Computational Chemical Science Center
Computational Chemical Science Center

PAST EVENTS

CSI Workshop: Deep Modeling for Molecular Simulation 2023

Our first in-person workshop “Deep Modeling for Molecular Simulation 2023”, July 11 – 14, 2023 was a success!

We appreciate our invited speakers, David Ceperley (University of Illinois), Robert DiStastio (Cornell University), Mark Tuckerman (New York University), Renata Wentzcovitch (Columbia University), Omar Valsson (University of North Texas), David Vanderbilt (Rutgers University), Xifan Wu (Temple University), Linfeng Zhang (AI for Science Institute, Beijing), and Roberto Car (Princeton), who took time out of their busy schedules to present their scientific lectures.  During the four days, we will have lectures in the mornings and hands-on sessions in the afternoons.

We had more than 80 participants apply and 40 participants were selected.  Participants registered from Russia, Taiwan, India, China, Nigeria, Hungary, Germany, France, Italy, Sri Lanka, and the United States.  We thank all of the participants who were excited to hear the lectures, participate in the hands-on tutorial sessions and the poster session make our first in-person workshop successful!  Congratulations to our 2 winners for the best posters, Lune Maillard (Sorbonne Université) and Hong-Zhou Ye (Columbia University)!

See the program here.

Special thanks to our tutors and organizers for their dedication in organizing this workshop. 

Organizers: Roberto Car, Pablo Piaggi, and Clarice Gethers-Mubarak (Princeton University)

Tutorial preparation and tutoring: Abhinav Raman, Chunyi Zhang, Iman Ahmadabadi, Jiayan Xu, Pablo Piaggi, Pinchen Xie, Ruiqi Gao, Taehun Lee, Yifan Li and Zachary Goldsmith

Virtual machine software setup: Yifan Li

Conference & Events: Emily Crosby (Princeton University)

Research Computing Cloud Architect: Irene Kopaliani (Princeton Research Computing)

Chemistry Department IT: Doug Russo and William Brown (Workshop website)

Hosts: Pablo Piaggi, Chunyi Zhang and Zachary Goldsmith (Princeton University, CSI center)

 

2023 CSI Center Summer Internship, June 4 – August 4, 2023

This program was offered to 3 undergraduates of underrepresented institutions interested in hands-on mentored research experience through the summer months. The proposed research project aimed to illustrate recent advances in the application of machine learning to molecular dynamics simulations based on quantum-mechanical electronic structure theory. The students will apply these techniques to gain insight into materials, such as graphene and aluminum.

Welcome to our 2023 summer interns Gabriel Diaz-Espinoza (The City College of New York), Katrina Mejia (Rutgers-Newark) and Yusef Wray (Macaulay Honors College at Hunter College, City University of New York)!

 

January 10th, 2023 

CSI Kickoff Meeting, Princeton University, Princeton, NJ

 

2022 Chemistry in Solution and at Interfaces (CSI) Workshop:  Modeling for Molecular Simulation, July 7 – 8, 2022

Our Modeling for Molecular Simulation workshop held on July 7-8, 2022 was a success!  The two-day virtual workshop covered recent developments in the application of deep learning to molecular simulation. The workshop consisted of lectures covering the theoretical foundations of the methods and hands-on tutorials for the relevant software packages (DeePMD-kit, DP-GEN, LAMMPS, and Quantum ESPRESSO). The lectures were given by well-known researchers in the community, including Stefano Baroni, Roberto Car, Robert DiStasio and Darrin York. The hands-on sessions covered the use of deep neural network models to learn the potential energy surface based on electronic density-functional theory calculations, an active learning approach to training, the learning of electronic properties based on maximally localized Wannier functions, and training models with long range electrostatic interactions.  Workshop flyer.

We had a total of 461 registered participants (USA+Canada (156), Europe (127), South America (107), Asia (46), and other countries (25)).  Most attendees registered were graduate students (202) and postdocs (117), followed by others (142) in academic or research positions.

Please see the workshop videos below.  You can also find the workshop which was funded by DOE on YouTube.  Click on this link for the videos.

Click here for the workshop tutorial link.

