arXiv subjects

Xiaoxi Liu

Publications and source records attributed to Xiaoxi Liu.

At least 19 recordsLinked to original sources

arXiv2025

Nanofluidic logic based on chiral skyrmion flows

Particle-like chiral magnetic skyrmions can flow in nanotracks and behave like chiral fluids. Using interacting flows to perform logical operations is an important topic in microfluidics and nanofluidics. Here, we report a basic nanofluidic logic computing system based on chiral magnetic skyrmions flowing in parallel pipelines connected by an H-shaped junction. The flow behaviors could be manipulated by adjusting the spin polarization angle, which controls the intrinsic skyrmion Hall angle. We demonstrate that within certain range of the spin polarization angle, fully developed skyrmion flows could lead to fluidic logical operations, which significantly reduce the complexity of skyrmion logic as there is no need for deterministic creation, precise control, and detection of a single isolated skyrmion. Our results suggest that the chiral flow behaviors of magnetic quasiparticles may offer possibilities for spintronic and nanofluidic functions.

cond-mat.mes-hall↗

arXiv2025

Knowledge-Driven Feature Selection and Engineering for Genotype Data with Large Language Models

Predicting phenotypes with complex genetic bases based on a small, interpretable set of variant features remains a challenging task. Conventionally, data-driven approaches are utilized for this task, yet the high dimensional nature of genotype data makes the analysis and prediction difficult. Motivated by the extensive knowledge encoded in pre-trained LLMs and their success in processing complex biomedical concepts, we set to examine the ability of LLMs in feature selection and engineering for tabular genotype data, with a novel knowledge-driven framework. We develop FREEFORM, Free-flow Reasoning and Ensembling for Enhanced Feature Output and Robust Modeling, designed with chain-of-thought and ensembling principles, to select and engineer features with the intrinsic knowledge of LLMs. Evaluated on two distinct genotype-phenotype datasets, genetic ancestry and hereditary hearing loss, we find this framework outperforms several data-driven methods, particularly on low-shot regimes. FREEFORM is available as open-source framework at GitHub: https://github.com/PennShenLab/FREEFORM.

cs.LG↗

arXiv2024

Initial Experience of Metabolic Imaging with Hyperpolarized [1-13C]pyruvate MRI in Kidney Transplant Patients

BACKGROUND: Kidney transplant is the treatment of choice for patients with end-stage renal disease. Early detection of allograft injury is important to delay or prevent irreversible damage. PURPOSE: To investigate the feasibility of hyperpolarized (HP) [1-13C]pyruvate MRI for assessing kidney allograft metabolism. SUBJECTS: 6 participants (mean age, 45.2 +- 12.4 years, 2 females) scheduled for kidney allograft biopsy and 5 patients (mean age, 59.6 +- 10.4 years, 2 females) with renal cell carcinoma (RCC). ASSESSMENT: Five of the six kidney allograft participants underwent biopsy after MRI. Estimated glomerular filtration rate (eGFR) and urine protein-to-creatine ratio (uPCR) were collected within 4 weeks of MRI. Kidney metabolism was quantified from HP [1-13C]pyruvate MRI using the lactate-to-pyruvate ratio in allograft kidneys and non-tumor bearing kidneys from RCC patients. RESULTS: Biopsy was performed a mean of 9 days (range 5-19 days) after HP [1-13C]pyruvate MRI. Three biopsies were normal, one showed low-grade fibrosis and one showed moderate microvascular inflammation. All had stable functioning allografts with eGFR > 60 mL/min/1.73 m2 and normal uPCR. One participant who did not undergo biopsy had reduced eGFR of 49 mL/min/1.73 m2 and elevated uPCR. The mean lactate-to-pyruvate ratio was 0.373 in participants with normal findings (n = 3) and 0.552 in participants with abnormal findings (n = 2). The lactate-to-pyruvate ratio was highest (0.847) in the participant with reduced eGFR and elevated uPRC. Native non-tumor bearing kidneys had a mean lactate-to-pyruvate ratio of 0.309. DATA CONCLUSION: Stable allografts with normal findings at biopsy showed lactate-to-pyruvate ratios similar to native non-tumor bearing kidneys, whereas allografts with abnormal findings showed higher lactate-to-pyruvate ratios.

