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At least 469 records · Page 26

Redox conditions correlated with vibronic coupling modulate quantum beats in photosynthetic pigment–protein complexes

Significance Photosynthetic organisms evolved their light-harvesting antenna complexes to optimize energy transfer. It was recently shown that the redox environment can tune the mixing of electronic and vibrational states to steer energy through different pathways of a pigment–protein complex. Quantum beating signals in the spectra of pigment–protein complexes have been used to probe the excited-state dynamics within the complexes, but the microscopic dynamics that generate these signals and their role in promoting energy transfer are not fully understood. Here, we show that the redox environment that tunes energy transfer similarly tunes the quantum beating signals in the same complex. We find that the beats report on excited-state vibrations that maintain coherence through the vibronically enhanced energy transfer process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanistic roles of metal- and ligand-protonated species in hydrogen evolution with [Cp*Rh] complexes

Protonation reactions involving organometallic complexes are ubiquitous in redox chemistry and often result in the generation of reactive metal hydrides. However, some organometallic species supported by η 5 -pentamethylcyclopentadienyl (Cp*) ligands have recently been shown to undergo ligand-centered protonation by direct proton transfer from acids or tautomerization of metal hydrides, resulting in the generation of complexes bearing the uncommon η 4 -pentamethylcyclopentadiene (Cp*H) ligand. Here, time-resolved pulse radiolysis (PR) and stopped-flow spectroscopic studies have been applied to examine the kinetics and atomistic details involved in the elementary electron- and proton-transfer steps leading to complexes ligated by Cp*H, using Cp*Rh(bpy) as a molecular model (where bpy is 2,2′-bipyridyl). Stopped-flow measurements coupled with infrared and UV-visible detection reveal that the sole product of initial protonation of Cp*Rh(bpy) is [Cp*Rh(H)(bpy)] + , an elusive hydride complex that has been spectroscopically and kinetically characterized here. Tautomerization of the hydride leads to the clean formation of [(Cp*H)Rh(bpy)] + . Variable-temperature and isotopic labeling experiments further confirm this assignment, providing experimental activation parameters and mechanistic insight into metal-mediated hydride-to-proton tautomerism. Spectroscopic monitoring of the second proton transfer event reveals that both the hydride and related Cp*H complex can be involved in further reactivity, showing that [(Cp*H)Rh] is not necessarily an off-cycle intermediate, but, instead, depending on the strength of the acid used to drive catalysis, an active participant in hydrogen evolution. Identification of the mechanistic roles of the protonated intermediates in the catalysis studied here could inform design of optimized catalytic systems supported by noninnocent cyclopentadienyl-type ligands.

08 HYDROGEN↗

Path integrals, complex probabilities and the discrete Weyl representation

Abstract A discrete formulation of the real-time path integral as the expectation value of a functional of paths with respect to a complex probability on a sample space of discrete valued paths is explored. The formulation in terms of complex probabilities is motivated by a recent reinterpretation of the real-time path integral as the expectation value of a potential functional with respect to a complex probability distribution on cylinder sets of paths. The discrete formulation in this work is based on a discrete version of the Weyl algebra that can be applied to any observable with a finite number of outcomes. The origin of the complex probability in this work is the completeness relation. In the discrete formulation the complex probability exactly factors into products of conditional probabilities and exact unitarity is maintained at each level of approximation. The approximation of infinite dimensional quantum systems by discrete systems is discussed. The method is illustrated by applying it to scattering theory and quantum field theory. The implications of these applications for quantum computing is discussed.

Physics↗

The structure of the high-affinity nickel-binding site in the Ni,Zn-HypA•UreE2 complex

