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Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the $\lambda$-dynamics approach by Brooks and co-workers was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the $\lambda$-coordinates, not only reduces the complexity associated with parameterizing the intra-molecular interactions between the sites, but is also easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.

Molecular dynamics (MD) computer simulations are used routinely to compute atomistic trajectories of complex systems. Systems are simulated in various ensembles, depending on the experimental conditions one aims to mimic. While constant energy, temperature, volume, and pressure are rather straightforward to model, pH, which is an equally important parameter in experiments, is more difficult to account for in simulations. Although a constant pH algorithm based on the $\lambda$-dynamics approach by Brooks and co-workers was implemented in a fork of the GROMACS molecular dynamics program, uptake has been rather limited, presumably due to the poor scaling of that code with respect to the number of titratable sites. To overcome this limitation, we implemented an alternative scheme for interpolating the Hamiltonians of the protonation states that makes the constant pH molecular dynamics simulations almost as fast as a normal MD simulation with GROMACS. In addition, we implemented a simpler scheme, called multisite representation, for modeling side chains with multiple titratable sites, such as imidazole rings. This scheme, which is based on constraining the sum of the $\lambda$-coordinates, not only reduces the complexity associated with parameterizing the intra-molecular interactions between the sites, but is also easily extendable to other molecules with multiple titratable sites. With the combination of a more efficient interpolation scheme and multisite representation of titratable groups, we anticipate a rapid uptake of constant pH molecular dynamics simulations within the GROMACS user community.

The aim of this study was to evaluate climate impacts of a typical Finnish wind farm. Three research questions were: 1) What is the typical Finnish wind farm’s carbon footprint? 2) what is the energy payback time of the typical Finnish wind farm? and 3) does the typical Finnish wind farm have a better net-negative impact on climate than the commercial forest area on which it was built? Data for the study were collected via academic literature, wind turbine life cycle assessment reports, geographic information system (GIS) analysis and through the Natural Resources Institute Finland’s Statistics database. The GIS analysis was conducted to retrieve the volume of roundwood on the wind farm’s site. The carbon footprint of the typical Finnish wind farm was found to be 7,18 g CO2e/kWh and the wind farm’s energy payback time 7,06 months. This study found that during 22 years (consisting of the wind farm’s construction and operation phases) the typical Finnish wind farm had a net-negative impact on climate change of at least 169 767,72 t CO2. In the absence of the typical Finnish wind farm, producing the equivalent amount of electricity by Finnish electricity mix was considered in calculating the net impact of the commercial forest area. This resulted in a net-positive impact on climate change of 192 393,42 t CO2. However, the typical Finnish wind farm did not represent a carbon sink. Climate impacts represent only a part of environmental impacts caused by wind power. The results of this study might have implications for the acceptability of wind power by general society as well as used for calculating climate impact assessment. Tutkimuksen tavoitteena oli arvioida tyypillisen suomalaisen tuulivoimapuiston ilmastovaikutuksia. Aihetta lähestyttiin kolmella tutkimuskysymyksellä selvittäen tuulivoimapuiston 1) hiilijalanjälki ja 2) energiantakaisinmaksuaika sekä 3) onko puistolla parempi nettonegatiivinen ilmastovaikutus kuin talousmetsällä, johon se on rakennettu. Tutkimuksen aineisto kerättiin akateemisen kirjallisuuden, elinkaariarviointi-raporttien, paikkatieto-analyysin (GIS) ja Luonnonvarakeskuksen tietokannan avulla. GIS-analyysillä selvitettiin runkopuun määrä tuulivoimapuistoalueella. Tyypillisen suomalaisen tuulivoimapuiston hiilijalanjälki on tulosten perusteella 7,18 g CO2e/kWh ja tuulivoimapuiston energiantakaisinmaksuaika 7,06 kuukautta. Tutkimuksessa havaittiin, että 22 vuoden aikana (puiston rakentaminen ja tuotantovaihe) tyypillisellä suomalaisella tuulivoimapuistolla on nettonegatiivinen ilmastovaikutus, joka on vähintään 169 767,72 t CO2. Skenaariossa, että tuulivoimapuistoa ei rakennettaisi, talousmetsän ilmastovaikutusten laskennassa on huomioitu vastaava sähkömäärän tuotto suomalaisella energialähteiden yhdistelmällä. Tässä tapauksessa netto-positiivinen vaikutus on tulosten perusteella 192 393,42 t CO2. Tuloksia ei voi kuitenkaan tulkita niin, että tuulivoimapuisto olisi hiilinielu. Ilmastovaikutukset ovat yksi osa tuulivoiman aiheuttamista ympäristövaikutuksista. Tämän tutkielman tuloksilla voidaan hyödyntää ilmastovaikutusten arvioinnin laskennassa ja niillä olla osaltaan vaikutuksia siihen, kuinka tuulivoima nähdään yhteiskunnassa. ei tietoa saavutettavuudesta unknown accessibility