physics.med-ph↗

arXiv2024

Transformation of a cellular skyrmion to polyomino-like structures

Topological spin structures with transformable shapes may have potential implications on data storage and computation. Here, we demonstrate that a square cellular skyrmion on an artificial grid pinning pattern can be manipulated by programmed current pulses. We find that parallel short pulses could result in the elongation of the skyrmion mainly in the current direction, while parallel long pulses are able to induce the elongation in the direction perpendicular to the current due to the intrinsic skyrmion Hall effect. Consequently, a programmed sequence of parallel pulses could lead to the transformation of the skyrmion to I-, L-, and Z-shaped polyomino-like structures without affecting the topological charge. In addition, we find that orthogonal pulses could lead to the transformation to more complex polyomino-like structures, including the T-shaped and irregular ones. Particularly, when a small T-shaped structure is formed, the topological charge of the system is found to be non-integer due to incomplete compensation of local topological charge densities; however, the T-shaped structure is stable on the attractive pinning pattern. Our results offer an effective way to create polyomino-like spin structures toward functional applications.

cond-mat.mes-hall↗

arXiv2024

Data Format Standardization and DICOM Integration for Hyperpolarized 13C MRI

Hyperpolarized (HP) 13C MRI has shown promise as a valuable modality for in vivo measurements of metabolism and is currently in human trials at 15 research sites worldwide. With this growth it is important to adopt standardized data storage practices as it will allow sites to meaningfully compare data. In this paper we (1) describe data that we believe should be stored and (2) demonstrate pipelines and methods that utilize the Digital Imaging and Communications in Medicine (DICOM) standard. This includes proposing a set of minimum set of information that is specific to HP 13C MRI studies. We then show where the majority of these can be fit into existing DICOM Attributes, primarily via the "Contrast/Bolus" module. We also demonstrate pipelines for utilizing DICOM for HP 13C MRI. DICOM is the most common standard for clinical medical image storage and provides the flexibility to accommodate the unique aspects of HP 13C MRI, including the HP agent information but also spectroscopic and metabolite dimensions. The pipelines shown include creating DICOM objects for studies on human and animal imaging systems with various pulse sequences. We also show a python-based method to efficiently modify DICOM objects to incorporate the unique HP 13C MRI information that is not captured by existing pipelines. Moreover, we propose best practices for HP 13C MRI data storage that will support future multi-site trials, research studies and technical developments of this imaging technique.

physics.med-ph↗

arXiv2023

Chiral Skyrmions Interacting with Chiral Flowers

The chiral nature of active matter plays an important role in the dynamics of active matter interacting with chiral structures. Skyrmions are chiral objects, and their interactions with chiral nanostructures can lead to intriguing phenomena. Here, we explore the random-walk dynamics of a thermally activated chiral skyrmion interacting with a chiral flower-like obstacle in a ferromagnetic layer, which could create topology-dependent outcomes. It is a spontaneous mesoscopic order-from-disorder phenomenon driven by the thermal fluctuations and topological nature of skyrmions that exists only in ferromagnetic and ferrimagnetic systems. The interactions between the skyrmions and chiral flowers at finite temperatures can be utilized to control the skyrmion position and distribution without applying any external driving force or temperature gradient. The phenomenon that thermally activated skyrmions are dynamically coupled to chiral flowers may provide a new way to design topological sorting devices.

