publications

2020

1. Technical Note: Dosimetric feasibility of lattice radiotherapy for breast cancer using GammaPod

   B. Kopchick, H. Xu, Y. Niu, and 3 more authors

   2020

   Kopchick, Benjamin Xu, Huijun Niu, Ying Becker, Stewart Qiu, Xiangyun Yu, Cedric eng Med Phys. 2020 Sep;47(9):3928-3934. doi: 10.1002/mp.14379. Epub 2020 Jul 28.

   Abs DOI

   PURPOSE: Studies on Lattice radiotherapy (LRT) for breast cancer have been largely lacking. This study investigates the dosimetric feasibility of using Gamma Pod, a stereotactic radiotherapy apparatus originally designed for breast SBRT, to deliver LRT to large, bulky breast tumor as a noninvasive treatment option. METHODS: The GammaPod-based LRT was simulated using Geant4 Gate Monte Carlo software. The simulated GammaPod was equipped with 5 mm diameter non-coplanar circular beams that span 28 degrees latitudinally from 18 degrees to 43 degrees off the horizontal plane. Two degrees longitudinal intervals were used to simulate rotating sources. To simulate the treatments to different breast sizes, three water-equivalent hemisphere volumes with diameters of 10, 15, and 20 cm were analyzed. The lattice was planned by spacing focal points 2 cm apart in the transverse and sagittal planes and 2.5 cm in the coronal plane. This resulted in 22-172 shots for full breast treatment. The maximum dose for each individual shot was 20 Gy. The peak-to-valley dose differences and skin dose were analyzed. To verify the feasibility of delivering LRT, a test plan was created and delivered to a commercial diode array dose verification device using a clinical GammaPod system with 15 mm collimators. RESULTS: The dose profiles showed the average peak-to-valley dose percent differences of 94.10% in the 10 cm hemispherical volume, 88.95% in the 15 cm hemispherical volume, and 83.60% in the 20 cm hemispherical volume. Average skin dose was 1.27, 1.72, and 2.13 Gy for the 10, 15, and 20 cm irradiation volumes, respectively. The LRT plan delivered using a clinical GammaPod system with larger collimators verified the feasibility of LRT plan delivery. CONCLUSION: GammaPod-based lattice radiotherapy is a viable treatment option and its application can be extended to treating large bulky breast tumors.

2. Touch-Spun Nanofibers for Nerve Regeneration

   S. J. Lee, D. Asheghali, B. Blevins, and 9 more authors

   2020

   Lee, Se-Jun Asheghali, Darya Blevins, Brianna Timsina, Raju Esworthy, Timothy Zhou, Xuan Cui, Haitao Hann, Sung Yun Qiu, Xiangyun Tokarev, Alexander Minko, Sergiy Zhang, Lijie Grace eng ACS Appl Mater Interfaces. 2020 Jan 15;12(2):2067-2075. doi: 10.1021/acsami.9b18614. Epub 2020 Jan 3.

   Abs DOI

   In the current study, we examined the potential for neural stem cell (NSCs) proliferation on novel aligned touch-spun polycaprolactone (PCL) nanofibers. Electrospun PCL nanofibers with similar diameter and alignment were used as a control. Confocal microscopy images showed that NSCs grew and differentiated all over the scaffolds up to 8 days. Neurite quantification analysis revealed that the NSCs cultured on the touch-spun fibers with incorporated bovine serum albumin promoted the expression of neuron-specific class III beta-tubulin after 8 days. More importantly, NSCs grown on the aligned touch-spun PCL fibers exhibited a bipolar elongation along the direction of the fiber, while NSCs cultured on the aligned electrospun PCL fibers expressed a multipolar elongation. The structural characteristics of the PCL nanofibers analyzed by X-ray diffraction indicated that the degree of crystallinity and elastic modulus of the touch-spun fiber are significantly higher than those of electrospun fibers. These findings indicate that the aligned and stiff touch-spun nanofibrous scaffolds show considerable potential for nerve injury repair.

