Yair Augusto Gutiérrez Fosado
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View article: Link to Densify: Topological Transitions and Origin of Hysteresis During the Compression and Decompression of Amorphous Ices
Link to Densify: Topological Transitions and Origin of Hysteresis During the Compression and Decompression of Amorphous Ices Open
In this Letter, we study the phase transition between amorphous ices and the nature of the hysteresis cycle separating them. We discover that a topological transition takes place as the system transforms from low-density amorphous ice (LDA…
View article: Fluidification of entangled polymers by loop extrusion
Fluidification of entangled polymers by loop extrusion Open
Loop extrusion is one of the main processes shaping chromosome organization across the cell cycle, yet its role in regulating deoxyribonucleic acid (DNA) entanglement and nucleoplasm viscoelasticity remains overlooked. We simulate entangle…
View article: Link to Densify: Topological Transitions and Origin of Hysteresis During the (De)Compression of Amorphous Ices
Link to Densify: Topological Transitions and Origin of Hysteresis During the (De)Compression of Amorphous Ices Open
In this Letter we study the phase transition between amorphous ices and the nature of the hysteresis cycle separating them. We discover that a topological transition takes place as the system transforms from low-density amorphous ice (LDA)…
View article: Runaway transition in irreversible polymer condensation with cyclization
Runaway transition in irreversible polymer condensation with cyclization Open
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 polymer condensation in competition with cyclization. Using…
View article: Entangled nematic disclinations using multi-particle collision dynamics
Entangled nematic disclinations using multi-particle collision dynamics Open
Colloids dispersed in nematic liquid crystals form topological composites in which colloid-associated defects mediate interactions while adhering to fundamental topological constraints. Better realising the promise of such materials requir…
View article: Single-Molecule Morphology of Topologically Digested Olympic Networks
Single-Molecule Morphology of Topologically Digested Olympic Networks Open
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 evolution, replication, and self-assembly of this structure…
View article: Entangled nematic disclinations using multi-particle collision dynamics
Entangled nematic disclinations using multi-particle collision dynamics Open
The kinetics of colloids embedded in a fluctuating nematohydrodynamic medium are shown to reproduce far-field interactions, topological properties of entangled disclination loops and topological transitions during relaxation towards ground…
View article: Single-Molecule Morphology of Topologically Digested Olympic Networks
Single-Molecule Morphology of Topologically Digested Olympic Networks Open
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 evolution, replication and self-assembly of this structure …
View article: Single-Molecule Morphology of Topologically Digested Olympic Networks
Single-Molecule Morphology of Topologically Digested Olympic Networks Open
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 evolution, replication and self-assembly of this structure …
View article: Geometric learning of knot topology
Geometric learning of knot topology Open
Unambiguous knot classification is a long-standing problem. In this paper, the authors use Machine Learning to classify all knots up to 10 crossings with more than 95% accuracy and also to distinguish knots with multiple identical knot pol…
View article: Topological Elasticity in Physical Gels with Limited Valence
Topological Elasticity in Physical Gels with Limited Valence Open
Understanding the connection between a material’s microscopic network topology and its macroscopic properties is a fundamental open challenge across a wide range of physical systems. Here, we investigate the elasticity of DNA nanostar hydr…
View article: Topological Linking Determines Elasticity in Limited Valence Networks
Topological Linking Determines Elasticity in Limited Valence Networks Open
Understanding the relationship between the microscopic structure and topology of a material and its macroscopic properties is a fundamental challenge across a wide range of systems. Here, we investigate the viscoelasticity of DNA nanostar …
View article: Geometric Learning of Knot Topology
Geometric Learning of Knot Topology Open
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 distinguish any two knotted curves. Additionally, the conjec…
View article: Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization
Programmed Self-Assembly of DNA Nanosheets with Discrete Single-Molecule Thickness and Interfacial Mechanics: Design, Simulation, and Characterization Open
DNA is programmed to hierarchically self-assemble into superstructures spanning from nanometer to micrometer scales. Here, we demonstrate DNA nanosheets assembled out of a rationally designed flexible DNA unit (F-unit), whose shape resembl…
View article: Fluidification of Entanglements by a DNA Bending Protein
Fluidification of Entanglements by a DNA Bending Protein Open
In spite of the nanoscale and single-molecule insights into nucleoid associated proteins (NAPs), their role in modulating the mesoscale viscoelasticity of entangled DNA has been overlooked so far. By combining microrheology and molecular d…
View article: Nanostars planarity modulates the rheology of DNA hydrogels
Nanostars planarity modulates the rheology of DNA hydrogels Open
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars depend on the precise geometry of their building blocks and the topology of the network.
View article: Runaway Transition in Irreversible Polymer Condensation with Cyclisation
Runaway Transition in Irreversible Polymer Condensation with Cyclisation Open
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 polymer condensation in competition with cyclisation. Using …
View article: Geometric Predictors of Knotted and Linked Arcs
Geometric Predictors of Knotted and Linked Arcs Open
Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here, we ask if local geometric features that may be used as a readout of the underlying topology of generic polymers exist. We perform molecular simulation…
View article: Geometric Predictors of Knotted and Linked Arcs
Geometric Predictors of Knotted and Linked Arcs Open
Inspired by how certain proteins "sense" knots and entanglements in DNA molecules, here we ask if there exist local geometric features that may be used as a read-out of the underlying topology of generic polymers. We perform molecular simu…
View article: Coarse-graining DNA: Symmetry, non-local elasticity and persistence length
Coarse-graining DNA: Symmetry, non-local elasticity and persistence length Open
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein …
View article: Fluidification of entanglements by a DNA bending protein
Fluidification of entanglements by a DNA bending protein Open
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 entangled genome in vivo has been overlooked so far. By co…
View article: Dynamic and facilitated binding of topoisomerase accelerates topological relaxation.
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation. Open
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is expe…
View article: Dynamic and facilitated binding of topoisomerase accelerates topological relaxation
Dynamic and facilitated binding of topoisomerase accelerates topological relaxation Open
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is expe…
View article: Nanostars planarity modulates the elasticity of DNA hydrogels
Nanostars planarity modulates the elasticity of DNA hydrogels Open
In analogy with classic rigidity problems of networks and frames, the elastic properties of hydrogels made of DNA nanostars (DNAns) are expected to strongly depend on the precise geometry of their building blocks. However, it is currently …
View article: Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation Open
How type 2 Topoisomerase (TopoII) proteins relax and simplify the topology of DNA molecules is one of the most intriguing open questions in genome and DNA biophysics. Most of the existing models neglect the dynamics of TopoII which is char…
View article: Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation
Dynamic and Facilitated Binding of Topoisomerase Accelerates Topological Relaxation Open
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 neglect the dynamics of TopoII which is characteristics for…
View article: Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling
Nonequilibrium dynamics and action at a distance in transcriptionally driven DNA supercoiling Open
Significance Positive and negative supercoiling refers to the overwinding or underwinding, respectively, of a DNA double helix. Supercoiling is important and ubiquitous, as all cells, from bacterial to human, deploy proteins to keep their …
View article: Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending
Twist dynamics and buckling instability of ring DNA: Effect of groove asymmetry and anisotropic bending Open
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxatio…
View article: Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance
Transcription-driven DNA Supercoiling: Non-Equilibrium Dynamics and Action-at-a-distance Open
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 double stranded DNA. By accounting for the action of a tran…