About

Professor Alan T. Charlie Johnson, Jr. leads a research group at the University of Pennsylvania focused on experimental nanoscale physics. His group's interests encompass transport phenomena including charge, energy, and spin in nanoscale systems such as carbon nanotubes, graphene, transition metal dichalcogenides, and hybrid nanostructures that integrate these materials with biological molecules like proteins, synthetic peptides, and DNA. These nanoscale systems are significant both for their potential technological applications in future nanoelectronics and for fundamental scientific understanding. To investigate the electronic properties of these molecular circuits, the group employs advanced nanofabrication techniques including photolithography, electron beam lithography, thin film deposition, and etching. Their experimental work heavily utilizes the facilities at the University of Pennsylvania Singh Center for Nanotechnology. Once fabricated, the molecular circuits are characterized using a variety of measurement techniques such as low-temperature magneto-transport, thermal conductivity measurements, and hybrid scanning probe methods that provide local electronic property data with nanometer-scale resolution. Professor Johnson's research thus bridges cutting-edge nanofabrication and nanoscale measurement techniques to explore the fundamental physics and potential applications of novel nanoscale materials and devices.

Research topics

• Materials science
• Optoelectronics
• Optics
• Nanotechnology
• Physics
• Chemistry
• Condensed matter physics
• Chromatography
• Electrical engineering
• Quantum mechanics
• Medicine
• Pathology
• Chemical physics
• Internal medicine
• Engineering
• Biochemistry

Selected publications

• High‐Density and Scalable Graphene Hall Sensor Arrays Through Monolithic CMOS Integration

  Advanced Electronic Materials · 2026-03-28

  articleOpen access

  ABSTRACT Electronic devices made from two‐dimensional materials (2DMs) significantly outperform their silicon counterparts; however, silicon CMOS technology remains commercially predominant as it offers the capability to operate dense arrays of devices in a scalable fashion. In particular, graphene Hall sensors (GHSs) offer great improvements in magnetic field sensitivity and resolution compared to silicon Hall‐effect sensors, making them extremely appealing for magnetic field imaging and biosensing. At present, GHS arrays have limited scalability compared to silicon CMOS since they require planar routing for biasing and multiplexing. In this work, we explore strategies to realize high‐density graphene Hall sensor arrays by vertically connecting GHSs with silicon CMOS biasing and multiplexing circuitry, allowing the routing and circuitry to scale with the array. We investigate the importance of design choices in the chip layout and post‐fabrication process in maximizing the reliability of graphene integration onto mm‐scale CMOS dies. Using this integration process, we show that GHSs and CMOS circuits can be monolithically integrated with high yield, creating high‐density magnetic sensing arrays with vertical biasing and readout connections. We expect that these results will lead to further improvements in magnetic sensing technology and broader advancements in large‐scale heterogeneous 2DM‐CMOS systems.

  PublisherDOI

• Quantitative Modeling of Nanopore Formation in 2D MoS ₂ by Swift Heavy-Ion Irradiation

  ACS Applied Materials & Interfaces · 2026-01-20 · 1 citations

  article

  Swift heavy-ion irradiation provides a versatile route for nanostructuring two-dimensional (2D) materials, with potential applications ranging from membrane engineering to electronic and sensing technologies. Here, we combine high-resolution scanning transmission electron microscopy with atomistic simulations to demonstrate controlled nanopore formation in monolayer MoS2, with pore sizes governed by stochastic energy transfer. By incorporating electron bunching, spatial straggling, and energy loss through escaping particles, our energy-transfer model quantitatively reproduces experimental pore size distributions and surpasses conventional stopping power predictions. These results deepen our understanding of ion–matter interactions in 2D systems and enable the controlled fabrication of functional nanostructures via ion irradiation.