3. Additive Modulation of DNA-DNA Interactions by Interstitial Ions

   W. Meng, R. Timsina, A. Bull, and 2 more authors

   2020

   Meng, Wei Timsina, Raju Bull, Abby Andresen, Kurt Qiu, Xiangyun eng Research Support, U.S. Gov’t, Non-P.H.S. Biophys J. 2020 Jun 16;118(12):3019-3025. doi: 10.1016/j.bpj.2020.05.001. Epub 2020 May 16.

   Abs DOI

   Quantitative understanding of biomolecular electrostatics, particularly involving multivalent ions and highly charged surfaces, remains lacking. Ion-modulated interactions between nucleic acids provide a model system in which electrostatics plays a dominant role. Using ordered DNA arrays neutralized by spherical cobalt(3+) hexammine and Mg(2+) ions, we investigate how the interstitial ions modulate DNA-DNA interactions. Using methods of ion counting, osmotic stress, and x-ray diffraction, we systematically determine thermodynamic quantities, including ion chemical potentials, ion partition, DNA osmotic pressure and force, and DNA-DNA spacing. Analyses of the multidimensional data provide quantitative insights into their interdependencies. The key finding of this study is that DNA-DNA forces are observed to linearly depend on the partition of interstitial ions, suggesting the dominant role of ion-DNA coupling. Further implications are discussed in light of physical theories of electrostatic interactions and like-charge attraction.

4. Structure-guided DNA-DNA attraction mediated by divalent cations

   A. Srivastava, R. Timsina, S. Heo, and 3 more authors

   2020

   Srivastava, Amit Timsina, Raju Heo, Seung Dewage, Sajeewa W Kirmizialtin, Serdal Qiu, Xiangyun eng Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. England Nucleic Acids Res. 2020 Jul 27;48(13):7018-7026. doi: 10.1093/nar/gkaa499.

   Abs DOI

   Probing the role of surface structure in electrostatic interactions, we report the first observation of sequence-dependent dsDNA condensation by divalent alkaline earth metal cations. Disparate behaviors were found between two repeating sequences with 100% AT content, a poly(A)-poly(T) duplex (AA-TT) and a poly(AT)-poly(TA) duplex (AT-TA). While AT-TA exhibits non-distinguishable behaviors from random-sequence genomic DNA, AA-TT condenses in all alkaline earth metal ions. We characterized these interactions experimentally and investigated the underlying principles using computer simulations. Both experiments and simulations demonstrate that AA-TT condensation is driven by non-specific ion-DNA interactions. Detailed analyses reveal sequence-enhanced major groove binding (SEGB) of point-charged alkali ions as the major difference between AA-TT and AT-TA, which originates from the continuous and close stacking of nucleobase partial charges. These SEGB cations elicit attraction via spatial juxtaposition with the phosphate backbone of neighboring helices, resulting in an azimuthal angular shift between apposing helices. Our study thus presents a distinct mechanism in which, sequence-directed surface motifs act with cations non-specifically to enact sequence-dependent behaviors. This physical insight allows a renewed understanding of the role of repeating sequences in genome organization and regulation and offers a facile approach for DNA technology to control the assembly process of nanostructures.

2019

1. Development of 3D printable conductive hydrogel with crystallized PEDOT:PSS for neural tissue engineering

   D. N. Heo, S. J. Lee, R. Timsina, and 3 more authors

   2019

   Heo, Dong Nyoung Lee, Se-Jun Timsina, Raju Qiu, Xiangyun Castro, Nathan J Zhang, Lijie Grace eng Netherlands Mater Sci Eng C Mater Biol Appl. 2019 Jun;99:582-590. doi: 10.1016/j.msec.2019.02.008. Epub 2019 Feb 2.

