About

Peng Chen is the Peter J. W. Debye Professor in the Department of Chemistry and Chemical Biology at Cornell University. His research focuses on developing and applying single-molecule imaging and manipulation approaches to investigate the function and dynamics of nanomaterials and biomacromolecules. His work aims to acquire fundamental chemical knowledge to improve strategies for energy conversion and to develop methods for curing and preventing diseases. Professor Chen's group specializes in studying molecular processes of physical, bioinorganic, and biophysical nature, utilizing single-molecule techniques to capture transient intermediates and heterogeneous subpopulations that are often obscured in traditional ensemble measurements. His research projects are divided into three main areas: single-molecule catalysis, where he studies nanoscale materials and small-molecule catalysts at high temporal and spatial resolution to enhance chemical processing and energy conversion; single-molecule bioinorganic and biophysical chemistry, focusing on the dynamics and mechanisms of protein machineries involved in cellular metal regulation, trafficking, and electron transport pathways related to energy conversion and biomass synthesis; and method development, where he develops new techniques and improves existing methods to enable experiments at the single-molecule, single-particle, and single-cell levels. Professor Chen's contributions have been recognized through numerous honors, including the 2024 ISE-Elsevier Prize in Experimental Electrochemistry, election to the American Academy of Arts and Sciences, and the 2019 Chemical Pioneer Award, among others.

Research topics

• Chemistry
• Biology
• Materials science
• Nanotechnology
• Cell biology

Selected publications

• Arbuscular mycorrhizal fungi regulate ion homeostasis and the AsA-GSH cycle to enhance saline-alkaline tolerance in apple rootstock M9-T337

