About

Shiheng Zhang holds a Ph.D. from Purdue University, where he studied numerical analysis with a focus on constructing structure preserving schemes for partial differential equations (PDEs). His research interests include dynamical systems, kinetic equations, neural networks, numerical analysis, optimization, scientific computing, spectral methods, and related fields. Currently, he is engaged in studying kinetic equations and their applications in neural networks. As an acting instructor at the University of Washington's Department of Applied Mathematics, he teaches courses such as Applied Linear Algebra and Numerical Analysis, as well as Introduction to Differential Equations and Applications. His work aims to advance the understanding and development of numerical methods for complex mathematical models, contributing to the fields of applied mathematics and computational science.

Research topics

• Chemistry
• Materials science
• Nanotechnology
• Chemical engineering
• Chemical physics

Selected publications

• Templating and confining calcium phosphate mineralization within designed protein assemblies

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-14

  articleOpen access

  Bone formation involves the deposition of ordered hydroxyapatite (HAp) on collagen fibrils, but the underlying molecular mechanisms remain largely unresolved, limiting the design of protein-apatite hybrid materials. Here we show that computationally designed de novo proteins can template and confine HAp mineralization with molecular level precision. We design C3-symmetric oligomers with inner surfaces chemically complementary to the HAp {010} facet, and assemble these through additional interfaces into D3 oligomers, one-dimensional nanotubes, and two-dimensional arrays. Electron microscopy revealed templated mineralization and confinement at each hierarchical level, with mineral shape guided by the underlying protein architecture. Phase conversion to HAp is driven by the designed protein-mineral interface. Our results establish a framework for programmable protein-guided mineralization, providing a foundation for next-generation biomaterials in regenerative medicine and nanotechnology.

  PublisherDOI

• Promotion of CaCO ₃ Nucleation by Carboxyl- and Amine-Terminated Peptoid Nanotubes

  Langmuir · 2026-04-22

  article

  The use of surfaces to promote heterogeneous nucleation of CaCO3 has been extensively studied to better understand natural processes of biomineralization, to develop bioinspired approaches for synthesizing composite materials with diverse functionalities, and as a route toward accelerating CO2 mineralization. Peptoids have emerged as a material of particular interest, because they offer tunable side chain chemistry while maintaining a constant long-range self-assembled architecture. Here, we investigate the ability of films of self-assembled -NH2 and −COOH terminated peptoid nanotubes to promote the nucleation of CaCO3. Using a combination of atomic force, scanning electron, and optical microscopy, we find that interwoven films of nanotubes formed from peptoids with -NH2 side chains promote the preferential formation of vaterite with the (001) plane parallel to the film and exhibit a lower interfacial energy than that reported for inorganic surfaces. In contrast, the film of −COOH-functionalized peptoid nanotubes is a much stronger promoter, giving a particle density 5 orders of magnitude larger than for the -NH2 terminated peptoid nanotubes and enabling complete coverage of individual peptoid tubes with CaCO3 nanoparticles that results in a composite material with a 50-fold increase in Young’s modulus. Thus, interwoven films of peptoid nanotubes provide a useful platform for investigating the impact of specific chemical groups on nucleation and offer potential application to accelerated mineralization of CO2 for removal from the environment or modulation of mineralogy and properties of carbonate-based building materials.

  PublisherDOI

• Ion Transport in Self-Assembled Peptoid Membranes with Carbon Nanotube Porin Channels

  Nano Letters · 2025-11-19

  article

  Artificial membranes that combine high ionic selectivity with mechanical robustness remain a key challenge for next-generation separation technologies. Here, we report ion transport measurements in biomimetic membranes composed of crystalline peptoid nanosheets co-assembled with carbon nanotube porins (CNTPs). Pure peptoid sheets formed defect-free, ion-impermeable membranes, which were then suspended over small SiNx nanopore apertures for ion transport measurements. Incorporation of CNTPs into the peptoid sheet matrix made these membranes ion permeable, with ion conductance values consistent with ion transport through individual and multiple carbon nanotube channels. The modularity and molecular order of peptoid membranes, combined with the exceptional conductance properties of CNTPs, position this platform as a versatile framework for assembling programmable, selective, and robust nanofluidic membranes that can bridge the performance gap between biological and synthetic membrane materials.