   Abs DOI

   Bioelectronic devices enable efficient and effective communication between medical devices and human tissue in order to directly treat patients with various neurological disorders. Due to the mechanical similarity to human tissue, hydrogel-based electronic devices are considered to be promising for biological signal recording and stimulation of living tissues. Here, we report the first three-dimensionally (3D) printable conductive hydrogel that can be photocrosslinked while retaining high electrical conductivity. In addition, we prepared dorsal root ganglion (DRG) cell-encapsulated gelatin methacryloyl (GelMA) hydrogels which were integrated with the 3D printed conductive structure and evaluated for efficiency neural differentiation under electrical stimulation (ES). For enhanced electrical conductivity, a poly(3,4-ethylenedioxythiophene) (PEDOT): polystyrene sulfonate (PSS) aqueous solution was freeze-dried and mixed with polyethylene glycol diacrylate (PEGDA) as the photocurable polymer base. Next, the conductive hydrogel was patterned on the substrate by using a table-top stereolithography (SLA) 3D printer. The fabricated hydrogel was characterized for electrochemical conductivity. After printing with the PEDOT:PSS conductive solution, the patterned hydrogel exhibited decreased printing diameters with increasing of PEDOT:PSS concentration. Also, the resultant conductive hydrogel had significantly increased electrochemical properties with increasing PEDOT:PSS concentration. The 3D printed conductive hydrogel provides excellent structural support to systematically transfer the ES toward encapsulated DRG cells for enhanced neuronal differentiation. The results from this study indicate that the conductive hydrogel can be useful as a 3D printing material for electrical applications.

2017

1. Combined Monte Carlo/torsion-angle molecular dynamics for ensemble modeling of proteins, nucleic acids and carbohydrates

   W. Zhang, S. C. Howell, D. W. Wright, and 4 more authors

   2017

   Zhang, Weihong Howell, Steven C Wright, David W Heindel, Andrew Qiu, Xiangyun Chen, Jianhan Curtis, Joseph E eng Research Support, U.S. Gov’t, Non-P.H.S. Research Support, Non-U.S. Gov’t J Mol Graph Model. 2017 May;73:179-190. doi: 10.1016/j.jmgm.2017.02.010. Epub 2017 Feb 23.

   Abs DOI

   We describe a general method to use Monte Carlo simulation followed by torsion-angle molecular dynamics simulations to create ensembles of structures to model a wide variety of soft-matter biological systems. Our particular emphasis is focused on modeling low-resolution small-angle scattering and reflectivity structural data. We provide examples of this method applied to HIV-1 Gag protein and derived fragment proteins, TraI protein, linear B-DNA, a nucleosome core particle, and a glycosylated monoclonal antibody. This procedure will enable a large community of researchers to model low-resolution experimental data with greater accuracy by using robust physics based simulation and sampling methods which are a significant improvement over traditional methods used to interpret such data.

2016

1. Monte Carlo simulation algorithm for B-DNA

   S. C. Howell, X. Qiu, and J. E. Curtis

   2016

   Howell, Steven C Qiu, Xiangyun Curtis, Joseph E eng Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. J Comput Chem. 2016 Nov 5;37(29):2553-63. doi: 10.1002/jcc.24474.

   Abs DOI

   Understanding the structure-function relationship of biomolecules containing DNA has motivated experiments aimed at determining molecular structure using methods such as small-angle X-ray and neutron scattering (SAXS and SANS). SAXS and SANS are useful for determining macromolecular shape in solution, a process which benefits by using atomistic models that reproduce the scattering data. The variety of algorithms available for creating and modifying model DNA structures lack the ability to rapidly modify all-atom models to generate structure ensembles. This article describes a Monte Carlo algorithm for simulating DNA, not with the goal of predicting an equilibrium structure, but rather to generate an ensemble of plausible structures which can be filtered using experimental results to identify a sub-ensemble of conformations that reproduce the solution scattering of DNA macromolecules. The algorithm generates an ensemble of atomic structures through an iterative cycle in which B-DNA is represented using a wormlike bead-rod model, new configurations are generated by sampling bend and twist moves, then atomic detail is recovered by back mapping from the final coarse-grained configuration. Using this algorithm on commodity computing hardware, one can rapidly generate an ensemble of atomic level models, each model representing a physically realistic configuration that could be further studied using molecular dynamics. (c) 2016 Wiley Periodicals, Inc.

