Bingqian Xu - Profile on Academia.edu (original) (raw)

Papers by Bingqian Xu

arXiv (Cornell University), May 28, 2015

One of the ultimate goals of molecular electronics is to create technologies that will complement... more One of the ultimate goals of molecular electronics is to create technologies that will complementand eventually supersede -Si-based microelectronics technologies . To reach this goal, electronic properties that mimic at least some of the electrical behaviors of today's semiconductor components must be recognized and characterized. An outstanding example for one such behavior is negative differential conductance (NDC), in which an increase in the voltage across the device terminals results in a decrease in the electric current passing through the device. This overview focuses on the NDC phenomena observed in metal-single molecule-metal molecular junctions, and is roughly divided into two parts. In the first part, the central experiments which demonstrate NDC in single-molecule junctions are critically reviewed, with emphasis on the main observations and their possible physical origins. The second part is devoted to the t heory of NDC in single-molecule junctions, where simple models are employed to shed light on the different possible mechanisms leading to NDC.

Nano Letters, 2006

We have studied the current-induced local heating effects in single molecules covalently bound to... more We have studied the current-induced local heating effects in single molecules covalently bound to two electrodes by measuring the force required to break the molecule-electrode bonds under various conditions. The breakdown process is thermally activated, which is used to extract the effective temperature of the molecular junction as a function of applied bias voltage. We have also performed first-principles calculations of both local heating and current-induced force effects, and the results are in good agreement with the experimental findings.

Surface-enhanced Raman spectroscopic studies of the Au-pentacene interface: A combined experimental and theoretical investigation

The Journal of Chemical Physics, 2013

It has recently been shown [D. Adil and S. Guha, J. Phys. Chem. C 116, 12779 (2012)]10.1021/jp303... more It has recently been shown [D. Adil and S. Guha, J. Phys. Chem. C 116, 12779 (2012)]10.1021/jp3031804 that a large enhancement in the Raman intensity due to surface-enhanced Raman scattering (SERS) is observed from pentacene when probed through the Au contact in organic field-effect transistors (OFET) structures. Here, the SERS spectrum is shown to exhibit a high sensitivity to disorder introduced in the pentacene film by Au atoms. The Raman signature of the metal-semiconductor interface in pentacene OFETs is calculated with density-functional theory by explicitly considering the Au-pentacene interaction. The observed enhancement in the 1380 cm−1 and the 1560 cm−1 regions of the experimental Raman spectrum of pentacene is successfully modeled by Au-pentacene complexes, giving insights into the nature of disorder in the pentacene sp2 network. Finally, we extend our previous work on high-operating voltage pentacene OFETs to low-operating voltage pentacene OFETs. No changes in the SERS...

Biomicrofluidics, 2010

In this paper, thermal mixing characteristics of two miscible fluids in a T-shaped microchannel a... more In this paper, thermal mixing characteristics of two miscible fluids in a T-shaped microchannel are investigated theoretically, experimentally, and numerically. Thermal mixing processes in a T-shaped microchannel are divided into two zones, consisting of a T-junction and a mixing channel. An analytical two-dimensional model was first built to describe the heat transfer processes in the mixing channel. In the experiments, de-ionized water was employed as the working fluid. Laser induced fluorescence method was used to measure the fluid temperature field in the microchannel. Different combinations of flow rate ratios were studied to investigate the thermal mixing characteristics in the microchannel. At the T-junction, thermal diffusion is found to be dominant in this area due to the striation in the temperature contours. In the mixing channel, heat transfer processes are found to be controlled by thermal diffusion and convection. Measured temperature profiles at the T-junction and mix...