Abstract The maturation pathway for the nickel-dependent enzyme urease utilizes the protein UreE as a metallochaperone to supply Ni(II) ions. In Helicobacter pylori urease maturation also requires HypA and HypB, accessory proteins that are commonly associated with hydrogenase maturation. Herein we report on the characterization of a protein complex formed between HypA and the UreE2 dimer. Nuclear magnetic resonance (NMR) coupled with molecular modelling show that the protein complex apo, Zn-HypA•UreE2, forms between the rigorously conserved Met-His-Glu (MHE motif) Ni-binding N-terminal sequence of HypA and the two conserved His102A and His102B located at the dimer interface of UreE2. This complex forms in the absence of Ni(II) and is supported by extensive protein contacts that include the use of the C-terminal sequences of UreE2 to form additional strands of β-sheet with the Ni-binding domain of HypA. The Ni-binding properties of apo, Zn-HypA•UreE2 and the component proteins were investigated by isothermal titration calorimetry using a global fitting strategy that included all of the relevant equilibria, and show that the Ni,Zn-HypA•UreE2 complex contains a single Ni(II)-binding site with a sub-nanomolar KD. The structural features of this novel Ni(II) site were elucidated using proteins produced with specifically deuterated amino acids, protein point mutations, and the analyses of X-ray absorption spectroscopy, hyperfine shifted NMR features, as well as molecular modeling coupled with quantum-mechanical calculations. The results show that the complex contains a six-coordinate, high-spin Ni(II) site with ligands provided by both component proteins.

Zambelli, Barbara (ORCID:0000000238760051)↗

Carbon complexes in highly C-doped GaN

We investigate the properties of heavily C-doped GaN grown by hydride vapor phase epitaxy using both optical experiments and hybrid density functional theory calculations. Previous work has established that carbon acceptors (C N ) give rise to a yellow luminescence band near 2.2 eV along with a blue luminescence band near 2.9 eV. Photoluminescence measurements show the yellow band shifting as a function of carbon concentration, suggesting a change in the behavior of carbon species as carbon content increases. With hybrid density functional theory we calculate the electrical and optical behavior of carbon centers containing multiple carbon impurities, which may arise in heavily doped material. We compare the behavior of these complexes to the isolated centers, and find that the dicarbon donor-acceptor (C Ga –C N ) complex is a candidate to explain the shift in the yellow luminescence peak. Tricarbon complexes have high formation energies and modest binding energies, and also give rise to optical transitions that are inconsistent with the observed spectra. We also identify the split dicarbon interstitial on the gallium site as a low-energy species with a large binding energy that may act to compensate carbon acceptors. Here, local vibrational modes are calculated for carbon impurity centers, and we compare these results to recent experiments. Dicarbon and tricarbon complexes involving C Ga and C N exhibit modes that are only slightly higher than the isolated species, while carbon interstitials and related complexes give rise to vibrational modes much higher than C Ga and C N .

36 MATERIALS SCIENCE↗

Carbon-nitrogen complex as an alternative to the 𝑇 center in Si

A first-principles study of a carbon-nitrogen (CN) impurity complex in silicon is presented as an isoelectronic alternative to the T center [(CCH) Si ]. The latter has been pursued for applications in quantum information science, yet its sensitivity to the presence of hydrogen is still problematic. Our proposed complex has no hydrogen, thereby eliminating this issue. First, we show that the CN complex is stable against decomposition into substitutional and interstitial defects. Next, we show that due to being isoelectronic to the T center, the CN complex has a similar electronic structure, and therefore could be used in similar applications. We assess several low-energy configurations of the CN complex, finding (CN) Si to be stable and have the largest Debye-Waller factor. We predict a zero-phonon line (ZPL) of 828 meV (in the telecom S-band) and a radiative lifetime of 4.2 μs, comparable to the T center. Due to the presence of a bound exciton, choice of the exchange-correlation functional and also supercell-size scaling of the ZPL and transition dipole moment require special scrutiny; we rigorously justify our extrapolation schemes that allow computing values in the dilute limit.

36 MATERIALS SCIENCE↗

Molecular Structure and Electron Affinity of Metal-Solvent Complexes: Insights from Density Functional Theory Simulations

A molecular level understanding of the structure and energetics of the monovalent and divalent metal ion complexes is of great importance for development of next-generation batteries. Here, Density Functional Theory (DFT) simulations at the ωb97xD/6-31 + G(d,p) level of theory are performed to investigate the interaction of metal ions (Li + , Na + , K + , Mg 2+ , Ca 2+ , Zn 2+ ) with 26 organic solvent molecules. The reduction energetics (electron affinity and reduction potential) and structural responses of the solvent molecules and the molecular complexes are discussed. The DFT calculations are carried out to investigate the structure, energetics and electron affinities of chelated complexes of water (H 2 O), tetrahydrofuran (THF) and di-methoxy ethane (DME) solvent molecules. Additionally, ab initio dynamic simulations (AIMD) at 298 K using atom centered density matrix propagation (ADMP) formalism are performed to understand the spontaneous structure formation upon electron attachment of the metal ion-solvent complexes. The ADMP simulations indicate the decomposition of Mg + -(DME) 3 complex via cleavage of C–O bond of one of the three DME molecules indicating irreversible decomposition of DME in the presence of the Mg + radical. We believe that the data collected as part of this investigation serves as a library of fundamental knowledge towards a deeper understanding of the electrode-electrolyte interfacial reactions.