2. Attractive Interactions between DNA–Carbon Nanotube Hybrids in Monovalent Salts

   Xiangyun Qiu, Fuyou Ke, Raju Timsina, and 2 more authors

   2016

   Dq8jk Times Cited:11 Cited References Count:33

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   DNA carbon nanotube (DNA-CNT) hybrids are nanometer-sized, highly charged, rodlike molecules with complex surface chemistry, and their behaviors in aqueous solutions are governed by multifactorial interactions with both solvent and cosolutes. We have previously measured the force between DNA-CNTs as a function of their interaxial distance in low monovalent salts where interhybrid electrostatic repulsion dominates. The characteristics of DNA-CNT forces were further shown to closely resemble that of double-stranded DNA (dsDNA) in low salts. However, contrasting behaviors emerge at elevated monovalent salts: DNA-CNT condenses spontaneously, whereas dsDNA remains soluble. Here we report force distance dependencies of DNA-CNTs across wide-ranging monovalent salt concentrations. DNA-CNT force curves are observed to deviate from dsDNA curves above 300 mmol/L NaCl, and the deviation grows with increasing salts. Most notably, DNA-CNT forces become net attractive above 1 mol/L NaCl, whereas dsDNA forces are repulsive at all salt concentrations. We further discuss possible physical origins for the observed DNA-CNT attraction in monovalent salts, in consideration of the complex surface chemistry and unique polyelectrolyte properties of DNA-CNT hybrids.

2015

1. Nanoscale Structure and Interaction of Condensed Phases of DNA–Carbon Nanotube Hybrids

   Fuyou Ke and Xiangyun Qiu

   2015

   Cm8pu Times Cited:0 Cited References Count:39

   Abs DOI

   Condensation of DNA carbon nanotube (CNT) hybrids dispersed in aqueous solutions can be induced by elevated hybrid concentrations, salts, or crowding agents. DNA CNT condensates exhibit either nematic ordering or amorphous aggregates, dependent on the nature of interhybrid interactions. This study employed X-ray diffraction (XRD) to determine nanoscale structures of the condensates, including the presence of positional ordering, interaxial distances, and the range of ordered domains. To probe the effects of DNA sequence, two types of CNT hybrids, dispersed by genomic DNA of random sequence and synthetic oligonucleotides respectively, were studied under identical conditions. The osmotic stress method was further used to quantify force distance dependencies of the DNA-CNT hybrids to elucidate the relation between interhybrid interactions and condensate structures. We observed that, independent of DNA sequence, lyotropic DNA-CNT phases showed weak positional ordering with long interhybrid distances, salt-induced condensates were amorphous, crowding-condensed DNA-CNTs were the most ordered with pronounced XRD peaks, and interhybrid interactions were defined by short-range hydration repulsion and long-range electrostatic repulsion. Conversely, the effects of DNA sequence became evident as to their quantitative force-distance relationships. Genomic DNA of random sequence consistently gave longer interhybrid distances than synthetic oligonucleotides, which we attribute to the likely differences in their hybrid diameters.

2. Ionic switch controls the DNA state in phage lambda

   D. Li, T. Liu, X. Zuo, and 3 more authors

   2015

   Li, Dong Liu, Ting Zuo, Xiaobing Li, Tao Qiu, Xiangyun Evilevitch, Alex eng Research Support, U.S. Gov’t, Non-P.H.S. England Nucleic Acids Res. 2015 Jul 27;43(13):6348-58. doi: 10.1093/nar/gkv611. Epub 2015 Jun 19.

   Abs DOI

   We have recently found that DNA packaged in phage lambda undergoes a disordering transition triggered by temperature, which results in increased genome mobility. This solid-to-fluid like DNA transition markedly increases the number of infectious lambda particles facilitating infection. However, the structural transition strongly depends on temperature and ionic conditions in the surrounding medium. Using titration microcalorimetry combined with solution X-ray scattering, we mapped both energetic and structural changes associated with transition of the encapsidated lambda-DNA. Packaged DNA needs to reach a critical stress level in order for transition to occur. We varied the stress on DNA in the capsid by changing the temperature, packaged DNA length and ionic conditions. We found striking evidence that the intracapsid DNA transition is ’switched on’ at the ionic conditions mimicking those in vivo and also at the physiologic temperature of infection at 37 degrees C. This ion regulated on-off switch of packaged DNA mobility in turn affects viral replication. These results suggest a remarkable adaptation of phage lambda to the environment of its host bacteria in the human gut. The metastable DNA state in the capsid provides a new paradigm for the physical evolution of viruses.

