experiments, have illuminated the molecular mechanisms behind these processes and suggest how remodelling of macromolecular complexes by AAA+ enzymes could occur without global denaturation. …”
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Nonequilibrium Work Relations and Response Theories in Ensemble Quantum Systems by Dodin, Amro, Willard, Adam P

“…We contrast these developments with their ρ-ensemble analogs, and we discuss how these P-ensemble theories provide a guide for an effective application of single molecule experiments.…”
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