EVENTS

Upcoming Events

November 4, 2024

CCTCh Seminar

3:45 PM | Kent 120

Professor Marco De Vivo, Italian Institute of Technology
“From Mechanistic Insights to Drug Discovery: The Power of Computation“

My lab develops and applies computational methods to investigate how pharmaceutically relevant (bio)chemical systems operate at the atomic level. We use these mechanistic insights to design and synthesize small molecules to initiate drug discovery efforts. With these premises, I will first describe our work on understanding the molecular mechanism of the Na–K–Cl cotransporter 1 (NKCC1), which regulates ion transport across cell membranes. Alterations in chloride concentrations in neurons are linked to neurological conditions, making NKCC1 inhibition a promising strategy for neuroscience drug discovery. By integrating molecular modeling and medicinal chemistry, we have identified a new class of small molecules specifically targeting NKCC1 to treat core symptoms of neurodevelopmental disorders. One of these molecules derived from this effort, IAMA-6, is now in Phase 1 clinical trials with Iama Therapeutics. Then, I will present our current efforts in designing RNA splicing modulators, which hold therapeutic potential for various congenital diseases and cancer. I will again start from mechanistic insights for splicing in group II introns and then move to the computer-aided structure-based design of potent RNA-targeted compounds. I will discuss how such novel compounds act at the core of the splicing catalytic site with an unprecedented mode of action. This is confirmed by multiple RNA-ligand X-ray complexes combined with free energy perturbation calculations.

Past Events

October 7, 2024

CCTCh Seminar

2:00 PM | GCIS W301/W303 and Zoom

Professor Roel Tempelaar, Northwestern University
“Mixed quantum–classical modeling of quantum materials”

Quantum materials are poised to unlock new technological opportunities, but it remains unclear how their behavior is driven by lattice vibrations (phonons). I will present our efforts towards studying phonon-driven dynamics of quantum materials based on inexpensive mixed quantum–classical (MQC) models. While such models have traditionally been developed for molecules, we have recently reformulated them in momentum space tailored to solids. In addition, we have extended the applicability of MQC models to topologically-nontrivial systems. The resulting framework is readily applicable to semiconducting quantum materials, yielding encouraging results for monolayer transition-metal dichalcogenides. Time permitting, I will also present an extension of our MQC framework to (semi)metallic systems, by adopting a mean-field approach to electron correlation effects.

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September 26, 2024

CCTCh Seminar

1:00 PM | Kent 102 and Zoom

Professor Donald Truhlar, University of Minnesota
“Multiconfiguration Nonclassical-Energy Density Functional Theory”

Multiconfiguration nonclassical-energy density functional theory (MC-NEFT) is a form of density functional theory specifically developed for electronic structure calculations on strongly correlated systems [1,2]. This lecture will present an introduction to MC-NEFT, and it will summarize the current status. The lecture will begin with a review of some issues in Kohn-Sham density functional theory (a single-configuration method) that call for a multiconfiguration approach, and the lecture will also contain an introduction to strong correlation. Then it will review the first version of MC-NEFT, namely multiconfiguration pair-density density functional theory. This will lead up to a presentation of three recent developments:

MC23: a new meta functional for MC-PDFT with much higher accuracy than the previously available functionals;
DC24: a density coherence functional for MC-NEFT that has the advantage of only needing the one-particle reduced density matrix (1-RDM), not the two-particle one;
L-PDFT: a multistate version extending MC-PDFT to excited electronic states in a way suitable for modeling photodynamics.

MC-NEFT is a joint research program carried out in collaboration with Professor Laura Gagliardi of the University of Chicago. In addition to Professor Gagliardi, credit for the three new projects is given to the following:

MC23: Dayou Zhang and Jie Bao, University of Minnesota
DC24: Dayou Zhang, University of Minnesota
L-PDFT: Matthew Hennefarth and Mathew Hermes, University of Chicago.