 

Day 1 – Thursday July 7, 2022

9:00 – 9:35 | Lecture: Roberto Car (Princeton University) “Deep potential method for molecular simulations”

9:35 – 10:10 | Lecture: Linfeng Zhang (DP Technology/AI for Science Institute) “Deep potential at scale: towards a framework for joint development of model, data, and software”

10:10 – 10:45 | Lecture: Robert DiStasio (Cornell University) “Towards a realistic description of H3O+ and OH− transport through confined environments using machine learning and an order-N framework for condensed-phase hybrid density functional theory”

Day 2 – Friday July 8, 2022

9:00 – 9:35 | Lecture: Darrin York (Rutgers University) “Next generation quantum and deep learning potentials for enzyme catalysis and drug discovery”

9:35 – 10:10 | Lecture: Stefano Baroni (SISSA) “Linear response theory of transport”

10:10 – 10:45 | Lecture: Chunyi Zhang (Temple University) “Deep modeling with long range electrostatic interactions”

 

January 20-22, 2022

2022 CSI Center Scientific Advisory Board Meeting

 

2020 Chemistry in Solution and at Interfaces (CSI) Workshop: Molecular Simulation with Machine Learning workshop

Our Molecular Simulation with Machine Learning workshop held on July 13 – 14, 2020 was a success!  The two-day workshop covered theory and hands-on tutorials on the software package for molecular simulation with machine learning (ML) tools developed at the Computational Chemical Science Center “Chemistry in Solution and at Interfaces”.  The package included codes to construct and use deep neural network models of the potential energy surface and electronic properties of multi-atomic systems that reproduce the results of electronic density functional theory.

We had a total of 584 registered participants (USA+Canada: 156; other American countries: 238; Europe: 101; Asia: 72; Africa: 17).  Most attendees registered were graduate students (242) and postdocs (159), followed by others (183) in academic or research positions. The workshop’s program included lectures and hands-on tutorials for students and postdocs.

The workshop videos are in the links below.

July 13th, 2020 – Molecular Simulation with Machine Learning Workshop (presentations & discussions)

Morning session 1, Chair: Thomas Gartner 

Weinan E (Princeton University): “Machine learning assisted modeling”

Roberto Car (Princeton University): “Molecular simulation with the deep potential method”

Pablo Piaggi (Princeton University): “The art of non-Boltzmann sampling”

 

Morning session 2, Chair: Amartya Bose

Gary Grest /Aidan Thompson (Sandia National Laboratories): “Introduction to LAMMPS molecular dynamics simulator” 

Thomas Kuhne (University of Paderborn): “CP2K/Quickstep: The Swiss Army Knife of Molecular Simulation”

Menno Bokdam (University of Vienna): “Entropy-driven phase transformations in hybrid perovskites simulated by on-the-fly machine-learning force fields” 

July 13th, 2020 – Molecular Simulation with Machine Learning Workshop (Tutorials) – Part 1 & Part 2

 

July 13, 2020, TUTORIAL SESSION 1, HOSTS: Marcos Calegari Andrade, Yixiao Chen, Tom Gartner, Pablo Piaggi, Shuwen Yue, Linfeng Zhang

Hands-on tutorials on the software package for molecular simulation with machine learning (ML) tools developed at the Computational Chemical Science Center “Chemistry in Solution and at Interfaces” (CSI).    The package includes codes to construct and use deep neural network models of the potential energy surface and electronic properties of multi-atomic systems that reproduce the results of electronic density functional theory. ML codes need interfacing with community codes for electronic structure and ab-initio simulation, classical molecular dynamics, path-integral molecular dynamics, and enhanced sampling of rare events. 

July 13th, 2020 – Afternoon sessions (Tutorials) – Part 1

July 13th, 2020 – Afternoon sessions (Tutorials) – Part 2

July 14th, 2020 – Molecular Simulation with Machine Learning Workshop (presentations & discussions)

 

Morning session 3, Chair: Pablo Piaggi

Michele Ceriotti (EPFL): “Equivariant representations for atomistic machine learning”

Sebastian Dick (SUNY): “Machine learned XC potentials in Siesta: NeuralXC”

Davide Tisi (SISSA): “Green Kubo simulation of transport properties from ab initio to neural networks”  

 

Morning session 4, Chair: Zachary Goldsmith

Robert A. DiStasio (Cornell U.): “DFT and Beyond: Benchmark Data for Next-Generation Machine Learning of Intra- and Inter-Molecular Interactions”

J. Mark Martirez (UCLA): “Density-functional-theory-based embedding theories for embedded correlated wavefunction description of molecules and surfaces”

 

Round table discussion. Panelists: All the speakers plus Stefano Baroni  (SISSA), Paolo Giannozzi (U. Udine), Aidan Thompson (Sandia  National Laboratories), L. Zhang