cond-mat.mes-hall↗

arXiv2023

Laminar and transiently disordered dynamics of a magnetic skyrmion pipe flow

The world is full of fluids that flow. The fluid nature of flowing skyrmionic quasiparticles is of fundamental physical interest and plays an essential role in the transport of many skyrmions. Here, we report the laminar and transiently disordered dynamic behaviors of many magnetic skyrmions flowing in a pipe channel. The skyrmion flow driven by a uniform current may show a lattice structural transition. The skyrmion flow driven by a non-uniform current shows a dynamically varying lattice structure. A large uniform current could result in the compression of skyrmions toward the channel edge, leading to the transition of the skyrmion pipe flow into an open-channel flow with a free surface. Namely, the width of the skyrmion flow could be adjusted by the driving current. Skyrmions on the free surface may form a single shear layer adjacent to the main skyrmion flow. In addition, although we focus on the skyrmion flow dynamics in a clean pipe channel without any pinning or defect effect, we also show that a variation of magnetic anisotropy in the pipe channel could lead to more complicated skyrmion flow dynamics and pathlines. Our results reveal the fluid nature of skyrmionic quasiparticles that may motivate future research on the complex flow physics of magnetic textures.

cond-mat.mes-hall↗

arXiv2023

Reversible magnetic domain reorientation induced by magnetic field pulses with fixed direction

Nanoscale magnetic domains with controllable configurations could be used for classical and quantum applications, where the switching of magnetization configurations is an essential operation for information processing. Here, we report that the magnetic domain reorientation in a notched ferromagnetic nanotrack can be realized and effectively controlled by applying uniform magnetic field pulses in a fixed in-plane direction perpendicular to the nanotrack. Our micromagnetic simulation results show that the configurations of magnetic domains in the notched nanotrack can be switched between a head-to-head state and a tail-to-tail state in a reversible manner driven by magnetic field pulses, while it is unnecessary to reverse the direction of the magnetic field. Such a unique magnetic domain reorientation dynamics is found to depend on magnetic parameters and nanotrack geometries. The reorientation dynamics of magnetic domains also depends on the strength and length of the applied magnetic field pulse. In addition, we point out that the notches at the center of the nanotrack play an important role for the stabilization of the head-to-head and tail-to-tail states during the magnetic domain reorientation. We also qualitatively explain the field-induced reorientation phenomenon with a simplified two-dimensional macrospin model. Our results may make it possible to build spintronic devices driven by a fixed magnetic field. Our findings may also motivate future studies to investigate the classical and quantum applications based on nanoscale magnetic domains.

cond-mat.mes-hall↗

arXiv2022

Reversible Transformation between Isolated Skyrmions and Bimerons

Skyrmions and bimerons are versatile topological spin textures that can be used as information bits for both classical and quantum computing. The transformation between isolated skyrmions and bimerons is an essential operation for computing architecture based on multiple different topological bits. Here we report the creation of isolated skyrmions and their subsequent transformation to bimerons by harnessing the electric current-induced Oersted field and temperature-induced perpendicular magnetic anisotropy variation. The transformation between skyrmions and bimerons is reversible, which is controlled by the current amplitude and scanning direction. Both skyrmions and bimerons can be created in the same system through the skyrmion-bimeron transformation and magnetization switching. Deformed skyrmion bubbles and chiral labyrinth domains are found as nontrivial intermediate transition states. Our results may provide a unique way for building advanced information-processing devices using different types of topological spin textures in the same system.

cond-mat.mes-hall↗

arXiv2022

Particle-like skyrmions interacting with a funnel obstacle

The skyrmion-substrate interaction is an important issue to consider when studying particle-like skyrmions in nanostructures, which may strongly affect the skyrmion dynamics and lead to complex dynamic phenomena. Here, we report the current-driven dynamic behaviors of particle-like skyrmions interacting with the funnel obstacle in a ferromagnetic layer. We computationally demonstrate that a funnel obstacle with enhanced perpendicular magnetic anisotropy can be used to modify the dynamics of skyrmions due to the repulsive skyrmion-funnel interaction, which could generate several nontrivial effects, including the compression, clogging, annihilation, guided motion, and capturing of skyrmions. It is also found that the funnel obstacle can separate an incoming flow of skyrmions into two asymmetric flows. Moreover, we show that it is possible to capture skyrmions by the funnel obstacle in both static and dynamic ways. Our results are useful for understanding the skyrmion dynamics interacting with the substrate and could provide guidelines for the control of skyrmion flows in a transmission channel.

