| 1. |
- Galván, Ignacio Fdez., et al.
(författare)
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OpenMolcas : From Source Code to Insight
- 2019
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Tidskriftsartikel (refereegranskat)abstract
- In this Article we describe the OpenMolcas environment and invite the computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during the transition from the commercial MOLCAS product to the open-source platform. The paper initially describes the technical details of the new software development platform. This is followed by brief presentations of many new methods, implementations, and features of the OpenMolcas program suite. These developments include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) methods, and hybrid multiconfigurational wave function and density functional theory models. Some of these implementations include an array of additional options and functionalities. The paper proceeds and describes developments related to explorations of potential energy surfaces. Here we present methods for the optimization of conical intersections, the simulation of adiabatic and nonadiabatic molecular dynamics, and interfaces to tools for semiclassical and quantum mechanical nuclear dynamics. Furthermore, the Article describes features unique to simulations of spectroscopic and magnetic phenomena such as the exact semiclassical description of the interaction between light and matter, various X-ray processes, magnetic circular dichroism, and properties. Finally, the paper describes a number of built-in and add-on features to support the OpenMolcas platform with postcalculation analysis and visualization, a multiscale simulation option using frozen-density embedding theory, and new electronic and muonic basis sets.
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| 2. |
- Levin, Malin, 1973, et al.
(författare)
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Rip2 deficiency leads to increased atherosclerosis despite decreased inflammation.
- 2011
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Ingår i: Circulation research. - 1524-4571. ; 109:11, s. 1210-8
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Tidskriftsartikel (refereegranskat)abstract
- The innate immune system and in particular the pattern-recognition receptors Toll-like receptors have recently been linked to atherosclerosis. Consequently, inhibition of various signaling molecules downstream of the Toll-like receptors has been tested as a strategy to prevent progression of atherosclerosis. Receptor-interacting protein 2 (Rip2) is a serine/threonine kinase that is involved in multiple nuclear factor-κB (NFκB) activation pathways, including Toll-like receptors, and is therefore an interesting potential target for pharmaceutical intervention.
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| 3. |
- Zheng, Guishan, et al.
(författare)
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Parameter calibration of transition-metal elements for the spin-polarized self-consistent-charge density-functional tight-binding (DFTB) method : Sc, Ti, Fe, Co, and Ni
- 2007
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 3:4, s. 1349-1367
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Tidskriftsartikel (refereegranskat)abstract
- Recently developed parameters for five first-row transition-metal elements (M = Sc, Ti, Fe, Co, and Ni) in combination with H, C, N, and O as well as the same metal (M-M) for the spin-polarized self-consistent-charge density-functional tight-binding (DFTB) method have been calibrated. To test their performance a couple sets of compounds have been selected to represent a variety of interactions and bonding schemes that occur frequently in transition-metal containing systems. The results show that the DFTB method with the present parameters in most cases reproduces structural properties very well, but the bond energies and the relative energies of different spin states only qualitatively compared to the B3LYP/SDD+6-31G(d) density functional (DFT) results. An application to the ONIOM(DFT:DFTB) indicates that DFTB works well as the low level method for the ONIOM calculation.
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| 4. |
- Ablyasova, Olesya S., et al.
(författare)
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Electronic Structure of the Complete Series of Gas-Phase Manganese Acetylacetonates by X-ray Absorption Spectroscopy
- 2023
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 127:34, s. 7121-7131
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Tidskriftsartikel (refereegranskat)abstract
- Metal centers in transition metal–ligand complexes occur in a variety of oxidation states causing their redox activity and therefore making them relevant for applications in physics and chemistry. The electronic state of these complexes can be studied by X-ray absorption spectroscopy, which is, however, due to the complex spectral signature not always straightforward. Here, we study the electronic structure of gas-phase cationic manganese acetylacetonate complexes Mn(acac)1–3+ using X-ray absorption spectroscopy at the metal center and ligand constituents. The spectra are well reproduced by multiconfigurational wave function theory, time-dependent density functional theory as well as parameterized crystal field and charge transfer multiplet simulations. This enables us to get detailed insights into the electronic structure of ground-state Mn(acac)1–3+ and extract empirical parameters such as crystal field strength and exchange coupling from X-ray excitation at both the metal and ligand sites. By comparison to X-ray absorption spectra of neutral, solvated Mn(acac)2,3 complexes, we also show that the effect of coordination on the L3 excitation energy, routinely used to identify oxidation states, can contribute about 40–50% to the observed shift, which for the current study is 1.9 eV per oxidation state.
