arXiv subjects

Andrew R. Lupini

Publications and source records attributed to Andrew R. Lupini.

At least 19 recordsLinked to original sources

arXiv2026

A versatile generalized digital twin for Electron Microscopy

Development of specialized imaging and spectroscopy states in transmission electron microscopy is needed for novel applications, such as flexible momentum-resolved high energy-resolution spectroscopy. This task is complicated by the need to align and configure many different lenses, and by ambiguity as to the locations of various imaging and diffraction planes, which are often not well documented. Here we develop a versatile digital twin for simulating the electron beam trajectory throughout an electron microscope. Our code package contains simple tools for modeling the microscope column, and we present multiple procedures for dialing in precise lens locations and calibrating lens models. This enables use of the model as a predictive tool, allowing the user to quickly and easily determine the correct lens values for setting up new condenser or projector modes. Automatic procedures to change lens settings and measure the resulting changes can be used to close the loop. With the accelerating development of machine learning and artificial intelligence tools, we also believe a physically-informed model of the microscope can serve as a valuable tool for automated microscopy and AI/ML integration.

cond-mat.mtrl-sci↗

arXiv2026

Inference-Sufficient Representations for High-Throughput Measurement: Lessons from Lossless Compression Benchmarks in 4D-STEM

Four-dimensional scanning transmission electron microscopy (4D-STEM) generates multi-gigabyte datasets, creating a growing mismatch between acquisition rates and practical storage, transfer, and interactive visualization capabilities. We systematically benchmark 13 lossless compression implementations across 5 representative datasets (8~MiB to 8~GiB, 49.5--92.8\% sparsity), with 10 independent runs per method. HDF5 provides built-in gzip compression, of which gzip-9 typically achieves the highest compression ratio but is slow. We therefore evaluate widely available alternatives (via hdf5plugin), including the Blosc family. As a representative comparison, blosc\_zstd achieves compression comparable to gzip-9 (mean 13.5$\times$ vs 12.3$\times$) while compressing 19--69$\times$ faster and reading 1.9--2.6$\times$ faster across datasets. Compression ratios are deterministic, and timing measurements are highly reproducible (CV $<$2\%). Compression performance follows a power law with sparsity ($R^2 = 0.99$), ranging from 5$\times$ for moderately sparse data to 35$\times$ for highly sparse data. We identify six top-performing implementations optimized for different use cases and demonstrate that 4D-STEM data can be routinely compressed by $>$10$\times$. While these results provide practical guidance for lossless compression selection, the broader conclusion is that lossless compression preserves measurements but does not by itself guarantee sustainable high-throughput workflows. As detector rates rise, data handling will increasingly require inference-driven representations -- i.e., deciding what must be preserved to support a scientific inference, rather than defaulting to storing fully dense raw measurements.

eess.SP↗

arXiv2026

Atomically Precise Electron Beam Sculpting of Bilayer h-BN: The Role of Crystallographic Orientation and Milling Strategy

Achieving atomic precision in top-down manufacturing remains a fundamental challenge nanofabrication technology. Here, the focused electron beam of a scanning transmission electron microscope is used to demonstrate atomically precise sculpting of hexagonal boron nitride (h-BN) bilayers, achieving nanoribbons as narrow as 6 Å with atomically smooth edges. The key to this precision lies in understanding how the underlying atomic structure, particularly in twisted bilayer systems, influences the milling process. High-angle annular dark-field imaging combined with multislice simulations reveals distinct intensity signatures that allow identification of different stacking arrangements within moiré patterns. Mathematical analysis of moiré lattices provides a predictive framework for determining optimal cutting directions, with cuts along armchair directions yielding superior edge quality compared to zigzag orientations. Surprisingly, a sequential milling approach, where a small electron beam subscan area is translated during the process, produces significantly better results than parallel milling of the entire target region. To understand these differences we implemented a stochastic milling model that reveals that sequential milling minimizes unwanted exposure to surrounding material through beam tail effects. These findings establish a framework for achieving atomic precision in electron beam sculpting of two-dimensional materials and provide fundamental insights applicable to the broader challenge of top-down nanofabrication.