25 ENERGY STORAGE↗

Performance of explicit and IMEX MRI multirate methods on complex reactive flow problems within modern parallel adaptive structured grid frameworks

Large-scale multiphysics simulations are computationally challenging due to the coupling of multiple processes with widely disparate time scales. The advent of exascale computing systems exacerbates these challenges since these systems enable ever-increasing size and complexity. In recent years, there has been renewed interest in developing multirate methods as a means to handle the large range of time scales, as these methods may afford greater accuracy and efficiency than more traditional approaches of using implicit-explicit (IMEX) and low-order operator splitting schemes. However, to date there have been few performance studies that compare different classes of multirate integrators on complex application problems. In this work, we study the performance of several newly developed multirate infinitesimal (MRI) methods, implemented in the SUNDIALS solver package, on two reacting flow model problems built on structured mesh frameworks. The first model revisits prior work on a compressible reacting flow problem with complex chemistry that is implemented using BoxLib but where we now include comparisons between a new explicit MRI scheme with the multirate spectral deferred correction (SDC) methods in the original paper. The second problem uses the same complex chemistry as the first problem, combined with a simplified flow model, but runs at a large spatial scale where explicit methods become infeasible due to stability constraints. Two recently developed IMEX MRI multirate methods are tested. These methods rely on advanced features of the AMReX framework on which the model is built, such as multilevel grids and multilevel preconditioners. The results from these two problems show that MRI multirate methods can offer significant performance benefits on complex multiphysics application problems and that these methods may be combined with advanced spatial discretization to compound the advantages of both.

97 MATHEMATICS AND COMPUTING↗

Relaxation behavior in low-frequency complex conductivity of sands caused by bacterial growth and biofilm formation by Shewanella oneidensis under a high-salinity condition

Complex electrical conductivity is increasingly used to monitor subsurface processes associated with microbial activities because microbial cells mostly have surface charges and thus electrical double layers. Although highly saline environments are frequently encountered in coastal and marine sediments, there are limited data available on the complex conductivity associated with microbial activities under a high-salinity condition. Therefore, we have developed the spectral responses of complex conductivity of sand associated with bacterial growth and biofilm formation under a highly saline condition of approximately 1% salinity and approximately 2 S/m pore water conductivity with an emphasis on relaxation behavior. A column test is performed, in which the model bacteria Shewanella oneidensis MR-1 are stimulated for cell growth and biofilm formation in a sand pack, whereas the complex conductivity is monitored from 0.01 Hz to 10 kHz. The test results indicate that the real conductivity increases in the early stage due to the microbial metabolites and the increased surface conduction with cell growth but soon begin to decrease because of the reduction of charge passages due to bioclogging. However, the imaginary conductivity significantly increases with time, and clear bell-shaped relaxation behaviors are observed with the peak frequency of 0.1–1 Hz, associated with the double-layer polarization of cells and electrically conductive pili and biofilms. The Cole-Cole relaxation model appears to capture such relaxation behaviors well, and the modeling results indicate gradual increases in normalized chargeability and decreases in relaxation time during bacterial growth and biofilm formation in the highly saline condition. Comparison with previous literature confirms that the high-salinity condition further increases the normalized chargeability, whereas it suppresses the phase shift and thus the imaginary conductivity. Our results suggest that the complex conductivity can effectively capture microbial biomass formation in sands under a highly saline condition.

