CLAS-NS: Biological Physics, Center for

Research Output

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

12 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

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., Feb 1 2019, In : Nature Chemical Biology. 15, 2, 1 p.

Research output: Contribution to journalComment/debate

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
2 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

XFEL structures of the human MT 2 melatonin receptor reveal the basis of subtype selectivity

Johansson, L. C., Stauch, B., McCorvy, J. D., Han, G. W., Patel, N., Huang, X. P., Batyuk, A., Gati, C., Slocum, S. T., Li, C., Grandner, J. M., Hao, S., Olsen, R. H. J., Tribo, A. R., Zaare, S., Zhu, L., Zatsepin, N., Weierstall, U., Yous, S., Stevens, R. C. & 4 others, Liu, W., Roth, B. L., Katritch, V. & Cherezov, V., May 9 2019, In : Nature. 569, 7755, p. 289-292 4 p.

Research output: Contribution to journalLetter

22 Scopus citations

X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis

Jensen, S. C., Sullivan, B., Hartzler, D. A., Aguilar, J. M., Awel, S., Bajt, S., Basu, S., Bean, R., Chapman, H. N., Conrad, C., Frank, M., Fromme, R., Martin-Garcia, J. M., Grant, T. D., Heymann, M., Hunter, M. S., Ketawala, G., Kirian, R. A., Knoska, J., Kupitz, C. & 23 others, Li, X., Liang, M., Lisova, S., Mariani, V., Mazalova, V., Messerschmidt, M., Moran, M., Nelson, G., Oberthür, D., Schaffer, A., Sierra, R. G., Vaughn, N., Weierstall, U., Wiedorn, M. O., Xavier, P. L., Yang, J. H., Yefanov, O., Zatsepin, N. A., Aquila, A., Fromme, P., Boutet, S., Seidler, G. T. & Pushkar, Y., Feb 7 2019, In : Journal of Physical Chemistry Letters. 10, 3, p. 441-446 6 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

25 Scopus citations

A biometric usability evaluation of instrument cluster and infotainment systems in two hybrid cars

Kula, I., Atkinson, R., Roscoe, R. & Branaghan, R., Jun 26 2018, 2017 IEEE SmartWorld Ubiquitous Intelligence and Computing, Advanced and Trusted Computed, Scalable Computing and Communications, Cloud and Big Data Computing, Internet of People and Smart City Innovation, SmartWorld/SCALCOM/UIC/ATC/CBDCom/IOP/SCI 2017 - Conference Proceedings. Institute of Electrical and Electronics Engineers Inc., p. 1-6 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Accessibility progress and perspectives

Elliott, S., Kettler, R. J., Beddow, P. A. & Kurz, A., Mar 8 2018, Handbook of Accessible Instruction and Testing Practices: Issues, Innovations, and Applications. Springer International Publishing, p. 263-267 5 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

Accessible instruction and testing today

Kettler, R. J., Elliott, S., Beddow, P. A. & Kurz, A., Mar 8 2018, Handbook of Accessible Instruction and Testing Practices: Issues, Innovations, and Applications. Springer International Publishing, p. 1-16 16 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 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

A multi-Dimensional analysis of writing flexibility in an automated writing evaluation system

Allen, L. K., Likens, A. D. & McNamara, D., Mar 7 2018, Proceedings of the 8th International Conference on Learning Analytics and Knowledge: Towards User-Centred Learning Analytics, LAK 2018. Association for Computing Machinery, p. 380-388 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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., Sep 1 2018, In : Reading and Writing. 31, 7, p. 1449-1477 29 p.

Research output: Contribution to journalArticle

2 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

20 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

1 Scopus citations

Biotechnological and protein-engineering implications of ancestral protein resurrection

Risso, V. A., Sanchez-Ruiz, J. M. & Ozkan, S., Aug 1 2018, In : Current Opinion in Structural Biology. 51, p. 106-115 10 p.

Research output: Contribution to journalReview article

7 Scopus citations

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

8 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

Confronting the known unknown: How the concept of opportunity to learn can advance tier 1 instruction

Kurz, A., Mar 8 2018, Handbook of Accessible Instruction and Testing Practices: Issues, Innovations, and Applications. Springer International Publishing, p. 135-156 22 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations

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

34 Scopus citations

Erratum: Author Correction: Supersaturation-controlled microcrystallization and visualization analysis for serial femtosecond crystallography (Scientific reports (2018) 8 1 (2541))

Lee, D. B., Kim, J. M., Seok, J. H., Lee, J. H., Jo, J. D., Mun, J. Y., Conrad, C., Coe, J., Nelson, G., Hogue, B., White, T. A., Zatsepin, N., Weierstall, U., Barty, A., Chapman, H., Fromme, P., Spence, J., Chung, M. S., Oh, C. H. & Kim, K. H., Apr 17 2018, In : Scientific reports. 8, 1, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Erratum to: Plant-expressed cocaine hydrolase variants of butyrylcholinesterase exhibit altered allosteric effects of cholinesterase activity and increased inhibitor sensitivity (Scientific Reports, (2017), 7, 1, (10419), 10.1038/s41598-017-10571-z)

Larrimore, K. E., Kazan, I. C., Kannan, L., Kendle, R. P., Jamal, T., Barcus, M., Bolia, A., Brimijoin, S., Zhan, C. G., Ozkan, S. & Leket-Mor, T., Dec 1 2018, In : Scientific Reports. 8, 1, 17223.

Research output: Contribution to journalComment/debate

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 2018, In : Journal of Applied Crystallography. 51, 1, p. 133-139 7 p.

Research output: Contribution to journalArticle

10 Scopus citations