# Scientific Publications

## Performance of Reservoir Discretizations in Quantum Transport Simulations

### J. E. Elenewski, G. Wojtowicz, M. M. Rams, and M. Zwolak

The Journal of Chemical Physics, 155, 124117 (2021)

Quantum transport simulations often use explicit, yet finite, electronic reservoirs. These should converge to the correct continuum limit, albeit with a trade-off between discretization and computational cost. Here, we study this interplay for extended reservoir simulations, where relaxation maintains a bias or temperature drop across the system. Our analysis begins in the non-interacting limit, where we parameterize different discretizations to compare them on an even footing. For many-body systems, we develop a method to estimate the relaxation that best approximates the continuum by controlling virtual transitions in Kramers' turnover for the current. While some discretizations are more efficient for calculating currents, there is little benefit with regard to the overall state of the system. Any gains become marginal for many-body, tensor network simulations, where the relative performance of discretizations varies when sweeping other numerical controls. These results indicate that a given reservoir discretization may have little impact on numerical efficiency for certain computational tools. The choice of a relaxation parameter, however, is crucial, and the method we develop provides a reliable estimate of the optimal relaxation for finite reservoirs.

## Dual current anomalies and quantum transport within extended reservoir simulations

### G. Wojtowicz, J. E. Elenewski, M. M. Rams, and M. Zwolak

Physical Review B, 104, 165131 (2021)

Quantum transport simulations are rapidly evolving and now encompass well-controlled tensor network techniques for many-body transport. One powerful approach combines matrix product states with extended reservoirs. In this method, continuous reservoirs are represented by explicit, discretized counterparts where a chemical potential or temperature drop is maintained by relaxation. Currents are strongly influenced by relaxation when it is very weak or strong, resulting in a simulation-analog of Kramers' turnover in solution-phase chemical reactions. At intermediate relaxation, the intrinsic conductance-that given by the Landauer or Meir-Wingreen expressions-moderates the current. We demonstrate that strong impurity scattering (i.e., a small steady-state current) reveals anomalous transport regimes within this methodology at weak-to-moderate and moderate-to-strong relaxation. The former is due to virtual transitions and the latter to unphysical broadening of the populated density of states. The Kramers' turnover analog thus has five standard transport regimes, further constraining the parameters that lead to the intrinsic conductance. In particular, a relaxation strength proportional to the reservoir level spacing-the commonly assumed strategy-can prevent convergence to the continuum limit. This underscores that the turnover profiles enable identification of simulation parameters that achieve proper physical behavior.

Open System Tensor Networks and Kramers' Crossover for Quantum Transport

### G. Wojtowicz, J. E. Elenewski, M. M. Rams, and M. Zwolak

Physical Review A, 101, 050301(R) (2020)

Tensor networks are a powerful tool for many-body ground states with limited entanglement. These methods can, nonetheless, fail for certain time-dependent processes–such as quantum transport or quenches—where entanglement growth is linear in time. Matrix-product-state decompositions of the resulting out-of-equilibrium states require a bond dimension that grows exponentially, imposing a hard limit on simulation timescales. However, in the case of transport, if the reservoir modes of a closed system are arranged according to their scattering structure, the entanglement growth can be made logarithmic. Here, we apply this ansatz to open systems via extended reservoirs that have explicit relaxation. This enables transport calculations that can access steady states, time dynamics and noise, and periodic driving (e.g., Floquet states). We demonstrate the approach by calculating the transport characteristics of an open, interacting system. These results open a path to scalable and numerically systematic many-body transport calculations with tensor networks.