July 14th, 2020 – Molecular Simulation with Machine Learning Workshop (Tutorials)

July 13, 2020, TUTORIAL SESSION 1, HOSTS: Marcos Calegari Andrade, Yixiao Chen, Tom Gartner, Pablo Piaggi, Shuwen Yue, Linfeng Zhang

Hands-on tutorials on the software package for molecular simulation with machine learning (ML) tools developed at the Computational Chemical Science Center “Chemistry in Solution and at Interfaces” (CSI).    The package includes codes to construct and use deep neural network models of the potential energy surface and electronic properties of multi-atomic systems that reproduce the results of electronic density functional theory. ML codes need interfacing with community codes for electronic structure and ab-initio simulation, classical molecular dynamics, path-integral molecular dynamics, and enhanced sampling of rare events. 

 

September 27, 2019 – Princeton University
1st CSI Tutorial Session

 

April 12 – 13, 2019

2019 CSI Center Scientific Advisory Board Meeting

 

PAST SEMINAR SERIES

2023

Friday, July 28, 2023 (virtual, in-person)
Simone Perego, Istituto Italiano di Tecnologia
Title: Exploring the adsorption and decomposition of ammonia on iron-based surfaces from a dynamic perspective

Ali Khosravi, Scuola Internazionale Superiore di Studi Avanzati
Title:

Friday, May 26, 2023 (virtual, in-person)
Yifan Li, CSI Graduate Student, Princeton University
Title: Ab initio Study of Nuclear Quantum Effects in Water and Ice with Deep Learning Potentials 

Friday, May 12, 2023 (virtual, in-person)
Chunyi Zhang, CSI Postdoc, Temple University
Title: Dielectric properties of water and sodium chloride solutions

Alec Wills, CSI Graduate Student, Stony Brook University
Title: Learning Solvation: The Transition from Machine Learned Potentials of Bulk Solvent to Aqueous Solution

Friday, April 14, 2023 (virtual, in-person)
Will Jacobs, Professor, Chemical and Biological Engineering, Princeton University
Title: Controlling phase transitions away from equilibrium

Friday, March 31, 2023 (virtual, in-person)
Ruiqi Gao, CSI Graduate Student, Princeton University
Title: Methodology and some preliminary results on simulating excess electrons in water

Abhinav S. Raman, Postdoc, Department of Chemistry, Princeton University
Title: Proton transfer and acidity at the aqueous IrO2(110) interface from deep potential molecular dynamics

Friday, March 17, 2023 (virtual, in-person)
Aaron Kaplan, Postdoc, Department of Physics, Temple University
Title: Simulating the electronic structure of water with chemical accuracy at DFT cost

Friday, March 3, 2023 (virtual, in-person)
Zach Goldsmith, CSI Postdoc, Princeton University
Title: Voltage-Dependent Dynamics and Surface-Specific IR Spectra of Water at Gold Electrodes from Deep Neural Network-Assisted Ab Initio Calculations

Friday, February 24, 2023 (virtual, in-person)
Zach Michiel Sprik (University of Cambridge, Department of Chemistry)
Title: Continuum model of the simple dielectric fluid: consistency between density based and continuum mechanics methods

Friday, February 17, 2023 (virtual, in-person)
Jan Niklas Boyn, CSI Postdoc, Princeton University
Title: Probing pH-Dependent Dehydration Dynamics of Mg and Ca Cations in Aqueous Solutions with Multi-Level Quantum Mechanics/Molecular Dynamics Simulations

Pinchen Xie, CSI Graduate Student, Princeton University
Title: Ab initio generalized Langevin equation

Friday, February 3, 2023 (virtual, in-person)
Boris Kozinsky, Professor, Harvard School of Engineering and Applied Physics
Title: Dynamics of realistic materials from first principles and machine learning computations

2022

Friday, December 16, 2022 (virtual, in-person)
Maria Muniz, CSI Graduate Student, Princeton University
Title: Vapor-Liquid Equilibrium and Nucleation Studies of Water from First Principles-Based Machine Learning Models

Friday, December 2, 2022 (virtual, in-person)
Fujie Tang, CSI Postdoc, Temple University
Title: Molecular insights into optical spectroscopy of liquid water and ice

Mark DellStritto,  CSI Postdoc, Temple University
Title: Inferred Charges from Machine Learning

Friday, November 18, 2022 (virtual, in-person)
Abhinav S. Raman, Postdoc, Department of Chemistry, Princeton University
Title: Modeling the solvation and acidity of carboxylic acids using deep neural-network potentials