[1] “Multiconfiguration Pair-Density Functional Theory: A New Way to Treat Strongly Correlated Systems,” L. Gagliardi, D. G. Truhlar, G. Li Manni, R. K. Carlson, C. E. Hoyer, and J. L. Bao, Accounts of Chemical Research 50, 66-73 (2017). doi.org/10. 1021/acs.accounts.6b00471

[2] “Electronic Structure of Strongly Correlated Systems: Recent Developments in Multiconfiguration Pair-Density Functional Theory and Multiconfiguration Nonclassical-Energy Functional Theory,” C. Zhou, M. R. Hermes, D. Wu, J. J. Bao, R. Pandharkar, D. S. King, D. Zhang, T. R. Scott, A. O. Lykhin, L. Gagliardi, and D. G. Truhlar, Chemical Science 13, 7685-7706 (2022). doi.org/1039/D2SC01022D

June 3, 2024

CCTCh Group Meeting

Matthew Du – (Vaikuntanathan Group)
2:00 PM | Kent 120 and Zoom
“Stabilizing equilibrium configurations using nonequilibrium forces“

May 6, 2024

CCTCh Group Meeting

Curt Waltmann – (Voth Group)

2:00 PM | GCIS W301/303 and Zoom

“Genome Packaging by the Mature HIV-1 Capsid”

April 15, 2024

CCTCh Seminar

12:00 PM | Kent 107 and Zoom

Professor Daniel Neuhauser, University of California (UCLA)
“Bringing Many Body Spectra to the Massive Molecules“

In this talk, we detail the journey to extend many-body perturbation linear
response methods to large molecular systems, including the canonically hard
cyanine dye problem. Molecular excitons in large extended systems are often
not well described by local or optimally-tuned TD-DFT due to highly delocalized
states valence and conduction states with long range electronic coupling and
charge transfer character. We have developed a stochastic formalism of the
Bethe-Salpeter equation, the linear response formalism that follows from the GW
approximation of many-body perturbation theory. Through a series of algorithmic
improvements to the method, we have developed new approximations to capture
the screened Coulomb interaction at lower computational cost, leading to the
study of systems with several thousand electrons.

April 1, 2024

CCTCh Seminar

2:00 PM | GCIS W301/303 and Zoom

Ping Yang, Theoretical Division, Los Alamos National Laboratory
“Data-driven Separation Design for 5f-Elements”

Advanced separation technologies are essential in the context of critical materials and spent nuclear fuels reprocessing, allowing for an increase in the supply of key elements, minimization of nuclear waste production, optimization of storage conditions, and alleviation of proliferation concerns. However, rationally designing advanced separation schemes has traditionally been a time-consuming and expensive endeavor. This complexity is partly due to intricate electronic structure of f-elements which contributes to their versatile chemical bonding, reactivity, and spectral properties. In this talk, I will begin by discussing the unique chemical bonding enabled by 5f-electrons and its implication for separation chemistry. Beyond the fundamental bonding interactions with extractants, numerous other factors impact the solvent extraction efficiency. We deploy a multidisciplinary effort that integrates modern data-centric approaches to develop new predictive capabilities for separations. In this presentation, I will share our recent progress on these integrated tasks, leveraging automated high-throughput simulations and robotic measurements.

March 4, 2024

CCTCh Seminar

2:00 PM | GCIS W301/303 and Zoom

Professor Christian Schilling
Arnold Sommerfeld Centre for Theoretical Physics, LMU Munich
“The Elecron Correlation Problem from a Quantum Information Perspective”

Describing strongly interacting electrons is one of the crucial challenges of modern quantum physics. A comprehensive solution to this electron correlation problem would simultaneously exploit both the pairwise interaction and its spatial decay. By taking a quantum information perspective, we explain how this structure of realistic Hamiltonians gives rise to two conceptually different notions of correlation and entanglement. The first one describes correlations between orbitals while the second one refers more to the particle picture. We illustrate those two concepts of orbital and particle correlation and present measures thereof. Our results for different molecular systems reveal that the total correlation between molecular orbitals is mainly classical, raising questions about the general significance of entanglement in chemical bonding. Finally, we also speculate on a promising relation between orbital and particle correlation and explain why this may replace the obscure but widely used concept of static and dynamic correlation.