## Topology, Landscapes, and Biomolecular Energy Transport

### J. E. Elenewski, K. Velizhanin, and M. Zwolak

Nature Communications, **10**, 4662 (2019)

While ubiquitous, energy redistribution remains a poorly understood facet of the nonequilibrium thermodynamics of biomolecules. At the molecular level, finite-size effects, pronounced nonlinearities, and ballistic processes produce behavior that diverges from the macroscale. Here, we show that transient thermal transport reflects macromolecular energy landscape architecture through the topological characteristics of molecular contacts and the nonlinear processes that mediate dynamics. While the former determines transport pathways via pairwise interactions, the latter reflects frustration within the landscape for local conformational rearrangements. Unlike transport through small-molecule systems, such as alkanes, nonlinearity dominates over coherent processes at even quite short time- and length-scales. Our exhaustive all-atom simulations and novel local-in-time and space analysis, applicable to both theory and experiment, permit dissection of energy migration in biomolecules. The approach demonstrates that vibrational energy transport can probe otherwise inaccessible aspects of macromolecular dynamics and interactions that underly biological function.

## Optimal transport and colossal ionic mechano-conductance in graphene crown ethers.

### S. Sahu, J. E. Elenewski, C. Rohmann, and M. Zwolak

Science Advances, 5, eaaw5478 (2019)

Biological ion channels balance electrostatic and dehydration effects to yield large ion selectivity alongside high transport rates. These macromolecular systems are often interrogated through point mutations of their pore domain, limiting the scope of mechanistic studies. In contrast, we demonstrate that graphene crown ether pores afford a simple platform to directly investigate optimal ion transport conditions, i.e., maximum current densities and selectivity. Crown ethers are known for selective ion adsorption. When embedded in graphene, however, transport rates lie below the drift-diffusion limit. We show that small pore strains (1%) give rise to a colossal (100%) change in conductance. This process is electromechanically tunable, with optimal transport in a primarily diffusive regime, tending toward barrierless transport, as opposed to a knock-on mechanism. These observations suggest a novel setup for nanofluidic devices while giving insight into the physical foundation of evolutionarily optimized ion transport in biological pores.

## A Spin-1 Representation for Dual-Funnel Energy Landscapes

### J. E. Elenewski, K. Velizhanin, and M. Zwolak

The Journal of Chemical Physics, **149**, 035101 (2018)

The interconversion between the left- and right-handed helical folds of a polypeptide defines a dual-funneled free energy landscape. In this context, the funnel minima are connected through a continuum of unfolded conformations, evocative of the classical helix-coil transition. Physical intuition and recent conjectures suggest that this landscape can be mapped by assigning a left- or right-handed helical state to each residue. We explore this possibility using all-atom replica exchange molecular dynamics and an Ising-like model, demonstrating that the energy landscape architecture is at odds with a two-state picture. A three-state model—left, right, and unstructured—can account for most key intermediates during chiral interconversion. Competing folds and excited conformational states still impose limitations on the scope of this approach. However, the improvement is stark: Moving from a two-state to a three-state model decreases the fit error from 1.6 *kT* to 0.3 *kT* along the left-to-right interconversion pathway.

## Master Equations for Electron Transport: The Limits of the Markovian Limit

### J. E. Elenewski, D. Gruss, and M. Zwolak

The Journal of Chemical Physics, **147**, 151101 (2017)

Master equations are increasingly popular for the simulation of time–dependent electronic transport in nanoscale devices. Several recent Markovian approaches use “extended reservoirs” – explicit degrees of freedom associated with the electrodes – distinguishing them from many previous classes of master equations. Starting from a Lindblad equation, we develop a common foundation for these approaches. Due to the incorporation of explicit electrode states, these methods do not require a large bias or even “true Markovianity” of the reservoirs. Nonetheless, their predictions are only physically relevant when the Markovian relaxation is weaker than the thermal broadening and when the extended reservoirs are “sufficiently large,” in a sense that we quantify. These considerations hold despite complete positivity and respect for Pauli exclusion at any relaxation strength.