  PublisherDOI

• Targeting Virulence to Disarm the Pathogen: Enzyme-Activated-Substrate Inhibition of Anthrax Edema Factor

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access1st authorCorresponding
  PublisherDOI

• Molecular characterisation of common <i>Culicoides</i> Biting Midges (Diptera: Ceratopogonidae) in Ireland

  bioRxiv (Cold Spring Harbor Laboratory) · 2025-01-08

  preprintOpen access

  Abstract Background Biting midges in the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including Bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoides species. This study represents the first attempt to characterise Culicoides in this region using molecular techniques. Methods Adult Culicoides samples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. Additionally, using both markers, we inferred the population genetic structure and potential colonisation pathways of Culicoides obsoletus sensu stricto (s. str.) , the major vector species in Ireland. Results DNA barcoding facilitated identification of 177 specimens. Eight common Culicoides species were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of Bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenus Avaritia ( C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi ) and subgenus Culicoides s. str. ( C. pulicaris and C. punctatus ). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement of Culicoides sp. which could not be identified to species level through DNA barcoding. Haplotype network analysis of C. obsoletus showed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector. Conclusion DNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifying Culicoides , especially species within the obsoletus complex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure of Culicoides spp. could be used to model the potential introduction routes of midge-borne pathogens into the country.

  PublisherOA PDFDOI

• Surface properties of copper oxytelluride thin films with different composition ratios fabricated by RF magnetron co-sputtering

  Physica B Condensed Matter · 2025-01-25 · 2 citations

  article
  PublisherDOI

• Targeting virulence to disarm the pathogen: Enzyme-activated-substrate inhibition of Anthrax edema factor

  Bioorganic & Medicinal Chemistry Letters · 2025-09-02

  articleOpen accessSenior author
  PublisherOA PDFDOI

• Molecular characterisation of common Culicoides biting midges (Diptera: Ceratopogonidae) in Ireland

  Parasites & Vectors · 2025-04-23 · 2 citations

  articleOpen access

  BACKGROUND: Biting midges of the genus Culicoides (Diptera: Ceratopogonidae) act as vectors for several arboviruses, including bluetongue virus (BTV) and Schmallenberg virus (SBV), which affect livestock health and productivity. In Ireland, limited genetic data are available regarding the diversity of Culicoides species. This study represents the first attempt to characterise Culicoides in this region using molecular techniques. METHODS: Adult Culicoides samples were captured using Onderstepoort Veterinary Institute (OVI) traps across six locations in Ireland. Subsequent molecular analyses involved polymerase chain reaction (PCR) and sequencing of the cytochrome oxidase subunit 1 (CO1) and the internal transcriber spacer (ITS) barcoding regions to obtain species identities. In addition, using both markers, we inferred the population genetic structure and potential colonisation pathways of Culicoides obsoletus sensu stricto (s. str.), the major vector species in Ireland. RESULTS: DNA barcoding facilitated identification of 177 specimens. Eight common Culicoides species were identified through DNA barcoding of CO1 and ITS gene regions. The presence of putative vectors of bluetongue virus (BTV) and Schmallenberg virus (SBV) were also confirmed, including species in the subgenus Avaritia (C. obsoletus s. str., C. scoticus, C. chiopterus, and C. dewulfi) and subgenus Culicoides s. str. (C. pulicaris and C. punctatus). Phylogenetic analysis confirmed the relationship between these vector species and facilitated the placement of Culicoides spp. that could not be identified to species level through DNA barcoding. Haplotype network analysis of C. obsoletus showed that some haplotypes of these species are shared between Continental Europe, the UK, and Ireland, suggesting a possible incursion pathway for this vector. CONCLUSIONS: DNA barcoding employing a combination of two barcodes, CO1 and ITS, proved effective in identifying Culicoides, especially species within the obsoletus complex, which are difficult to morphologically distinguish. Our findings also suggest that investigation of the population genetic structure of Culicoides spp. could be used to model the potential introduction routes of midge-borne pathogens into the country.

  PublisherOA PDFDOI

• Investigation on the Surface Properties of Annealed Copper Selenide Thin Films with Various Compositional Ratios

  physica status solidi (a) · 2024-10-29 · 2 citations

  article

  Copper‐based metal chalcogenides are versatile materials used for a variety of electronic devices, yet realizing the full scope of copper‐based composite materials is hindered by limited understanding of their chemical properties. In this work, copper selenide thin films (TFs) are fabricated using radio frequency (RF) magnetron co‐sputtering to investigate the effects of composition and annealing temperature on the films. The surface composition of the TFs is examined using energy dispersive X‐Ray spectroscopy (EDS) and X‐Ray photoelectron spectroscopy (XPS). In the unannealed films, an increase in Se composition leads to smaller grain sizes and smoother surfaces. The influence of higher Se content on the dispersive surface free energy (SFE) is shown through contact angle measurements. Work functions (WFs), determined by Kelvin probe (KP) and ultraviolet photoelectron spectroscopy (UPS), rose with increasing Se content. After annealing, the TFs exhibited opposite trends. As the films transitioned from an amorphous to a crystalline phase due to annealing, their roughness significantly increased.