September 11, 2023

CCTCh Group Meeting

Anna Schouten – (Mazzioti Group)
1:00 PM | Searle 240A and Zoom

“Exciton-condensate-like Amplification of Energy Transport in Light-harvesting”

July 25, 2023

CCTCh & Mazzioti Group Joint Seminar

2:00 PM | GCIS W301

Dr. Carlos L. Benavides-Riveros
“Quantum Parallelizing Quantum Eingensolvers for Excited States”

Dr. Benavides-Riveros is currently working at the University of Trento in Italy on method development projects for calculating excited-state properties of molecules and solids on quantum devices. His research spans a wide range of topics, from excited-state quantum chemistry and superconductivity to quantum computing and machine learning.

July 10, 2023

CCTCh Group Meeting

2:00 PM | Searle 240A and Zoom

Bohak Yoon – (Voth Group)
“Mechanistic Insights into CO2 Capture by Amino Acid Ionic Liquids through Multiscale Simulations.”

March 6, 2023

CCTCh Seminar

4:00 PM | ERC 161 and Zoom

Professor William James Glover, New York University Shanghai
“Pushing (QM/MM) boundaries: simulations of solvent-supported electronic states”

Three pillars of theoretical chemistry are quantum mechanics (governing the physics of light particles, especially electrons), statistical mechanics (providing the connections between microscopic interactions and macroscopic observables), and chemical dynamics (describing the motions of atoms on potential energy surfaces). As theoretical tools have developed, simultaneously with exponential increases in computational power, the boundaries between these three fields have blurred. In this talk, I will use the example of the hydrated electron, a solvent-supported excess electron embedded in liquid water, to showcase how these developments now allow for the simulation of the real-time dynamics of thousands of atoms with a large active region treated quantum mechanically. Recent experiments on the dynamical response of this system to the absorption of light have shown that previous theories give predictions that overestimate the dynamical timescale by an order of magnitude. Our simulations close the gap between theory and experiment and provide new physical insight into the dynamics of the hydrated electron.

February 6, 2023

CCTCh Seminar

2:00 PM | ERC 161 and Zoom

2:00 PM | Zoom

Cal Floyd – (Dinner and Vaikuntanathan Groups)

“Signatures of odd dynamics in viscoelastic systems: from spatiotemporal pattern formation to odd rheology”

September 19, 2022

CCTCh Group Meeting

2:00 PM | Zoom

Leeann Sager-Smith – (Mazziotti Group)

“Entangled phase of simultaneous fermion and exciton condensations realized”

June 17, 2022

CCTCh Seminar

11:00 AM | GCIS W301/W303

Professor Biman Bagchi, Solid State and Structural Chemistry Unit of the Indian Institute of Science

“Diffusion-Entropy Scaling through a Multidimensional Rate Theory”

Professor Biman Bagchi is currently serving as the India National Science Chair (DST-SERB) and holds a Honorary Professorship at the Solid State and Structural Chemistry Unit (SSCU), Indian Institute of Science (IISc), Bangalore. He received his PhD from Brown University, RI and carried out postdoctoral work at the University of Chicago and University of Maryland, before returning to India in 1984 to join the Indian Institute of Science. He is a Fellow of all the three National Science Academies of India, an elected Fellow of the third world academy of sciences (TWAS) and Elected Foreign Member of the American Academy of Arts and Sciences (2020) [AAA&S] He is the recipient of the 2021 Joel Henry Hildebrand Award from the American Chemical Society in Theoretical and Experimental Chemistry of Liquids, Humboldt Science Research Award of Alexander von Humboldt Foundation (2019). He has also received a fair number of Awards in India. And J. Physical Chemistry brought out a Festschrift special issue J. Phys. Chem. B, 2015, Vol.: 119, in his honour. Bagchi has authored three books on different aspects of statistical mechanics and currently writing a 4th book on nonequilibrium statistical mechanics. He has also published two non-technical books available at Amazon Kindle.

