Amr Dodin completed his BSc in Chemical Physics and Mathematics and MSc in Theoeretical Chemistry at the University of Toronto. During this time, he studied the quantum dynamics of molecules excited by sunlight, such as photosynthetic light harvesting complexes and retinal in the human eye. He then received his PhD in Theoretical Chemistry at MIT under the supervision of Prof. Adam Willard where his research focused on developing new mathematical theories and computer simulations for understanding how energy or charge move through disordered molecular materials and nano-materials, and for understanding information processing in realistic quantum computers. Most recently, as a postdoctoral scholar at UC Berkeley and Lawrence Berkeley National Lab under the supervision of Prof. Phill Geissler and Prof. David Limmer, Amr used Machine Learning-powered computer simulations alongside statistical mechanical theories to understand the speciation and reactivity of ions near electrochemical and atmospheric interfaces.
Research Overview
Nearly every process of interest in chemistry, biology, and physics is characterized by a system interacting strongly with its environment. Solvent fluctuations drive the interfacial dynamics of molecules that govern electrochemistry and atmospheric chemistry. The protein machinery of photosynthesis continuously adapts to changing light intensities. The performance of a quantum device degrades severely every time it interacts with its surroundings. The Dodin group studies these diverse processes through the statistics of the environments that drive them, formulating our insights mathematically as statistical mechanical theories. In many cases, the surroundings we consider are complex and far from equilibrium, involving the interplay of quantum and classical systems, with dynamics spanning many length and time scales. Simulating such complex systems is often intractable with existing tools, requiring the development of new computational methods and models, such as Machine Learning based interaction potentials, and thermodynamically consistent mutliscale models. Our research consists of 3 major areas of interest:
1. Chemical Reactions at Liquid Interfaces: A surprising pattern of discoveries has recently emerged in many areas of chemistry. Some chemical reactions that occur very slowly in a bulk liquid can be significantly accelerated at interfaces where the liquid meets another phase of matter. In organic synthesis, chemical reactions that can take a day in pure toluene proceed to completion in minutes by stirring in a small amount of water, indicating that the water-toluene interface can act as the ultimate "green catalyst". Unique chemistry can occur at the liquid-vapor interface of aerosol droplets in the atmosphere and in our indoor environments, playing an important role in the composition of gases that affect our climate and health. Electrochemical reactions that are responsible for the performance of batteries in electric vehicles and the grid scale energy storage we need to sustainably power our cities primarily occur within a nanometer of the liquid-electrode interface of these devices. These liquid interfaces are unique nanoscale chemical environment that can be very different from the bulk liquid, driving this enhanced reactivity. The Dodin group builds computational tools, such as electrochemical Neural Network Potentials, and mathematical theories, such as interfacial liquid state theory, that can describe the unique properties of these environments and explain how they can drive such remarkable acceleration of chemical reactions.
2. Biological Control of Photosynthesis: When a photosynthetic organism absorbs sunlight, it must decide if the absorbed energy is transported to a reaction center, where it drives reactions that store the energy, or if it is dissipated into the environment. The ability to balance these outcomes under varying light intensity is essential to the survival of the organism. If too much energy is dissipated, the organism will not generate the energy required to survive. If too much is directed to the reaction center, side-reactions generate toxic byproducts that destroy the cell’s proteins. Photosynthetic organisms are amazingly effective at making this decision, evolving a variety of mechanisms for regulating energy transport, known collectively as nonphotochemical quenching (NPQ), which allow a limited cast of pigments and proteins to respond to large variations in light intensity spanning many time scales. The Dodin group develops multi-scale models that span the quantum dynamics of excited electrons on the femtosecond timescale to evolutionary dynamics of photosynthetic organisms on the timescale of centuries in order to understand how these extraordinary biological control mechanisms operate and evolved. We combine these models with the latest theories from non-equilibrium statistical mechanics, such as thermodynamic uncertainty relations and far from equilibrium fluctuation theorems to gain a fundamental understanding of the biophysics of homeostasis - how biological systems are able to maintain their internal state in the face of fluctuating external environments.
3. Noisy Quantum Devices: Quantum devices exploit interference and entanglement to perform tasks that would not be possible with a classical device. The interaction of these systems with their environments stochastically perturbs their dynamics, typically destroying the quantum effects on which they rely. The loss of these quantum effects is a key barrier to the implementation of useful quantum computers and other quantum technologies. However, it has recently been discovered that in some cases, a noisy environment can generate rather than destroy these quantum interference effects, raising the remarkable possibility that we can harness such noise-induced coherences to build robust quantum devices that can operate at high temperatures or without isolating them from their surroundings. The Dodin group combines the tools of open systems quantum dynamics with recent developments in non-equilibrium thermodynamics to understand the statistics of dynamics produced by noisy environments. In doing so, we have two main goals (1) designing the world's first noise-driven quantum devices that exploit noise-induced coherences to exceed classical limits, and (2) derive the thermodynamic limits that govern quantum computing and use them to develop better quantum computers, similarly to how the laws of thermodynamics taught us how to build better heat engines.
Teaching (if applicable)
Publications (if applicable):
Selected Publications:
1. Heelweg, H.J.; Dodin, A.; Willard, A.P.; Deriving the Landauer Principle From the Quantum Shannon Entropy. J. Phys. Chem. Lett. 16 (5) 1397-1402 (2025).
2. Cohen, L.; Dodin, A.; Wilson, K.R.; Limmer, D.T.; Accelerated Chlorination at the Air-Organic Interface Revealed by Molecular Simulations and Kinetic Modeling. J. Phys. Chem. Lett.16 (29) 7498-7505 (2025).
3. Dodin, A.; NaCl Ion Pairing at Liquid-Insulator and Liquid-Conductor Interfaces. J. Phys. Chem. C 129 (20) 9572-9579 (2025).
4. Bernal, F.; Dodin, A.; Kyprianou, C.; Limmer, D.T.; Saykally, R.J.; Strong adsorption of guanidinium cations to the air–water interface. Proc. Natl. Acad. Sci.122 (2) e2418443122 (2025).
5. Dodin, A.; Brumer, P.; Generalized adiabatic theorems: Quantum systems driven by modulated time-varying fields. Phys. Rev. X Quantum 2 (3) 030302 (2021).
6. Anderson, M.C.; Dodin, A.; Fay, T.P.; Limmer, D.T.; Coherent control from quantum commitment probabilities. J. Chem. Phys. 161 (2) 024115 (2024).
7. Dodin, A.; Willard, A.P.; Nonequilibrium work relations and response theories in ensemble quantum systems. J. Phys. Chem. Lett. 12 (45) 11151-11157 (2021).
8. Dodin, A.; Brumer, P.; Noise-induced coherences in molecular processes. J. Phys. B 54 (22) 223001 (2022).
9. Dodin, A.; Geissler, P.L.; Symmetriced Drude oscillator force fields improve numerical performance of polarizable molecular dynamics. J. Chem. Theor. Comp. 19 (10) 2906-2917 (2023).
10. Castellanos, M.A.; Dodin, A.; Willard, A.P.; On the design of molecular excitonic circuits for quantum computing: the universal quantum gates. Phys. Chem. Chem. Phys. 22 (5) 2048-2057 (2020).
A full publication list is available on Google Scholar.