J Chem Theory Comput
December 2024
We present a massively parallel GPU-accelerated implementation of the Bethe-Salpeter equation (BSE) for the calculation of the vertical excitation energies (VEEs) and optical absorption spectra of condensed and molecular systems, starting from single-particle eigenvalues and eigenvectors obtained with density functional theory. The algorithms adopted here circumvent the slowly converging sums over empty and occupied states and the inversion of large dielectric matrices through a density matrix perturbation theory approach and a low-rank decomposition of the screened Coulomb interaction, respectively. Further computational savings are achieved by exploiting the nearsightedness of the density matrix of semiconductors and insulators to reduce the number of screened Coulomb integrals.
View Article and Find Full Text PDFPurpose: Chronic rhinosinusitis (CRS) has been distinguished in primary CRS, a primary inflammatory disorder limited to airways and secondary CRS, in which the sinonasal pathology is caused by a systemic disease or a local pathologic condition. Primary CRS is in turn classified in Type 2 and Non-type 2 on the basis of the endotype and of the pattern of the immune response. Advance in the knowledge of CRS has led to new therapeutic options, among which Dupilumab (anti-IL4R).
View Article and Find Full Text PDFWe present a theoretical study of the formation of self-trapped excitons (STEs) and the associated broadband emission in metal-halide perovskites CsSnBr and CsAgInCl, using time-dependent density functional theory (TDDFT) with the dielectric-dependent hybrid (DDH) functional. Our approach allows for an accurate description of the excitonic effect and geometry relaxation in the electronic excited states and yields optical gap, STE emission energy, and emission spectra in reasonable agreement with experiments. We point out the significance of considering geometry relaxations in the electronic excited state by showing that the exciton-phonon coupling computed in the ground-state atomic geometry is insufficient to describe the physical properties of STEs.
View Article and Find Full Text PDFWe present a formulation of spin-conserving and spin-flip hybrid time-dependent density functional theory (TDDFT), including the calculation of analytical forces, which allows for efficient calculations of excited state properties of solid-state systems with hundreds to thousands of atoms. We discuss an implementation on both GPU- and CPU-based architectures along with several acceleration techniques. We then apply our formulation to the study of several point defects in semiconductors and insulators, specifically the negatively charged nitrogen-vacancy and neutral silicon-vacancy centers in diamond, the neutral divacancy center in 4H silicon carbide, and the neutral oxygen-vacancy center in magnesium oxide.
View Article and Find Full Text PDFJ Chem Theory Comput
September 2023
Electronic structure calculations based on density functional theory (DFT) have successfully predicted numerous ground-state properties of a variety of molecules and materials. However, exchange and correlation functionals currently used in the literature, including semilocal and hybrid functionals, are often inaccurate to describe the electronic properties of heterogeneous solids, especially systems composed of building blocks with large dielectric mismatch. Here, we present a dielectric-dependent range-separated hybrid functional, screened-exchange range-separated hybrid (SE-RSH), for the investigation of heterogeneous materials.
View Article and Find Full Text PDFPeriprosthetic joint infections (PJIs) in arthroplasty and osteosynthesis-associated infections (OAIs) in reconstructive surgery still represent a challenging complication in orthopaedics and traumatology causing a burden worsening the patient's quality of life, for caregiver and treating physicians, and for healthcare systems. PJIs and OAIs are the result of bacterial adhesion over an implant surface with subsequent biofilm formation. Therefore, the clinical pathological outcome is a difficult-to-eradicate persistent infection.
View Article and Find Full Text PDFExtracorporeal membrane oxygenation (ECMO) is an invasive medical technique used to provide life support in persons with insufficient cardiac and respiratory functionalities, or to preserve, postmortem, and organ function addressing organ/tissue transplant. Although a lot of information is available about organs in their entirety, the safety and effectiveness of allogeneic tissues collected from ECMO donors have not been fully elucidated. In this preliminary study, samples of tibial and peroneal human tendons were analyzed along their length with Raman microspectroscopy and attenuated total reflection-Fourier transform infrared micro-imaging.
