ArticleProceedings of the National Academy of Sciences of the United States of America2018
Butane dihedral angle dynamics in water is dominated by internal friction.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 91 citations in OpenAlex.
- Hierarchical friction memory leads to subdiffusive configurational dynamics of fast-folding proteins.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Non-Markovian equilibrium and non-equilibrium barrier-crossing kinetics in asymmetric double-well potentials.The European physical journal. E, Soft matter · 2025Article
- Accuracy of Reaction Coordinate Based Rate Theories for Modelling Chemical Reactions: Insights From the Thermal Isomerization in Retinal.Journal of computational chemistry · 2025Article
- The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media.Nature communications · 2024Article
- Accurate Memory Kernel Extraction from Discretized Time-Series Data.Journal of chemical theory and computation · 2024Article
- Score Dynamics: Scaling Molecular Dynamics with Picoseconds Time Steps via Conditional Diffusion Model.Journal of chemical theory and computation · 2024Article
- Activation and friction in enzymatic loop opening and closing dynamics.Nature communications · 2024Article
- Fast protein folding is governed by memory-dependent friction.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Pair-Reaction Dynamics in Water: Competition of Memory, Potential Shape, and Inertial Effects.The journal of physical chemistry. B · 2022Review
- Likelihood-based non-Markovian models from molecular dynamics.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Time-Dependent Friction Effects on Vibrational Infrared Frequencies and Line Shapes of Liquid Water.The journal of physical chemistry. B · 2022Article
- Non-Markovian modeling of protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Does Electric Friction Matter in Living Cells?The journal of physical chemistry. B · 2021Article
- Negative friction memory induces persistent motion.The European physical journal. E, Soft matter · 2020Article
- Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems.Journal of chemical theory and computation · 2020Review
- Non-Markovian barrier crossing with two-time-scale memory is dominated by the faster memory component.The European physical journal. E, Soft matter · 2019Article
- Origin of Internal Friction in Disordered Proteins Depends on Solvent Quality.The journal of physical chemistry. B · 2018Article
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4 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The dihedral dynamics of butane in water is known to be rather insensitive to the water viscosity; possible explanations for this involve inertial effects or Kramers' turnover, the finite memory time of friction, and the presence of so-called internal friction. To disentangle these factors, we introduce a method to directly extract the friction memory function from unconstrained simulations in the presence of an arbitrary free-energy landscape. By analysis of the dihedral friction in butane for varying water viscosity, we demonstrate the existence of an internal friction contribution that does not scale linearly with water viscosity. At normal water viscosity, the internal friction turns out to be eight times larger than the solvent friction and thus completely dominates the effective friction. By comparison with simulations of a constrained butane molecule that has the dihedral as the only degree of freedom, we show that internal friction comes from the six additional degrees of freedom in unconstrained butane that are orthogonal to the dihedral angle reaction coordinate. While the insensitivity of butane's dihedral dynamics to water viscosity is solely due to the presence of internal friction, inertial effects nevertheless crucially influence the resultant transition rates. In contrast, non-Markovian effects due to the finite memory time are present but do not significantly influence the dihedral barrier-crossing rate of butane. These results not only settle the character of dihedral dynamics in small solvated molecular systems such as butane, they also have important implications for the folding of polymers and proteins.
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