32 citations · 107 across the 11 of their papers we have counts for
11 papers
Topological Signatures of Hardness and Structural Order in Network-Forming Materials
Yair Augusto Gutiérrez Fosado, Ayobami Daramola, Davide Marenduzzo +1
Understanding how the topology of network forming materials influences their physical properties remains a longstanding challenge. Here, we investigate the topology of experimental…
Entangled nematic disclinations using multi-particle collision dynamics
Louise C. Head, Yair A. G. Fosado, Davide Marenduzzo +1
Colloids dispersed in nematic liquid crystals form topological composites in which colloid-associated defects mediate interactions while adhering to fundamental topological constra…
Single-Molecule Morphology of Topologically Digested Olympic Networks
Saminathan Ramakrishnan, Zihao Chen, Yair Augusto Gutierrez Fosado +5
The kinetoplast DNA (kDNA) is the archetype of a two-dimensional Olympic network, composed of thousands of DNA minicircles and found in the mitochondrion of certain parasites. The…
Geometric Learning of Knot Topology
Joseph Lahoud Sleiman, Filippo Conforto, Yair Augusto Gutierrez Fosado +1
Knots are deeply entangled with every branch of science. One of the biggest open challenges in knot theory is to formalise a knot invariant that can unambiguously and efficiently d…
Runaway Transition in Irreversible Polymer Condensation with Cyclisation
Maria Panoukidou, Simon Weir, Valerio Sorichetti +3
The process of polymer condensation, i.e. the formation of bonds between reactive end-groups, is ubiquitous in both industry and biology. Here we study generic systems undergoing p…
Fluidification of entanglements by a DNA bending protein
Yair A. G. Fosado, Jamieson Howard, Simon Weir +3
In spite of the nanoscale and single-molecule insights into how nucleoid associated proteins (NAPs) interact with DNA, their role in modulating the mesoscale viscoelasticity of the…
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
Davide Michieletto, Yair Fosado, Elias Melas +3
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in biophysics. Most of the existing models…
Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance
Y. A. G. Fosado, D. Michieletto, C. A. Brackley +1
We study the effect of transcription on the kinetics of DNA supercoiling in 3D by means of Brownian dynamics simulations of a single nucleotide resolution coarse-grained model for…
A Numerical Study of Three-Armed DNA Hydrogel Structures
Yair Augusto Gutierrez Fosado, Zhongyang Xing, Erika Eiser +2
We present a numerical analysis of a DNA hydrogel that consists of three-valent Y-shaped DNA molecules. The building blocks self-assemble fully reversibly from complementary single…
Dynamical Scaling and Phase Coexistence in Topologically-Constrained DNA Melting
Y. A. G. Fosado, D. Michieletto, D. Marenduzzo
There is a long-standing experimental observation that the melting of topologically constrained DNA, such as circular-closed plasmids, is less abrupt than that of linear molecules.…
A Single Nucleotide Resolution Model for Large-Scale Simulations of Double Stranded DNA
Y. A. G. Fosado, D. Michieletto, J. Allan +3
The computational modelling of DNA is becoming crucial in light of new advances in DNA nanotechnology, single-molecule experiments and in vivo DNA tampering. Here we present a meso…