Publications - Revision history

Doye at 15:38, 16 April 2025

2025-04-16T15:38:20Z

← Older revision		Revision as of 15:38, 16 April 2025
Line 552:		Line 552:
	#: DNA origami 2.0 ([https://doi.org/10.1101/2022.12.29.522100 bioRxiv])		#: DNA origami 2.0 ([https://doi.org/10.1101/2022.12.29.522100 bioRxiv])
	# J.M. Weck and A. Heuer-Jungemann, ''Nat. Commun.'' '''16''', 1556 (2025)		# J.M. Weck and A. Heuer-Jungemann, ''Nat. Commun.'' '''16''', 1556 (2025)
	#: Fully addressable, designer superstructures assembled from a single modular DNA origami ([https://doi.org/10.1101/2023.09.14.557688 bioRxiv])		#: [https://doi.org/10.1038/s41467-025-56846-2 Fully addressable, designer superstructures assembled from a single modular DNA origami] ([https://doi.org/10.1101/2023.09.14.557688 bioRxiv])
	# Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li, S. Wang, H. Yan, P. Sulc, N. Stephanopoulos, submitted		# Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li, S. Wang, H. Yan, P. Sulc, N. Stephanopoulos, submitted
	#: High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody ([https://doi.org/10.1101/2023.09.18.558353 bioRxiv])		#: High-affinity binding to the SARS-CoV-2 spike trimer by a nanostructured, trivalent protein-DNA synthetic antibody ([https://doi.org/10.1101/2023.09.18.558353 bioRxiv])

Doye at 15:37, 16 April 2025

2025-04-16T15:37:39Z

← Older revision		Revision as of 15:37, 16 April 2025
Line 551:		Line 551:
	# N.P. Agarwal and A. Gopinath, submited		# N.P. Agarwal and A. Gopinath, submited
	#: DNA origami 2.0 ([https://doi.org/10.1101/2022.12.29.522100 bioRxiv])		#: DNA origami 2.0 ([https://doi.org/10.1101/2022.12.29.522100 bioRxiv])
	# J.M. Weck and A. Heuer-Jungemann, ~~submitted~~		# J.M. Weck and A. Heuer-Jungemann, ''Nat. Commun.'' '''16''', 1556 (2025)
	#: Fully addressable, designer superstructures assembled from a single modular DNA origami ([https://doi.org/10.1101/2023.09.14.557688 bioRxiv])		#: Fully addressable, designer superstructures assembled from a single modular DNA origami ([https://doi.org/10.1101/2023.09.14.557688 bioRxiv])
	# Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li, S. Wang, H. Yan, P. Sulc, N. Stephanopoulos, submitted		# Y. Xu, R. Zheng, A. Prasad, M. Liu, Z. Wan, X. Zhou, R.M. Porter, M. Sample, E. Poppleton, J. Procyk, H. Liu, Y. Li, S. Wang, H. Yan, P. Sulc, N. Stephanopoulos, submitted

Doye at 15:34, 16 April 2025

2025-04-16T15:34:58Z

← Older revision		Revision as of 15:34, 16 April 2025
Line 616:		Line 616:
	#: [https://doi.org/10.1017/qrd.2024.26 Unzipping of knotted DNA via nanopore translocation] ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])		#: [https://doi.org/10.1017/qrd.2024.26 Unzipping of knotted DNA via nanopore translocation] ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])
	# G. Mattiotti, M. Micheloni, L. Petrolli, L. Rovigatti, L. Tubiana, S. Pasquali, R. Potestio, ''Macromol. Rapid Commun.'' '''45''', 2400639 (2024).		# G. Mattiotti, M. Micheloni, L. Petrolli, L. Rovigatti, L. Tubiana, S. Pasquali, R. Potestio, ''Macromol. Rapid Commun.'' '''45''', 2400639 (2024).
	#: [https://doi.org/10.1002/marc.202400639 Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])		#: [https://doi.org/10.1002/marc.202400639 Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model] ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])
	# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, ''Discover Nano'' '''20''', 13 (2025)		# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, ''Discover Nano'' '''20''', 13 (2025)
	#: [https://doi.org/10.1186/s11671-025-04188-9 How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])		#: [https://doi.org/10.1186/s11671-025-04188-9 How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])
Line 632:		Line 632:
	#: Economical and versatile subunit design principles for self-assembled DNA origami structures ([https://doi.org/10.48550/arXiv.2411.09801 arXiv])		#: Economical and versatile subunit design principles for self-assembled DNA origami structures ([https://doi.org/10.48550/arXiv.2411.09801 arXiv])
	# C. LaRock, P. Sorensen, D. Blair, D. Murphy, J. O’Connor, S. Armentrout, submitted		# C. LaRock, P. Sorensen, D. Blair, D. Murphy, J. O’Connor, S. Armentrout, submitted
	#: inSēquio: A Programmable 3D CAD Application for Designing DNA Nanostructures ([https://doi.org/10.1101/2024.03.27.586810 bioRxiv]		#: inSēquio: A Programmable 3D CAD Application for Designing DNA Nanostructures ([https://doi.org/10.1101/2024.03.27.586810 bioRxiv])


