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THE XU LAB
Single Molecule Study: Molecular Electronics & Single Molecular Biophysics and Mechanics
Welcome to the XU LAB at the University of Georgia!
RESEARCH PROJECTS
Schematic description of the research projects
Research Schematics
  •          Nano/Molecular Electronics (Up Panel): The death of the famous Moore’s Law after it lasted 50 years, on one hand,  will cause economic crisis, on the other hand, however,  will spur innovation.  The original considerations of molecular electronics, overcome the prediction of Moore’s Law, led researchers to single-molecule scale devices. 32 years passed since Aviram and Ratner proposed the famous molecular rectifier. Though a great deal of researchers have been conducted in single molecular transport properties using molecular breakjunction methods, devices of single molecules are still conceptual. This opportunity will spur many innovations in molecular electronics and my research is well positioned to grasp this opportunity (see the aove schametic figure, top right, our research projects  highlighted in yellow) with my national and international collaborators from UGA, Georgia State University, University of Liverpool, Lancaster University and Ben-Gurion University. 
1.   Single molecular optoelectronic transport, thermo transport, and spin transport: As stated above, we have developed the STM break junction methods and data analysis strategies (Schematic Figure) and demonstrated many electronic properties of the junctions, from the method delopment to single molecule conductance measuremts, from determing the molecule-electrode contact details to fabricate and characterizing the functional junction devices, from simple mechanistic understanding to unraveling the quantum effcets in the molecular junction devices.  We are now interested in furthering our study on the transport properties of single molecular junction devices under addition of photonic emission, temperature gradient, and magnetic field. The combined optical/thermo/magnetic and electron-transport experimental measurements will reveal a wealth of new findings beyond what has been found in previous sole electronic measurements. Such studies will generate new insights into the molecular transport mechanisms which are imperative to advance research in single molecular devices and gain new insights into the processes in bulk organic devices. For example, the potential applications of the Opto-electronic transport include photovoltaic cells for solar energy harvesting and organic light emitting diodes for flat panel and flexible displays.

Selected Publications:
  •   K Wang, BQ Xu, 2016 Electron tunneling through molecule-electrode contacts of single alkane molecular junctions: experimental determination and a practical barrier model Phys. Chem. Chem. Phys.                      18 9569-9576 (pdf)
  • A Vezzoli,  G Lain, C Brooke, K Wang, C Lambert, BQ Xu, R Nichols, S Higgins, 2015 Gating of single molecule junction conductance by charge transfer complex formation Nanoscale, 7,18949-18955 (pdf)
  •  K Wang,  J Hamill,  JF Zhou, BQ Xu, 2014 Mapping the details of contact effect of modulated Au-octanedithiol-Au break junction by force-conductance cross-correlation ,  J. Am. Chem. Soc., 136 (50), pp 17406–17409 (pdf)
  • K Wang, JF Zhou, J Hamill,  BQ Xu, 2014 Measurement and understanding of  single molecule junction retification caused by asymmetric contacts ,  J. Chem. Phys., 141, 054712/1-054712/7 (pdf)
  •  JF Zhou, S Samanta, CL Guo, J Locklin, BQ Xu, 2013 Measurements of contact specific low-bias negative differential resistance of single metalorganic molecular junctions, Nanoscale, 3,  5715-5719 (pdf)
  •  JF Zhou, CL Guo, BQ Xu, 2012 Electron transport properties of single molecular junctions under mechanical modulations, J. Phys. Condens. Matt. 24, 164029/1-164029/9  (pdf)
  • JF Zhou, BQ Xu, 2011. Determining contact potential barrier effects on electronic transport in single molecular junctions, Appl. Phys. Lett. 99(4): 042104/1-042104/3 (pdf)
  • JF Zhou, GJ Chen, BQ Xu, 2010. Probing the Molecule-Electrode Interface of Single-Molecule Junctions by Controllable Mechanical Modulations, J. Phys. Chem. C., 114(18), 8587-8592 (pdf)
  • JF Zhou, F Chen, BQ Xu*, 2009. Fabrication and electronic characterization of single molecular junction devices: A comprehensive approach, J. Am. Chem. Soc., 131 (30): 10439-10446(pdf)
  • BQ Xu. 2007. Modulating the Conductance of a Au-octanedithiol-Au Molecular Junction, Small, 3 (12) 2061-2065 (pdf)

