Publications

Mutations in signal transduction pathways lead to various diseases including cancers. MEK1 kinase, encoded by the human MAP2K1 gene, is one of the central components of the MAPK pathway and more than a hundred somatic mutations in MAP2K1 gene were identified in various tumors. Germline mutations deregulating MEK1 also lead to congenital abnormalities, such as the Cardiofaciocutaneous Syndrome and Arteriovenous Malformation. Evaluating variants associated with a disease is a challenge and computational genomic approaches aid in this process. Establishing evolutionary history of a gene improves computational prediction of disease-causing mutations; however, the evolutionary history of MEK1 is not well understood. Here, by revealing a precise evolutionary history of MEK1 we construct a well-defined dataset of MEK1 metazoan orthologs, which provides sufficient depth to distinguish between conserved and variable amino acid positions. We used this dataset to match known and predicted disease-causing and benign mutations to evolutionary changes observed in corresponding amino acid positions. We found that all known and the vast majority of suspected disease-causing mutations are evolutionarily intolerable. We selected several MEK1 mutations that cannot be unambiguously assessed by automated variant prediction tools, but that are confidently identified as evolutionary intolerant and thus “damaging” by our approach, for experimental validation in Drosophila. In all cases, evolutionary intolerant variants caused increased mortality and severe defects in fruit fly embryos confirming their damaging nature predicted by out computational strategy. We anticipate that our analysis will serve as a blueprint to help evaluate known and novel missense variants in MEK1 and that our approach will contribute to improving automated tools for disease-associated variant interpretation.

During cell division, the mitotic spindle forms inside cells and segregates chromosomes. The spindle's position sets the division plane, which is essential for proper growth and development. Force mechanisms regulating the position of the spindle are not yet understood. Here, we develop a coarse-grained model of spindles in cells, which accounts for microtubule dynamics, pulling forces from cortically bounded motor proteins, and fluid drag. We show that the spindle's resistance to rotation is largely driven by pulling forces from the motor proteins rather than the drag imposed by the cytoplasm. We also show that the arrangement of motor proteins affects the spindle's resistance to rotation for configurations where multiple motors stack at the same region, the spindle's resistance to rotation significantly reduces. Our findings are consistent with measurements in human tissue culture cells, where the spindle resistance to the rotation has been quantified.

Observer motion and continuous deformations of objects and surfaces imbue natural videos with distinct temporal structures, enabling partial prediction of future frames from past ones. Conventional methods first estimate local motion, or optic flow, and then use it to predict future frames by warping or copying content. Here, we explore a more direct methodology, in which each frame is mapped into a learned representation space where the structure of temporal evolution is more readily accessible. Motivated by the geometry of the Fourier shift theorem and its group-theoretic generalization, we formulate a simple architecture that represents video frames in learned local polar coordinates. Specifically, we construct networks in which pairs of convolutional channel coefficients are treated as complex-valued, and are optimized to evolve with slowly varying amplitudes and linearly advancing phases. We train these models on next-frame prediction in natural videos, and compare their performance with that of conventional methods using optic flow as well as predictive neural networks. We find that the polar predictor achieves better performance while remaining interpretable and fast, thereby demonstrating the potential of a flow-free video processing methodology that is trained end-to-end to predict natural video content.

Neuroscience has long been an essential driver of progress in artificial intelligence (AI). We propose that to accelerate progress in AI, we must invest in fundamental research in NeuroAI. A core component of this is the embodied Turing test, which challenges AI animal models to interact with the sensorimotor world at skill levels akin to their living counterparts. The embodied Turing test shifts the focus from those capabilities like game playing and language that are especially well-developed or uniquely human to those capabilities – inherited from over 500 million years of evolution – that are shared with all animals. Building models that can pass the embodied Turing test will provide a roadmap for the next generation of AI.

We consider the quantum electrodynamics of single photons in arrays of one-way waveguides, each containing many atoms. We investigate both chiral and antichiral arrays, in which the group velocities of the waveguides are the same or alternate in sign, respectively. We find that in the continuum limit, the one-photon amplitude obeys a Dirac equation. In the chiral case, the Dirac equation is hyperbolic, while in the antichiral case it is elliptic. This distinction has implications for the nature of photon transport in waveguide arrays. Our results are illustrated by numerical simulations.

Neuroscience has long been an essential driver of progress in artificial intelligence (AI). We propose that to accelerate progress in AI, we must invest in fundamental research in NeuroAI. A core component of this is the embodied Turing test, which challenges AI animal models to interact with the sensorimotor world at skill levels akin to their living counterparts. The embodied Turing test shifts the focus from those capabilities like game playing and language that are especially well-developed or uniquely human to those capabilities – inherited from over 500 million years of evolution – that are shared with all animals. Building models that can pass the embodied Turing test will provide a roadmap for the next generation of AI.

We propose a new method to extend the size of a quantum computation beyond the number of physical qubits available on a single device. This is accomplished by randomly inserting measure-and-prepare channels to express the output state of a large circuit as a separable state across distinct devices. Our method employs randomized measurements, resulting in a sample overhead that is O(4

Correlated electron states are at the root of many important phenomena including unconventional superconductivity (USC), where electron-pairing arises from repulsive interactions. Computing the properties of correlated electrons, such as the critical temperature T

Ion transport measurements are widely used as an indirect probe for various properties of confined electrolytes. It is generally assumed that the ion concentration in a nanoscale channel is equal to the ion concentration in the macroscopic reservoirs it connects to, with deviations arising only in the presence of surface charges on the channel walls. Here, we show that this assumption may break down even in a neutral channel, due to electrostatic correlations between the ions arising in the regime of interaction confinement, where Coulomb interactions are reinforced due to the presence of the channel walls. We focus on a one-dimensional channel geometry, where an exact evaluation of the electrolyte's partition function is possible with a transfer operator approach. Our exact solution reveals that in nanometre-scale channels, the ion concentration is generally lower than in the reservoirs, and depends continuously on the bulk salt concentration, in contrast to conventional mean-field theory that predicts an abrupt filling transition. We develop a modified mean-field theory taking into account the presence of ion pairs that agrees quantitatively with the exact solution and provides predictions for experimentally-relevant observables such as the ionic conductivity. Our results will guide the interpretation of nanoscale ion transport measurements.

Irradiating solids with ultrashort laser pulses is known to initiate femtosecond timescale magnetization dynamics. However, sub-femtosecond spin dynamics have not yet been observed or predicted. Here, we explore ultrafast light-driven spin dynamics in a highly non-resonant strong-field regime. Through state-of-the-art ab-initio calculations, we predict that a non-magnetic material can be transiently transformed into a magnetic one via dynamical extremely nonlinear spin-flipping processes, which occur on attosecond timescales and are mediated by a combination of multi-photon and spin-orbit interactions. These are non-perturbative non-resonant analogues to the inverse Faraday effect that build up from cycle-to-cycle as electrons gain angular momentum. Remarkably, we show that even for linearly polarized driving, where one does not intuitively expect any magnetic response, the magnetization transiently oscillates as the system interacts with light. This oscillating response is enabled by transverse anomalous light-driven currents in the solid, and typically occurs on timescales of 500 attoseconds. We further demonstrate that the speed of magnetization can be controlled by tuning the laser wavelength and intensity. An experimental set-up capable of measuring these dynamics through pump-probe transient absorption spectroscopy is outlined and simulated. Our results pave the way for new regimes of ultrafast manipulation of magnetism.