Strain and rupture of HIV-1 capsids during uncoating.

SignificanceThe mature capsids of HIV-1 are transiently stable complexes that self-assemble around the viral genome during maturation, and uncoat to release preintegration complexes that archive a double-stranded DNA copy of the virus in the host cell genome. However, a detailed view of how HIV cores rupture remains lacking. Here, we elucidate the physical properties involved in capsid rupture using a combination of large-scale all-atom molecular dynamics simulations and cryo-electron tomography. We find that intrinsic strain on the capsid forms highly correlated patterns along the capsid surface, along which cracks propagate. Capsid rigidity also increases with high strain. Our findings provide fundamental insight into viral capsid uncoating.

GaSI: A Wide-Gap Non-centrosymmetric Helical Crystal.

The complex non-centrosymmetric and chiral nature of helical structures endow materials that possess such motifs with unusual properties. However, despite their ubiquity in biological and organic systems, there is a severe lack of inorganic crystals that display helicity in extended lattices, where these unusual properties are expected to be most pronounced. Here, we report a new inorganic helical structure, gallium sulfur iodide (GaSI), within the exfoliable class of III-VI-VII (1:1:1) one-dimensional (1D) van der Waals (vdW) crystals. Through detailed structural analyses, including single-crystal X-ray diffraction, electron microscopy, and density functional theory (DFT), we elucidate the apparent noncrystallographic screw axis and the first example of an atomic scale helical structure bearing a "squircular" cross-section in GaSI. Crystallizing in the non-centrosymmetric P4̅ space group, we found that GaSI crystals exhibit pronounced second-harmonic generation. From diffuse reflectance spectroscopy, GaSI displays a sizeable bandgap of 3.69 eV, owing tostrong covalent interactions arising from the smaller sulfur atoms within the helix core. These results position GaSI as a promising exfoliable nonlinear optical material across a broad optical window.

Improving MR Image Quality in Patients with Metallic Implants.

The number of implanted devices such as orthopedic hardware and cardiac implantable devices continues to increase with an increase in the age of the patient population, as well as an increase in the number of indications for specific devices. Many patients with these devices have or will develop clinical conditions that are best depicted at MRI. However, implanted devices containing paramagnetic or ferromagnetic substances can cause significant artifact, which could limit the diagnostic capability of this modality. Performing imaging with MRI when an implant is present may be challenging, and there are numerous techniques the radiologist and technologist can use to help minimize artifacts related to implants. First, knowledge of the presence of an implant before patient arrival is critical to ensure safety of the patient when the device is subjected to a strong magnetic field. Once safety is ensured, the examination should be performed with the MRI system that is expected to provide the best image quality. The selection of the MRI system includes multiple considerations such as the effects of field strength and availability of specific sequences, which can reduce metal artifact. Appropriate patient positioning, attention to MRI parameters (including bandwidth, voxel size, and echo), and appropriate selection of sequences (those with less metal artifact and advanced metal reduction sequences) are critical to improve image quality. Patients with implants can be successfully imaged with MRI with appropriate planning and understanding of how to minimize artifacts. This improves image quality and the diagnostic confidence of the radiologist. ©RSNA, 2021.

Charge Carrier Hopping Dynamics in Homogeneously Broadened PbS Quantum Dot Solids.

Energetic disorder in quantum dot solids adversely impacts charge carrier transport in quantum dot solar cells and electronic devices. Here, we use ultrafast transient absorption spectroscopy to show that homogeneously broadened PbS quantum dot arrays (σhom2:σinh2 > 19:1, σinh/kBT < 0.4) can be realized if quantum dot batches are sufficiently monodisperse (δ ≲ 3.3%). The homogeneous line width is found to be an inverse function of quantum dot size, monotonically increasing from ∼25 meV for the largest quantum dots (5.8 nm diameter/0.92 eV energy) to ∼55 meV for the smallest (4.1 nm/1.3 eV energy). Furthermore, we show that intrinsic charge carrier hopping rates are faster for smaller quantum dots. This finding is the opposite of the mobility trend commonly observed in device measurements but is consistent with theoretical predictions. Fitting our data to a kinetic Monte Carlo model, we extract charge carrier hopping times ranging from 80 ps for the smallest quantum dots to over 1 ns for the largest, with the same ethanethiol ligand treatment. Additionally, we make the surprising observation that, in slightly polydisperse (δ ≲ 4%) quantum dot solids, structural disorder has a greater impact than energetic disorder in inhibiting charge carrier transport. These findings emphasize how small improvements in batch size dispersity can have a dramatic impact on intrinsic charge carrier hopping behavior and will stimulate further improvements in quantum dot device performance.