2. DNA Electronics: From fabrication to measuring and understanding of their electronic transport properties:  .  In addition to the molecule’s high density of genetic information, the inherent structural and molecular recognition properties of DNA render it ideal for molecular electronics applications. Because the predictability, diversity, and programmability, DNA is leading candidate for the design of functional electronic devices using single molecules. Building upon our research on DNA molecules on its structure determined charge properties (Chem. Sci., 5 (9) 3425-3431) and demonstrated device properties as diode (Nat. Chem. 8, 484–490 (2016)), we will develop novel approaches to dope DNA with atoms  and small molecules with the goal to bring the single DNA device to the level that is comparable to that of workable devices.

 Selected Publications:
    o     CL Guo, K  Wang,  E Zerah-Harush, J Hamill, B Wang, Y Dubi, BQ Xu, 2016 Single-molecule rectifier composed of DNA with high rectification ratio enabled by structure                                modification,          Nat. Chem., 8, 484-490  (pdf).

    o  K Wang, J Hamill, B Wang, CL Guo, S Jiang, Z Huang, BQ Xu, 2014 Structure determined charge transport in single DNA molecule break junctions,  Chem. Sci., 5 (9) 3425-3431              (pdf)

  • Single Molecular Biophysics and Mechanics (Bottom Panel): Probing and understanding the molecular basis of biomolecules and their interactions are critical to both fundamental scientific understanding and advances in identifying, and developing therapies that promote human health. We have been successfully using the single molecular chemo-mechanical techniques we developed to address the molecular basis involved in single molecular structure evolving and their interaction processes. In such research programs, we have been collaborating with UGA chemists, biologists, especially the researchers in the world well-known Complex Carbohydrate Research Center (CCRC), and scientists from other universities nationally and internationally.

3. Molecular basis of single molecular DNA-protein interactions: Interactions between proteins and nucleic acids are critical to many biochemical and biophysical processes in living cells, such as gene expression, DNA repair, and cell replication. For most of these interactions the nucleic acids show complex behaviors, such as flexible folding structures, which often cause the interaction to be multiple energy barriers, and multiple reaction pathways. The greatest challenge facing today is how to measure and understand these structure-determined single molecule interactions under physiological conditions. In this research we are quantitatively studying the molecular details of structure and functions of single DNA aptamer protein interactions by combining the SPM-based experimental and MD based theoretical expertise to elucidate the fundamental mechanisms.

Selected Publications:

  • B Wang, Z Lou, B Park, YK Kwon, HQ Zhang, BQ Xu, 2015 Surface conformations of anti-ricin aptamer and its affinity to ricin determined by atomic force microscopy and surface plasmon resonance, Phys. Chem. Chem.Phys., 17 (1) 307-314(pdf)
  • B Wang, B Park, YK Kwon, BQ Xu, 2014 Determining the Elastic Properties of Aptamer-Ricin Single Molecule Mutiple Pathway Intercations, Appl. Phys. Lett.  104, 193702/1-193702/4(pdf)
  • B Wang, BQ Xu, 2014 Transition Model for ricin-aptamer interactions with multiple pathways and energy barriers,  Phys. Rev. E. 89, 022720(1)-022720(10)(pdf)
  • B. Wang, Cl Guo, GJ Chen, B Park, BQ Xu, 2012 Following aptamer–ricin specific binding by single molecule recognition and force spectroscopy measurements, Chem. Commun., 48, 1644–1646(pdf)
  • GJ Chen, XH Ning, B Park, GJ Boons, BQ Xu. 2009. Simple, clickable protocol for AFM tip modification and its application for trace ricin detection by recognition imagingLangmuir, 25, 2860-2864(pdf)