	We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].		We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].

Doye at 15:34, 16 April 2025

2025-04-16T15:34:32Z

← Older revision		Revision as of 15:34, 16 April 2025
Line 615:		Line 615:
	# A. Suma and C. Micheletti, ''QRB Discovery'' '''6''', e4 (2025)		# A. Suma and C. Micheletti, ''QRB Discovery'' '''6''', e4 (2025)
	#: [https://doi.org/10.1017/qrd.2024.26 Unzipping of knotted DNA via nanopore translocation] ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])		#: [https://doi.org/10.1017/qrd.2024.26 Unzipping of knotted DNA via nanopore translocation] ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])
	# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, ~~submitted~~.		# G. Mattiotti, M. Micheloni, L. Petrolli, L. Rovigatti, L. Tubiana, S. Pasquali, R. Potestio, ''Macromol. Rapid Commun.'' '''45''', 2400639 (2024).
	#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])		#: [https://doi.org/10.1002/marc.202400639 Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])
	# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, ''Discover Nano'' '''20''', 13 (2025)		# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, ''Discover Nano'' '''20''', 13 (2025)
	#: [https://doi.org/10.1186/s11671-025-04188-9 How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])		#: [https://doi.org/10.1186/s11671-025-04188-9 How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])

Doye at 15:31, 16 April 2025

2025-04-16T15:31:54Z

← Older revision		Revision as of 15:31, 16 April 2025
Line 559:		Line 559:
	# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, ''Nat. Nanotechnol.'' '''20''', 303–310 (2025) (2024)		# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, ''Nat. Nanotechnol.'' '''20''', 303–310 (2025) (2024)
	#: [https://doi.org/10.1038/s41565-024-01804-0 Engineering modular and tunable single-molecule sensors by decoupling sensing from signal output] ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv])		#: [https://doi.org/10.1038/s41565-024-01804-0 Engineering modular and tunable single-molecule sensors by decoupling sensing from signal output] ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv])
	~~# F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted~~
	~~#: nNxB: a new coarse-grained model for RNA and DNA nanotechnology ([https://doi.org/10.48550/arXiv.2311.03317 arXiv])~~
	# E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, ''J. Chem. Phys.'' '''160''', 115101 (2024)		# E.J. Ratajczyk, P. Šulc, A.J. Turberfield, J.P.K. Doye and A.A. Louis, ''J. Chem. Phys.'' '''160''', 115101 (2024)
	#: [https://doi.org/10.1063/5.0199558 Coarse-grained modelling of DNA-RNA hybrids] ([https://doi.org/10.48550/arXiv.2311.07709 arXiv])		#: [https://doi.org/10.1063/5.0199558 Coarse-grained modelling of DNA-RNA hybrids] ([https://doi.org/10.48550/arXiv.2311.07709 arXiv])

