arXiv subjects

David Pekker

Publications and source records attributed to David Pekker.

At least 19 recordsLinked to original sources

arXiv2026

Polyformer: a generative framework for thermodynamic modeling of polymeric molecules

The classic paradigm of structural biology is that the sequence of a biomolecule (protein, nucleic acid, lipid, etc) determines its conformation (shape) which determines its biological function. Protein folding programs like AlphaFold address this paradigm by predicting the single best conformation given a sequence that defines the molecule. However, biomolecules are not static structures, and their conformational ensemble determines their function. We present the Polyformer -- a generative framework for thermodynamic modeling of polymeric molecules. Given the sequence and temperature (or another thermodynamic variable), the Polyformer generates conformations faithful to the molecule's thermodynamic conformational ensemble. It is the first generative model that solves three problems simultaneously: how does a molecule fold, what is its conformational ensemble, and how does the conformational ensemble change as we change physical temperature. As a concrete test case, we apply Polyformer to protein domains with 50-111 residues and report good agreement of model predictions to Molecular Dynamics (MD) trajectories.

q-bio.BM↗

arXiv2026

A superconducting quantum circuit single artificial atom maser

We demonstrate a circuit QED analog of an atomic micromaser that utilizes an artificial, multi level atom, pumped into a population-inverted state by a microwave tone, as the gain medium. Our demonstration is enabled by the flexibility of the circuit QED platform, which allowed us to precisely engineer the level-structure, coupling, and dissipation of the micromaser components. Our device shows rich physics and perhaps points to ways to use the recent developments in the domain of microwave quantum circuits to probe the domain of maser physics.

quant-ph↗

arXiv2026

Achieving Sub-Zeptonewton Force Sensitivity and Spin-Motion Entanglement in Levitated Diamond via Pulsed Backaction Evasion

We propose a system to achieve sub-zeptonewton force sensing and robust spin-mechanical entanglement in a levitated diamond system. By coupling a nitrogen-vacancy (NV) center spin to the motion of its host diamond within a magnetic trap, we develop a platform designed to surpass the standard quantum limit. We develop and compare three distinct pulse sequences -- Ramsey, Hahn echo, and Carr-Purcell-Meiboom-Gill (CPMG) -- to create increasing amounts of backaction evasion while mitigating the effects of shot noise and thermal decoherence. Our results show that the CPMG sequences yield the most significant performance gains, reaching a force sensitivity of better than $10^{-23} \text{ N}/\sqrt{\text{Hz}}$ for broadband sensing around $10^4 \text{ Hz}$. Furthermore, we derive an entanglement witness protocol that accounts for pulsed dynamical decoupling, proving that spin-motion entanglement remains detectable even when occurring much faster than the mechanical period. These findings provide a more practical path for using levitated nanodiamonds both as high-precision sensors and as non-classical mechanical systems for fundamental tests of quantum mechanics.

quant-ph↗

arXiv2025

KTaO3-Based Supercurrent Diode

The supercurrent diode effect (SDE), characterized by nonreciprocal critical currents, represents a promising building block for future dissipationless electronics and quantum circuits. Realizing SDE requires breaking both time-reversal and inversion symmetry in the device. Here we use conductive atomic force microscopy (c-AFM) lithography to pattern reconfigurable superconducting weak links (WLs) at the LaAlO3/KTaO3 (LAO/KTO) interface. By deliberately engineering the WL geometry at the nanoscale, we realize SDE in these devices in the presence of modest out-of-plane magnetic fields. The SDE polarity can be reversed by simply changing the WL position, and the rectification efficiency reaches up to 13% under optimal magnetic field conditions. Time-dependent Ginzburg-Landau simulations reveal that the observed SDE originates from asymmetric vortex motion in the inversion-symmetry-breaking device geometry. This demonstration of SDE in the LAO/KTO system establishes a versatile platform for investigating and engineering vortex dynamics, forming the basis for engineered quantum circuit elements.

