publications

2025

2025

1. Robust RNA secondary structure prediction with a mixture of deep learning and physics-based experts

   X Qiu

   Biology Methods and Protocols 10 (1), bpae097, 2025

2023

2023

1. Sequence similarity governs generalizability of de novo deep learning models for RNA secondary structure prediction

   X Qiu

   PLOS Computational Biology 19 (4), e1011047, 2023
2. Sequence-Dependent Orientational Coupling and Electrostatic Attraction in Cation-Mediated DNA-DNA Interactions

   W He, X Qiu, and S Kirmizialtin

   Journal of chemical theory and computation 19 (19), 6827-6838, 2023

2020

2020

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

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

   Nucleic acids research 48 (13), 7018-7026, 2020
2. Dosimetric Feasibility of Lattice Radiotherapy for Breast Cancer Using GammaPod

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

   Medical physics, 2020
3. Additive Modulation of DNA-DNA Interactions by Interstitial Ions

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

   Biophysical Journal 118 (12), 3019-3025, 2020

2019

2019

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

   DN Heo, SJ Lee, R Timsina, and 3 more authors

   Materials Science and Engineering: C 99, 582-590, 2019
2. Touch-Spun Nanofibers for Nerve Regeneration

   SJ Lee, D Asheghali, B Blevins, and 5 more authors

   ACS Applied Materials & Interfaces 12 (2), 2067-2075, 2019

2017

2017

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

   W Zhang, SC Howell, DW Wright, and 4 more authors

   Journal of Molecular Graphics and Modelling 73, 179-190, 2017

2016

2016

1. Attractive Interactions between DNA-Carbon Nanotube Hybrids in Monovalent Salts

   X Qiu, F Ke, R Timsina, and 2 more authors

   The Journal of Physical Chemistry C 120 (25), 13831-13835, 2016
2. Monte Carlo simulation algorithm for B-DNA

   SC Howell, X Qiu, and JE Curtis

   Journal of Computational Chemistry 37 (29), 2553-2563, 2016

2015

2015

1. Structure and Interaction of Graphene Oxide-Cetyltrimethylammonium Bromide Complexation

   W Meng, E Gall, F Ke, and 4 more authors

   The Journal of Physical Chemistry C 119 (36), 21135-21140, 2015
2. DNA under Force: Mechanics, Electrostatics, and Hydration

   J Li, SS Wijeratne, X Qiu, and 1 more author

   Nanomaterials 5 (1), 246-267, 2015
3. Ionic switch controls the DNA state in phage lambda

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

   Nucleic acids research 43 (13), 6348-6358, 2015
4. Nanoscale structure and interaction of condensed phases of DNA-carbon nanotube hybrids

   F Ke and X Qiu

   The Journal of Physical Chemistry C 119 (27), 15763-15769, 2015

2014

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

   Chemical Communications 50 (67), 9525-9528, 2014

2013

2013

1. DNA methylation regulated nucleosome dynamics

   I Jimenez-Useche, J Ke, Y Tian, and 4 more authors

   Scientific reports 3 (1), 2121, 2013
2. Solution scattering and FRET studies on nucleosomes reveal DNA unwrapping effects of H3 and H4 tail removal

   K Andresen, I Jimenez-Useche, SC Howell, and 2 more authors

   PLoS One 8 (11), e78587, 2013
3. Electrostatically driven interactions between hybrid DNA-carbon nanotubes

   X Qiu, CY Khripin, F Ke, and 2 more authors

   Physical review letters 111 (4), 048301, 2013
4. Elucidating internucleosome interactions and the roles of histone tails

   SC Howell, K Andresen, I Jimenez-Useche, and 2 more authors

   Biophysical journal 105 (1), 194-199, 2013
5. Ion competition in condensed DNA arrays in the attractive regime

   X Qiu, J Giannini, SC Howell, and 3 more authors

   Biophysical journal 105 (4), 984-992, 2013

2012

2012

1. Heat induced capsid disassembly and DNA release of bacteriophage lambda

   X Qiu

   PLoS One 7 (7), e39793, 2012

2011

2011

1. Salt-Dependent DNA-DNA Spacings in Intact Bacteriophage Reflect Relative Importance of DNA Self-Repulsion and Bending Energies

   X Qiu, DC Rau, VA Parsegian, and 3 more authors

   Physical review letters 106 (2), 028102, 2011

2010

2010

1. Divalent counterion-induced condensation of triple-strand DNA

   X Qiu, VA Parsegian, and DC Rau

   Proceedings of the National Academy of Sciences 107 (50), 21482-21486, 2010

2009

2009

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

   SA Pabit, X Qiu, JS Lamb, and 3 more authors

   Nucleic acids research 37 (12), 3887-3896, 2009
2. Structural and genetic analysis of X-ray scattering by spores of Bacillus subtilis