  PublisherDOI

• Klein tunneling of gigahertz elastic waves in nanoelectromechanical metamaterials

  Device · 2024-08-01 · 1 citations

  articleOpen accessCorresponding

  The Klein tunneling effect describes the transmission of a relativistic particle with normal incidence through an energy barrier. It has been observed and tested in various electronic, photonic, and phononic systems, but its potential in guiding and filtering classical waves in the ultrahigh frequency regime has not been explored. Here, we report the realization of acoustic Klein tunneling in a nanoelectromechanical metamaterial system operating at gigahertz frequencies. The piezoelectric potential profiles are obtained by transmission-mode microwave impedance microscopy, from which reciprocal-space maps are extracted. The transmission rate of normally incident elastic waves is near unity in the Klein tunneling regime and drops significantly outside this frequency range, consistent with microwave network analysis. Strong angular dependent transmission is possible by controlling the launching angle of the emitter interdigital transducer. This work broadens the horizon for exploiting high-energy-physics phenomena for practical circuit applications in both classical and quantum regimes.

  PublisherOA PDFDOI

• Electrical Characterization and Ammonia Gas Response of a p‐Si/n<i>‐</i>poly[benzimidazobenzophenanthroline] Thin‐Film Junction Diode

  physica status solidi (a) · 2024-03-09 · 3 citations

  articleSenior author

  The electrical characterization and ammonia vapor (NH 3 ) response of a p‐Si/n‐poly[benzimidazobenzophenanthroline] (n‐BBL) thin‐film junction diode are reported. The presence of a depletion layer at the n‐BBL/p‐Si interface is verified via capacitance–voltage measurements, and the built‐in potential is ≈1.8 V. Using the standard diode equation for data analysis, the turn‐on voltage, rectification ratio, and ideality parameter are found to be 2 V, 16, and 6, respectively. The diode is also tested in the presence of NH 3 vapor where it retained its asymmetric J – V behavior with increased currents and an insignificant change in device parameters. NH 3 is believed to interact with the adsorbed O 2 − species on the n‐BBL surface liberating electrons that enhance the diode current. The response time, recovery time, and sensitivity of the diode are 65 s, 121 s, and 52%, respectively. The removal of the gas restores the diode characteristics to their near original shape making it reusable. The diode is also electrically characterized as a function of temperature and is found to retain its rectifying behavior down to 150 K. The rectifying and gas‐sensing features make the diode multifunctional, which expands the range of applications of this ladder‐type conducting polymer.

  PublisherDOI

Recent grants

• Graphene- and Metal-based Atomically Precise Nanoelectronics

  NSF · $488k · 2008–2012

• NIH Grant R44AI052587

  NIH · $8.0M · 2011

• EFRI 2-DARE: Functionalized Monolayer Heterostructures for Biosensors with Optical Readout

  NSF · $2.2M · 2015–2020

• NIH Grant R43AI069584

  NIH · $988k · 2009

• AIR Option 2: Research Alliance Bio-enabled Nanosensors with Fully Programmable Ligand Detection

  NSF · $812k · 2013–2016

Frequent coauthors

• Carl H. Naylor

  Intel (United States)

  62 shared

• Guan‐Sheng Jiao

  Hawaii Biotech (United States)

  57 shared

• Danvers E. Johnston

  Florida Gulf Coast University

  50 shared

• Nicholas J. Pinto

  49 shared

• Zhaoli Gao

  Chinese University of Hong Kong

  47 shared

• W. F. Smith

  44 shared

• Meng‐Qiang Zhao

  New Jersey Institute of Technology

  41 shared

• Jinglei Ping

  40 shared

Labs

• Charlie Johnson GroupPI

Education

• Ph.D., Physics

  University of Pennsylvania

  1994

• M.S., Physics

  University of Pennsylvania

  1991

• B.S., Physics

  University of California, Berkeley

  1987