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2019

A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer

Sgouralis, I., Madaan, S., Djutanta, F., Kha, R., Hariadi, R. & Presse, S., Jan 24 2019, In : Journal of Physical Chemistry B. 123, 3, p. 675-688 14 p.

Research output: Contribution to journalArticle

3 Scopus citations

A broader view on jamming: from spring networks to circle packings

F. Hagh, V., Corwin, E. I., Stephenson, K. & Thorpe, M., Jan 1 2019, In : Soft Matter. 15, 15, p. 3076-3084 9 p.

Research output: Contribution to journalArticle

A method for single molecule tracking using a conventional single-focus confocal setup

Jazani, S., Sgouralis, I. & Presse, S., Mar 21 2019, In : Journal of Chemical Physics. 150, 11, 114108.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Autonomous dynamic control of DNA nanostructure self-assembly

Green, L. N., Subramanian, H. K. K., Mardanlou, V., Kim, J., Hariadi, R. & Franco, E., Jan 1 2019, In : Nature Chemistry.

Research output: Contribution to journalArticle

10 Scopus citations

Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor

Audet, M., White, K. L., Breton, B., Zarzycka, B., Han, G. W., Lu, Y., Gati, C., Batyuk, A., Popov, P., Velasquez, J., Manahan, D., Hu, H., Weierstall, U., Liu, W., Shui, W., Katritch, V., Cherezov, V., Hanson, M. A. & Stevens, R. C., Jan 1 2019, In : Nature Chemical Biology. 15, 1, p. 11-17 7 p.

Research output: Contribution to journalArticle

9 Scopus citations

Effective Dielectric Constant of Water at the Interface with Charged C 60 Fullerenes

Sarhangi, S. M., Waskasi, M. M., Hashemianzadeh, S. M. & Matyushov, D., Apr 11 2019, In : Journal of Physical Chemistry B. 123, 14, p. 3135-3143 9 p.

Research output: Contribution to journalArticle

2 Scopus citations

Identification of point defects using high-resolution electron energy loss spectroscopy

Wang, S., March, K., Ponce, F. & Rez, P., Mar 18 2019, In : Physical Review B. 99, 11, 115312.

Research output: Contribution to journalArticle

2 Scopus citations

Non-cryogenic structure of a chloride pump provides crucial clues to temperature-dependent channel transport efficiency

Yun, J. H., Li, X., Park, J. H., Wang, Y., Ohki, M., Jin, Z., Lee, W., Park, S. Y., Hu, H., Li, C., Zatsepin, N., Hunter, M. S., Sierra, R. G., Koralek, J., Yoon, C. H., Cho, H. S., Weierstall, U., Tang, L., Liu, H. & Lee, W., Jan 1 2019, In : Journal of Biological Chemistry. 294, 3, p. 794-804 11 p.

Research output: Contribution to journalArticle

2 Scopus citations
1 Scopus citations

Quantitative Mapping of Endosomal DNA Processing by Single Molecule Counting

Prakash, V., Tsekouras, K., Venkatachalapathy, M., Heinicke, L., Presse, S., Walter, N. G. & Krishnan, Y., Mar 4 2019, In : Angewandte Chemie - International Edition. 58, 10, p. 3073-3076 4 p.

Research output: Contribution to journalArticle

1 Scopus citations

Selective Transmission of Phonons in Molecular Junctions with Nanoscopic Thermal Baths

Medrano Sandonas, L., Rodríguez Méndez, Á., Gutierrez, R., Ugalde, J. M., Mujica, V. & Cuniberti, G., Apr 18 2019, In : Journal of Physical Chemistry C. 123, 15, p. 9680-9687 8 p.

Research output: Contribution to journalArticle

1 Scopus citations

Single Molecule Identification and Quantification of Glycosaminoglycans Using Solid-State Nanopores

Im, J., Lindsay, S., Wang, X. & Zhang, P., Jan 1 2019, In : ACS Nano.

Research output: Contribution to journalArticle

5 Scopus citations

SPIND: A reference-based auto-indexing algorithm for sparse serial crystallography data

Li, C., Li, X., Kirian, R., Spence, J., Liu, H. & Zatsepin, N., Jan 1 2019, In : IUCrJ. 6, p. 72-84 13 p.

