About

Sahar Sharifzadeh is an Affiliate Faculty and Associate Professor in the Department of Electrical and Computer Engineering at Boston University. Her research focuses on understanding and predicting functional material properties through the use of first-principles electronic structure methods. She develops and applies these methods to accurately predict the electronic, magnetic, and structural properties of materials based on the fundamental laws of quantum mechanics. The primary goal of her work is to extract physical intuition about materials and to facilitate the design of new outstanding materials. Dr. Sharifzadeh holds a Ph.D. in Electrical Engineering from Princeton University and a B.S. in Electrical Engineering and Computer Science from the University of California, Berkeley. Her research contributes to the advancement of computational materials science, aiming to enable the discovery and development of novel materials with desirable properties.

Research topics

• Physics
• Condensed matter physics
• Materials science

Selected publications

• Chemical Mapping of Nanoparticle–Ligand Interfaces in Optical Nanocavities

  Journal of the American Chemical Society · 2025-06-13

  articleOpen access

  Understanding processes in photon-phonon scattering, absorption, and chemical reactions in optical nanocavities is important for single-molecule sensors, single-photon emitters, and photocatalysis. However, the influence of electromagnetic fields, charge transfer, and molecular geometry is challenging to probe by ensemble-averaged spectroscopic techniques over multiple nanocavities. Photoinduced force microscopy (PiFM), which measures photoinduced polarizability under infrared excitation of a sample in the nanocavity between the scanning probe microscopy tip and sample surface, is used here for simultaneous nanoscale topological and chemical characterization. First-principles density functional theory (DFT) simulations of the vibrational spectra of gold nanoparticle surfaces functionalized with benzenedithiol (Au-BDT) elucidate molecular orientation, charge transfer, and oxidation state for understanding molecular and adatom reconfiguration in optical nanocavities in response to external fields.

  PublisherDOI

• Ferroelectric phase transition in group-IV monochalcogenides from an equivariant machine learned force field

  Physical Review Materials · 2025-10-10

  articleSenior author

  Group-IV monochalcogenides are a class of layered ferroelectric semiconductors that have demonstrated spontaneous intrinsic polarization above room temperature. Here, we use the multiatomic cluster expansion machine learning architecture to train and test a force field capable of modeling the structural properties and second-order ferroelectric-to-paraelectric phase transition in a group-IV monochalcogenide, GeSe. The model captures the double-well potential energy surface associated with the onset of macroscopic polarization in bulk GeSe within $12.5\phantom{\rule{0.28em}{0ex}}\mathrm{meV}/\mathrm{atom}$, as well as near-equilibrium properties like the phonon dispersion. The development of this quantitatively accurate force field enables long-time molecular dynamics simulations, which predict the critical temperature of the ferroelectric-to-paraelectric phase transition in bulk GeSe to be ${T}_{c}=600\phantom{\rule{0.28em}{0ex}}\mathrm{K}$. This study demonstrates the capabilities of equivariant force fields to accurately describe phenomena associated with structural symmetry breaking.

  PublisherDOI

• Mo Atom Rearrangement Drives Layer-Dependent Reactivity in Two-Dimensional MoS2

  ArXiv.org · 2025-09-04

  preprintOpen access

  Two-dimensional (2D) materials offer a valuable platform for manipulating and studying chemical reactions at atomic level, owing to the ease of controlling their microscopic structure at the nanometer scale. While extensive research has been conducted on the structure-dependent chemical activity of 2D materials, the influence of structural transformation during the reaction remains largely unexplored. In this work, we report the layer-dependent chemical reactivity of MoS2 during a nitridation atomic substitution reaction and attribute it to the rearrangement of Mo atoms. Our results show that the chemical reactivity of MoS2 decreases as the number of layers is reduced in the few-layer regime. In particular, monolayer MoS2 exhibits significantly lower reactivity compared to its few-layer and multilayer counterparts. Atomic-resolution transmission electron microscope (TEM) reveals that MoN nanonetworks form as reaction products from monolayer and bilayer MoS2, with the continuity of the MoN crystals increasing with layer number, consistent with the local conductivity mapping data. The layer-dependent reactivity is attributed to the relative stability of the hypothetically formed MoN phase which retain the number of Mo atomic layers present in the precursor. Specifically, the low chemical reactivity of monolayer MoS2 is attributed to the high energy cost associated with Mo atom diffusion and migration necessary to form multi-layer Mo lattices in the thermodynamically stable MoN phase. This study underscores the critical role of lattice rearrangement in governing chemical reactivity and highlights the potential of 2D materials as versatile platforms for advancing the understanding of materials chemistry at atomic scale.