58 GEOSCIENCES↗

Effects on Human Non-Small Lung Cancer Cell growth of Cu(II), Au(III) and Re(I) Complexes Containing N-donor Pyridyl Ligands: A Senior Undergraduate Research Project

Hands-on synthetic laboratory experiences are critically important for undergraduate chemistry majors. A senior undergraduate research experience at the College of Wooster is presented in the current work. The inorganic complexes [Cu(phenan) 2 (NO 3 ) 2 ] (1; phenan = phenanthridine) and [Au(phenan)Cl 3 ](2) were prepared by metallation of the phenan ligand in a 1:1 CH 3 OH/CH 2 Cl 2 mixture at room temperature. Complex 1 is a new inorganic coordination compound. The structures were confirmed by X-ray crystallography. Complex 1 reveals a distorted octahedral geometry around the central Cu (II) metal ion. In complex 2, the Au(III) atom exhibits a square planar geometry. In addition, we investigated [Cu(dmeobpy)(H 2 O) 2 ][NO 3 ] 2 (3; dmeobpy = 4,4’-dimethoxy-2,2’-bipyridine), [Cu(bap)(NO 3 ) 2 ](4; bap = 2,6-bis(azaindole)pyridine) and [Re(CO) 3 (dmeobpy)Cl] (5). The cytoxocities of 1-5, phenan, dmeobpy, bap and cisplatin were evaluated against several human non-small cell lung cancer cell lines (NCI-H1975, HCC827, NCI-H460, and NCI-A549). Compound 1 exhibited modest antitumor activity against the HCC827 cell line, with an IC 50 value of 19 µM. Compound 3 exhibits lower cytotoxic activity than 1. Finally, the cytotoxic activity of complex 5 (IC 50 < 11 µM) is significantly greater than 1 and 3 against the H1975 cancer cell line.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Mechanical coupling in the nitrogenase complex

The enzyme nitrogenase reduces dinitrogen to ammonia utilizing electrons, protons, and energy obtained from the hydrolysis of ATP. Mo-dependent nitrogenase is a symmetric dimer, with each half comprising an ATP-dependent reductase, termed the Fe Protein, and a catalytic protein, known as the MoFe protein, which hosts the electron transfer P-cluster and the active-site metal cofactor (FeMo-co). A series of synchronized events for the electron transfer have been characterized experimentally, in which electron delivery is coupled to nucleotide hydrolysis and regulated by an intricate allosteric network. We report a graph theory analysis of the mechanical coupling in the nitrogenase complex as a key step to understanding the dynamics of allosteric regulation of nitrogen reduction. This analysis shows that regions near the active sites undergo large-scale, large-amplitude correlated motions that enable communications within each half and between the two halves of the complex. Computational predictions of mechanically regions were validated against an analysis of the solution phase dynamics of the nitrogenase complex via hydrogen-deuterium exchange. These regions include the P-loops and the switch regions in the Fe proteins, the loop containing the residue β-188Ser adjacent to the P-cluster in the MoFe protein, and the residues near the protein-protein interface. In particular, it is found that: (i) within each Fe protein, the switch regions I and II are coupled to the [4Fe-4S] cluster; (ii) within each half of the complex, the switch regions I and II are coupled to the loop containing β-188Ser; (iii) between the two halves of the complex, the regions near the nucleotide binding pockets of the two Fe proteins (in particular the P-loops, located over 130 Å apart) are also mechanically coupled. Notably, we found that residues next to the P-cluster (in particular the loop containing β-188Ser) are important for communication between the two halves.

59 BASIC BIOLOGICAL SCIENCES↗

Eligibility Assessment of TA-52-1 and TA-52-11: The Ultra-High Temperature Reactor Experiment (UHTREX) Complex

