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Item Trapped-ion quantum simulation of electron transfer models with tunable dissipation(AAAS, 2024) So, Visal; Duraisamy Suganthi, Midhuna; Menon, Abhishek; Zhu, Mingjian; Zhuravel, Roman; Pu, Han; Wolynes, Peter G.; Onuchic, José N.; Pagano, Guido; Center for Theoretical Biological PhysicsElectron transfer is at the heart of many fundamental physical, chemical, and biochemical processes essential for life. The exact simulation of these reactions is often hindered by the large number of degrees of freedom and by the essential role of quantum effects. Here, we experimentally simulate a paradigmatic model of molecular electron transfer using a multispecies trapped-ion crystal, where the donor-acceptor gap, the electronic and vibronic couplings, and the bath relaxation dynamics can all be controlled independently. By manipulating both the ground-state and optical qubits, we observe the real-time dynamics of the spin excitation, measuring the transfer rate in several regimes of adiabaticity and relaxation dynamics. Our results provide a testing ground for increasingly rich models of molecular excitation transfer processes that are relevant for molecular electronics and light-harvesting systems.Item Impact of Surface Enhanced Raman Spectroscopy in Catalysis(American Chemical Society, 2024) Stefancu, Andrei; Aizpurua, Javier; Alessandri, Ivano; Bald, Ilko; Baumberg, Jeremy J.; Besteiro, Lucas V.; Christopher, Phillip; Correa-Duarte, Miguel; de Nijs, Bart; Demetriadou, Angela; Frontiera, Renee R.; Fukushima, Tomohiro; Halas, Naomi J.; Jain, Prashant K.; Kim, Zee Hwan; Kurouski, Dmitry; Lange, Holger; Li, Jian-Feng; Liz-Marzán, Luis M.; Lucas, Ivan T.; Meixner, Alfred J.; Murakoshi, Kei; Nordlander, Peter; Peveler, William J.; Quesada-Cabrera, Raul; Ringe, Emilie; Schatz, George C.; Schlücker, Sebastian; Schultz, Zachary D.; Tan, Emily Xi; Tian, Zhong-Qun; Wang, Lingzhi; Weckhuysen, Bert M.; Xie, Wei; Ling, Xing Yi; Zhang, Jinlong; Zhao, Zhigang; Zhou, Ru-Yu; Cortés, EmilianoCatalysis stands as an indispensable cornerstone of modern society, underpinning the production of over 80% of manufactured goods and driving over 90% of industrial chemical processes. As the demand for more efficient and sustainable processes grows, better catalysts are needed. Understanding the working principles of catalysts is key, and over the last 50 years, surface-enhanced Raman Spectroscopy (SERS) has become essential. Discovered in 1974, SERS has evolved into a mature and powerful analytical tool, transforming the way in which we detect molecules across disciplines. In catalysis, SERS has enabled insights into dynamic surface phenomena, facilitating the monitoring of the catalyst structure, adsorbate interactions, and reaction kinetics at very high spatial and temporal resolutions. This review explores the achievements as well as the future potential of SERS in the field of catalysis and energy conversion, thereby highlighting its role in advancing these critical areas of research.Item Whole-cell multi-target single-molecule super-resolution imaging in 3D with microfluidics and a single-objective tilted light sheet(Springer Nature, 2024) Saliba, Nahima; Gagliano, Gabriella; Gustavsson, Anna-Karin; Smalley-Curl Institute;Center for Nanoscale Imaging SciencesMulti-target single-molecule super-resolution fluorescence microscopy offers a powerful means of understanding the distributions and interplay between multiple subcellular structures at the nanoscale. However, single-molecule super-resolution imaging of whole mammalian cells is often hampered by high fluorescence background and slow acquisition speeds, especially when imaging multiple targets in 3D. In this work, we have mitigated these issues by developing a steerable, dithered, single-objective tilted light sheet for optical sectioning to reduce fluorescence background and a pipeline for 3D nanoprinting microfluidic systems for reflection of the light sheet into the sample. This easily adaptable microfluidic fabrication pipeline allows for the incorporation of reflective optics into microfluidic channels without disrupting efficient and automated solution exchange. We combine these innovations with point spread function engineering for nanoscale localization of individual molecules in 3D, deep learning for analysis of overlapping emitters, active 3D stabilization for drift correction and long-term imaging, and Exchange-PAINT for sequential multi-target imaging without chromatic offsets. We then demonstrate that this platform, termed soTILT3D, enables whole-cell multi-target 3D single-molecule super-resolution