View Article and Find Full Text PDFIntroduction: The impairment of the sense of smell is often related to chronic rhinosinusitis (CRS) with or without nasal polyps (CRSwNP, CRSsNP). CRSwNP is a frequent condition that drastically worsens the quality of life of those affected; it has a higher prevalence than CRSsNP. CRSwNP patients experience severe loss of smell with earlier presentation and are more likely to experience recurrence of their symptoms, often requiring revision surgery.
View Article and Find Full Text PDFOver the last decade, evidence has mounted for a prominent etiologic role of femoroacetabular impingement (FAI) in the development of early hip osteoarthritis (OA). The aim of this study was to compare the ultrastructure and tissue composition of the hip labrum in healthy and pathological conditions, as FAI and OA, to provide understanding of structural changes which might be helpful in the future to design targeted therapies and improve treatment indications. We analyzed labral tissue samples from five healthy multi-organ donors (MCDs) (median age, 38 years), five FAI patients (median age, 37 years) and five late-stage OA patients undergoing total hip replacement (median age, 56 years).
View Article and Find Full Text PDFJ Chem Theory Comput
March 2023
We propose a computational protocol for quantum simulations of fermionic Hamiltonians on a quantum computer, enabling calculations on spin defect systems which were previously not feasible using conventional encodings and a unitary coupled-cluster ansatz of variational quantum eigensolvers. We combine a qubit-efficient encoding scheme mapping Slater determinants onto qubits with a modified qubit-coupled cluster ansatz and noise-mitigation techniques. Our strategy leads to a substantial improvement in the scaling of circuit gate counts and in the number of required qubits, and to a decrease in the number of required variational parameters, thus increasing the resilience to noise.
View Article and Find Full Text PDFIn this study, Brillouin and Raman micro-Spectroscopy (BRamS) and Machine Learning were used to set-up a new diagnostic tool for Osteoarthritis (OA), potentially extendible to other musculoskeletal diseases. OA is a degenerative pathology, causing the onset of chronic pain due to cartilage disruption. Despite this, it is often diagnosed late and the radiological assessment during the routine examination may fail to recognize the threshold beyond which pharmacological treatment is no longer sufficient and prosthetic replacement is required.
View Article and Find Full Text PDFIn spine surgery, allogenic bone grafts are often required to ensure bone fusion, however, the main concern regarding their use is the infection risk: therefore, an intraoperative swab for culture test is performed. The cost-effectiveness of these swabs and their influence on the patients' postoperative course have often been questioned. This study aims at determining whether positive spine allograft culture results are predictive of an increased risk of surgical site infection and whether they influence the surgeon's choices in postoperative management.
View Article and Find Full Text PDFOne of the greatest challenges of hip revision surgery is the need to restore extensive bone loss by creating a stable reconstruction with long-term durability. The present observational, investigator-initiated prospective study was carried out to evaluate the clinical and radiological results of the use of a commercial biomimetic collagen-hydroxyapatite composite biomaterial (RegenOss) applied in hip revision surgery. Thirty-three patients who underwent hip revision were included in this study, and 29 received up to 2 years of follow-up.
View Article and Find Full Text PDFWe present a computational protocol, based on density matrix perturbation theory, to obtain non-adiabatic, frequency-dependent electron-phonon self-energies for molecules and solids. Our approach enables the evaluation of electron-phonon interaction using hybrid functionals, for spin-polarized systems, and the computational overhead to include dynamical and non-adiabatic terms in the evaluation of electron-phonon self-energies is negligible. We discuss results for molecules, as well as pristine and defective solids.
View Article and Find Full Text PDFMany-body perturbation theory is a powerful method to simulate electronic excitations in molecules and materials starting from the output of density functional theory calculations. By implementing the theory efficiently so as to run at scale on the latest leadership high-performance computing systems it is possible to extend the scope of GW calculations. We present a GPU acceleration study of the full-frequency GW method as implemented in the WEST code.
