arXiv subjects

Benjamin K. Miller

Publications and source records attributed to Benjamin K. Miller.

3 recordsLinked to original sources

arXiv2026

Quantum-accurate atomistic modeling of enzyme catalysis using a machine learned potential

Electronic rearrangements associated with bond forming/breaking in catalytic enzymes require quantum mechanical (QM) treatment beyond classical molecular mechanics (MM). Hybrid QM/MM methods enable tractable simulations but require system-specific setup and are sensitive to the QM region choice and treatment of the QM/MM interface. We demonstrate quantum-accurate treatment of all-atom, complete enzymes in explicit solvent comprising up to 54k atoms and 1 microsecond of total simulation time using the machine-learned interatomic potential (MLIP) eSEN-omol. We reproduce experimental barrier trends for Claisen rearrangement in chorismate mutase, resolve critical intermediate states in PETase catalyzed polymer depolymerization, and distinguish mechanistic alternatives for metal-activated phosphoryl transfer in nucleoside diphosphate kinase. We realize 1000x speedups relative to typical QM/MM calculations without system-specific tuning. These results establish MLIPs as a practical route to QM-accurate simulations of enzyme catalysis.

physics.chem-ph↗

arXiv2025

FastCSP: Accelerated Molecular Crystal Structure Prediction with Universal Model for Atoms

Molecular crystal structure prediction (CSP) is essential for applications in pharmaceuticals and organic electronics. However, CSP remains challenging and computationally intensive due to the need to explore a large search space with sub-kJ/mol accuracy to distinguish between competing polymorphs. While dispersion-inclusive density functional theory (DFT) offers the necessary precision, its computational cost is impractical for a large number of putative structures. Here, we present FastCSP, an open-source, end-to-end CSP workflow driven entirely by a single pretrained universal machine learning interatomic potential (MLIP), the Universal Model for Atoms (UMA), without any system-specific fine-tuning or DFT calculations. FastCSP integrates conformer generation, random structure generation via Genarris 3, geometry optimization, free energy evaluation, and conformer energy corrections, all powered by UMA. Benchmarked on 28 semi-rigid and 10 flexible molecules spanning 74 experimental polymorphs, FastCSP reliably recovers all known structures, ranking them within 9 kJ/mol of the global minimum. UMA reproduces dispersion-inclusive DFT results with high fidelity across chemically diverse compounds. Conformer corrections are particularly beneficial for flexible compounds with conformational polymorphism, such as ROY. UMA's accuracy, transferability, and computational cost thus eliminate the need for classical force fields in early-stage screening and DFT-based re-ranking in CSP workflows. The open-source release of the entire FastCSP workflow lowers the barrier to accessing CSP, enabling both pharmaceutical-grade and high-throughput polymorph screening within practical computational reach.

physics.chem-ph↗

arXiv2020

Chemical Kinetics for Operando Electron Microscopy of Catalysts: 3D Modeling of Gas and Temperature Distributions During Catalytic Reactions

$\textit{In situ}$ environmental transmission electron microscopy (ETEM) is a powerful tool for observing structural modifications taking place in heterogeneous catalysts under reaction conditions. However, to strengthen the link between catalyst structure and functionality, an $\textit{operando}$ measurement must be performed in which reaction kinetics and catalyst structure are simultaneously determined. To determine chemical kinetics for gas-phase catalysis, it is necessary to develop a reliable chemical engineering model to describe catalysis as well as heat and mass transport processes within the ETEM cell. Here, we establish a finite element model to determine the gas and temperature profiles during catalysis in an open-cell operando ETEM experiment. The model is applied to a $SiO_2$-supported Ru catalyst performing CO oxidation. Good agreement is achieved between simulated compositions and those measured experimentally across a temperature range of 25 - 350 °C. In general, for lower conversions, the simulations show that the temperature and gas are relatively homogeneous within the hot zone of the TEM holder where the catalyst is located. The uniformity of gas and temperature indicates that the ETEM reactor system behavior approximates that of a continuously stirred tank reactor. The large degree of gas-phase uniformity also allows one to estimate the catalytic conversion of reactants in the cell to within 10 percent using electron energy-loss spectroscopy. Moreover, the findings indicate that for reactant conversions below 30 percent, one can reliably evaluate the steady-state reaction rate of catalyst nanoparticles that are imaged on the TEM grid.

cond-mat.mtrl-sci↗