Including surface ligand effects in continuum elastic models of nanocrystal vibrations.

The measured low frequency vibrational energies of some quantum dots (QDs) deviate from the predictions of traditional elastic continuum models. Recent experiments have revealed that these deviations can be tuned by changing the ligands that passivate the QD surface. This observation has led to speculation that these deviations are due to a mass-loading effect of the surface ligands. In this article, we address this speculation by formulating a continuum elastic theory that includes the dynamical loading by elastic surface ligands. We demonstrate that this model is capable of accurately reproducing the l = 0 phonon energy across a variety of different QD samples, including cores with different ligand identities and epitaxially grown CdSe/CdS core/shell heterostructures. We highlight that our model performs well even in the small QD regime, where traditional elastic continuum models are especially prone to failure. Furthermore, we show that our model combined with Raman measurements can be used to infer the elastic properties of surface bound ligands, such as sound velocities and elastic moduli, that are otherwise challenging to measure.

Pharmacogenomic incidental findings in 308 families: The NIH Undiagnosed Diseases Program experience.

PURPOSE: Using single-nucleotide polymorphism (SNP) chip and exome sequence data from individuals participating in the National Institutes of Health (NIH) Undiagnosed Diseases Program (UDP), we evaluated the number and therapeutic informativeness of incidental pharmacogenetic variants. METHODS: Pharmacogenomics Knowledgebase (PharmGKB) annotated sequence variants were identified in 1,101 individuals. Medication records of participants were used to identify individuals prescribed medications with a genetic variant that might alter efficacy. RESULTS: A total of 395 sequence variants, including 19 PharmGKB 1A and 1B variants, were identified in SNP chip sequence data, and 388 variants, including 21 PharmGKB 1A and 1B variants, were identified in the exome sequence data. Nine participants had incidental pharmacogenetic variants associated with altered efficacy of a prescribed medication. CONCLUSIONS: Despite the small size of the NIH UDP patient cohort, we identified pharmacogenetic incidental findings potentially useful for guiding therapy. Consequently, groups conducting clinical genomic studies might consider reporting of pharmacogenetic incidental findings.Genet Med 18 12, 1303-1307.

Computational evaluation of exome sequence data using human and model organism phenotypes improves diagnostic efficiency.

PURPOSE: Medical diagnosis and molecular or biochemical confirmation typically rely on the knowledge of the clinician. Although this is very difficult in extremely rare diseases, we hypothesized that the recording of patient phenotypes in Human Phenotype Ontology (HPO) terms and computationally ranking putative disease-associated sequence variants improves diagnosis, particularly for patients with atypical clinical profiles. METHODS: Using simulated exomes and the National Institutes of Health Undiagnosed Diseases Program (UDP) patient cohort and associated exome sequence, we tested our hypothesis using Exomiser. Exomiser ranks candidate variants based on patient phenotype similarity to (i) known disease-gene phenotypes, (ii) model organism phenotypes of candidate orthologs, and (iii) phenotypes of protein-protein association neighbors. RESULTS: Benchmarking showed Exomiser ranked the causal variant as the top hit in 97% of known disease-gene associations and ranked the correct seeded variant in up to 87% when detectable disease-gene associations were unavailable. Using UDP data, Exomiser ranked the causative variant(s) within the top 10 variants for 11 previously diagnosed variants and achieved a diagnosis for 4 of 23 cases undiagnosed by clinical evaluation. CONCLUSION: Structured phenotyping of patients and computational analysis are effective adjuncts for diagnosing patients with genetic disorders.Genet Med 18 6, 608-617.

Temperature dependence of acoustic vibrations of CdSe and CdSe-CdS core-shell nanocrystals measured by low-frequency Raman spectroscopy.