4. Prion Proteins (PrP) assembly and nanomedicine:  PrP are related to neurodegenerative diseases, such as Alzhemer’s disease (AD), Parkinson’s disease (PD), and transmissible spongiform encephalopathies (TSEs, including Creutzfeldt-Jakob disease and mad-cow disease). In the living cell, all of these proteins exist and function at the single-molecule level.  Especially, the initial step of the aggregation of IDPs inside cells is critical for those diseases but many questions are still unknown. We are conducting a systematic study of how PrP assemble by in-situ, real-time imaging and the unbinding mechanisms of prion-aptamer complexes. The results will reveal whether the unbinding processes follow single pathway or multiple pathways. The energy landscapes of these unbinding pathways will be constructed. The stretching behaviors or the prion protein and aptamer during the unbinding process will be analyzed. We will develop specific models for the single-molecule behaviors of PrP and the anti-prion aptamers. This research will potentially provide a new avenue to develop drugs for neurodegenerative diseases.

Selected Publications:

  • Y Pan, B Wang, T Zhang,  Y Zhang, H Wang BQ Xu, 2016 Nonoscale Insights into Full-length Prion Protein Aggregation on Model Lipid Membranes, Chem. Commun,52, 8533-8536 (pdf)
  • B Wang, Z Lou, HQ Zhang, BQ Xu, 2016 Effect of the electrostatic surface  potentianl on the oligomerization of full-length human recombinant prion protein at single-molecule level  J. Chem. Phys.,144 114701 (pdf)
  • Z Lou,  B Wang, CL Guo, K Wang, HQ Zhang, BQ Xu, 2015 Molecualr-level Insight of Early-stage Prion Protein   Aggregation  on Mica and God Surface by AFM Imaging and Molecular Simulation  Colloids Surf., B 135 371-378(pdf)
  • B Wang, CL Guo, Z Lou,  BQ Xu, 2015 Following the Aggregation of Human Prion Protein on Au (111) Surface in Real-time, Chem. Commun., 51, 2088-2090(pdf)

5. Bio-catalytic process in biomass for biofuel: We have used our recently developed carbohydrate binding module (CBM) functionalized Atomic Force Microscopy (AFM) to perform measurements on a series of enzymatic hydrolysis (e.g. various reaction time, various pretreated biomass) to directly detect dynamics of lignocellulosic fine structure and its interactions with hydrolytic enzymes. Such detailed understanding and in-depth knowledge revealed the molecular mechanisms of biomass recalcitrance. In the upcoming study, we will (1) test and verify such understanding and knowledge through hydrolysis process optimization with improved conversion efficiency; (2) map out the structure of the plant cell wall surface, including the chemical components and their distributions; and (3) recognize and follow the developments of components (cellulose, extensin, AGP, pectin) during the cell wall growth of Arabidonsis Thaliana T87 Cell protoplast by AFM function imaging and interaction methods using antibody functionalized AFM tips.

Selected Publications:

  • Y Zhang, M Zhang, RA Reese, H Zhang, BQ Xu, 2016 Real-time single molecular study of a pretreated cellulose hydrolysis mode and individual enzyme movement,Biotechnol. Biofuels, 9, 85 (pdf)
  • MM Zhang, B Wang, BQ Xu, 2014 Mapping single molecular binding kinetics of carbohydrate-binding module with crystalline cellulose by atomic force microscopy recognition imaging,J. Phys. Chem. B.,  118 (24), 6714-1720(pdf)
  • MM Zhang, GJ Chen, G. Kumar, BQ Xu, 2013 Mapping out the structural changes of natural and pretreated plant cell wall surfaces by atomic force microscopy single molecular recognition  imaging, Biotechnol. Biofuels, 6, 147(pdf)
  • MM Zhang, B Wang, BQ Xu, 2013 Measurements of Single Molecular Affinity  Interacctions between Carbohydrate-Binding Module Crystalline Cellulose Fibrils, Phys. Chem. Chem.Phys., 15(17), 6508-6515(pdf)
  • MM Zhang, SC Wu, W Zhou, BQ Xu, 2012 Imaging and Measuring Single-Molecule Intercation between a Carbohydrate-Binding Module and Natural Plant Cell Wall Cellulose,   J. Phys. Chem. B., 116, 9949-9956(pdf)