Research output: Contribution to journalArticle

4 Scopus citations

Structural recovery and fictive variables: The fictive electric field

Riechers, B. & Richert, R., Jan 1 2019, (Accepted/In press) In : Thermochimica Acta.

Research output: Contribution to journalArticle

The influence of electrically conductive and non-conductive nanocomposite scaffolds on the maturation and excitability of engineered cardiac tissues

Navaei, A., Rahmani Eliato, K., Ros, R., Migrino, R. Q., Willis, B. C. & Nikkhah, M., Feb 1 2019, In : Biomaterials Science. 7, 2, p. 585-595 11 p.

Research output: Contribution to journalArticle

1 Scopus citations
2018

3D heterogeneous islet organoid generation from human embryonic stem cells using a novel engineered hydrogel platform

Candiello, J., Grandhi, T. S. P., Goh, S. K., Vaidya, V., Lemmon-Kishi, M., Eliato, K. R., Ros, R., Kumta, P. N., Rege, K. & Banerjee, I., Sep 1 2018, In : Biomaterials. 177, p. 27-39 13 p.

Research output: Contribution to journalArticle

23 Scopus citations

A comparison of methods to assess cell mechanical properties

Wu, P. H., Aroush, D. R. B., Asnacios, A., Chen, W. C., Dokukin, M. E., Doss, B. L., Durand-Smet, P., Ekpenyong, A., Guck, J., Guz, N. V., Janmey, P. A., Lee, J. S. H., Moore, N. M., Ott, A., Poh, Y. C., Ros, R., Sander, M., Sokolov, I., Staunton, J. R., Wang, N. & 2 others, Whyte, G. & Wirtz, D., Jun 18 2018, (Accepted/In press) In : Nature Methods. p. 1-8 8 p.

Research output: Contribution to journalArticle

52 Scopus citations

A course-embedded comparison of instructor-generated videos of either an instructor alone or an instructor and a student

Cooper, K. M., Ding, L., Stephens, M. D., Chi, M. & Brownell, S., Jun 1 2018, In : CBE life sciences education. 17, 2, ar31.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Ancient thioredoxins evolved to modern-day stability–function requirement by altering native state ensemble

Modi, T., Huihui, J., Ghosh, K. & Ozkan, S., Jun 19 2018, In : Philosophical Transactions of the Royal Society B: Biological Sciences. 373, 1749, 20170184.

Research output: Contribution to journalArticle

7 Scopus citations

A novel modelling mechanism of PAEL receptor and GABARAPL2 interaction involved in Parkinson's disease

Dutta, P., Dargahi, L., O'Connell, K. E., Bolia, A., Ozkan, S., Sailer, A. W. & Dev, K. K., Apr 23 2018, In : Neuroscience Letters. 673, p. 12-18 7 p.

Research output: Contribution to journalArticle

2 Scopus citations

Are working memory and behavioral attention equally important for both reading and listening comprehension? A developmental comparison

Language, Lomax, R., O’Connell, A., Pentimonti, J., Petrill, S. A., Piasta, S. B., Gray, S., Restrepo, M., Cain, K., Catts, H., Bridges, M., Nielsen, D., Hogan, T., Bovaird, J., Nelson, J. R., Jiang, H. & Farquharson, K., May 7 2018, (Accepted/In press) In : Reading and Writing. p. 1-29 29 p.

Research output: Contribution to journalArticle

1 Scopus citations

Auxiliary field diffusion Monte Carlo calculations of light and medium-mass nuclei with local chiral interactions

Lonardoni, D., Gandolfi, S., Lynn, J. E., Petrie, C., Carlson, J., Schmidt, K. & Schwenk, A., Apr 24 2018, In : Physical Review C. 97, 4, 044318.

Research output: Contribution to journalArticle

18 Scopus citations

A Y-Shaped Three-Arm Structure for Probing Bivalent Interactions between Protein Receptor-Ligand Using AFM and SPR

Senapati, S., Biswas, S., Manna, S., Ros, R., Lindsay, S. & Zhang, P., Jun 12 2018, In : Langmuir. 34, 23, p. 6930-6940 11 p.