cond-mat.supr-con↗

arXiv2025

Electron spin dynamics guide cell motility

Diverse organisms exploit the geomagnetic field (GMF) for migration. Migrating birds employ an intrinsically quantum mechanical mechanism for detecting the geomagnetic field: absorption of a blue photon generates a radical pair whose two electrons precess at different rates in the magnetic field, thereby sensitizing cells to the direction of the GMF. In this work, using an in vitro injury model, we discovered a quantum-based mechanism of cellular migration. Specifically, we show that migrating cells detect the GMF via an optically activated, electron spin-based mechanism. Cell injury provokes acute emission of blue photons, and these photons sensitize muscle progenitor cells to the magnetic field. We show that the magnetosensitivity of muscle progenitor cells is (a) activated by blue light, but not by green or red light, and (b) disrupted by the application of an oscillatory field at the frequency corresponding to the energy of the electron-spin/magnetic field interaction. A comprehensive analysis of protein expression reveals that the ability of blue photons to promote cell motility is mediated by activation of calmodulin calcium sensors. Collectively, these data suggest that cells possess a light-dependent magnetic compass driven by electron spin dynamics.

physics.bio-ph↗

arXiv2024

Engineering a multi-level bath for transmons with three-wave mixing and parametric drives

A quantum system with a tunable bath temperature provides an additional degree of freedom for quantum simulators. Such a system can be realized by parametrically modulating the coupling between the system and the bath. Here, by coupling a transmon qubit to a lossy Superconducting Nonlinear Asymmetric Inductive eLement (SNAIL) mode, we experimentally create a tunable bath for the qubit mode. The effective temperature of this bath can be precisely controlled, ranging from negative to positive values. We show that the qubit can be thermalized to equilibrium with different population distributions under different parametric pumping conditions. We further extend our method to the third level of the transmon, demonstrating its potential utility beyond the two-level case. Our results provide a useful tool that can be readily integrated with quantum simulators that would benefit from a nontrivial photon population distribution.

quant-ph↗

arXiv2024

Analysis of the Pressure-Velocity boundary conditions for the projection method solution of the incompressible Navier-Stokes Equations

The projection method is the standard approach for numerically integrating the incompressible Navier-Stokes equation initial-boundary-value problem. Typical boundary conditions specify either the velocity or the gradient velocity on the boundary. Here, we consider the pressure-tangential-velocity boundary condition in which the tangential components of the velocity and the pressure at the boundary are specified.

physics.flu-dyn↗

arXiv2024

Simple, High Saturation Power, Quantum-limited, RF SQUID Array-based Josephson Parametric Amplifiers

High-fidelity quantum non-demolition qubit measurement is critical to error correction and rapid qubit feedback in large-scale quantum computing. High-fidelity readout requires passing a short and strong pulse through the qubit's readout resonator, which is then processed by a sufficiently high bandwidth, high saturation power, and quantum-limited amplifier. We have developed a design pipeline that combines time-domain simulation of the un-truncated device Hamiltonian, fabrication constraints, and maximization of saturation power. We have realized an amplifier based on a modified NIST tri-layer Nb fabrication suite which utilizes an array of 25 radio frequency Superconducting QUantum Interference Devices (rf SQUIDs) embedded within a low-Q resonator powered by a high-power voltage pump delivered via a diplexer on the signal port. We show that, despite the intensity of the pump, the device is quantum-efficient and capable of high-fidelity measurement limited by state transitions in the transmon. We present experimental data demonstrating up to -91.2 dBm input saturation power with 20 dB gain, up to 28 MHz instantaneous bandwidth, and phase-preserving qubit measurements with 62% quantum efficiency.

quant-ph↗

arXiv2024

Pump-efficient Josephson parametric amplifiers with high saturation power

Circuit QED based quantum information processing relies on low noise amplification for signal readout. In the realm of microwave superconducting circuits, this amplification is often achieved via Josephson parametric amplifiers (JPA). In the past, these amplifiers exhibited low power added efficiency (PAE), which is roughly the fraction of pump power that is converted to output signal power. This is increasingly relevant because recent attempts to build high saturation power amplifiers achieve this at the cost of very low PAE, which in turn puts a high heat load on the cryostat and limits the number of these devices that a dilution refrigerator can host. Here, we numerically investigate upper bounds on PAE. We focus on a class of parametric amplifiers that consists of a capacitor shunted by a nonlinear inductive block. We first set a benchmark for this class of amplifiers by considering nonlinear blocks described by an arbitrary polynomial current-phase relation. Next, we propose two circuit implementations of the nonlinear block. Finally, we investigate chaining polynomial amplifiers. We find that while amplifiers with higher gain have a lower PAE, regardless of the gain there is considerable room to improve as compared to state of the art devices. For example, for a phase-sensitive amplifier with a power gain of 20 dB, the PAE is ~0.1% for typical JPAs, 5.9% for our simpler circuit JPAs, 34% for our more complex circuit JPAs, 48% for our arbitrary polynomial amplifiers, and at least 95% for our chained amplifiers.