3. DNA under Force: Mechanics, Electrostatics, and Hydration

   J. Li, S. S. Wijeratne, X. Qiu, and 1 more author

   2015

   Li, Jingqiang Wijeratne, Sithara S Qiu, Xiangyun Kiang, Ching-Hwa eng Review Switzerland Nanomaterials (Basel). 2015 Feb 25;5(1):246-267. doi: 10.3390/nano5010246.

   Abs DOI

   Quantifying the basic intra- and inter-molecular forces of DNA has helped us to better understand and further predict the behavior of DNA. Single molecule technique elucidates the mechanics of DNA under applied external forces, sometimes under extreme forces. On the other hand, ensemble studies of DNA molecular force allow us to extend our understanding of DNA molecules under other forces such as electrostatic and hydration forces. Using a variety of techniques, we can have a comprehensive understanding of DNA molecular forces, which is crucial in unraveling the complex DNA functions in living cells as well as in designing a system that utilizes the unique properties of DNA in nanotechnology.

4. Structure and Interaction of Graphene Oxide– Cetyltrimethylammonium Bromide Complexation

   Wei Meng, Elizabeth Gall, Fuyou Ke, and 4 more authors

   2015

   Cr3td Times Cited:41 Cited References Count:36

   Abs DOI

   Complexation of graphene oxide (GO) and cetyltrimethylammonium bromide (CTAB), a model amphiphile, was quantitatively studied to elucidate the governing forces and resulting structures of their self-assembly. We systematically varied pertinent self-assembly parameters, including GO size, mixing ratio, salt, and osmotic stress, and quantified the nanoscale structures of GO:CTAB using X-ray diffraction. Multi lamellar stacking of GO and CTAB layers persists in all GO:CTAB assemblies exhibiting structural order. While driven by hydrophobic interactions between the hydrocarbon tails, the CTAB layer displays a series of structural transitions from a Mayer with in-plane ordering to a more fluidic bilayer and to an interdigitated monolayer. Interaction between GO and CTAB layers shows domination by electrostatics, and osmotic stress studies indicate the absence of continuous hydration layers in GO:CTAB assemblies. Adding salt increases the interlayer spacing by intercalating between GO and CTAB layers, and this ion layer can be expelled by high osmotic stress. These studies provide quantitative knowledge of the structure and interaction of GO:CTAB complexation, which lays foundation for precise control and rational design of their nanoscale self-assemblies.

2014

1. Capsules with a hierarchical shell structure assembled by aminoglycosides and DNA via the kinetic path

   J. Zhou, H. Wen, F. Ke, and 6 more authors

   2014

   Zhou, Jihan Wen, Hao Ke, Fuyou Shi, Dong Brisky, April A Wang, Nan Zhu, Lin Qiu, Xiangyun Liang, Dehai eng Research Support, Non-U.S. Gov’t England Chem Commun (Camb). 2014 Aug 28;50(67):9525-8. doi: 10.1039/c4cc03508a.

   Abs DOI

   Aminoglycosides are capable of expelling water molecules when forming a complex with DNA via electrostatic interaction. The "water-proof" nature of the complex leads to the formation of capsules, which possess hierarchical shell structures with a smooth and rigid outer layer and a viscoelastic inner layer.

2013

1. Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal

   K. Andresen, I. Jimenez-Useche, S. C. Howell, and 2 more authors

   2013

   Andresen, Kurt Jimenez-Useche, Isabel Howell, Steven C Yuan, Chongli Qiu, Xiangyun eng Research Support, Non-U.S. Gov’t PLoS One. 2013 Nov 12;8(11):e78587. doi: 10.1371/journal.pone.0078587. eCollection 2013.