  PublisherDOI

• Two-Dimensional Silk Crystal Films as Matrix Layer for High-Performance Microelectronics

  2025-09-30

  reportOpen access1st authorCorresponding

  This study explores a bio-inspired approach for memristive devices by combining Keggin-type polyoxometalates (POMs)-[SiW12O40]4 (POM-T) and [PW12O40]3 (POM-P), with silk fibroin (SF) to create 2D SF–POM layers on highly ordered pyrolytic graphite (HOPG) as resistive switching layers for memristors. We propose that the ordered SF layer template 0D POMs facilitate the formation of conductive filaments, thereby enhancing the variability of the manufactured memristors. AFM analysis revealed that both SF and SF–POM layers shared similar morphologies, while SF–POM–T formed larger aggregates, likely due to the stronger acidity of POM-T, which probably caused SF to aggregate and alter its secondary structure. Scanning Kelvin probe microscopy (SKPM) revealed that POMs reduced the contact potential difference of HOPG, resulting in lower work functions. Compared to an SF device, the SF–POM–P device showed improved memristive behavior, with a larger current gap and good repeatability over multiple sweeps; whereas the SF–POM–T device did not exhibit memristor activity, likely due to acidity-induced disruption of the SF template’s order and CF formation. More importantly, SF–POM–P devices also demonstrated programmable memristive states. Finally, combining simulation-driven memristor modeling, we showcase a co-design workflow for advancing bioinspired memristors through new materials design, synthesis, and device modeling and development.

  PublisherOA PDFDOI

• Oil-based micro-sized extraction system designed from O/W Pickering emulsion template for highly efficient nanoplastics removal in the gastrointestinal tract

  Food Hydrocolloids · 2025-03-19 · 1 citations

  articleCorresponding
  PublisherDOI

• Insight into the promotion mechanism of the surface plasmon resonance aptasensor based on ultrathin MBene nanosheets embedded with aptamer-templated silver nanoclusters for aptasensing exosomal marker

  Talanta · 2025-02-14 · 7 citations

  article
  PublisherDOI

• Persistent El Niño-like conditions over the western Pacific during the Bølling–Allerød interstadial

  Communications Earth & Environment · 2025-11-29

  articleOpen access

  Abstract Projecting El Niño-Southern Oscillation responses to future climate change are hindered by limited paleoclimate records spanning past abrupt climate transitions. This study combines multi-proxy records from the Northwest Borneo Trough over the past 30 kyr with transient climate simulations, reconstructing tropical western Pacific hydroclimate during Heinrich events and Bølling–Allerød warming. Results show contrasting responses: Heinrich events saw stronger winter monsoons bringing northern moisture for Borneo’s orographic rain, while Bølling–Allerød warming initiated central Pacific El Niño-like conditions tied to Northern Hemisphere ice-sheet retreat beyond a critical threshold and subsequently sustained by insolation minimum, combined with Southern Hemisphere forcing, leading to regional dryness/seasonal aridity. We demonstrate dual high-latitude controls on western Pacific variability during Dansgaard–Oeschger cycles: hemispheric thermal gradients and ice-sheet topography. These findings reveal the links between ice sheets, insolation, and western Pacific El Niño-like conditions, offering valuable insights into long-term El Niño-Southern Oscillation dynamics and future behavior.

  PublisherOA PDFDOI

• Integrating High- <i>Z</i> Thorium Nodes with AIEgens in a Metal–Organic Framework for Superior X-ray Scintillation