6. Drug-cell interaction: Recent years, understanding the molecular basis of diseases plays an important role in the development of modern medicine. In order to deep characterize the distinct molecular features of disease state, new molecular tools are demanded. These advances in AFM have led rapidly to in situ investigations of drug-induced changes in cell structure, membrane stability, and receptor interaction forces. Although the near-molecular image resolution and single-molecule interaction force resolution of these approaches are impressive, it is important to note several current limitations of this contact-based approach for efficient discovery of new pharmaceutical solutions and understanding of existing mechanisms of drug action. These include restriction to two-dimensional, in vitro cell culture environments; low throughput relative to the timescale of many cell responses (e.g. translational diffusion of receptors along membranes) and to the variability among cells within a population; and the potential to induce confounding cell responses by mechanical perturbing of the cell surface and its receptors. We are to address these important current constraints through experimental and computational innovations and data processing and analysis to nanomechanically mapp the dynamics of drug-cell interactions. Our recent study of heparan sulfate-antithrombin interaction on single endothelial cell surface (Phys. Chem. Chem.Phys., 17 13301-13306) demonstrated the feasibility of the proposed study.  This research is key to scientific advances in understanding, identifying, and developing therapies that promote human health.

 Selected Publications:

  • CL Guo, X Fan,  H Qiu, W Xiao, L Wang, BQ Xu, 2015 High-resolution probing heparan sulfate-antithrombin interaction on single endothelial cell surface:  Single-molecule AFM studies, Phys. Chem. Chem.Phys., 17 13301-13306 (pdf)
  • Cl Guo, B Wang,LC Wang, BQ Xu, 2012 Structural Basis of Single Molecular Heparin-FX06 Interaction Revealed by SPM Measurements and Molecular Simulations, Chem. Commun., 48, 12222–12224(pdf)
  • Self-assembly of giant supermolecules: The field of supramolecular chemistry witnessed significant growth in the past few decades. Understanding of the genesis, attributes, and principles of mathematic geometry can provide a foundation for comprehending the structure design of supramolecular chemistry. Further, the connection between mathematic geometry and supramolecular chemistry appears to hold the key to an innovative and intriguing source from which to create a diverse array of structures to facilitate material applications. With the collaborative efforts, together with a group of scientists worldwide, we are characterizing the supermolecules using our single atomic/molecule imaging methods and exploring the applications of these assemblies in diverse fields, such as host−guest chemistry, molecular electronics, molecular recognition, reactivity modulation, catalysis, template-directed synthesis and biology.
Selected Publications:
  • M Wang, K Wang, C wang,  M Huang, X Hao, M Shen, G Shi, Z Zhang, B Song, A Cisneros, M Song, BQ Xu, X Li, 2016 Self-assembly of Concentric Hexagons and hierarchical Self-Assembly of Superamolecular Metal-Organic Nanoribbons (SMON) at solid/Liquid Interface,  J. Am. Chem. Soc.,  138 (29), 9258-9268 (pdf)
  • B Sun,  M Wang,  Z Lou, M Huang, C Xu, X Li, L Chen, Y Yu, GL Davis, BQ Xu, HB Yang, XP Li, 2015 From Ring-in-Ring to Sphere-in-Spahere: Self-Assembly of Discrit 2D and 3D Archtitectures with Increasing Stability,  J. Am. Chem. Soc., 137 (5) 1556-15640(pdf)
  • C Wang, X Hao, C. Guor, B Xu, E Tan, Y Zhang, Y Yu, Z Li, M. Song, X Li, 2014 Self-assembly of Giant Supramolecular Cubes with Terpyridine Ligands as Vertices and Metals on Edges,Chem. Sci. 5, 1221-1226(pdf)
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