arXiv subjects

Nathan S. Babcock

Publications and source records attributed to Nathan S. Babcock.

5 recordsLinked to original sources

arXiv2025

Physical Principles of Quantum Biology

This technical monograph provides a comprehensive overview of the field of quantum biology. It approaches quantum biology from a physical perspective with core quantum mechanical concepts presented foremost to provide a theoretical foundation for the field. An extensive body of research is covered to clarify the significance of quantum biology as a scientific field, outlining the field's long-standing importance in the historical development of quantum theory. This lays the essential groundwork to enable further advances in nanomedicine and biotechnology. Written for academics, biological science researchers, physicists, biochemists, medical technologists, and students of quantum mechanics, this text brings clarity to fundamental advances being made in the emerging science of quantum biology.

physics.bio-ph↗

arXiv2024

Quantum-enhanced photoprotection in neuroprotein architectures emerges from collective light-matter interactions

We study here the collective quantum optical effect of superradiance in neuroprotein architectures. This phenomenon arises from the interaction of the electromagnetic field with an organized network of tryptophan chromophores, where each can be effectively modeled as a two-level quantum emitter. Building on our prior experimental confirmation of single-photon superradiance in microtubules, we predict that bright superradiant states will also emerge in simulated actin filament bundles and amyloid fibrils, which manifests in the form of high quantum yields that are robust to static disorder up to five times that of room temperature. For microtubules and amyloid fibrils, the quantum yield is enhanced with increasing system size, contrary to the conventional expectations of quantum effects in a thermally equilibrated environment. We conduct our analyses using a non-Hermitian Hamiltonian derived from the Lindblad equation for an open quantum system that describes the interaction of a chromophore network with the electromagnetic field, in the single-photon limit. Our detailed quantum yield predictions in realistic neuroprotein structures -- including analysis of the potential information-processing applications of correlated superradiant and subradiant states at divergent timescales -- provide motivation for a range of in vitro experiments to confirm these quantum enhancements, which can serve in vivo as a mechanism for dissipating or downconverting high-energy UV metabolic photon emissions in intensely oxidative pathological environments, including those found in Alzheimer's disease and related dementias.

physics.bio-ph↗

arXiv2011

Improved Error-Scaling for Adiabatic Quantum State Transfer

We present a technique that dramatically improves the accuracy of adiabatic state transfer for a broad class of realistic Hamiltonians. For some systems, the total error scaling can be quadratically reduced at a fixed maximum transfer rate. These improvements rely only on the judicious choice of the total evolution time. Our technique is error-robust, and hence applicable to existing experiments utilizing adiabatic passage. We give two examples as proofs-of-principle, showing quadratic error reductions for an adiabatic search algorithm and a tunable two-qubit quantum logic gate.

quant-ph↗

arXiv2010

Surface residues dynamically organize water bridges to enhance electron transfer between proteins

Cellular energy production depends on electron transfer (ET) between proteins. In this theoretical study, we investigate the impact of structural and conformational variations on the electronic coupling between the redox proteins methylamine dehydrogenase and amicyanin from Paracoccus denitrificans. We used molecular dynamics simulations to generate configurations over a duration of 40ns (sampled at 100fs intervals) in conjunction with an ET pathway analysis to estimate the ET coupling strength of each configuration. In the wild type complex, we find that the most frequently occurring molecular configurations afford superior electronic coupling due to the consistent presence of a water molecule hydrogen-bonded between the donor and acceptor sites. We attribute the persistence of this water bridge to a "molecular breakwater" composed of several hydrophobic residues surrounding the acceptor site. The breakwater supports the function of nearby solvent-organizing residues by limiting the exchange of water molecules between the sterically constrained ET region and the more turbulent surrounding bulk. When the breakwater is affected by a mutation, bulk solvent molecules disrupt the water bridge, resulting in reduced electronic coupling that is consistent with recent experimental findings. Our analysis suggests that, in addition to enabling the association and docking of the proteins, surface residues stabilize and control interprotein solvent dynamics in a concerted way.

physics.bio-ph↗

arXiv2007

Entangling identical bosons in optical tweezers via exchange interaction

We first devise a scheme to perform a universal entangling gate via controlled collisions between pairs of atomic qubits trapped with optical tweezers. Second, we present a modification to this scheme to allow the preparation of atomic Bell pairs via selective excitation, suitable for quantum information processing applications that do not require universality. Both these schemes are enabled by the inherent symmetries of identical composite particles, as originally proposed by Hayes et al. Our scheme provides a technique for producing weighted graph states, entangled resources for quantum communication, and a promising approach to performing a "loophole free" Bell test in a single laboratory.

quant-ph↗