   Abs DOI

   Using a combination of small-angle X-ray scattering (SAXS) and fluorescence resonance energy transfer (FRET) measurements we have determined the role of the H3 and H4 histone tails, independently, in stabilizing the nucleosome DNA terminal ends from unwrapping from the nucleosome core. We have performed solution scattering experiments on recombinant wild-type, H3 and H4 tail-removed mutants and fit all scattering data with predictions from PDB models and compared these experiments to complementary DNA-end FRET experiments. Based on these combined SAXS and FRET studies, we find that while all nucleosomes exhibited DNA unwrapping, the extent of this unwrapping is increased for nucleosomes with the H3 tails removed but, surprisingly, decreased in nucleosomes with the H4 tails removed. Studies of salt concentration effects show a minimum amount of DNA unwrapping for all complexes around 50-100mM of monovalent ions. These data exhibit opposite roles for the positively-charged nucleosome tails, with the ability to decrease access (in the case of the H3 histone) or increase access (in the case of the H4 histone) to the DNA surrounding the nucleosome. In the range of salt concentrations studied (0-200mM KCl), the data point to the H4 tail-removed mutant at physiological (50-100mM) monovalent salt concentration as the mononucleosome with the least amount of DNA unwrapping.

2. Ion competition in condensed DNA arrays in the attractive regime

   X. Qiu, J. Giannini, S. C. Howell, and 3 more authors

   2013

   Qiu, Xiangyun Giannini, John Howell, Steven C Xia, Qi Ke, Fuyou Andresen, Kurt eng Research Support, Non-U.S. Gov’t Biophys J. 2013 Aug 20;105(4):984-92. doi: 10.1016/j.bpj.2013.07.004.

   Abs DOI

   Physical origin of DNA condensation by multivalent cations remains unsettled. Here, we report quantitative studies of how one DNA-condensing ion (Cobalt(3+) Hexammine, or Co(3+)Hex) and one nonDNA-condensing ion (Mg(2+)) compete within the interstitial space in spontaneously condensed DNA arrays. As the ion concentrations in the bath solution are systematically varied, the ion contents and DNA-DNA spacings of the DNA arrays are determined by atomic emission spectroscopy and x-ray diffraction, respectively. To gain quantitative insights, we first compare the experimentally determined ion contents with predictions from exact numerical calculations based on nonlinear Poisson-Boltzmann equations. Such calculations are shown to significantly underestimate the number of Co(3+)Hex ions, consistent with the deficiencies of nonlinear Poisson-Boltzmann approaches in describing multivalent cations. Upon increasing the concentration of Mg(2+), the Co(3+)Hex-condensed DNA array expands and eventually redissolves as a result of ion competition weakening DNA-DNA attraction. Although the DNA-DNA spacing depends on both Mg(2+) and Co(3+)Hex concentrations in the bath solution, it is observed that the spacing is largely determined by a single parameter of the DNA array, the fraction of DNA charges neutralized by Co(3+)Hex. It is also observed that only approximately 20% DNA charge neutralization by Co(3+)Hex is necessary for spontaneous DNA condensation. We then show that the bath ion conditions can be reduced to one variable with a simplistic ion binding model, which is able to describe the variations of both ion contents and DNA-DNA spacings reasonably well. Finally, we discuss the implications on the nature of interstitial ions and cation-mediated DNA-DNA interactions.

2009

1. Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA

   S. A. Pabit, X. Qiu, J. S. Lamb, and 3 more authors

   2009

   Pabit, Suzette A Qiu, Xiangyun Lamb, Jessica S Li, Li Meisburger, Steve P Pollack, Lois eng P01-GM066275/GM/NIGMS NIH HHS/ T32-GM008267/GM/NIGMS NIH HHS/ Comparative Study Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S. England Nucleic Acids Res. 2009 Jul;37(12):3887-96. doi: 10.1093/nar/gkp257. Epub 2009 Apr 24.

