David Yllanes
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View article: Microcanonical simulated annealing: Massively parallel Monte Carlo simulations with sporadic random-number generation
Microcanonical simulated annealing: Massively parallel Monte Carlo simulations with sporadic random-number generation Open
Numerical simulations of models and theories that describe complex experimental systems $\unicode{x2014}$in fields like high-energy and condensed-matter physics$\unicode{x2014}$ are becoming increasingly important. Examples include lattice…
Markov-bridge generation of transition paths and its application to cell-fate choice Open
We present a method to sample Markov-chain trajectories constrained to both the initial and final conditions, which we term Markov bridges. The trajectories are conditioned to end in a specific state at a given time. We derive the master e…
View article: Quantifying Memory in Spin Glasses
Quantifying Memory in Spin Glasses Open
Rejuvenation and memory, long considered the distinguishing features of spin glasses, have recently been proven to result from the growth of multiple length scales. This insight, enabled by simulations on the Janus II supercomputer, has op…
View article: Spin-glass dynamics: experiment, theory and simulation
Spin-glass dynamics: experiment, theory and simulation Open
The study of spin-glass dynamics, long considered the paradigmatic complex system, has reached important milestones. The availability of single crystals has allowed the experimental measurement of spin-glass coherence lengths of almost mac…
Scaling study of diffusion in dynamic crowded spaces Open
We formulate a scaling theory for the long-time diffusive motion in a space occluded by a high density of moving obstacles in dimensions 1, 2 and 3. Our tracers diffuse anomalously over many decades in time, before reaching a diffusive ste…
Phase transition in the computational complexity of the shortest common superstring and genome assembly Open
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle form…
Vibrations and transitions across barrier of strained nanoribbons at finite temperature Open
Crystalline sheets (e.g., graphene and transition metal dichalcogenides) liberated from a substrate are a paradigm for materials at criticality, because flexural phonons can fluctuate into the third dimension. Although studies of static cr…
View article: Multifractality in spin glasses
Multifractality in spin glasses Open
We unveil the multifractal behavior of Ising spin glasses in their low-temperature phase. Using the Janus II custom-built supercomputer, the spin-glass correlation function is studied locally. Dramatic fluctuations are found when pairs of …
Markov-bridge generation of transition paths and its application to cell-fate choice Open
We present a method to sample Markov-chain trajectories constrained to both the initial and final conditions, which we term Markov bridges. The trajectories are conditioned to end in a specific state at a given time. We derive the master e…
View article: Quantifying memory in spin glasses
Quantifying memory in spin glasses Open
Rejuvenation and memory, long considered the distinguishing features of spin glasses, have recently been proven to result from the growth of multiple length scales. This insight, enabled by simulations on the Janus~II supercomputer, has op…
Configurational entropy is an intrinsic driver of tissue structural heterogeneity Open
SUMMARY Tissues comprise ordered arrangements of cells that can be surprisingly disordered in their details. How the properties of single cells and their microenvironment contribute to the balance between order and disorder at the tissue-s…
View article: Superposition principle and nonlinear response in spin glasses
Superposition principle and nonlinear response in spin glasses Open
The extended principle of superposition has been a touchstone of spin-glass dynamics for almost 30 years. Here the Uppsala group has demonstrated its validity for the metallic spin glass, CuMn, for magnetic fields H up to 10 Oe at the redu…
View article: Multifractality in spin glasses
Multifractality in spin glasses Open
We unveil the multifractal behavior of Ising spin glasses in their low-temperature phase. Using the Janus II custom-built supercomputer, the spin-glass correlation function is studied locally. Dramatic fluctuations are found when pairs of …
Vibrations and tunneling of strained nanoribbons at finite temperature Open
Crystalline sheets (e.g., graphene and transition metal dichalcogenides) liberated from a substrate are a paradigm for materials at criticality because flexural phonons can fluctuate into the third dimension. Although studies of static cri…
Statistical topology of the streamlines of a two-dimensional flow Open
Recent experiments on mucociliary clearance, an important defense against airborne pathogens, have raised questions about the topology of two-dimensional (2D) flows, such as the proportion of topologically closed and open streamlines. We i…
Phase transition in the computational complexity of the shortest common superstring and genome assembly Open
Genome assembly, the process of reconstructing a long genetic sequence by aligning and merging short fragments, or reads, is known to be NP-hard, either as a version of the shortest common superstring problem or in a Hamiltonian-cycle form…
On the superposition principle and non-linear response in spin glasses Open
The extended principle of superposition has been a touchstone of spin glass dynamics for almost thirty years. The Uppsala group has demonstrated its validity for the metallic spin glass, CuMn, for magnetic fields $H$ up to 10 Oe at the red…
Memory and rejuvenation in spin glasses: aging systems are ruled by more than one length scale Open
Memory and rejuvenation effects in the magnetic response of off-equilibrium spin glasses have been widely regarded as the doorway into the experimental exploration of ultrametricity and temperature chaos (maybe the most exotic features in …
View article: A high-resolution flux-matrix model describes the spread of diseases in a spatial network and the effect of mitigation strategies
A high-resolution flux-matrix model describes the spread of diseases in a spatial network and the effect of mitigation strategies Open
Propagation of an epidemic across a spatial network of communities is described by a variant of the SIR model accompanied by an intercommunity infectivity matrix. This matrix is estimated from fluxes between communities, obtained from cell…
Statistical topology of the streamlines of a two-dimensional flow Open
Recent experiments on mucociliary clearance, an important defense against airborne pathogens, have raised questions about the topology of two-dimensional (2D) flows. We introduce a framework for studying ensembles of 2D time-invariant flow…
View article: Epidemic dynamics in inhomogeneous populations and the role of superspreaders
Epidemic dynamics in inhomogeneous populations and the role of superspreaders Open
A variant of the susceptible-infected-recovered model for an inhomogeneous population is introduced to account for the effect of variability in susceptibility and infectiousness across a population. An initial formulation of this dynamics …
Polysomally protected viruses Open
It is conceivable that an RNA virus could use a polysome, that is, a string of ribosomes covering the RNA strand, to protect the genetic material from degradation inside a host cell. This paper discusses how such a virus might operate, and…
A scaling law describes the spin-glass response in theory, experiments and simulations Open
The correlation length xi, a key quantity in glassy dynamics, can now be precisely measured for spin glasses both in experiments and in simulations. However, known analysis methods lead to discrepancies either for large external fields or …
Polymorphism of Genetic Ambigrams Open
Double synonyms in the genetic code can be used as a tool to test competing hypotheses regarding ambigrammatic narnavirus genomes. Applying the analysis to recent observations of Culex narnavirus 1 and Zhejiang mosquito virus 3 ambigrammat…
View article: Epidemic dynamics in inhomogeneous populations and the role of superspreaders
Epidemic dynamics in inhomogeneous populations and the role of superspreaders Open
A variant of the SIR model for an inhomogeneous population is introduced in order to account for the effect of variability in susceptibility and infectiousness across a population. An initial formulation of this dynamics leads to infinitel…
Spin-glass dynamics in the presence of a magnetic field]{Spin-glass dynamics in the presence of a magnetic field: exploration of microscopic properties Open
The synergy between experiment, theory, and simulations enables a microscopic
analysis of spin-glass dynamics in a magnetic field in the vicinity of and
below the spin-glass transition temperature $T_\mathrm{g}$. The spin-glass
correlation…