cond-mat.mtrl-sci↗

arXiv2025

Topology-Driven Vibrations in a Chiral Polar Vortex Lattice

The ordering of magnetic or electric dipoles leading to real-space topological structures is at the forefront of materials research as their quantum mechanical nature often lends itself to emergent properties. Atomic lattice vibrations (phonons) are often a key contributor to the formation of long-range dipole textures based on ferroelectrics and impact the properties of the emergent phases. Here, using monochromated, momentum-resolved electron energy-loss spectroscopy (qEELS) with nanometer spatial resolution and meV-spectral-precision, we demonstrate that polar vortex lattices in PbTiO$_3$ spatially modulate the material's vibrational spectrum in patterns that directly reflect the overlying symmetry of the topological patterns. Moreover, by combining experiments with molecular dynamics simulations using machine learned potentials we reveal how these structures modify phonon modes across the vibrational spectrum. Beyond simple intensity modulation, we find that the chirality of the vortex topology imparts its unique symmetry onto phonons, producing a distinctive asymmetrical spectral shift across the vortex unit cell. Finally, the high spatial resolution of the technique enables topological defects to be probed directly, demonstrating a return to trivial PbTiO$_3$ modes at vortex dislocation cores. These findings establish a fundamental relationship between ferroelectric-ordering-induced topologies and phonon behavior, opening new avenues for engineering thermal transport, electron-phonon coupling, and other phonon-mediated properties in next-generation nanoscale devices.

cond-mat.mtrl-sci↗

arXiv2025

Antiferroelectric Hafnia Down to the 2D Limit

Antiferroelectricity is a material property characterized by alternating electric dipoles spontaneously ordered in antiparallel directions. Antiferroelectrics are promising for energy storage, solid-state cooling, and memory technologies; however, these materials are scarce, and their scalability remains largely unexplored. In this work, we demonstrate that single-crystalline hafnia, a lead-free CMOS-compatible material, exhibits antiferroelectricity under compressive-strain conditions. We observe antiparallel sublattice polarization and stable double-hysteresis in single-crystalline (111)-oriented epitaxial La-doped hafnia films grown on yttrium-stabilized zirconia and show that the antipolar orthorhombic phase of hafnia adheres to the Kittel model of antiferroelectricity. Notably, compressive strain strengthens the antiferroelectric order in thinner La-doped hafnia films, achieving an unprecedented 850 C ordering temperature in the two-dimensional limit, highlighting hafnia's potential for advanced antiferroelectric devices.

cond-mat.mtrl-sci↗

arXiv2025

Towards Atomic-Scale Control over Structural Modulations in Quasi-1D Chalcogenides for Colossal Optical Anisotropy

Optically anisotropic materials are sought after for tailoring the polarization of light. Recently, colossal optical anisotropy was reported in a quasi-one-dimensional chalcogenide, Sr1.125TiS3. Compared to SrTiS3, the excess Sr in Sr1.125TiS3 leads to periodic structural modulations and introduces additional electrons that undergo charge ordering on select Ti atoms to form a highly polarizable cloud oriented along the c-axis, hence, resulting in the colossolal optical anisotropy. Here, further enhancement of the colossal optical anisotropy to 2.5 in Sr1.143TiS3 is reported through control over the periodicity of the atomic-scale modulations. The role of structural modulations in tuning the optical properties in a series of SrxTiS3 compounds has been investigated using DFT calculations. The structural modulations arise from various stacking sequences of face-sharing TiS6 octahedra and twist-distorted trigonal prisms, and are found to be thermodynamically stable for x larger than 1 but smaller than 1.5. As x increases, an indirect-to-direct band gap transition is predicted for x equal to and larger than 1.143 along with an increased occupancy of Ti-dz2 states. Together, these two factors result in a theoretically predicted maximum birefriengence of 2.5 for Sr1.143TiS3. Single crystals of Sr1.143TiS3 were grown using a molten-salt flux method. Atomic-scale observations using scanning transmission electron microscopy confirm the feasibility of synthesizing SrxTiS3 with varied modulation periodicities. Overall, these findings demonstrate compositonal tunability of optical properties in SrxTiS3 compounds, and potentially in other hexagonal perovskites having structural modulations.

cond-mat.mtrl-sci↗

arXiv2025

Defect Engineering in Large-Scale CVD-Grown Hexagonal Boron Nitride: Formation, Spectroscopy, and Spin Relaxation Dynamics

