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Objectives: The development of new drugs for the treatment of progressive multiple sclerosis (MS) highlights the need for new prognostic biomarkers. Phase-rim lesions (PRLs) have been proposed as markers of progressive disease but are difficult to identify and quantify. Previous studies have identified T1-hypointensity in PRLs. The aim of this study was to compare the intensity profiles of PRLs and non-PRL white-matter lesions (nPR-WMLs) on three-dimensional T1-weighted turbo field echo (3DT1TFE) MRI. We then evaluated the performance of a derived metric as a surrogate for PRLs as potential markers for risk of disease progression. Methods: This study enrolled a cohort of relapsing–remitting (n = 10) and secondary progressive MS (n = 10) patients for whom 3 T MRI was available. PRLs and nPR-WMLs were segmented, and voxel-wise normalized T1-intensity histograms were analyzed. The lesions were divided equally into training and test datasets, and the fifth-percentile (p5)-normalized T1-intensity of each lesion was compared between groups and used for classification prediction. Results: Voxel-wise histogram analysis showed a unimodal histogram for nPR-WMLs and a bimodal histogram for PRLs with a large peak in the hypointense limit. Lesion-wise analysis included 1075 nPR-WMLs and 39 PRLs. The p5 intensity of PRLs was significantly lower than that of nPR-WMLs. The T1 intensity-based PRL classifier had a sensitivity of 0.526 and specificity of 0.959. Conclusions: Profound hypointensity on 3DT1TFE MRI is characteristic of PRLs and rare in other white-matter lesions. Given the widespread availability of T1-weighted imaging, this feature might serve as a surrogate biomarker for smoldering inflammation. Clinical relevance statement: Quantitative analysis of 3DT1TFE may detect deeply hypointense voxels in multiple sclerosis lesions, which are highly specific to PRLs. This could serve as a specific indicator of smoldering inflammation in MS, aiding in early detection of disease progression. Key Points: • Phase-rim lesions (PRLs) in multiple sclerosis present a characteristic T1-hypointensity on 3DT1TFE MRI. • Intensity-normalized 3DT1TFE can be used to systematically identify and quantify these deeply hypointense foci. • Deep T1-hypointensity may act as an easily detectable, surrogate marker for PRLs. [ABSTRACT FROM AUTHOR]

A multiple time step (MTS) algorithm for trajectory surface hopping molecular dynamics has been developed, implemented, and tested. The MTS scheme is an extension of the ab initio implementation for Born–Oppenheimer molecular dynamics presented in the work of Liberatore et al. [J. Chem. Theory Comput. 14, 2834 (2018)]. In particular, the MTS algorithm has been modified to enable the simulation of non-adiabatic processes with the trajectory surface hopping (TSH) method and Tully's fewest switches algorithm. The specificities of the implementation lie in the combination of Landau–Zener and Tully's transition probabilities during the inner MTS time steps. The new MTS-TSH method is applied successfully to the photorelaxation of protonated formaldimine, showing that the important characteristics of the process are recovered by the MTS algorithm. A computational speed-up between 1.5 and 3 has been obtained compared to standard TSH simulations, which is close to the ideal values that could be obtained with the computational settings considered. [ABSTRACT FROM AUTHOR]

The cluster perturbation series, CPS(D), for coupled cluster singles and doubles excitation energies is considered. It is demonstrated that the second-order model CPS(D-2) is identical to the configuration interaction singles with perturbative doubles, CIS(D) model. The third-order model, CPS(D-3), provides excitation energies of coupled cluster singles and doubles (CCSD) quality in the sense that the difference between CPS(D-3) and CCSD excitation energies is of the same size or smaller than the effect of adding triples corrections to CCSD excitation energies. We further show that the third-order corrections can be efficiently implemented, in particular, when the resolution of the identity approximation is used for integrals. We also show that the CPS(D-3) excitation energies can be determined for system sizes that are far beyond what can be considered in conventional CCSD excitation energy calculations. [ABSTRACT FROM AUTHOR]