Research output: Contribution to journalArticle

Catalytic conversion of cyanobacteria-derived fatty acids to alkanes for biorenewable synthetic paraffinic kerosene

Schulz, T. C., Oelschlager, M., Thompson, S. T., Vermaas, W., Nielsen, D. & Lamb, H. H., Jan 1 2018, In : Sustainable Energy and Fuels. 2, 4, p. 882-893 12 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Chirality-Induced Electron Spin Polarization and Enantiospecific Response in Solid-State Cross-Polarization Nuclear Magnetic Resonance

Santos, J. I., Rivilla, I., Cossío, F. P., Matxain, J. M., Grzelczak, M., Mazinani, S. K. S., Ugalde, J. M. & Mujica, V., Nov 27 2018, In : ACS Nano. 12, 11, p. 11426-11433 8 p.

Research output: Contribution to journalArticle

7 Scopus citations

Coevolving residues inform protein dynamics profiles and disease susceptibility of nSNVs

Butler, B. M., Kazan, I. C., Kumar, A. & Ozkan, S., Nov 1 2018, In : PLoS Computational Biology. 14, 11, e1006626.

Research output: Contribution to journalArticle

Complex Dynamics of Water in Protein Confinement

Martin, D. R., Forsmo, J. E. & Matyushov, D., Apr 5 2018, In : Journal of Physical Chemistry B. 122, 13, p. 3418-3425 8 p.

Research output: Contribution to journalArticle

8 Scopus citations

Comprehension and Writing Strategy Training Improves Performance on Content-Specific Source-Based Writing Tasks

Weston-Sementelli, J. L., Allen, L. K. & McNamara, D., Mar 1 2018, In : International Journal of Artificial Intelligence in Education. 28, 1, p. 106-137 32 p.

Research output: Contribution to journalArticle

5 Scopus citations

Comprehension in a Scenario-Based Assessment: Domain and Topic-Specific Background Knowledge

McCarthy, K. S., Guerrero, T. A., Kent, K. M., Allen, L. K., McNamara, D., Chao, S. F., Steinberg, J., O’Reilly, T. & Sabatini, J., May 3 2018, (Accepted/In press) In : Discourse Processes. p. 1-15 15 p.

Research output: Contribution to journalArticle

Dipolar susceptibility of protein hydration shells

Seyedi, S. & Matyushov, D., Dec 1 2018, In : Chemical Physics Letters. 713, p. 210-214 5 p.

Research output: Contribution to journalArticle

4 Scopus citations

Direct observation of cargo transfer from HDL particles to the plasma membrane

Plochberger, B., Axmann, M., Röhrl, C., Weghuber, J., Brameshuber, M., Rossboth, B. K., Mayr, S., Ros, R., Bittman, R., Stangl, H. & Schütz, G. J., Oct 1 2018, In : Atherosclerosis. 277, p. 53-59 7 p.

Research output: Contribution to journalArticle

3 Scopus citations
4 Scopus citations

Disordered auxetic networks with no reentrant polygons

Hagh, V. F. & Thorpe, M., Sep 24 2018, In : Physical Review B. 98, 10, 100101.

Research output: Contribution to journalArticle

3 Scopus citations

Electrode redox reactions with polarizable molecules

Matyushov, D., Apr 21 2018, In : Journal of Chemical Physics. 148, 15, 154501.

Research output: Contribution to journalArticle

3 Scopus citations

Electronic Structure and Triplet–Triplet Energy Transfer in Artificial Photosynthetic Antennas

Tejeda-Ferrari, M. E., Brown, C. L., Coutinho, G. C. C. C., Gomes de Sá, G. A., Palma, J. L., Llansola-Portoles, M. J., Kodis, G., Mujica, V., Ho, J., Gust, D., Moore, T. & Moore, A., Jan 1 2018, (Accepted/In press) In : Photochemistry and Photobiology.

Research output: Contribution to journalArticle

5 Scopus citations

Enhanced Magnetoresistance in Chiral Molecular Junctions

Maslyuk, V. V., Gutierrez, R., Dianat, A., Mujica, V. & Cuniberti, G., Sep 20 2018, In : Journal of Physical Chemistry Letters. 9, 18, p. 5453-5459 7 p.