Recently, numerous techniques have been reported for generating optically active defects in exfoliated hexagonal boron nitride (hBN), which hold transformative potential for quantum photonic devices. However, achieving on-demand generation of desirable defect types in scalable hBN films remains a significant challenge. Here, we demonstrate that formation of negative boron vacancy defects, VB-, in suspended, large-area CVD-grown hBN is strongly dependent on the type of bombarding particles (ions, neutrons, and electrons) and irradiation conditions. In contrast to suspended hBN, defect formation in substrate-supported hBN is more complex due to the uncontrollable generation of secondary particles from the substrate, and the outcome strongly depends on the thickness of the hBN. We identify different defect types by correlating spectroscopic and optically detected magnetic resonance features, distinguishing boron vacancies (formed by light ions and neutrons) from other optically active defects emitting at 650 nm assigned to anti-site nitrogen vacancy (NBVN) and reveal the presence of additional dark paramagnetic defects that influence spin-lattice relaxation time (T1) and zero-field splitting parameters, all of which strongly depend on the defect density. These results underscore the potential for precisely engineered defect formation in large-scale CVD-grown hBN, paving the way for the scalable fabrication of quantum photonic devices.

cond-mat.mtrl-sci↗

arXiv2024

Strain-driven stabilization of a room-temperature chiral multiferroic with coupled ferroaxial and ferroelectric order

Noncollinear ferroic materials are sought after as testbeds to explore the intimate connections between topology and symmetry, which result in electronic, optical and magnetic functionalities not observed in collinear ferroic materials. For example, ferroaxial materials have ordered rotational structural distortions that break mirror symmetry and induce chirality. When ferroaxial order is coupled with ferroelectricity arising from a broken inversion symmetry, it offers the prospect of electric-field-control of the ferroaxial distortions and opens up new tunable functionalities. However, chiral multiferroics, especially ones stable at room temperature, are rare. We report the discovery of a strain-stabilized, room-temperature chiral multiferroic phase in single crystals of BaTiS$_3$, a quasi-one-dimensional (1D) hexagonal chalcogenide. Using first-principles calculations, we predict the stabilization of this multiferroic phase having $P6_3$ space group for biaxial tensile strains exceeding 1.5% applied on the basal ab-plane of the room temperature $P6_3cm$ phase of BaTiS$_3$. The chiral multiferroic phase is characterized by rotational distortions of select TiS$_6$ octahedra around the long $c$-axis and polar displacement of Ti atoms along the $c$-axis. We used an innovative approach using focused ion beam milling to make appropriately strained samples of BaTiS$_3$. The ferroaxial and ferroelectric distortions, and their domains in $P6_3$-BaTiS$_3$ were directly resolved using atomic resolution scanning transmission electron microscopy. Landau-based phenomenological modeling predicts a strong coupling between the ferroelectric and the ferroaxial order making $P6_3$-BaTiS$_3$ an attractive test bed for achieving electric-field control of chirality-related phenomena such as circular photo-galvanic current and the Rashba effect.

cond-mat.mtrl-sci↗

arXiv2024

A Versatile Side Entry Laser System for Scanning Transmission Electron Microscopy

We present the design and implementation of a side entry laser system designed for an ultra-high vacuum scanning transmission electron microscope. This system uses a versatile probe design enclosed in a vacuum envelope such that parts can be easily aligned, modified, or exchanged without disturbing the vacuum. The system uses a mirror mounted on the sample holder such that the sample can be illuminated without being tilted. Notably the mirror can be removed and replaced with an ablation target and a higher power laser used to ablate material directly onto the sample. We argue that new capabilities hold the potential to transform the electron microscope from an analysis tool towards a more flexible synthesis system, where atomic scale fabrication and atom-by-atom experiments can be performed.

physics.app-ph↗

arXiv2024

Your Clean Graphene is Still Not Clean

Efforts aimed at scaling fabrication processes to the level of single atoms, dubbed atom-by-atom fabrication or atomic fabrication, invariably encounter the obstacle of atomic scale cleanliness. When considering atomic fabrication, cleanliness of the base material and purity of the source reservoir from which atomic structures will be built are invariable constraints imposed by laws of physics and chemistry. As obvious as such statements may be, and regardless of the inevitable consequences for successful atomic fabrication, there is a poignant lack of understanding of the "dirt" (contamination/impurities). Here, we examine hydrocarbon contamination on graphene. Graphene has formed the base substrate for many e-beam-based atomic fabrication studies and many strategies for cleaning graphene have been presented in the literature. One popular method is heating to high temperatures (>500 °C). It is usually inferred that volatile hydrocarbons evaporate into the microscope vacuum system leaving behind pristine graphene. Here, we show through direct image intensity analysis that what appears to be clean graphene can be coated with a thin layer of dynamically diffusing hydrocarbons. This result holds significant implications for approaches to e-beam based atomic fabrication, updates the conceptual model of e-beam induced hydrocarbon deposition, and may extend to hot surfaces generally.

