Publications

115

Kim HM, Omer M, Knappe GA, McMullen P, Le DA, Pasupathy A, Anderson DG, Bathe M. Programmable Lipid Functionalization of Nucleic Acid Nanoparticles Modulates Liver Cell-Type Targeting. ACS Applied Materials & Interfaces. 2026 18(13):18721-18739.

114

Shah A, Lee XK, Li K, Knappe GA, Bathe M, Barbastathis G, Doyle PS. Interpretable Deep Learning for Single-Molecule Nanopore Fingerprinting Using Physics-Guided Preprocessing. ACS sensors. 2026 40 (XXX), XXX-XXX.

113

Berleant JD, Banal JL, Rao DK, Bathe M. Enabling global-scale nucleic acid repositories through versatile, scalable biochemical selection from room-temperature archives. Nat Commun. 2026 17:2807.

112

Romanov A, Knappe GA, Ronsard L, Cottrell CA, Zhang YJ, Suh H, Duhamel L, Omer M, Chapman AP, Spivakovsky K, Skog P, Flynn CT, Lee JH, Kalyuzhniy O, Liguori A, Parsons MF, Lewis VR, Canales J, Reizis B, Tingle RD, Schiffner T, Schief WR, Lingwood D, Bathe M, Irvine DJ. DNA origami vaccines program antigen-focused germinal centers. Science. 2026 391(6785):eadx6291.

111

Scott MN, Banal JL, Chen WJ, Brooks C, Wang X, Hart SM, Dodin A, Bathe M, Willard AP, Schlau-Cohen GS. Transport of Delocalized Excitons through DNA-Based Molecular Photonic Wires. ACS nano. 2025 19:44.

110

Wei W, Mo Q, Chen C, Bathe M, Hernandez R. DNA Origami Nanostructures Observed in Transmission Electron Microscopy Images can be Characterized through Convolutional Neural Networks. J. Chem. Inf. and Model. 2025 65:6526-6536.

109

Knappe GA, Gorman J, Bigley AN, Harvey SP, Bathe M. Heterovalent Click Reactions on DNA Origami. Bioconjugate Chemistry. 2025 36:476-485.

108

Romanov A, Knappe GA, Ronsard L, Suh H, Omer M, Chapman AP, Lewis VR, Spivakovsky K, Canales J, Reizis B, Tingle RD, Cottrell CA, Schiffner T, Lingwood D, Bathe M, Irvine DJ. DNA origami vaccines program antigen-focused germinal centers. bioRxiv. 2025 2025.02. 21.639354.

107

Luo X, Ranno L, Sverko T, Lee JY, Sbalbi N, Jones A, Chen C, Bawendi MG, Hu J, Macfarlane RJ, Bathe M. DNA origami directed integration of colloidal nanophotonic materials with silicon photonics. bioRxiv. 2025 2025.01. 23.634416.

106

Chen C, Luo X, Bathe M. Versatile Dehydration-Assisted Functionalization of Quantum Dots and Rods. Angew. Chem. Int. Ed. 2024 2024:63,e202410247.

105

Falkovich R, Aryal S, Wang J, Sheng M, Bathe M. Synaptic composition, activity, mRNA translation and dynamics in combined single-synapse profiling using multimodal imaging. bioRxiv. 2024 2024.10. 28.620504.

104

Ofoegbu PC, Knappe GA, Romanov A, Draper BE, Bathe M, Jarrold MF. Charge Detection Mass Spectrometry Enables Molecular Characterization of Nucleic Acid Nanoparticles. ACS Nano. 2024 18:23301-23309.

103

Rouskin, S., Allan, M., Aruda, J., Plung, J., Grote, S., Martin, Y., de Lajarte, A., Bathe, M. (2024). Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA

102

Wei X, Chen C, Popov AV, Bathe M, Hernandez R. Binding Site Programmable Self-Assembly of 3D Hierarchical DNA Origami Nanostructures. The Journal of Physical Chemistry A. 2024 128(25):4999-5008.

101

Kim HM, Bathe M. Force-free activation of Notch with DNA origami. Trends in Genetics. 2024 10.1016/j.tig.2024.03.001.

100

Berleant JD, Banal JL, Rao DK, Bathe M. Scalable search of massively pooled nucleic acid samples enabled by a molecular database query language. medRxiv. 2024. DOI: https://doi.org/10.1101/2024.04.12.24305660.

