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| 2. |
- Manni, Giovanni Li, et al.
(författare)
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The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
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Tidskriftsartikel (refereegranskat)abstract
- The developments of the open-source OpenMolcas chemistry software environment since spring 2020 are described, with a focus on novel functionalities accessible in the stable branch of the package or via interfaces with other packages. These developments span a wide range of topics in computational chemistry and are presented in thematic sections: electronic structure theory, electronic spectroscopy simulations, analytic gradients and molecular structure optimizations, ab initio molecular dynamics, and other new features. This report offers an overview of the chemical phenomena and processes OpenMolcas can address, while showing that OpenMolcas is an attractive platform for state-of-the-art atomistic computer simulations.
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| 3. |
- Aquilante, Francesco, et al.
(författare)
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Molcas 8 : New capabilities for multiconfigurational quantum chemical calculations across the periodic table
- 2016
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Ingår i: Journal of Computational Chemistry. - : Wiley. - 0192-8651 .- 1096-987X. ; 37:5, s. 506-541
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Tidskriftsartikel (refereegranskat)abstract
- In this report, we summarize and describe the recent unique updates and additions to the Molcas quantum chemistry program suite as contained in release version 8. These updates include natural and spin orbitals for studies of magnetic properties, local and linear scaling methods for the Douglas-Kroll-Hess transformation, the generalized active space concept in MCSCF methods, a combination of multiconfigurational wave functions with density functional theory in the MC-PDFT method, additional methods for computation of magnetic properties, methods for diabatization, analytical gradients of state average complete active space SCF in association with density fitting, methods for constrained fragment optimization, large-scale parallel multireference configuration interaction including analytic gradients via the interface to the Columbus package, and approximations of the CASPT2 method to be used for computations of large systems. In addition, the report includes the description of a computational machinery for nonlinear optical spectroscopy through an interface to the QM/MM package Cobramm. Further, a module to run molecular dynamics simulations is added, two surface hopping algorithms are included to enable nonadiabatic calculations, and the DQ method for diabatization is added. Finally, we report on the subject of improvements with respects to alternative file options and parallelization.
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| 4. |
- Araujo, C. M., et al.
(författare)
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Electrical resistivity, MNM transition and band-gap narrowing of cubic GaN : Si
- 2002
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Ingår i: Microelectronics Journal. - 0026-2692. ; 33:4, s. 365-369
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Tidskriftsartikel (refereegranskat)abstract
- The electrical resistivity of the Si-donor cubic GaN is investigated theoretically at low temperature. The critical impurity concentration, N-c, for the metal-nonmetal transition is estimated in three different ways: from using the generalized Drude approach (GDA) for the resistivity; from the vanishing of the chemical potential calculated using the dielectric function model with a Lorentz-Lorenz correction; from finding the crossing point between the energy in the insulating and metallic states. The bandgap narrowing (BGN) has been determined theoretically and experimentally above the MNM transition, The experimental data have been obtained with photoluminescence measurements. Theoretical and experimental results are in rough agreement in the range of impurity concentration of interest.
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| 6. |
- Fernandez, J. R. L., et al.
(författare)
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Electrical resistivity and band-gap shift of Si-doped GaN and metal-nonmetal transition in cubic GaN, InN and AlN systems
- 2001
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Ingår i: Journal of Crystal Growth. - 0022-0248 .- 1873-5002. ; 231:3, s. 420-427
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Tidskriftsartikel (refereegranskat)abstract
- The critical impurity concentration N-c of the metal-nonmetal (MNM) transition for the cubic GaN, InN and AIN systems. is calculated using the following two different criteria: vanishing of the donor binding energy and the crossing point between the energies in the metallic and insulating phases. A dielectric function model with a Lorentz-Lorenz correction is used for the insulating phase. The InN presents an order of magnitude increase in N-c as compared to the other two systems. The electrical resistivity of the Si-donor system GaN is investigated theoretically and experimentally from room temperature down to 10K. It presents a metallic character above a certain high impurity concentration identified as N-c. The samples were grown by plasma assisted molecular beam epitaxy (MBE) on GaAs (0 0 1) substrate. The model calculation is carried out from a recently proposed generalized Drude approach (GDA) presenting a very good estimation for the metallic region. The band-gap shift (BGS) of Si-doped GaN has also been investigated above the MNM transition where this shift is observed. Theoretical and experimental results have a rough agreement in a range of impurity concentration of interest.
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| 8. |
- Liegmann, AS, et al.
(författare)
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Single Cell Genetic Profiling of Tumors of Breast Cancer Patients Aged 50 Years and Older Reveals Enormous Intratumor Heterogeneity Independent of Individual Prognosis
- 2021
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Ingår i: Cancers. - : MDPI AG. - 2072-6694. ; 13:13
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Tidskriftsartikel (refereegranskat)abstract
- Purpose: Older breast cancer patients are underrepresented in cancer research even though the majority (81.4%) of women dying of breast cancer are 55 years and older. Here we study a common phenomenon observed in breast cancer which is a large inter- and intratumor heterogeneity; this poses a tremendous clinical challenge, for example with respect to treatment stratification. To further elucidate genomic instability and tumor heterogeneity in older patients, we analyzed the genetic aberration profiles of 39 breast cancer patients aged 50 years and older (median 67 years) with either short (median 2.4 years) or long survival (median 19 years). The analysis was based on copy number enumeration of eight breast cancer-associated genes using multiplex interphase fluorescence in situ hybridization (miFISH) of single cells, and by targeted next-generation sequencing of 563 cancer-related genes. Results: We detected enormous inter- and intratumor heterogeneity, yet maintenance of common cancer gene mutations and breast cancer specific chromosomal gains and losses. The gain of COX2 was most common (72%), followed by MYC (69%); losses were most prevalent for CDH1 (74%) and TP53 (69%). The degree of intratumor heterogeneity did not correlate with disease outcome. Comparing the miFISH results of diploid with aneuploid tumor samples significant differences were found: aneuploid tumors showed significantly higher average signal numbers, copy number alterations (CNAs) and instability indices. Mutations in PIKC3A were mostly restricted to luminal A tumors. Furthermore, a significant co-occurrence of CNAs of DBC2/MYC, HER2/DBC2 and HER2/TP53 and mutual exclusivity of CNAs of HER2 and PIK3CA mutations and CNAs of CCND1 and PIK3CA mutations were revealed. Conclusion: Our results provide a comprehensive picture of genome instability profiles with a large variety of inter- and intratumor heterogeneity in breast cancer patients aged 50 years and older. In most cases, the distribution of chromosomal aneuploidies was consistent with previous results; however, striking exceptions, such as tumors driven by exclusive loss of chromosomes, were identified.
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