cond-mat.mtrl-sci↗

arXiv2024

Giant Modulation of Refractive Index from Picoscale Atomic Displacements

Structural disorder has been shown to enhance and modulate magnetic, electrical, dipolar, electrochemical, and mechanical properties of materials. However, the possibility of obtaining novel optical and optoelectronic properties from structural disorder remains an open question. Here, we show unambiguous evidence of disorder in the form of anisotropic, picoscale atomic displacements modulating the refractive index tensor and resulting in the giant optical anisotropy observed in BaTiS$_3$, a quasi-one-dimensional hexagonal chalcogenide. Single crystal X-ray diffraction studies reveal the presence of antipolar displacements of Ti atoms within adjacent TiS$_6$ chains along the c-axis, and three-fold degenerate Ti displacements in the a-b plane. $^{47/49}$Ti solid-state NMR provides additional evidence for those Ti displacements in the form of a three-horned NMR lineshape resulting from a low symmetry local environment around Ti atoms. We used scanning transmission electron microscopy to directly observe the globally disordered Ti a-b plane displacements and find them to be ordered locally over a few unit cells. First-principles calculations show that the Ti a-b plane displacements selectively reduce the refractive index along the ab-plane, while having minimal impact on the refractive index along the chain direction, thus resulting in a giant enhancement in the optical anisotropy. By showing a strong connection between structural disorder with picoscale displacements and the optical response in BaTiS$_3$, this study opens a pathway for designing optical materials with high refractive index and functionalities such as large optical anisotropy and nonlinearity.

cond-mat.mtrl-sci↗

arXiv2023

Controlling hydrocarbon transport and electron beam induced deposition on single layer graphene: toward atomic scale synthesis in the scanning transmission electron microscope

Focused electron beam induced deposition (FEBID) is a direct write technique for depositing materials on a support substrate akin to 3D printing with an electron beam (e-beam). Opportunities exist for merging this existing technique with aberration-corrected scanning transmission electron microscopy to achieve molecular- or atomic-level spatial precision. Several demonstrations have been performed using graphene as the support substrate. A common challenge that arises during this process is e-beam-induced hydrocarbon deposition, suggesting greater control over the sample environment is needed. Various strategies exist for cleaning graphene in situ. One of the most effective methods is to rapidly heat to high temperatures, e.g., 600 C or higher. While this can produce large areas of what appears to be atomically clean graphene, mobile hydrocarbons can still be present on the surfaces. Here, we show that these hydrocarbons are primarily limited to surface migration and demonstrate an effective method for interrupting the flow using e-beam deposition to form corralled hydrocarbon regions. This strategy is effective for maintaining atomically clean graphene at high temperatures where hydrocarbon mobility can lead to substantial accumulation of unwanted e-beam deposition.

cond-mat.mtrl-sci↗

arXiv2023

Doping transition-metal atoms in graphene for atomic-scale tailoring of electronic, magnetic, and quantum topological properties

Atomic-scale fabrication is an outstanding challenge and overarching goal for the nanoscience community. The practical implementation of moving and fixing atoms to a structure is non-trivial considering that one must spatially address the positioning of single atoms, provide a stabilizing scaffold to hold structures in place, and understand the details of their chemical bonding. Free-standing graphene offers a simplified platform for the development of atomic-scale fabrication and the focused electron beam in a scanning transmission electron microscope can be used to locally induce defects and sculpt the graphene. In this scenario, the graphene forms the stabilizing scaffold and the experimental question is whether a range of dopant atoms can be attached and incorporated into the lattice using a single technique and, from a theoretical perspective, we would like to know which dopants will create technologically interesting properties. Here, we demonstrate that the electron beam can be used to selectively and precisely insert a variety of transition metal atoms into graphene with highly localized control over the doping locations. We use first-principles density functional theory calculations with direct observation of the created structures to reveal the energetics of incorporating metal atoms into graphene and their magnetic, electronic, and quantum topological properties.