The aim of this study was to evaluate climate impacts of a typical Finnish wind farm. Three research questions were: 1) What is the typical Finnish wind farm’s carbon footprint? 2) what is the energy payback time of the typical Finnish wind farm? and 3) does the typical Finnish wind farm have a better net-negative impact on climate than the commercial forest area on which it was built? Data for the study were collected via academic literature, wind turbine life cycle assessment reports, geographic information system (GIS) analysis and through the Natural Resources Institute Finland’s Statistics database. The GIS analysis was conducted to retrieve the volume of roundwood on the wind farm’s site. The carbon footprint of the typical Finnish wind farm was found to be 7,18 g CO2e/kWh and the wind farm’s energy payback time 7,06 months. This study found that during 22 years (consisting of the wind farm’s construction and operation phases) the typical Finnish wind farm had a net-negative impact on climate change of at least 169 767,72 t CO2. In the absence of the typical Finnish wind farm, producing the equivalent amount of electricity by Finnish electricity mix was considered in calculating the net impact of the commercial forest area. This resulted in a net-positive impact on climate change of 192 393,42 t CO2. However, the typical Finnish wind farm did not represent a carbon sink. Climate impacts represent only a part of environmental impacts caused by wind power. The results of this study might have implications for the acceptability of wind power by general society as well as used for calculating climate impact assessment. Tutkimuksen tavoitteena oli arvioida tyypillisen suomalaisen tuulivoimapuiston ilmastovaikutuksia. Aihetta lähestyttiin kolmella tutkimuskysymyksellä selvittäen tuulivoimapuiston 1) hiilijalanjälki ja 2) energiantakaisinmaksuaika sekä 3) onko puistolla parempi nettonegatiivinen ilmastovaikutus kuin talousmetsällä, johon se on rakennettu. Tutkimuksen aineisto kerättiin akateemisen kirjallisuuden, elinkaariarviointi-raporttien, paikkatieto-analyysin (GIS) ja Luonnonvarakeskuksen tietokannan avulla. GIS-analyysillä selvitettiin runkopuun määrä tuulivoimapuistoalueella. Tyypillisen suomalaisen tuulivoimapuiston hiilijalanjälki on tulosten perusteella 7,18 g CO2e/kWh ja tuulivoimapuiston energiantakaisinmaksuaika 7,06 kuukautta. Tutkimuksessa havaittiin, että 22 vuoden aikana (puiston rakentaminen ja tuotantovaihe) tyypillisellä suomalaisella tuulivoimapuistolla on nettonegatiivinen ilmastovaikutus, joka on vähintään 169 767,72 t CO2. Skenaariossa, että tuulivoimapuistoa ei rakennettaisi, talousmetsän ilmastovaikutusten laskennassa on huomioitu vastaava sähkömäärän tuotto suomalaisella energialähteiden yhdistelmällä. Tässä tapauksessa netto-positiivinen vaikutus on tulosten perusteella 192 393,42 t CO2. Tuloksia ei voi kuitenkaan tulkita niin, että tuulivoimapuisto olisi hiilinielu. Ilmastovaikutukset ovat yksi osa tuulivoiman aiheuttamista ympäristövaikutuksista. Tämän tutkielman tuloksilla voidaan hyödyntää ilmastovaikutusten arvioinnin laskennassa ja niillä olla osaltaan vaikutuksia siihen, kuinka tuulivoima nähdään yhteiskunnassa. ei tietoa saavutettavuudesta unknown accessibility