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| 5. |
- Aquilante, Francesco, et al.
(författare)
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Modern quantum chemistry with [Open]Molcas
- 2020
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
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Tidskriftsartikel (refereegranskat)abstract
- MOLCAS/OpenMolcas is an ab initio electronic structure program providing a large set of computational methods from Hartree-Fock and density functional theory to various implementations of multiconfigurational theory. This article provides a comprehensive overview of the main features of the code, specifically reviewing the use of the code in previously reported chemical applications as well as more recent applications including the calculation of magnetic properties from optimized density matrix renormalization group wave functions.
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| 6. |
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| 7. |
- Bengtson, Charlotta, et al.
(författare)
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Kursutveckling i partnerskap mellan lärare och studenter
- 2018
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- En kurs på grundutbildningsnivå har omformats i partnerskap mellan studenter och lärare vilket lett till mer omfattande förändringar än motsvarande lärarledd process.(Bengtson et al., 2017) Den nya kursen har getts två gånger och resultatet blev avsevärt bättre betyg på kursvärderingarna och viss förbättring av examensresultateten jämfört med tidigare år. Fokus på presentationen är att diskutera lärdomar och utmaningar för att genomföra lyckade partnerskap i kursutveckling. Målet med projektet var att göra om en fysikkurs på kandidatprogrammet i kemi som studenterna uppfattade som svår och med bristande koppling till deras utbildning i kemi. I den första delen av projektet hördes studentens röst genom intervjuer kring kursens roll i utbildningsprogrammet. Intervjuerna gav inspiration till fortsatt arbete med högre grad av studentmedverkan. I den andra delen av projektet bildades därför en utvecklingsgrupp bestående av sex studenter och två lärare för att utveckla kursplan och läromedel i partnerskap (Mihans et al., 2008). Partnerskap kan leda till ökad motivation och självförtroende hos studenterna och att de tar större ansvar för sitt lärande (Bovill et al., 2011). Samtidigt drar lärarna nytta av att se inlärningsprocessen från studentens perspektiv (Cook-Sather, 2014). Hela gruppen träffades en gång i veckan under sju veckor. Dessutom bildades fyra separata arbetsgrupper som tog fram nytt kursmaterial. Samtliga beslut om förändringar togs genom omröstningar i hela gruppen där allas röster vägde lika. Lärarna kunde behålla ansvaret för kursens kvalitet genom att bestämma vilka förslag som var tillräckligt bra för omröstning, men det blev aldrig aktuellt eftersom det nya materialet höll genomgående hög kvalitet. Bland de genomförda förändringarna var nya seminarier för ökad begreppsmässig förståelse, omformning av alla föreläsningar med mer aktivt studentdeltagande, samt byte av kurslitteratur. Projektet har krävt betydande resurser från både lärare och studenter och med tanke på arbetsinsatsen passar liknande projekt bäst för att periodvis genomföra större förändringar i en kurs. Studenterna arvoderades för de timmar de lagt ned på kursutveckling och projektet finansierades med bidrag från en pedagogisk fond. Viktiga framgångsfaktorer var deltagande av studenter att rekrytera till projektet, finansiellt stöd från fakulteten, tidigt urval av konkreta utvecklingsuppgifter samt att låta gruppens medlemmar själva välja vad de ville utveckla utifrån deras egen kompetens. En rekommendation är att dela in utvecklingsprocessen i flera steg och öka partnerskap över tid för att hitta balans mellan behovet av vägledning och studenternas frihet att utveckla på egen hand. Nästa steg är att tillsammans med en ny studentgrupp fokuserat arbeta med att förbättra examinationsformerna. Samarbetet mellan lärare och studenter ledde till en djupare förståelse för varandras roller i en akademisk utbildningsmiljö och gav studenterna inspiration att arbeta med förbättring även i andra delar av utbildningen. Bengtson, C., Ahlkvist, M., Ekeroth, W., Nilsen-Moe, A., Proos Vedin, N., Rodiuchkina, K., Ye, S. & Lundberg, M. 2017. Working as Partners: Course Development by a Student–Teacher Team. International Journal for the Scholarship of Teaching and Learning, 11, 6.Bovill, C., Bulley, C. J. & Morss, K. 2011. Engaging and empowering first-year students through curriculum design: perspectives from the literature. Teaching in Higher Education, 16, 197-209.Cook-Sather, A. 2014. Multiplying perspectives and improving practice: what can happen when undergraduate students collaborate with college faculty to explore teaching and learning. Instructional Science, 42, 31-46.Mihans, I., Richard, J., Long, D. T. & Felten, P. 2008. Power and expertise: Student-faculty collaboration in course design and the scholarship of teaching and learning. International Journal for the Scholarship of Teaching and Learning, 2, 16.