Friday, November 4, 2022 (virtual, in-person)
Jie Deng, Assistant Professor of Geosciences, Princeton University
Title: Simulating water (H2O) and rock (MgSiO3) in the deep Earth

Friday, June 3, 2022 (virtual, in-person)
Chunyi Zhang, CSI Postdoc, Temple University
Title: Dielectric properties of liquid water and NaCl solutions

Friday, May 13, 2022 (virtual, in-person)
Patricia Vindel-Zandbergen, CSI Postdoc, Rutgers University – Newark
Title: Mixed quantum-classical methods derived from the exact factorization approach: A case study on the uracil cation

Friday, April 29, 2022 (virtual, in-person)
Pablo Piaggi, CSI Postdoc, Princeton University
Title: Effect of proton disorder and liquid-liquid criticality on the melting lines of ice polymorphs

Friday, April 15, 2022 (virtual, in-person)
Taehun Lee, Postdoc, Princeton University
Title: Theoretical Insights into Photoelectrochemical Water Reduction on Delafossite CuRhO2

Friday, April 1, 2022 (virtual, in-person)
Zach Goldsmith, CSI Postdoc, Princeton University
Title: Ab initio characterization of charge carriers at the aqueous interface of doped hematite

Friday, March 4, 2022 (virtual, in-person)
Kewei Zhao, Graduate student, Geosciences, Princeton University
Title: Journey of calcium in seawater: From dissolved ion complexes to biomineralization

Friday, December 10, 2021 (virtual, in-person)
Marivi Fernandez-Serra, CSI PI, Stony Brook University
Title: Photocatalytic water oxidation in SrTiO3 [001] surfaces

Friday, November 12, 2021 (virtual, in-person)
Maria Muniz, CSI Graduate Student, Princeton University
Title: Vapor-liquid equilibrium studies of water with an ab initio deep neural network model

Zhutian (Clarissa) Ding , CSI Graduate Student, Princeton University
Title: Pathways for Electron Transfer at the MgO-Water Interface

Friday, October 29, 2021 (virtual, in-person)
Tom Underwood, Postdoc, Civil & Environmental Engineering, Princeton University
Title: Why Clays Swell: Understanding the Dielectric Properties of Confined Water

Friday, October 15, 2021 (virtual, in-person)
Tom Gartner, CSI Postdoc, Princeton University
Title: Sampling water’s liquid-liquid transition from first

John Mark P. Martirez, Assistant Project Scientist, Chemical & Biomolecular Engineering, UCLA
Title: Hydration of CO2 in water from first principles

Friday, October 1, 2021 (virtual)
Robert Wexler, CSI Postdoc, Princeton University
Title: Searching for seawater splitting anodes that break O-Cl chemisorption scaling

2021
Friday, May 28, 2021 (virtual)
Sebastian Dick, CSI Grad Student, Stonybrook University
Title: Machine Learning in Density Functional Theory: NeuralXC and xc-diff

Friday, May 14, 2021 (virtual)
Amartya Bose, CSI Postdoc, Princeton University
Title: Nuclear quantum effects in ab initio water

Friday, April 30, 2021 (virtual)
Fujie Tang , CSI Postdoc, Temple University
Title: Theoretical X-ray Absorption Spectroscopy of Liquid Water by the GW plus Bethe-Salpeter equation (GW-BSE) method

Chunyi Zhang, CSI Postdoc, Temple University
Title: Modeling liquid water by climbing up Jacob’s ladder in density functional theory facilitated by deep neural network

Friday, April 16, 2021 (virtual)
Zachary Goldsmith, CSI Postdoc, Princeton University
Title: Effects of applied voltage on water at gold electrodes from first-principles simulations

Friday, April 2, 2021 (virtual)
Chunyi Zhang, CSI Postdoc, Temple University
Title: An investigation of the “pressure effect” in NaCl solution

Friday, March 19, 2021 (virtual)
Sal Torquato, Professor/CSI PI, Princeton University
Title: Local Number Fluctuations in Hyperuniform and Nonhyperuniform Systems: Higher-Order Moments and Distribution Functions

Friday, March 5, 2021 (virtual)
Yixiao Chen, CSI Grad Student, Princeton University
Title: DeePKS: a comprehensive data-driven approach towards chemically accurate density functional theory