  PublisherOA PDFDOI

• Investigating electron conductivity regimes in the bacterial cytochrome wire OmcS

  arXiv (Cornell University) · 2025-04-07 · 1 citations

  preprintOpen accessSenior author

  The anaerobic bacterium \textit{Geobacter sulfurreducens} produces extracellular, electronically conductive cytochrome polymer wires that are conductive over micron length scales. Structure models from cryo-electron microscopy data show OmcS wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. The geometric arrangement of heme along OmcS wires is conserved in many multiheme c-type cytochromes and other recently discovered microbial cytochrome wires. However, the mechanism by which this arrangement of heme molecules support electron transport through proteins and supramolecular heme wires is unclear. Here, we investigate the site energies, inter-heme coupling, and long-range electronic conductivity within OmcS. We introduce an approach to extract charge carrier site information directly from Kohn-Sham density functional theory, without employing projector schemes. We show that site and coupling energies are highly sensitive to changes in inter-heme geometry and the surrounding electrostatic environment, as intuitively expected. These parameters serve as inputs for a quantum charge carrier model that includes decoherence corrections with which we predict a diffusion coefficient comparable with other organic-based electronic materials. Based on these simulations, we propose that dynamic disorder, particularly due to perturbative inter-heme vibrations allow the carrier to overcome trapping due to the presence of static disorder \textit{via} small frequency-dependent fluctuations. These studies provide insights into molecular and electronic determinants of long-range electronic conductivity in microbial cytochrome wires and highlight design principles for bioinspired, heme-based conductive materials.

  PublisherDOI

• Investigating Electron Conductivity Regimes in the Bacterial Cytochrome Wire OmcS

  The Journal of Physical Chemistry B · 2025-11-08 · 2 citations

  articleOpen accessSenior authorCorresponding

  produces extracellular, electronically conductive cytochrome polymer wires that are conductive over micron length scales. Structure models from cryo-electron microscopy data show OmcS wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. However, the mechanism by which this heme arrangement supports long-range electronic conduction remains unknown. Structure models from cryo-electron microscopy data show these wires form a linear chain of hemes along the protein wire axis, which is proposed as the structural basis supporting their electronic properties. Existing computational models using static heme redox potentials and coupling energies fail to explain experimental observations, predicting conductances 10,000 to 100,000 times lower than measured values. Here, we investigate how dynamic disorder affects site energies, interheme coupling, and long-range electronic conductivity within these cytochrome wires. We introduce an approach to extract charge carrier site information directly from Kohn-Sham density functional theory, without employing projector schemes, and show that site and coupling energies are highly sensitive to changes in interheme geometry and the surrounding electrostatic environment. Unlike models that incorporate dynamic disorder as a thermally averaged quantity, our quantum charge carrier model incorporates proxies for dynamic disorder through decoherence corrections, yielding predicted diffusion coefficient closer to what is expected from experiment and comparable with other organic-based electronic materials. Based on these simulations, we propose that the instantaneous fluctuations of the local electrostatic environment can transiently lift energy degeneracies and delocalize charge carriers. These studies reveal how incorporating dynamic fluctuations associated with the environment resolves the discrepancy between theory and experiment in microbial cytochrome wires and highlight design principles for bioinspired, heme-based conductive materials.

  PublisherOA PDFDOI

• Near-Infrared Emission from Sulfur Heteroatom Defects in Single-Walled Carbon Nanotubes

  The Journal of Physical Chemistry C · 2025-09-19

  article
  PublisherDOI

• Mo Atom Rearrangement Drives Layer-Dependent Reactivity in Two-Dimensional MoS₂

  Journal of the American Chemical Society · 2025-09-09 · 4 citations

  article

  Two-dimensional (2D) materials offer a valuable platform for manipulating and studying chemical reactions at the atomic level, owing to the ease of controlling their microscopic structure at the nanometer scale. While extensive research has been conducted on the structure-dependent chemical activity of 2D materials, the influence of structural transformation during the reaction has remained largely unexplored. In this work, we report the layer-dependent chemical reactivity of MoS2 during a nitridation atomic substitution reaction and attribute it to the rearrangement of Mo atoms. Our results show that the chemical reactivity of MoS2 decreases as the number of layers is reduced in the few-layer regime. In particular, monolayer MoS2 exhibits significantly lower reactivity compared with its few-layer and multilayer counterparts. Atomic-resolution transmission electron microscopy (TEM) reveals that MoN nanonetworks form as reaction products from monolayer and bilayer MoS2, with the continuity of the MoN crystals increasing with layer number, consistent with the local conductivity mapping data. The layer-dependent reactivity is attributed to the relative stability of the hypothetically formed MoN phase, which retains the number of Mo atomic layers present in the precursor. Specifically, the low chemical reactivity of monolayer MoS2 is attributed to the high energy cost associated with Mo atom diffusion and migration necessary to form multilayer Mo lattices in the thermodynamically stable MoN phase. This study underscores the critical role of lattice rearrangement in governing chemical reactivity and highlights the potential of 2D materials as versatile platforms for advancing the understanding of materials chemistry at the atomic scale.

