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Hybrid quantum mechanics / molecular mechanics (QM/MM) models successfully describe the properties of biological macromolecules. However, most QM/MM methodologies are constrained to unrealistic gas phase models, thus limiting their…
Electronic polarization and dispersion are decisive actors in determining interaction energies between molecules. These interactions have a particularly profound effect on excitation energies of molecules in complex environments, especially…
Analytic second derivatives of electrostatic embedding (EE) quantum mechanics/molecular mechanics (QM/MM) energy are important for performing vibrational analysis and simulating vibrational spectra of quantum systems interacting with an…
Given a partition of a large system into an active quantum mechanical (QM) region and its environment, we present a simple way of embedding the QM region into an effective electrostatic potential representing the environment. This potential…
The coherence of quantum dot qubits fabricated in semiconductors is often limited by charge noise from defects in gate dielectrics, which are material- and process-dependent. Characterizing these defects is an important step towards…
A kernel-based method (kernelized minimal distributed charge model - kMDCM) to represent the molecular electrostatic potential (ESP) in terms of off-center point charges whose positions adapts to the molecular geometry. Using Gaussian…
Quantum-mechanically-driven charge polarization and charge transfer are ubiquitous in biomolecular systems, controlling reaction rates, allosteric interactions, ligand-protein binding, membrane transport, and dynamically-driven structural…
We present an implementation of the quantum mechanics/molecular mechanics (QM/MM) method for periodic systems using GPU accelerated QM methods, a distributed multipole formulation of the electrostatics, and a pseudo-bond treatment of the…
We developed a general framework for hybrid quantum-classical computing of molecular and periodic embedding approaches based on an orbital space separation of the fragment and environment degrees of freedom. We demonstrate its potential by…
Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from…
Quantum embedding approaches involve the self-consistent optimization of a local fragment of a strongly correlated system, entangled with the wider environment. The `energy-weighted' density matrix embedding theory (EwDMET) was established…
This thesis synthesizes probability and entropic inference with Quantum Mechanics (QM) and quantum measurement [1-6]. It is shown that the standard and quantum relative entropies are tools designed for the purpose of updating probability…
We propose Electrostatic Field Matching (EFM), a novel method that is suitable for both generative modeling and distribution transfer tasks. Our approach is inspired by the physics of an electrical capacitor. We place source and target…
Atomic partial charges are crucial parameters in molecular dynamics (MD) simulation, dictating the electrostatic contributions to intermolecular energies, and thereby the potential energy landscape. Traditionally, the assignment of partial…
Predictive simulation of electrochemical interfaces requires atomistic models that capture reactive bond rearrangements, long-range electrostatics, and charge distributions reflecting the electronic distinctness of electrode and…
Quantum embedding is an appealing route to fragment a large interacting quantum system into several smaller auxiliary `cluster' problems to exploit the locality of the correlated physics. In this work we critically review approaches to…
To further develop accurate and large-scale simulations of electrochemical interfaces, we propose a unified explicit electric potential framework to simultaneously predict atomic forces and electron density distributions. The framework…
Electric charge detection by atomic force microscopy (AFM) with single- electron resolution (e-EFM) is a promising way to investigate the electronic level structure of individual quantum dots (QD). The oscillating AFM tip modulates the…
We introduce the multivariate decomposition finite element method for elliptic PDEs with lognormal diffusion coefficient $a=\exp(Z)$ where $Z$ is a Gaussian random field defined by an infinite series expansion $Z(\boldsymbol{y}) =…
Gaussian process (GP) emulator has been used as a surrogate model for predicting force field and molecular potential, to overcome the computational bottleneck of molecular dynamics simulation. Integrating both atomic force and energy in…