Doye at 15:28, 16 April 2025

2025-04-16T15:28:22Z

← Older revision		Revision as of 15:28, 16 April 2025
Line 619:		Line 619:
	# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.		# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.
	#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])		#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])
	# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, ~~submitted.~~		# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, ''Discover Nano'' '''20''', 13 (2025)
	#: How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])		#: [https://doi.org/10.1186/s11671-025-04188-9 How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])
	# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, ''Discover Nano'' '''20''', 13 (2025)		# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, ''Discover Nano'' '''20''', 13 (2025)
	#: [https://doi.org/10.1186/s11671-025-04188-9 Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])		#: [https://doi.org/10.1186/s11671-025-04188-9 Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
			# M.O. Ogieva, W.G. Pfeifer and S. Sensale, ''Sci Rep'' '''15''', 9450 (2025)
			#: [https://doi.org/10.1038/s41598-025-93269-x Enhancing the speed of DNA walkers through soft confinement]
			# Y. Ochi, W. Kato, Y. Tsutsui, Y. Gomibuchi, D. Tominaga, K. Sakai, T. Araki, S. Yoshitake, T. Yasunaga, Y.V. Morimoto, K. Maeda, J. Taira, Y. Sato, ChemBioChem, accepted (2025)
			#: [https://doi.org/10.1002/cbic.202401071 Wireframe DNA Origami Capable of Vertex-protruding Transformation]
	# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)		# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
	#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv])		#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv])
Line 629:		Line 633:
	# W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted		# W.-S. Wei, T.E. Videbæk, D. Hayakawa, R. Saha, W.B. Rogers, S. Fraden, submitted
	#: Economical and versatile subunit design principles for self-assembled DNA origami structures ([https://doi.org/10.48550/arXiv.2411.09801 arXiv])		#: Economical and versatile subunit design principles for self-assembled DNA origami structures ([https://doi.org/10.48550/arXiv.2411.09801 arXiv])
			# C. LaRock, P. Sorensen, D. Blair, D. Murphy, J. O’Connor, S. Armentrout, submitted
			#: inSēquio: A Programmable 3D CAD Application for Designing DNA Nanostructures ([https://doi.org/10.1101/2024.03.27.586810 bioRxiv]


	We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].		We are also maintaining a list of all published papers using oxDNA at [https://publons.com/researcher/3051012/oxdna-oxrna/ publons].

Doye at 15:24, 16 April 2025

2025-04-16T15:24:17Z

← Older revision		Revision as of 15:24, 16 April 2025
Line 621:		Line 621:
	# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.		# S. Haggenmueller, M. Matthies, M. Sample and P. Šulc, submitted.
	#: How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])		#: How we simulate DNA origami ([https://doi.org/10.48550/arXiv.2409.13206 arXiv])
	# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, ~~submitted~~		# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, ''Discover Nano'' '''20''', 13 (2025)
	#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])		#: [https://doi.org/10.1186/s11671-025-04188-9 Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
	# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)		# R.K. Krueger, M.C. Engel, R. Hausen, M.P. Brenner, submitted (2024)
	#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv])		#: A Differentiable Model of Nucleic Acid Dynamics ([https://arxiv.org/abs/2411.09216 arXiv])
	~~# Y. Guo, T. Xiong, H. Yan and R.X. Zhang, submitted~~
	#: Correlation of precisely fabricated geometric characteristics of DNA-origami nanostructures with their cellular entry in human lens epithelial cells ([https://doi.org/10.21203/rs.3.rs-4897446/v1 ResearchSquare])
	# K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.		# K. Zhou, M. Chung, J. Cheng, J.T. Powell, J. Liu, Y. Xiong, M.A. Schwartz and C. Lin, submitted.
	#: DNA nanodevice for analysis of force-activated protein extension and interactions ([https://doi.org/10.1101/2024.10.25.620262 bioRxiv])		#: DNA nanodevice for analysis of force-activated protein extension and interactions ([https://doi.org/10.1101/2024.10.25.620262 bioRxiv])