  DOAJ (DOAJ: Directory of Open Access Journals) · 2026-01-01

  article1st authorCorresponding

  【Objective】Salt-alkali stress, involving elevated sodium (Na+) levels and high pH conditions, poses a significant threat to crop growth and productivity in saline-alkali soils, which are widespread in many regions of the world. Finding effective strategies to mitigate the harmful effects of such stress on crops is crucial for sustainable agricultural development. This study aimed to investigate the effects of arbuscular mycorrhizal fungi (AMF) inoculation on the growth, physiological responses, and salt-alkali stress tolerance of apple rootstock M9-T337. The primary objective was to explore how AMF inoculation enhances salt-alkali tolerance, particularly by regulating ion homeostasis and modulating the ascorbate-glutathione (AsA-GSH) cycle in plants subjected to saline-alkali stress. The study provides a deeper understanding of the mechanisms underlying AMF-mediated tolerance in apple rootstocks, which are important for fruit production in marginal environmental conditions.【Methods】The experiment was conducted using one-year-old M9-T337 apple rootstock seedlings, which were transplanted into pots containing a sterilized substrate composed of soil, perlite, and vermiculite (3∶1∶1). These pots were sterilized in an autoclave at 121 ℃ for 2 hours to eliminate any microbial contaminants. The seedlings were subject to three treatments: (1)a control group receiving clean water irrigation(CK), (2)a saline-alkali stress group irrigated with 300 mL of a solution of 200 mmol·L-1NaCl∶NaHCO2(1∶1, pH 8.36)(SA)every 6 days, and(3)a saline-alkali stress group treated with AMF inoculation(SA+AMF). The AMF inoculum used was Claroideoglomus etunicatum(Ce, BGC G203C), with a spore count of 40 spores·g-1. A total of 90 seedlings were used, with 10 seedlings per treatment and three biological replicates for each treatment. The AMF inoculum was added to the substrate after transplantation, and after 45 days. The seedlings were harvested 30 days after the onset of saline-alkali stress to measure growth parameters, ion content, and the antioxidant system response.【Results】The results revealed that saline-alkali stress severely inhibited the growth of M9-T337 seedlings, as evidenced by significant reductions in biomass, stem thickness, leaf area, plant height increment, and leaf relative water content. However, AMF inoculation alleviated these negative effects. Specifically, the shoot and root biomass of AMF-treated seedlings increased by 35.7% and 28.6%, respectively, compared to those under saline-alkali stress alone. Additionally, stem thickness, leaf area, plant height increment, and leaf relative water content were significantly higher in the AMF-treated seedlings, demonstrating the positive impact of AMF on plant growth under stress conditions. The physiological responses of AMF-treated seedlings were also significantly enhanced, as indicated by substantial increases in antioxidant enzyme activities. The activities of superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) increased by 30.45%, 38.87%, and 19.35%, respectively, compared to the saline-alkali stressed group. This increase in antioxidant enzyme activities resulted in a reduction in hydrogen peroxide(H2O2)and superoxide anion(O2-·)accumulation by 18.09% and 27.03%, respectively, thus mitigating the oxidative damage caused by salt-alkali stress. In terms of ion homeostasis, AMF inoculation had a significant effect on the ion content in the seedlings. The AMF-treated seedlings exhibited a marked reduction in the sodium ion(Na+)content in the leaves by 18.02%, and a decrease in the sodium-to-potassium(Na+/K+)ratio by 28.96%, suggesting that AMF helped to maintain an optimal ion balance under saline-alkali conditions. The potassium ion (K+) content in the leaves of AMF-treated seedlings also increased by 15.40%, indicating that AMF promoted K+uptake and enhanced its transport to the leaves. These changes in ion balance are critical for reducing the toxic effects of Na+accumulation in the plant tissues. AMF likely facilitated the efflux of Na+from the root system and its compartmentalization into vacuoles, and improved the selective uptake of K+. Gene expression analysis further confirmed the role of AMF in regulating ion transport. Key genes involved in Na+ exclusion (MdSOS2), Na+ sequestration (MdNHX2), and K+uptake(MdGORK1)were upregulated in AMF-treated seedlings, contributing to improved ionic balance under stress conditions. Moreover, AMF inoculation enhanced the activity of the AsA-GSH cycle, which plays a vital role in plant responses to oxidative stress. The activities of ascorbate peroxidase (APX)and glutathione reductase(GR)in AMF-treated seedlings increased by 48.89% and 21.38%, respectively, leading to a more efficient AsA-GSH cycle, which might help to scavenge reactive oxygen species (ROS) and reduce oxidative damage. The increased antioxidant capacity in the AMF-treated seedlings was associated with a lower level of oxidative stress markers, such as H2O2and O2-·, in the plant tissues. These findings suggest that AMF inoculation not only improves ion homeostasis but also enhances the plant's ability to cope with oxidative stress under saline-alkali conditions.【Conclusion】The findings of this study demonstrate that AMF inoculation significantly enhanced the salt-alkali tolerance of apple rootstock M9-T337 by improving both ion homeostasis and antioxidant capacity. AMF treatment effectively reduced Na+accumulation in the leaves, enhanced K+uptake, and lowered the Na+/K+ratio, thereby mitigating ion toxicity. Additionally, AMF inoculation enhanced the AsA-GSH cycle, improving the plant's antioxidant defense system and reducing oxidative damage caused by salt-alkali stress. These results suggest that AMF can be a powerful tool to enhance the growth and stress tolerance of apple rootstocks in saline-alkali soils, offering potential applications in sustainable fruit production. The insights gained from this study also provide a theoretical basis for the practical use of mycorrhizal symbiosis technology to improve the resilience of crops in saline-alkali soils.

  PublisherDOI

• Microhomology-Mediated Tandem Duplication Drives Tandem Repeat Formation Across Life

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-03-02

  article

  Abstract Tandem repeats (TR) are common genomic elements that are highly variable and with major functional consequences. Yet, the evolutionary trajectory for their formation remains poorly understood. One proposed mechanism is microhomology-mediated tandem duplication (MTD), in which single-copy DNA segments flanked by microhomology undergo tandem duplication (TD) and can further expand into TRs. Although MTD was first identified in the fission yeast Schizosaccharomyces pombe , its universal occurrence and postulated role in TR evolution have not been established. Using whole-genome deep sequencing and new analytical tools, we show that MTDs occur de novo universally across bacteria, archaea, fungi, and viruses. Further analysis of 2,245 reference genomes and millions of isolate genomes from 103 prokaryotic and eukaryotic microbial species, combined with human population TD data, somatic-germline mutations, and disease-associated variants, reveals that MTDs are consistently the dominant TD-forming mechanism across domains of life. Evidence suggests that MTDs have initiated the formation of the majority of existing TRs in genomes. Importantly, MTDs also prevail in human pathogenic TR mutations, including those linked to cancers. Mechanistically, deletion of the conserved mutator gene Rad27 specifically increased de novo MTD frequency in the budding yeast Saccharomyces cerevisiae , implicating Rad27-mediated Okazaki fragment maturation in MTD formation. These findings establish MTD as a universal and functionally significant mechanism for TR genesis. Graphic abstract Significance Statement Microhomology-mediated tandem duplications (MTDs) represent a universal mechanism driving tandem repeat formation across all domains of life—from viruses to humans. These duplications initiate genome evolution by expanding into functional tandem repeats and are the predominant form of pathogenic tandem duplications in human cancers and heritable disorders. Critically, disruption of the conserved Okazaki fragment processing pathway promotes MTD formation, establishing a fundamental link between DNA replication fidelity and genomic plasticity.

