Greater Boston Area Theoretical Chemistry Lecture Series

2022-2023 Speaker Schedule

Making sense of polarons and electron localization in solids

11/2/22 4:00 pm EST at MIT building 32 room 124

Feliciano Giustino

Oden Institute and Department of Physics, The University of Texas at Austin, Austin, TX




GiustinoF

Polarons are fascinating realizations of emergent quasiparticles resulting from the interaction between fermions and bosons [1]. In crystals, polarons form when electrons or holes become dressed by phonons in the form of lattice distortions. In the presence of weak electron-phonon interactions, polarons behave like conventional Bloch waves with heavier effective masses. In the presence of strong interactions, on the other hand, polarons become localized wavepackets and profoundly alter the transport, electrical, and optical properties of the host material. In this talk I will describe recent explorations of polaron physics from the point of view of first-principles atomic-scale calculations [2,3]. In the first part of the talk, I will provide a general introduction to the electron-phonon problem, and show that we can now perform predictive non-empirical calculations of many materials properties relating to electron-phonon physics using density functional theory and many-body Green's functions methods [4,5]. In the second part, I will present a recently-developed ab initio theory of polarons and its applications to simple ionic insulators. I will make the connection with historical developments such as Feynman's polaron theory, and discuss implications on our current understanding of electron localization in solids.

References
[1] F. Giustino, Rev. Mod. Phys. 89, 015003 (2017).
[2] W. H. Sio, C. Verdi, S. Poncé, and F. Giustino, Phys. Rev. Lett. 122, 246403 (2019).
[3] J. Lafuente-Bartolome, C. Lian, W. H. Sio, I. G. Gurtubay, A. Eiguren, and F. Giustino, Phys. Rev. Lett. 129, 076402 (2022).
[4] S. Poncé, W. Li, S. Reichardt, and F. Giustino, Rep. Prog. Phys. 83, 036501 (2020).
[5] M. Zacharias and F. Giustino, Phys. Rev. Res. 2, 013357 (2020).

Rare Conformational transitions in Biomolecular Systems

12/7/22 4:00 pm EST at MIT building 32 room 124

Benoît Roux

University of Chicago, Chicago, IL




RouxB

Classical molecular dynamics (MD) simulations based on atomic models play an increasingly important role in a wide range of applications in physics, biology and chemistry. The approach consists of constructing detailed atomic models of the macromolecular system, and having described the microscopic forces with a potential function, using Newton's classical equation, F=MA, to literally "simulate" the dynamical motions of all the atoms as a function of time. The calculated trajectory, though an approximation to the real world, provides detailed information about the time course of the atomic motions, which is impossible to access experimentally. While great progress has been made, producing genuine knowledge about biological systems using MD simulations remains enormously challenging. Among the most difficult problems is the characterization of large conformational transitions occurring over long-time scales. Issues of force field accuracy, the neglect of induced polarization, in particular, are also a constant concern. Transition path theory offers a powerful paradigm for mapping the conformational landscape of biomolecular systems is to combine free energy methods, string method, transition pathway techniques, and stochastic Markov State Model based massively distributed simulations.[1-5] These concepts will be illustrated with a few recent computational studies of biomolecular systems.

References
[1] Pan, A. C., Sezer, D. & Roux, B. Finding transition pathways using the string method with swarms of trajectories. J. Phys. Chem. B 112, 3432-3440, (2008).
[2] Pan, A. C. & Roux, B. Building Markov state models along pathways to determine free energies and rates of transitions. J. Chem. Phys. 129, 064107, (2008).
[3] Roux, B. String Method with Swarms-of-Trajectories, Mean Drifts, Lag Time, and Committor. J. Phys. Chem. A 125, 7558-7571, (2021).
[4] Roux, B. Transition rate theory, spectral analysis, and reactive paths. J. Chem. Phys. 156, 134111, (2022).
[5] He, Z., Chipot, C. & Roux, B. Committor-Consistent Variational String Method. J. Phys. Chem. Lett. 13, 9263−9271, (2022).