quant-ph↗

arXiv2023

Equilibrium Contact Angles and Dewetting in Capillaries

In this work, we extend the model of contact angles that we have previously developed for sessile drops on a wetted surface to the case of a meniscus in a capillary. The underlying physics of our model describe the intermolecular forces between the fluid and the surface of the capillary that result in the formation of a thin, non-removable fluid layer that coats the capillary wall. We describe the shape of the meniscus using a Young-Laplace equation and an incompressible, two-phase, CFD calculation, both modified to take into account intermolecular forces using the disjoining pressure model. We find that our numerical solutions of the Young-Laplace equation and equilibrium meniscus shapes obtained by CFD agree well with each other. Furthermore, for capillaries that are sufficiently larger than the thickness of the non-removable film, our numerical solutions agree well with the effective contact angle model that we previously developed for sessile drops. Finally, we observe that it is possible to tune the disjoining pressure model parameters so that the intermolecular forces between the liquid and solid molecules becomes so strong compared to the surface tension that our formula for effective contact angle gives an imaginary solution. We analyze this situation using CFD and find that it corresponds to dewetting, where the bulk liquid detaches from the walls of the capillary leaving behind the non-removable thin liquid film.

physics.flu-dyn↗

arXiv2023

Sketched Nanoscale KTaO3-Based Superconducting Quantum Interference Device

The discovery of two-dimensional superconductivity in LaAlO3/KTaO3 (111) and (110) interfaces has raised significant interest in this system. In this manuscript we report the first successful fabrication of a superconducting quantum interference device (DC-SQUID) in the KTO system. The key device elements, superconducting weak links, are created by conductive atomic force microscope (c-AFM) lithography which can reversibly control the conductivity at the LAO/KTO(110) interface with nanoscale resolution. The periodic modulation of the SQUID critical current, Ic(B), with magnetic field corresponds well with our theoretical modeling, which reveals a large kinetic inductance of the superconducting two-dimensional electron gas in KTO. The kinetic inductance of the SQUID is tunable by electrical gating from the back, due to the large dielectric constant of KTO. The demonstration of weak links and SQUIDs in KTO broadens the scope for exploring the underlying physics of KTO superconductivity, including the role of spin-orbit-coupling, pairing symmetry, and inhomogeneity. It also promotes KTO as a versatile platform for a growing family of quantum devices, which could be applicable in the realm of quantum computing and information.

cond-mat.supr-con↗

arXiv2023

Fast superconducting qubit control with sub-harmonic drives

Increasing the fidelity of single-qubit gates requires a combination of faster pulses and increased qubit coherence. However, with resonant qubit drive via a capacitively coupled port, these two objectives are mutually contradictory, as higher qubit quality factor requires a weaker coupling, necessitating longer pulses for the same applied power. Increasing drive power, on the other hand, can heat the qubit's environment and degrade coherence. In this work, by using the inherent nonlinearity of the transmon qubit, we circumvent this issue by introducing a new parametric driving scheme to perform single-qubit control. We achieve rapid gate speed by pumping the transmon's native Kerr term at approximately one third of the qubit's resonant frequency. Given that transmons typically operate within a fairly narrow range of anharmonicity, this technique is applicable to all transmons. In both theory and experiment, we show that the Rabi rate of the process is proportional to applied drive amplitude cubed, allowing for rapid gate speed with only modest increases in applied power. In addition, we demonstrate that filtering can be used to protect the qubit's coherence while performing rapid gates, and present theoretical calculations indicating that decay due to multi-photon losses, even in very strongly coupled drive lines, will not limit qubit lifetime. We demonstrate single qubit gates as short as 37.4ns with fidelity as high as 99.91%. We also present calculations indicating that this technique could reduce cryostat heating for fast gates, a vital requirement for large-scale quantum computers.

quant-ph↗

arXiv2022

Machine Learning 1- and 2-electron reduced density matrices of polymeric molecules