The U.S. Department of Energy (DOE), National Nuclear Security Administration, Los Alamos Field Office (NA-LA) requests the State Historic Preservation Officer (SHPO) to concur with the eligibility determinations contained in this report for Buildings 1 and 11 in Technical Area 52 (TA-52) at Los Alamos National Laboratory (LANL or the Laboratory). Triad National Security LLC cultural resources staff have completed the evaluation of two buildings, called the UHTREX Complex, for inclusion in the National Register of Historic Places (Register). This complex includes the UHTREX Reactor Building (TA-52-1), and an associated Mechanical Assembly Building (TA-52-11). As part of LANL’s Footprint Reduction Program, both facilities of the UHTREX Complex are scheduled for characterization and demolition. In addition to evaluating their eligibility in the Register, the properties at TA-52 were assessed for potential adaptive reuse, long-term preservation, and public interpretation. Based on the findings in this assessment report, both TA-52-1 and TA-52-11 have been determined to not be eligible for inclusion in the Register. The history of the UHTREX Complex lacks association with exceptionally significant Cold War events of scientific developments. Both TA-52-1 and TA-52-11 lack the necessary internal historic integrity suitable for long-term preservation or public interpretation. And both facilities contain legacy radioactive contamination, which prohibits their reuse. In addition to its loss of integrity and context, TA-52- 11 has been determined ineligible due to its status as a support building of secondary or minor importance. In compliance with Section 106 and Section 110 of the National Historic Preservation Act of 1966, as amended, and with the Programmatic Agreement among the U.S. Department of Energy, National Nuclear Security Administration, Los Alamos Field Office, the New Mexico State Historic Preservation Office, and the Advisory Council on Historic Preservation Concerning Management of the Historic Properties at Los Alamos National Laboratory, Los Alamos, New Mexico, the SHPO is requested to concur with the eligibility determinations contained in this report for the UHTREX Complex in TA-52.

99 GENERAL AND MISCELLANEOUS↗

Deep Learning Prediction of Protein Complex Structures

Proteins interact to form protein complex to carry out biological functions such as catalytic chemical reaction. Therefore, it is important to develop computational methods to predict protein-protein interaction and the structures of protein complexes to study and enhance protein function. In this project, we successfully developed several deep learning methods to predict inter-protein contacts and the reinforcement learning and optimization methods to reconstruct protein complex structures from predicted inter-chain contacts. The methods were integrated with the MULTICOM protein complex structure prediction system and applied to predict the complex structures of biomass production-related proteins of green algae. During the two and a half years of research and development, all the specific milestones of the project were achieved successfully. 16 publications/manuscripts were produced. 10 software tools were developed. A patent application was submitted. Our MULTICOM predictors leveraging some tools developed in this project were ranked among the top predictors in the 15th Critical Assessment of Techniques for Protein Structure Prediction (CASP15) in 2022.

59 BASIC BIOLOGICAL SCIENCES↗

Predictive Complexity of Quantum Subsystems

We define predictive states and predictive complexity for quantum systems composed of distinct subsystems. This complexity is a generalization of entanglement entropy. It is inspired by the statistical or forecasting complexity of predictive state analysis of stochastic and complex systems theory but is intrinsically quantum. Predictive states of a subsystem are formed by equivalence classes of state vectors in the exterior Hilbert space that effectively predict the same future behavior of that subsystem for some time. As an illustrative example, we present calculations in the dynamics of an isotropic Heisenberg model spin chain and show that, in comparison to the entanglement entropy, the predictive complexity better signifies dynamically important events, such as magnon collisions. It can also serve as a local order parameter that can distinguish long and short range entanglement.

Asplund, Curtis T. (ORCID:0000000305575850)↗

Scalable Simulation of Pressure Gradient-Driven Transport of Rarefied Gases in Complex Permeable Media Using Lattice Boltzmann Method

Accurate representations of slip and transitional flow regimes present a challenge in the simulation of rarefied gas flow in confined systems with complex geometries. In these regimes, continuum-based formulations may not capture the physics correctly. This work considers a regularized multi-relaxation time lattice Boltzmann (LB) method with mixed Maxwellian diffusive and halfway bounce-back wall boundary treatments to capture flow at high Kn. The simulation results are validated against atomistic simulation results from the literature. We examine the convergence behavior of LB for confined systems as a function of inlet and outlet treatments, complexity of the geometry, and magnitude of pressure gradient and show that convergence is sensitive to all three. The inlet and outlet boundary treatments considered in this work include periodic, pressure, and a generalized periodic boundary condition. Compared to periodic and pressure treatments, simulations of complex domains using a generalized boundary treatment conserve mass but require more iterations to converge. Convergence behavior in complex domains improves at higher magnitudes of pressure gradient across the computational domain, and lowering the porosity deteriorates the convergence behavior for complex domains.

