CLAS-NS: Biological Physics, Center for

Research Output 1870 2019

2019
3 Citations (Scopus)

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

Bayes Theorem
Energy Transfer
Photons
Energy transfer
energy transfer

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

jamming
Jamming
Elastic moduli
Triangulation
bulk modulus
3 Citations (Scopus)

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
Molecules
spatial resolution
Sensors
Fluorescence
molecules
6 Citations (Scopus)

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

Self assembly
Nanostructures
DNA
Nucleic acids
Nanotechnology
7 Citations (Scopus)

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

Prostaglandin Receptors
Misoprostol
Dinoprostone
Induced Labor
Myometrium
2 Citations (Scopus)

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

Fullerenes
fullerenes
Permittivity
permittivity
Hydration

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

Prostaglandin Receptors
Misoprostol
Moscow
Russia
Dinoprostone
2 Citations (Scopus)

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

Electron energy loss spectroscopy
Point defects
point defects
energy dissipation
electron energy
1 Citation (Scopus)

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

Chlorides
Pumps
Rhodopsin
X ray lasers
Temperature
1 Citation (Scopus)
Free energy
Thermodynamics
Bandwidth
vibration
Molecules
1 Citation (Scopus)

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

DNA
Molecules
Processing
Deoxyribonucleases
Fluorescence microscopy
1 Citation (Scopus)

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

Phonons
baths
phonons
molecular chains
Energy harvesting
4 Citations (Scopus)

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

heparins
Nanopores
Glycosaminoglycans
solid state
Molecules
2 Citations (Scopus)

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

Crystallography
Diffraction patterns
crystallography
Boidae
Proteins

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

recovery
Electric fields
Recovery
electric fields
Calorimetry
1 Citation (Scopus)

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

Nanostructured materials
Scaffolds
Nanocomposites
Tissue
Stiffness matrix
13 Citations (Scopus)

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

Melatonin Receptors
Lasers
X-Rays
Electrons
Ligands
2018
23 Citations (Scopus)

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

Organoids
Hydrogel
Stem cells
Hydrogels
Stem Cells

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

infotainment
biometry
Biometrics
Automobile instruments
automobile

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 Citation (Scopus)

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

instruction
44 Citations (Scopus)

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

Mechanical properties
Cell adhesion
Rheology
Stretching
Monolayers
1 Citation (Scopus)

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
instructor
video
Students
Physiology
physiology

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

Linguistics
Feedback
Students
6 Citations (Scopus)

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

Thioredoxins
protein
Proteins
proteins
Catalytic Domain
1 Citation (Scopus)

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

Endothelin Receptors
Parkinson Disease
Autophagy
Receptor Aggregation
Aminobutyrates
1 Citation (Scopus)

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

listening comprehension
Short-Term Memory
Reading
school grade
comprehension
15 Citations (Scopus)

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

nuclei
interactions
cut-off
sum rules
Monte Carlo method

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

Streptavidin
Surface plasmon resonance
surface plasmon resonance
biotin
Atomic force microscopy
7 Citations (Scopus)

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

Protein Engineering
Proteins
3 Citations (Scopus)

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
Kerosene
Fatty acids
Paraffins
Purification
Acids
6 Citations (Scopus)

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

Spin polarization
Chirality
cross polarization
chirality
electron spin

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

Disease Susceptibility
Susceptibility
disease resistance
Proteins
Protein
8 Citations (Scopus)

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

Powders
proteins
Proteins
Water
water
3 Citations (Scopus)

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

comprehension
Students
performance
Intelligent systems
instruction

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

comprehension
Students
scenario
Ecosystems
student
1 Citation (Scopus)

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

instruction
4 Citations (Scopus)

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

Hydration
hydration
Permittivity
permittivity
proteins
3 Citations (Scopus)

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

HDL Lipoproteins
Cell Membrane
Observation
CD36 Antigens
Cholesterol
4 Citations (Scopus)
X ray absorption spectroscopy
Cobalt
Ground state
absorption spectroscopy
cobalt
3 Citations (Scopus)

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

polygons
Poisson ratio
Triangulation
Elastic moduli
triangulation
3 Citations (Scopus)

Electrode redox reactions with polarizable molecules

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

Research output: Contribution to journalArticle

Redox reactions
electron transfer
Electrodes
Molecules
electrodes
5 Citations (Scopus)

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

carotenoids
Energy Transfer
Carotenoids
Energy transfer
Electronic structure
13 Citations (Scopus)

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

Enhanced magnetoresistance
Spin polarization
Chirality
Conformations
chirality
28 Citations (Scopus)

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

crystallography
Crystallography
Diptera
X-radiation
X-Rays

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
Crystallography

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

Prostaglandin Receptors
Misoprostol
Moscow
Russia
Dinoprostone

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

Butyrylcholinesterase
Cholinesterases
Hydrolases
Cocaine
9 Citations (Scopus)

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

X-Ray Diffraction
Nanoparticles
Nanocrystals
Granulovirus
Jet Injections
6 Citations (Scopus)
enzymes
electron transfer
Enzymes
Aging of materials
proteins