Doye at 15:21, 16 April 2025

2025-04-16T15:21:37Z

Doye at 15:01, 16 April 2025

2025-04-16T15:01:24Z

Doye at 14:55, 16 April 2025

2025-04-16T14:55:52Z

← Older revision		Revision as of 14:55, 16 April 2025
Line 591:		Line 591:
	# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted		# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, submitted
	#: DNA nanostar structures with tunable auxetic properties ([https://doi.org/10.1101/2023.12.22.573109 bioRxiv])		#: DNA nanostar structures with tunable auxetic properties ([https://doi.org/10.1101/2023.12.22.573109 bioRxiv])
	# G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro, ''Sci. Adv.'' 10, ~~???~~ (2024)		# G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro, ''Sci. Adv.'' 10, eadn9423 (2024)
	#: [https://doi.org/10.1126/sciadv.~~adn94~~ Piggybacking functionalized DNA nanostructures into live cell nuclei] ([https://doi.org/10.1101/2023.12.30.573746 bioRxiv])		#: [https://doi.org/10.1126/sciadv.adn9423 Piggybacking functionalized DNA nanostructures into live cell nuclei] ([https://doi.org/10.1101/2023.12.30.573746 bioRxiv])
	# A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, ''Nat. Commun.'' '''15''', 7564 (2024)		# A. Walbrun, T. Wang, M. Matthies, P. Šulc, F.C. Simmel, M. Rief, ''Nat. Commun.'' '''15''', 7564 (2024)
	#: [https://doi.org/10.1038/s41467-024-51813-9 Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement] ([https://doi.org/10.1101/2024.01.16.575816 bioRxiv])		#: [https://doi.org/10.1038/s41467-024-51813-9 Single-Molecule Force Spectroscopy of Toehold-Mediated Strand Displacement] ([https://doi.org/10.1101/2024.01.16.575816 bioRxiv])

← Older revision		Revision as of 15:21, 16 April 2025
Line 589:		Line 589:
	# G. Nava, T. Carzaniga, L. Casiraghi, E. Bot, G. Zanchetta, F. Damin, M. Chiari, G. Weber, T. Bellini, L. Mollica and M. Buscaglia, ''Nucl. Acids Res.'' '''52''', 8661–8674 (2024)		# G. Nava, T. Carzaniga, L. Casiraghi, E. Bot, G. Zanchetta, F. Damin, M. Chiari, G. Weber, T. Bellini, L. Mollica and M. Buscaglia, ''Nucl. Acids Res.'' '''52''', 8661–8674 (2024)
	#: [https://doi.org/10.1093/nar/gkae576 Weak-cooperative binding of a long single-stranded DNA chain on a surface]		#: [https://doi.org/10.1093/nar/gkae576 Weak-cooperative binding of a long single-stranded DNA chain on a surface]
	# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, ~~submitted~~		# Y. Du, R. Li, A.S. Madhvacharyula, A.A. Swett, J.H. Choi, ''Mol. Syst. Des. Eng.'' '''9''', 765-774 (2024)
	#: DNA nanostar structures with tunable auxetic properties ([https://doi.org/10.1101/2023.12.22.573109 bioRxiv])		#: [https://doi.org/10.1039/D3ME00202K DNA nanostar structures with tunable auxetic properties] ([https://doi.org/10.1101/2023.12.22.573109 bioRxiv])
	# G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro, ''Sci. Adv.'' 10, eadn9423 (2024)		# G.M. Roozbahani, P. Colosi, A. Oravecz, E.M. Sorokina, W. Pfeifer, S. Shokri, Y. Wei, P. Didier, M. DeLuca, G. Arya, L. Tora, M. Lakadamyali, M.G. Poirier, C. E. Castro, ''Sci. Adv.'' 10, eadn9423 (2024)
	#: [https://doi.org/10.1126/sciadv.adn9423 Piggybacking functionalized DNA nanostructures into live cell nuclei] ([https://doi.org/10.1101/2023.12.30.573746 bioRxiv])		#: [https://doi.org/10.1126/sciadv.adn9423 Piggybacking functionalized DNA nanostructures into live cell nuclei] ([https://doi.org/10.1101/2023.12.30.573746 bioRxiv])
