Bourns College of Engineering

We present an open-source software package, VAN-DAMME (Versatile Approaches to Numerically Design, Accelerate, and Manipulate Magnetic Excitations), for massively-parallelized quantum optimal control (QOC) calculations of multi-qubit systems. To enable large QOC calculations, the VAN-DAMME software package utilizes symmetry-based techniques with custom GPU-enhanced algorithms. This combined approach allows for the simultaneous computation of hundreds of matrix exponential propagators that efficiently leverage the intra-GPU parallelism found in high-performance GPUs. In addition, to maximize the computational efficiency of the VAN-DAMME code, we carried out several extensive tests on data layout, computational complexity, memory requirements, and performance. These extensive analyses allowed us to develop computationally efficient approaches for evaluating complex-valued matrix exponential propagators based on Padé approximants. To assess the computational performance of our GPU-accelerated VAN-DAMME code, we carried out QOC calculations of systems containing 10 - 15 qubits, which showed that our GPU implementation is 18.4× faster than the corresponding CPU implementation. Our GPU-accelerated enhancements allow efficient calculations of multi-qubit systems, which can be used for the efficient implementation of QOC applications across multiple domains. Program summary: Program Title: VAN-DAMME CPC Library link to program files:: https://doi.org/10.17632/zcgw2n5bjf.1 Licensing provisions: GNU General Public License 3 Programming language: C++ and CUDA Nature of problem: The VAN-DAMME software package utilizes GPU-accelerated routines and new algorithmic improvements to compute optimized time-dependent magnetic fields that can drive a system from a known initial qubit configuration to a specified target state with a large (≈1) transition probability. Solution method: Quantum control, GPU acceleration, analytic gradients, matrix exponential, and gradient ascent optimization.

Polymer/ceramic nanocomposites integrated the advantages of both polymers and ceramics for a wide range of biomedical applications, such as bone tissue repair. Here, we reported triphasic poly(lactic-co-glycolic acid) (PLGA, LA/GA = 90:10) nanocomposites with improved dispersion of hydroxyapatite (HA) and magnesium oxide (MgO) nanoparticles using a process that integrated the benefits of ultrasonic energy and dual asymmetric centrifugal mixing. We characterized the microstructure and composition of the nanocomposites and evaluated the effects of the HA/MgO ratios on degradation behavior and cell-material interactions. The PLGA/HA/MgO nanocomposites were composed of 70 wt % PLGA and 30 wt % nanoparticles made of 20:10, 25:5, and 29:1% by weight of HA and MgO, respectively. The results showed that the nanocomposites had a homogeneous nanoparticle distribution and as-designed elemental composition. The cell study indicated that reducing the MgO content in the triphasic nanocomposite increased the BMSC adhesion density under both direct and indirect contact conditions. Specifically, after the 24 and 48 h of culture, the PLGA/HA/MgO group with a weight ratio of 70:29:1 (P70/H29/M1) exhibited the greatest average cell adhesion density under direct and indirect contact conditions among triphasic nanocomposites. During a 28-day degradation study, the mass loss of triphasic nanocomposites was 18 ± 2% for P70/H20/M10, 9 ± 2% for P70/H25/M5, and 7 ± 1% for P70/H29/M1, demonstrating that MgO nanoparticles accelerated the degradation of the nanocomposites. Postculture analysis showed that the pH values and Mg2+ ion concentrations in the media increased with increasing MgO content in the nanocomposites. Triphasic nanocomposites provided different degradation profiles that can be tuned for different biomedical applications, especially when a shorter or longer period of degradation would be desirable for optimal bone tissue regeneration. The concentration and ratio of nanoparticles should be adjusted and optimized when other polymers with different degradation modes and rates are used in the nanocomposites.