   Abs DOI

   The recent discovery of the RNA interference mechanism emphasizes the biological importance of short, isolated, double-stranded (ds) RNA helices and calls for a complete understanding of the biophysical properties of dsRNA. However, most previous studies of the electrostatics of nucleic acid duplexes have focused on DNA. Here, we present a comparative investigation of electrostatic effects in RNA and DNA. Using resonant (anomalous) and non-resonant small-angle X-ray scattering, we characterized the charge screening efficiency and counterion distribution around short (25 bp) dsDNA and RNA molecules of comparable sequence. Consistent with theoretical predictions, we find counterion mediated screening to be more efficient for dsRNA than dsDNA. Furthermore, the topology of the RNA A-form helix alters the spatial distribution of counterions relative to B-form DNA. The experimental results reported here agree well with ion-size-corrected non-linear Poisson-Boltzmann calculations. We propose that differences in electrostatic properties aid in selective recognition of different types of short nucleic acid helices by target binding partners.

2007

1. Inter-DNA attraction mediated by divalent counterions

   X. Qiu, K. Andresen, L. W. Kwok, and 3 more authors

   2007

   Qiu, Xiangyun Andresen, Kurt Kwok, Lisa W Lamb, Jessica S Park, Hye Yoon Pollack, Lois eng Research Support, N.I.H., Extramural Research Support, U.S. Gov’t, Non-P.H.S. 2007/08/07 Phys Rev Lett. 2007 Jul 20;99(3):038104. doi: 10.1103/PhysRevLett.99.038104. Epub 2007 Jul 20.

   Abs DOI

   Can nonspecifically bound divalent counterions induce attraction between DNA strands? Here, we present experimental evidence demonstrating attraction between short DNA strands mediated by Mg2+ ions. Solution small angle x-ray scattering data collected as a function of DNA concentration enable model independent extraction of the second virial coefficient. As the [Mg2+] increases, this coefficient turns from positive to negative reflecting the transition from repulsive to attractive inter-DNA interaction. This surprising observation is corroborated by independent light scattering experiments. The dependence of the observed attraction on experimental parameters including DNA length provides valuable clues to its origin.

2006

1. Achieving uniform mixing in a microfluidic device: hydrodynamic focusing prior to mixing

   H. Y. Park, X. Qiu, E. Rhoades, and 5 more authors

   2006

   Park, Hye Yoon Qiu, Xiangyun Rhoades, Elizabeth Korlach, Jonas Kwok, Lisa W Zipfel, Warren R Webb, Watt W Pollack, Lois eng 9 P41 EB001976/EB/NIBIB NIH HHS/ P01-GM066275/GM/NIGMS NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. 2006/07/01 Anal Chem. 2006 Jul 1;78(13):4465-73. doi: 10.1021/ac060572n.

   Abs DOI

   We describe a microfluidic mixer that is well-suited for kinetic studies of macromolecular conformational change under a broad range of experimental conditions. The mixer exploits hydrodynamic focusing to create a thin jet containing the macromolecules of interest. Kinetic reactions are triggered by molecular diffusion into the jet from adjacent flow layers. The ultimate time resolution of these devices can be restricted by premature contact between co-flowing solutions during the focusing process. Here, we describe the design and characterization of a mixer in which hydrodynamic focusing is decoupled from the diffusion of reactants, so that the focusing region is free from undesirable contact between the reactants. Uniform mixing on the microsecond time scale is demonstrated using a device fabricated by imprinting optical-grade plastic. Device characterization is carried out using fluorescence correlation spectroscopy (FCS) and two-photon microscopy to measure flow speeds and to quantify diffusive mixing by monitoring the collisional fluorescence quenching, respectively. Criteria for achieving microsecond time resolution are described and modeled.

2. Measuring inter-DNA potentials in solution

   X. Qiu, L. W. Kwok, H. Y. Park, and 3 more authors

   2006

   Qiu, Xiangyun Kwok, Lisa W Park, Hye Yoon Lamb, Jessica S Andresen, Kurt Pollack, Lois eng P01-GM066275/GM/NIGMS NIH HHS/ Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov’t Research Support, U.S. Gov’t, Non-P.H.S. 2006/05/23 Phys Rev Lett. 2006 Apr 7;96(13):138101. doi: 10.1103/PhysRevLett.96.138101. Epub 2006 Apr 3.