Physical Chemistry Chemical Physics, 2015

Heparan sulfate (HS) plays diverse functions in multiple biological processes by interacting with... more Heparan sulfate (HS) plays diverse functions in multiple biological processes by interacting with a wide range of important protein ligands, such as the key anticoagulant factor, antithrombin (AT). The specific interaction of HS with a protein ligand is determined mainly by the sulfation patterns on HS chain. Here, we reported the probing single-molecule interaction of AT and HS (both wild type and mutated) expressed on endothelial cell surface under near-physiological condition by atomic force microscopy (AFM). Functional AFM imaging revealed the uneven distribution of HS on endothelial cell surface though they are highly expressed. Force spectroscopy measurement with an AT-functionalized AFM tip revealed AT interacts with endothelial HS on the cell surface through multiple binding sites. The interaction essentially requires HS to be N-, 2-O-and/or 6-Osulfated. This work provides a new tool to probe the HS-protein ligand interaction at a singlemolecular level on cell surface to elucidate the functional roles of HS.

Plant Methods, Nov 3, 2020

Background: Recent interest in Populus as a source of renewable energy, combined with its numerou... more Background: Recent interest in Populus as a source of renewable energy, combined with its numerous available pretreatment methods, has enabled further research on structural modification and hydrolysis. To improve the biodegradation efficiency of biomass, a better understanding of the relationship between its macroscopic structures and enzymatic process is important. This study investigated mutant cell wall structures compared with wild type on a molecular level. Furthermore, a novel insight into the structural dynamics occurring on mutant biomass was assessed in situ and in real time by functional Atomic Force Microscopy (AFM) imaging. High-resolution AFM images confirmed that genetic pretreatment effectively inhibited the production of irregular lignin. The average roughness values of the wild type are 78, 60, and 30 nm which are much higher than that of the mutant cell wall, approximately 10 nm. It is shown that the action of endoglucanases would expose pure crystalline cellulose with more cracks for easier hydrolysis by cellobiohydrolase I (CBHI). Throughout the entire CBHI hydrolytic process, when the average roughness exceeded 3 nm, the hydrolysis mode consisted of a peeling action. Functional AFM imaging is helpful for biomass structural characterization. In addition, the visualization of the enzymatic hydrolysis process will be useful to explore the cell wall structure-activity relationships.

Processes, Aug 12, 2023

Biological interactions often involve the transport of molecules, ions, or other species across b... more Biological interactions often involve the transport of molecules, ions, or other species across biological membranes or between interacting proteins. The understanding of these transport phenomena is crucial for the development of therapies for various diseases. Atomic force microscopy is a powerful tool that has been increasingly used to study biological systems at the nano scale. The high resolution, quantitative measurements, and the ability to probe biological interactions under near-physiological conditions make AFM an attractive tool for investigating transport phenomena in biological systems. In this article, we focus on the use of AFM in the study of the transport phenomena in biological systems. We discuss the principles of AFM, its instrumentation, and its application in the study of biomolecules and biological systems. We also provide a comprehensive overview of recent articles that have utilized AFM in the study of biomarkers in biological systems.

The manipulation of electron transport through single-molecule junctions via light illumination i... more The manipulation of electron transport through single-molecule junctions via light illumination is a critical step towards molecular hybrid devices. However, most kinds of molecules are nonphotoresponsive without photo absorption upon a specific light illumination. Here, a strategy for high efficiently gating electron transport through a nonphotoresponsive molecular junction with a general light source is provided by introducing nanogap plasmons and molecular design. It is found the conductance of the triphenylamine-based molecules, a nonphotoresponsive molecule with buried anchoring groups, can be enhanced by two orders of magnitude under a general light illumination, which should be the greatest enhancement in the family of nonphotoresponsive molecules. It is further revealed that the giant conductance modulation originates from the coupling of the buried anchoring groups and plasmon-excited hot electrons. This work would contribute to the understanding of the interaction mechanis...

Plant Methods, 2020

Background Recent interest in Populus as a source of renewable energy, combined with its numerous... more Background Recent interest in Populus as a source of renewable energy, combined with its numerous available pretreatment methods, has enabled further research on structural modification and hydrolysis. To improve the biodegradation efficiency of biomass, a better understanding of the relationship between its macroscopic structures and enzymatic process is important. Results This study investigated mutant cell wall structures compared with wild type on a molecular level. Furthermore, a novel insight into the structural dynamics occurring on mutant biomass was assessed in situ and in real time by functional Atomic Force Microscopy (AFM) imaging. High-resolution AFM images confirmed that genetic pretreatment effectively inhibited the production of irregular lignin. The average roughness values of the wild type are 78, 60, and 30 nm which are much higher than that of the mutant cell wall, approximately 10 nm. It is shown that the action of endoglucanases would expose pure crystalline ce...