imaging with improved precision and imaging speed.Item Pleozymes: Pleiotropic Oxidized Carbon Nanozymes Enhance Cellular Metabolic Flexibility(MDPI, 2024) Vo, Anh T. T.; Mouli, Karthik; Liopo, Anton V.; Lorenzi, Philip; Tan, Lin; Wei, Bo; Martinez, Sara A.; McHugh, Emily A.; Tour, James M.; Khan, Uffaf; Derry, Paul J.; Kent, Thomas A.; Smalley-Curl Institute;Rice Advanced Materials Institute;The NanoCarbon CenterOur group has synthesized a pleiotropic synthetic nanozyme redox mediator we term a “pleozyme” that displays multiple enzymatic characteristics, including acting as a superoxide dismutase mimetic, oxidizing NADH to NAD+, and oxidizing H2S to polysulfides and thiosulfate. Benefits have been seen in acute and chronic neurological disease models. The molecule is sourced from coconut-derived activated charcoal that has undergone harsh oxidization with fuming nitric acid, which alters the structure and chemical characteristics, yielding 3–8 nm discs with broad redox potential. Prior work showed pleozymes localize to mitochondria and increase oxidative phosphorylation and glycolysis. Here, we measured cellular NAD+ and NADH levels after pleozyme treatment and observed increased total cellular NADH levels but not total NAD+ levels. A 13C-glucose metabolic flux analysis suggested pleozymes stimulate the generation of pyruvate and lactate glycolytically and from the tricarboxylic acid (TCA) cycle, pointing to malate decarboxylation. Analysis of intracellular fatty acid abundances suggests pleozymes increased fatty acid β-oxidation, with a concomitant increase in succinyl- and acetyl-CoA. Pleozymes increased total ATP, potentially via flexible enhancement of NAD+-dependent catabolic pathways such as glycolysis, fatty acid β-oxidation, and metabolic flux through the TCA cycle. These effects may be favorable for pathologies that compromise metabolism such as brain injury.Item Determining the N-Representability of a Reduced Density Matrix via Unitary Evolution and Stochastic Sampling(American Chemical Society, 2024) Massaccesi, Gustavo E.; Oña, Ofelia B.; Capuzzi, Pablo; Melo, Juan I.; Lain, Luis; Torre, Alicia; Peralta, Juan E.; Alcoba, Diego R.; Scuseria, Gustavo E.The N-representability problem consists in determining whether, for a given p-body matrix, there exists at least one N-body density matrix from which the p-body matrix can be obtained by contraction, that is, if the given matrix is a p-body reduced density matrix (p-RDM). The knowledge of all necessary and sufficient conditions for a p-body matrix to be N-representable allows the constrained minimization of a many-body Hamiltonian expectation value with respect to the p-body density matrix and, thus, the determination of its exact ground state. However, the number of constraints that complete the N-representability conditions grows exponentially with system size, and hence, the procedure quickly becomes intractable for practical applications. This work introduces a hybrid quantum-stochastic algorithm to effectively replace the N-representability conditions. The algorithm consists of applying to an initial N-body density matrix a sequence of unitary evolution operators constructed from a stochastic process that successively approaches the reduced state of the density matrix on a p-body subsystem, represented by a p-RDM, to a target p-body matrix, potentially a p-RDM. The generators of the evolution operators follow the well-known adaptive derivative-assembled pseudo-Trotter method (ADAPT), while the stochastic component is implemented by using a simulated annealing process. The resulting algorithm is independent of any underlying Hamiltonian, and it can be used to decide whether a given p-body matrix is N-representable, establishing a criterion to determine its quality and correcting it. We apply the proposed hybrid ADAPT algorithm to alleged reduced density matrices from a quantum chemistry electronic Hamiltonian, from the reduced Bardeen–Cooper–Schrieffer model with constant pairing, and from the Heisenberg XXZ spin model. In all cases, the proposed method behaves as expected for 1-RDMs and 2-RDMs, evolving the initial matrices toward different targets.Item Neuroprotective Effects of Functionalized Hydrophilic Carbon Clusters: Targeted Therapy of Traumatic Brain Injury in an Open Blast Rat Model(MDPI, 2024) Padmanabhan, Parasuraman; Lu, Jia; Ng, Kian Chye; Srinivasan, Dinesh Kumar; Sundramurthy, Kumar; Nilewski, Lizanne Greer; Sikkema, William K. A.; Tour, James M.; Kent, Thomas A.; Gulyás, Balázs; Carlstedt-Duke, JanTraumatic brain injury (TBI) causes multiple cerebrovascular disruptions and oxidative stress. These pathological