Physical Principles of Protein Phase Separation in Biomolecular Condensates Explored by Theory and Computation

1/25/23 4:00 pm EST at MIT building 32 room 124

Hue Sun Chan

University of Toronto, Toronto




HSChan

Compartmentalization at the cellular and sub-cellular levels is essential for biological functions. Some of the intra-organismic compartmentalized bodies are devoid of a lipid membrane (hence sometimes called “membrane-less organelles”) and possess material properties similar to those of mesoscopic liquid droplets. Referred to collectively as “biomolecular condensates”, their assembly is underpinned to a significant degree by liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs), intrinsically disordered regions (IDRs) of proteins, globular protein domains, and nucleic acids—though other physicochemical processes also contribute [1]. To gain physical insights, our group has developed analytical theories [2]—including Flory-Huggins formulations, random phase approximation [3], Kuhn-length renormalization [4], and new formulations of field-theoretic simulation that account for both short- and long-spatial-range interactions [5,6]—as well as coarse-grained explicit-chain molecular dynamics models for sequence-specific LLPS of IDPs/IDRs [7]. This effort has elucidated the effect of sequence charge pattern [2-7], π-related interactions [7], pH, salt [4], and osmolytes [8] on biomolecular LLPS. Moreover, our results point to a “fuzzy” mode of molecular recognition by charge pattern matching [9] modulated by excluded-volume effects [10], which is relevant to deciphering how different IDP species may de-mix upon LLPS to achieve functional sub-compartmentalization. A first step has also been taken toward rationalizing the temperature and pressure dependence of LLPS by empirical and atomic models of solvent-mediated hydrophobic interactions [11] and the interplay between stoichiometric and less-specific multivalent interactions in the assembly of biomolecular condensates [12]. Biological ramifications of our findings will be discussed, including how the pressure sensitivity of an in vitro model of postsynaptic densities might offer biophysical insights into pressure-related neurological disorders in terrestrial vertebrates [13].

References
[1] Lyson, Peeple, Rosen (2021) Nat Rev Mol Cell Biol 22:215-235.
[2] Lin, Forman-Kay, Chan (2018) Biochemistry 57:2499-2508.
[3] Lin, Forman-Kay, Chan (2016) Phys Rev Lett 117: 178101.
[4] Lin et al. (2020) J Chem Phys 152:045102.
[5] Lin et al. (2023) In: Methods in Molecular Biology (Springer-Nature), Vol. 2563, Ch. 3, pp.51-94.
[6] Wessén et al. (2022) J Phys Chem B 126:9222-9245.
[7] Das et al. (2020) Proc Natl Acad Sci USA 117:28795-28805.
[8] Cinar et al. (2019) J Am Chem Soc 141:7347-7354.
[9] Lin et al. (2017) New J Phys 19:115003.
[10] Pal et al. (2021) Phys Rev E 103:042406.
[11] Cinar et al. (2019) Chem Eur J 25:13049-13069.
[12] Lin et al. (2022) Biophys J 121:157-171.
[13] Cinar et al. (2020) Chem Eur J 26:11024-11031.

TBD

3/15/23 4:30 pm EST at MIT building 32 room 144

Eran Rabani

University of California Berkeley, Berkeley, CA




ERabani

TBD

Ab-initio solid state chemistry as a new frontier of theory

3/22/23 4:30 pm EST at MIT building 32 room 144

Dominika Zgid

University of Michigan, Ann Arbor, MI




DZgid

The search for new materials is at the core of the technological advancement of our society. While many newly synthesized materials can be analyzed by current quantum chemical techniques, mostly based on the density functional theory (DFT), there is a large number of materials that cannot be treated successfully by existing methodologies. This is mostly due to the presence of strong electron correlation, relativistic effects, and disorder. These materials require a post-DFT description that explicitly includes electron-electron interactions.
[In my talk, I will discuss current theoretical challenges in the study of solid state materials and I will describe my group’s contributions to the development of post-DFT methods. In the first part, I will present the newest relativistic methodologies for solids. In the second part, I will talk about the treatment of strongly correlated electrons residing in d- and f-orbitals of crystals with transition metals. Finally, I will sketch future directions for computational ab-initio solid state chemistry.