Line 605:		Line 605:
	# C. Karfusehr, M. Eder, F.C. Simmel		# C. Karfusehr, M. Eder, F.C. Simmel
	#: Self-assembled cell-scale containers made from DNA origami membranes ([https://doi.org/10.1101/2024.02.09.579479 bioRxiv])		#: Self-assembled cell-scale containers made from DNA origami membranes ([https://doi.org/10.1101/2024.02.09.579479 bioRxiv])
	# M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, ~~submitted~~		# M.T. Luu, J.F. Berengut, J.K.D. Singh, K.C.D. Glieze, M. Turner, K. Skipper, S. Meppat, H. Fowler, W. Close, J.P.K. Doye, A. Abbas, S.F.J. Wickham, ''Sci. Robot.'' '''9''', eadp2309 (2024)
	#: Reconfigurable ~~multi-component nanostructures built~~ from DNA origami voxels ([https://doi.org/10.1101/2024.03.10.584331 bioRxiv])		#: [https://doi.org/10.1126/scirobotics.adp2309 Reconfigurable nanomaterials folded from multicomponent chains of DNA origami voxels] ([https://doi.org/10.1101/2024.03.10.584331 bioRxiv])
	# M.P. Tran, T. Chakraborty, E. Poppleton, L. Monari, F. Giessler and K. Göpfrich, ~~submitted~~		# M.P. Tran, T. Chakraborty, E. Poppleton, L. Monari, F. Giessler and K. Göpfrich, ''Nat. Nanotechnol.'' accepted (2025)
	#: Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells ([https://doi.org/10.1101/2024.06.12.598448 bioRxiv])		#: [https://doi.org/10.1038/s41565-025-01879-3 Genetic encoding and expression of RNA origami cytoskeletons in synthetic cells] ([https://doi.org/10.1101/2024.06.12.598448 bioRxiv])
	# V. Bukina and A. Božič, ''Biophys. J.'' '''123''', 3397-3407 (2024)		# V. Bukina and A. Božič, ''Biophys. J.'' '''123''', 3397-3407 (2024)
	#: [https://doi.org/10.1016/j.bpj.2024.08.004 Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA] ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])		#: [https://doi.org/10.1016/j.bpj.2024.08.004 Context-dependent structure formation of hairpin motifs in bacteriophage MS2 genomic RNA] ([https://doi.org/10.1101/2024.04.17.589867 bioRxiv])
Line 615:		Line 615:
	# E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted		# E.J. Ratajczyk, J. Bath, P. Sulc, J.P.K. Doye, A.A. Louis, A.J. Turberfield, submitted
	#: Controlling DNA-RNA strand displacement kinetics with base distribution ([https://doi.org/10.1101/2024.08.06.606789 bioRxiv])		#: Controlling DNA-RNA strand displacement kinetics with base distribution ([https://doi.org/10.1101/2024.08.06.606789 bioRxiv])
	# A. Suma and C. Micheletti, ~~submitted~~		# A. Suma and C. Micheletti, ''QRB Discovery'' '''6''', e4 (2025)
	#: Unzipping of knotted DNA via nanopore translocation ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])		#: [https://doi.org/10.1017/qrd.2024.26 Unzipping of knotted DNA via nanopore translocation] ([https://doi.org/10.48550/arXiv.2407.11567 arXiv])
	# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.		# G. Mattiotti, M. Micheloni, L. Petrolli, L. Tubiana, S. Pasquali, R. Potestio, submitted.
	#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])		#: Molecular dynamics characterization of the free and encapsidated RNA2 of CCMV with the oxRNA model ([https://doi.org/10.48550/arXiv.2408.03662 arXiv])