Relationship between entropy and relaxation has been a subject of inquiry since the time of Boltzmann who introduced his famous H-Theorem and remarked on its relation with entropy. This relationship has been further established through Adam-Gibbs relation and also Rosenfeld scaling hypothesis. We shall discuss a derivation of the diffusion-entropy scaling in a two-dimensional periodic lattice, using the multidimensional rate theory. We shall discuss a two-dimensional periodic system that displays interesting coherences in trajectories, leading to a non-monotonic friction dependence of diffusion. We discuss a simple random walk model that surprisingly could capture the non-monotonicity of diffusion (partly) and the behaviour at large friction (quantitatively). We shall also discuss, if time permits, a few biophysical problems that we are studying in our group.

June 6, 2022

CCTCh Group Meeting

2:00 PM | Zoom

Daniel Beckett (Voth Group)

“Multiscale Investigations of Microtubule Catastrophe”

May 2, 2022

CCTCh Seminar

2:00 PM | Zoom

Professor Shaama Sharada, University of Southern California

2:00 PM | Zoom

Professor Stuart Rice, University of Chicago

2:00 PM | Zoom

Chatipat Lorpaiboon, Graduate Student (Dinner Group)
“Improving transition path theory with extended committors”

TBD (Roux Group)

CCTCh Seminar

Professor Pratyush Tiwary, University of Maryland, College Park

“Can artificial intelligence help understand and predict molecular dynamics?”

2:00 PM | Zoom

The ability to rapidly learn from high-dimensional data to make reliable predictions about the future is crucial to life. This could be a fly avoiding predators, or the retina processing terabytes of data guiding complex human actions. Modern day artificial intelligence (AI) aims to mimic this fidelity and has been successful in many domains. It is tempting to ask if AI could also be used to understand and predict the dynamics of complex molecules with millions of atoms. In this talk I will show that certain flavors of AI can indeed help us understand generic molecular dynamics and also predict it even in situations with arbitrary long memories. However this requires close integration of AI with old and new ideas in statistical mechanics. I will talk about such methods developed by my group (1-3). I will demonstrate the methods on different problems, where we predict mechanisms at timescales much longer than milliseconds while keeping all-atom/femtosecond resolution. These include ligand dissociation from flexible protein/RNA and crystal nucleation with competing polymorphs. I will conclude by discussing some generic challenges and solutions regarding reliability, interpretability and extrapolative powers of AI when used in molecular simulations.

References:

1. Wang, Y., Ribeiro, J.M.L. & Tiwary, P. Past–future information bottleneck for sampling molecular reaction coordinate simultaneously with thermodynamics and kinetics. Nat. Commun. 10, 3573 (2019). https://doi.org/10.1038/s41467-019-11405-4

2. Tsai, S.T, Kuo, E.J. & Tiwary, P. Learning Molecular Dynamics with Simple Language Model built upon Long Short-Term Memory Neural Network. Nat. Commun. 11, 5115 (2020). https://doi.org/10.1038/s41467-020-18959-8

3. Wang, Y., Ribeiro, J.M.L. and Tiwary, P. Machine learning approaches for analyzing and enhancing molecular dynamics simulations. Curr. Op. Sruc. Bio., 61, 139 (2020). https://doi.org/10.1016/j.sbi.2019.12.016

March 1, 2021

CCTCh Seminar

Professor David Limmer, University of California, Berkeley

“Computing and decoding fluctuations in systems far from equilibrium”

3:00 PM | Zoom

In this talk, I will discuss some recent efforts to develop a set of theoretical and simulation tools to study many body systems driven away from equilibrium. This work leverages recent advancements in the study of large deviations and control theory, as well as the burgeoning area of stochastic thermodynamics. Generalizations of the fluctuation-dissipation theorem, and variational statements of stability for nonequilibrium systems, will be demonstrated. Specific questions concerning electrokinetic phenomena in ionic solutions confined to nanoscale dimensions and the self assembly of active and proliferating matter will be addressed.

