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176 results
2022
Ella M. King, Zizhao Wang, DavidA. Weitz, Frans Spaepen, and Michael P. Brenner. 2022. “Correlation Tracking: Using Simulations to Interpolate Highly Correlated Particle Tracks ”. PHYSICAL REVIEW E, 105, 044608
Ella M. King, Zizhao Wang, DavidA. Weitz, Frans Spaepen, and Michael P. Brenner. 2022. “Correlation Tracking: Using Simulations to Interpolate Highly Correlated Particle Tracks ”. PHYSICAL REVIEW E, 105, 044608
Despite significant advances in particle imaging technologies over the past two decades, few advances have been made in particle tracking, i.e., linking individual particle positions across time series data. The state-of-the-art tracking algorithm is...
Chrisy Xiyu Du, Hanyu Alice Zhang, Tanner Pearson, Jakin Ng, Paul McEuen, Itai Cohen, and Michael Brenner. 2022. “Programming Interactions in Magnetic Handshake Materials ”. Soft Matter, 18, 34
Chrisy Xiyu Du, Hanyu Alice Zhang, Tanner Pearson, Jakin Ng, Paul McEuen, Itai Cohen, and Michael Brenner. 2022. “Programming Interactions in Magnetic Handshake Materials ”. Soft Matter, 18, 34
The ability to rapidly manufacture building blocks with specific binding interactions is a key aspect of programmable assembly. Recent developments in DNA nanotechnology and colloidal particle synthesis have significantly advanced our ability to create...
2021
Carl P. Goodrich, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. 2021. “Designing Self-Assembling Kinetics With Differentiable Statistical Physics Models”. Proceedings of the National Academy of Sciences of the United States of America, 118, 10. doi:10.1073/pnas.2024083118
Carl P. Goodrich, Ella M. King, Samuel S. Schoenholz, Ekin D. Cubuk, and Michael P. Brenner. 2021. “Designing Self-Assembling Kinetics With Differentiable Statistical Physics Models”. Proceedings of the National Academy of Sciences of the United States of America, 118, 10. doi:10.1073/pnas.2024083118
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing emergent...
Mor Nitzan and Michael P. Brenner. 2021. “Revealing Lineage-Related Signals in Single-Cell Gene Expression Using Random Matrix Theory”. Proceedings of the National Academy of Sciences of the United States of America, 118, 11. doi:10.1073/pnas.1913931118
Mor Nitzan and Michael P. Brenner. 2021. “Revealing Lineage-Related Signals in Single-Cell Gene Expression Using Random Matrix Theory”. Proceedings of the National Academy of Sciences of the United States of America, 118, 11. doi:10.1073/pnas.1913931118
Gene expression profiles of a cellular population, generated by single-cell RNA sequencing, contains rich information about biological state, including cell type, cell cycle phase, gene regulatory patterns, and location within the tissue of origin. A...
Ofer Kimchi, Rees Garmann, Timothy Chiang, Megan Engel, Michael P. Brenner, and Vinothan N. Manoharan. 2021. “Secondary Structures of Very Large RNAs via High-Throughput Oligonucleotide-Binding Microarrays”. Biophysical Journal, 120, 3, 1, Pp. 316A
Ofer Kimchi, Rees Garmann, Timothy Chiang, Megan Engel, Michael P. Brenner, and Vinothan N. Manoharan. 2021. “Secondary Structures of Very Large RNAs via High-Throughput Oligonucleotide-Binding Microarrays”. Biophysical Journal, 120, 3, 1, Pp. 316A
Krishna Shrinivas and Michael P. Brenner. 2021. “Phase Separation in Fluids With Many Interacting Components ”. Proceedings of the National Academy of Sciences of the United States of America, 118, 45
Krishna Shrinivas and Michael P. Brenner. 2021. “Phase Separation in Fluids With Many Interacting Components ”. Proceedings of the National Academy of Sciences of the United States of America, 118, 45
Fluids in natural systems, like the cytoplasm of a cell, often contain thousands of molecular species that are organized into multiple coexisting phases that enable diverse and specific functions. How interactions between numerous molecular species encode...