← Older revision		Revision as of 15:01, 16 April 2025
Line 557:		Line 557:
	# H. Liu, M. Matthies, J. Russo, L. Rovigatti, R.P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano and P. Šulc, ''Science'' '''384''', 776-781 (2024)		# H. Liu, M. Matthies, J. Russo, L. Rovigatti, R.P. Narayanan, T. Diep, D. McKeen, O. Gang, N. Stephanopoulos, F. Sciortino, H. Yan, F. Romano and P. Šulc, ''Science'' '''384''', 776-781 (2024)
	#: [https://doi.org/10.1126/science.adl5549 Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments] ([https://doi.org/10.48550/arXiv.2310.10995 arXiv])		#: [https://doi.org/10.1126/science.adl5549 Inverse design of a pyrochlore lattice of DNA origami through model-driven experiments] ([https://doi.org/10.48550/arXiv.2310.10995 arXiv])
	# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, ''Nat. Nanotechnol.'' ~~accepted~~ (2024)		# L. Grabenhorst, M. Pfeiffer, T. Schinkel, M. Kümmerlin, J.B. Maglic, G.A. Brüggenthies, F. Selbach, A.T. Murr, P. Tinnefeld, V. Glembockyte, ''Nat. Nanotechnol.'' '''20''', 303–310 (2025) (2024)
	#: [https://doi.org/10.1038/s41565-024-01804-0 Engineering modular and tunable single-molecule sensors by decoupling sensing from signal output] ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv])		#: [https://doi.org/10.1038/s41565-024-01804-0 Engineering modular and tunable single-molecule sensors by decoupling sensing from signal output] ([https://doi.org/10.1101/2023.11.06.565795 bioRxiv])
	# F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted		# F. Tosti Guerra, E. Poppleton, P. Šulc, L. Rovigatti, submitted
Line 577:		Line 577:
	# W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, ''Nat. Chem.'' '''16''', 1408–1417 (2024)		# W. Ji, X. Xiong, M. Cao, Y. Zhu, L. Li, F. Wang, C. Fan and H. Pei, ''Nat. Chem.'' '''16''', 1408–1417 (2024)
	#: [https://doi.org/10.1038/s41557-024-01565-2 Encoding signal propagation on topology-programmed DNA origami]		#: [https://doi.org/10.1038/s41557-024-01565-2 Encoding signal propagation on topology-programmed DNA origami]
	# M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, ''Nat. Chem.'' ~~accepted~~ (2024)		# M. van Galen, A. Bok, T. Peshkovsky, J. van der Gucht, B. Albada and J. Sprakel, ''Nat. Chem.'' '''16''', 1943–1950 (2024)
	#: [https://doi.org/10.1038/s41557-024-01571-4 De novo DNA-based catch bonds]		#: [https://doi.org/10.1038/s41557-024-01571-4 De novo DNA-based catch bonds]
	# Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, ''Nat. Nanotechnol.'' '''19''', 1674–1685 (2024)		# Y. Hu, J. Rogers, Y. Duan, A. Velusamy, S. Narum, S. Al Abdullatif and K. Salaita, ''Nat. Nanotechnol.'' '''19''', 1674–1685 (2024)
	#: [https://doi.org/10.1038/s41565-024-01723-0 Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors]		#: [https://doi.org/10.1038/s41565-024-01723-0 Quantifying T cell receptor mechanics at membrane junctions using DNA origami tension sensors]
	# D. Svenšek, J. Sočan and M. Praprotnik, ''Macromol. Rapid Commun.'' ~~accepted~~ 2400382 (2024)		# D. Svenšek, J. Sočan and M. Praprotnik, ''Macromol. Rapid Commun.'' '''45''', 2400382 (2024)
	#: [https://doi.org/10.1002/marc.202400382 Density–nematic coupling in isotropic solution of DNA: Multiscale model]		#: [https://doi.org/10.1002/marc.202400382 Density–nematic coupling in isotropic solution of DNA: Multiscale model]
	# M. Mogheiseh and R.H. Ghasemi, ''J. Chem. Phys.'' '''161''', 045101 (2024)		# M. Mogheiseh and R.H. Ghasemi, ''J. Chem. Phys.'' '''161''', 045101 (2024)
Line 601:		Line 601:
	# L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, ''Nano Lett.'' '''24''', 13481–13486 (2024)		# L. Yang, G. Pecastaings, C. Drummond and J. Elezgaray, ''Nano Lett.'' '''24''', 13481–13486 (2024)
	#: [https://doi.org/10.1021/acs.nanolett.4c02302 Driving DNA nanopore membrane insertion through dipolar coupling]		#: [https://doi.org/10.1021/acs.nanolett.4c02302 Driving DNA nanopore membrane insertion through dipolar coupling]
	# J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ''ACM Trans. Evol. Learn. Optim.'' ~~accepted~~ (2024)		# J.-Y. Liou, M. Awan, K. Leyba, P. Šulc, S. Hofmeyr, C.-J. Wu and S. Forrest, ''ACM Trans. Evol. Learn. Optim.'' '''4''', 1-29 (2024)
	#: [https://doi.org/10.1145/3703920 Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications]		#: [https://doi.org/10.1145/3703920 Evolving to find optimizations humans miss: Using evolutionary computation to improve GPU code for bioinformatics applications]
	# C. Karfusehr, M. Eder, F.C. Simmel		# C. Karfusehr, M. Eder, F.C. Simmel