We measure the temperature dependence of breathing-mode acoustic vibrations of semiconductor nanocrystals using low-frequency Raman spectroscopy. In CdSe core-only nanocrystals, the lowest-energy l = 0 mode red-shifts with increasing temperature by ∼5% between 77-300 K. Changes to the interatomic bond distances in the inorganic crystal lattice, with corresponding changes to the bulk modulus and density of the material, contribute to the observed energy shift but do not fully explain its magnitude across all nanocrystal sizes. Invariance of the Raman linewidth over the same temperature range suggests that the acoustic breathing mode is inhomogeneously broadened. The acoustic phonons of CdSe/CdS core-shell composite nanocrystals display similar qualitative behavior. However, for large core-shell nanocrystals, we observe a higher-order Raman peak at approximately twice the energy of the l = 0 mode, which we identify as a higher spherical harmonic-the n = 2, l = 0 eigenmode-rather than a two-phonon scattering event.

Subdiffusive exciton transport in quantum dot solids.

Colloidal quantum dots (QDs) are promising materials for use in solar cells, light-emitting diodes, lasers, and photodetectors, but the mechanism and length of exciton transport in QD materials is not well understood. We use time-resolved optical microscopy to spatially visualize exciton transport in CdSe/ZnCdS core/shell QD assemblies. We find that the exciton diffusion length, which exceeds 30 nm in some cases, can be tuned by adjusting the inorganic shell thickness and organic ligand length, offering a powerful strategy for controlling exciton movement. Moreover, we show experimentally and through kinetic Monte Carlo simulations that exciton diffusion in QD solids does not occur by a random-walk process; instead, energetic disorder within the inhomogeneously broadened ensemble causes the exciton diffusivity to decrease over time. These findings reveal new insights into exciton dynamics in disordered systems and demonstrate the flexibility of QD materials for photonic and optoelectronic applications.

NASCI case of the month: "Unroofed coronary sinus without persistent left-sided superior vena cava".

Unroofed sinus is categorized into four subtypes. Types I and II represent complete unroofing with or without an LSVC, respectively [1]. Types III and IV are partial unroofing involving the mid-CS (type III) or near the LA appendage and left superior pulmonary vein (type IV) [1]. CT has advantages over echocardiography in detection of this anomaly (illustrated in this case) as well as in precise delineation of defect and associated findings (presence or absence of LSVC). Short axis reconstructions at the level of CS are helpful in diagnosis. Considerations for repair include location of CS defect, presence of LSVC and other abnormalities as well as comorbidity risks [2].

On the electronic structure of the low lying electronic states of vanadium trioxide.

The electronic structure of transition metal oxides is frequently studied using density functional theory. Nonetheless, the electronic structure of VO3 has been found to be sensitive to the choice of functional. As a consequence, the basic question of whether or not the ground electronic state exhibits a Jahn-Teller distortion has yet to be resolved. Using basis sets of triple zeta quality and multireference configuration interaction wave functions as large as 700 million configuration state functions, we determine that the ground electronic state of VO3 is a (2)A2 state in C3v symmetry. The first two excited electronic states are also characterized and found to be the components of a degenerate (2)E state, in C3v symmetry, which exhibits a small Jahn-Teller distortion. The Jahn-Teller stabilization energy is only 40 cm(-1) and the barrier to pseudo-rotation is 9 cm(-1). This (2)E state exhibits some unexpected properties. In the vicinity of the minimum energy conical intersection, the local topography appears almost quadratic, rather than linear, in the Jahn-Teller active coordinates. This gives rise to three symmetry-related seams of conical intersections in addition to the symmetry-required seam and results in the suppression of the geometric phase effect. These features, attributable to small linear Jahn-Teller parameters, are usually found in states characterized by e(2) (or e(3)e(')) electron configurations rather than the e(3) configuration found here. In addition to its Jahn-Teller minimum, the first excited state exhibits a second minimum with a structure significantly distorted from C3v. A conical intersection with Cs symmetry connects the two minima and puts an upper limit of 190 cm(-1) on the barrier connecting these minima.

