Structure and inhibition of SARS-CoV-2 spike refolding in membranes

M. W. Grunst, Z. Qin, E. Dodero-Rojas, S. Ding, J. Prévost, Y. Chen, Y. Hu, M. Pazgier, S. Wu, X. Xie, A. Finzi, J. N. Onuchic, P. C. Whitford, W. Mothes, W. Li. Science, 2024, 385, 757-765.

Press Releases: National Science Foundation, Rice University, Yale University

Reconstruction of single-cell lineage trajectories and identification of diversity in fates during the epithelial-to-mesenchymal transition

Y.C. Cheng, Y. Zhang, S. Tripathi, B. V. Harshavardhan, M. K. Jolly, G. Schiebinger, H. Levine, T. O. McDonald, F. Michor. Proceedings of the National Academy of Sciences USA, 2024, 121, e2406842121.

Cell Division and Motility Enable Hexatic Order in Biological Tissues

Y. Tang, S. Chen, M. J. Bowick, D. Bi. Physical Review Letters, 2024, 132, 218402.

Three-dimensional genome architecture persists in a 52,000-year-old wooly mammoth skin sample

M. Sandoval-Velasco et al. Cell, 2024, 187, P3541-3562.E51.

New York Times coverage

Machine learning meets physics: A two-way street

H. Levine, Y. Tu. Proceedings of the National Academy of Sciences USA, 2024, 121, e2403580121.

HIV-1 uncoating requires long double-stranded reverse transcription products

R. C. Burdick, M. Morse, I. Rouzina, M. C. Williams, W.-S. Hu, V. K. Pathak. Science Advances, 2024, 10, eadn7033.

News story

Network physics of attractive colloidal gels: Resilience, rigidity, and phase diagram

M. Nabizadeh, F. Nasirian, X. Li, Y. Saraswat, R. Waheibi, L. C. Hsiao, D. Bi, B. Ravandi, S. Jamali. Proceedings of the National Academic of Sciences USA, 2024, 121, e2316394121.

RACER-m leverages structural features for sparse T cell specificity prediction

A. Wang, X. Lin, K. N. Chau, J. N. Onuchic, H. Levine, J. T. George. Science Advances, 2024, 10, eadl0161.

Experimentally probing the effect of confinement geometry on lipid diffusion

N. Voce, P. Stevenson. Journal of Physical Chemistry B, 2024, 128, 4404-4413.

C-terminal domain of T4 gene 32 protein enabled rapid filament reorganization and dissociation

B. A. Cashen, M. Morse, I. Rouzina, R. L. Karpel, M. C. Williams. Journal of Molecular Biology, 2024, 436, 168544.

A shape-driven reentrant jamming transition in confluent monolayers of synthetic cell-mimics

P. Arora, S. Sadhukhan, S. K. Nandi, D. Bi, A. K. Sood, R. Ganapathy. Nature Communications, 2024, 15, 5645.

Spatial confinement affects the heterogeneity and interactions between shoaling fish

G. Kuntz, J. Huang, M. Rask, A. Lindgren-Ruby, J. Y. Shinsato, D. Bi, A. P. Tabatabai. Scientific Reports, 2024, 14, 12296.

Cationic residues of the HIV-1 nucleocapsid protein enable DNA condensation to maintain viral core particle stability during reverse transcription

H. Gien, M. Morse, M. J. McCauley, I. Rouzina, R. J. Gorelick, M. C. Williams. Viruses, 2024, 16, 872.

Nucleosomes play a dual role in regulating transcription dynamics

S. Brahmachari, S. Tripathi, J. N. Onuchic, H. Levine. Proceedings of the National Academic of Sciences USA, 2024, 121, e2319772121.

Selective temperature sensing in nanodiamonds using dressed states

N. M. Beaver, P. Stevenson. Advanced Quantum Technologies, 2024, DOI: 10.1002/qute.202400271.

Vibrational coherence and tunneling in proteins

A. Benabbas, P. M. Champion. Chapter 14 in Ultrafast electronic and structural dynamics, 2024.

Effect of non-linear strain stiffening in eDAH and unjamming

X. Xie, F. Sauer, S. Grosser, J. Lippoldt, E. Warmt, A. Das, D. Bi, T. Fuhs, J. Kas. Soft Matter, 2024, 20, 1996-2007.

Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk

V. Singh, Y. Itoh, S. Del’Olio, A. Hassan, A. Naschberger, R. K. Flygaard, Y. Nobe, K. Izumikawa, S. Aibara, J. Andrell, P. C. Whitford, A. Barrientos, M. Taoka, A. Amunts. Nature Communications, 2024, 15, 4272.

Ephaptic coupling as a resolution to the paradox of action potential wave speed and discordant alternans spatial scales in the heart

N. F. Otani, E. Figueroa, J. Garrison, M. Hewson, L. Munoz, F. H. Fenton, A. Karma, S. H. Weinberg. Phys. Rev. Lett., 2023, 130, 218401.

