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 Appl Mater 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 Sens. 2026 [Epub ahead of print]. doi:10.1021/acssensors.5c04784.

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). doi:10.1021/acsnano.5c11986.

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 Model. 2025;65:6526-6536.

109

Knappe GA, Gorman J, Bigley AN, Harvey SP, Bathe M. Heterovalent Click Reactions on DNA Origami. Bioconjug Chem. 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 [Preprint]. 2025. doi:10.1101/2025.02.21.639354.

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 [Preprint]. 2025. doi:10.1101/2025.01.23.634416.

106

Chen C, Luo X, Bathe M. Versatile Dehydration-Assisted Functionalization of Quantum Dots and Rods. Angew Chem Int Ed Engl. 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 [Preprint]. 2024. doi:10.1101/2024.10.28.620504.

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. Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA. Res Sq [Preprint]. 2024. doi:10.21203/rs.3.rs-4814547/v1.

102

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

101

Kim HM, Bathe M. Force-free activation of Notch with DNA origami. Trends Genet. 2024. doi: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 [Preprint]. 2024. doi: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:10.1016/j.chempr.2024.03.007.

98

Wamhoff EC, 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. Nat Commun. 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. Sci Adv. 2023;9:eadh8508.

96

Hart SM, Gorman J, Bathe M, Schlau-Cohen GS. Engineering exciton dynamics with synthetic DNA scaffolds. Acc Chem Res. 2023;56:2051.

95

Falkovich R, Danielson EW, Perez de Arce K, Wamhoff EC, 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 Rep. 2023;42:112430.

94

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

93

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

92

Berleant J, Sheridan K, Condon A, Williams VV, Bathe M. Isometric Hamming embeddings of weighted graphs. Discrete Appl Math. 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. Nat Commun. 2023;14:382.

90

Knappe GA, Wamhoff EC, Bathe M. Functionalizing DNA origami to investigate and interact with biological systems. Nat Rev Mater. 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. Nat Commun. 2022;13:4935.

87

Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, 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. Sci Adv. 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. Nat Commun. 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. J Am Chem Soc. 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. J Phys Chem Lett. 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. Adv Drug Deliv Rev. 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 Res. 2022;50:717.

79

Lavi R, Bathe M, Hosoi AE, Mitra A, Crawley EF. The NEET ways of thinking: Implementing them at MIT and assessing their efficacy. Adv Eng Educ. 2021.

78

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

77

Banal JL, Bathe M. Scalable nucleic acid storage and retrieval using barcoded microcapsules. ACS Appl Mater 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 Res. 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. Commun Biol. 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. Nat Mater. 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. 2021;7:752.

70

Danielson E, Perez de Arce K, Cimini BA, Wamhoff EC, Singh S, Cottrell JR, Carpenter AE, Bathe M. Molecular diversity of glutamatergic and GABAergic synapses from multiplexed fluorescence imaging. eNeuro. 2021;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 Nanomed Nanobiotechnol. 2021;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. Commun Biol. 2020;3:370.

66

Veneziano R, Moyer TJ, Stone MB, Wamhoff EC, Read BJ, 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. Nat Nanotechnol. 2020;15:716.

65

Hart SM, Banal JL, Bathe M, Schlau-Cohen GS. Identification of non-radiative decay pathways in Cy3. J Phys Chem Lett. 2020;11:5000.

64

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

63

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

62

Wamhoff EC, Banal JL, Bricker WP, Parsons MF, Veneziano R, Stone MB, Jun H, Wang X, Bathe M. Programming structured DNA assemblies to probe biophysical processes. Annu Rev Biophys. 2019;48:395.

61

Shepherd TR, Du RR, Huang H, Wamhoff EC, Bathe M. Bioproduction of pure, kilobase-scale single-stranded DNA. Sci Rep. 2019;9:6121.

60

Kulikov V, Guo SM, Stone MB, Goodman A, Carpenter AE, Bathe M, Lempitsky V. DoGNet: A deep architecture for synapse detection in multiplexed fluorescence images. PLoS Comput Biol. 2019;15:e1007012.

59

Jun H, Zhang F, Shepherd TR, Ratanalert S, Qi X, Yan H, Bathe M. Autonomously designed free-form 2D DNA origami. Sci Adv. 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 DJC, 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. 2019;35(1):118-127.

55

Bricker WP, Banal JL, Stone MB, Bathe M. Molecular model of J-aggregated pseudoisocyanine fibers. J Chem Phys. 2018;149:024905.

54

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

53

Veneziano R, Shepherd TR, Ratanalert S, Bellou L, Tao C, Bathe M. In vitro synthesis of gene-length single-stranded DNA. Sci Rep. 2018;8:6548.