The observed difference in the selectivity towards alkane, ketone, and alcohol hydrodeoxygenation products over Ru and Rh catalysts is explored using a combination of density functional theory and microkinetics. Using γ-valerolactone as a model compound, we investigate the reaction mechanism in order to identify selectivity determining species. The effect of the coadsorbed water molecule as well as the higher adsorbate surface coverage on reaction barriers and energies is explored as well. The performed calculations suggest that the desired alkane product is formed from a ketone intermediate on Ru, and through both ketone and alcohol on Rh, although the selectivity towars alkane on Rh is much lower than on Ru. peerReviewed

The observed difference in the selectivity towards alkane, ketone, and alcohol hydrodeoxygenation products over Ru and Rh catalysts is explored using a combination of density functional theory and microkinetics. Using γ-valerolactone as a model compound, we investigate the reaction mechanism in order to identify selectivity determining species. The effect of the coadsorbed water molecule as well as the higher adsorbate surface coverage on reaction barriers and energies is explored as well. The performed calculations suggest that the desired alkane product is formed from a ketone intermediate on Ru, and through both ketone and alcohol on Rh, although the selectivity towars alkane on Rh is much lower than on Ru. peerReviewed

AbstractThis article reports on the inclusive production cross section of several quarkonium states, $$\textrm{J}/\psi $$ J / ψ , $$\psi \mathrm{(2S)}$$ ψ ( 2 S ) , $$\Upsilon \mathrm (1S)$$ Υ ( 1 S ) , $$\Upsilon \mathrm{(2S)}$$ Υ ( 2 S ) , and $$\Upsilon \mathrm{(3S)}$$ Υ ( 3 S ) , measured with the ALICE detector at the LHC, in pp collisions at $$\sqrt{s} = 5.02$$ s = 5.02  TeV. The analysis is performed in the dimuon decay channel at forward rapidity ($$2.5< y < 4$$ 2.5 < y < 4 ). The integrated cross sections and transverse-momentum ($$p_{\textrm{T}}$$ p T ) and rapidity ($$y$$ y ) differential cross sections for $$\textrm{J}/\psi $$ J / ψ , $$\psi \mathrm{(2S)}$$ ψ ( 2 S ) , $$\Upsilon \mathrm (1S)$$ Υ ( 1 S ) , and the $$\psi \mathrm{(2S)}$$ ψ ( 2 S ) -to-$$\textrm{J}/\psi $$ J / ψ cross section ratios are presented. The integrated cross sections, assuming unpolarized quarkonia, are: $$\sigma _{\textrm{J}/\psi }$$ σ J / ψ  ($$p_{\textrm{T}} <20$$ p T < 20  GeV/c) = 5.88 ± 0.03 ± 0.34$$ ~\mu $$ μ b, $$\sigma _{\psi \mathrm{(2S)}}$$ σ ψ ( 2 S )  ($$p_{\textrm{T}} <12$$ p T < 12  GeV/c) = 0.87 ± 0.06 ± 0.10$$~\mu $$ μ b, $$\sigma _{\Upsilon \mathrm (1S)}$$ σ Υ ( 1 S )  ($$p_{\textrm{T}} <15$$ p T < 15  GeV/c) = 45.5 ± 3.9 ± 3.5 nb, $$\sigma _{\Upsilon \mathrm{(2S)}}$$ σ Υ ( 2 S )  ($$p_{\textrm{T}} <15$$ p T < 15  GeV/c) = 22.4 ± 3.2 ± 2.7 nb, and $$\sigma _{\Upsilon \mathrm{(3S)}}$$ σ Υ ( 3 S )  ($$p_{\textrm{T}} <15$$ p T < 15  GeV/c) = 4.9 ± 2.2 ± 1.0 nb, where the first (second) uncertainty is the statistical (systematic) one. For the first time, the cross sections of the three $$\Upsilon $$ Υ states, as well as the $$\psi \mathrm{(2S)}$$ ψ ( 2 S ) one as a function of $$p_{\textrm{T}}$$ p T and $$y$$ y , are measured at $$\sqrt{s} = 5.02$$ s = 5.02  TeV at forward rapidity. These measurements also significantly extend the $$\textrm{J}/\psi $$ J / ψ $$p_{\textrm{T}}$$ p T reach and supersede previously published results. A comparison with ALICE measurements in pp collisions at $$\sqrt{s} = 2.76$$ s = 2.76 , 7, 8, and 13 TeV is presented and the energy dependence of quarkonium production cross sections is discussed. Finally, the results are compared with the predictions from several production models.