Sibel Ebru Yalcin, PhD
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Biography
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Extensive Research Description
Dr. Sibel Ebru Yalcin is a Turkish-American biochemical physicist & spectroscopist who develops nanoscopic imaging tools to visualize extracellular electron transfer pathways in diverse microbes such as soil bacteria, infectious bacteria and the microbes involved in climate change. She is the recipient of 2024 AAUW Research and 2022 Laura Bassi Fellowships. Dr Yalcin is also Alan Alda Center's STEM Professional dedicated to Empower Women in STEM Leadership since 2023.Her research focuses on building a new multimodal chemical and functional imaging capability to study microbial nanowires and their interactions with geochemically important soil minerals in physiologically relevant conditions such as pH and humidity. Using multimodal nanoscopy she correlated structure of the microbial nanowires with their functions that led to the discoveries of the identity of the proteins that make the conductive "Geobacter" OmcS nanowires (Cell, 2019) and electric field stimulated production of 1000 times more conductive OmcZ nanowires (Nature Chemical Biology, 2020). Discovery of cytochrome OmcZ nanowires explains the mystery of high biofilm conductivity scientists observed even in the absence of cytochrome OmcS! Highlights to this work can be found at Nature Chemical Biology News and Views article, LiveScience, YaleNews, Yale Scientific and Yale's Microbial Sciences Institute. The team also solved the mystery of electron transfer mechanism in OmcS nanowires (Science Advances, 2022). Additionally, Dr. Yalcin was part of the team that worked on solving the structure of Geobacter pili that revealed secretory rather than nanowire behavior (Nature, 2021). Highlights to this work can be found at Proteopedia, YaleNews & EurekAlert!. Dr. Yalcin also designed, developed and carried out the first photoconductivity measurements on individual OmcS nanowires using Photoconductive Atomic Force Microscopy (pc-AFM) (Nature Communications, 2022). Reviewers called her nanoscale measurements “very innovative approach and brilliantly combined with bulk measurements”. In her work she showed that individual nanowires can have up to 100-fold increase in conductance upon photoexcitation suggesting that these protein nanowires can serve as intrinsic photoconductors. Highlight to this work can be found at EurekAlert! and Phys.Org.
In addition to working on naturally produced conductive microbial nanowires, Dr. Yalcin also worked with a team that engineered conductivity to bacterial filaments. The team's work laid the foundation of how to turn nonconductive E-coli pili into bionanowires using non-natural amino acids with click chemistry functionality, a method not accessible in nature and only accessible through chemical based synthesis. In this work, the team demonstrated sequence-defined production of highly-conductive protein nanowires and hybrid organic-inorganic biomaterials with genetically-programmable electronic functionalities (Nature Communications, 2022).
Other than biological systems, Dr. Yalcin performed the first Nanoscale Chemical Imaging on reactive minerals (Gibbsite, Lepidocrocite) through their water binding chemistry. Her discoveries are critical to understand how mineral morphology and the defect sites affect the water growth over the mineral surface (Science Advances, 2020). Highlights to this work can be found at Yale West Campus, Yale's Microbial Sciences Institute, Yale's MB&B News and Umea University.
Dr. Yalcin has considerable experiences in Ultrafast Spectroscopy and Nanoscale Near-field Imaging of many low dimensional systems. She was part of user facility (Center for Integrated Nanotechnologies) at Los Alamos National Laboratory (LANL) where she built single molecule spectroscopy setup to study Carbon Nanotubes (Nanoscale, 2015) working with Steve Doorn and other low dimension materials such as Graphene Oxide (ACS Nano, 2015), MoS2 (Nature Materials, 2014) working with Manish Chhowalla. At University of Massachusetts Amherst, Dr. Yalcin has developed an Electrostatic Force Microscopy (EFM) based imaging method that has enabled the first visualization of electron transport in individual bacterial protein nanowires under biologically relevant conditions (Nature Nanotechnology, 2014) working with Nikhil Malvankar.