## Simulation of Singlet Fission in Single Crystalline Pentacene via Functional Mode Vibronic Theory

### J. E. Elenewski, U. S. Cubeta, E. Ko, and H. Chen

The Journal of Physical Chemistry C, **121**, 11159 (2017)

We have applied our functional mode framework for singlet fission to pentacene, a prototypical organic material for multiple exciton generation. It was found that singlet fission in pentacene occurs predominantly through a coherent process mediated by a virtual charge-transfer (CT) intermediate, which lies slightly above the photoexcited S1S0 state. This energetic near-degeneracy facilitates a substantial vibronic superposition, leading to a rapid transition rate of 25.1 ps–1. By contrast, the direct S1S0 → T1T1 path constitutes a much more sluggish route with a rate of 2.6 ps–1, largely due to the weak diabatic coupling between participant states. These data collectively afford an experimentally consistent rate of 27.7 ps–1 for the entire singlet fission process. The presence of this low-lying CT intermediate suggests that enhanced electronic coupling between S1S0 and T1T1 states may collude with coherent vibrational mixing to expedite the formation of triplet pairs. The knowledge gleaned from our investigations heralds a new approach to charge transfer-mediated singlet fission, a rapidly growing research field that holds great promise to circumvent the Shockley–Queisser thermodynamic limit for solar energy conversion.

## Functional Mode Singlet Fission

### J. E. Elenewski, U. S. Cubeta, E. Ko, and H. Chen

The Journal of Physical Chemistry C, **121**, 4130 (2017)

Singlet fission is a multiple exciton generation process that splits a singlet exciton (S0S1) into a correlated triplet pair (T1T1), affording a route to overcome the long-standing Shockley–Queisser thermodynamic limit for solar energy conversion. A new theory, based on multiconfiguration-constrained density functional theory and functional mode analysis, has been developed to model intermolecular singlet fission in organic photovoltaics. Specifically, constrained density functional theory is first employed to construct molecular orbitals for the six spin configurations comprising T1T1, the diabatic product state. In a subsequent step, linear response time-dependent density functional theory is utilized to formulate the S0S1 diabatic reactant state. Functional mode analysis is then applied to a thermalized ensemble of diabatic energy gaps to ascertain the reaction coordinate for the S0S1 → T1T1 transition. If singlet fission is assumed to follow a direct route, its rate may be evaluated using a modified Jortner formula within strong vibronic coupling regime. In contrast, second-order perturbation theory must be adopted to treat alternate pathways that are mediated by a charge-transfer (CT) intermediate. As shown through numerical simulations of single crystal tetracene, our theory reveals the direct mechanism to be the primary transition path, with an experimentally consistent singlet fission rate of 0.02 ps–1. CT pathways are effectively blocked due to a substantially diminished vibrational resonance among participating states. Our results have broad applicability, as only trivial alterations are needed to enable our new theory to model vibrationally modulated singlet fission using time-delayed pulse sequences.

## Visible-Light-Responsive Graphitic Carbon Nitride (g-C3N4): Tailored Synthesis and Photocatalytic Applications for Water Treatment

### Q. Zheng, D. P. Durkin, J. E. Elenewski, H. Chen, Y. Sun, N. A. Banek, M. J. Wagner, W. Zhang, and D. Shuai

Environmental Science and Technology, **50**, 12938 (2016)