Effects of Mitral Valve Prolapse on Quantification of Mitral Regurgitation and Ejection Fraction Using Cardiac MRI.

Purpose: To determine the impact of prolapsed volume on regurgitant volume (RegV), regurgitant fraction (RF), and left ventricular ejection fraction (LVEF) in patients with mitral valve prolapse (MVP) using cardiac MRI. Materials and Methods: Patients with MVP and mitral regurgitation who underwent cardiac MRI from 2005 to 2020 were identified retrospectively from the electronic record. RegV is the difference between left ventricular stroke volume (LVSV) and aortic flow. Left ventricular end-systolic volume (LVESV) and LVSV were obtained from volumetric cine images, with prolapsed volume inclusion (LVESVp, LVSVp) and exclusion (LVESVa, LVSVa) providing two estimates of RegV (RegVp, RegVa), RF (RFp, RFa), and LVEF (LVEFa, LVEFp). Interobserver agreement for LVESVp was assessed using intraclass correlation coefficient (ICC). RegV was also calculated independently using measurements from mitral inflow and aortic net flow phase-contrast imaging as the reference standard (RegVg). Results: The study included 19 patients (mean age, 28 years ± 16 [SD]; 10 male patients). Interobserver agreement for LVESVp was high (ICC, 0.98; 95% CI: 0.96, 0.99). Prolapsed volume inclusion resulted in higher LVESV (LVESVp: 95.4 mL ± 34.7 vs LVESVa: 82.4 mL ± 33.8; P < .001), lower LVSV (LVSVp: 100.5 mL ± 33.8 vs LVSVa: 113.5 mL ± 35.9; P < .001), and lower LVEF (LVEFp: 51.7% ± 5.7 vs LVEFa: 58.6% ± 6.3; P < .001). RegV was larger in magnitude when prolapsed volume was excluded (RegVa: 39.4 mL ± 21.0 vs RegVg: 25.8 mL ± 22.8; P = .02), with no evidence of a difference when including prolapsed volume (RegVp: 26.4 mL ± 16.4 vs RegVg: 25.8 mL ± 22.8; P > .99). Conclusion: Measurements that included prolapsed volume most closely reflected mitral regurgitation severity, but inclusion of this volume resulted in a lower LVEF.Keywords: Cardiac, MRI© RSNA, 2023See also commentary by Lee and Markl in this issue.

Electronic structure calculations in arbitrary electrostatic environments.

Modeling of electronic structure of molecules in electrostatic environments is of considerable relevance for surface-enhanced spectroscopy and molecular electronics. We have developed and implemented a novel approach to the molecular electronic structure in arbitrary electrostatic environments that is compatible with standard quantum chemical methods and can be applied to medium-sized and large molecules. The scheme denoted CheESE (chemistry in electrostatic environments) is based on the description of molecular electronic structure subject to a boundary condition on the system/environment interface. Thus, it is particularly suited to study molecules on metallic surfaces. The proposed model is capable of describing both electrostatic effects near nanostructured metallic surfaces and image-charge effects. We present an implementation of the CheESE model as a library module and show example applications to neutral and negatively charged molecules.

Stability and molecular pathways to the formation of spin defects in silicon carbide.

Spin defects in wide-bandgap semiconductors provide a promising platform to create qubits for quantum technologies. Their synthesis, however, presents considerable challenges, and the mechanisms responsible for their generation or annihilation are poorly understood. Here, we elucidate spin defect formation processes in a binary crystal for a key qubit candidate-the divacancy complex (VV) in silicon carbide (SiC). Using atomistic models, enhanced sampling simulations, and density functional theory calculations, we find that VV formation is a thermally activated process that competes with the conversion of silicon (VSi) to carbon monovacancies (VC), and that VV reorientation can occur without dissociation. We also find that increasing the concentration of VSi relative to VC favors the formation of divacancies. Moreover, we identify pathways to create spin defects consisting of antisite-double vacancy complexes and determine their electronic properties. The detailed view of the mechanisms that underpin the formation and dynamics of spin defects presented here may facilitate the realization of qubits in an industrially relevant material.

Neural Network Sampling of the Free Energy Landscape for Nitrogen Dissociation on Ruthenium.

