arXiv subjects

David Yllanes

Publications and source records attributed to David Yllanes.

12 recordsLinked to original sources

arXiv2026

On the true low-energy excitations of the three-dimensional spin glass

We study the low-energy excitations of the three dimensional spin glass through a large-scale Monte Carlo simulation on lattices up to $L=18$. We find smooth extrapolations down to zero temperature, which, in the case of the energy and of the link overlap, can be directly -- and favourably -- compared with previous investigations featuring ground states (i.e., at zero temperature). The best fit for the fractal dimension of the excitations is provided by Replica-Symmetry Breaking theory, but we also consider the alternative TNT description. The $P(q)$ is found to verify the Parisi-Toulouse temperature scaling. Our data provides a spectacular confirmation of the overlap-equivalence hypothesis.

cond-mat.dis-nn↗

arXiv2026

Cluster moves with an entropic reservoir accelerate low-temperature simulations of three-dimensional spin glasses

We present an algorithm for the simulation of three-dimensional spin glasses deep in the low-temperature phase: Parallel Tempering enhanced with Houdayer moves and with an entropic reservoir (PTHR). Although differences with the standard Houdayer algorithm are small, PTHR allows us to equilibrate a large number of samples of $L=16$ lattices with Gaussian couplings for temperatures $T\geq 0.2$. We show that the computational complexity displays better size scaling than standard Parallel Tempering. For finite sizes, our method outperforms other cluster algorithms by a speedup factor of around 64. In close analogy with standard Parallel Tempering, PTHR's computational complexity strongly relates to temperature chaos.

cond-mat.dis-nn↗

arXiv2023

Markov-bridge generation of transition paths and its application to cell-fate choice

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 equation for Markov bridges, which exhibits the original transition rates scaled by a time-dependent factor. Trajectories can then be generated using a refined version of the Gillespie algorithm. We illustrate the benefits of our method by sampling trajectories in the M\"uller-Brown potential. This allows us to generate transition paths which would otherwise be obtained at a high computational cost with standard Kinetic Monte Carlo methods because commitment to a transition path is essentially a rare event. We then apply our method to a single-cell RNA sequencing dataset from mouse pancreatic cells to investigate the cell differentiation pathways of endocrine-cell precursors. By sampling Markov bridges for a specific differentiation pathway we obtain a time-resolved dynamics that can reveal features such as cell types which behave as bottlenecks. The ensemble of trajectories also gives information about the fluctuations around the most likely path. For example, we quantify the statistical weights of different branches in the differentiation pathway to alpha cells.

cond-mat.stat-mech↗

arXiv2023

Vibrations and tunneling of strained nanoribbons at finite temperature

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 critical behaviors (e.g., the scale-dependent elastic constants) are plentiful, investigations of dynamics remain limited. Here, we use molecular dynamics to study the time dependence of the midpoint (the height center-of-mass) of doubly clamped nanoribbons, as prototypical graphene resonators, under a wide range of temperature and strain conditions. By treating the ribbon midpoint as a Brownian particle confined to a nonlinear potential (which assumes a double-well shape beyond the buckling transition), we formulate an effective theory describing the ribbon's tunneling rate across the two wells and its oscillations inside a given well. We find that, for nanoribbbons compressed above the Euler buckling point and thermalized above a temperature at which the non-linear effects due to thermal fluctuations become significant, the exponential term (the ratio between energy barrier and temperature) depends only on the geometry, but not the temperature, unlike the usual Arrhenius behavior. Moreover, we find that the natural oscillation time for small strain shows a non-trivial scaling $τ_{\rm o}\sim L_0^{\,z}T^{-η/4}$, with $L_0$ being the ribbon length, $z=2-η/2$ being the dynamic critical exponent, $η=0.8$ being the scaling exponent describing scale-dependent elastic constants, and $T$ being the temperature. These unusual scale- and temperature-dependent dynamics thus exhibit dynamic criticality and could be exploited in the development of graphene-based nanoactuators.

cond-mat.mtrl-sci↗

arXiv2021

Polysomally Protected Viruses

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 how its presence might be detected by ribosome profiling. There are two possible forms for such a polysomally protected virus, depending upon whether just the forward strand or both the forward and complementary strands can be encased by ribosomes (these will be termed type 1 and type 2, respectively). It is argued that in the type 2 case the viral RNA would evolve an ambigrammatic property, whereby the viral genes are free of stop codons in a reverse reading frame (with forward and reverse codons aligned). Recent observations of ribosome profiles of ambigrammatic narnavirus sequences are consistent with our predictions for the type 2 case.

q-bio.SC↗

arXiv2020

Thermal buckling and symmetry breaking in thin ribbons under compression

Understanding thin sheets, ranging from the macro to the nanoscale, can allow control of mechanical properties such as deformability. Out-of-plane buckling due to in-plane compression can be a key feature in designing new materials. While thin-plate theory can predict critical buckling thresholds for thin frames and nanoribbons at very low temperatures, a unifying framework to describe the effects of thermal fluctuations on buckling at more elevated temperatures presents subtle difficulties. We develop and test a theoretical approach that includes both an in-plane compression and an out-of-plane perturbing field to describe the mechanics of thermalised ribbons above and below the buckling transition. We show that, once the elastic constants are renormalised to take into account the ribbon's width (in units of the thermal length scale), we can map the physics onto a mean-field treatment of buckling, provided the length is short compared to a ribbon persistence length. Our theoretical predictions are checked by extensive molecular dynamics simulations of thin thermalised ribbons under axial compression.