mechanisms are often accompanied by serious impairment of cerebral blood flow autoregulation and neuronal and glial degeneration. Background/Objectives: Multiple biochemical cascades are triggered by brain damage, resulting in reactive oxygen species production alongside blood loss and hypoxia. However, most currently available early antioxidant therapies lack capacity and hence sufficient efficacy against TBI. The aim of this study was to test a novel catalytic antioxidant nanoparticle to alleviate the damage occurring in blast TBI. Methods: TBI was elicited in an open blast rat model, in which the rats were exposed to the effects of an explosive blast. Key events of the post-traumatic chain in the brain parenchyma were studied using immunohistochemistry. The application of a newly developed biologically compatible catalytic superoxide dismutase mimetic carbon-based nanocluster, a poly-ethylene-glycol-functionalized hydrophilic carbon cluster (PEG-HCC), was tested post-blast to modulate the components of the TBI process. Results: The PEG-HCC was shown to significantly ameliorate neuronal loss in the brain cortex, the dentate gyrus, and hippocampus when administered shortly after the blast. There was also a significant increase in endothelial activity to repair blood–brain barrier damage as well as the modulation of microglial and astrocyte activity and an increase in inducible NO synthase in the cortex. Conclusions: We have demonstrated qualitatively and quantitatively that the previously demonstrated antioxidant properties of PEG-HCCs have a neuroprotective effect after traumatic brain injury following an explosive blast, acting at multiple levels of the pathological chain of events elicited by TBI.Item Laser-induced high-entropy alloys as long-duration bifunctional electrocatalysts for seawater splitting(Royal Society of Chemistry, 2024) Xie, Yunchao; Xu, Shichen; Meng, Andrew C.; Zheng, Bujingda; Chen, Zhenru; Tour, James M.; Lin, Jian; NanoCarbon Center;Rice Advanced Materials InstituteElectrocatalytic seawater splitting has garnered significant attention as a promising approach for eco-friendly, large-scale green hydrogen production. Development of high-efficiency and cost-effective electrocatalysts remains a frontier in this field. Herein, we report a rapid in situ synthesis of FeNiCoCrRu high-entropy alloy nanoparticles (HEA NPs) by direct CO2 laser induction of metal precursors on carbon paper under ambient conditions. Due to the induced ultrahigh temperature and ultrafast heating/quenching rates, FeNiCoCrRu HEA NPs with sizes ranging from 5 to 40 nm possess uniform phase homogeneity. FeNiCoCrRu HEA NPs exhibit exceptional bifunctional electrocatalytic activities, delivering overpotentials of 0.148 V at 600 mA cm−2 for the hydrogen evolution reaction and 0.353 V at 300 mA cm−2 for the oxygen evolution reaction in alkaline seawater. When assembled FeNiCoCrRu HEA NPs to an electrolyzer, it shows a negligible voltage increase at 250 mA cm−2 even after over 3000-hour operation. This superior performance can be attributed to the high-entropy design, large electrochemical specific area, and excellent chemical and structural stability. An operando Raman spectroscopy study discloses that the Ni and Ru sites serve as active sites for hydrogen evolution, while the Ni site acts as an active site for oxygen evolution. This work demonstrates a laser-induced eco-friendly nanomaterial synthesis. The systematic studies offer an in-depth understanding of HEA design and its correlation with high-efficiency seawater splitting.Item SOD1 Is an Integral Yet Insufficient Oxidizer of Hydrogen Sulfide in Trisomy 21 B Lymphocytes and Can Be Augmented by a Pleiotropic Carbon Nanozyme(MDPI, 2024) Mouli, Karthik; Liopo, Anton V.; Suva, Larry J.; Olson, Kenneth R.; McHugh, Emily A.; Tour, James M.; Derry, Paul J.; Kent, Thomas A.; Smalley-Curl Institute;NanoCarbon Center;Rice Advanced Materials InstituteDown syndrome (DS) is a multisystemic disorder that includes accelerated aging caused by trisomy 21. In particular, overexpression of cystathionine-β-synthase (CBS) is linked to excess intracellular hydrogen sulfide (H2S), a mitochondrial toxin at higher concentrations, which impairs cellular viability. Concurrent overexpression of superoxide dismutase 1 (SOD1) may increase oxidative stress by generating excess hydrogen peroxide (H2O2) while also mitigating the toxic H2S burden via a non-canonical sulfide-oxidizing mechanism. We investigated the phenotypic variability in basal H2S levels in relation to DS B lymphocyte cell health and SOD1 in H2S detoxification. The H2S levels were negatively correlated