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| 8. |
- Bengtson, Charlotta, et al.
(författare)
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Working as Partners : Course Development by a Student–Teacher Team
- 2017
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Ingår i: International Journal for the Scholarship of Teaching & Learning. - : Georgia Southern University. - 1931-4744. ; 11:2
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Tidskriftsartikel (refereegranskat)abstract
- A first-year undergraduate course at Uppsala University has been redesigned in a process exploring differentlevels of student participation. In the first part of the project, the student voice was heard through interviewsfocusing on the role of the course in the degree program. In the second part, a student-teacher team wasformed to develop course curriculum and teaching material in partnership. Among the implemented changeswere new seminars focusing on conceptual understanding, redesign of all lectures to include active studentparticipation, and a change of the course literature. The redesigned course significantly increased studentsatisfaction compared to previous years. Important success factors were involvement of the studentorganization to promote the project, institutional support, early selection of concrete development tasks, andallowing team members to choose what they wanted to develop according to their own expertise.
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| 9. |
- Blachucki, Wojciech, et al.
(författare)
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Approaching the Attosecond Frontier of Dynamics in Matter with the Concept of X-ray Chronoscopy
- 2022
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Ingår i: Applied Sciences. - : MDPI AG. - 2076-3417. ; 12:3
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Tidskriftsartikel (refereegranskat)abstract
- Featured Application Herein, an innovative methodology, called X-ray chronoscopy, is proposed for exploration of ultrafast processes in matter with attosecond precision using current XFEL sources. The method is based on measuring the change in an X-ray pulse temporal profile induced by interaction with a medium. X-ray free electron lasers (XFELs) have provided scientists opportunities to study matter with unprecedented temporal and spatial resolutions. However, access to the attosecond domain (i.e., below 1 femtosecond) remains elusive. Herein, a time-dependent experimental concept is theorized, allowing us to track ultrafast processes in matter with sub-fs resolution. The proposed X-ray chronoscopy approach exploits the state-of-the-art developments in terahertz streaking to measure the time structure of X-ray pulses with ultrahigh temporal resolution. The sub-femtosecond dynamics of the saturable X-ray absorption process is simulated. The employed rate equation model confirms that the X-ray-induced mechanisms leading to X-ray transparency can be probed via measurement of an X-ray pulse time structure.
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| 10. |
- Blachucki, W., et al.
(författare)
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Inception of electronic damage of matter by photon-driven post-ionization mechanisms
- 2019
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Ingår i: Structural Dynamics. - : AIP Publishing. - 2329-7778. ; 6:2
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Tidskriftsartikel (refereegranskat)abstract
- "Probe-before-destroy" methodology permitted diffraction and imaging measurements of intact specimens using ultrabright but highly destructive X-ray free-electron laser (XFEL) pulses. The methodology takes advantage of XFEL pulses ultrashort duration to outrun the destructive nature of the X-rays. Atomic movement, generally on the order of >50 fs, regulates the maximum pulse duration for intact specimen measurements. In this contribution, we report the electronic structure damage of a molecule with ultrashort X-ray pulses under preservation of the atoms' positions. A detailed investigation of the X-ray induced processes revealed that X-ray absorption events in the solvent produce a significant number of solvated electrons within attosecond and femtosecond timescales that are capable of coulombic interactions with the probed molecules. The presented findings show a strong influence on the experimental spectra coming from ionization of the probed atoms' surroundings leading to electronic structure modification much faster than direct absorption of photons. This work calls for consideration of this phenomenon in cases focused on samples embedded in, e.g., solutions or in matrices, which in fact concerns most of the experimental studies.
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