Sampling the proteome by emerging single-molecule and mass spectrometry methods

M. J. MacCoss, J. A. Alfaro, D. A. Faivre, C. C. Wu, M. Wanunu, N. Slavov. Nature Methods, 2023, 20, 339-346.

Multi-objective optimization of custom compound prism arrays for multiplexed optical imaging

L. Price, J. Tatz, J. Sutin J, B.Q. Spring BQ. Optics Express 2023, 31, 9739–9749.

Dynamic structure of T4 gene 32 protein filaments facilitates rapid noncooperative protein dissociation

B. A. Cashen, M. Morse, I. Rouzina, R. L. Karpel, M. C. Williams. Nucleic Acids Research., 2023, 51, 8587-8605.

Chromatin alternates between A and B compartments at kilobase scale for sub-genic organization 

H.L. Harris., H. Gu, A. Wang, … ,M. Di Pierro,…, et al  Nature Communications 2023, 14, 3303. 

Functional imaging and quantification of multineuronal olfactory responses in C. elegans

A. Lin, S. Qin, H. Casademunt, M. Wu, W. Hung, G. Cain, N. Z. Tan, R. Valenzuela, L. Lesanpezeshki, V. Venkatachalam, C. Pehlevan, M. Zhen, A. D. T. Samuel. Science Advances, 2023, 9, DOI: 10.1126/sciadv.ade1249

Semi-quantitative detection of pseudouridine modifications and type I/II hypermodifications in human mRNAs using direct long-read sequencing

S. Tavakoli, M. Nabizadeh, A. Makhamreh, H. Gamper, C. A. McCormick, N. K. Rezapour, Y.-M. Jou, M. Wanunu, S. H. Rouhanifard. Nature Communications, 2023, 14, 334.

Bridging the Gap Between Collective Motility and Epithelial-Mesenchymal Transitions through the Active Finite Voronoi Model

J. Huang, H. Levine, D. Bi. Soft Matter, 2023.

An Associative Memory Hamiltonian Model for DNA and Nucleosomes 

W. Lu, J.N. Onuchic, M. Di Pierro. PLOS Computational Biology 2023, 19, e1011013. 

A Marcus-type inverted region in the translocation kinetics of a knotted protein

P. Tripathi, B. Mehrafrooz, A. Aksimentiev, S. E. Jackson, M. Gruebele, M. Wanunu. J. Phys. Chem. Lett. 2023, 14, 10719-10726.

Nature-inspired designs for disordered acoustic bandgap materials

Z. Li, D. Bi. Soft Matter, 2023.

Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues 

V.G. Contessoto, O. Dudchenko, E.L. Aiden, P.G. Wolynes, J.N. Onuchic, M. Di Pierro Nature Communications 2023, 14, 326. 

Structural domains of SARS-CoV-2 nucleocapsid protein coordinate to compact long nucleic acid substrates

M. Morse, J. Sefcikova, I. Rouzina, P. J. Beuning, M. C. Williams. Nucleic Acids Research, 2023, 51, 290-303.

Unidirectional single-file transport of full-length proteins through a nanopore

L. Yu, X. Kang, F. Li, B. Mehrafrooz, A. Makhamreh, A. Fallahi, J. C. Foster, A. Aksimentiev, M. Chen, M. Wanunu. Nature Biotechnology, 2023, 41, 1130-1139.

Ratchet, swivel, tilt and roll: A complete description of subunit rotation in the ribosome

A. Hassan, S. Byju, F. C. Campos, C. Roc, N. Pender, K. Nguyen, E. M. Kimbrough, J. M. Mattingly, R. L. Gonzalez Jr, R. J. Oliveira, C. M. Dunham, P. C. Whitford. Nucleic Acids Research, 2023, 51, 919-934.

Minimal frustration underlies the usefulness of incomplete regulatory network models in biology

S. Tripathi, D. A. Kessler, H. Levine. Proc. Natl. Acad. Sci. USA, 2022, 120, e2216109120.

Diffuse ions coordinate dynamics in a ribonucleoprotein assembly

A. Wang, M. Levi, U. Mohanty, P. C. Whitford. J. Amer. Chem. Soc. 2022, 144, 9510-9522.

This study reported a new theoretical model for the treatment of ionic interactions with biopolymers.

Shaping the genome via lengthwise compaction, phase separation, and lamina adhesion 

S. Brahmachari, V.G. Contessoto, M. Di Pierro, J.N. Onuchic. Nucleic Acids Research, 2022, 50, 4258-42714.

Epigenetic factor competition reshapes the EMT landscape

M. A. Al-Radhawi, S. Tripathi, Y. Zhang, H. Levine. Proc. Natl. Acad. Sci. USA 2022, 119, e2210844119

An open-source LED array illumination system for automated multiwell plate cell culture photodynamic therapy experiments

K. Zhang, S. Timilsina, M. Waguespack M, E.M. Kercher, B.Q. Spring. Scientific Reports 2022, 12 19341.

Human FACT subunits coordinate to catalyze both disassembly and reassembly of nucleosomes

M. J. McCauley, M. Morse, N. Becker, …, J. Maher III, M. C. Williams. Cell Reports, 2022, 41, 111858.

The L1-ORF1p coiled coil enables formation of a tightly compacted nucleic acid-bound complex that is associated with retrotransposition

B. A. Cashen, M. N. Naufer, M. Morse, C. E. Jones, M. C. Williams, A. V. Furano. Nucleic Acids Research, 2022, 50, 8690-8699.