cond-mat.mes-hall↗

arXiv2022

Bifurcation of a Topological Skyrmion String

Manipulation of three-dimensional (3D) topological objects is of both fundamental interest and practical importance in many branches of physics. Here, we show by spin dynamics simulations that the bifurcation of a 3D skyrmion string in a layered frustrated system could be induced by the dampinglike spin-orbit torque. The bifurcation of a skyrmion string happens when the skyrmion string carries a minimal topological charge of $Q=2$. We demonstrate that three types of bifurcations could be realized by applying different current injection geometries, which lead to the transformation from I-shaped skyrmion strings to Y-, X-, and O-shaped ones. Besides, different branches of a bifurcated skyrmion string may merge into an isolated skyrmion string spontaneously. The mechanism of bifurcation should be universal to any skyrmion strings with $Q\geq 2$ in the layered frustrated system and could offer a general approach to manipulate 3D stringlike topological objects for spintronic functions.

cond-mat.mes-hall↗

arXiv2022

Qubits based on merons in magnetic nanodisks

Merons and skyrmions are classical topological solitons. However, they will become quantum mechanical objects when their sizes are of the order of nanometers. Recently, quantum computation based on nanoscale skyrmions was proposed. Here, we propose to use a nanoscale meron in a magnetic nanodisk as a qubit, where the up and down directions of the core spin are assigned to be the qubit states $|0\rangle$ and $|1\rangle$. First, we show numerically that a meron with the radius containing only $7$ spins can be stabilized in a ferromagnetic nanodisk classically. Then, we show theoretically that universal quantum computation is possible based on merons by explicitly constructing the arbitrary phase-shift gate, the Hadamard gate, and the CNOT gate. They are executed by magnetic field or electric current. It would serve as a qubit with long coherence time as a remnant of topological stability from its classical counterpart.

cond-mat.mes-hall↗

arXiv2022

Structural transition of skyrmion quasiparticles under compression

The competition between external drives and interparticle interactions are important for the static and dynamic properties of topological quasiparticles in confined geometries. Here, we study the dynamics of particlelike skyrmions under a current-induced compression, where skyrmions are stabilized in a confined space and form a skyrmion solid. We find that a lattice structural transition of nanoscale skyrmions could be induced by the compression, which depends on the initial lattice configuration and the compression level. The compression effect in the skyrmion solid with strong skyrmion-skyrmion repulsion could produce a wave front showing an abrupt change of the skyrmion density, which may propagate through the skyrmion solid depending on the compression level. Besides, a chain of skyrmions on the surface of the compressed skyrmion solid could show a fast and stable motion along the surface as long as it remains within the driving region. Some skyrmions may collapse during the compression due to the destructive skyrmion-skyrmion collision, which mainly happens in the area around the skyrmion injection boundary between the driving and compressive regions. Our results are useful for understanding the compression physics of quasiparticles carrying nontrivial topology.

cond-mat.mes-hall↗

arXiv2022

Universal quantum computation based on nanoscale skyrmion helicity qubits in frustrated magnets

Skyrmions in frustrated magnets have the helicity degree of freedom, where two different configurations of Bloch-type skyrmions are energetically favored by the magnetic dipole-dipole interaction and characterized by opposite helicities. A skyrmion must become a quantum-mechanical object when its radius is of the order of nanometer. We construct a qubit based on the two-fold degeneracy of the Bloch-type nanoscale skyrmions in frustrated magnets. It is shown that the universal quantum computation is possible based on nanoscale skyrmions in a multilayered system. We explicitly show how to construct the $π/4$ phase-shift gate, the Hadamard gate, and the CNOT gate. The one-qubit quantum gates are materialized by temporally controlling the electric field and the spin current. The two-qubit gate is materialized with the use of the Ising-type exchange coupling by controlling the distance between the skyrmion centers in two adjacent layers. The merit of the present mechanism is that an external magnetic field is not necessary. Our results may open a possible way toward universal quantum computations based on nanoscale topological spin textures.