Nanoscale, 2019

PrP-lipid membrane interactions are critical to PrP structure conversion and neurotoxicity, but i... more PrP-lipid membrane interactions are critical to PrP structure conversion and neurotoxicity, but its molecular mechnism remains unclear. Two-dimensional histogram of force-distance curves and worm-like chain model revealed three binding regions...

Nanoscale Horizons, 2018

Single-molecule glucose transport was illuminated using both experimental and theoretical methods.

Nature communications, Nov 1, 2018

Coordination-driven self-assembly as a bottom-up approach has witnessed a rapid growth in buildin... more Coordination-driven self-assembly as a bottom-up approach has witnessed a rapid growth in building giant structures in the past few decades. Challenges still remain, however, within the construction of giant architectures in terms of high efficiency and complexity from simple building blocks. Inspired by the features of DNA and protein, which both have specific sequences, we herein design a series of linear building blocks with specific sequences through the coordination between terpyridine ligands and Ru(II). Different generations of polycyclic supramolecules (C1 to C5) with increasing complexity are obtained through the self-assembly with Cd(II), Fe(II) or Zn(II). The assembled structures are characterized via multi-dimensional mass spectrometry analysis as well as multi-dimensional and multinuclear NMR (H, COSY, NOESY) analysis. Moreover, the largest two cycles C4 and C5 hierarchically assemble into ordered nanoscale structures on a graphite based on their precisely-controlled sh...

Journal of nanobiotechnology, Jan 17, 2017

The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. ... more The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. The atomic force microscopy (AFM) has been used to study the molecular mechanism of the reactions for protein and aptamers. The surface plasmon resonance (SPR) have been used in fast detections of various pathogens such as bacteria. This study used both AFM and SPR to investigate the complex reactions between aptamers and outer membrane proteins (OMPs) on the surface of S. typhimurium. Two DNA aptamers were used for the label-free detections of S. typhimurium by AFM and SPR. The aptamers have specific binding affinities to the OMPs of S. typhimurium. At single-molecule level, the high resolution AFM topography and recognition images distinguished the OMPs on the bacteria surface, which is the first time the location of individual outer membrane protein have been determined on Salmonella surface. E. coli in the control experiments didn't generate recognition signals, which proved the ...

The Journal of chemical physics, Jan 21, 2016

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggre... more The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the confo...

Physical Chemistry Chemical Physics, 2015

Using an antithrombin functionalized AFM probe, the specific interactions between antithrombin an... more Using an antithrombin functionalized AFM probe, the specific interactions between antithrombin and heparan sulfate on endothelial cell surface were determined, revealing previously unexpected diverse binding sites as well as critical roles ofN-, 2-O- and 6-O-sulfation in the interactions.

Physical chemistry chemical physics : PCCP, Jan 7, 2015

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface co... more We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and...

Applied Physics Letters, 2014

We report on the elastic properties of ricin and anti-ricin aptamer interactions, which showed th... more We report on the elastic properties of ricin and anti-ricin aptamer interactions, which showed three stable binding conformations, each of which has its special elastic properties. These different unbinding pathways were investigated by the dynamic force spectroscopy. A series-spring model combining the worm-like-chain model and Hook's law was used to estimate the apparent spring constants of the aptamer and linker molecule polyethylene glycol. The aptamer in its three different unbinding pathways showed different apparent spring constants. The two reaction barriers in the unbinding pathways also influence the apparent spring constant of the aptamer. This special elastic behavior of aptamer was used to distinguish its three unbinding pathways under different loading rates. This method also offered a way to distinguish and discard the non-specific interactions in single molecule experiments.

Chemical communications (Cambridge, England), Jan 7, 2015

Aggregations of human prion protein (23-231) were monitored by atomic force microscopy in real-ti... more Aggregations of human prion protein (23-231) were monitored by atomic force microscopy in real-time under pH 4. Prion dimers and trimers were determined as the basic units by AFM images and simulated structures. Aggregates aligned with the herringbone structures of an Au(111) reconstructed surface via Au-S bonds as the first layer, while the second layer was formed by non-covalent interactions.

