News
The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media
In our recent publication in Nature Communications, we reveal the complex relationship between molecular isomerization kinetics, dihedral friction, and solvent viscosity in viscogenic solvent environments. We demonstrate that deviations from a linear dependence of isomerization rates on solvent viscosity, typically attributed to internal friction effects, are actually due to the simultaneous violation of both the Stokes-Einstein relation for dihedral dynamics and Kramers’ theory for isomerization kinetics. Such a detailed decomposition of internal friction effects has not been previously possible due to the difficulties associated with calculating one critical quantity: friction.
Oct 15, 2024
Fast protein folding is governed by memory-dependent friction
In this paper, we evaluate the time-dependent friction kernels for the folding dynamics of eight fast-folding proteins and show that friction relaxation times are long, comparable to protein folding times. By applying memory-kernel extraction techniques to the dynamics of well-characterized reaction coordinates, we directly access the folding friction, which is typically otherwise evaluated by fitting some reaction kinetic model. As such, we parameterize a range of reaction kinetic models and show that models explicitly accounting for non-Markovian effects are the most accurate for predicting the population of protein folding rates.
Oct 15, 2024
Nanoscopic Interfacial Hydrogel Viscoelasticity Revealed from Comparison of Macroscopic and Microscopic Rheology
Our publication in Nano Letters investigates the discrepancies between macrorheological and particle-based microrheological measurements in aqueous poly(ethylene oxide) (PEO) hydrogels. By analyzing hydrogels with varying PEO concentrations and chain lengths, we reveal that these deviations expose the nanoscopic viscoelastic properties at the particle–hydrogel interface. We show that an interfacial shell with distinct viscoelastic properties explains the experimental results by utilizing a generalized Stokes-Einstein relation and ruling out alternative explanations such as finite particle radius or surface-slip effects. Our approach provides insights into the nanoscopic interfacial rheology of hydrogels and can be extended to other viscoelastic materials. Robert F. Schmidt, Henrik Kiefer, Robert Dalgliesh, Michael Gradzielski, Roland R. Netz - Nano Lett. 24, 4758-4765 - Published April 9, 2024.
Oct 15, 2024
Non-Markovian Modeling of Nonequilibrium Fluctuations and Dissipation in Active Viscoelastic Biomatter
In our recent paper published in Physical Review Letters we have developed a model for viscoelastic active biomatter. This model incorporates the elastic coupling between a tracer bead and an active viscoelastic medium, yielding closed-form analytical predictions for the tracer autocorrelation and response function. We have demonstrated that these analytical predictions are in excellent agreement with experimental data for red blood cells (RBCs) and actomyosin networks. Amir Abbasi, Roland R. Netz, Ali Naji – Phys. Rev. Lett. 131, 228202 – Published November 30, 2023 – DOI: 10.1103/PhysRevLett.131.228202
Dec 01, 2023
Proton transfer insights from IR spectroscopy
In a recent publication in Nature Communications, we show how the infrared spectroscopic signatures of hydrochloric acid solutions are related to proton-transfer processes between water molecules, the elementary step of the long-range Grotthus transport. In a second work that just appeared in the Journal of Chemical Physics, the IR band shapes produced by proton-transfer events are derived using analytical models for the barrier-crossing dynamics as a proton moves from one water molecule to a neighboring one. You can check out the articles here! https://www.nature.com/articles/s41467-022-31700-x https://aip.scitation.org/doi/10.1063/5.0116686
Jan 18, 2023
Visiting Professors Marie-Laure Bocquet and Lyderic Bocquet
The AG Netz is pleased to host Professors Marie-Laure Bocquet and Lyderic Bocquet from the Ecole Normale Superieure in Paris, for the months of May and June 2022. Prof. Lyderic Bocquet is visiting thanks to an Alexander von Humboldt Research Award and was also just awarded the 2022 Gentner-Kastler Prize by the DPG
May 02, 2022
How Ions Evaporate from Water
Our new paper in Nature Communications Chemistry gives insights on the evaporation energetics and kinetics of a chloride ion from liquid water using molecular simulations. Check out this blog entry to watch cool videos.
Apr 26, 2022
Keywords
- AG Roland Netz, Bio Soft Matter Theory