   X Qiu and P Setlow

   Journal of bacteriology 191 (24), 7620-7622, 2009

2008

2008

1. Mono-and trivalent ions around DNA: a small-angle scattering study of competition and interactions

   K Andresen, X Qiu, SA Pabit, and 4 more authors

   Biophysical journal 95 (1), 287-295, 2008
2. Abrupt transition from a free, repulsive to a condensed, attractive DNA phase, induced by multivalent polyamine cations

   X Qiu, K Andresen, JS Lamb, and 2 more authors

   Physical review letters 101 (22), 228101, 2008
3. Reconstructing three-dimensional shape envelopes from time-resolved small-angle X-ray scattering data

   J Lamb, L Kwok, X Qiu, and 3 more authors

   Journal of applied crystallography 41 (6), 1046-1052, 2008

2007

2007

1. Inter-DNA attraction mediated by divalent counterions

   X Qiu, K Andresen, LW Kwok, and 3 more authors

   Physical review letters 99 (3), 038104, 2007
2. Focusing capillary optics for use in solution small-angle X-ray scattering

   JS Lamb, S Cornaby, K Andresen, and 5 more authors

   Journal of Applied Crystallography 40 (1), 193-195, 2007
3. Local lattice dynamics in the Mg0. 5Al0. 5B2 superconductor

   G Campi, T Proffen, X Qiu, and 5 more authors

   Journal of Superconductivity and Novel Magnetism 20 (7-8), 505-510, 2007
4. Utilizing total scattering to study the Jahn-Teller transition in La1-xCaxMnO3

   ES Bozin, X Qiu, RJ Worhatch, and 4 more authors

   Z. Kristallogr 26, 429-434, 2007

2006

2006

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

   HY Park, X Qiu, E Rhoades, and 5 more authors

   Analytical chemistry 78 (13), 4465-4473, 2006
2. Measuring inter-DNA potentials in solution

   X Qiu, LW Kwok, HY Park, and 3 more authors

   Physical review letters 96 (13), 138101, 2006
3. Study of temperature dependent atomic correlations in MgB2

   G Campi, E Cappelluti, T Proffen, and 4 more authors

   The European Physical Journal B-Condensed Matter and Complex Systems 52, 15-21, 2006
4. Local structural aspects of the orthorhombic to pseudo-cubic phase transformation in La1-xCaxMnO3

   ES Bozin, X Qiu, M Schmidt, and 5 more authors

   Physica B: Condensed Matter 385, 110-112, 2006

2005

2005

1. Orbital correlations in the pseudocubic O and rhombohedral R phases of LaMnO 3

   X Qiu, T Proffen, JF Mitchell, and 1 more author

   Physical review letters 94 (17), 177203, 2005

2004

2004

1. PDFgetX2: a GUI-driven program to obtain the pair distribution function from X-ray powder diffraction data

   X Qiu, JW Thompson, and SJL Billinge

   Journal of Applied Crystallography 37 (4), 678-678, 2004
2. Reciprocal-space instrumental effects on the real-space neutron atomic pair distribution function

   X Qiu, ES Bozin, P Juhas, and 2 more authors

   Journal of Applied Crystallography 37 (1), 110-116, 2004
3. Probing local and long-range structure simultaneously: An in situ study of the high-temperature phase transition of alpha-AlF3

   PJ Chupas, S Chaudhuri, JC Hanson, and 4 more authors

   Journal of the American Chemical Society 126 (15), 4756-4757, 2004
4. Planar nets of Ti atoms comprising squares and rhombs in the new binary antimonide Ti2Sb

   S Derakhshan, A Assoud, KM Kleinke, and 4 more authors

   Journal of the American Chemical Society 126 (26), 8295-8302, 2004
5. Local structure study of disordered crystalline materials with the atomic pair distribution function method

   X Qiu

   Michigan State University, 2004

2003

2003

1. Rapid-acquisition pair distribution function (RA-PDF) analysis

   PJ Chupas, X Qiu, JC Hanson, and 3 more authors

   Journal of Applied Crystallography 36 (6), 1342-1347, 2003
2. In-situ time resolved powder diffraction studies in heterogenous catalysis; coupling the study of long range and local structural changes. Commission on Powder Diffraction ...

   PJ Chupas, CP Grey, JC Hanson, and 4 more authors

   International Union of Crystallography 29, 24-25, 2003