99

Gorman J, Hart SM, John T, Castellanos MA, Harris D, Parsons MF, Banal JL, Willard AP, Schlau-Cohen GS, Bathe M. Sculpting photoproducts with DNA origami. Chem. 2024. DOI: https://doi.org/10.1016/j.chempr.2024.03.007.

98

Wamhoff E-C, Ronsard L, Feldman J, Knappe GA, Hauser BM, Romanov A, Case JB, Sanapala S, Lam EC, St. Denis KJ, Boucau J, Barczak AK, Balazs AB, Diamond MS, Schmidt AG, Lingwood D, Bathe M. Enhancing antibody responses by multivalent antigen display on thymus-independent DNA origami scaffolds. Nature Communications. 2024 15:795.

97

Chen C, Luo X, Kaplan AEK, Bawendi MG, Macfarlane RJ, Bathe M. Ultrafast dense DNA functionalization of quantum dots and rods for scalable 2D array fabrication with nanoscale precision. Science Advances. 2023 32:eadh8508.

96

Hart SM, Gorman J, Bathe M, Schlau-Cohen GS. Engineering exciton dynamics with synthetic DNA scaffolds. Accounts of Chemical Research. 2023 56:2051.

95

Falkovich R, Danielson EW, Perez de Arce K, Wamhoff E-C, Strother J, Lapteva AP, Sheng M, Cottrell JR, Bathe M. A synaptic molecular dependency network in knockdown of autism- and schizophrenia-associated genes revealed by multiplexed imaging. Cell Reports. 2023 42:112430.

94

Wamhoff E-C, Knappe GA, Burds AA, Du RR, Neun B, Difilipppantonio S, Sanders C, Edmondson E, Matta JL, Dobrovolskaia M, Bathe M. Evaluation of non-modified wireframe DNA origami for acute toxicity and biodistribution in mice. ACS Applied Bio Materials. 2023 6:1960.

93

Sheridan K, Berleant J, Bathe M, Condon A, Williams VV. Factorization and pseudofactorization of weighted graphs. Discrete Applied Mathematics. 2023 337:81.

92

Berleant J, Sheridan K, Condon A, Williams VV, Bathe M. Isometric Hamming embeddings of weighted graphs. Discrete Applied Mathematics. 2023 332:119.

91

Parsons MF, Allan MF, Li S, Shepherd TR, Ratanalert S, Zhang S, Pullen KM, Chiu W, Rouskin S, Bathe M. 3D RNA-scaffolded wireframe origami. Nature Communications. 2023 14:382.

90

Knappe GA, Wamhoff E-C, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. Nature Reviews Materials. 2023 8:123.

89

Du RR, Cedrone E, Romanov A, Falkovich R, Dobrovolskaia MA, Bathe M. Innate immune stimulation using 3D wireframe DNA origami. ACS Nano. 2022 16:20340.

88

Chen C, Wei X, Parsons MF, Guo J, Banal JL, Zhao Y, Scott MN, Schlau-Cohen GS, Hernandez R, Bathe M. Nanoscale 3D spatial addressing and valence control of quantum dots using wireframe DNA origami. Nature Communications. 2022 13:4935.

87

Wamhoff E-C, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim H-M, Farrell NP, Irvine DJ, Bathe M. Controlling nuclease degradation of wireframe DNA origami with minor groove binders. ACS Nano. 2022 16:8954.

86

Wang X, Li S, Jun H, John T, Zhang K, Fowler H, Doye JPK, Chiu W, Bathe M. Planar wireframe 2D origami. Science Advances. 2022 8:eabn0039.

85

Lan TCT, Allan MF, Malsick LE, Woo JZ, Zhu C, Zhang F, Khandwala S, Nyeo SSY, Sun Y, Guo JU, Bathe M, Näär A, Griffiths A, Rouskin S. Secondary structural ensembles of the SARS-CoV-2 RNA genome in infected cells. Nature Communications. 2022 13:1128.

84

Wei X, Chen C, Zhao Y, Harazinska E, Bathe M, Hernandez R. Molecular structure of single-stranded DNA on the ZnS surface of quantum dots. ACS Nano. 2022 16:6666.

83

Wang X, Jun H, Bathe M. Programming 2D supramolecular assemblies with wireframe DNA origami. Journal of the American Chemical Society. 2022 144:4403.

82

Hart SM, Wang X, Guo J, Bathe M, Schlau-Cohen GS. Tuning optical absorption and emission using strongly coupled dimers in programmable DNA scaffolds. The Journal of Physical Chemistry Letters. 2022 13:1863.