Graphitic carbon nitride (g-C3N4) has recently emerged as a promising visible-light-responsive polymeric photocatalyst; however, a molecular-level understanding of material properties and its application for water purification were underexplored. In this study, we rationally designed nonmetal doped, supramolecule-based g-C3N4 with improved surface area and charge separation. Density functional theory (DFT) simulations indicated that carbon-doped g-C3N4 showed a thermodynamically stable structure, promoted charge separation, and had suitable energy levels of conduction and valence bands for photocatalytic oxidation compared to phosphorus-doped g-C3N4. The optimized carbon-doped, supramolecule-based g-C3N4 showed a reaction rate enhancement of 2.3–10.5-fold for the degradation of phenol and persistent organic micropollutants compared to that of conventional, melamine-based g-C3N4 in a model buffer system under the irradiation of simulated visible sunlight. Carbon-doping but not phosphorus-doping improved reactivity for contaminant degradation in agreement with DFT simulation results. Selective contaminant degradation was observed on g-C3N4, likely due to differences in reactive oxygen species production and/or contaminant-photocatalyst interfacial interactions on different g-C3N4 samples. Moreover, g-C3N4 is a robust photocatalyst for contaminant degradation in raw natural water and (partially) treated water and wastewater. In summary, DFT simulations are a viable tool to predict photocatalyst properties and oxidation performance for contaminant removal, and they guide the rational design, fabrication, and implementation of visible-light-responsive g-C3N4 for efficient, robust, and sustainable water treatment.

## Functional Mode Hot Electron Transfer Theory

### J. E. Elenewski, J. Cai, J. Wei, and H. Chen

The Journal of Physical Chemistry C, **120**, 20579 (2016)

Charge carriers that have been driven out of thermal equilibrium by their excessive vibrational energies are termed hot carriers. A theory has been developed to model the injection of these vibrationally excited electrons by explicitly accounting for the time-dependent thermal relaxation of the electron-transfer driving vibrational mode, as ascertained using functional mode analysis. Specifically, the thermal relaxation rate of the driving mode is first determined through the so-called frozen-phonon approach after which the energy-dependent line shape function is revisited to include memory effects for the vibrational quanta within the framework of Fermi’s golden rule. As shown by the numerical simulations of a 6-methyl-azulene-2-carboxylic acid dye molecule bound to an anatase TiO2[101] surface, our new theory not only yields persistently faster electron injection rates with higher incident photon energy but also exhibits a sharp increase when the vibrational quanta of the photoexcited dye molecule changes from 2 to 3, in excellent agreement with a recent femtosecond pump–probe spectroscopy study. These methods comprise a practical first-principles simulation protocol to model vibrationally resolved electron injection by accommodating the subtle coupling between molecular vibration, thermal relaxation, and electron transfer under arbitrary thermalization conditions. Moreover, only trivial extensions are needed to enable the application of our new theory to vibrationally controlled electron-transfer reactions in a wide range of chemical and biological systems, particularly those engineered using time-delayed laser pulses.

## Computational Modeling of Shallow Electron Polarons in Rutile TiO2

### L. Yan, J. E. Elenewski, J. Wei, and H. Chen.

Physical Chemistry Chemical Physics, **17**, 29949 (2015)

In conjunction with the constrained density functional theory, a valence-bond representation has been employed to model the migration of anionic polaron in bulk rutile TiO2. It was found that the charge delocalization of a self-trapped electron proceeded predominately along the *c* crystal axis of rutile, thus exhibiting pronounced directional heterogeneity of polaron migration. As a result, the extrapolated polaron activation energies are 0.026 eV and 0.195 eV along the [001] and [111] lattice vectors, respectively. According to the Holstein theory, the difference on the activation energy makes the polaron drift over 100 times faster along the *c* crystal axis than on the *ab* crystal plane at room temperature. The notable anisotropy of the anionic polaron was also reflected through the electron paramagnetic resonance (EPR) *g*-matrix, whose principal component along [001] is substantially smaller than that along [110] or [10]. Finally, the extent of polaron charge was probed by our calculated isotropic hyperfine coupling constants on two groups of crystallographically inequivalent 17O atoms, which manifest distinct strengths of spin–orbit interaction with the unpaired electron.