cond-mat.stat-mech↗

arXiv2019

A self-driven phase transition drives Myxococcus xanthus fruiting body formation

Combining high-resolution single cell tracking experiments with numerical simulations, we show that starvation-induced fruiting body (FB) formation in Myxococcus xanthus is a phase separation driven by cells that tune their motility over time. The phase separation can be understood in terms of cell density and a dimensionless Peclet number that captures cell motility through speed and reversal frequency. Our work suggests that M. xanthus take advantage of a self-driven non-equilibrium phase transition that can be controlled at the single cell level.

physics.bio-ph↗

arXiv2018

Curvature-dependent tension and tangential flows at the interface of motility-induced phases

Purely repulsive active particles spontaneously undergo motility-induced phase separation (MIPS) into condensed and dilute phases. Remarkably, the mechanical tension measured along the interface between these phases is negative. In equilibrium this would imply an unstable interface that wants to expand, but these out-of-equilibrium systems display long-time stability and have intrinsically stiff boundaries. Here, we study this phenomenon in detail using active Brownian particle simulations and a novel frame of reference. By shifting from the global (or laboratory) frame to a local frame that follows the dynamics of the phase boundary, we observe correlations between the local curvature of the interface and the measured value of the tension. Importantly, our analysis reveals the presence of sustained local tangential motion of particles within a surface layer in both the gas and the dense regions. The combined tangential current in the gas and self-shearing of the surface of the dense phase suggest a stiffening interface that redirects particles along itself to heal local fluctuations. These currents restore the otherwise wildly fluctuating interface through an out-of-equilibrium Marangoni effect. We discuss the implications of our observations on phenomenological models of interfacial dynamics.

cond-mat.soft↗

arXiv2016

Kinetics of motility-induced phase separation and swim pressure

Active Brownian particles (ABPs) represent a minimal model of active matter consisting of self-propelled spheres with purely repulsive interactions and rotational noise. Here, we examine the pressure of ABPs in two dimensions in both closed boxes and systems with periodic boundary conditions and show that its nonmonotonic behavior with density is a robust feature, independent of system size. We correlate the time evolution of the mean pressure towards its steady state value with the kinetics of motility-induced phase separation. For parameter values corresponding to phase separated steady states, we identify two dynamical regimes. The pressure grows monotonically in time during the initial regime of rapid cluster formation, overshooting its steady state value and then quickly relaxing to it, and remains constant during the subsequent slower period of cluster coalescence and coarsening. The overshoot is a distinctive feature of active systems.

cond-mat.soft↗

arXiv2016

Minimal model of active colloids highlights the role of mechanical interactions in controlling the emergent behavior of active matter

Minimal models of active Brownian colloids consisting of self-propelled spherical particles with purely repulsive interactions have recently been identified as excellent quantitative testing grounds for theories of active matter and have been the subject of extensive numerical and analytical investigation. These systems do not exhibit aligned or flocking states, but do have a rich phase diagram, forming active gases, liquids and solids with novel mechanical properties. This article reviews recent advances in the understanding of such models, including the description of the active gas and its swim pressure, the motility-induced phase separation and the high-density crystalline and glassy behavior.

cond-mat.soft↗

arXiv2009

A cluster Monte Carlo algorithm with a conserved order parameter

We propose a cluster simulation algorithm for statistical ensembles with fixed order parameter. We use the tethered ensemble, which features Helmholtz's effective potential rather than Gibbs's free energy, and in which canonical averages are recovered with arbitrary accuracy. For the D = 2,3 Ising model our method's critical slowing down is comparable to that of canonical cluster algorithms. Yet, we can do more than merely reproduce canonical values. As an example, we obtain a competitive value for the 3D Ising anomalous dimension from the maxima of the effective potential.

cond-mat.stat-mech↗

arXiv2008

The Invar tensor package: Differential invariants of Riemann

The long standing problem of the relations among the scalar invariants of the Riemann tensor is computationally solved for all 6x10^23 objects with up to 12 derivatives of the metric. This covers cases ranging from products of up to 6 undifferentiated Riemann tensors to cases with up to 10 covariant derivatives of a single Riemann. We extend our computer algebra system Invar to produce within seconds a canonical form for any of those objects in terms of a basis. The process is as follows: (1) an invariant is converted in real time into a canonical form with respect to the permutation symmetries of the Riemann tensor; (2) Invar reads a database of more than 6x10^5 relations and applies those coming from the cyclic symmetry of the Riemann tensor; (3) then applies the relations coming from the Bianchi identity, (4) the relations coming from commutations of covariant derivatives, (5) the dimensionally-dependent identities for dimension 4, and finally (6) simplifies invariants that can be expressed as product of dual invariants. Invar runs on top of the tensor computer algebra systems xTensor (for Mathematica) and Canon (for Maple).

cs.SC↗