The journal of physical chemistry. B, Jan 19, 2014

We studied the binding kinetics of family 3 carbohydrate-binding module (CBM3a) molecules to crys... more We studied the binding kinetics of family 3 carbohydrate-binding module (CBM3a) molecules to crystalline cellulose fibrils extracted from the poplar cell wall by atomic force microscopy (AFM) recognition imaging. The free CBM3a molecules of different concentrations were added to the buffer solution to bind to the crystalline cellulose sample immobilized on the AFM substrate. During in-situ AFM imaging, the CBM molecules were observed to bind to cellulose efficiently and regularly, especially in the first 60-120 min. A 1:1 single-molecule binding model was used to study the kinetics of the CBM3a-cellulose interaction. The saturation time when the concentration of occupied binding sites is 99% of the maximum bound CBM3a concentration at the end of reaction, t(0.99), was determined by fitting different concentrations of CBM3a against reaction time using the high resolution AFM images and the single-molecule kinetics equations. Based on the experimental data and kinetics calculations, t...

arXiv (Cornell University), May 28, 2015

One of the ultimate goals of molecular electronics is to create technologies that will complement... more One of the ultimate goals of molecular electronics is to create technologies that will complementand eventually supersede -Si-based microelectronics technologies . To reach this goal, electronic properties that mimic at least some of the electrical behaviors of today's semiconductor components must be recognized and characterized. An outstanding example for one such behavior is negative differential conductance (NDC), in which an increase in the voltage across the device terminals results in a decrease in the electric current passing through the device. This overview focuses on the NDC phenomena observed in metal-single molecule-metal molecular junctions, and is roughly divided into two parts. In the first part, the central experiments which demonstrate NDC in single-molecule junctions are critically reviewed, with emphasis on the main observations and their possible physical origins. The second part is devoted to the t heory of NDC in single-molecule junctions, where simple models are employed to shed light on the different possible mechanisms leading to NDC.

Nano Letters, 2006

We have studied the current-induced local heating effects in single molecules covalently bound to... more We have studied the current-induced local heating effects in single molecules covalently bound to two electrodes by measuring the force required to break the molecule-electrode bonds under various conditions. The breakdown process is thermally activated, which is used to extract the effective temperature of the molecular junction as a function of applied bias voltage. We have also performed first-principles calculations of both local heating and current-induced force effects, and the results are in good agreement with the experimental findings.

Surface-enhanced Raman spectroscopic studies of the Au-pentacene interface: A combined experimental and theoretical investigation

The Journal of Chemical Physics, 2013

It has recently been shown [D. Adil and S. Guha, J. Phys. Chem. C 116, 12779 (2012)]10.1021/jp303... more It has recently been shown [D. Adil and S. Guha, J. Phys. Chem. C 116, 12779 (2012)]10.1021/jp3031804 that a large enhancement in the Raman intensity due to surface-enhanced Raman scattering (SERS) is observed from pentacene when probed through the Au contact in organic field-effect transistors (OFET) structures. Here, the SERS spectrum is shown to exhibit a high sensitivity to disorder introduced in the pentacene film by Au atoms. The Raman signature of the metal-semiconductor interface in pentacene OFETs is calculated with density-functional theory by explicitly considering the Au-pentacene interaction. The observed enhancement in the 1380 cm−1 and the 1560 cm−1 regions of the experimental Raman spectrum of pentacene is successfully modeled by Au-pentacene complexes, giving insights into the nature of disorder in the pentacene sp2 network. Finally, we extend our previous work on high-operating voltage pentacene OFETs to low-operating voltage pentacene OFETs. No changes in the SERS...

