Published:
2025
Giorgia Palombo, Simon Weir, Davide Michieletto and Yair Augusto Gutiérrez-Fosado. Topological linking determines elasticity in limited valence networks. Nature Materials.
2024
Yair Augusto Gutiérrez Fosado, Davide Michieletto, and Fausto Martelli. Link to Densify: Topological Transitions and Origin of Hysteresis During the Compression and Decompression of Amorphous Ices. Phys. Rev. Lett. 133, 266102
Louise C. Head, Yair Augusto Gutiérrez Fosado, Davide Marenduzzo and Tyler N. Shendruk. Entangled nematic disclinations using multi-particle collision dynamics. Soft Matter, 2024,20, 7157-7173
Filippo Conforto, Yair Augusto Gutiérrez Fosado, and Davide Michieletto. Fluidification of entangled polymers by loop extrusion. Phys. Rev. Research 6, 033160
Maria Panoukidou, Simon Weir, Valerio Sorichetti, Yair Augusto Gutiérrez-Fosado, Martin Lenz and Davide Michieletto. Runaway transition in irreversible polymer condensation with cyclization. Phys. Rev. Research 6, 023189
Saminathan Ramakrishnan, Zihao Chen, Yair Augusto Gutiérrez Fosado, Luca Tubiana, Willem Vanderlinden, Nicholas Jon Savill, Achim Schnaufer, and Davide Michieletto. Single-Molecule Morphology of Topologically Digested Olympic Networks. PRX Life 2, 013009
2023
Joseph Lahoud Sleiman, Filippo Conforto, Yair Augusto Gutiérrez-Fosado, and Davide Michieletto. Geometric Learning of Knot Topology. Soft Matter, 2024,20, 71-78. Selected as the main cover of the Journal .
Yair Augusto Gutiérrez-Fosado. Nanostars planarity modulates the rheology of DNA hydrogels. Soft Matter, 2023,19, 4820. Selected as the main cover of the Journal .
Keitel Cervantes-Salguero, Yair Augusto Gutiérrez Fosado, William Megone, Julien E. Gautrot, and Matteo Palma. Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization, Molecules 28, no. 9: 3686.
Yair A. G. Fosado, Jamieson Howard, Simon Weir, Agnes Noy, Mark C. Leake, and Davide Michieletto, Fluidification of Entanglements by a DNA Bending Protein, Phys. Rev. Lett. 130, 058203
Yair Augusto Gutiérrez Fosado, Fabio Landuzzi, and Takahiro Sakaue, Coarse Graining DNA: Symmetry, Nonlocal Elasticity, and Persistence Length, Phys. Rev. Lett. 130, 058402
2022
Joseph L. Sleiman, Robin H. Burton, Michele Caraglio, Yair Augusto Gutierrez Fosado, and Davide Michieletto, Geometric Predictors of Knotted and Linked Arcs, ACS Polym. Au 2022, 2, 5, 341–350. Selected as the main cover of the Journal .
Davide Michieletto, Yair Augusto Gutierrez-Fosado, Elias Melas, Marco Baiesi, Luca Tubiana, and Enzo Orlandini, Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation, Nucleic Acids Research 50 (8), 4659-4668.
2021
Yair A. G. Fosado, Davide Michieletto, Chris A. Brackley, and Davide Marenduzzo, Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling, PNAS 118 (10) e1905215118
Yair Augusto Gutierrez-Fosado, Fabio Landuzzi, and Takahiro Sakaue, Twist dynamics and buckling instability of ring DNA: the effect of groove asymmetry and anisotropic bending, Soft Matter 17, 1530-1537
2018
Yair Augusto Gutierrez Fosado, Double-stranded coarse grained model for DNA: applications to supercoiling and denaturation, PhD Thesis
Oliver Henrich, Yair Augusto Gutierrez Fosado, Tine Curk, and Thomas E. Ouldridge, Coarse-Grained Simulation of DNA using LAMMPS, an implementation of the oxDNA model and its applications, The European Physical Journal E 41:57
Charles S. Cockell, Yair Augusto Gutierrez-Fosado, James Hitchen, Hanna Landenmark, Liam Pereraand, and Teun Vissers, Life Beyond–A Program to Use Astrobiology to Teach Science and Advance Space Exploration through Prisons, Journal of Correctional Education, Vol. 69, No. 1
2017
Y.A.G. Fosado, D. Michieletto, and D. Marenduzzo, Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting. Phys. Rev. Lett. 119, 118002
2016
Y.A.G. Fosado, D. Michieletto, J. Allan, C.A. Brackley, O. Henrich, and D. Marenduzzo, A single nucleotide resolution model for large-scale simulations of double stranded DNA, Soft Matter 12,9458
2014, book
Ariel Ayala R., Jazmín Castillo L., Pamela Villamil Sapien and Yair A. Gutierrez Fosado, Fisica 2. McMillan Education Press, ISBN 978-607-463-199-9.