81

Afonin KA, Dobrovolskaia MA, Ke W, Grodzinski P, Bathe M. Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation. Advanced Drug Delivery Reviews. 2022 181:114081.

80

Adendorff MR, Tang GQ, Millar DP, Bathe M, Bricker WP. Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics. Nucleic Acids Research. 2022 50:717.

79

Lavi R, Bathe M, Hosoi A, Mitra A, Crawley E. The NEET ways of thinking: Implementing them at MIT and assessing their efficacy. Advances in Engineering Education. 2021.

78

Bathe M. Nanoscale 2D and 3D patterning using programmed DNA assemblies. Novel Patterning Technologies. 2021 11610:1161012.

77

Banal J, Bathe M. Scalable nucleic acid storage and retrieval using barcoded microcapsules. ACS Applied Materials & Interfaces. 2021 13:49729.

76

Jun H, Wang X, Parsons MF, Bricker WP, John T, Li S, Jackson S, Chiu W, Bathe M. Rapid prototyping of arbitrary 2D and 3D wireframe DNA origami. Nucleic Acids Research. 2021 49:10265.

75

Knappe GA, Wamhoff EC, Read BJ, Irvine DJ, Bathe M. In situ covalent functionalization of DNA origami virus-like particles. ACS Nano. 2021 15:14316.

74

Tomov ML, O’Neil A, Abbasi HS, Cimini BA, Carpenter AE, Rubin LL, Bathe M. Resolving cell state in iPSC-derived human neural samples with multiplexed fluorescence imaging. Communications Biology. 2021 4:786.

73

Banal JL, Shepherd TY, Berleant J, Huang H, Reyes M, Ackerman CM, Blainey PC, Bathe M. Random access DNA memory using Boolean search in an archival file storage system. Nature Materials. 2021 20:1272.

72

Bathe M, Hernandez R, Komiyama T, Machiraju R, Neogi S. Autonomous Computing Materials. ACS Nano. 2021 15:3586.

71

Hart SM, Chen WJ, Banal JL, Bricker WP, Dodin A, Markova L, Vyborna Y, Willard AP, Häner R, Bathe M, Schlau-Cohen GS. Engineering couplings for exciton transport using synthetic DNA scaffolds. Chem. 2020 7:752.

70

Danielson E, Perez de Arce K, Cimini B, Wamhoff EC, Singh S, Cottrell JR, Carpenter AE, Bathe M. Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging. eNeuro. 2020 8:ENEURO.0286-20.2020.

69

Afonin KA, Dobrovolskaia MA, Church G, Bathe M. Opportunities, barriers, and a strategy for overcoming translational challenges to therapeutic nucleic acid nanotechnology. ACS Nano. 2020 14:9221.

68

Dobrovolskaia MA, Bathe M. Opportunities and challenges for the clinical translation of structured DNA assemblies as gene therapeutic delivery and vaccine vectors. WIREs Nanomedicine and Nanobiotechnology. 2020 13:e1657.

67

Pisharady KP, Eberly LE, Cheong I, Manousakis G, Guliani G, Clark HB, Bathe M, Walk D, Lenglet C. Tract-specific analysis improves sensitivity of spinal cord diffusion MRI to cross-sectional and longitudinal changes in amyotrophic lateral sclerosis. Communications Biology. 2020 3:370.

66

Veneziano R, Moyer TJ, Stone MB, Mukherjee, S. Shepherd TR, Das J, Schief WR, Irvine DJ, Bathe M. Role of nanoscale antigen organization on B-cell activation probed using DNA origami. Nature Nanotechnology. 2020 15:716.

65

Hart SM, Banal JL, Bathe M, Schlau-Cohen GS. Identification of non-radiative decay pathways in cy3. The Journal of Physical Chemistry Letters. 2020 11:5000.

64

Jun H, Wang X, Bricker WP, Bathe M. Automated sequence design of 2D wireframe DNA origami with honeycomb edges. Nature Communications. 2019 10:5419.

63

Guo S-M, Veneziano R, Gordonov S, Li L, Danielson E, Perez de Arce K, Park D, Kulesa AB, Wamhoff E-C, Blainey PC, Boyden ES, Cottrell JR, Bathe M. Multiplexed and high-throughput neuronal fluorescence imaging with diffusible probes. Nature Communications. 2019 10:4377.

62

Wamhoff E-C, Banal JL, Bricker TR, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming structured DNA assemblies to probe biophysical processes. Annual Review of Biophysics. 2019 48:395.

