arXiv subjects

Travis J. A. Craddock

Publications and source records attributed to Travis J. A. Craddock.

7 recordsLinked to original sources

arXiv2026

Quantum in Biology, Quantum for Biology, and Biology for Quantum: Mapping the Evidence and the Road Ahead

Quantum science and biology now intersect in three complementary directions: quantum in biology, quantum for biology, and biology for quantum. This review provides a structured narrative evidence map of that interface rather than an exhaustive catalogue or formal systematic review. For each topic, we ask what the mechanistic or technological claim is, which quantum resource is invoked, what the strongest experiments and models establish, which classical alternatives or engineering confounds remain competitive, and what decisive tests or benchmarks would most strongly change confidence. The most mature quantum-in-biology cases remain mechanistically constrained tunneling in some enzymatic hydrogen-transfer reactions and radical-pair spin chemistry as a viable framework for magnetoreception, whereas several higher-visibility topics remain suggestive but unresolved under physiological conditions. In quantum for biology, the central issue is whether quantum-enabled tools improve biological inference relative to strong classical baselines under realistic calibration, dose, throughput, and uncertainty constraints. In biology for quantum, the strongest claims arise when biomolecular structure or self-assembly measurably improves fabrication, integration, or robustness in quantum devices. Summary tables in the Appendix provide a compact cross-map view of the current evidence, major confounds, and the experiments or benchmarks most likely to discriminate between competing explanations.

quant-ph↗

arXiv2026

A quantum-like benchmark for context-sensitive associative memory with adaptive plasticity

Learning and memory require a balance between plasticity and stability: synaptic connections must encode new information without collapsing, saturating, or erasing previously useful structure. Associative-memory models can appear to learn successfully when fixed background connectivity already carries part of the task, making it difficult to distinguish genuine recall dynamics from structural assistance. We test this issue using an order-sensitive adaptive-plasticity benchmark for staged associative recall. The benchmark compares a quantum-like associative-memory model with matched real-valued no-phase and Markov-rate controls under the same task schedule, perturbation profiles, weak-support conditions, and plasticity settings. Here, "quantum-like" refers to the modeling formalism, not to a biological claim about quantum computation. We first screen weak structural support and then fix a conservative operating point for factorial comparisons across model families and plasticity mechanisms. The useful weak-support regime is narrow and non-monotonic. Weak structure alone does not rescue recall in the no-plasticity ablation, whereas most useful recall gains arise from adaptive plasticity, especially homeostatic stabilization. The Markov-rate control often achieves stronger raw recall, but the quantum-like model more consistently preserves order sensitivity and stage-dependent organization. These results do not support a universal quantum-like advantage. Instead, they show that model classes are better distinguished by a multi-objective profile combining recall, temporal organization, and context sensitivity than by any single recall score. The benchmark therefore provides a controlled framework for studying context-sensitive memory dynamics under weak support, regulated plasticity, and matched classical comparison.

q-bio.NC↗

arXiv2026

Engineering quantum optical responses of microtubules through tryptophan-network simulations and ultraviolet spectroscopy

Microtubules host dense ultraviolet-absorbing aromatic networks, suggesting an opportunity to engineer their optical response for biotechnology. Here we assess the feasibility of tuning microtubule fluorescence by combining an excitonic radiative-coupling model with molecular-dynamics-derived microtubule-like assemblies and steady-state absorbance and fluorescence measurements in microplate geometries. Simulations quantify how positional and orientational fluctuations reshape radiative rates and quantum yield, and predict how perturbing the tryptophan network by removing a specific site, adding an extra tryptophan at candidate binding pockets, or using mixed modification fractions can modulate emission. Experiments on porcine tubulin dimers and taxol-stabilized microtubules support these trends: polymerization enhances microtubule quantum yield at 280 nm and yields bounded changes at 295 nm due to scattering, while added L-tryptophan reproducibly quenches microtubules at both wavelengths. Together, theory and experiment provide evidence for chemically addressable tuning of microtubule quantum yield and motivate design rules for engineered microtubule photonics.