  PublisherDOI

• Effect of a Grinding Method in the Preparation of CuO-ZnO-Al2O3@HZSM-5 Catalyst for CO2 Hydrogenation

  Catalysts · 2025-11-10

  articleOpen access

  There are many obstacles to the industrial application of CO2 hydrogenation reduction technology, the most important of which is the high economic cost. The purpose of this study is to explore the interaction mechanism between the active component CuO-ZnO-Al2O3(CZA) and the zeolite carrier Zeolite Socony Mobil-5(ZSM-5), screen the simplified preparation method of catalysts with high catalytic performance, and further promote the industrial application of CO2 hydrogenation reduction technology. In this study, the effects of the gas velocity of the feedstock, the reaction temperature, the content of acidic sites in the carrier, the filling amount of active component, and the mixing mode of the active component and the carrier on catalytic CO2 hydrogenation reduction were investigated. The structure of the catalysts was analyzed by X-ray diffractometer (XRD), Brunauer-Emmett-Teller (BET), Fourier-transform infrared spectroscopy (FTIR), scanning electron microscope (SEM) and transmission electron microscopy (TEM). The catalyst surface properties were analyzed by X-ray photoelectron spectroscopy (XPS), ammonia temperature programmed desorption (NH3-TPD), hydrogen temperature programed reduction (H2-TPR) and other characterization methods. The research found that the grinding treatment led to the insertion of CZA between ZSM-5 zeolite particles in CZA@HZ5-20-GB, which was prepared via grinding both CZA and H-ZSM-5 with an Si/Al ratio of 20, inhibiting the action of strongly acidic sites in the zeolite, resulting in only CO and MeOH in the catalytic products, with no Dimethyl Ether (DME) generation.

  PublisherOA PDFDOI

• CombatVLA: An Efficient Vision-Language-Action Model for Combat Tasks in 3D Action Role-Playing Games

  2025-10-19

  articleOpen access1st authorCorresponding

  Recent advances in Vision-Language-Action models (VLAs) have expanded the capabilities of embodied intelligence. However, significant challenges remain in real-time decision-making in complex 3D environments, which demand second-level responses, high-resolution perception, and tactical reasoning under dynamic conditions. To advance the field, we introduce CombatVLA, an efficient VLA model optimized for combat tasks in 3D action role-playing games(ARPGs). Specifically, our CombatVLA is a 3B model trained on video-action pairs collected by an action tracker, where the data is formatted as action-of-thought (AoT) sequences. Thereafter, CombatVLA seamlessly integrates into an action execution framework, allowing efficient inference through our truncated AoT strategy. Experimental results demonstrate that CombatVLA not only outperforms all existing models on the combat understanding benchmark but also achieves a 50-fold acceleration in game combat. Moreover, it has a higher task success rate than human players. We will open-source all resources, including the action tracker, dataset, benchmark, model weights, training code, and the implementation of the framework at https://combatvla.github.io/.