61

Shepherd TR, Du R, R. Huang H, Wamhoff E-C, Bathe M. Bioproduction of pure, kilobase-scale single-stranded DNA. Scientific Reports. 2019 9:6121.

60

Kulikov V, Guo S-M, Stone MB, Goodman A, Carpenter A, Bathe M, Lempitsky V. DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. PLoS Computational Biology. 2019 15:e1007012.

59

Jun H, Zhang F, Shepherd T, Ratalanert S, Qi X, Yan H, Bathe M. Autonomously designed free-form 2D DNA origami. Science Advances. 2019 5:eaav0655.

58

Jun H, Shepherd TR, Zhang K, Bricker WP, Li S, Chiu W, Bathe M. Automated sequence design of 3D polyhedral wireframe DNA origami with honeycomb edges. ACS Nano. 2019 13:2083.

57

Bathe M, Chrisey LA, Herr DJ, Lin Q, Rasic D, Woolley AT, Zadegan R, Zhirnov VV. Roadmap on biological pathways for electronic nanofabrication and materials. Nano Futures. 2019 3:012001.

56

Holec PV, Berleant J, Bathe M, Birnbaum ME. A Bayesian framework for high-throughput T cell receptor pairing. Bioinformatics. 2018 149:024905.

55

Bricker WP, Banal JL, Stone MB, Bathe M. Molecular model of J-aggregated pseudoisocyanine fibers. The Journal of Chemical Physics. 2018 149:024905.

54

Bathe M, Guo S-M, Li L, Veneziano R, Gordonov S, Cottrell JC. Multiplexed imaging of neuronal synapses using nucleic acid probe exchange. Protocol Exchange. 2018. DOI: 10.1038/protex.2018.066.

53

Veneziano R, Shepherd T, Ratanalert S, Bellou L, Tao C, Bathe M. In vitro synthesis of gene-length single-stranded DNA. Scientific Reports. 2018 8:6548.

52

Bathe M, Rothemund P. DNA Nanotechnology: A foundation for programmable nanoscale materials. MRS Bulletin. 2017 42:882.

51

Boulais E, Sawaya N, Veneziano R, Andreoni A, Banal JL, Kondo T, Mandal S, Lin S, Schlau-Cohen GS, Woodbury N, Yan H, Aspuru-Guzik A, Bathe M. Programmed coherent coupling in a synthetic DNA-based excitonic circuit. Nature Materials. 2018 17:159.

50

Banal JL, Kondo T, Veneziano R, Bathe M, Schlau-Cohen GS. Photophysics of J-aggregate-mediated energy transfer on DNA. The Journal of Physical Chemistry Letters. 2017 8:5827.

49

Cunningham P, Bricker W, Diaz S, Medintz I, Bathe M, Melinger JS. Optical determination of the electronic coupling and intercalation geometry of Thiazole Orange homodimer in DNA. The Journal of Chemical Physics. 2017 147:055101.

48

Pan K, Bricker W, Ratanalert S, Bathe M. Structure and conformational dynamics of scaffolded DNA origami nanoparticles. Nucleic Acids Research. 2017 45:6284.

47

Su KC, Barry Z, Schweizer N, Maiato H, Bathe M, Cheeseman I. A regulatory switch alters chromosome motions at the metaphase to anaphase transition. Cell Reports. 2016 17:728.

46

Veneziano R, Ratanalert S, Zhang K, Zhang F, Yan H, Chiu W, Bathe M. Designer nanoscale DNA assemblies programmed from the top down. Science. 2016 352:1534.

45

Wang P, Gaitanaros S, Lee S, Bathe M, Shih WM, Ke Y. Programming self-assembly of DNA origami honeycomb lattices and plasmonic metamaterials. JACS. 2016 138:7733.

44

Katz ZB, English BP, Lionnet T, Yoon YJ, Monnier N, Ovryn B, Bathe M, Singer RH. Mapping translation ‘hot-spots’ in live cells by tracking single molecules of mRNA and ribosomes. eLife. 2016 e10415.

43

Dhakal S, Adendorff M, Liu M, Yan H, Bathe M, Walter N. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. Nanoscale. 2016 8:3125.

42

Hogstrom L, Guo SM, Murugadoss K, Bathe M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length-scales. Journal of The Royal Society Interface. 2016 6:20150081.

