Publications

Phase separation of proteins plays a critical role in cellular organization. How phase-separated protein condensates underpin biological function and how condensates achieve specificity remain elusive. We investigated the phase separation of MUT-16, a scaffold protein in Mutator foci, and its role in recruiting the client protein MUT-8, a key component in RNA silencing in Caenorhabditis elegans. We employed a multi-scale approach that combined coarse-grained (residue-level CALVADOS2 and near-atomistic Martini3) and atomistic simulations. Simulations across different resolutions provide a consistent perspective on how MUT-16 condensates recruit MUT-8, enabling the fine-tuning of chemical details and balancing the computational cost. Both coarse-grained models (CALVADOS2 and Martini3) predicted the relative phase-separation propensities of MUT-16’s disordered regions, which we confirmed through in vitro experiments. Simulations also identified key sequence features and residues driving phase separation and revealed differences in residue interaction propensities between CALVADOS2 and Martini3. Furthermore, Martini3 and 350-μs atomistic simulations on Folding@Home of MUT-8’s N-terminal prion-like domain with MUT-16 M8BR cluster highlighted the importance of cation-interactions between Tyr residues of MUT-8 and Arg residues of MUT-16 M8BR. Lys residues were observed to be more prone to interact in Martini3. Atomistic simulations revealed that the guanidinium group of Arg also engages in interactions and hydrogen bonds with the backbone of Tyr, possibly contributing to the greater strength of Arg-Tyr interactions compared to Lys-Tyr, where these additional favorable contacts are absent. In agreement with our simulations, in vitro co-expression pull-down experiments demonstrated a progressive loss of MUT-8 recruitment after the mutation of Arg in MUT-16 M8BR to Lys or Ala, confirming the critical role of Arg in this interaction. These findings advance our understanding of MUT-16 phase separation and subsequent MUT-8 recruitment, key processes in assembling Mutator foci that drive RNA silencing in C. elegans.

Phase separation of proteins plays a critical role in cellular organization. How phase-separated protein condensates underpin biological function and how condensates achieve specificity remain elusive. We investigated the phase separation of MUT-16, a scaffold protein in Mutator foci, and its role in recruiting the client protein MUT-8, a key component in RNA silencing in Caenorhabditis elegans. We employed a multi-scale approach that combined coarse-grained (residue-level CALVADOS2 and near-atomistic Martini3) and atomistic simulations. Simulations across different resolutions provide a consistent perspective on how MUT-16 condensates recruit MUT-8, enabling the fine-tuning of chemical details and balancing the computational cost. Both coarse-grained models (CALVADOS2 and Martini3) predicted the relative phase-separation propensities of MUT-16’s disordered regions, which we confirmed through in vitro experiments. Simulations also identified key sequence features and residues driving phase separation and revealed differences in residue interaction propensities between CALVADOS2 and Martini3. Furthermore, Martini3 and 350-μs atomistic simulations on Folding@Home of MUT-8’s N-terminal prion-like domain with MUT-16 M8BR cluster highlighted the importance of cation-interactions between Tyr residues of MUT-8 and Arg residues of MUT-16 M8BR. Lys residues were observed to be more prone to interact in Martini3. Atomistic simulations revealed that the guanidinium group of Arg also engages in interactions and hydrogen bonds with the backbone of Tyr, possibly contributing to the greater strength of Arg-Tyr interactions compared to Lys-Tyr, where these additional favorable contacts are absent. In agreement with our simulations, in vitro co-expression pull-down experiments demonstrated a progressive loss of MUT-8 recruitment after the mutation of Arg in MUT-16 M8BR to Lys or Ala, confirming the critical role of Arg in this interaction. These findings advance our understanding of MUT-16 phase separation and subsequent MUT-8 recruitment, key processes in assembling Mutator foci that drive RNA silencing in C. elegans.