Food packaging (FP) is essential for preserving food quality, safety, and extending shelf-life. However, growing concerns about the environmental and health impacts of conventional packaging materials, particularly per- and polyfluoroalkyl substances (PFAS) and microplastics, are driving a major transformation in FP design. PFAS, synthetic compounds with dual hydro- and lipophobicity, have been widely employed in food packaging materials (FPMs) to impart desirable water and grease repellency. However, PFAS bioaccumulate in the human body and have been linked to multiple health effects, including immune system dysfunction, cancer, and developmental problems. The detection of microplastics in various FPMs has raised significant concerns regarding their potential migration into food and subsequent ingestion. This comprehensive review examines the current landscape of FPMs, their functions, and physicochemical properties to put into perspective why there is widespread use of PFAS and microplastics in FPMs. The review then addresses the challenges posed by PFAS and microplastics, emphasizing the urgent need for sustainable and bio-based alternatives. We highlight promising advancements in sustainable and renewable materials, including plant-derived polysaccharides, proteins, and waxes, as well as recycled and upcycled materials. The integration of these sustainable materials into active packaging systems is also examined, indicating innovations in oxygen scavengers, moisture absorbers, and antimicrobial packaging. The review concludes by identifying key research gaps and future directions, including the need for comprehensive life cycle assessments and strategies to improve scalability and cost-effectiveness. As the FP industry evolves, a holistic approach considering environmental impact, functionality, and consumer acceptance will be crucial in developing truly sustainable packaging solutions.

African Swine Fever Virus (ASFV) is a highly contagious pathogen with nearly 100% mortality in swine, causing severe global economic loss. Current detection methods rely on nucleic acid amplification, which requires specialized equipment and skilled operators, limiting accessibility in resource-constrained settings. To address these challenges, we developed the Covalently Immobilized Magnetic Nanoparticles Enhanced CRISPR (CIMNE-CRISPR) system. This amplification-free diagnostic system seamlessly combines target recognition, sequence-specific enrichment, and signal generation. This approach uses covalent immobilization of CRISPR-LbCas12a-crRNA complexes on Fe₃O₄@SiO₂ core-shell magnetic nanoparticles, which improves enzyme specificity and robustness over traditional adsorption. The CIMNE-CRISPR assay reached a limit of detection (LOD) of 8.1 × 10⁴ copies/μL and a limit of quantification (LOQ) of 4.2 × 10⁵ copies/μL, with a dynamic range spanning 10⁵ to 10¹⁰ copies/μL and a matrix factor of 100.29% in porcine plasma. It maintained great specificity and accurately detecting 10⁵ copies/μL of ASFV DNA even with high mutant concentrations (10¹³ copies/μL). The method demonstrated decent reproducibility across different nanoparticle synthesis batches, with an RSD of 9.63% and recovery rates between 97% and 103%, and features rapid processing well-suited for field diagnostics. Overall, this system's cost-effectiveness, simplicity, and reliability highlight its potential to pave the way for advanced CRISPR-based diagnostics, particularly for diverse viral and bacterial targets in agricultural, environmental, and zoonotic disease contexts.

The recently synthesized monolayer fullerene network in a quasi-hexagonal phase (qHP-C₆₀) exhibits superior electron mobility and optoelectronic properties compared to molecular fullerene (C₆₀), making it highly promising for a variety of applications. However, the microscopic carrier dynamics of qHP-C₆₀ remain unclear, particularly in realistic environments, which are of significant importance for applications in optoelectronic devices. Unfortunately, traditional ab initio methods are prohibitive for capturing the real-time carrier dynamics of such large systems due to their high computational cost. In this work, we present the first real-time electron-nuclear dynamics study of qHP-C₆₀ using velocity-gauge density functional tight binding, which enables us to perform several picoseconds of excited-state electron-nuclear dynamics simulations for nanoscale systems with periodic boundary conditions. When applied to C₆₀, qHP-C₆₀, and their solvated counterparts, we demonstrate that water/moisture significantly increases the electron-hole recombination time in C₆₀ but has little impact on qHP-C₆₀. Our excited-state electron-nuclear dynamics calculations show that qHP-C₆₀ is extremely unique and enable exploration of time-resolved dynamics for understanding excited-state processes of large systems in complex, solvated environments.