41

Gordonov S, Hwang MK, Wells A, Gertler FB, Lauffenburger D, Bathe M. Time-series modeling of live-cell shape dynamics for image-based phenotypic profiling. Integrative Biology. 2016 8:73.

40

Sedeh R, Pan K, Adendorff M, Hallatschek O, Bathe KJ, Bathe M. Computing nonequilibrium conformational dynamics of structured nucleic acid assemblies. Journal of Chemical Theory & Computation. 2016 12:261.

39

Monnier N, Barry Z, Park HY, Su KC, Katz Z, English B, Dey A, Pan K, Cheeseman I, Singer R, Bathe M. Inferring transient particle transport dynamics in live cells. Nature Methods. 2015 12:838.

38

Sun G, Guo SM, Teh C, Korzh V, Bathe M, Wohland T. Bayesian model selection applied to the analysis of FCS data of fluorescent proteins in vitro and in vivo. Analytical Chemistry. 2015 87:4326.

37

Zhou Z, Munteanu EL, He J, Ursell T, Bathe M, Huang KC, Chang F. The contractile ring coordinates curvature dependent septum assembly during fission yeast cytokinesis. Molecular Biology of the Cell. 2015 26:78.

36

Pan K, Kim DN, Zhang F, Adendorff M, Yan H, Bathe M. Lattice-free prediction of three-dimensional structure of programmed DNA assemblies. Nature Communications. 2014 5:5578.

35

Klingner C, Cherian AV, Diesinger PM, Aufschnaiter R, Maghelli N, Keil T, Beck G, Tolic-Norrelykke I, Bathe M, Wedlich-Soldner R. An isotropic acto-myosin network promotes organization of the apical cell cortex in epithelial cells. The Journal of Cell Biology. 2014 207:107.

34

Sun W, Boulais E, Hakobyan Y, Wang W, Guan A, Bathe M, Yin P. Casting inorganic structures with DNA molds. Science. 2014 346:717.

33

Mori M, Somogyi K, Kondo H, Monnier N, Falk H, Machado P, Bathe M, Nedelec F, Lenart P. An Arp2/3 nucleated F-actin shell fragments nuclear membranes at nuclear envelope breakdown. Current Biology. 2014 24:1421.

32

Oh HS, Bryant KF, Nieland T, Mazumder A, Bagul M, Bathe M, Root DE, Knipe DM. Targeted RNAi screen reveals novel epigenetic factors that regulate herpesviral gene expression in U2OS osteosarcoma cells. mBio. 2014 5:e01086.

31

Guo SM, Bag N, Mishra A, Wohland T, Bathe M. Bayesian total internal reflection fluorescence correlation spectroscopy reveals hIAPP-induced plasma membrane domain organization in live cells. Biophysical Journal. 2014 106:190.

30

Pan K, Boulais E, Yang L, Bathe M. Structure-based model for light-harvesting properties of nucleic acid nanostructures. Nucleic Acids Research. 2014 42:2159.

29

Subramanian V, Mazumder A, Surface LE, Butty V, Fields PA, Alwan A, Torrey L, Thai KK, Levine S, Bathe M, Boyer L. H2A.Z acidic patch couples chromatin dynamics to regulation of developmental gene expression programs during lineage commitment. PLoS Genetics. 2013 9:e1003725.

28

Mazumder A, Pesudo LQ, McRee S, Bathe M, Samson L. Genome-wide single-cell-level screen for protein abundance and localization changes in response to DNA damage in S. cerevisiae. Nucleic Acids Research. 2013 41:9310.

27

Johnson-Buck A, Nangreave J, Kim DN, Bathe M, Yan H, Walter N. Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. Nano Letters. 2013 13:728.

26

Mazumder A, Tummler K, Bathe M, Samson LD. Single-cell analysis of RNR transcriptional and translational response to DNA damage. Molecular & Cellular Biology. 2013 33:635.

25

Krishnan Y, Bathe M. Designer nucleic acids to probe and program the cell. Trends in Cell Biology. 2013 22:624.

24

Schmidt JC, Arthanari H, Boeszoermenyi A, Dashkevich NM, Wilson-Kubalek E, Monnier N, Markus M, Oberer M, Milligan R, Bathe M, Wagner G, Grishchuk EL, Cheeseman IM. The kinetochore-bound Ska1 complex tracks depolymerizing microtubules by binding to curved protofilaments. Developmental Cell. 2012 23:968.

23

Monnier N, Guo SM, Mori M, He J, Lenart P, Bathe M. Bayesian approach to MSD-based analysis of particle motion in live cells. Biophysical Journal. 2012 103:616.