Research output: Contribution to journalArticle

13 Scopus citations

Enzyme intermediates captured "on the fly" by mix-and-inject serial crystallography

Olmos, J. L., Pandey, S., Martin-Garcia, J. M., Calvey, G., Katz, A., Knoska, J., Kupitz, C., Hunter, M. S., Liang, M., Oberthuer, D., Yefanov, O., Wiedorn, M., Heyman, M., Holl, M., Pande, K., Barty, A., Miller, M. D., Stern, S., Roy-Chowdhury, S., Coe, J. & 30 others, Nagaratnam, N., Zook, J., Verburgt, J., Norwood, T., Poudyal, I., Xu, D., Koglin, J., Seaberg, M. H., Zhao, Y., Bajt, S., Grant, T., Mariani, V., Nelson, G., Subramanian, G., Bae, E., Fromme, R., Fung, R., Schwander, P., Frank, M., White, T. A., Weierstall, U., Zatsepin, N., Spence, J., Fromme, P., Chapman, H. N., Pollack, L., Tremblay, L., Ourmazd, A., Phillips, G. N. & Schmidt, M., May 31 2018, In : BMC Biology. 16, 1, 59.

Research output: Contribution to journalArticle

32 Scopus citations

Erratum to: Crystal structure of misoprostol bound to the labor inducer prostaglandin E2 receptor (Nature Chemical Biology, (2019), 15, 1, (11-17), 10.1038/s41589-018-0160-y)

Audet, M., White, K. L., Breton, B., Zarzycka, B., Han, G. W., Lu, Y., Gati, C., Batyuk, A., Popov, P., Velasquez, J., Manahan, D., Hu, H., Weierstall, U., Liu, W., Shui, W., Katritch, V., Cherezov, V., Hanson, M. A. & Stevens, R. C., Jan 1 2018, (Accepted/In press) In : Nature Chemical Biology.

Research output: Contribution to journalArticle

Femtosecond X-ray diffraction from an aerosolized beam of protein nanocrystals

Awel, S., Kirian, R., Wiedorn, M. O., Beyerlein, K. R., Roth, N., Horke, D. A., Oberthür, D., Knoska, J., Mariani, V., Morgan, A., Adriano, L., Tolstikova, A., Xavier, P. L., Yefanov, O., Aquila, A., Barty, A., Roy-Chowdhury, S., Hunter, M. S., James, D., Robinson, J. S. & 5 others, Weierstall, U., Rode, A. V., Bajt, S., Küpper, J. & Chapman, H. N., Feb 1 2018, In : Journal of Applied Crystallography. 51, 1, p. 133-139 7 p.

Research output: Contribution to journalArticle

10 Scopus citations
6 Scopus citations

Free-electron laser data for multiple-particle fluctuation scattering analysis

Pande, K., Donatelli, J. J., Malmerberg, E., Foucar, L., Poon, B. K., Sutter, M., Botha, S., Basu, S., Doak, R. B., Dörner, K., Epp, S. W., Englert, L., Fromme, R., Hartmann, E., Hartmann, R., Hauser, G., Hattne, J., Hosseinizadeh, A., Kassemeyer, S., Lomb, L. & 16 others, Carron Montero, S. F., Menzel, A., Rolles, D., Rudenko, A., Seibert, M. M., Sierra, R. G., Schwander, P., Ourmazd, A., Fromme, P., Sauter, N. K., Bogan, M., Bozek, J., Bostedt, C., Schlichting, I., Kerfeld, C. A. & Zwart, P. H., Jan 1 2018, In : Scientific data. 5, 180201.

Research output: Contribution to journalArticle

1 Scopus citations

From the volcano effect to banding: A minimal model for bacterial behavioral transitions near chemoattractant sources

Javens, G., Jashnsaz, H. & Presse, S., Apr 30 2018, In : Physical Biology. 15, 4, 046002.

Research output: Contribution to journalArticle

Gordon Research Conference on photosynthesis: photosynthetic plasticity from the environment to synthetic systems

Gisriel, C., Saroussi, S., Ramundo, S., Fromme, P. & Govindjee, Jan 2 2018, (Accepted/In press) In : Photosynthesis Research. p. 1-13 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

Half Reactions with Multiple Redox States Do Not Follow the Standard Theory: A Computational Study of Electrochemistry of C60

Sarhangi, S. M., Waskasi, M. M., Hashemianzadeh, S. M., Martin, D. R. & Matyushov, D., May 18 2018, (Accepted/In press) In : Journal of Physical Chemistry C.