Biomicrofluidics, 2010

In this paper, thermal mixing characteristics of two miscible fluids in a T-shaped microchannel a... more In this paper, thermal mixing characteristics of two miscible fluids in a T-shaped microchannel are investigated theoretically, experimentally, and numerically. Thermal mixing processes in a T-shaped microchannel are divided into two zones, consisting of a T-junction and a mixing channel. An analytical two-dimensional model was first built to describe the heat transfer processes in the mixing channel. In the experiments, de-ionized water was employed as the working fluid. Laser induced fluorescence method was used to measure the fluid temperature field in the microchannel. Different combinations of flow rate ratios were studied to investigate the thermal mixing characteristics in the microchannel. At the T-junction, thermal diffusion is found to be dominant in this area due to the striation in the temperature contours. In the mixing channel, heat transfer processes are found to be controlled by thermal diffusion and convection. Measured temperature profiles at the T-junction and mix...

Physical Chemistry Chemical Physics, 2015

Heparan sulfate (HS) plays diverse functions in multiple biological processes by interacting with... more Heparan sulfate (HS) plays diverse functions in multiple biological processes by interacting with a wide range of important protein ligands, such as the key anticoagulant factor, antithrombin (AT). The specific interaction of HS with a protein ligand is determined mainly by the sulfation patterns on HS chain. Here, we reported the probing single-molecule interaction of AT and HS (both wild type and mutated) expressed on endothelial cell surface under near-physiological condition by atomic force microscopy (AFM). Functional AFM imaging revealed the uneven distribution of HS on endothelial cell surface though they are highly expressed. Force spectroscopy measurement with an AT-functionalized AFM tip revealed AT interacts with endothelial HS on the cell surface through multiple binding sites. The interaction essentially requires HS to be N-, 2-O-and/or 6-Osulfated. This work provides a new tool to probe the HS-protein ligand interaction at a singlemolecular level on cell surface to elucidate the functional roles of HS.

Plant Methods, Nov 3, 2020

Background: Recent interest in Populus as a source of renewable energy, combined with its numerou... more Background: Recent interest in Populus as a source of renewable energy, combined with its numerous available pretreatment methods, has enabled further research on structural modification and hydrolysis. To improve the biodegradation efficiency of biomass, a better understanding of the relationship between its macroscopic structures and enzymatic process is important. This study investigated mutant cell wall structures compared with wild type on a molecular level. Furthermore, a novel insight into the structural dynamics occurring on mutant biomass was assessed in situ and in real time by functional Atomic Force Microscopy (AFM) imaging. High-resolution AFM images confirmed that genetic pretreatment effectively inhibited the production of irregular lignin. The average roughness values of the wild type are 78, 60, and 30 nm which are much higher than that of the mutant cell wall, approximately 10 nm. It is shown that the action of endoglucanases would expose pure crystalline cellulose with more cracks for easier hydrolysis by cellobiohydrolase I (CBHI). Throughout the entire CBHI hydrolytic process, when the average roughness exceeded 3 nm, the hydrolysis mode consisted of a peeling action. Functional AFM imaging is helpful for biomass structural characterization. In addition, the visualization of the enzymatic hydrolysis process will be useful to explore the cell wall structure-activity relationships.

Processes, Aug 12, 2023

Biological interactions often involve the transport of molecules, ions, or other species across b... more Biological interactions often involve the transport of molecules, ions, or other species across biological membranes or between interacting proteins. The understanding of these transport phenomena is crucial for the development of therapies for various diseases. Atomic force microscopy is a powerful tool that has been increasingly used to study biological systems at the nano scale. The high resolution, quantitative measurements, and the ability to probe biological interactions under near-physiological conditions make AFM an attractive tool for investigating transport phenomena in biological systems. In this article, we focus on the use of AFM in the study of the transport phenomena in biological systems. We discuss the principles of AFM, its instrumentation, and its application in the study of biomolecules and biological systems. We also provide a comprehensive overview of recent articles that have utilized AFM in the study of biomarkers in biological systems.