In a recent work [P. Baudin and K. Kristensen, J. Chem. Phys. 144, 224106 (2016)], we introduced a local framework for calculating excitation energies (LoFEx), based on second-order approximated coupled cluster (CC2) linear-response theory. LoFEx is a black-box method in which a reduced excitation orbital space (XOS) is optimized to provide coupled cluster (CC) excitation energies at a reduced computational cost. In this article, we present an extension of the LoFEx algorithm to the calculation of CC2 oscillator strengths. Two different strategies are suggested, in which the size of the XOS is determined based on the excitation energy or the oscillator strength of the targeted transitions. The two strategies are applied to a set of medium-sized organic molecules in order to assess both the accuracy and the computational cost of the methods. The results show that CC2 excitation energies and oscillator strengths can be calculated at a reduced computational cost, provided that the targeted transitions are local compared to the size of the molecule. To illustrate the potential of LoFEx for large molecules, both strategies have been successfully applied to the lowest transition of the bivalirudin molecule (4255 basis functions) and compared with time-dependent density functional theory. [ABSTRACT FROM AUTHOR]

Transient absorption spectra (TAS) of lead halide perovskites can provide important insights into the nature of the photoexcited state dynamics of this prototypical class of materials. Here, we perform ground and excited state molecular dynamics (MD) simulations within a restricted open shell Kohn‐Sham (ROKS) approach in order to interpret the characteristic features of the TAS of CsPbBr3. Our results reveal that properties such as the finite temperature band gap, the Stokes shift, and therefore, also the TAS are strongly size‐dependent. Our TAS simulations show an early positive red‐shifted feature on the fs scale that can be explained by geometric relaxation in the excited state. As excited‐state processes can crucially affect the electronic properties of this class of photoactive materials, our observations are an important ingredient for further optimization of lead halide based optoelectronic devices. [ABSTRACT FROM AUTHOR]

Transient absorption spectra (TAS) of lead halide perovskites can provide important insights into the nature of the photoexcited state dynamics of this prototypical class of materials. Here, we perform ground and excited state molecular dynamics (MD) simulations within a restricted open shell Kohn‐Sham (ROKS) approach in order to interpret the characteristic features of the TAS of CsPbBr3. Our results reveal that properties such as the finite temperature band gap, the Stokes shift, and therefore, also the TAS are strongly size‐dependent. Our TAS simulations show an early positive red‐shifted feature on the fs scale that can be explained by geometric relaxation in the excited state. As excited‐state processes can crucially affect the electronic properties of this class of photoactive materials, our observations are an important ingredient for further optimization of lead halide based optoelectronic devices. [ABSTRACT FROM AUTHOR]

We present a local framework for the calculation of coupled cluster excitation energies of large molecules (LoFEx). The method utilizes time-dependent Hartree-Fock information about the transitions of interest through the concept of natural transition orbitals (NTOs). The NTOs are used in combination with localized occupied and virtual Hartree-Fock orbitals to generate a reduced excitation orbital space (XOS) specific to each transition where a standard coupled cluster calculation is carried out. Each XOS is optimized to ensure that the excitation energies are determined to a predefined precision. We apply LoFEx in combination with the RI-CC2 model to calculate the lowest excitation energies of a set of medium-sized organic molecules. The results demonstrate the black-box nature of the LoFEx approach and show that significant computational savings can be gained without affecting the accuracy of CC2 excitation energies. [ABSTRACT FROM AUTHOR]

The theoretical foundation for solving coupled cluster singles and doubles (CCSD) amplitude equations to a desired precision in terms of independent fragment calculations using restricted local orbital spaces is reinvestigated with focus on the individual error sources. Four different error sources are identified theoretically and numerically and it is demonstrated that, for practical purposes, local orbital spaces for CCSD calculations can be identified from calculations at the MP2 level. The development establishes a solid theoretical foundation for local CCSD calculations for the independent fragments, and thus for divide-expand-consolidate coupled cluster calculations for large molecular systems with rigorous error control. Based on this theoretical foundation, we have developed an algorithm for determining the orbital spaces needed for obtaining the single fragment energies to a requested precision and numerically demonstrated the robustness and precision of this algorithm. [ABSTRACT FROM AUTHOR]