## Ab Initio Dynamics of the Cytochrome P450 Hydroxylation Reaction

### J. E. Elenewski and J. C Hackett

The Journal of Chemical Physics, 142, 064307 (2015)

The iron(IV)-oxo porphyrin *π*-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, *ab initio* molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of *ab initio* simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

## Real-Time Transport in Open Quantum Systems from PT-Symmetric Quantum Mechanics

### J. E. Elenewski and H. Chen

Physical Review B, 90, 085104 (2014)

Nanoscale electronic transport is of intense technological interest, with applications ranging from semiconducting devices and molecular junctions to charge migration in biological systems. Most explicit theoretical approaches treat transport using a combination of density functional theory (DFT) and non-equilibrium Green's functions. This is a static formalism, with dynamic response properties accommodated only through complicated extensions. To circumvent this limitation, the carrier density may be propagated using real-time time-dependent DFT (RT-TDDFT), with boundary conditions corresponding to an open quantum system. Complex absorbing potentials can emulate outgoing particles at the simulation boundary, although these do not account for introduction of charge density. It is demonstrated that the desired positive particle flux is afforded by a class of PT-symmetric generating potentials that are characterized by anisotropic transmission resonances. These potentials add density every time a particle traverses the cell boundary, and may be used to engineer a continuous pulse train for incident packets. This is a first step toward developing a complete transport formalism unique to RT-TDDFT.

## Spin equilibrium and O2-binding kinetics of Mycobacterium tuberculosis CPYP51

### G. K. Jennings, A. Modi, J. E. Elenewski, C. M. Richie, T. Nguyen, K. C. Ellis, and J. C Hackett

Journal of Inorganic Biochemistry, 136, 81 (2014)

The acidic residues of the “acid–alcohol pair” in CYP51 enzymes are uniformly replaced with histidine. Herein, we adopt the *Mycobacterium tuberculosis* (mt) enzyme as a model system to investigate these residues’ roles in finely tuning the heme conformation, iron spin state, and formation and decay of the oxyferrous enzyme. Properties of the mtCYP51 and the T260A, T260V, and H259A mutants were interrogated using UV–Vis and resonance Raman spectroscopies. Evidence supports that these mutations induce comprehensive changes in the heme environment. The heme iron spin states are differentially sensitive to the binding of the substrate, dihydrolanosterol (DHL). DHL and clotrimazole perturb the local environments of the heme vinyl and propionate substituents. Molecular dynamics (MD) simulations of the DHL–enzyme complexes support that the observed perturbations are attributable to changes in the DHL binding mode. Furthermore, the rates of the oxyferrous formation were measured using stopped-flow methods. These studies demonstrate that both HT mutations and DHL modulate the rates of oxyferrous formation. Paradoxically, the binding rate to the H259A mutant–DHL complex was approximately four-fold that of mtCYP51, a phenomenon that is predicted to result from the creation of an additional diffusion channel from loss of the H259–E173 ion pair in the mutant. Oxyferrous enzyme auto-oxidation rates were relatively constant, with the exception of the T260V-DHL complex. MD simulations lead us to speculate that this behavior may be attributed to the distortion of the heme macrocycle by the substrate.

## Solvatochromism and the solvation structure of benzophenone

### J. E. Elenewski and J. C Hackett

The Journal of Chemical Physics, 138, 224308 (2013)

Many complex molecular phenomena, including macromolecular association, protein folding, and chemical reactivity, are determined by the nuances of their electrostatic landscapes. The measurement of such electrostatic effects is nonetheless difficult, and is typically accomplished by exploiting a spectroscopic probe within the system of interest, such as through the vibrational Stark effect. Raman spectroscopy and solvatochromism afford an alternative to this method, circumventing the limitations of infrared spectroscopy, providing a lower detection limit, and permitting measurement in a native chemical environment. To explore this possibility, the solvatochromism of the C=O and aromatic C–H stretching modes of benzophenone are investigated using Raman spectroscopy. In conjunction with density functional theory calculations, these observations are sufficient to determine the probe electrostatic environment as well as contributions from halogen and hydrogen bonding. Further analysis using a detailed Kubo–Anderson lineshape model permits the detailed assignment of distinct hydrogen bonding configurations for water in the benzophenone solvation shell. These observations reinforce the use of benzophenone as an effective electrostatic probe for complex chemical systems.

