Bounding phenotype transition probabilities via conditional complexity
Journal of The Royal Society Interface The Royal Society 22:231 (2025) 20240916
Abstract:
By linking genetic sequences to phenotypic traits, genotype-phenotype maps represent a key layer in biological organization. Their structure modulates the effects of genetic mutations which can contribute to shaping evolutionary outcomes. Recent work based on algorithmic information theory introduced an upper bound on the likelihood of a random genetic mutation causing a transition between two phenotypes, using only the conditional complexity between them. Here we evaluate how well this bound works for a range of genotype-phenotype maps, including a differential equation model for circadian rhythm, a matrix-multiplication model of gene regulatory networks, a developmental model of tooth morphologies for ringed seals, a polyomino-tile shape model of biological self-assembly, and the hydrophobic/polar (HP) lattice protein model. By assessing three levels of predictive performance, we find that the bound provides meaningful estimates of phenotype transition probabilities across these complex systems. These results suggest that transition probabilities can be predicted to some degree directly from the phenotypes themselves, without needing detailed knowledge of the underlying genotype-phenotype map.Gate-tunable double-dome superconductivity in twisted trilayer graphene
Nature Physics Springer Nature 21:11 (2025) 1773-1779
Abstract:
Graphene moiré systems are ideal environments for investigating complex phase diagrams and gaining fundamental insights into the mechanisms that underlie them, as they permit controlled manipulation of electronic properties. Magic-angle twisted trilayer graphene has emerged as a key platform for exploring moiré superconductivity due to the robustness of its superconducting order and the ability to tune its energy bands with an electric field. Here we report the direct observation of two domes of superconductivity in the phase diagram of magic-angle twisted trilayer graphene. The dependence of the superconductivity of doped holes on the temperature, magnetic field and bias current shows that it is suppressed near a specific filling of the moiré flat band, leading to a double dome in the phase diagram within a finite range of the displacement field. The transport properties are also indicative of a phase transition and the potentially distinct nature of superconductivity in the two domes. Hartree–Fock calculations incorporating mild strain yield an incommensurate Kekulé spiral state whose effective spin polarization peaks in the regime where superconductivity is suppressed in the experiments.Continuous-time multifarious systems. I. Equilibrium multifarious self-assembly
The Journal of Chemical Physics AIP Publishing 163:12 (2025) 124904
Abstract:
Multifarious assembly models consider multiple structures assembled from a shared set of components, reflecting the efficient usage of components in biological self-assembly. These models are subject to a high-dimensional parameter space, with only a finite region of parameter space giving reliable self-assembly. Here, we use a continuous-time Gillespie simulation method to study multifarious self-assembly and find that the region of parameter space in which reliable self-assembly can be achieved is smaller than what was obtained previously using a discrete-time Monte Carlo simulation method. We explain this discrepancy through a detailed analysis of the stability of assembled structures against chimera formation. We find that our continuous-time simulations of multifarious self-assembly can expose this instability in large systems even at moderate simulation times. In contrast, discrete-time simulations are slow to show this instability, particularly for large system sizes. For the remaining state space, we find good agreement between the predictions of continuous- and discrete-time simulations. We present physical arguments that can help us predict the state boundaries in the parameter space and gain a deeper understanding of multifarious self-assembly.Continuous-time multifarious systems. II. Non-reciprocal multifarious self-organization
The Journal of Chemical Physics AIP Publishing 163:12 (2025) 124905
Abstract:
In the context of self-assembly, where complex structures can be assembled from smaller units, it is desirable to devise strategies toward disassembly and reassembly processes that reuse the constituent parts. A non-reciprocal multifarious self-organization strategy has been recently introduced and shown to have the capacity to exhibit this complex property. In this work, we study the model using continuous-time Gillespie simulations and compare the results against discrete-time Monte Carlo simulations investigated previously. Furthermore, using the continuous-time simulations, we explore important features in our system, namely, the nucleation time and interface growth velocity, which comprise the timescale of shape-shifting. We develop analytical calculations for the associated timescales and compare the results to those measured in simulations, allowing us to pin down the key mechanisms behind the observed timescales at different parameter values.
Quantum Hall Antidot as a Fractional Coulombmeter
preprint, arXiv:2509.04209
Abstract:
The detection of fractionally charged quasiparticles, which arise in the fractional quantum Hall regime, is of fundamental importance for probing their exotic quantum properties. While electronic interferometers have been central to probe their statistical properties, their interpretation is often complicated by bulk-edge interactions. Antidots, potential hills in the quantum Hall regime, are particularly valuable in this context, as they overcome the geometric limitations of conventional designs and act as controlled impurities within a quantum point contact. Furthermore, antidots allow for quasiparticle charge detection through straightforward conductance measurements, replacing the need for more demanding techniques. In this work, we employ a gate-defined bilayer graphene antidot operating in the Coulomb-dominated regime to study quasiparticle tunneling in both integer and fractional quantum Hall states. We show that the gate-voltage period and the oscillation slope directly reveal the charge of the tunneling quasiparticles, providing a practical method to measure fractional charge in graphene. We report direct measurements of fractional charge, finding q=e/3 at ν=4/3, 5/3 and 7/3, q=2e/3 at ν=2/3 and q=3e/5 at ν=3/5, while at ν=8/3 we observe signatures of both e/3 and 2e/3 tunneling charge. The simplicity and tunability of this design open a pathway to extend antidot-based charge measurements to other van der Waals materials, establishing antidots as a powerful and broadly applicable platform to study the quantum Hall effect.