arXiv subjects

Maria Yampolskaya

Publications and source records attributed to Maria Yampolskaya.

5 recordsLinked to original sources

arXiv2026

Collective gene dynamics leave signatures of decision landscapes in cell fate coordinates

Multicellular organisms contain a wide variety of highly specialized cell types. The consistency and robustness of developmental trajectories suggest that complex gene regulatory networks effectively act as low-dimensional cell fate landscapes. Prior work inspired by dynamical systems theory argues that cell fate transitions fall into universal decision-making classes, but the theory connecting these geometric landscapes to high-dimensional gene expression space is still in its infancy. Here, we introduce a phenomenological model that identifies experimental signatures of decision-making classes in single-cell RNA-sequencing time-series data. The model combines low-dimensional gradient-like dynamics with high-dimensional Hopfield networks to capture the interplay between cell fate, gene expression, and signaling. We apply the framework to experimental mouse data on maturing lung alveolar cells and lineage-traced hematopoietic differentiation and show that the measured cell fate dynamics are consistent with developmental landscapes containing intermediate progenitors and saddle points. We further show that the framework can be used to understand spatial patterning and cell fate organization, focusing on Notch signaling in lung airways. Together, these results provide evidence that collective transcriptomic dynamics carry signatures of landscape features associated with universal decision-making classes.

q-bio.CB↗

arXiv2025

Hopfield Networks as Models of Emergent Function in Biology

Hopfield models, originally developed to study memory retrieval in neural networks, have become versatile tools for modeling diverse biological systems in which function emerges from collective dynamics. In this review, we provide a pedagogical introduction to both classical and modern Hopfield networks from a biophysical perspective. After presenting the underlying mathematics, we build physical intuition through three complementary interpretations of Hopfield dynamics: as noise discrimination, as a geometric construction defining a natural coordinate system in pattern space, and as gradient-like descent on an energy landscape. We then survey recent applications of Hopfield networks a variety of biological setting including cellular differentiation and epigenetic memory, molecular self-assembly, and spatial neural representations.

physics.bio-ph↗

arXiv2021

Order-of-Magnitude Beam Current Improvement in Compact Cyclotrons

There is great need for high intensity proton beams from compact particle accelerators in particle physics, medical isotope production, and materials- and energy-research. To address this need, we present, for the first time, a design for a compact isochronous cyclotron that will be able to deliver 10 mA of 60 MeV protons - an order of magnitude higher than on-market compact cyclotrons and a factor four higher than research machines. A key breakthrough is that vortex motion is incorporated in the design of a cyclotron, leading to clean extraction. Beam losses on the septa of the electrostatic extraction channels stay below 50 W (a factor four below the required safety limit), while maintaining good beam quality. We present a set of highly accurate particle-in-cell simulations, and an uncertainty quantification of select beam input parameters using machine learning, showing the robustness of the design. This design can be utilized for beams for experiments in particle and nuclear physics, materials science and medical physics as well as for industrial applications.

physics.acc-ph↗

arXiv2018

First Commissioning Results of the Multicusp Ion Source at MIT (MIST-1) for H$_2^+$

IsoDAR is an experiment under development to search for sterile neutrinos using the isotope Decay-At-Rest (DAR) production mechanism, where protons impinging on $^9$Be create neutrons which capture on $^7$Li which then beta-decays producing $\barν_e$. As this will be an isotropic source of $\barν_e$, the primary driver current must be large (10 mA cw) for IsoDAR to have sufficient statistics to be conclusive within 5 years of running. H$_2^+$ was chosen as primary ion to overcome some of the space-charge limitations during low energy beam transport and injection into a compact cyclotron. The H$_2^+$ will be stripped into protons before the target. At MIT, a multicusp ion source (MIST-1) was designed and built to produce a high intensity beam with a high H$_2^+$ fraction. MIST-1 is now operational at the Plasma Science and Fusion Center (PSFC) at MIT and under commissioning.

physics.acc-ph↗

arXiv2018

The Isostatic Conjecture

We show that a jammed packing of disks with generic radii, in a generic container, is such that the minimal number of contacts occurs and there is only one dimension of equilibrium stresses. We also point out some connections to packings with different radii and results in the theory of circle packings whose graph forms a triangulation of a given topological surface. We also point out a counterexample, due to F. Nazarov, to a previous conjecture that that triangulated packings with fixed numbers of disks with fixed numbers of disks for each radius claiming that such packings were the most dense.

math.MG↗