with the DS B lymphocyte growth rates but not with CBS protein. Pharmacological inhibition of SOD1 using LCS-1 significantly increased the H2S levels to a greater extent in DS cells while also decreasing the polysulfide products of H2S oxidation. However, DS cells exhibited elevated H2O2 and lipid peroxidation, representing potential toxic consequences of SOD1 overexpression. Treatment of DS cells with a pleiotropic carbon nanozyme (pleozymes) decreased the total oxidative stress and reduced the levels of the H2S-generating enzymes CBS and 3-mercaptopyruvate sulfurtransferase (MPST). Our results indicate that pleozymes may bridge the protective and deleterious effects of DS SOD1 overexpression on H2S metabolism and oxidative stress, respectively, with cytoprotective benefits.Item Intermolecular Interactions and their Implications in Solid-State Photon Interconversion(Swiss Chemical Society, 2024) Nienhaus, Lea; Rice Advanced Materials InstitutePhoton interconversion promises to alleviate thermalization losses for high energy photons and facilitates utilization of sub-bandgap photons – effectively enabling the optimal use of the entire solar spectrum. However, for solid-state device applications, the impact of intermolecular interactions on the energetic landscape underlying singlet fission and triplet-triplet annihilation upconversion cannot be neglected. In the following, the implications of molecular arrangement, intermolecular coupling strength and molecular orientation on the respective processes of solid-state singlet fission and triplet-triplet annihilation are discussed.Item Persistent flat band splitting and strong selective band renormalization in a kagome magnet thin film(Springer Nature, 2024) Ren, Zheng; Huang, Jianwei; Tan, Hengxin; Biswas, Ananya; Pulkkinen, Aki; Zhang, Yichen; Xie, Yaofeng; Yue, Ziqin; Chen, Lei; Xie, Fang; Allen, Kevin; Wu, Han; Ren, Qirui; Rajapitamahuni, Anil; Kundu, Asish K.; Vescovo, Elio; Kono, Junichiro; Morosan, Emilia; Dai, Pengcheng; Zhu, Jian-Xin; Si, Qimiao; Minár, Ján; Yan, Binghai; Yi, Ming; Smalley-Curl InstituteMagnetic kagome materials provide a fascinating playground for exploring the interplay of magnetism, correlation and topology. Many magnetic kagome systems have been reported including the binary FemXn (X = Sn, Ge; m:n = 3:1, 3:2, 1:1) family and the rare earth RMn6Sn6 (R = rare earth) family, where their kagome flat bands are calculated to be near the Fermi level in the paramagnetic phase. While partially filling a kagome flat band is predicted to give rise to a Stoner-type ferromagnetism, experimental visualization of the magnetic splitting across the ordering temperature has not been reported for any of these systems due to the high ordering temperatures, hence leaving the nature of magnetism in kagome magnets an open question. Here, we probe the electronic structure with angle-resolved photoemission spectroscopy in a kagome magnet thin film FeSn synthesized using molecular beam epitaxy. We identify the exchange-split kagome flat bands, whose splitting persists above the magnetic ordering temperature, indicative of a local moment picture. Such local moments in the presence of the topological flat band are consistent with the compact molecular orbitals predicted in theory. We further observe a large spin-orbital selective band renormalization in the Fe $${{{{\rm{d}}}}}_{{xy}}+{{{{\rm{d}}}}}_{{x}^{2}-{y}^{2}}$$spin majority channel reminiscent of the orbital selective correlation effects in the iron-based superconductors. Our discovery of the coexistence of local moments with topological flat bands in a kagome system echoes similar findings in magic-angle twisted bilayer graphene, and provides a basis for theoretical effort towards modeling correlation effects in magnetic flat band systems.Item Theoretical study of adsorption properties and CO oxidation reaction on surfaces of higher tungsten boride(Springer Nature, 2024) Radina, Aleksandra D.; Baidyshev, Viktor S.; Chepkasov, Ilya V.; Matsokin, Nikita A.; Altalhi, Tariq; Yakobson, Boris I.; Kvashnin, Alexander G.Most modern catalysts are based on precious metals and rear-earth elements, making some of organic synthesis reactions economically insolvent. Density functional theory calculations are used here to describe several differently oriented surfaces of the higher tungsten boride WB5-x, together with their catalytic activity for the CO oxidation reaction. Based on our findings, WB5-x appears to be an efficient alternative catalyst for CO oxidation. Calculated surface energies allow the use of the Wulff construction to determine the equilibrium shape of WB5-x particles. It is