Encoding the electronic structure of molecules using 2-electron reduced density matrices (2RDMs) as opposed to many-body wave functions has been a decades-long quest as the 2RDM contains sufficient information to compute the exact molecular energy but requires only polynomial storage. We focus on linear polymers with varying conformations and numbers of monomers and show that we can use machine learning to predict both the 1-electron and the 2-electron reduced density matrices. Moreover, by applying the Hamiltonian operator to the predicted reduced density matrices we show that we can recover the molecular energy. Thus, we demonstrate the feasibility of a machine learning approach to predicting electronic structure that is generalizable both to new conformations as well as new molecules. At the same time our work circumvents the N-representability problem that has stymied the adaption of 2RDM methods, by directly machine-learning valid Reduced Density Matrices.

physics.chem-ph↗

arXiv2022

An Improved Self-Consistent One-Dimensional Slender Jet Model

In 1994, Eggers and Dupont suggested the slender jet model, a one-dimensional model that describes the motion of a thin axisymmetric column of viscous, incompressible fluid with a free surface. In their model, the momentum equation was derived in a manner that was not completely self-consistent. Consequently, the viscosity term was described with less accuracy than the surface tension term. In this paper, we derive a novel slender jet momentum equation in completely self-consistent manner that allows us to describe both the viscosity and the surface tension forces with the same accuracy as the surface tension term in the Eggers-Dupont model. Our derivation does not affect the volume conservation equation, which remains identical to the one in the Eggers-Dupont model. We show that our model predicts different Plateau-Rayleigh instability dynamics as compared to the Eggers-Dupont's model. The differences between the models are particularly large at small Reynolds numbers, where the viscosity plays a prominent role in development the Plateau-Rayleigh instability.

physics.flu-dyn↗

arXiv2022

Equilibrium Contact Angle at the Wetted Substrate

We construct a novel model for the steady-state contact angles of liquid droplets at the wetted substrate. The non-removable, thin liquid film covering the substrate is governed by the intermolecular forces between molecules of liquid and solid, which we describe using the standard disjoining pressure approximation. Balancing the disjoining pressure against the surface tension we find the smooth shape of the surface of the liquid. We show that we can extract an effective contact angle from the region where the film and the droplet meet. Crucially, we find that for large droplets the contact angle is independent of the droplet size. Instead, the contact angle is determined by the surface tension and the disjoining pressure parameters through a simple formula that works for both small and large contact angles. We suggest that comparing predictions of our model to experimentally measured contact angles will enable constraining the parameters of the disjoining pressure models.

physics.flu-dyn↗

arXiv2022

Simulating spectroscopy experiments with a superconducting quantum computer

We present a novel method for solving eigenvalue problems on a quantum computer based on spectroscopy. The method works by coupling a "probe" qubit to a set of system simulation qubits and then time evolving both the probe and the system under Hamiltonian dynamics. In this way, we simulate spectroscopy on a quantum computer. We test our method on the IBM quantum hardware for a simple single spin model and an interacting Kitaev chain model. For the Kitaev chain, we trace out the pseudo-topological phase boundary for a two-site model.

quant-ph↗

arXiv2021

One-dimensional repulsive Hubbard model with mass imbalance: Orders and filling anomaly

We investigate the phase diagram of the one-dimensional repulsive Hubbard model with mass imbalance. Using DMRG, we show that this model has a "triplet" paired phase (dubbed $π\mathrm{SG}$) at generic fillings, consistent with previous theoretical analysis. We study the topological aspect of $π\mathrm{SG}$ phase, determining long-range string orders and the filling anomaly which refers to the relation among the single particle gap, inversion symmetry, and filling imbalance for open chains. We also find, using DMRG, that at $1/3$ filling, commensurate effects lead to two additional phases: a crystal phase and a trion phase; we construct a description of these phases using Tomonaga-Luttinger liquid theory.

cond-mat.str-el↗

arXiv2021

Theory of engineering flat bands in graphene using doubly-periodic electrostatic gating

We explore the use of applied electrical potentials to induce band flattening in graphene for bands near zero energy. We consider various families of doubly periodic potentials and simulate their effect on the electronic band structure using a tight-binding and a continuum approach. From these families, we find that an applied potential with symmetries of wallpaper group 17, in particular a Kagome potential, works best for inducing a high degree of band flattening for a range of realistic potential amplitudes and periods. Our work indicates that it should be possible to engineer the band structure of graphene using electrostatic gating, thus enabling a new approach to the development of graphene-based metamaterials.

cond-mat.mes-hall↗