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AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.

The reactive uptake of N2O5 to aqueous aerosol is a major loss channel for nitrogen oxides in the troposphere. Despite its importance, a quantitative picture of the uptake mechanism is missing. Here we use molecular dynamics simulations with a data-driven many-body model of coupled-cluster accuracy to quantify thermodynamics and kinetics of solvation and adsorption of N2O5 in water. The free energy profile highlights that N2O5 is selectively adsorbed to the liquid-vapor interface and weakly solvated. Accommodation into bulk water occurs slowly, competing with evaporation upon adsorption from gas phase. Leveraging the quantitative accuracy of the model, we parameterize and solve a reaction-diffusion equation to determine hydrolysis rates consistent with experimental observations. We find a short reaction-diffusion length, indicating that the uptake is dominated by interfacial features. The parameters deduced here, including solubility, accommodation coefficient, and hydrolysis rate, afford a foundation for which to consider the reactive loss of N2O5 in more complex solutions.

The reactive uptake of N2O5 to aqueous aerosol is a major loss channel for nitrogen oxides in the troposphere. Despite its importance, a quantitative picture of the uptake mechanism is missing. Here we use molecular dynamics simulations with a data-driven many-body model of coupled-cluster accuracy to quantify thermodynamics and kinetics of solvation and adsorption of N2O5 in water. The free energy profile highlights that N2O5 is selectively adsorbed to the liquid-vapor interface and weakly solvated. Accommodation into bulk water occurs slowly, competing with evaporation upon adsorption from gas phase. Leveraging the quantitative accuracy of the model, we parameterize and solve a reaction-diffusion equation to determine hydrolysis rates consistent with experimental observations. We find a short reaction-diffusion length, indicating that the uptake is dominated by interfacial features. The parameters deduced here, including solubility, accommodation coefficient, and hydrolysis rate, afford a foundation for which to consider the reactive loss of N2O5 in more complex solutions.

Cytochrome bd-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the Mycobacterium tuberculosis (Mtb) bacterium that causes tuberculosis (TB) in humans, the Vibrio cholerae bacterium that causes cholera, the Pseudomonas aeruginosa bacterium that contributes to antibiotic resistance and sepsis, and the Campylobacter jejuni bacterium that causes food poisoning. Escherichia coli (E. coli) is another organism exhibiting the cytochrome bd oxidase. Since it has the highest sequence identity to Mtb (36%) and we are ultimately interested in finding drug targets for TB, we have built parameters for the E. coli bd oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome bd-type oxidases (heme b 558 , heme b 595 , and heme d) along with their axial ligands. This data report includes the parameter and library files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions.

Cytochrome bd-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the Mycobacterium tuberculosis (Mtb) bacterium that causes tuberculosis (TB) in humans, the Vibrio cholerae bacterium that causes cholera, the Pseudomonas aeruginosa bacterium that contributes to antibiotic resistance and sepsis, and the Campylobacter jejuni bacterium that causes food poisoning. Escherichia coli (E. coli) is another organism exhibiting the cytochrome bd oxidase. Since it has the highest sequence identity to Mtb (36%) and we are ultimately interested in finding drug targets for TB, we have built parameters for the E. coli bd oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome bd-type oxidases (heme b 558 , heme b 595 , and heme d) along with their axial ligands. This data report includes the parameter and library files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions.

Cytochrome bd-type quinol oxidase is an important metalloenzyme that allows many bacteria to survive in low oxygen conditions. Since bd oxidase is found in many prokaryotes but not in eukaryotes, it has emerged as a promising bacterial drug target. Examples of organisms containing bd oxidases include the Mycobacterium tuberculosis (Mtb) bacterium that causes tuberculosis (TB) in humans, the Vibrio cholerae bacterium that causes cholera, the Pseudomonas aeruginosa bacterium that contributes to antibiotic resistance and sepsis, and the Campylobacter jejuni bacterium that causes food poisoning. Escherichia coli (E. coli) is another organism exhibiting the cytochrome bd oxidase. Since it has the highest sequence identity to Mtb (36%) and we are ultimately interested in finding drug targets for TB, we have built parameters for the E. coli bd oxidase (Protein Data Bank ID number: 6RKO) that are compatible with the all-atom Amber ff14SB force field for molecular dynamics (MD) simulations. Specifically, we built parameters for the three heme cofactors present in all species of bacterial cytochrome bd-type oxidases (heme b 558 , heme b 595 , and heme d) along with their axial ligands. This data report includes the parameter and library files that can be used with Amber's LEaP program to generate input files for MD simulations using the Amber software package. We also provide the PDB data files of the initial model both by itself and solvated with TIP3P water molecules and counterions.

Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches that have not been validated against extensive first-principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from icelike layers, and an MD simulation of an interface between a c(4 × 6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.

Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches that have not been validated against extensive first-principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from icelike layers, and an MD simulation of an interface between a c(4 × 6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface.

