More Like this

1. Transferable and Polarizable Coarse Grained Model for Proteins─ProMPT

   https://doi.org/10.1021/acs.jctc.2c00269  

   Sahoo, Abhilash; Lee, Pei-Yin; Matysiak, Silvina (August 2022, Journal of Chemical Theory and Computation)
2. Contrasting Dielectric Properties of Electrolyte Solutions with Polar and Polarizable Solvents

   https://doi.org/10.1103/PhysRevLett.122.128007  

   Grzetic, Douglas J.; Delaney, Kris T.; Fredrickson, Glenn H. (March 2019, Physical Review Letters)
3. Decoherence and Brownian motion of a polarizable particle near a medium

   https://doi.org/10.1103/6m4t-jm4x  

   Jakubec, Clemens; Jarzynski, Christopher; Sinha, Kanu (October 2025, Physical Review A)

   Optically levitated nanoparticles are ideal experimental testbeds for investigating macroscopic superpositions and microscopic thermodynamics. Integrating such levitated nanoparticles with photonic structures can enable strong coupling between their center-of-mass motion and guided photonic modes, facilitating enhanced control and probing of their motion. When coupling a particle to a photonic structure, such as a waveguide, the effects of fluctuations become prominent at nanoscales. In this work, we analyze the classical and quantized center-of-mass motion of a polarizable particle interacting with the fluctuations of the electromagnetic field in the presence of a medium. We derive a position localization master equation for the particle's quantized center of mass, and examine its classical center-of-mass momentum diffusion, elucidating correspondences between classical and quantum Brownian motion of polarizable particles near media. We study the decoherence rate of the particle in the presence of a planar surface as a function of temperature and distance from the surface, comparing it to common sources of decoherence. Our results are pertinent to experiments aimed at preparing levitated nanospheres in macroscopic quantum states and investigating their Brownian dynamics. 

   more » « less
4. Polarizable embedding for simulating redox potentials of biomolecules

   https://doi.org/10.1039/c9cp01533g  

   Tazhigulov, Ruslan N.; Gurunathan, Pradeep Kumar; Kim, Yongbin; Slipchenko, Lyudmila V.; Bravaya, Ksenia B. (June 2019, Physical Chemistry Chemical Physics)

   Redox reactions play a key role in various biological processes, including photosynthesis and respiration. Quantitative and predictive computational characterization of redox events is therefore highly desirable for enriching our knowledge on mechanistic features of biological redox-active macromolecules. Here, we present a computational protocol exploiting polarizable embedding hybrid quantum-classical approach and resulting in accurate estimates of redox potentials of biological macromolecules. A special attention is paid to fundamental aspects of the theoretical description such as the effects of environment polarization and of the long-range electrostatic interactions on the computed energetic parameters. Environment (protein and the solvent) polarization is shown to be crucial for accurate estimates of the redox potential: hybrid quantum-classical results with and without account for environment polarization differ by 1.4 V. Long-range electrostatic interactions are shown to contribute significantly to the computed redox potential value even at the distances far beyond the protein outer surface. The approach is tested on simulating reduction potential of cryptochrome 1 protein from Arabidopsis thaliana . The theoretical estimate (0.07 V) of the midpoint reduction potential is in good agreement with available experimental data (−0.15 V). 

   more » « less
5. Polarizable AMOEBA force field predicts thin and dense hydration layer around monosaccharides

   https://doi.org/10.1039/D4CC04415K  

   Newman, Luke A; Patton, Mackenzie G; Rodriguez, Breyanna A; Sumner, Ethan W; Vaissier_Welborn, Valerie (December 2024, Chemical Communications)

   Stephan, Douglas; Ackermann, Lutz; Bonifazi, Davide; D_Alessandro, Deanna; Fan, Fengtao; Hamachi, Itaru; Hardi, Michaele; Jelfs, Kim; Li, Chao_Jun; Lou, David (Ed.)

   Polarizable force fields improve the modeling of carbohydrates in polar media. 

   more » « less