cond-mat.mes-hall↗

arXiv2022

Nonlinear dynamics of topological helicity wave in a frustrated skyrmion string

A skyrmion in frustrated magnetic system has the helicity degree of freedom. A skyrmion string is formed in a frustrated layered system, which is well described by the $XY$ model owing to the exchange coupling between adjacent layers. We consider a system where the interlayer exchange couplings are alternating, where the dimerized $XY$ model is materialized, whose linear limit is the Su-Schrieffer-Heeger model. We argue that it is a nonlinear topological system. We study the quench dynamics of the helicity wave under the initial condition that the helicity of the skyrmion in the bottommost layer is rotated. It yields a good signal to detect whether the system is topological or trivial. Our results show that the helicity dynamics of the skyrmion string have a rich physics in the modulated exchange-coupled system.

cond-mat.mes-hall↗

arXiv2022

Nonreciprocal dynamics of ferrimagnetic bimerons

Magnetic bimerons are topologically nontrivial spin textures in in-plane easy-axis magnets, which can be used as particle-like information carriers. Here, we report a theoretical study on the nonreciprocal dynamics of asymmetrical ferrimagnetic (FiM) bimerons induced by spin currents. The FiM bimerons have the ability to move at a speed of kilometers per second and do not show the skyrmion Hall effect at the angular momentum compensation point. Our micromagnetic simulations and analytical results demonstrate that spin currents are able to induce the nonreciprocal transport and a drift motion of the FiM bimeron even if the system is at the angular momentum compensation point. By analyzing the current-induced effective fields, we find that the nonreciprocal transport is attributed to the asymmetry of the bimeron structure. Our results are useful for understanding the physics of bimerons in ferrimagnets and may provide guidelines for building bimeron-based spintronic devices.

cond-mat.mes-hall↗

arXiv2021

Dynamic transformation between a skyrmion string and a bimeron string in a layered frustrated system

Frustrated topological spin textures have unique properties that may enable novel spintronic applications, such as helicity-based information storage and computing. Here, we report the statics and current-induced dynamics of two-dimensional (2D) pancake skyrmions in a stack of weakly coupled frustrated magnetic monolayers, which form a three-dimensional (3D) skyrmion string. The Bloch-type skyrmion string is energetically more stable than its Néel-type counterpart. It can be driven into translational motion by the dampinglike spin-orbit torque and shows the damping-dependent skyrmion Hall effect. Most notably, the skyrmion string can be transformed to a dynamically stable bimeron string by the dampinglike spin-orbit torque. The current-induced bimeron string rotates stably with respect to its center, which can spontaneously transform back to a skyrmion string when the current is switched off. Our results reveal unusual physical properties of 3D frustrated spin textures, and may open up different possibilities for spintronic applications based on skyrmion and bimeron strings.

cond-mat.mes-hall↗

arXiv2021

Configurable pixelated skyrmions on nanoscale magnetic grids

Topological spin textures can serve as non-volatile information carriers. Here we study the current-induced dynamics of an isolated magnetic skyrmion on a nanoscale square-grid pinning pattern formed by orthogonal defect lines with reduced magnetic anisotropy. The skyrmion on the square grid can be pixelated with a quantized size of the grid. We demonstrate that the position, size, and shape of skyrmion on the square grid are electrically configurable. The skyrmion center is quantized to be on the grid and the skyrmion may show a hopping motion instead of a continuous motion. We find that the skyrmion Hall effect can be perfectly prohibited due to the pinning effect of the grid. The pixelated skyrmion can be harnessed to build future programmable racetrack memory, multistate memory, and logic computing device. Our results will be a basis for digital information storage and computation based on pixelated topological spin textures on artificial pinning patterns.

cond-mat.mes-hall↗