cond-mat.mtrl-sci↗

arXiv2023

The role of temperature on defect diffusion and nanoscale patterning in graphene

Graphene is of great scientific interest due to a variety of unique properties such as ballistic transport, spin selectivity, the quantum hall effect, and other quantum properties. Nanopatterning and atomic scale modifications of graphene are expected to enable further control over its intrinsic properties, providing ways to tune the electronic properties through geometric and strain effects, introduce edge states and other local or extended topological defects, and sculpt circuit paths. The focused beam of a scanning transmission electron microscope (STEM) can be used to remove atoms, enabling milling, doping, and deposition. Utilization of a STEM as an atomic scale fabrication platform is increasing; however, a detailed understanding of beam-induced processes and the subsequent cascade of aftereffects is lacking. Here, we examine the electron beam effects on atomically clean graphene at a variety of temperatures ranging from 400 to 1000 C. We find that temperature plays a significant role in the milling rate and moderates competing processes of carbon adatom coalescence, graphene healing, and the diffusion (and recombination) of defects. The results of this work can be applied to a wider range of 2D materials and introduce better understanding of defect evolution in graphite and other bulk layered materials.

cond-mat.mes-hall↗

arXiv2023

Doping of Cr in Graphene Using Electron Beam Manipulation for Functional Defect Engineering

Chromium atoms in graphene have been proposed to exhibit magnetic moments and spin-selective conducting states depending on the local bonding geometry within the graphene structure, which could lead to interesting applications in spintronics. Despite this interest, there are few direct experimental reports of Cr dopants in graphene even though it is theorized to be stable. Here, we demonstrate the introduction of single Cr dopant atoms into the graphene lattice and onto graphene edges through the controlled use of a focused electron beam in a scanning transmission electron microscope. We show local control of doping locations and when coupled with targeted in situ milling during scanning of the e-beam, these strategies demonstrate an important component of the fabrication of tailored nanostructured devices in the electron microscope. The approach is validated with first principles calculations to understand synthesis pathways during fabrication and reveal the energetics and local properties of Cr atoms embedded in graphene; e.g., Cr doping can convert graphene into a magnetic and semiconducting material, which suggests Cr-doped graphene can be used as a building block for potential electronic devices and a means to construct them.

cond-mat.mtrl-sci↗

arXiv2023

The Synthescope: A Vision for Combining Synthesis with Atomic Fabrication

The scanning transmission electron microscope, a workhorse instrument in materials characterization, is being transformed into an atomic-scale material manipulation platform. With an eye on the trajectory of recent developments and the obstacles toward progress in this field, we provide a vision for a path toward an expanded set of capabilities and applications. We reconceptualize the microscope as an instrument for fabrication and synthesis with the capability to image and characterize atomic-scale structural formation as it occurs. Further development and refinement of this approach may have substantial impact on research in microelectronics, quantum information science, and catalysis where precise control over atomic scale structure and chemistry of a few "active sites" can have a dramatic impact on larger scale functionality and where developing a better understanding of atomic scale processes can help point the way to larger scale synthesis approaches.

physics.app-ph↗

arXiv2023

Direct-Writing Atom-by-Atom

Direct-write processes enable the alteration or deposition of materials in a continuous, directable, sequential fashion. In this work we demonstrate an electron beam direct-write process in an aberration-corrected scanning transmission electron microscope. This process has several fundamental differences from conventional electron beam induced deposition techniques, where the electron beam dissociates precursor gases into chemically reactive products that bond to a substrate. Here, we use elemental tin (Sn) as a precursor and employ a different mechanism to facilitate deposition. The atomic-sized electron beam is used to generate chemically reactive point defects at desired locations in a graphene substrate. Temperature control of the sample is used to enable the precursor atoms to migrate across the surface and bond to the defect sites thereby enabling atom-by-atom direct-writing.

cond-mat.mtrl-sci↗

arXiv2023

A platform for in situ synthesis in a STEM

The engineering of quantum materials requires the development of tools able to address various synthesis and characterization challenges. These include the establishment and refinement of growth methods, material manipulation, and defect engineering. Material modification at the atomic level will be a key enabling factor for the engineering of quantum materials where desired phenomena are critically determined by local atomic structures. Successful use of scanning transmission electron microscopes (STEMs) for atomic scale material manipulation has opened the door for a transformed view of what can be accomplished using electron-beam-based strategies. However, serious obstacles exist on the pathway from possibility to practical reality. One such obstacle is the in situ delivery of atomized material in the STEM to the region of interest for further fabrication processes. Here, we present progress on this front with a view toward performing synthesis (deposition and growth) processes in a scanning transmission electron microscope. An in situ thermal deposition platform is presented, tested, and deposition and growth processes are demonstrated. In particular, we show that isolated Sn atoms can be evaporated from a filament and caught on the nearby sample, demonstrating atomized material delivery. This platform, and future variations, are envisioned to facilitate real-time atomic resolution imaging of growth processes and open new pathways toward atomic fabrication.

cond-mat.mtrl-sci↗