Machine-learning models are key to modern biology, yet models trained on one dataset are often not generalizable to other datasets from different cohorts or laboratories due to both technical and biological differences. Domain adaptation, a type of transfer learning, alleviates this problem by aligning different datasets so that models can be applied across them. However, most state-of-the-art domain adaptation methods were designed for large-scale data such as images, whereas biological datasets are smaller and have more features, and these are also complex and heterogeneous. This Review discusses domain adaptation methods in the context of such biological data to inform biologists and guide future domain adaptation research. We describe the benefits and challenges of domain adaptation in biological research and critically explore some of its objectives, strengths, and weaknesses. We argue for the incorporation of domain adaptation techniques to the computational biologists toolkit, with further development of customized approaches.

CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were developed by combining CRISPR-Cas9 with a transfer RNA (tRNA) adenosine deaminase enzyme and through directed evolution, conferring the ability to deaminate DNA. However, the molecular mechanisms driving the efficient DNA deamination in the evolved ABEs remain unresolved. Here, extensive molecular simulations and biochemical experiments reveal the biophysical basis behind the astonishing base editing efficiency of ABE8e, the most efficient ABE to date. We demonstrate that the ABE8es DNA deaminase domain, TadA8e, forms remarkably stable dimers compared to its tRNA-deaminating progenitor and that the strength of TadA dimerization is crucial for DNA deamination. The TadA8e dimer forms robust interactions involving its R98 and R129 residues, the RuvC domain of Cas9 and the DNA. These locking interactions are exclusive to ABE8e, distinguishing it from its predecessor, ABE7.10, and are indispensable to boost DNA deamination. Additionally, we identify three critical residues that drive the evolution of ABE8e toward improved base editing by balancing the enzymes activity and stability, reinforcing the TadA8e dimer and improving the ABE8es functionality. These insights offer new directions to engineer superior ABEs, advancing the design of safer precision genome editing tools.

Thermal treatment of perfluoroalkyl and polyfluoroalkyl substances (PFASs) presents a promising opportunity to halt the PFAS cycle. However, how co-occurring materials such as granular activated carbon (GAC) influence thermal decomposition products of PFASs, and underlying mechanisms remain unclear. We studied the pyrolysis of two potassium salts of perfluoroalkanesulfonates (PFSAs, C_nF_2n+1SO₃K), perfluorobutanesulfonate (PFBS-K), and perfluorooctanesulfonate (PFOS-K), with or without GAC. PFBS-K is more stable than PFOS-K for pure standards, but when it is adsorbed onto GAC, its thermal stabilities and decomposition behaviors are similar. Temperatures and heating rates can significantly influence the decomposition mechanisms and products for pure standards, while these effects are less pronounced when PFSAs are adsorbed onto GAC. We further studied the underlying decomposition mechanisms. Pure standards of C_nF_2n+1SO₃K can decompose directly in their condense phase by reactions: F(CF₂)_nSO₃K → F(CF₂)_n-2CF═CF₂ + KFSO₃ or F(CF₂)_nSO₃K → F(CF₂)_n^- + K⁺ + SO₃. GAC appears to facilitate breakage of the C-S bond to release SO₂ at temperatures as low as 280 °C. GAC promotes fluorine mineralization through functional reactive sites. SiO₂ is particularly important for the surface-mediated mineralization of PFASs into SiF₄. These findings offer valuable insights into optimizing thermal treatment strategies for PFAS-contaminated waste.

Manta rays use wing-like pectoral fins for intriguing oscillatory swimming. It provides rich inspiration for designing potentially fast, efficient, and maneuverable soft swimming robots, which, however, have yet to be realized. It remains a grand challenge to combine fast speed, high efficiency, and high maneuverability in a single soft swimmer while using simple actuation and control. Here, we report leveraging spontaneous snapping stroke in the monostable flapping wing of a manta-like soft swimmer to address the challenge. The monostable wing is pneumatically actuated to instantaneously snap through to stroke down, and upon deflation, it will spontaneously stroke up by snapping back to its initial state, driven by elastic restoring force, without consuming additional energy. This largely simplifies designs, actuation, and control for achieving a record-high speed of 6.8 body length per second, high energy efficiency, and high maneuverability and collision resilience in navigating through underwater unstructured environments with obstacles by simply tuning single-input actuation frequencies.