Collective curvature sensing and fluidity in three-dimensional multicellular systems

W. Tang, A. Das, A. F. Pegoraro, Y. L. Han, J. Huang, D. A. Roberts, H. Yang, J. F. Fredberg, D. N. Kotton, D. Bi, M. Guo. Nature Physics, 2022, 18, 1371-1378.

Imaging whole-brain activity to understand behavior

A. Lin, D. Witvliet, L. Hernandez-Nunez, S. W. Linderman, A. D. T. Samuel, V. Venkatachalam. Nature Reviews Physics, 2022, 4, 292-305.

Spatiotemporal organization of electromechanical phase singularities during high-frequency cardiac arrhythmias

A. M. Tabrizi, A. Mesgarnejad, M. Bazzi, S. Luther, J. Christoph, A. Karma. Phys. Rev. X, 2022, 12, 021052.

Denoising multiplexed microscopy images in n-dimensional spectral space

R. C. Harman, R. T. Lang, E. M. Kercher, P. Leven, B. Q. Spring. Biomed. Opt. Exp. 2022, 13, 4298-4309.

3D genomics across the tree of life reveals condensin II as a determinant of architecture type

C. Hoencamp, … M. Di Pierro, E. L. Aiden, B. D. Rowland. Science, 2021, 372, 984-989.

NeuroPAL: A multicolor atlas for whole-brain neuronal identification in C. elegans

E. Yemeni, A. Lin, A. Nejatbakhsh, E. Varol, R. Sun, G. E. Mena, A. D. T. Samuel, L. Paninski, V. Venkatachalam, O. Hobert. Cell, 2021, 184, 272-288.e11

Natural sensory context drives diverse brain-wide activity during C. elegans mating

V. Susoy, W. Hung, D. Witvliet, J. E. Whitener, M. Wu, C. F. Park, B. J. Graham, M. Zhen, V. Venkatachalam, A. D. T. Samuel. Cell, 2021, 184, 5122-5137.

HIV-1 nucleocapsid protein binds double-stranded DNA in multiple modes to regulate compaction and capsid uncoating

H. Gien, M. Morse, M. J. McCauley, …, M. C. Williams. Viruses, 2021, 14, 235.

Sterically-confined rearrangements of SARS-CoV-2 spike protein control cell invasion

E. Dodero-Rojas, J. N. Onuchic, P. C. Whitford. eLife 2021, DOI: 10.7554/eLife.70362

This theoretical study provided the first description of how the SARS-CoV-2 virus is able to fuse with a host cell.
eLife Press Release
Rice U press Release

Noise in neurons and synapses enable reliable associative memory storage in local cortical circuits

C. Zhang, D. Zhang, A. Stepanyants. eNeuro 2021, 8, ENEURO.0302-20.2020

Two-photon peak molecular brightness spectra reveal long-wavelenth enhancements of multiplexed imaging depth and photostability

R. T. Lang, B. Q. Spring. Biomed. Opt. Exp. 2021, 12, 5909-5919.

A steric gate controls P/E hybrid formation of tRNA on the ribosome

M. Levi, K. Walak, A. Wang, U. Mohanty, P. C. Whitford. Nature Comm. 2020, 11, 5706.

Using simulations to apply a perturbation strategy, this showed how a small set of atoms is able to control the dynamics of a large-scale molecular machine.

Custom fabrication and mode-locked operation of a femtosecond fiber laser for multiphoton microscopy

N. Davoudzadeh, G. Docourthial, B. Q. Spring. Scientific Reports 2019, 9, 4233.

Robust associative learning is sufficient to explain the structural and dynamical properties of local cortical circuits

D. Zhang, C. Zhang, A. Stepanyants. JNeurosci 2019, 39, 6888-6904.

Artificial neural network filters for enhancing 3D optical microscopy images of neuritis

S.-L. Wang, S. M. M. Kahaki, A. Stepanyants. SPIE Medical Imaging, 2019, 10949, 109490G.

Accurate registration of in vivo time-lapse images

S. M. M. Kahaki, S.-L. Wang, A. Stepanyants. SPIE Medical Imaging, 2019, 10949, 109491D.

The Ca²⁺ transient as a feedback sensor controlling cardiomyocyte ionic conductances in mouse populations.

C. M. Rees, J.-H. Yang, M. Santolini, A. J. Lusis, J. N. Weiss, A. Karma. eLife, 2018, DOI: 10.7554/eLife.36717

Computer-assisted detection of axonal bouton structural plasticity in in vivo time-lapse images

R. Gala, D. Lebrecht, D. A. Sahlender, A. Jorstad, G. Knott, A. Holtmaat, A. Stepanyants. eLife, 2017, DOI: 10.7554/eLife.29315.