October to November 2020

Symposium on Theoretical Chemistry

PKU-UChicago Joint Lecture Series

Lecture 1 (October 19/20): Frontiers of Biomolecular Theory & Simulation
Speakers: Gregory Voth, University of Chicago & Yiqin Gao, Peking University
Moderator: Chen Li, Peking University

Lecture 2 (October 26/27): Quantum Simulations of Heterogeneous Materials on Classical and Near-term Quantum Computers & Ensemble-based Thermodynamics of the Fuzzy Binding between Intrinsically Disordered Proteins and Small Molecule Ligands: Principle and Application
Speakers: Giulia Galli, University of Chicago & Zhirong Liu, Peking University
Moderator: Chen Li, Peking University

Lecture 3 (November 2/3): Complex Reaction Mechanisms and Drug Design
Speakers: Aaron Dinner, University of Chicago & Luhua Lai, Peking University
Moderator: Chen Li, Peking University

Lecture 4 (November 9/10): When Quantum Computing Meets DFT
Speakers: David A. Mazziotti, University of Chicago & Chen Li, Peking University

Lecture 5 (November 16/17): Non-equilibrium Thermodynamic and Quantum Dynamics
Speakers: Suriyanarayanan Vaikuntanathan, University of Chicago & Jian Liu, Peking University
Moderator: Chen Li, Peking University

Lecture 6 (November 23/24): Strong Correlation and Band Structure
Speakers: Laura Gagliardi, University of Chicago & Hong Jiang, Peking University
Moderator: Chen Li, Peking University

December 10, 2019

2019 Rice-Berry Lecture of the CCTCh

Professor John D. Weeks, University of Maryland, College Park

“Solvation, Structure, and Simulations of Systems with Strong Coulomb Interactions: The Long and Short of It”

3:45 PM | GCIS W301/W303

John D. Weeks is a Distinguished University Professor in the Department of Chemistry and the Institute for Physical Science and Technology at the University of Maryland, College Park. He earned his bachelor’s degree from Harvard University (1965) and then completed his PhD at the University of Chicago working with Stuart Rice (1969). John then moved to the University of California, San Diego for a postdoctoral fellowship in the group of Kurt Shuler. There, along with another postdoc in the group, David Chandler, and Hans Andersen (then an assistant professor at Stanford), he put together an elegant, powerful, and definitive framework to understand the structure of strongly interacting uniform simple liquids. This framework—commonly referred to as WCA in honor of Weeks, Chandler, and Andersen—has been used for understanding the properties of many nonpolar molecular liquids. John then moved to AT&T Bell Labs and pioneered work on the statistical mechanics of interfaces. In particular, John and his co-workers developed a statistical mechanics framework to describe a new transition governing the roughness of crystal interface. They showed that this “roughening” transition falls in the same class as the KTHNY transition that governs topological defect formation in two-dimensional solids. In 1990, John moved to the University of Maryland, College Park where he has been ever since. His recent work focuses on the conceptual development of a general theory of nonuniform ionic and dipolar fluids, focusing on hydrophobic and ionic solvation properties in aqueous solutions. John’s work has been recognized by multiple awards and honors, including elections to the National Academy of Sciences and American Academy of Arts and Sciences, as well as the Joel Henry Hildebrand Award from the American Chemical Society.

May 6, 2019

Inaugural Rice-Berry Lecture of the CCTCh

Professor Bruce J. Berne, Columbia University