Dr. Yalcin holds a research faculty position at Yale’s Department of Molecular Biophysics & Biochemistry and Microbial Sciences Institute. She leads the effort of nanoscale functional imaging research to understand structural, physical and biochemical components and pathways involved in biological electron transfer. She is interested in understanding at nanoscopic level how bacteria interact with soil minerals to perform extracellular electron transfer for their respiration. She has PhD in Physics, and extensive experience in Biochemistry, Geochemistry and Microbiology. Dr. Yalcin is also a mother of a toddler boy. She has given many invited talks about the difficulties women scientists experience on how to achieve a work-life balance. Her passion is to inspire young female scientists who aspire to do impactful research and also have a family and kids.
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Selected Publications
- Microbial biofilms as living photoconductors due to ultrafast electron transfer in cytochrome OmcS nanowiresNeu J, Shipps CC, Guberman-Pfeffer MJ, Shen C, Srikanth V, Spies JA, Kirchhofer ND, Yalcin SE, Brudvig GW, Batista VS, Malvankar NS. Microbial biofilms as living photoconductors due to ultrafast electron transfer in cytochrome OmcS nanowires. Nature Communications 2022, 13: 5150. PMID: 36071037, PMCID: PMC9452534, DOI: 10.1038/s41467-022-32659-5.
- A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networksDahl PJ, Yi SM, Gu Y, Acharya A, Shipps C, Neu J, O’Brien J, Morzan UN, Chaudhuri S, Guberman-Pfeffer MJ, Vu D, Yalcin SE, Batista VS, Malvankar NS. A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks. Science Advances 2022, 8: eabm7193. PMID: 35544567, PMCID: PMC9094664, DOI: 10.1126/sciadv.abm7193.
- Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesisShapiro DM, Mandava G, Yalcin SE, Arranz-Gibert P, Dahl PJ, Shipps C, Gu Y, Srikanth V, Salazar-Morales AI, O’Brien J, Vanderschuren K, Vu D, Batista VS, Malvankar NS, Isaacs FJ. Protein nanowires with tunable functionality and programmable self-assembly using sequence-controlled synthesis. Nature Communications 2022, 13: 829. PMID: 35149672, PMCID: PMC8837800, DOI: 10.1038/s41467-022-28206-x.
- Structure of Geobacter pili reveals secretory rather than nanowire behaviourGu Y, Srikanth V, Salazar-Morales AI, Jain R, O’Brien J, Yi SM, Soni RK, Samatey FA, Yalcin SE, Malvankar NS. Structure of Geobacter pili reveals secretory rather than nanowire behaviour. Nature 2021, 597: 430-434. PMID: 34471289, PMCID: PMC9127704, DOI: 10.1038/s41586-021-03857-w.
- Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formationWong GCL, Antani JD, Lele PP, Chen J, Nan B, Kühn MJ, Persat A, Bru JL, Høyland-Kroghsbo NM, Siryaporn A, Conrad JC, Carrara F, Yawata Y, Stocker R, Brun Y, Whitfield GB, Lee CK, de Anda J, Schmidt WC, Golestanian R, O’Toole G, Floyd KA, Yildiz FH, Yang S, Jin F, Toyofuku M, Eberl L, Nomura N, Zacharoff LA, El-Naggar MY, Yalcin SE, Malvankar NS, Rojas-Andrade MD, Hochbaum AI, Yan J, Stone HA, Wingreen NS, Bassler BL, Wu Y, Xu H, Drescher K, Dunkel J. Roadmap on emerging concepts in the physical biology of bacterial biofilms: from surface sensing to community formation. Physical Biology 2021, 18: 10.1088/1478-3975/abdc0e. PMID: 33462162, PMCID: PMC8506656, DOI: 10.1088/1478-3975/abdc0e.
- The blind men and the filament: Understanding structures and functions of microbial nanowiresYalcin SE, Malvankar NS. The blind men and the filament: Understanding structures and functions of microbial nanowires. Current Opinion In Chemical Biology 2020, 59: 193-201. PMID: 33070100, PMCID: PMC7736336, DOI: 10.1016/j.cbpa.2020.08.004.
- Electric field stimulates production of highly conductive microbial OmcZ nanowiresYalcin SE, O’Brien J, Gu Y, Reiss K, Yi SM, Jain R, Srikanth V, Dahl PJ, Huynh W, Vu D, Acharya A, Chaudhuri S, Varga T, Batista VS, Malvankar NS. Electric field stimulates production of highly conductive microbial OmcZ nanowires. Nature Chemical Biology 2020, 16: 1136-1142. PMID: 32807967, PMCID: PMC7502555, DOI: 10.1038/s41589-020-0623-9.