   Abs DOI

   Interactions between short strands of DNA can be tuned from repulsive to attractive by varying solution conditions and have been quantified using small angle x-ray scattering techniques. The effective DNA interaction charge was extracted by fitting the scattering profiles with the generalized one-component method and inter-DNA Yukawa pair potentials. A significant charge is measured at low to moderate monovalent counterion concentrations, resulting in strong inter-DNA repulsion. The charge and repulsion diminish rapidly upon the addition of divalent counterions. An intriguing short range attraction is observed at surprisingly low divalent cation concentrations, approximately 16 mM Mg2+. Quantitative measurements of inter-DNA potentials are essential for improving models of fundamental interactions in biological systems.

2005

1. Orbital correlations in the pseudocubic O and rhombohedral R phases of LaMnO3

   X. Qiu, T. Proffen, J. F. Mitchell, and 1 more author

   2005

   Qiu, Xiangyun Proffen, Th Mitchell, J F Billinge, S J L eng Phys Rev Lett. 2005 May 6;94(17):177203. doi: 10.1103/PhysRevLett.94.177203. Epub 2005 May 5.

   Abs DOI

   The local and intermediate structure of stoichiometric LaMnO3 has been studied in the pseudocubic and rhombohedral phases at high temperatures (300-1150 K). Neutron powder diffraction data were collected and a combined Rietveld and high real space resolution atomic pair distribution function analysis was carried out. The nature of the Jahn-Teller (JT) transition around 750 K is confirmed to be orbital order to disorder. In the high-temperature orthorhombic (O) and rhombohedral (R) phases, the MnO6 octahedra are still fully distorted locally. More importantly, the intermediate structure suggests the presence of local ordered clusters of diameter approximately 16 A ( approximately 4 MnO6 octahedra) implying strong nearest-neighbor JT antiferrodistortive coupling. These clusters persist well above the JT transition temperature even into the high-temperature R phase.

2004

1. Probing local and long-range structure simultaneously: an in situ study of the high-temperature phase transition of alpha-AlF3

   P. J. Chupas, S. Chaudhuri, J. C. Hanson, and 5 more authors

   2004

   Chupas, Peter J Chaudhuri, Santanu Hanson, Jonathan C Qiu, Xiangyun Lee, Peter L Shastri, Sarvjit D Billinge, Simon J L Grey, Clare P eng J Am Chem Soc. 2004 Apr 21;126(15):4756-7. doi: 10.1021/ja031553n.

   Abs DOI

   We show in this Communication that the combination of Rietveld and pair distribution function (PDF) analyses allows unique insight into the nature and driving force of the phase transition of alpha-AlF3, which was not available from conventional structural analysis methods alone. The use of image plate technology allows structural changes to be followed in "real time" and reduces the time required to collect high-resolution PDF data from hours (with a conventional solid state detector) to seconds. This methodology produces raw data that can simultaneously be analyzed by both Rietveld and PDF analysis.

2. Planar nets of Ti atoms comprising squares and rhombs in the new binary antimonide Ti2Sb

   S. Derakhshan, A. Assoud, K. M. Kleinke, and 4 more authors

   2004

   Derakhshan, Shahab Assoud, Abdeljalil Kleinke, Katja M Dashjav, Enkhtsetseg Qiu, Xiangyun Billinge, Simon J L Kleinke, Holger eng J Am Chem Soc. 2004 Jul 7;126(26):8295-302. doi: 10.1021/ja048262e.

   Abs DOI

   The new binary antimonide Ti(2)Sb was found to crystallize in a distorted variant of the La(2)Sb type, which contains a square planar La net with short La-La bonds. In the Ti(2)Sb structure, the corresponding Ti net is deformed to squares and rhombs in order to enhance Ti-Ti bonding, as proven by single-crystal X-ray investigation in combination with the real-space pair distribution function technique utilizing both X-ray and neutron powder diffraction data. Electronic structure calculations revealed a lowering of the total energy caused by the disorder, the major driving force being strengthened Ti-Ti interactions along the diagonal of the Ti(4) rhombs.