  PublisherOA PDFDOI

• Transporter excess and clustering facilitate adaptor protein shuttling for bacterial efflux

  Cell Reports Physical Science · 2025-02-01 · 5 citations

  articleOpen accessSenior author

  cells, there is a large excess of MacB (and TolC) driving the limiting adaptor protein MacA mostly into the MacAB-TolC assembly. Moreover, the excess MacB transporters can dynamically cluster around the assembly, and MacA can dynamically disassemble from the MacAB-TolC assembly, leading to an adaptor protein shuttling mechanism for efficient substrate sequestration from the periplasm toward efflux. We further show that both MacB clustering and MacAB-TolC assembly can be perturbed chemically or physically via microfluidics-based extrusion loading for compromised antibiotic tolerance. These insights may provide opportunities for countering the activities of multidrug efflux systems for antimicrobial treatments.

  PublisherDOI

• Conformation-gated binding underlies kinetic asymmetry and negative cooperativity in ATP:cob(I)alamin adenosyltransferase

  Cell Reports Physical Science · 2025-08-01 · 1 citations

  articleOpen access

  (cobalamin) is a high-value yet scarce cofactor critical for metabolic homeostasis, necessitating efficient handling mechanisms. ATP:cob(I)alamin adenosyltransferase (MMAB) plays a central role in synthesizing, delivering, and repairing 5'-deoxyadenosylcobalamin (AdoCbl), but the kinetic mechanisms regulating this process, including negative cooperativity, remain unclear. Using single-molecule relative fluorescence spectroscopy, we reveal that conformation-gated binding mechanism, involving a required structural rearrangement prior to the first cofactor association, dictates MMAB's interaction kinetics. This mechanism slows the association of a second AdoCbl, resulting in strong negative cooperativity, favoring the singly bound state, and optimizing AdoCbl handling. This gating mechanism, supported by direct observation of a kinetic intermediate, also contributes to MMAB's preferential handling of AdoCbl over hydroxocobalamin, highlighting MMAB's effective cofactor utilization, supporting bacterial survival in nutrient-limited environments. Furthermore, our approach offers a platform to study cofactor interactions, including cobalamin sensing and gene regulation, shedding light on bacterial adaptation to nutrient fluctuations.

  PublisherDOI

• Photocatalytic Overall Water Splitting at the Integrated Rh–MoRhO <i> _x </i> Cluster Heterostructure on InGaN/GaN Nanowires

  Angewandte Chemie International Edition · 2025-11-10 · 3 citations

  articleOpen accessCorresponding

  Abstract The quest for efficient solar‐driven water splitting, a promising avenue for clean fuel production, faces challenges due to limited solar energy conversion efficiency. Traditional approaches study the overall water splitting as two spatially separate half reactions on two unrelated sites, hindering full utilization of photogenerated charge and water molecules. To overcome these limitations, an integrated cluster heterostructure catalyst on InGaN/GaN semiconductor nanowires is proposed for the effective utilization of photogenerated charge carriers and water molecules on the same redox localization. By establishing the fast charge extraction kinetics based on InGaN/GaN nanowires, the integration of Rh and MoRhO x clusters on the nanowire surface enables simultaneous and fast hydrogen/oxygen evolution reactions at the cluster heterostructure. Furthermore, the integrated strategy can enhance the charge redistribution across the heterostructure between the two clusters, further optimizing adsorption of reaction intermediates on each cluster for boosted photocatalytic water splitting activity. Consequently, the integrated heterostructure triggers a 40‐fold increased hydrogen production efficiency in an artificial leaf system. This study provides valuable insights for the rational design of advanced heterostructured photocatalysts for water splitting and beyond.

  PublisherOA PDFDOI

• Circ-ITCH promotes the ubiquitination degradation of HOXC10 to facilitate osteogenic differentiation in disuse osteoporosis through stabilizing BRCA1 mRNA via IGF2BP2-mediated m6A modification