  PublisherDOI

• First-principles investigation of sulfur and sulfur-oxide compounds as potential optically active defects on (6,5) SWCNT

  Materials Advances · 2025-12-23

  articleOpen accessSenior author

  The adsorption of SO x on (6,5) SWCNT was studied within density functional theory. While S and SO adsorb strongly on the tube and lead to a red-shift in the band gap, SO 2 and SO 3 are weakly bound and do not.

  PublisherOA PDFDOI

• Identifying Driving and Spectator Phonon Modes in Pentacene Exciton Transport

  Journal of the American Chemical Society · 2025-06-27 · 2 citations

  article

  In organic semiconductors, the crystal packing motif is known to modify electronic properties, such as exciton transport dynamics. Phonon vibrations can drive or hinder exciton transport, and understanding the role of these intermolecular vibrations can aid in the rational design of materials for improved solar cell efficiency. In this article, we use double pulse spatially offset femtosecond stimulated Raman spectroscopy (SOFSRS) to identify the functional role of phonon modes in pentacene exciton transport. In SOFSRS, we photoexcite our sample at a spatially offset position relative to the Raman pump and probe, which allows us to track changes in the excited state structure over micrometer length scales and femtosecond time scales during exciton transport. We first measure the phonon modes in a single crystal and then use optical pulse shaping to selectively amplify each mode and measure the resulting exciton transport dynamics along the fast and slow transport axes using SOFSRS. We compare the resulting dynamics with a single pulse excitation SOFSRS to assign driving and spectator phonon modes. We find that a 91 cm–1 phonon mode drives exciton transport preferentially along the slow transport axis. We also find two modes at 161 and 176 cm–1 that drive an increase in the overall excited state population. By comparing these to first-principles density functional theory calculations, we assign a plausible mechanism for exciton–phonon coupling. This study presents a new experimental method that can determine the functional role of phonon vibrations in mediating exciton transport.

  PublisherDOI

• Dynamic electronic structure fluctuations in the de novo peptide ACC-dimer revealed by first-principles theory and machine learning

  ChemRxiv · 2025-02-10

  preprintSenior author

  Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex molecular environment of biomolecular building blocks, however, it is unclear which chemical and structural dynamic features support electronic conductivity. Here, we investigate the role of finite temperature fluctuations on the electronic structure and its implications for conductivity in a peptide-based fiber material composed of an antiparallel coiled coil hexamer, ACC-Hex, building block. All-atom classical molecular dynamics (MD) and first-principles density functional theory (DFT) are combined with interpretable machine learning (ML) to understand the relationship between physical and electronic structure of the peptide dimer subunit of ACC-Hex. For 1,101 unique MD ``snapshots" of the ACC peptide dimer, hybrid DFT calculations predict a significant variation of near-gap orbital energies among snapshots, with an increase in the predicted number of nearly degenerate states near the highest occupied molecular orbital (HOMO), which suggests improved conductivity. Interpretable ML is then used to investigate which nuclear conformations increase number of nearly-degenerate states. We find that molecular conformation descriptors of inter-phenylalanine distance and orientation are, as expected, highly correlated with increased state density near the HOMO. Unexpectedly, we also find that descriptors of tightly coiled peptide backbones, as well as those describing the change in the electrostatic environment around the peptide dimer, are important for predicting the number of hole-accessible states near the HOMO. Our study illustrates the utility of interpretable ML as a tool for understanding complex trends in large-scale \textit{ab initio} simulations.

  PublisherDOI

Recent grants

• CAREER: First-Principles Investigation of Energy Transport Within Ordered Organic Assemblies

  NSF · $542k · 2019–2024

• First-Principles Investigation of Energy Transport within Highly Ordered Organic Molecular Arrays

  NSF · $284k · 2016–2019

Frequent coauthors

• Jeffrey B. Neaton

  University of California, Berkeley

  58 shared

• Leeor Kronik

  Weizmann Institute of Science

  24 shared

• Pierre Darancet

  Argonne National Laboratory

  19 shared

• Anubhab Haldar

  Boston University

  15 shared

• Marios Zacharias

  Université de Rennes

  15 shared

• Xuedan Ma

  Argonne National Laboratory

  11 shared

• Sebastian Fernández-Alberti

  Consejo Nacional de Investigaciones Científicas y Técnicas

  11 shared

• Sergei Tretiak

  Los Alamos National Laboratory

  11 shared