- Direct observation of anisotropic growth of water films on minerals driven by defects and surface tensionYalcin SE, Legg BA, Yeşilbaş M, Malvankar NS, Boily JF. Direct observation of anisotropic growth of water films on minerals driven by defects and surface tension. Science Advances 2020, 6: eaaz9708. PMID: 32832658, PMCID: PMC7439304, DOI: 10.1126/sciadv.aaz9708.
- Probing the Role of Metal Coordination and pH in Assembly and Function of Cytochrome NanowiresSrikanth V, Gu Y, O'Brien J, Jain R, Yalcin S, Yi S, Samatey F, Malvankar N. Probing the Role of Metal Coordination and pH in Assembly and Function of Cytochrome Nanowires. Biophysical Journal 2020, 118: 335a-336a. DOI: 10.1016/j.bpj.2019.11.1872.
- Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over MicrometersWang F, Gu Y, O’Brien J, Yi SM, Yalcin SE, Srikanth V, Shen C, Vu D, Ing NL, Hochbaum AI, Egelman EH, Malvankar NS. Structure of Microbial Nanowires Reveals Stacked Hemes that Transport Electrons over Micrometers. Cell 2019, 177: 361-369.e10. PMID: 30951668, PMCID: PMC6720112, DOI: 10.1016/j.cell.2019.03.029.
- Femtosecond Dynamics of Nanoscale Molecular HeterogeneityAtkin J, Pollard B, Metzger B, Sass P, Yalcin S, Lea A, Teichen P, Eaves J, Raschke M. Femtosecond Dynamics of Nanoscale Molecular Heterogeneity. 2016, uw1a.3. DOI: 10.1364/up.2016.uw1a.3.
- Photoluminescence imaging of solitary dopant sites in covalently doped single-wall carbon nanotubesHartmann NF, Yalcin SE, Adamska L, Hároz EH, Ma X, Tretiak S, Htoon H, Doorn SK. Photoluminescence imaging of solitary dopant sites in covalently doped single-wall carbon nanotubes. Nanoscale 2015, 7: 20521-20530. PMID: 26586162, DOI: 10.1039/c5nr06343d.
- (Invited) Photoluminescence Carrier Dynamics and Photon Statistics of Covalent Dopant-Induced Trap States in Single Wall Carbon NanotubesDoorn S, Ma X, Hartmann N, Yalcin S, Htoon H. (Invited) Photoluminescence Carrier Dynamics and Photon Statistics of Covalent Dopant-Induced Trap States in Single Wall Carbon Nanotubes. ECS Meeting Abstracts 2015, MA2015-01: 803-803. DOI: 10.1149/ma2015-01/6/803.
- Dynamic and Steady State Optical Studies of Individual Covalent Dopant Sites in Single-Wall Carbon NanotubesHartmann N, Yalcin S, Haroz E, Ma X, Htoon H, Doorn S. Dynamic and Steady State Optical Studies of Individual Covalent Dopant Sites in Single-Wall Carbon Nanotubes. ECS Meeting Abstracts 2015, MA2015-01: 805-805. DOI: 10.1149/ma2015-01/6/805.
- Bench-top aqueous two-phase extraction of isolated individual single-walled carbon nanotubesSubbaiyan N, Parra-Vasquez A, Cambré S, Cordoba M, Yalcin S, Hamilton C, Mack N, Blackburn J, Doorn S, Duque J. Bench-top aqueous two-phase extraction of isolated individual single-walled carbon nanotubes. Nano Research 2015, 8: 1755-1769. DOI: 10.1007/s12274-014-0680-z.
- Direct Imaging of Charge Transport in Progressively Reduced Graphene Oxide Using Electrostatic Force MicroscopyYalcin SE, Galande C, Kappera R, Yamaguchi H, Martinez U, Velizhanin KA, Doorn SK, Dattelbaum AM, Chhowalla M, Ajayan PM, Gupta G, Mohite AD. Direct Imaging of Charge Transport in Progressively Reduced Graphene Oxide Using Electrostatic Force Microscopy. ACS Nano 2015, 9: 2981-2988. PMID: 25668323, DOI: 10.1021/nn507150q.
