arXiv subjects

Michael Lynch

Publications and source records attributed to Michael Lynch.

11 recordsLinked to original sources

arXiv2026

The Emergence of Life in the Light of Evolution

The origin of life is often framed primarily as a chemical problem, yet life s defining feature is evolution. Advances in geochemistry, prebiotic chemistry and molecular biology have suggested diverse scenarios for the emergence of genomes, metabolism and cellular compartments on the early Earth, but most of these models ignore the relevance of a population genetics perspective. Here, we argue that origin of life research must expand from asking simply how life began to exploring how it evolved from pre biological systems. Synthesizing evidence from comparative genomics, phylogenetics, biochemistry, and geoscience, we emphasize that the last universal common ancestor (LUCA) was already a complex, ecologically adapted population of cells far removed from the starting point of life, implying a deep, pre LUCA evolutionary history. We highlight how population genetics, ecology, and synthetic biology can constrain origin of life scenarios by making explicit the roles of selection, drift, mutation, horizontal gene transfer, parasites and compartmentalization in shaping early communities. Finally, we outline an evolutionary research agenda spanning proto metabolic autocatalytic networks, protocells, and the emergence of translation and the transition to DNA genomes, such that qualitative models can be formalized through evolution driven hypotheses testable with theory and laboratory experiments, including those with synthetic cells.

q-bio.PE↗

arXiv2026

Hadronic contributions to $\alpha(Q^{2})$ and $\sin^{2}\theta_{W}(Q^{2})$ from spectral reconstruction of lattice-QCD data

We present preliminary results from a lattice-QCD study of the hadronic contributions to the running of the electromagnetic coupling, $\Delta\alpha(Q^2)$, and the electroweak mixing angle, $\Delta\sin^2\theta_{W}(Q^2)$. Using $N_f = 2+1+1$ HISQ ensembles at physical quark masses, we discuss the challenges posed by strong statistical correlations in the time-momentum representation and propose a spectral-reconstruction strategy to obtain controlled continuum-extrapolated results across the full energy range.

hep-lat↗

arXiv2025

High-Precision Scale Setting with the Omega-Baryon Mass and Gradient Flow

The gradient-flow scale $w_0$ in lattice QCD is determined using the mass of the $\Omega^-$ baryon to set the physical scale. Nine ensembles using the highly improved staggered quark (HISQ) action with lattice spacings of 0.15 fm down to 0.04 fm are used, seven of which have nearly physical light-quark masses. Electromagnetic corrections to the $\Omega^-$ mass are defined in order to compute a pure-QCD $\Omega$ mass. The final result is $w_0 = 0.17187(68)$ fm, corresponding to a relative uncertainty of 0.40% and a central value in good agreement with previous calculations in the literature.

hep-lat↗

arXiv2025

Decoding the Hot-Mitochondrion Paradox

In a 2018 paper and a subsequent article published in 2023, researchers reported that mitochondria maintain temperatures 10oC-15oC higher than the surrounding cytoplasm-a finding that deviates by five to six orders of magnitude from theoretical predictions based on Fourier's law of heat conduction. In 2022, we proposed a solution to this apparent paradox. In the present perspective, we build upon that framework and introduce new ideas to further unravel how a biological membrane-whether of an organelle or a whole cell-can become significantly warmer than its environment. We propose that ion-translocating proteins embedded in the inner mitochondrial membrane (IMM) can be modeled as ratchet engines, introducing a novel, previously overlooked mode of heat transfer. This mechanism, coupled with localized heat release during the cyclical dehydration-translocation-hydration of ions through membrane proteins, may generate transient but substantial temperature spikes. The cumulative thermal occupancy of these microscopic events across the three-dimensional surface of the IMM can account for the elevated temperatures detected by molecular probes.