  Journal of Translational Medicine · 2025-03-27 · 12 citations

  articleOpen access

  Osteogenic differentiation of bone marrow mesenchymal stem cells (BM-MSCs) facilitated by mechanical loading is a promising therapy for disuse osteoporosis (DOP), however, it is difficult to implement mechanical loading for a majority of patients. Our study aims to identify circ-ITCH-mediated novel approach to facilitate osteogenic differentiation in DOP. A rat DOP model and human BM-MSCs under microgravity condition were generated as in vivo and in vitro models of DOP, respectively. The bone mineral density (BMD) and bone parameters were examined in rats. The histological changes of bones and mineralization were monitored by H&E, Alcian blue and Alizarin red S staining. Co-IP was employed to examine the ubiquitination of HOXC10 and the interaction between HOXC10 and BRCA1. The direct associations among circ-ITCH, IGFBP2 and BRCA1 mRNA were assessed by RIP, FISH and RNA pull-down assays. Circ-ITCH was downregulated in rat model of DOP and BM-MSCs under microgravity stimulation. Circ-ITCH overexpression promoted osteogenic differentiation in BM-MSCs under microgravity condition. The altered bone parameters, such as BMD, trabecular number (Tb.N), trabecular separation (Tb.Sp), trabecular thickness (Tb.Th), and bone microstructure in DOP rats were rescued by circ-ITCH overexpression. Mechanistically, circ-ITCH enhanced the ubiquitination degradation of HOXC10 through enhancing BRCA1 mRNA stability. Circ-ITCH directly bound to IGF2BP2 protein to stabilize BRCA1 mRNA via m6A modification, thus facilitating osteogenic differentiation in BM-MSCs under microgravity condition. Circ-ITCH stabilized BRCA1 mRNA via IGF2BP2-mediated m6A modification, thereby facilitating the ubiquitination degradation of HOXC10 to promote osteogenic differentiation in DOP.

  PublisherOA PDFDOI

• Association and Threshold Effect between Serum 25-Hydroxyvitamin D and Osteoporosis in Adults: A Cross-Sectional Study

  SSRN Electronic Journal · 2025-01-01

  preprintOpen access
  PublisherDOI

• Elucidating Energy Conversion Pathways at Biotic/Abiotic Interfaces in Microbe–Semiconductor Hybrids

  Journal of the American Chemical Society · 2025-06-07 · 9 citations

  reviewOpen accessCorresponding

  Biotic/abiotic hybrid systems integrating microbes with light-absorbing semiconductor materials offer promising solutions for sustainable energy conversion and value-added chemical production. In this Perspective, we discuss the mechanistic insights into upstream energy conversion processes at the biotic-abiotic interfaces, underscoring their pivotal roles in determining biohybrid performance. We explore how biological, physicochemical, and electrochemical characterization techniques have advanced our understanding of energy conversion pathways and electron transport mechanisms within these complex systems. Moreover, we emphasize the growing importance of spatiotemporally resolved imaging in linking biological activity to physicochemical dynamics at the single-cell level. Moving forward, we propose that interdisciplinary collaborations and innovative methodologies will be critical in deepening the mechanistic understanding and unlocking the full potential of artificial photosynthetic biohybrid systems.

  PublisherOA PDFDOI

Recent grants

• Single-Molecule Investigation of Nanocatalysis

  NSF · $281k · 2009–2012

• Unusual mechanisms of metal regulation in bacteria: from single molecules to single cells to cell communities

  NIH · $3.6M · 2014–2027

• CAREER: Bioinorganic Chemistry on a Single-Molecule Basis

  NSF · $555k · 2007–2012

• Nanoscale Mapping and Manipulation of Activity on Single Catalytic Nanocrystals/Nanostructures

  NSF · $319k · 2013–2016

• NIH Grant R21AI117295

  NIH · $440k · 2017

Frequent coauthors

• Xianwen Mao

  19 shared

• Won Jung

  Seoul National University

  18 shared

• Nesha May Andoy

  The Scarborough Hospital

  18 shared

• Jaime J. Benítez

  Cornell University

  16 shared

• Tai‐Yen Chen

  University of Houston

  13 shared

• Zhanqi Dong

  Southwest University

  13 shared

• Cheng Lu

  12 shared

• Aaron M. Keller

  Thomas More College

  12 shared

Labs

• Peng Chen GroupPI

Education

• Postdoc, Chemistry and Chemical Biology

  Harvard University

  2005

• PhD, Chemistry

  Stanford University

  2003

• graduate student, Chemistry & Biochemistry

  University of California San Diego

  1998

• BS, Chemistry

  Nanjing University

  1997

Awards & honors

• ISE-Elsevier Prize in Experimental Electrochemistry (2024)
• Member, American Academy of Arts and Sciences (2024)
• MilliporeSigma Lecture, St. Louis University (2024)
• Chemistry Honors Program Lecture, Kent State University (202…
• Chemical Pioneer Award (2019)