The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem.2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks.

The description of aggregation processes with molecular dynamics simulations is a playground for testing biomolecular force fields, including a new generation of force fields that explicitly describe electronic polarization. In this work, we study a system consisting of 50 glycyl-l-alanine (Gly-Ala) dipeptides in solution with 1001 water molecules. Neutron diffraction experiments have shown that at this concentration, Gly-Ala aggregates into large clusters. However, general-purpose force fields in combination with established water models can fail to correctly describe this aggregation process, highlighting important deficiencies in how solute-solute and solute-solvent interactions are parametrized in these force fields. We found that even for the fully polarizable AMOEBA force field, the degree of association is considerably underestimated. Instead, a fixed point-charge approach based on the newly developed IPolQ scheme [Cerutti et al. J. Phys. Chem.2013, 117, 2328] allows for the correct modeling of the dipeptide aggregation in aqueous solution. This result should stimulate interest in novel fitting schemes that aim to improve the description of the solvent polarization effect within both explicitly polarizable and fixed point-charge frameworks.

We re-investigate the image charge model of Iori and Corni (Iori and Corni, J. Comput. Chem. 2008, 29, 1656). We find that a simple symmetrization of their model allows to obtain quantitatively correct results for the electrostatic interaction of a water molecule with a metallic surface. This symmetrization reduces the magnitude of the electrostatic interaction to less than 10% of the total interaction energy. © 2017 Wiley Periodicals, Inc.

We re-investigate the image charge model of Iori and Corni (Iori and Corni, J. Comput. Chem. 2008, 29, 1656). We find that a simple symmetrization of their model allows to obtain quantitatively correct results for the electrostatic interaction of a water molecule with a metallic surface. This symmetrization reduces the magnitude of the electrostatic interaction to less than 10% of the total interaction energy. © 2017 Wiley Periodicals, Inc.

Aktuell finden umfangreiche Neuerungen und Veränderungen im Elektroenergiesystem statt. Dabei stellen die Netzintegration von Energiespeichern, EE-Anlagen und Elektrofahrzeugen sowie die Realisierung von Energiemanagementsystemen wichtige Neuerungen in der Niederspannungsebene dar. Analysen der Ladevorgänge von Elektrofahrzeugen zeigen einen nennenswerten Einfluss auf den Lastbedarf. Als ein Ergebnis wird die maximal zulässige Anzahl an Elektrofahrzeugen ermittelt, bei der kein Netzumbau notwendig wird. Neben der Untersuchung verschiedener Ladevarianten wird die zufällige Ladung als innovative Ladevariante vorgestellt und deren Nutzen simuliert., Currently, fundamental innovations and changes are occurring in the power system. The grid integration of energy storage systems, renewable energy systems and electric vehicles as well as the implementation of energy management systems are important innovations in the low-voltage grid. Analyses of charging processes for electric vehicles show significant impacts on the load demand. As one result, the maximum number of electric vehicles is determined assuming that no grid expansion is needed. Besides studying various charging options, a random charging method is proposed as an innovative charging option and its benefits are shown by simulations.

Aktuell finden umfangreiche Neuerungen und Veränderungen im Elektroenergiesystem statt. Dabei stellen die Netzintegration von Energiespeichern, EE-Anlagen und Elektrofahrzeugen sowie die Realisierung von Energiemanagementsystemen wichtige Neuerungen in der Niederspannungsebene dar. Analysen der Ladevorgänge von Elektrofahrzeugen zeigen einen nennenswerten Einfluss auf den Lastbedarf. Als ein Ergebnis wird die maximal zulässige Anzahl an Elektrofahrzeugen ermittelt, bei der kein Netzumbau notwendig wird. Neben der Untersuchung verschiedener Ladevarianten wird die zufällige Ladung als innovative Ladevariante vorgestellt und deren Nutzen simuliert., Currently, fundamental innovations and changes are occurring in the power system. The grid integration of energy storage systems, renewable energy systems and electric vehicles as well as the implementation of energy management systems are important innovations in the low-voltage grid. Analyses of charging processes for electric vehicles show significant impacts on the load demand. As one result, the maximum number of electric vehicles is determined assuming that no grid expansion is needed. Besides studying various charging options, a random charging method is proposed as an innovative charging option and its benefits are shown by simulations.

Aktuell finden umfangreiche Neuerungen und Veränderungen im Elektroenergiesystem statt. Dabei stellen die Netzintegration von Energiespeichern, EE-Anlagen und Elektrofahrzeugen sowie die Realisierung von Energiemanagementsystemen wichtige Neuerungen in der Niederspannungsebene dar. Analysen der Ladevorgänge von Elektrofahrzeugen zeigen einen nennenswerten Einfluss auf den Lastbedarf. Als ein Ergebnis wird die maximal zulässige Anzahl an Elektrofahrzeugen ermittelt, bei der kein Netzumbau notwendig wird. Neben der Untersuchung verschiedener Ladevarianten wird die zufällige Ladung als innovative Ladevariante vorgestellt und deren Nutzen simuliert., Currently, fundamental innovations and changes are occurring in the power system. The grid integration of energy storage systems, renewable energy systems and electric vehicles as well as the implementation of energy management systems are important innovations in the low-voltage grid. Analyses of charging processes for electric vehicles show significant impacts on the load demand. As one result, the maximum number of electric vehicles is determined assuming that no grid expansion is needed. Besides studying various charging options, a random charging method is proposed as an innovative charging option and its benefits are shown by simulations.