Friday, February 19, 2021 (virtual)
Mark DelloStritto, CSI Postdoc, Temple University
Title: Building Better Neural Network Potentials: Impact of Symmetry and Activation Functions

Friday, February 5, 2021 (virtual)
Pablo Piaggi, CSI Postdoc, Princeton University
Title: Towards the simulation of ice nucleation from first principles

Friday, January 22, 2021 (virtual)
Patricia Vindel Zandbergen, CSI Postdoc, Rutgers(Newark) University
Title: Mixed quantum-classical dynamics based on the Exact Factorization approach

Friday, January 8, 2021 (virtual)
Cate Anstöter, CSI Postdoc, Temple University
Title: Modelling the electron capture dynamics of micro-hydrated uracil

2020
Friday, November 13, 2020 (virtuall)
Michael Webb, Assistant Professor, Princeton University
Title: Integrating Coarse-Grained Modeling, Machine Learning, and Optimization for Biopolymer Design

Friday, October 30, 2020 (virtual)
William Jacobs, Assistant Professor, Princeton University
Title: Programmable phase behavior in biopolymer solutions

Friday, October 16, 2020 (virtual)
Shuwen Yue, CSI Graduate Student, Princeton University
Title: Dynamic and thermodynamic properties of water and aqueous electrolyte solutions using empirical and machine-learning models

Friday, October 2, 2020 (virtual)
GĂŒl Zerze, Postdoc, Princeton University
Title: Liquid-liquid critical point in realistic classical models of water

Friday, September 18, 2020 (virtual)
Yuan Ping, Assistant Professor, University of California, Santa Cruz
Title: Spin and exciton dynamics for quantum materials from first-principles

Friday, September 11, 2020 (special seminar-virtual)
Weile Jia,  Postdoc, University of California, Berkeley
Title: HPC+AI: pushing ab initio MD to 100 million atoms on the Summit supercomputer

Friday, September 4, 2020 (virtual)
Thomas Gartner, CSI Postdoc, Princeton University
Title: Signatures of a liquid-liquid transition in neural network and empirical models of water

Friday, February 21, 2020 – Princeton University
Lesheng Li, CSI Postdoc, Princeton University
Title: First-Principles Modeling of Sodium Ion Intercalation into TiS2 Interlayers for Water Desalination

Friday, February 7, 2020 – Princeton University
Ian C Bourg, Assistant Professor, Princeton University
Title: MD simulations of charge screening, hydrophobic adsorption, and colloidal mechanics at Earth’s most abundant interface

Friday, January 24, 2020 – Temple University
Mark DelloStritto, CSI Postdoc, Temple University
Title: Volume Scaling for Improving the Performance of Neural Network Potentials

Friday, December 13, 2019 – Temple University
Fujie Tang, CSI Postdoc, Temple University
Title: Molecular Modeling of Interfacial Water at Water-Air Interface and Ice-Air Interface

2019
Friday, November 15, 2019
Pablo Piaggi, CSI Postdoc – Princeton University
Title: Calculation of liquid-solid free energy differences: the case of hexagonal ice

Friday, November 1, 2019
Thomas Gartner III, CSI Postdoc – Princeton University
Title: Molecular dynamics simulation of the emulsion assembly of nanoparticle mixtures; and, a look ahead

Friday, October 18, 2019
Amartya Bose, CSI Postdoc – Princeton University
Title: Phase space and path integral methods in quantum dynamics

Friday, October 4, 2019 – Princeton University
Zachary Goldsmith, CSI Postdoc, Princeton University
Title: Model and Computational Studies of Nuclear Quantum Effects in Photo- and Electrochemical Energy Conversion Processes

Friday, April 26, 2019 – Princeton University
Jianing Li, Associate Professor, The University of Vermont
Title: Advancing Rational Design of Nanomedicines from Biomolecular Self-Assembly

Friday, February 15, 2019 – Princeton University
Pablo G. Debenedetti, Dean for Research, Princeton University
Title: Computational Investigation of the Phase Behavior of Supercooled Water

Friday, January 11, 2019 – Princeton University
Marivi Fernandez-Serra, Professor, Stony Brook University
Title: Learning from the Density to Correct Total Energy and Forces in First Principle Simulations

2018
Friday, December 7, 2018 – Princeton University
Spiridoula Matsika, Professor, Temple University
Title: Nonadiabatic effects in electron transfer in DNA

Friday, November 2, 2018 – Princeton University
Neepa Maitra, Professor, City University of New York
Title: Non-adiabatic dynamics via the exact factorization approach