| 1. |
- Galván, Ignacio Fdez., et al.
(author)
-
OpenMolcas : From Source Code to Insight
- 2019
-
In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
-
Journal article (peer-reviewed)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.
|
|
| 2. |
- Manni, Giovanni Li, et al.
(author)
-
The OpenMolcas Web : A Community-Driven Approach to Advancing Computational Chemistry
- 2023
-
In: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 19:20, s. 6933-6991
-
Journal article (peer-reviewed)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.
|
|
| 3. |
- Ahlen, Anders, et al.
(author)
-
Toward Wireless Control in Industrial Process Automation : A Case Study at a Paper Mill
- 2019
-
In: IEEE Control Systems. - : Institute of Electrical and Electronics Engineers (IEEE). - 1066-033X .- 1941-000X. ; 39:5, s. 36-57
-
Journal article (peer-reviewed)abstract
- Wireless sensors and networks are used only occasionally in current control loops in the process industry. With rapid developments in embedded and highperformance computing, wireless communication, and cloud technology, drastic changes in the architecture and operation of industrial automation systems seem more likely than ever. These changes are driven by ever-growing demands on production quality and flexibility. However, as discussed in "Summary," there are several research obstacles to overcome. The radio communication environment in the process industry is often troublesome, as the environment is frequently cluttered with large metal objects, moving machines and vehicles, and processes emitting radio disturbances [1], [2]. The successful deployment of a wireless control system in such an environment requires careful design of communication links and network protocols as well as robust and reconfigurable control algorithms.
|
|
| 4. |
- Ahlén, Anders, et al.
(author)
-
Towards Wireless Control in Industrial Process Automation : A Case Study at a Paper Mill
- 2019
-
In: IEEE CONTROL SYSTEMS MAGAZINE. - : IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC. - 1066-033X .- 1941-000X. ; 39:5, s. 36-57
-
Journal article (peer-reviewed)abstract
- Wireless sensors and networks are used only occasionally in current control loops in the process industry. With rapid developments in embedded and highperformance computing, wireless communication, and cloud technology, drastic changes in the architecture and operation of industrial automation systems seem more likely than ever. These changes are driven by ever-growing demands on production quality and flexibility. However, as discussed in "Summary," there are several research obstacles to overcome. The radio communication environment in the process industry is often troublesome, as the environment is frequently cluttered with large metal objects, moving machines and vehicles, and processes emitting radio disturbances [1], [2]. The successful deployment of a wireless control system in such an environment requires careful design of communication links and network protocols as well as robust and reconfigurable control algorithms.
|
|
| 5. |
- Akram, Neelam, et al.
(author)
-
Regulation of proteorhodopsin gene expression by nutrient limitation in the marine bacterium Vibrio sp AND4
- 2013
-
In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 15:5, s. 1400-1415
-
Journal article (peer-reviewed)abstract
- Proteorhodopsin (PR), a ubiquitous membrane photoprotein in marine environments, acts as a light-driven proton pump and can provide energy for bacterial cellular metabolism. However, knowledge of factors that regulate PR gene expression in different bacteria remains strongly limited. Here, experiments with Vibrio sp. AND4 showed that PR phototrophy promoted survival only in cells from stationary phase and not in actively growing cells. PR gene expression was tightly regulated, with very low values in exponential phase, a pronounced peak at the exponential/stationary phase intersection, and a marked decline in stationary phase. Thus, PR gene expression at the entry into stationary phase preceded, and could therefore largely explain, the stationary phase light-induced survival response in AND4. Further experiments revealed nutrient limitation, not light exposure, regulated this differential PR expression. Screening of available marine vibrios showed that the PR gene, and thus the potential for PR phototrophy, is found in at least three different clusters in the genus Vibrio. In an ecological context, our findings suggest that some PR-containing bacteria adapted to the exploitation of nutrient-rich micro-environments rely on a phase of relatively slowly declining resources to mount a cellular response preparing them for adverse conditions dispersed in the water column.
|
|
| 6. |
- Alneberg, Johannes, et al.
(author)
-
Genomes from uncultivated prokaryotes : a comparison of metagenome-assembled and single-amplified genomes
- 2018
-
In: Microbiome. - : BioMed Central. - 2049-2618. ; 6
-
Journal article (peer-reviewed)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
|
|
| 7. |
- Alneberg, Johannes, et al.
(author)
-
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
-
Other publication (other academic/artistic)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
|
|
| 8. |
- Andersson, Agneta, et al.