found that the (010) and (101) facets terminated by boron and tungsten, respectively, are the most exposed surfaces for which the adsorption of different gaseous agents (CO, CO2, H2, N2, O2, NO, NO2, H2O, NH3, SO2) is evaluated to reveal promising prospects for applications. CO oxidation on B-rich (010) and W-rich (101) surfaces is further investigated by analyzing the charge redistribution during the adsorption of CO and O2 molecules. It is found that CO oxidation has relatively low energy barriers. The implications of the present results, the effects of WB5-x on CO oxidation and potential application in the automotive, chemical, and mining industries are discussed.Item The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes(National Academy of Sciences, 2024) Jaafari, Hana; Bueno, Carlos; Schafer, Nicholas P.; Martin, Jonathan; Morcos, Faruck; Wolynes, Peter G.; Center for Theoretical BiophysicsProtein evolution is guided by structural, functional, and dynamical constraints ensuring organismal viability. Pseudogenes are genomic sequences identified in many eukaryotes that lack translational activity due to sequence degradation and thus over time have undergone “devolution.” Previously pseudogenized genes sometimes regain their protein-coding function, suggesting they may still encode robust folding energy landscapes despite multiple mutations. We study both the physical folding landscapes of protein sequences corresponding to human pseudogenes using the Associative Memory, Water Mediated, Structure and Energy Model, and the evolutionary energy landscapes obtained using direct coupling analysis (DCA) on their parent protein families. We found that generally mutations that have occurred in pseudogene sequences have disrupted their native global network of stabilizing residue interactions, making it harder for them to fold if they were translated. In some cases, however, energetic frustration has apparently decreased when the functional constraints were removed. We analyzed this unexpected situation for Cyclophilin A, Profilin-1, and Small Ubiquitin-like Modifier 2 Protein. Our analysis reveals that when such mutations in the pseudogene ultimately stabilize folding, at the same time, they likely alter the pseudogenes’ former biological activity, as estimated by DCA. We localize most of these stabilizing mutations generally to normally frustrated regions required for binding to other partners.Item Preserving surface strain in nanocatalysts via morphology control(AAAS, 2024) Shi, Chuqiao; Cheng, Zhihua; Leonardi, Alberto; Yang, Yao; Engel, Michael; Jones, Matthew R.; Han, YimoEngineering strain critically affects the properties of materials and has extensive applications in semiconductors and quantum systems. However, the deployment of strain-engineered nanocatalysts faces challenges, in particular in maintaining highly strained nanocrystals under reaction conditions. Here, we introduce a morphology-dependent effect that stabilizes surface strain even under harsh reaction conditions. Using four-dimensional scanning transmission electron microscopy (4D-STEM), we found that cube-shaped core-shell Au@Pd nanoparticles with sharp-edged morphologies sustain coherent heteroepitaxial interfaces with larger critical thicknesses than morphologies with rounded edges. This configuration inhibits dislocation nucleation due to reduced shear stress at corners, as indicated by molecular dynamics simulations. A Suzuki-type cross-coupling reaction shows that our approach achieves a fourfold increase in activity over conventional nanocatalysts, owing to the enhanced stability of surface strain. These findings contribute to advancing the development of advanced nanocatalysts and indicate broader applications for strain engineering in various fields.Item Adsorption of aqueous insensitive munitions compounds by graphene nanoplatelets(Elsevier, 2024) Gurtowski, Luke A.; McLeod, Sheila J.; Zetterholm, Sarah Grace; Allison, Cleveland D.; Griggs, Chris S.; Gramm, Josh; Wyss, Kevin; Tour, James M.; Sanchez, Florence; Rice Advanced Materials Institute; Smalley-Curl InstituteMitigation strategies for potential environmental impacts of insensitive munition (IM) compounds, including 2,4-dinitroanisole (DNAN), 3-nitro-1,2,4-triazol-5-one (NTO), nitroguanidine (NQ), and methylnitroguanidine, (MeNQ) are being considered to enhance sustainability of current or potential IM formulations. Graphene nanoplatelets (GnPs) were investigated for adsorptive removal of each compound. GnPs were characterized to determine surface areas, along with particle size and zeta potential at different pH and ionic strength conditions. Adsorption