52

Bathe M, Rothemund PWK. DNA Nanotechnology: A foundation for programmable nanoscale materials. MRS Bull. 2017;42:882.

51

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

50

Banal JL, Kondo T, Veneziano R, Bathe M, Schlau-Cohen GS. Photophysics of J-aggregate-mediated energy transfer on DNA. J Phys Chem Lett. 2017;8:5827.

49

Cunningham PD, Bricker WP, Diaz SA, Medintz IL, Bathe M, Melinger JS. Optical determination of the electronic coupling and intercalation geometry of Thiazole Orange homodimer in DNA. J Chem Phys. 2017;147:055101.

48

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

47

Su KC, Barry Z, Schweizer N, Maiato H, Bathe M, Cheeseman IM. A regulatory switch alters chromosome motions at the metaphase to anaphase transition. Cell Rep. 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. J Am Chem Soc. 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;5:e10415.

43

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

42

Hogstrom LJ, Guo SM, Murugadoss K, Bathe M. Advancing multiscale structural mapping of the brain through fluorescence imaging and analysis across length-scales. Interface Focus. 2016;6:20150081.

41

Gordonov S, Hwang MK, Wells A, Gertler FB, Lauffenburger DA, Bathe M. Time-series modeling of live-cell shape dynamics for image-based phenotypic profiling. Integr Biol (Camb). 2016;8:73.

40

Sedeh RS, Pan K, Adendorff MR, Hallatschek O, Bathe KJ, Bathe M. Computing nonequilibrium conformational dynamics of structured nucleic acid assemblies. J Chem Theory Comput. 2016;12:261.

39

Monnier N, Barry Z, Park HY, Su KC, Katz ZB, English BP, Dey A, Pan K, Cheeseman IM, Singer RH, Bathe M. Inferring transient particle transport dynamics in live cells. Nat 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. Anal Chem. 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. Mol Biol Cell. 2015;26:78.

36

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

35

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

34

Sun W, Boulais E, Hakobyan Y, Wang WL, Guan A, Bathe M, Yin P. Casting inorganic structures with DNA molds. Science. 2014;346:1258361.

33

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

32

Oh HS, Bryant KF, Nieland TJF, 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. Biophys J. 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 Res. 2014;42:2159.

29

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

28

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

27

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

26

Mazumder A, Tümmler K, Bathe M, Samson LD. Single-cell analysis of RNR transcriptional and translational response to DNA damage. Mol Cell Biol. 2013;33:635.

25

Krishnan Y, Bathe M. Designer nucleic acids to probe and program the cell. Trends Cell Biol. 2012;22:624.

24

Schmidt JC, Arthanari H, Boeszoermenyi A, Dashkevich NM, Wilson-Kubalek EM, Monnier N, Markus M, Oberer M, Milligan RA, Bathe M, Wagner G, Grishchuk EL, Cheeseman IM. The kinetochore-bound Ska1 complex tracks depolymerizing microtubules by binding to curved protofilaments. Dev 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. Biophys J. 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. Anal Chem. 2012;84:3880.

21

He J, Guo SM, Bathe M. Bayesian approach to the analysis of fluorescence correlation spectroscopy data I: Theory. Anal Chem. 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 Res. 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. Nat 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. Curr Biol. 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 Res. 2011;39:D451.

16

Kim DN, Nguyen CT, Bathe M. Conformational dynamics of supramolecular protein assemblies. J Struct Biol. 2011;173:261.

15

Strehle D, Schnauss J, Heussinger C, Alvarado J, Bathe M, Käs J, Gentry B. Transiently crosslinked F-actin bundles. Eur Biophys J. 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. J Mol Biol. 2010;400:589.

13

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

12

Sedeh RS, Bathe M, Bathe KJ. The subspace iteration method in protein normal mode analysis. J Comput Chem. 2010;31:66.

11

Bathe M, Heussinger C, Claessens MMAE, Bausch AR, Frey E. Cytoskeletal bundle mechanics. Biophys J. 2008;94:2955.

10

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

9

Heussinger C, Bathe M, Frey E. Statistical mechanics of wormlike bundles. Phys Rev Lett. 2007;99:048101.

8

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

7

Bathe M, Rutledge GC, Grodzinsky AJ, Tidor B. Osmotic pressure of aqueous chondroitin sulfate solution: A molecular modeling investigation. Biophys J. 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. Biophys J. 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. J Chem Phys. 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. Comput Struct. 2003;81

3

Bathe M, Rutledge GC. Inverse Monte Carlo procedure for conformation determination of macromolecules. J Comput Chem. 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. Biophys J. 2002;83:1917.

1

Bathe M, Kamm RD. A fluid-structure interaction finite element analysis of pulsatile blood flow through a compliant stenotic artery. J Biomech Eng. 1999;121:361.