The Resolution of the Identity second-order Møller-Plesset perturbation theory (RI-MP2) method is implemented within the linear-scaling Divide-Expand-Consolidate (DEC) framework. In a DEC calculation, the full molecular correlated calculation is replaced by a set of independent fragment calculations each using a subset of the total orbital space. The number of independent fragment calculations scales linearly with the system size, rendering the method linear-scaling and massively parallel. The DEC-RI-MP2 method can be viewed as an approximation to the DEC-MP2 method where the RI approximation is utilized in each fragment calculation. The individual fragment calculations scale with the fifth power of the fragment size for both methods. However, the DEC-RI-MP2 method has a reduced prefactor compared to DEC-MP2 and is well-suited for implementation on massively parallel supercomputers, as demonstrated by test calculations on a set of medium-sized molecules. The DEC error control ensures that the standard RI-MP2 energy can be obtained to the predefined precision. The errors associated with the RI and DEC approximations are compared, and it is shown that the DECRI- MP2 method can be applied to systems far beyond the ones that can be treated with a conventional RI-MP2 implementation. [ABSTRACT FROM AUTHOR]

BACKGROUND AND PURPOSE: SARS‐CoV‐2 causes multiorgan disease due to altered coagulability and microangiopathy. Patients may have an increased risk of cerebrovascular accidents (CVA). Our objective was to analyze clinical and neuroimaging characteristics of patients with ischemic CVA during the pandemic peak in our region, in order to identify atypical presentations. METHODS: We performed a cross‐sectional analysis of patients admitted under code‐stroke protocol to our center with a final diagnosis of ischemic brain infarction. We analyzed the main imaging and demographic characteristics and reviewed neuroimaging for atypical presentations. RESULTS: One‐hundred patients with confirmed ischemic CVA were included. Nineteen had positive polymerase chain reaction testing for SARS‐CoV‐2 on admission. These patients had a lower prevalence of proximal arterial occlusion on imaging, higher in‐hospital mortality, and worse baseline disability. No differences were identified in affected vascular territory, volume of infarction, initial CT stroke score, prevalence of hemorrhagic transformation, gender, age, cardiovascular risk factors, time to admission, symptom severity on entry, or decision to treat with thrombolysis or mechanical thrombectomy. Prevalence of COVID‐19 in our code‐stroke sample was higher than that for our province during this time period. CONCLUSION: The COVID‐19 group had more in‐hospital mortality, less proximal arterial occlusion on CT or MR angiography, and lower baseline modified Rankin Scale score. We suggest a possibly higher proportion of microangiopathic involvement or undetected distal large‐vessel occlusion in the COVID‐19 stroke group. Excess mortality was explained by severe respiratory failure. Otherwise, stroke patients with COVID‐19 did not differ demographically or clinically from those without the illness. [ABSTRACT FROM AUTHOR]

A new implementation of the approximate coupled cluster singles and doubles CC2 linear response model is reported. It employs a Cholesky decomposition of the two-electron integrals that significantly reduces the computational cost and the storage requirements of the method compared to standard implementations. Our algorithm also exploits a partitioning form of the CC2 equations which reduces the dimension of the problem and avoids the storage of doubles amplitudes. We present calculation of excitation energies of benzene using a hierarchy of basis sets and compare the results with conventional CC2 calculations. The reduction of the scaling is evaluated as well as the effect of the Cholesky decomposition parameter on the quality of the results. The new algorithm is used to perform an extrapolation to complete basis set investigation on the spectroscopically interesting benzylallene conformers. A set of calculations on medium-sized molecules is carried out to check the dependence of the accuracy of the results on the decomposition thresholds. Moreover, CC2 singlet excitation energies of the free base porphin are also presented. [ABSTRACT FROM AUTHOR]