View Article and Find Full Text PDFQuantum computers hold promise to improve the efficiency of quantum simulations of materials and to enable the investigation of systems and properties that are more complex than tractable at present on classical architectures. Here, we discuss computational frameworks to carry out electronic structure calculations of solids on noisy intermediate-scale quantum computers using embedding theories, and we give examples for a specific class of materials, that is, solid materials hosting spin defects. These are promising systems to build future quantum technologies, such as quantum computers, quantum sensors and quantum communication devices.
View Article and Find Full Text PDFWe present a Green's function formulation of the quantum defect embedding theory (QDET) where a double counting scheme is rigorously derived within the approximation. We then show the robustness of our methodology by applying the theory with the newly derived scheme to several defects in diamond. Additionally, we discuss a strategy to obtain converged results as a function of the size and composition of the active space.
View Article and Find Full Text PDFThe use of massive bone allografts after the resection of bone tumours is still a challenging process. However, to overcome some issues related to the processing procedures and guarantee the best three-dimensional matching between donor and recipient, some tissue banks have developed a virtual tissue database based on the scanning of the available allografts for using their 3D shape during virtual surgical planning (VSP) procedures. To promote the use of future VSP bone-shaping protocols useful for machining applications within a cleanroom environment, in our work, we simulate a massive bone allograft machining with two different machines: a four-axes (computer numerical control, CNC) vs.
View Article and Find Full Text PDFAdipose tissue is an attractive source of stem cells due to its wide availability. They contribute to the stromal vascular fraction (SVF), which is composed of pre-adipocytes, tissue-progenitors, and pericytes, among others. Because its direct use in medical applications is increasing worldwide, new quality control systems are required.
View Article and Find Full Text PDF3D printing has opened exciting new opportunities for the in vitro fabrication of biocompatible hybrid pseudo-tissues. Technologies based on additive manufacturing herald a near future when patients will receive therapies delivering functional tissue substitutes for the repair of their musculoskeletal tissue defects. In particular, bone tissue engineering (BTE) might extensively benefit from such an approach.
View Article and Find Full Text PDFOsteoarthritis (OA) is the most common form of arthritis affecting both the elderly and the middle-aged population. Although various therapeutics have been developed to arrest the structural deterioration of cartilage, the current treatments are limited to delay the progress of OA clinically. Therefore, it is pivotal to study new therapeutic agents for chondroprotection and the prevention of cartilage degeneration.
View Article and Find Full Text PDFActa Otorhinolaryngol Ital
December 2021
Objective: Cochlear fistula (CF) is a rare finding, usually associated with extensive middle ear cholesteatoma. There is agreement on the fact that removing the cholesteatoma matrix on a CF exposes the ear to a high risk of sensorineural hearing loss or dead ear. The aim of the study is to describe the presentation, possible treatment strategies and related outcomes for patients with CF in chronic otitis media (COM).
View Article and Find Full Text PDFWe present a method to efficiently combine the computation of electron-electron and electron-phonon self-energies, which enables the evaluation of electron-phonon coupling at the level of theory for systems with hundreds of atoms. In addition, our approach, which is a generalization of a method recently proposed for molecules [ , , 6269-6275], enables the inclusion of nonadiabatic and temperature effects at no additional computational cost. We present results for diamond and defects in diamond and discuss the importance of numerically accurate band structures to obtain robust predictions of zero point renormalization (ZPR) of band gaps, and of the inclusion of nonadiabatic effects to accurately compute the ZPR of defect states in the band gap.
View Article and Find Full Text PDFOsteochondritis dissecans (OCD) is a chronic and painful joint condition that can occur from childhood through to adult life. Microtrauma, vascular insufficiency, or abnormal endochondral ossification are the most common causes of OCD. Reconstructive techniques for OCD of the knee are typically necessary when either non-operative or reparative/regenerative operative treatments fail, or when the OCD is irreversible.
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