q-bio.SC↗

arXiv2025

Costs and benefits of phytoplankton motility

The motility skills of phytoplankton have evolved and persisted over millions of years, primarily in response to factors such as nutrient and light availability, temperature and viscosity gradients, turbulence, and predation pressure. Phytoplankton motility is broadly categorized into swimming and buoyancy regulation. Despite studies in the literature exploring the motility costs and benefits of phytoplankton, there remains a gap in our integrative understanding of direct and indirect energy expenditures, starting from when an organism initiates movement due to any biophysical motive, to when the organism encounters intracellular and environmental challenges. Here we gather available pieces of this puzzle from literature in biology, physics, and oceanography to paint an overarching picture of our current knowledge. The characterization of sinking and rising behavior as passive motility has resulted in the concept of sinking and rising internal efficiency being overlooked. We define this efficiency based on any energy dissipation associated with processes of mass density adjustment, as exemplified in structures like vacuoles, gas vesicles, and frustules. We propose that sinking and rising are active motility processes involving non-visible mechanisms, as species demonstrate active and rapid strategies in response to turbulence, predation risk, and gradients of nutrients, light, temperature, and viscosity. In swimmers, internal and external motility efficiencies have been extensively explored in theoretical studies, yet they are largely neglected in energetic estimates within marine and freshwater sciences. Identifying the dissipative processes associated with swimming and buoyancy-regulating machinery offers deeper insight into motility costs relative to an organism's total metabolic rate.

physics.bio-ph↗

arXiv2024

Hadronic vacuum polarization for the muon $g-2$ from lattice QCD: Long-distance and full light-quark connected contribution

We present results for the dominant light-quark connected contribution to the long-distance window (LD) of the hadronic vacuum polarization contribution (HVP) to the muon $g-2$ from lattice quantum chromodynamics (QCD). Specifically, with a new determination of the lattice scale on MILC's physical-mass HISQ ensembles, using the $\Omega^-$ baryon mass, we obtain a result of $400.2(2.3)_{\mathrm{stat}}(3.7)_{\mathrm{syst}}[4.3]_{\mathrm{total}} \times 10^{-10}$. Summing this result with our recent determinations of the light-quark connected contributions to the short- (SD) and intermediate-distance (W) windows, we obtain a sub-percent precision determination of the light-quark-connected contribution to HVP of $655.5(2.3)_{\mathrm{stat}}(3.9)_{\mathrm{syst}}[4.5]_{\mathrm{total}} \times 10^{-10}$. Finally, as a consistency check, we verify that an independent analysis of the full contribution is in agreement with the sum of individual windows. We discuss our future plans for improvements of our HVP calculations to meet the target precision of the Fermilab $g-2$ experiment.

hep-lat↗

arXiv2024

Hadronic vacuum polarization for the muon $g-2$ from lattice QCD: Complete short and intermediate windows

We present complete results for the hadronic vacuum polarization (HVP) contribution to the muon anomalous magnetic moment $a_\mu$ in the short- and intermediate-distance window regions, which account for roughly 10% and 35% of the total HVP contribution to $a_\mu$, respectively. In particular, we perform lattice-QCD calculations for the isospin-symmetric connected and disconnected contributions, as well as corrections due to strong isospin-breaking. For the short-distance window observables, we investigate the so-called log-enhancement effects as well as the significant oscillations associated with staggered quarks in this region. For the dominant, isospin-symmetric light-quark connected contribution, we obtain $a^{ll,\,{\mathrm{SD}}}_{\mu}(\mathrm{conn.}) = 48.139(11)_{\mathrm{stat}}(91)_{\mathrm{syst}}[92]_{\mathrm{total}} \times 10^{-10}$ and $a^{ll,\,{\mathrm{W}}}_{\mu}(\mathrm{conn.}) = 206.90(14)_{\mathrm{stat}}(61)_{\mathrm{syst}}[63]_{\mathrm{total}} \times 10^{-10}$. We use Bayesian model averaging to fully estimate the covariance matrix between the individual contributions. Our determinations of the complete window contributions are $a^{{\mathrm{SD}}}_{\mu} = 69.05(1)_{\mathrm{stat}}(21)_{\mathrm{syst}}[21]_{\mathrm{total}} \times 10^{-10}$ and $a^{{\mathrm{W}}}_{\mu} = 236.45(17)_{\mathrm{stat}}(83)_{\mathrm{syst}}[85]_{\mathrm{total}} \times 10^{-10}$. This work is part of our ongoing effort to compute all contributions to HVP with an overall uncertainty at the few permille level.

hep-lat↗

arXiv2023

Light-quark connected intermediate-window contributions to the muon $g-2$ hadronic vacuum polarization from lattice QCD