## Cytochrome P450 Compound I in the Plane-Wave Pseudopotential Framework: GGA Electronic and Geometric Structure of Thiolate-Ligated Iron-Oxo (IV) Porphyrin

### J. E. Elenewski and J. C Hackett

The Journal of Computational Chemistry, 24, 1647 (2013)

The cytochromes P450 constitute a ubiquitous family of metalloenzymes, catalyzing manifold reactions of biological and synthetic importance via a thiolate-ligated iron-oxo (IV) porphyrin radical species denoted compound I (Cpd I). Experimental investigations have implicated this intermediate in a broad spectrum of biophysically interesting phenomena, further augmenting the importance of a Cpd I model system. Ab initio molecular dynamics, including Car-Parrinello and path integral methods, conjoin electronic structure theory with finite temperature simulation, affording tools most valuable to approach such enzymes. These methods are typically driven by density functional theory (DFT) in a plane-wave pseudopotential framework; however, existing studies of Cpd I have been restricted to localized Gaussian basis sets. The appropriate choice of density functional and pseudopotential for such simulations is accordingly not obvious. To remedy this situation, a systematic benchmarking of thiolate-ligated Cpd I is performed using several generalized-gradient approximation (GGA) functionals in the Martins-Troullier and Vanderbilt ultrasoft pseudopotential schemes. The resultant electronic and structural parameters are compared to localized-basis DFT calculations using GGA and hybrid density functionals. The merits and demerits of each scheme are presented in the context of reproducing existing experimental and theoretical results for Cpd I.

## A GGA+U approach to effective electronic correlations in thiolate-ligated iron-oxo (IV) porphyrin.

### J. E. Elenewski and J. C Hackett

The Journal of Chemical Physics, 137, 124311 (2012)

High-valent oxo-metal complexes exhibit correlated electronic behavior on dense, low-lying electronic state manifolds, presenting challenging systems for electronic structure methods. Among these species, the iron-oxo (IV) porphyrin denoted Compound I occupies a privileged position, serving a broad spectrum of catalytic roles. The most reactive members of this family bear a thiolate axial ligand, exhibiting high activity toward molecular oxygen activation and substrate oxidation. The default approach to such systems has entailed the use of hybrid density functionals or multi-configurational/multireference methods to treat electronic correlation. An alternative approach is presented based on the GGA+U approximation to density functional theory, in which a generalized gradient approximation (GGA) functional is supplemented with a localization correction to treat on-site correlation as inspired by the Hubbard model. The electronic structure of thiolate-ligated iron-oxo (IV) porphyrin and corresponding Coulomb repulsion U are determined both empirically and self-consistently, yielding spin-distributions, state level splittings, and electronic densities of states consistent with prior hybrid functional calculations. Comparison of this detailed electronic structure with model Hamiltonian calculations suggests that the localized 3d iron moments induce correlation in the surrounding electron gas, strengthening local moment formation. This behavior is analogous to strongly correlated electronic systems such as Mott insulators, in which the GGA+U scheme serves as an effective single-particle representation for the full, correlated many-body problem.

## Free Energy Landscape of the Retinol / Serum Retinol Binding Protein Complex: A Biological Host-Guest System

### J. E. Elenewski and J. C Hackett

The Journal of Physical Chemistry B, 114, 11315 (2010)

Small molecule host-guest complexes have traditionally provided model systems for biological ligand recognition. Nonetheless, direct extrapolation of these results is precluded by the comparative simplicity of these supramolecular assemblies. If energetic behavior analogous to small molecule host-guest chemistry exists, it is unclear how this would manifest for protein-small molecule interactions. To answer this question, we employ the retinol/serum retinol binding protein (sRBP) system as an analogue of a classical host-guest complex. Using a combination of molecular dynamics simulations and free energy methods, we decompose the potential of mean force for retinol unbinding from the sRBP into constituent interactions. Our calculations reveal an unexpected mechanism of host-guest complexation. Desolvation is sufficient to drive formation of an intermediate binding state; however, a combination of electrostatic and van der Waals interactions pull the intermediate into a stable configuration. Association is accompanied by a change in the conformational flexibility of the portal domains of sRBP and subsequent "stiffening" of the holo sRBP, reflecting an "order-disorder" transition in the protein.