The manipulation of electron transport through single-molecule junctions via light illumination i... more The manipulation of electron transport through single-molecule junctions via light illumination is a critical step towards molecular hybrid devices. However, most kinds of molecules are nonphotoresponsive without photo absorption upon a specific light illumination. Here, a strategy for high efficiently gating electron transport through a nonphotoresponsive molecular junction with a general light source is provided by introducing nanogap plasmons and molecular design. It is found the conductance of the triphenylamine-based molecules, a nonphotoresponsive molecule with buried anchoring groups, can be enhanced by two orders of magnitude under a general light illumination, which should be the greatest enhancement in the family of nonphotoresponsive molecules. It is further revealed that the giant conductance modulation originates from the coupling of the buried anchoring groups and plasmon-excited hot electrons. This work would contribute to the understanding of the interaction mechanis...

Plant Methods, 2020

Background Recent interest in Populus as a source of renewable energy, combined with its numerous... more Background Recent interest in Populus as a source of renewable energy, combined with its numerous available pretreatment methods, has enabled further research on structural modification and hydrolysis. To improve the biodegradation efficiency of biomass, a better understanding of the relationship between its macroscopic structures and enzymatic process is important. Results This study investigated mutant cell wall structures compared with wild type on a molecular level. Furthermore, a novel insight into the structural dynamics occurring on mutant biomass was assessed in situ and in real time by functional Atomic Force Microscopy (AFM) imaging. High-resolution AFM images confirmed that genetic pretreatment effectively inhibited the production of irregular lignin. The average roughness values of the wild type are 78, 60, and 30 nm which are much higher than that of the mutant cell wall, approximately 10 nm. It is shown that the action of endoglucanases would expose pure crystalline ce...

Nanoscale, 2019

PrP-lipid membrane interactions are critical to PrP structure conversion and neurotoxicity, but i... more PrP-lipid membrane interactions are critical to PrP structure conversion and neurotoxicity, but its molecular mechnism remains unclear. Two-dimensional histogram of force-distance curves and worm-like chain model revealed three binding regions...

Nanoscale Horizons, 2018

Single-molecule glucose transport was illuminated using both experimental and theoretical methods.

Nature communications, Nov 1, 2018

Coordination-driven self-assembly as a bottom-up approach has witnessed a rapid growth in buildin... more Coordination-driven self-assembly as a bottom-up approach has witnessed a rapid growth in building giant structures in the past few decades. Challenges still remain, however, within the construction of giant architectures in terms of high efficiency and complexity from simple building blocks. Inspired by the features of DNA and protein, which both have specific sequences, we herein design a series of linear building blocks with specific sequences through the coordination between terpyridine ligands and Ru(II). Different generations of polycyclic supramolecules (C1 to C5) with increasing complexity are obtained through the self-assembly with Cd(II), Fe(II) or Zn(II). The assembled structures are characterized via multi-dimensional mass spectrometry analysis as well as multi-dimensional and multinuclear NMR (H, COSY, NOESY) analysis. Moreover, the largest two cycles C4 and C5 hierarchically assemble into ordered nanoscale structures on a graphite based on their precisely-controlled sh...

Journal of nanobiotechnology, Jan 17, 2017

The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. ... more The emerging nanotechnologies have greatly facilitated the development of label-free biosensors. The atomic force microscopy (AFM) has been used to study the molecular mechanism of the reactions for protein and aptamers. The surface plasmon resonance (SPR) have been used in fast detections of various pathogens such as bacteria. This study used both AFM and SPR to investigate the complex reactions between aptamers and outer membrane proteins (OMPs) on the surface of S. typhimurium. Two DNA aptamers were used for the label-free detections of S. typhimurium by AFM and SPR. The aptamers have specific binding affinities to the OMPs of S. typhimurium. At single-molecule level, the high resolution AFM topography and recognition images distinguished the OMPs on the bacteria surface, which is the first time the location of individual outer membrane protein have been determined on Salmonella surface. E. coli in the control experiments didn't generate recognition signals, which proved the ...