  Inorganic Chemistry · 2025-11-19 · 2 citations

  article

  With the rapid progression of cutting-edge technologies, the demand for scintillator performance has become increasingly stringent, requiring enhancements across multiple dimensions, such as radioluminescence intensity, flexibility, and stability. Metal–organic frameworks (MOFs) have emerged as a promising class of materials capable of addressing these challenges through their tunable structures and their hybrid organic–inorganic nature. Here, we report the design of a thorium-based MOF scintillator, Th-TCBPE, constructed from high-atomic-number thorium nodes, and an aggregation-induced emission (AIE)-active linker (H4TCBPE). The rigid framework effectively suppresses nonradiative decay pathways of the AIE ligand, thereby affording an exceptional photoluminescence quantum yield (PLQY) of 90.83%, far surpassing that of the free ligand (56.78%). Under X-ray excitation, Th-TCBPE achieves a remarkably low detection limit of 3.46 μGy s–1, indicative of the outstanding sensitivity to low-dose radiation. Moreover, incorporation of Th-TCBPE into a flexible poly(dimethylsiloxane) (PDMS) matrix yielded composite films capable of high-fidelity X-ray imaging with a spatial resolution of 14.91 lp mm–1. These results underscore the promise of heavy-metal-based MOFs as efficient, multifunctional scintillators, opening new avenues for next-generation radiation detection and high-resolution imaging technologies.

  PublisherDOI

• An Electron Beam Irradiation Postsynthetic Lanthanide-Based Metal–Organic Framework for Extraction of U(VI)

  Inorganic Chemistry · 2025-04-29 · 2 citations

  article

  The development of highly efficient uranium adsorbents is pivotal for the sustainable advancement of nuclear energy. In this study, we present an innovative electron beam (EB) irradiation-assisted postsynthetic modification (PSM) strategy to engineer defects within a lanthanide-based metal–organic framework, MOF-76, significantly enhancing its U(VI) adsorption capacity. Compared to pristine MOF-76, the EB-modified MOF-76 demonstrates a remarkable increase in uranium removal efficiency, achieving the highest removal rate at a cumulative radiation dose of 120 kGy─twice that of the pristine material. A comprehensive suite of characterizations, including powder X-ray diffraction (PXRD), thermogravimetric analysis (TGA), CO2 sorption, electron paramagnetic resonance (EPR), X-ray photoelectron spectroscopy (XPS), and fluorescence lifetime and quantum yield measurements, confirms that the EB irradiation induces a high concentration of defects in MOF-76–120 kGy, primarily manifested as ligand vacancies, while preserving the overall framework structure and stability. XPS analysis further reveals that the irradiation-induced defects introduce numerous binding sites containing −COOH and −OH groups, which exhibit a strong affinity for U(VI). Our findings not only propel the development of advanced uranium extraction technologies but also offer valuable insights into the interactions between radiation and matter in porous crystalline systems.

  PublisherDOI

• Water Transportation through Nano/Microsized Lipid Protocells with a Significant Deviation from the van’t Hoff Osmotic Rule

  The Journal of Physical Chemistry B · 2025-03-12 · 1 citations

  article

  Osmotic pressure is known to be an important driving force that induces water transport through membranes, which is crucial for many biophysical processes. Here, we observed that under a relatively low osmotic pressure induced by sugars’ protocells (vesicles) with a diameter of ∼110 nm barely shrank. However, NaCl and CaCl2 at lower concentrations induced a rapid decrease in the vesicle size as evidence of water transportation through the membrane. An additional mechanical pressure resulting from the increase in interfacial tension of the lipid membrane was proposed to be the main driving force of this electrolyte-specific effect. These results indicate that osmotic pressure is not the only driving force of water transport in nano/microsized lipid protocells.

  PublisherDOI

Frequent coauthors

• James J. De Yoreo

  Pacific Northwest National Laboratory

  101 shared

• Chun‐Long Chen

  University of Washington

  76 shared

• James J. De Yoreo

  Pacific Northwest National Laboratory

  38 shared

• David Baker

  University of Washington

  31 shared

• Jim Pfaendtner

  North Carolina State University

  29 shared

• Zhihong Zhang

  Zhengzhou University of Light Industry

  28 shared

• Renyu Zheng

  Pacific Northwest National Laboratory

  28 shared

• Christopher J. Mundy

  Physical Sciences (United States)

  27 shared

Education

• PhD, iNANO Center

  Aarhus Universitet

  2014

• Graduate studnet, iNANO Center

  Aarhus Universitet

  2010

• Bachelor, Chemistry Department

  Jilin University

  2009