## Interaction of the Sigma-2 Receptor Ligand PB28 with the Human Nucleosome: Computational and Experimental Probes of Interaction with the H2A/H2B Dimer

### C. Abate, J. E. Elenewski, M. Niso, F. Berardi, N. A. Colabufo, A. Azzariti, R. Perrone, and R. A. Glennon

Sigma-2 binding sites are an emerging target for anti-neoplastic agents due to the strong apoptotic effect exhibited by sigma(2) agonists in vitro and the overexpression of these sites in tumor cells. Nonetheless, no sigma(2) receptor protein has been identified. Affinity chromatography using the high-affinity sigma(2) ligand PB28 and human SK-N-SH neuroblastoma cells was previously utilized to identify sigma(2) ligand binding proteins, specifically histones H1, H2A, H2B, and H3.3a. To rationalize this finding, homology modeling and automated docking studies were employed to probe intermolecular interactions between PB28 and human nucleosomal proteins. These studies predicted interaction of PB28 with the H2A/H2B dimer at a series of sites previously found to be implicated in chromatin compaction and nucleosomal assembly. To experimentally verify this prediction, a competitive binding assay was performed on the reconstituted H2A/H2B dimer using [(3)H]PB28 as radioligand, and an IC(50) value of 0.50 nM was determined for PB28 binding. In addition, [(3)H]PB28 was found to accumulate with up to a fivefold excess in nuclear fractions over cytosolic fractions of SK-N-SH and MCF7 cells, indicating that PB28 is capable of entering the nucleus to interact with histone proteins. In conjunction with computational results, these data suggest that PB28 may exert its cytotoxic effect through direct interaction with nuclear material.

## Depth-Controlled β-NMR of 8Li in a Thin Silver Film

### G. D. Morris, W. A. MacFarlane, K. H. Chow, Z. Salman, D. Arseneau, S. Daviel, A. Hatakeyama, S. R. Kreitzman, C. D. P. Levy, R. Poutissou, R. H. Heffner, J. E. Elenewski, L. H. Greene, and R. F. Kiefl

Physical Review Letters, 93, 157601 (2004)

Depth-controlled beta-NMR can be used to probe the magnetic properties of thin films and interfaces on a nanometer length scale. A 30 keV beam of highly spin-polarized 8Li+ ions was slowed down and implanted into a 50 nm film of Ag deposited on a SrTiO3 substrate. A novel high field beta-NMR spectrometer was used to observe two well resolved resonances which are attributed to Li occupying substitutional and octahedral interstitial sites in the Ag lattice. The temperature dependence of the Knight shifts and spin relaxation rates are consistent with the Korringa law for a simple metal, implying that the NMR of implanted 8Li reflects the spin suspectibility of bulk metallic silver.

## Subterahertz spectroscopy at He-3 temperatures

### D. N. Basov, S. V. Dordevic, E. J. Singley, W. J. Padilla, K. Burch, J. E. Elenewski, and L. H. Greene

Review of Scientific Instruments, 74, 4703 (2003)

We report on the design and implementation of an instrument for spectroscopic studies of materials at sub-terahertz (THz) frequencies at temperatures down to 340 mK. We achieved consistent operation under these rather extreme conditions by coupling a modified Martin–Puplett interferometer to a single cryogenic unit housing two independently controlled He-3 platforms: one as a sample stage and the other for bolometric detectors. Both the optical scheme of the interferometer and detector layout are tailored for the use of the two-channel data acquisition mode which is especially advantageous for measurement of absolute values of reflectance as well as for high-resolution spectroscopy. We document the reliable performance of the sub-THz apparatus with several experiments exploring electrodynamics of both conventional and high-Tc superconductors.