kinetics and isotherm studies were conducted, comparing results against granular activated carbon (GAC). Ionic strength, pH, and temperature were adjusted to inform impacts on adsorptive behaviors and performance. The results indicated that GnPs adsorbed IM compounds more rapidly than GAC. Additionally, GnPs removed DNAN with greater capacity compared to GAC, likely due to π-π interactions. GnPs removed other compounds via van der Waals forces, while GAC exhibited greater adsorption capacities due to higher surface area. Although negative charges associated with GnPs and dissociated NTO species hindered adsorption, pH and ionic strength did not impact other compounds. Moreover, this study reports the first environmental treatment technique for MeNQ. Overall, these findings suggest that GnPs are a promising treatment technology for IM-laden waters, particularly those with compounds like DNAN where specific interactions enhance removal efficiency.Item Accurate nuclear quantum statistics on machine-learned classical effective potentials(AIP Publishing, 2024) Zaporozhets, Iryna; Musil, Félix; Kapil, Venkat; Clementi, Cecilia; Center for Theoretical Biological PhysicsThe contribution of nuclear quantum effects (NQEs) to the properties of various hydrogen-bound systems, including biomolecules, is increasingly recognized. Despite the development of many acceleration techniques, the computational overhead of incorporating NQEs in complex systems is sizable, particularly at low temperatures. In this work, we leverage deep learning and multiscale coarse-graining techniques to mitigate the computational burden of path integral molecular dynamics (PIMD). In particular, we employ a machine-learned potential to accurately represent corrections to classical potentials, thereby significantly reducing the computational cost of simulating NQEs. We validate our approach using four distinct systems: Morse potential, Zundel cation, single water molecule, and bulk water. Our framework allows us to accurately compute position-dependent static properties, as demonstrated by the excellent agreement obtained between the machine-learned potential and computationally intensive PIMD calculations, even in the presence of strong NQEs. This approach opens the way to the development of transferable machine-learned potentials capable of accurately reproducing NQEs in a wide range of molecular systems.Item Superhard and Superconducting Bilayer Borophene(MDPI, 2024) Zhong, Chengyong; Sun, Minglei; Altalhi, Tariq; Yakobson, Boris I.Two-dimensional superconductors, especially the covalent metals such as borophene, have received significant attention due to their new fundamental physics, as well as potential applications. Furthermore, the bilayer borophene has recently ignited interest due to its high stability and versatile properties. Here, the mechanical and superconducting properties of bilayer-δ6 borophene are explored by means of first-principles computations and anisotropic Migdal–Eliashberg analytics. We find that the coexistence of strong covalent bonds and delocalized metallic bonds endows this structure with remarkable mechanical properties (maximum 2D-Young’s modulus of ~570 N/m) and superconductivity with a critical temperature of ~20 K. Moreover, the superconducting critical temperature of this structure can be further boosted to ~46 K by applied strain, which is the highest value known among all borophenes or two-dimensional elemental materials.Item Spin disorder control of topological spin texture(Springer Nature, 2024) Zhang, Hongrui; Shao, Yu-Tsun; Chen, Xiang; Zhang, Binhua; Wang, Tianye; Meng, Fanhao; Xu, Kun; Meisenheimer, Peter; Chen, Xianzhe; Huang, Xiaoxi; Behera, Piush; Husain, Sajid; Zhu, Tiancong; Pan, Hao; Jia, Yanli; Settineri, Nick; Giles-Donovan, Nathan; He, Zehao; Scholl, Andreas; N’Diaye, Alpha; Shafer, Padraic; Raja, Archana; Xu, Changsong; Martin, Lane W.; Crommie, Michael F.; Yao, Jie; Qiu, Ziqiang; Majumdar, Arun; Bellaiche, Laurent; Muller, David A.; Birgeneau, Robert J.; Ramesh, Ramamoorthy; Rice Advanced Materials InstituteStabilization of topological spin textures in layered magnets has the potential to drive the development of advanced low-dimensional spintronics devices. However, achieving reliable and flexible manipulation of the topological spin textures beyond skyrmion in a two-dimensional magnet system remains challenging. Here, we demonstrate the introduction of magnetic iron atoms between the van der Waals gap of a layered magnet, Fe3GaTe2, to modify local anisotropic magnetic interactions. Consequently, we present direct observations of the order-disorder skyrmion lattices