Prior work has demonstrated a consistent tendency in neural networks engaged in continual learning tasks, wherein intermediate task similarity results in the highest levels of catastrophic interference. This phenomenon is attributed to the network’s tendency to reuse learned features across tasks. However, this explanation heavily relies on the premise that neuron specialisation occurs, i.e. the emergence of localised representations. Our investigation challenges the validity of this assumption. Using theoretical frameworks for the analysis of neural networks, we show a strong dependence of specialisation on the initial condition. More precisely, we show that weight imbalance and high weight entropy can favour specialised solutions. We then apply these insights in the context of continual learning, first showing the emergence of a monotonic relation between task-similarity and forgetting in non-specialised networks. Finally, we show that specialisation by weight imbalance is beneficial on the commonly employed elastic weight consolidation regularisation technique.

During epithelial morphogenesis, cell polarity aligns individual cell behaviors into collective motions that shape developing tissues. Here, we combine experiments with computational modeling to investigate how cell-scale forces oriented by Planar Cell Polarity (PCP) direct the collective, counter-rotational cell flows that occur during hair placode morphogenesis. We rule out that PCP directs apical neighbor exchanges, as junctional myosin and PCP protein localization are not co-correlated with junction shrinkage. Instead, we find that PCP directs anterior-directed crawling of placode cells along the basal surface of the tissue through a mechanism that requires cell crawling regulator Rac1. Modeling the placode as a continuum viscoelastic fluid, we find that active forces from cell crawling at the basal surface is sufficient to generate the experimentally observed counter-rotational cell motion at the apical surface. Our results show an unexpected role for PCP in epithelial morphogenesis, centering the basal surface as the site of force generation.

Elliptic partial differential equations (PDEs) can model many physical phenomena, such as electrostatics, acoustics, wave propagation, and diffusion. In scientific machine learning settings, a high-throughput PDE solver may be required to generate a training dataset, run in the inner loop of an iterative algorithm, or interface directly with a deep neural network. To provide value to machine learning users, such a PDE solver must be compatible with standard automatic differentiation frameworks, scale efficiently when run on graphics processing units (GPUs), and maintain high accuracy for a large range of input parameters. We have designed the jaxhps package with these use-cases in mind by implementing a highly efficient and accurate solver for elliptic problems with native hardware acceleration and automatic differentiation support. This is achieved by expressing a highly-efficient solution method for elliptic PDEs in JAX (Bradbury et al., 2018). This software implements algorithms specifically designed for fast GPU execution of a family of elliptic PDE solvers, which are described in full in Melia et al. (2025).

3D chromatin structure is critical for the regulation of gene expression during development. Here we used Micro-C assays at 100-bp resolution to map genome organization in Drosophila melanogaster throughout the first half of embryogenesis. These high-resolution contact maps reveal fine-scale features such as loops and boundaries delineating topologically associating domains. Notably, we observe that 3D chromatin structures form prior to zygotic genome activation and persist during successive mitotic cycles. Integrative analysis with 149 public chromatin immunoprecipitation sequencing (ChIP-seq) datasets identifies four classes of chromatin structuring elements, including a distinct group enriched for GAGA-associated factor (GAF) and Zelda binding, associated with developmental-gene regulation. These elements are mitotically retained and exhibit sequence and structure similarity between D. melanogaster and D. virilis. We propose that 3D chromatin organization in the pre-cellular embryo facilitates deployment of developmentally regulated genes during Drosophila embryogenesis.

We present an efficient separation of variables algorithm for the evaluation of imaginary time Feynman diagrams appearing in the bold pseudo-particle strong coupling expansion of the Anderson impurity model. The algorithm uses a fitting method based on AAA rational approximation and numerical optimization to obtain a sum-of-exponentials expansion of the hybridization function, which is then used to decompose the diagrams. A diagrammatic formulation of the algorithm leads to an automated procedure for diagrams of arbitrary order and topology. We also present methods of stabilizing the self-consistent solution of the pseudo-particle Dyson equation. The result is a low-cost and high-order accurate impurity solver for quantum embedding methods using general multi-orbital hybridization functions at low temperatures, appropriate for low-to-intermediate expansion orders. In addition to other benchmark examples, we use our solver to perform a dynamical mean-field theory study of a minimal model of the strongly correlated compound Ca 2RuO4, describing the anti-ferromagnetic transition and the in- and out-of-plane anisotropy induced by spin-orbit coupling.

Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in vitrified samples have yet to reach maturity. With an increasing number of new methods to analyze the multitude of heterogeneous states captured in single particle images, a systematic approach to validation in this field is needed. With this motivation, we issued a challenge to the community to analyze two cryo-EM particle image sets of thyroglobulin that exhibit continuous conformational heterogeneity. The first dataset was experimental and the second was generated with a simulator, allowing control over the distribution of molecular structures and enabled direct comparison between participants’ submissions and the ground truth molecular structures and distributions. Participants were asked to submit 80 volumes representing the heterogeneous ensemble and estimate their respective populations in the image sets provided. Participation of the research community in the challenge was strong, with submissions from nearly all developers of heterogeneity methods, resulting in 41 submissions across both datasets. Submissions qualitatively exceeded expectations, with the molecular motions identified by methods resembling both each other and the ground truth motion. However, quantitatively assessing these similarities was a challenge in and of itself. In the process of assessing the submissions, we developed several validation metrics, most of which require reference to the underlying ground truth volumes. However, we have also explored the use of metrics that do not necessarily reference ground truth. This is particularly apt for experimental datasets where ground truth is inaccessible. These approaches allowed us to assess the similarity and accuracy in volume quality, molecular motions, and conformational distribution of di!erent submissions. These metrics and the e!orts of all participants help chart a path forward for the improvements of heterogeneity methods for cryo-EM and for future challenges to validate these new methods as they continue to be developed by the community.

Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in vitrified samples have yet to reach maturity. With an increasing number of new methods to analyze the multitude of heterogeneous states captured in single particle images, a systematic approach to validation in this field is needed. With this motivation, we issued a challenge to the community to analyze two cryo-EM particle image sets of thyroglobulin that exhibit continuous conformational heterogeneity. The first dataset was experimental and the second was generated with a simulator, allowing control over the distribution of molecular structures and enabled direct comparison between participants’ submissions and the ground truth molecular structures and distributions. Participants were asked to submit 80 volumes representing the heterogeneous ensemble and estimate their respective populations in the image sets provided. Participation of the research community in the challenge was strong, with submissions from nearly all developers of heterogeneity methods, resulting in 41 submissions across both datasets. Submissions qualitatively exceeded expectations, with the molecular motions identified by methods resembling both each other and the ground truth motion. However, quantitatively assessing these similarities was a challenge in and of itself. In the process of assessing the submissions, we developed several validation metrics, most of which require reference to the underlying ground truth volumes. However, we have also explored the use of metrics that do not necessarily reference ground truth. This is particularly apt for experimental datasets where ground truth is inaccessible. These approaches allowed us to assess the similarity and accuracy in volume quality, molecular motions, and conformational distribution of di!erent submissions. These metrics and the e!orts of all participants help chart a path forward for the improvements of heterogeneity methods for cryo-EM and for future challenges to validate these new methods as they continue to be developed by the community.

Septins can assemble into scaffolds at the plasma membrane to regulate cell morphology. While septins preferentially bind convex membranes via amphipathic helices, their assembly on varied geometries in cells suggests additional localization cues. We tested the hypothesis that lipid composition directs septin assembly through the property of lipid packing. We used pharmacological perturbations that alter fatty acid chain saturation to manipulate lipid packing and found septin structures were selectively disrupted at flat regions of the plasma membrane. To determine whether lipid packing is sufficient to impact septin assembly, molecular dynamics simulations were used to design lipid mixtures with varied packing to monitor septin adsorption in vitro. Septins strongly favored loosely packed lipid bilayers, but additional geometrical cues act in conjunction with this membrane property. This work demonstrates that packing defects and geometry jointly regulate septin localization, highlighting how distinct membrane properties are integrated to organize the septin cytoskeleton.