## Faceting of Single-Crystal SrTiO3 During Wet Chemical Etching

### G. C. Spalding, W. L. Murphy, T. M. Davidsmeier, and J. E. Elenewski

in *Substrate Engineering: Paving the Way to Epitaxy* (D. P. Norton, D. G. Schlom, N. Newman, and D. H. Matthiesen, Eds.) Materials Research Society, Boston, MA (2000)

We use an Atomic Force Microscopy (AFM) to study changes in the surface of single-crystal SrTiO_{3} etched in HF-based solutions. Attention in this work has been focused upon observations of *pyramidal pitting* – both because of an interest in avoiding etch pits during substrate preparation prior to heteroepitaxial growth, and because of an interest in micromachining this highly polarizable material. We note that (110) SrTiO_{3} is surprisingly robust against the formation of pits, while pitting is significant on {100} surfaces. Particular etch rates have been measured, and we discuss anisotropies in the rates of dissolution. These data are combined to extract a macroscopic model describing processes relevant to the most extreme pitting, which we show to be associated with surface defects.

# Unpublished Technical Notes

## Complex non-Hermitian Potentials and Real-Time Time-Dependent Density Functional Theory: A Master Equation Approach

### J. E. Elenewski, Y. Zhao, and H. Chen

The simulation of quantum transport in a realistic, many-particle system is a nontrivial problem with no quantitatively satisfactory solution. While real-time propagation has the potential to overcome the shortcomings of conventional transport methods, this approach is prone to finite size effects that are associated with modeling an open system on a closed spatial domain. Using a master equation framework, we exploit an equivalence between the superoperators coupling an open system to external particle reservoirs and non-Hermitian terms defined at the periphery of a quantum device. By taking the mean-field limit, the equation of motion for the single-particle reduced density matrix becomes equivalent to real-time time-dependent density functional theory in the presence of imaginary source and sink potentials. This method may be used to converge nonequilibrium steady states for a many-body quantum system using a previously reported constraint algorithm.

## Non-Equilibrium Transport in Open Quantum Systems via Dynamically Constrained non-Hermitian Boundary Domains

### J. E. Elenewski, Y. Zhao, and H. Chen

The accurate simulation of real-time quantum transport is notoriously difficult, requiring a consistent scheme to treat incoming and outgoing fluxes at the boundary of an open system. We demonstrate a method to converge non-equilibrium steady states using non-Hermitian source and sink potentials alongside the application of dynamic density constraints during wavefunction propagation. This scheme adds negligible cost to existing computational methods while exhibiting exceptional stability and numerical accuracy.

## Open System Tensor Networks and Kramers' Crossover for Quantum Transport

### G. Wojtowicz, J. E. Elenewski, M. M. Rams, and M. Zwolak

Phys. Rev. A **101**, 050301(R) (2020)

Tensor networks are a powerful tool for many-body ground states with limited entanglement. These methods can, nonetheless, fail for certain time-dependent processes–such as quantum transport or quenches—where entanglement growth is linear in time. Matrix-product-state decompositions of the resulting out-of-equilibrium states require a bond dimension that grows exponentially, imposing a hard limit on simulation timescales. However, in the case of transport, if the reservoir modes of a closed system are arranged according to their scattering structure, the entanglement growth can be made logarithmic. Here, we apply this ansatz to open systems via extended reservoirs that have explicit relaxation. This enables transport calculations that can access steady states, time dynamics and noise, and periodic driving (e.g., Floquet states). We demonstrate the approach by calculating the transport characteristics of an open, interacting system. These results open a path to scalable and numerically systematic many-body transport calculations with tensor networks.