The Journal of chemical physics, Jan 21, 2016

The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggre... more The electrostatic surface potential (ESP) of prion oligomers has critical influences on the aggregating processes of the prion molecules. The atomic force microscopy (AFM) and structural simulation were combined to investigate the molecular basis of the full-length human recombinant prion oligomerization on mica surfaces. The high resolution non-intrusive AFM images showed that the prion oligomers formed different patterns on mica surfaces at different buffer pH values. The basic binding units for the large oligomers were determined to be prion momoners (Ms), dimers (Ds), and trimers (Ts). The forming of the D and T units happened through the binding of hydrophobic β-sheets of the M units. In contrast, the α-helices of these M, D, and T units were the binding areas for the formation of large oligomers. At pH 4.5, the binding units M, D, and T showed clear polarized ESP distributions on the surface domains, while at pH 7.0, they showed more evenly distributed ESPs. Based on the confo...

Physical Chemistry Chemical Physics, 2015

Using an antithrombin functionalized AFM probe, the specific interactions between antithrombin an... more Using an antithrombin functionalized AFM probe, the specific interactions between antithrombin and heparan sulfate on endothelial cell surface were determined, revealing previously unexpected diverse binding sites as well as critical roles ofN-, 2-O- and 6-O-sulfation in the interactions.

Physical chemistry chemical physics : PCCP, Jan 7, 2015

We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface co... more We used atomic force microscopy (AFM) and surface plasmon resonance (SPR) to study the surface conformations of an anti-ricin aptamer and its specific binding affinity for ricin molecules. The effect of surface modification of the Au(111) substrate on the aptamer affinity was also estimated. The AFM topography images had a resolution high enough to distinguish different aptamer conformations. The specific binding site on the aptamer molecule was clearly located by the AFM recognition images. The aptamer on a Au(111) surface modified with carboxymethylated-dextran (CD) showed both similarities to and differences from the one without CD modification. The influence of CD modification was evaluated using AFM images of various aptamer conformations on the Au(111) surface. The affinity between ricin and the anti-ricin aptamer was estimated using the off-rate values measured using AFM and SPR. The SPR measurements of the ricin sample were conducted in the range from 83.3 pM to 8.33 nM, and...

Applied Physics Letters, 2014

We report on the elastic properties of ricin and anti-ricin aptamer interactions, which showed th... more We report on the elastic properties of ricin and anti-ricin aptamer interactions, which showed three stable binding conformations, each of which has its special elastic properties. These different unbinding pathways were investigated by the dynamic force spectroscopy. A series-spring model combining the worm-like-chain model and Hook's law was used to estimate the apparent spring constants of the aptamer and linker molecule polyethylene glycol. The aptamer in its three different unbinding pathways showed different apparent spring constants. The two reaction barriers in the unbinding pathways also influence the apparent spring constant of the aptamer. This special elastic behavior of aptamer was used to distinguish its three unbinding pathways under different loading rates. This method also offered a way to distinguish and discard the non-specific interactions in single molecule experiments.

Chemical communications (Cambridge, England), Jan 7, 2015

Aggregations of human prion protein (23-231) were monitored by atomic force microscopy in real-ti... more Aggregations of human prion protein (23-231) were monitored by atomic force microscopy in real-time under pH 4. Prion dimers and trimers were determined as the basic units by AFM images and simulated structures. Aggregates aligned with the herringbone structures of an Au(111) reconstructed surface via Au-S bonds as the first layer, while the second layer was formed by non-covalent interactions.

The journal of physical chemistry. B, Jan 19, 2014

We studied the binding kinetics of family 3 carbohydrate-binding module (CBM3a) molecules to crys... more We studied the binding kinetics of family 3 carbohydrate-binding module (CBM3a) molecules to crystalline cellulose fibrils extracted from the poplar cell wall by atomic force microscopy (AFM) recognition imaging. The free CBM3a molecules of different concentrations were added to the buffer solution to bind to the crystalline cellulose sample immobilized on the AFM substrate. During in-situ AFM imaging, the CBM molecules were observed to bind to cellulose efficiently and regularly, especially in the first 60-120 min. A 1:1 single-molecule binding model was used to study the kinetics of the CBM3a-cellulose interaction. The saturation time when the concentration of occupied binding sites is 99% of the maximum bound CBM3a concentration at the end of reaction, t(0.99), was determined by fitting different concentrations of CBM3a against reaction time using the high resolution AFM images and the single-molecule kinetics equations. Based on the experimental data and kinetics calculations, t...