transition. In addition, non-trivial topological solitons, such as skyrmioniums and skyrmion bags, are realized at room temperature. Our work highlights the influence of random spin control of non-trivial topological spin textures.Item RACER-m leverages structural features for sparse T cell specificity prediction(AAAS, 2024) Wang, Ailun; Lin, Xingcheng; Chau, Kevin Ng; Onuchic, José N.; Levine, Herbert; George, Jason T.; Center for Theoretical Biological PhysicsReliable prediction of T cell specificity against antigenic signatures is a formidable task, complicated by the immense diversity of T cell receptor and antigen sequence space and the resulting limited availability of training sets for inferential models. Recent modeling efforts have demonstrated the advantage of incorporating structural information to overcome the need for extensive training sequence data, yet disentangling the heterogeneous TCR-antigen interface to accurately predict MHC-allele-restricted TCR-peptide interactions has remained challenging. Here, we present RACER-m, a coarse-grained structural model leveraging key biophysical information from the diversity of publicly available TCR-antigen crystal structures. Explicit inclusion of structural content substantially reduces the required number of training examples and maintains reliable predictions of TCR-recognition specificity and sensitivity across diverse biological contexts. Our model capably identifies biophysically meaningful point-mutant peptides that affect binding affinity, distinguishing its ability in predicting TCR specificity of point-mutants from alternative sequence-based methods. Its application is broadly applicable to studies involving both closely related and structurally diverse TCR-peptide pairs.Item Reassessing the exon–foldon correspondence using frustration analysis(National Academy of Sciences, 2024) Galpern, Ezequiel A.; Jaafari, Hana; Bueno, Carlos; Wolynes, Peter G.; Ferreiro, Diego U.; Center for Theoretical Biological PhysicsProtein folding and evolution are intimately linked phenomena. Here, we revisit the concept of exons as potential protein folding modules across a set of 38 abundant and conserved protein families. Taking advantage of genomic exon–intron organization and extensive protein sequence data, we explore exon boundary conservation and assess the foldon-like behavior of exons using energy landscape theoretic measurements. We found deviations in the exon size distribution from exponential decay indicating selection in evolution. We show that when taken together there is a pronounced tendency to independent foldability for segments corresponding to the more conserved exons, supporting the idea of exon–foldon correspondence. While 45% of the families follow this general trend when analyzed individually, there are some families for which other stronger functional determinants, such as preserving frustrated active sites, may be acting. We further develop a systematic partitioning of protein domains using exon boundary hotspots, showing that minimal common exons correspond with uninterrupted alpha and/or beta elements for the majority of the families but not for all of them.Item Quantum simulation of an extended Dicke model with a magnetic solid(Springer Nature, 2024) Marquez Peraca, Nicolas; Li, Xinwei; Moya, Jaime M.; Hayashida, Kenji; Kim, Dasom; Ma, Xiaoxuan; Neubauer, Kelly J.; Fallas Padilla, Diego; Huang, Chien-Lung; Dai, Pengcheng; Nevidomskyy, Andriy H.; Pu, Han; Morosan, Emilia; Cao, Shixun; Bamba, Motoaki; Kono, JunichiroThe Dicke model describes the cooperative interaction of an ensemble of two-level atoms with a single-mode photonic field and exhibits a quantum phase transition as a function of light–matter coupling strength. Extending this model by incorporating short-range atom–atom interactions makes the problem intractable but is expected to produce new physical phenomena and phases. Here, we simulate such an extended Dicke model using a crystal of ErFeO3, where the role of atoms (photons) is played by Er3+ spins (Fe3+ magnons). Through terahertz spectroscopy and magnetocaloric effect measurements as a function of temperature and magnetic field, we demonstrated the existence of a novel atomically ordered phase in addition to the superradiant and normal phases that are expected from the standard Dicke model. Further, we elucidated the nature of the phase boundaries in the temperature–magnetic-field phase diagram, identifying both first-order and second-order phase transitions. These results lay the foundation for studying multiatomic quantum optics models using well-characterized many-body solid-state systems.