Research output: Contribution to journalArticle

1 Scopus citations

Hinge-Shift Mechanism Modulates Allosteric Regulations in Human Pin1

Campitelli, P., Guo, J., Zhou, H. X. & Ozkan, S., May 31 2018, In : Journal of Physical Chemistry B. 122, 21, p. 5623-5629 7 p.

Research output: Contribution to journalArticle

8 Scopus citations

Interfacial structural crossover and hydration thermodynamics of charged C60 in water

Sarhangi, S. M., Waskasi, M. M., Hashemianzadeh, S. M. & Matyushov, D., Jan 1 2018, In : Physical Chemistry Chemical Physics. 20, 42, p. 27069-27081 13 p.

Research output: Contribution to journalArticle

2 Scopus citations

Megahertz serial crystallography

Wiedorn, M. O., Oberthür, D., Bean, R., Schubert, R., Werner, N., Abbey, B., Aepfelbacher, M., Adriano, L., Allahgholi, A., Al-Qudami, N., Andreasson, J., Aplin, S., Awel, S., Ayyer, K., Bajt, S., Barák, I., Bari, S., Bielecki, J., Botha, S., Boukhelef, D. & 106 others, Brehm, W., Brockhauser, S., Cheviakov, I., Coleman, M. A., Cruz-Mazo, F., Danilevski, C., Darmanin, C., Doak, R. B., Domaracky, M., Dörner, K., Du, Y., Fangohr, H., Fleckenstein, H., Frank, M., Fromme, P., Gañán-Calvo, A. M., Gevorkov, Y., Giewekemeyer, K., Ginn, H. M., Graafsma, H., Graceffa, R., Greiffenberg, D., Gumprecht, L., Göttlicher, P., Hajdu, J., Hauf, S., Heymann, M., Holmes, S., Horke, D. A., Hunter, M. S., Imlau, S., Kaukher, A., Kim, Y., Klyuev, A., Knoška, J., Kobe, B., Kuhn, M., Kupitz, C., Küpper, J., Lahey-Rudolph, J. M., Laurus, T., Le Cong, K., Letrun, R., Xavier, P. L., Maia, L., Maia, F. R. N. C., Mariani, V., Messerschmidt, M., Metz, M., Mezza, D., Michelat, T., Mills, G., Monteiro, D. C. F., Morgan, A., Mühlig, K., Munke, A., Münnich, A., Nette, J., Nugent, K. A., Nuguid, T., Orville, A. M., Pandey, S., Pena, G., Villanueva-Perez, P., Poehlsen, J., Previtali, G., Redecke, L., Riekehr, W. M., Rohde, H., Round, A., Safenreiter, T., Sarrou, I., Sato, T., Schmidt, M., Schmitt, B., Schönherr, R., Schulz, J., Sellberg, J. A., Seibert, M. M., Seuring, C., Shelby, M. L., Shoeman, R. L., Sikorski, M., Silenzi, A., Stan, C. A., Shi, X., Stern, S., Sztuk-Dambietz, J., Szuba, J., Tolstikova, A., Trebbin, M., Trunk, U., Vagovic, P., Ve, T., Weinhausen, B., White, T. A., Wrona, K., Xu, C., Yefanov, O., Zatsepin, N., Zhang, J., Perbandt, M., Mancuso, A. P., Betzel, C., Chapman, H. & Barty, A., Dec 1 2018, In : Nature Communications. 9, 1, 4025.

Research output: Contribution to journalArticle

37 Scopus citations

Modeling the nature of grammar and vocabulary trajectories from prekindergarten to third grade

Language Reading Research Consortium (LARRC), Apr 1 2018, In : Journal of Speech, Language, and Hearing Research. 61, 4, p. 910-923 14 p.

Research output: Contribution to journalArticle

1 Scopus citations

Moved by reading in a spanish-speaking, dual language learner population

Adams, A. M., Glenberg, A. & Restrepo, M., Jul 1 2018, In : Language, Speech, and Hearing Services in Schools. 49, 3, p. 582-594 13 p.

Research output: Contribution to journalArticle

1 Scopus citations

Mutations utilize dynamic allostery to confer resistance in TEM-1 β-lactamase

Modi, T. & Ozkan, S., Dec 1 2018, In : International Journal of Molecular Sciences. 19, 12, 3808.

Research output: Contribution to journalArticle

3 Scopus citations