arXiv subjects

Amara McCune

Publications and source records attributed to Amara McCune.

7 recordsLinked to original sources

arXiv2026

Transcription rate dynamics and RNA copy number noise: General relations and data-driven predictions

Stochastic models of gene expression typically begin with a microscopic model of transcription and propagate its statistics to the RNA distribution. Here we develop a doubly stochastic framework in which RNA production is Poisson conditional on a time-varying transcription rate $\lambda(t)$. For RNA lifetimes drawn independently from an arbitrary finite-mean distribution, we derive the RNA Fano factor in terms of the lifetime survival function and the autocovariance of $\lambda(t)$. For a Poisson degradation process with rate $\mu$, the survival kernel provides an exponential temporal filter, and the result depends only on the mean, variance, and normalized autocorrelation of $\lambda(t)$. These quantities may be calculated from an explicit rate model or, under ergodicity and adequate sampling, estimated from a sufficiently long rate trajectory. We validate the data-driven estimator using simulated transcription-rate trajectories, without supplying the known autocorrelation to the estimator. We also obtain exact analytical results for transcription-rate dynamics modeled by a discrete M/M/1 process and by drift-diffusion with reflecting, periodic, or first-passage-reset boundaries, and verify each result by direct simulation of the coupled transcription-rate and RNA copy-number processes.

physics.bio-ph↗

arXiv2026

MolCryst-MLIPs: A Machine-Learned Interatomic Potentials Database for Molecular Crystals

We present an open Molecular Crystal (MC) database of Machine-Learned Interatomic Potentials (MLIP) called MolCryst-MLIPs. The first release comprises fine-tuned MACE models for nine molecular crystal systems---Benzamide, Benzoic acid, Coumarin, Durene, Isonicotinamide, Nicotinic acid , Niacinamide, Pyrazinamide, and Resorcinol---developed using the Automated Machine Learning Pipeline (AMLP), which streamlines the entire MLIP development workflow, from reference data generation to model training and validation, into a reproducible and user-friendly pipeline. Models are fine-tuned from the MACE-MH-1 foundation model omol head), yielding a mean energy MAE of 0.141 kJ/mol/atom and a mean force MAE of 0.648 kJ/mol/Angstrom across all systems. Benchmarked against three state-of-the-art foundation models on the DFT-labelled polymorph set, only the fine-tuned models resolve the polymorphic energy landscape. Dynamical stability and structural integrity, as assessed through energy conservation, P2 orientational order parameters, and radial distribution functions, are evaluated using molecular dynamics simulations. The released models and datasets constitute a growing open database of validated MLIPs, ready for production MD simulations of molecular crystal polymorphism across the polymorphic landscape of each target compound under different thermodynamic conditions.

cs.LG↗

arXiv2024

An Effective Cosmological Collider

Effective field theories (EFTs) of heavy particles coupled to the inflaton are rife with operator redundancies, frequently obscured by sensitivity to both boundary terms and field redefinitions. We initiate a systematic study of these redundancies by establishing a minimal operator basis for an archetypal example, the abelian gauge-Higgs-inflaton EFT. Working up to dimension 9, we show that certain low-dimensional operators are entirely redundant and identify new non-redundant operators with potentially interesting cosmological collider signals. Our methods generalize straightforwardly to other EFTs of heavy particles coupled to the inflaton.

hep-ph↗

arXiv2023

Dark Matter in A Mirror Solution to the Strong CP Problem

We study thermal production of dark matter (DM) in a realization of the minimal models of Ref.~\cite{Bonnefoy:2023afx}, where parity is used to solve the strong CP problem by transforming the entire Standard Model (SM) into a mirror copy. Although the mirror electron $e^{\prime}$ is a good DM candidate, its viability is mired by the presence of the mirror up-quark $u^{\prime}$, whose abundance is intimately related to the $e^{\prime}$ abundance and must be suppressed. This can be achieved through a sequential freeze-in mechanism, where mirror photons are first produced from SM gluons, and then the mirror photons produce $e'$. After computing the details of this double freeze-in, we discuss the allowed parameter space of the model, which lies at the threshold of experimental observations. We find that this origin of $e'$ DM requires a low reheating temperature after inflation and is consistent with the baryon asymmetry arising from leptogenesis, providing mirror neutrinos have a significant degeneracy. Finally, we show that this $e'$ DM is not compatible with Higgs Parity, the simplest scheme with exact parity, unless SM parameters deviate significantly from their central values or the minimal model is extended.

hep-ph↗

arXiv2023

Gravitational Waves from Stochastic Scalar Fluctuations

We present a novel mechanism for gravitational wave generation in the early Universe. Light spectator scalar fields during inflation can acquire a blue-tilted power spectrum due to stochastic effects. We show that this effect can lead to large curvature perturbations at small scales (induced by the spectator field fluctuations) while maintaining the observed, slightly red-tilted curvature perturbations at large cosmological scales (induced by the inflaton fluctuations). Along with other observational signatures, such as enhanced dark matter substructure, large curvature perturbations can induce a stochastic gravitational wave background (SGWB). The predicted strength of SGWB in our scenario, $\Omega_{\rm GW}h^2 \simeq 10^{-20} - 10^{-15}$, can be observed with future detectors, operating between $10^{-5}$ Hz and 10 Hz. We note that, in order to accommodate the newly reported NANOGrav observation, one could consider the same class of spectator models. At the same time, one would need to go beyond the simple benchmark considered here and consider a regime in which a misalignment contribution is also important.

astro-ph.CO↗

arXiv2021

The Muon Smasher's Guide

We lay out a comprehensive physics case for a future high-energy muon collider, exploring a range of collision energies (from 1 to 100 TeV) and luminosities. We highlight the advantages of such a collider over proposed alternatives. We show how one can leverage both the point-like nature of the muons themselves as well as the cloud of electroweak radiation that surrounds the beam to blur the dichotomy between energy and precision in the search for new physics. The physics case is buttressed by a range of studies with applications to electroweak symmetry breaking, dark matter, and the naturalness of the weak scale. Furthermore, we make sharp connections with complementary experiments that are probing new physics effects using electric dipole moments, flavor violation, and gravitational waves. An extensive appendix provides cross section predictions as a function of the center-of-mass energy for many canonical simplified models.

hep-ph↗

arXiv2020

P not PQ

Parity solutions to the strong CP problem are a compelling alternative to approaches based on Peccei-Quinn symmetry, particularly given the expected violation of global symmetries in a theory of quantum gravity. The most natural of these solutions break parity at a low scale, giving rise to a host of experimentally accessible signals. We assess the status of the simplest parity-based solution in light of LHC data and flavor constraints, highlighting the prospects for near-future tests at colliders, tabletop experiments, and gravitational wave observatories. The origin of parity breaking and associated gravitational effects play crucial roles, providing new avenues for discovery through EDMs and gravity waves. These experimental opportunities underline the promise of generalized parity, rather than Peccei-Quinn symmetry, as a robust and testable solution to the strong CP problem.

hep-ph↗