- Visualization of charge propagation along individual pili proteins using ambient electrostatic force microscopyMalvankar NS, Yalcin SE, Tuominen MT, Lovley DR. Visualization of charge propagation along individual pili proteins using ambient electrostatic force microscopy. Nature Nanotechnology 2014, 9: 1012-1017. PMID: 25326694, DOI: 10.1038/nnano.2014.236.
- Electronic Structure and Chemical Nature of Oxygen Dopant States in Carbon NanotubesMa X, Adamska L, Yamaguchi H, Yalcin SE, Tretiak S, Doorn SK, Htoon H. Electronic Structure and Chemical Nature of Oxygen Dopant States in Carbon Nanotubes. ACS Nano 2014, 8: 10782-10789. PMID: 25265272, DOI: 10.1021/nn504553y.
- Metallic 1T phase source/drain electrodes for field effect transistors from chemical vapor deposited MoS2Kappera R, Voiry D, Yalcin S, Jen W, Acerce M, Torrel S, Branch B, Lei S, Chen W, Najmaei S, Lou J, Ajayan P, Gupta G, Mohite A, Chhowalla M. Metallic 1T phase source/drain electrodes for field effect transistors from chemical vapor deposited MoS2. APL Materials 2014, 2: 092516. DOI: 10.1063/1.4896077.
- Phase-engineered low-resistance contacts for ultrathin MoS2 transistorsKappera R, Voiry D, Yalcin SE, Branch B, Gupta G, Mohite AD, Chhowalla M. Phase-engineered low-resistance contacts for ultrathin MoS2 transistors. Nature Materials 2014, 13: 1128-1134. PMID: 25173581, DOI: 10.1038/nmat4080.
- Invited Presentation: Photoluminescence Imaging Probes of Contrasting 1-D and 0-D Exciton Behavior in Doped Carbon NanotubesDoorn S, Yamaguchi H, Yalcin S, Ma X, Htoon H. Invited Presentation: Photoluminescence Imaging Probes of Contrasting 1-D and 0-D Exciton Behavior in Doped Carbon Nanotubes. ECS Meeting Abstracts 2014, MA2014-01: 1176-1176. DOI: 10.1149/ma2014-01/30/1176.
- Electrostatic Force Microscopy and Spectral Studies of Electron Attachment to Single Quantum Dots on Indium Tin Oxide SubstratesYalcin S, Yang B, Labastide J, Barnes M. Electrostatic Force Microscopy and Spectral Studies of Electron Attachment to Single Quantum Dots on Indium Tin Oxide Substrates. The Journal Of Physical Chemistry C 2012, 116: 15847-15853. DOI: 10.1021/jp305857d.
- Spectral Properties of Multiply Charged Semiconductor Quantum DotsYalcin SE, Labastide JA, Sowle DL, Barnes MD. Spectral Properties of Multiply Charged Semiconductor Quantum Dots. Nano Letters 2011, 11: 4425-4430. PMID: 21905683, DOI: 10.1021/nl2026103.
- Block-Copolymer-Based Plasmonic NanostructuresMistark PA, Park S, Yalcin SE, Lee DH, Yavuzcetin O, Tuominen MT, Russell TP, Achermann M. Block-Copolymer-Based Plasmonic Nanostructures. ACS Nano 2009, 3: 3987-3992. PMID: 19947582, DOI: 10.1021/nn901245w.
- Spectral bandwidth and phase effects of resonantly excited ultrafast surface plasmon pulsesYalcin S, Wang Y, Achermann M. Spectral bandwidth and phase effects of resonantly excited ultrafast surface plasmon pulses. Applied Physics Letters 2008, 93: 101103. DOI: 10.1063/1.2978399.
- Ultrafast surface plasmon pulses and their limitations using prism coupling excitationYalcin S, Wang Y, Ouellette D, Achermann M. Ultrafast surface plasmon pulses and their limitations using prism coupling excitation. 2008, 1-2. DOI: 10.1109/cleo.2008.4552002.