Nathan S. Babcock

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 40 ns (sampled at 100-fs 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.

Improved error-scaling for adiabatic quantum evolutions

We present a new technique that improves the scaling of the error in the adiabatic approximation with respect to the evolution duration, thereby permitting faster transfer at a fixed error tolerance. Our method is conceptually different from previously proposed techniques: it exploits a commonly overlooked phase interference effect that occurs predictably at specific evolution times, suppressing transitions away from the adiabatically transferred eigenstate. Our method can be used in concert with existing adiabatic optimization techniques, such as local adiabatic evolutions or boundary cancelation methods. We perform a full error analysis of our phase interference method along with existing boundary cancelation techniques and show a tradeoff between error-scaling and experimental precision. We illustrate these findings using two examples, showing improved error-scaling for an adiabatic search algorithm and a tunable two-qubit quantum logic gate.

Entanglement of group-II-like atoms with fast measurement for quantum information processing

We construct a scheme for the preparation, pairwise entanglement via exchange interaction, manipulation, and measurement of individual group-II-like neutral atoms (Yb, Sr, etc.). Group-II-like atoms proffer important advantages over alkali metals, including long-lived optical-transition qubits that enable fast manipulation and measurement. Our scheme provides a promising approach for producing weighted graph states, entangled resources for quantum communication, and possible application to fundamental tests of Bell inequalities that close both detection and locality loopholes.

Entanglement and rapid measurement of clock-state qubits in Yb or Sr for quantum information processing

We devise protocols for entangling and rapidly measuring qubits encoded in the clock transitions in Yb or Sr. Our work provides concrete guidelines for experimental realizations of quantum computing and fundamental tests of quantum mechanics.

Rapid measurement of atomic clock-state qubits for violating Bell inequalities

Optical clock-transitions such as the ones in Ytterbium are prime candidates for encoding qubits for quantum information processing applications due to very low decoherence rates. In this work, we investigate the challenges involved in using these prime candidates for fundamental tests of quantum mechanics. We design entangling operations for pairs of indistinguishable atoms trapped in optical tweezers, as well as determine the feasibility of rapid qubit rotation and measurement of qubits encoded in these desirable low-decoherence clock transitions. In particular, we propose multi-photon transitions for fast rotation of qubits, followed by ultrafast readout via resonant multiphoton ionization. The rapid measurement of atomic qubits is crucial for high-speed synchronization of quantum information processors, but is also of interest for tests of Bell inequalities. We investigate a Bell inequality test that avoids the detection loophole in entangled qubits, which are spacelike separated over only a few meters.