In heterogeneous catalysis, free energy profiles of reactions govern the mechanisms, rates, and equilibria. Energetics are conventionally computed using the harmonic approximation (HA), which requires determination of critical states a priori. Here, we use neural networks to efficiently sample and directly calculate the free energy surface (FES) of a prototypical heterogeneous catalysis reaction-the dissociation of molecular nitrogen on ruthenium-at density-functional-theory-level accuracy. We find that the vibrational entropy of surface atoms, often neglected in HA for transition metal catalysts, contributes significantly to the reaction barrier. The minimum free energy path for dissociation reveals an "on-top" adsorbed molecular state prior to the transition state. While a previously reported flat-lying molecular metastable state can be identified in the potential energy surface, it is absent in the FES at relevant reaction temperatures. These findings demonstrate the importance of identifying critical points self-consistently on the FES for reactions that involve considerable entropic effects.

Atomic-scale characterization of mature HIV-1 capsid stabilization by inositol hexakisphosphate (IP6).

Inositol hexakisphosphates (IP6) are cellular cofactors that promote the assembly of mature capsids of HIV. These negatively charged molecules coordinate an electropositive ring of arginines at the center of pores distributed throughout the capsid surface. Kinetic studies indicate that the binding of IP6 increases the stable lifetimes of the capsid by several orders of magnitude from minutes to hours. Using all-atom molecular dynamics simulations, we uncover the mechanisms that underlie the unusually high stability of mature capsids in complex with IP6 We find that capsid hexamers and pentamers have differential binding modes for IP6 Ligand density calculations show three sites of interaction with IP6 including at a known capsid inhibitor binding pocket. Free energy calculations demonstrate that IP6 preferentially stabilizes pentamers over hexamers to enhance fullerene modes of assembly. These results elucidate the molecular role of IP6 in stabilizing and assembling the retroviral capsid.

Solving the Trivial Crossing Problem While Preserving the Nodal Symmetry of the Wave Function.

In an adiabatic mixed quantum-classical simulation, the avoided crossing of weakly coupled eigenstates can lead to unphysical discontinuities in wave function dynamics, otherwise known as the trivial crossing problem. A standard solution to the trivial crossing problem eliminates spatial discontinuities in wave function dynamics by imposing changes to the eigenstate of the wave function. In this paper, we show that this solution has the side effect of introducing transient discontinuities in the nodal symmetry of the wave function. We present an alternative solution to the trivial crossing problem that preserves both the spatial and nodal structure of the adiabatic wave function. By considering a model of exciton dynamics on conjugated polymer systems, we show that failure to preserve wave function symmetry yields exciton dynamics that depends unphysically on polymer system size. We demonstrate that our symmetry-preserving solution to the trivial crossing problem yields more realistic dynamics and can thus improve the accuracy of simulations of larger systems that are prone to the trivial crossing problem.

Molecular engineered conjugated polymer with high thermal conductivity.

Traditional polymers are both electrically and thermally insulating. The development of electrically conductive polymers has led to novel applications such as flexible displays, solar cells, and wearable biosensors. As in the case of electrically conductive polymers, the development of polymers with high thermal conductivity would open up a range of applications in next-generation electronic, optoelectronic, and energy devices. Current research has so far been limited to engineering polymers either by strong intramolecular interactions, which enable efficient phonon transport along the polymer chains, or by strong intermolecular interactions, which enable efficient phonon transport between the polymer chains. However, it has not been possible until now to engineer both interactions simultaneously. We report the first realization of high thermal conductivity in the thin film of a conjugated polymer, poly(3-hexylthiophene), via bottom-up oxidative chemical vapor deposition (oCVD), taking advantage of both strong C=C covalent bonding along the extended polymer chain and strong π-π stacking noncovalent interactions between chains. We confirm the presence of both types of interactions by systematic structural characterization, achieving a near-room temperature thermal conductivity of 2.2 W/m·K, which is 10 times higher than that of conventional polymers. With the solvent-free oCVD technique, it is now possible to grow polymer films conformally on a variety of substrates as lightweight, flexible heat conductors that are also electrically insulating and resistant to corrosion.