42 ENGINEERING↗

A Structural Perspective on the RNA Editing of Plant Respiratory Complexes

The last steps of respiration, a core energy-harvesting process, are carried out by a chain of multi-subunit complexes in the inner mitochondrial membrane. Several essential subunits of the respiratory complexes are RNA-edited in plants, frequently leading to changes in the encoded amino acids. While the impact of RNA editing is clear at the sequence and phenotypic levels, the underlying biochemical explanations for these effects have remained obscure. Here, we used the structures of plant respiratory complex I, complex III2 and complex IV to analyze the impact of the amino acid changes of RNA editing in terms of their location and biochemical features. Through specific examples, we demonstrate how the structural information can explain the phenotypes of RNA-editing mutants. This work shows how the structural perspective can bridge the gap between sequence and phenotype and provides a framework for the continued analysis of RNA-editing mutants in plant mitochondria and, by extension, in chloroplasts.

59 BASIC BIOLOGICAL SCIENCES↗

Site Density Functional Theory and Structural Bioinformatics Analysis of the SARS-CoV Spike Protein and hACE2 Complex

The entry of the SARS-CoV-2, a causative agent of COVID-19, into human host cells is mediated by the SARS-CoV-2 spike (S) glycoprotein, which critically depends on the formation of complexes involving the spike protein receptor-binding domain (RBD) and the human cellular membrane receptor angiotensin-converting enzyme 2 (hACE2). Using classical site density functional theory (SDFT) and structural bioinformatics methods, we investigate binding and conformational properties of these complexes and study the overlooked role of water-mediated interactions. Analysis of the three-dimensional reference interaction site model (3DRISM) of SDFT indicates that water mediated interactions in the form of additional water bridges strongly increases the binding between SARS-CoV-2 spike protein and hACE2 compared to SARS-CoV-1-hACE2 complex. By analyzing structures of SARS-CoV-2 and SARS-CoV-1, we find that the homotrimer SARS-CoV-2 S receptor-binding domain (RBD) has expanded in size, indicating large conformational change relative to SARS-CoV-1 S protein. Protomer with the up-conformational form of RBD, which binds with hACE2, exhibits stronger intermolecular interactions at the RBD-ACE2 interface, with differential distributions and the inclusion of specific H-bonds in the CoV-2 complex. Further interface analysis has shown that interfacial water promotes and stabilizes the formation of CoV-2/hACE2 complex. This interaction causes a significant structural rigidification of the spike protein, favoring proteolytic processing of the S protein for the fusion of the viral and cellular membrane. Moreover, conformational dynamics simulations of RBD motions in SARS-CoV-2 and SARS-CoV-1 point to the role in modification of the RBD dynamics and their impact on infectivity.

3DRISM↗

ODIN: Characterizing the Three-dimensional Structure of Two Protocluster Complexes at z = 3.1

We present a detailed study of the 3D morphology of two extended associations of multiple protoclusters at z = 3.1. These protocluster "complexes," designated COSMOS-z3.1-A and COSMOS-z3.1-C, are the most prominent overdensities of z = 3.1 Lyα emitters (LAEs) identified in the COSMOS field by the One-hundred-deg$^{2}$ DECam Imaging in Narrowbands survey. These protocluster complexes have been followed up with extensive spectroscopy from Keck, Gemini, and DESI. Using a probabilistic method that combines photometrically selected and spectroscopically confirmed LAEs, we reconstruct the 3D structure of these complexes on scales of ≈50 cMpc. We validate our reconstruction method using the IllustrisTNG300-1 cosmological hydrodynamical simulation and show that it consistently outperforms approaches relying solely on spectroscopic data. The resulting 3D maps reveal that both complexes are irregular and elongated along a single axis, emphasizing the impact of sightline on our perception of structure morphology. The complexes consist of multiple density peaks, 10 in COSMOS-z3.1-A and 4 in COSMOS-z3.1-C. The former is confirmed to be a proto-supercluster, similar to Hyperion at z = 2.4 but observed at an even earlier epoch. Multiple "tails" connected to the cores of the density peaks are seen, likely representing cosmic filaments feeding into these extremely overdense regions. The 3D reconstructions further provide strong evidence that Lyα blobs preferentially reside in the outskirts of the highest density regions. Descendant mass estimates of the density peaks suggest that COSMOS-z3.1-A and COSMOS-z3.1-C will evolve to become ultramassive structures by z = 0, with total masses log ( M / M ,⊙ ,) ≳ 15.3 , exceeding that of Coma.

Ramakrishnan, Vandana [Purdue U., West Lafayette] ↗