Yipei Guo, Mor Nitzan, and Michael Brenner. 2021. “Programming Cell Growth into Different Cluster Shapes Using Diffusible Signals ”. PLoS Computational Biology, 17, 11
Yipei Guo, Mor Nitzan, and Michael Brenner. 2021. “Programming Cell Growth into Different Cluster Shapes Using Diffusible Signals ”. PLoS Computational Biology, 17, 11
Advances in genetic engineering technologies have allowed the construction of artificial genetic circuits, which have been used to generate spatial patterns of differential gene expression. However, the question of how cells can be programmed, and how...
2020
Alma Dal Co and Michael P. Brenner. 2020. “Tracing Cell Trajectories in a Biofilm”. Science, 369, 6499, Pp. 30-31. doi:10.1126/science.abd1225
Alma Dal Co and Michael P. Brenner. 2020. “Tracing Cell Trajectories in a Biofilm”. Science, 369, 6499, Pp. 30-31. doi:10.1126/science.abd1225
Ryan McKeown, Rodolfo Ostilla-Monico, Alain Pumir, Michael P. Brenner, and Shmuel M. Rubinstein. 2020. “Turbulence Generation through an Iterative Cascade of the Elliptical Instability”. Science Advances, 6, 9. doi:10.1126/sciadv.aaz2717
Ryan McKeown, Rodolfo Ostilla-Monico, Alain Pumir, Michael P. Brenner, and Shmuel M. Rubinstein. 2020. “Turbulence Generation through an Iterative Cascade of the Elliptical Instability”. Science Advances, 6, 9. doi:10.1126/sciadv.aaz2717
The essence of turbulent flow is the conveyance of energy through the formation, interaction, and destruction of eddies over a wide range of spatial scales-from the largest scales where energy is injected down to the smallest scales where it is dissipated...
Ofer Kimchi, Carl P. Goodrich, Alexis Courbet, Agnese Curatolo I, Nicholas B. Woodall, David Baker, and Michael P. Brenner. 2020. “Self-Assembly-Based Posttranslational Protein Oscillators”. Science Advances, 6, 51. doi:10.1126/sciadv.abc1939
Ofer Kimchi, Carl P. Goodrich, Alexis Courbet, Agnese Curatolo I, Nicholas B. Woodall, David Baker, and Michael P. Brenner. 2020. “Self-Assembly-Based Posttranslational Protein Oscillators”. Science Advances, 6, 51. doi:10.1126/sciadv.abc1939
Recent advances in synthetic posttranslational protein circuits are substantially impacting the landscape of cellular engineering and offer several advantages compared to traditional gene circuits. However, engineering dynamic phenomena such as...
2019
Martin J. Falk, Amy Duwel, Lucy J. Colwell, and Michael P. Brenner. 2019. “Collagen-Inspired Self-Assembly of Twisted Filaments”. Physical Review Letters, 123, 23. doi:10.1103/PhysRevLett.123.238102
Martin J. Falk, Amy Duwel, Lucy J. Colwell, and Michael P. Brenner. 2019. “Collagen-Inspired Self-Assembly of Twisted Filaments”. Physical Review Letters, 123, 23. doi:10.1103/PhysRevLett.123.238102
Collagen consists of three peptides twisted together through a periodic array of hydrogen bonds. Here we use this as inspiration to find design rules for programmed specific interactions for self-assembling synthetic collagen like triple helices, starting...
Ran Niu, Chrisy Xiyu Du, Edward Esposito, Jakin Ng, Michael P. Brenner, Paul L. McEuen, and Itai Cohen. 2019. “Magnetic Handshake Materials As a Scale-Invariant Platform for Programmed Self-Assembly”. Proceedings of the National Academy of Sciences of the United States of America, 116, 49, Pp. 24402-7. doi:10.1073/pnas.1910332116
Ran Niu, Chrisy Xiyu Du, Edward Esposito, Jakin Ng, Michael P. Brenner, Paul L. McEuen, and Itai Cohen. 2019. “Magnetic Handshake Materials As a Scale-Invariant Platform for Programmed Self-Assembly”. Proceedings of the National Academy of Sciences of the United States of America, 116, 49, Pp. 24402-7. doi:10.1073/pnas.1910332116
Programmable self-assembly of smart, digital, and structurally complex materials from simple components at size scales from the macro to the nano remains a long-standing goal of material science. Here, we introduce a platform based on magnetic encoding of...