(author)
-
DNA-streckkodning av marina växtplankton : Ett nytt verktyg i miljöövervakningen
- 2024
-
Reports (other academic/artistic)abstract
- Växtplankton utgör grunden i den marina näringsväven och används världen över för att bestämma miljöstatus i hav och sjöar. De ingår exempelvis som en kvalitetsfaktor i EU:s vattendirektiv och havsmiljödirektiv. Det finns långa tidsserier av växtplanktonövervakning där analyserna utförts med mikroskopi. Det sker nu en snabb internationell utveckling av DNA-metoder för att övervaka växtplankton. Målsättningen med detta projekt var att utveckla en praktisk och robust DNA analysmetod som kan implementeras i svensk marin miljöövervakning. Vårt tillvägagångssätt var att följa med på ordinarie marina miljöövervakningsexpeditioner under ett års tid (2019–2020) och ta parallella havsvattenprov för så kallad DNA-streckkodning av växtplankton. Sammanlagt tog vi prov vid 19 övervakningsstationer som var spridda från Bottenviken i norr till Skagerrak i söder. Provtagningsfrekvensen var cirka 1 gång per månad. Praktiska metoder utarbetades för fältprovtagning, DNA-extraktion, sekvensering, bioinformatisk analys och taxonomisk annotering. Vi har även tagit fram system för datahantering hos nationell datavärd och gett förslag på en ny datatyp för nationellt datavärdskap för marinbiologi och oceanografi vid Svenskt Oceanografiskt Datacentrum (https://sharkweb. smhi.se/hamta-data/). En viktig del har varit att jämföra resultaten av DNA-streckkodning och mikroskopi. Resultaten visar att DNA-streckkodning ger ungefär dubbelt så högt biodiversitetsmått än mikroskopering, även om det skiljer sig åt mellan olika grupper av växtplankton. För att undersöka om DNA-streckkodning kan användas för kvantitativ analys tillsatte vi en intern standard till proverna bestående av syntetiskt DNA, men eftersom resultatet varierade så behöver man arbeta vidare med detta. Den relativa fördelningen av vanliga eukaryota växtplanktongrupper visade sig ha relativt bra överensstämmelse mellan DNA-streckkodning och mikroskopimåttet kolbiomassa, medan biovolym och abundans skiljde sig åt mer. DNA-streckkodning visade sig ge detaljerade utbredningsmönster av skadliga alger, till exempel för släktet Prymnesium bland häftalgerna (Coccolithophyceae). Vi har inom projektet kunnat utvärdera ekologiska drivkrafter för växtplanktonsamhällets diversitet och artsammansättning, genom att miljöövervakningen mäter många fysikalisk-kemiska parametrar. Både salthalt och närsalter visade sig ha stor inverkan på växtplanktonsamhällets sammansättning och diversitet. Sammanfattningsvis ser vi att den framtagna DNA-streckkodningsmetoden skulle vara ett bra komplement till den etablerade växtplanktonövervakningen.
|
|
| 9. |
- Andersson, Kent, 1967-, et al.
(author)
-
Introduktion till Operationsanalys : En antologi med essäer av studerande i militärteknik 2011
- 2012
-
Other publication (other academic/artistic)abstract
- I ämnesplanen definieras militärteknik som ”den vetenskap som beskriver och förklarar hur tekniken inverkar på militär verksamhet på alla nivåer, strategisk, operativ och taktisk, samt hur officersprofessionen påverkar och påverkas av tekniken.”[1] En militärteknikers uppgift brukar, utgående från definitionen, uttryckas som att beskriva och förklara den militära nyttan med tekniken. För att kunna göra detta behövs verktyg. Och många av dem kommer från den vetenskapliga disciplinen Operationsanalys.Syftet med den här antologin är att introducera studerande i militärteknik på Försvarshögskolan till två av de mest refererade boktitlarna i operationsanalys – Methods for conducting military operational analysis editerad av Andrew G. Loerch och Larry B. Rainey samt Military Operations Research, quantitative decision making av N.K. Jaiswal.Kapitlen utgörs av essäer skrivna av studerande på den högre stabsofficersutbildningen med teknisk inriktning, som examinationsuppgift i en fördjupningskurs. Essäerna är till del referat av kapitel i de två böckerna ovan, men kryddade med exempel satta i svenskt sammanhang och med de studerandes egen värdering av metodernas användbarhet.[1]Försvarshögskolan, Ämnesplan militärteknik, 2007.
|
|
| 10. |
- Aquilante, Francesco, et al.
(author)
-
Modern quantum chemistry with [Open]Molcas
- 2020
-
In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 152:21
-
Journal article (peer-reviewed)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.
|
|