Aktuell finden umfangreiche Neuerungen und Veränderungen im Elektroenergiesystem statt. Dabei stellen die Netzintegration von Energiespeichern, EE-Anlagen und Elektrofahrzeugen sowie die Realisierung von Energiemanagementsystemen wichtige Neuerungen in der Niederspannungsebene dar. Analysen der Ladevorgänge von Elektrofahrzeugen zeigen einen nennenswerten Einfluss auf den Lastbedarf. Als ein Ergebnis wird die maximal zulässige Anzahl an Elektrofahrzeugen ermittelt, bei der kein Netzumbau notwendig wird. Neben der Untersuchung verschiedener Ladevarianten wird die zufällige Ladung als innovative Ladevariante vorgestellt und deren Nutzen simuliert., Currently, fundamental innovations and changes are occurring in the power system. The grid integration of energy storage systems, renewable energy systems and electric vehicles as well as the implementation of energy management systems are important innovations in the low-voltage grid. Analyses of charging processes for electric vehicles show significant impacts on the load demand. As one result, the maximum number of electric vehicles is determined assuming that no grid expansion is needed. Besides studying various charging options, a random charging method is proposed as an innovative charging option and its benefits are shown by simulations.

Placa homogeneizadora de temperatura para microdispositivos térmicamente aislados (ver figura en archivo de texto adjunto). El objeto de la presente invención es el desarrollo de una microestructura térmicamente aislada con zonas de temperatura muy homogénea y controlada. Dichas estructuras son la base de distintos tipos de sensores microelectrónicos ya existentes, en los que un cierto material o elemento sensible se deposita sobre una estructura térmica que debe trabajar a una temperatura conocida. Es aplicable a sistemas de medida microelectrónica basados en microsensores de silicio.

The characteristics of electrochemical etching of silicon in concentrated (25 wt.%) and dilute (2.5 wt.%) tetramethyl ammonium hydroxide (TMAH) and in 25 wt.% TMAH: 17 vol.% isopropyl alcohol (IPA) solutions are presented. I-V curves and the variation of the etch rate in the <100 > direction with the applied potential have been obtained for n- and p-type silicon. The difference in the passivation potential (PP) of n- and p-type silicon is more significant for dilute TMAH solutions and is practically unaffected by the presence of IPA. The silicon etch rate is smaller for n-type than for p-type silicon, the difference being more pronounced when no IPA is used. In any case, the etch rate decreases abruptly at potentials anodic to the PP. Surprisingly, a pronounced decrease in the etch rate of n-type silicon is observed for potentials negative with respect to the open-circuit potential. The results obtained are applied to the fabrication of thin membranes and for monocrystalline silicon microbridges. © 1994.

Auch im VD 18 verzeichnet unter: VD18 10202285, Schlüsselseiten aus dem Exemplar der SLUB Dresden: Coll.diss.A.111,45, Vorlageform des Erscheinungsvermerks: A.S.R. MDCXXXVIII. Altorfii Noricorvm Typis Et Impensis Iodoci Gvil. Kohlesii Acad. Typogr. - Erscheinungsjahr der Datierung des Vorwortes entnommen

Emendatvm Et Avctvm A Ioh. Frid. Fischero Qviet Praefationem De De Vitiis Lexicorvm N. T Addidit, Autopsie nach Exemplar der ULB Sachsen-Anhalt (Halle), Vorlageform des Erscheinungsvermerks: Lipsiae Ex officina Weidmann. et Reich A. C. N. MDCCLXXXI

Auch im VD 18 verzeichnet unter: VD18 10202285, Schlüsselseiten aus dem Exemplar der SLUB Dresden: Coll.diss.A.111,45, Vorlageform des Erscheinungsvermerks: A.S.R. MDCXXXVIII. Altorfii Noricorvm Typis Et Impensis Iodoci Gvil. Kohlesii Acad. Typogr. - Erscheinungsjahr der Datierung des Vorwortes entnommen

Emendatvm Et Avctvm A Ioh. Frid. Fischero Qviet Praefationem De De Vitiis Lexicorvm N. T Addidit, Autopsie nach Exemplar der ULB Sachsen-Anhalt (Halle), Vorlageform des Erscheinungsvermerks: Lipsiae Ex officina Weidmann. et Reich A. C. N. MDCCLXXXI