22

Guo SM, He J, Monnier N, Sun G, Wohland T, Bathe M. Bayesian approach to the analysis of fluorescence correlation spectroscopy data II: Application to simulated and in vitro data. Analytical Chemistry. 2012 84:3880.

21

He J, Guo SM, Bathe M. Bayesian approach to the analysis of fluorescence correlation spectroscopy data I: Theory. Analytical Chemistry. 2012 84:3871.

20

Kim DN, Kilchherr F, Dietz H, Bathe M. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures. Nucleic Acids Research. 2012 40:2862.

19

Castro CE, Kilchherr F, Kim DN, Lin Shiao E, Wauer T, Wortmann P, Bathe M, Dietz H. A primer to scaffolded DNA origami. Nature Methods. 2011 8:221.

18

Mori M, Monnier N, Daigle N, Bathe M, Ellenberg J, Lenart P. Intracellular transport by an anchored homogeneously contracting F-actin meshwork. Current Biology. 2011 21:606.

17

Kim DN, Altschuler J, Strong C, McGill G, Bathe M. Conformational dynamics data bank: a database for conformational dynamics of proteins and supramolecular protein assemblies. Nucleic Acids Research. 2011 39:D451.

16

Kim DN, Nguyen CT, Bathe M. Conformational dynamics of supramolecular protein assemblies. Journal of Structural Biology. 2011 173:261.

15

Strehle D, Schnauss J, Heussinger C, Alvarado J, Bathe M, Kaes J, Gentry B. Transiently crosslinked F-actin bundles. European Biophysical Journal. 2011 40:93.

14

Sedeh RS, Fedorov AA, Fedorov EV, Ono S, Matsumura F, Almo SC, Bathe M. Structure, evolutionary conservation, and conformational dynamics of Homo sapiens fascin-1, an F-actin crosslinking protein. Journal of Molecular Biology. 2010 400:589.

13

Bathe M, Chang FC. Cytokinesis and the contractile ring in fission yeast: towards a systems-level understanding. Trends in Microbiology. 2010 18:38.

12

Sedeh R, Bathe M, Bathe KJ. The subspace iteration method in protein normal mode analysis. Journal of Computational Chemistry. 2010 31:66.

11

Bathe M, Heussinger C, Claessens MMAE, Bausch AR, Frey E. Cytoskeletal bundle mechanics. Biophysical Journal. 2008 94:2955.

10

Bathe M. A Finite Element framework for computation of protein normal modes and mechanical response. Proteins: Structure, Function, and Bioinformatics. 2008 70:1595.

9

Heussinger C, Bathe M, Frey E. Statistical mechanics of wormlike bundles. Physical Review Letters. 2007 99:Art.No.048101.

8

Claessens MMAE, Bathe M, Frey E, Bausch AR. Actin-binding proteins sensitively mediate F-actin bundle stiffness. Nature Materials. 2006 5:748.

7

Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Osmotic pressure of aqueous chondroitin sulfate solution: A molecular modeling investigation. Biophysical Journal. 2005 89:2357.

6

Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. A coarse-grained molecular model for glycosaminoglycans: Application to chondroitin, chondroitin sulfate, and hyaluronic acid. Biophysical Journal. 2005 88:3870.

5

Bathe M, Grodzinsky AJ, Tidor B, Rutledge GC. Optimal linearized Poisson-Boltzmann theory applied to the simulation of flexible polyelectrolytes in solution. Journal of Chemical Physics. 2004 121:7557.

4

Kaazempur-Mofrad MR, Bathe M, Karcher H, Younis HF, Seong HC, Shim EB, Chan RC, Hinton DP, Isasi AG, Upadhyaya A, Powers MJ, Griffith LG, Kamm RD. Role of simulation in understanding biological systems. Computers & Structures. 2003 81:715.

3

Bathe M, Rutledge GC. Inverse Monte Carlo procedure for conformation determination of macromolecules. Journal of Computational Chemistry. 2003 24:876.

2

Bathe M, Shirai A, Doerschuk CM, Kamm RD. Neutrophil transit times through pulmonary capillaries: The effects of capillary geometry and fMLP-stimulation. Biophysical Journal. 2002 83:1917.

1

Bathe M, Kamm RD. A fluid-structure interaction finite element analysis of pulsatile blood flow through a compliant stenotic artery. Journal of Biomechanical Engineering. 1999 121:361.