physics.bio-ph↗

arXiv2026

Quantum Information Flow in Microtubule Tryptophan Networks

Networks of aromatic amino acid residues within microtubules, particularly those formed by tryptophan, may serve as pathways for optical information flow. Ultraviolet excitation dynamics in these networks are typically modeled with effective non-Hermitian Hamiltonians. By extending this approach to a Lindblad master equation that incorporates explicit site geometries and dipole orientations, we track how correlations are generated, routed, and dissipated, while capturing both energy dissipation and information propagation among coupled chromophores. We compare localized injections, fully delocalized preparations, and eigenmode-based initial states. To quantify the emerging quantum-informational structure, we evaluate the $L_1$ norm of coherence, the correlated coherence, and the logarithmic negativity within and between selected chromophore sub-networks. The results reveal a strong dependence of both the direction and persistence of information flow on the type of initial preparation. Superradiant components drive the rapid export of correlations to the environment, whereas subradiant components retain them and slow their leakage. Embedding single tubulin units into larger dimers and spirals reshapes pairwise correlation maps and enables site-selective routing. Scaling to larger ordered lattices strengthens both export and retention channels, whereas static energetic and structural disorder suppresses long-range transport and reduces overall correlation transfer. These findings provide a Lindbladian picture of information flow in cytoskeletal chromophore networks and identify structural and dynamical conditions that transiently preserve nonclassical correlations in microtubules.

quant-ph↗

arXiv2025

Magnetic Field-dependent Isotope Effect Supports Radical Pair Mechanism in Tubulin Polymerization

Weak magnetic fields and isotopes have been shown to influence biological processes; however, the underlying mechanisms remain poorly understood, particularly because the corresponding interaction energies are far below thermal energies, making classical explanations challenging or impossible. Microtubules, dynamic cytoskeletal fibers, offer an ideal system to test weak magnetic field effects due to their self-assembling capabilities, sensitivity to magnetic fields, and their central role in cellular processes. In this study, we use a combination of experiments and simulations to explore how nuclear spin dynamics affect microtubule polymerization by examining interactions between magnesium isotope substitution and weak magnetic fields. Our experiments reveal an isotope-dependent effect, which can be explained via a radical pair mechanism, explicitly arising from nuclear spin properties rather than isotopic mass differences. This nuclear spin-driven isotope effect is notably enhanced under an applied weak magnetic field of approximately 3 mT. Our theoretical model based on radical pairs achieves quantitative agreement with our experimental observations. These results establish a direct connection between quantum spin dynamics and microtubule assembly, providing new insights into how weak magnetic fields influence cellular and biomolecular functions.

physics.bio-ph↗

arXiv2022

Electronic Energy Migration in Microtubules

The repeating arrangement of tubulin dimers confers great mechanical strength to microtubules, which are used as scaffolds for intracellular macromolecular transport in cells and exploited in biohybrid devices. The crystalline order in a microtubule, with lattice constants short enough to allow energy transfer between amino acid chromophores, is similar to synthetic structures designed for light harvesting. After photoexcitation, can these amino acid chromophores transfer excitation energy along the microtubule like a natural or artificial light-harvesting system? Here, we use tryptophan autofluorescence lifetimes to probe inter-tryptophan energy hopping in tubulin and microtubules. By studying how quencher concentration alters tryptophan autofluorescence lifetimes, we demonstrate that electronic energy can diffuse over 6.6 nm in microtubules. We discover that while diffusion lengths are influenced by tubulin polymerization state (free tubulin versus tubulin in the microtubule lattice), they are not significantly altered by the average number of protofilaments (13 versus 14). We also demonstrate that the presence of the anesthetics etomidate and isoflurane reduce exciton diffusion. Energy transport as explained by conventional Förster theory (accommodating for interactions between tryptophan and tyrosine residues) does not sufficiently explain our observations. Our studies indicate that microtubules are, unexpectedly, effective light harvesters.

physics.bio-ph↗

arXiv2018

Water Bridging Dynamics of Polymerase Chain Reaction in the Gauge Theory Paradigm of Quantum Fields

We discuss the role of water bridging the DNA-enzyme interaction by resorting to recent results showing that London dispersion forces between delocalized electrons of base pairs of DNA are responsible for the formation of dipole modes that can be recognized by \textit{Taq} polymerase. We describe the dynamic origin of the high efficiency and precise targeting of \textit{Taq} activity in PCR. The spatiotemporal distribution of interaction couplings, frequencies, amplitudes, and phase modulations comprise a pattern of fields which constitutes the electromagnetic image of DNA in the surrounding water, which is what the polymerase enzyme actually recognizes in the DNA water environment. The experimental realization of PCR amplification, achieved through replacement of the DNA template by the treatment of pure water with electromagnetic signals recorded from viral and bacterial DNA solutions, is found consistent with the gauge theory paradigm of quantum fields.

q-bio.OT↗