We present a lattice-QCD calculation of the light-quark connected contribution to window observables associated with the leading-order hadronic vacuum polarization contribution to the anomalous magnetic moment of the muon, $a_\mu^{\mathrm{HVP,LO}}$. We employ the MILC Collaboration's isospin-symmetric QCD gauge-field ensembles, which contain four flavors of dynamical highly-improved-staggered quarks with four lattice spacings between $a\approx 0.06$-$0.15$~fm and close-to-physical quark masses. We consider several effective-field-theory-based schemes for finite-volume and other lattice corrections and combine the results via Bayesian model averaging to obtain robust estimates of the associated systematic uncertainties. After unblinding, our final results for the intermediate and ``W2'' windows are $a^{ll,{\mathrm W}}_{\mu}(\mathrm{conn.})=206.6(1.0) \times 10^{-10}$ and $a^{ll,\mathrm {W2}}_{\mu}(\mathrm{conn.}) = 100.7(3.2)\times 10^{-10}$, respectively.

hep-lat↗

arXiv2021

Fibrosis-Net: A Tailored Deep Convolutional Neural Network Design for Prediction of Pulmonary Fibrosis Progression from Chest CT Images

Pulmonary fibrosis is a devastating chronic lung disease that causes irreparable lung tissue scarring and damage, resulting in progressive loss in lung capacity and has no known cure. A critical step in the treatment and management of pulmonary fibrosis is the assessment of lung function decline, with computed tomography (CT) imaging being a particularly effective method for determining the extent of lung damage caused by pulmonary fibrosis. Motivated by this, we introduce Fibrosis-Net, a deep convolutional neural network design tailored for the prediction of pulmonary fibrosis progression from chest CT images. More specifically, machine-driven design exploration was leveraged to determine a strong architectural design for CT lung analysis, upon which we build a customized network design tailored for predicting forced vital capacity (FVC) based on a patient's CT scan, initial spirometry measurement, and clinical metadata. Finally, we leverage an explainability-driven performance validation strategy to study the decision-making behaviour of Fibrosis-Net as to verify that predictions are based on relevant visual indicators in CT images. Experiments using a patient cohort from the OSIC Pulmonary Fibrosis Progression Challenge showed that the proposed Fibrosis-Net is able to achieve a significantly higher modified Laplace Log Likelihood score than the winning solutions on the challenge. Furthermore, explainability-driven performance validation demonstrated that the proposed Fibrosis-Net exhibits correct decision-making behaviour by leveraging clinically-relevant visual indicators in CT images when making predictions on pulmonary fibrosis progress. While Fibrosis-Net is not yet a production-ready clinical assessment solution, we hope that its release in open source manner will encourage researchers, clinicians, and citizen data scientists alike to leverage and build upon it.

eess.IV↗

arXiv2018

The Supersingularity of Hurwitz Curves

We study when Hurwitz curves are supersingular. Specifically, we show that the curve $H_{n,\ell}: X^nY^\ell + Y^nZ^\ell + Z^nX^\ell = 0$, with $n$ and $\ell$ relatively prime, is supersingular over the finite field $\mathbb{F}_{p}$ if and only if there exists an integer $i$ such that $p^i \equiv -1 \bmod (n^2 - n\ell + \ell^2)$. If this holds, we prove that it is also true that the curve is maximal over $\mathbb{F}_{p^{2i}}$. Further, we provide a complete table of supersingular Hurwitz curves of genus less than 5 for characteristic less than 37.

math.NT↗

arXiv2000

The Spallation Neutron Source (SNS) Linac RF System

The SNS linac accelerates an average beam current of 2 mA to an energy of 968 MeV. The linac is pulsed at 60 Hz with an H- beam pulse of 1 ms. The first 185 Mev of the linac uses normal conducting cavities, and the remaining length of the linac uses superconducting cavities. The linac operates at 402.5 MHz up to 87 MeV and then changes to 805 MHz for the remainder. This paper gives an overview of the Linac RF system. The overview includes a description and configuration of the high power RF components, the HV converter/modulator, and the RF controls. Issues and tradeoffs in the RF system will be discussed, especially with regards to the use of pulsed superconducting cavities.

physics.acc-ph↗