| 1. |
- Gordon, I.E., et al.
(författare)
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The HITRAN2020 molecular spectroscopic database
- 2022
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Ingår i: Journal of Quantitative Spectroscopy and Radiative Transfer. - : Elsevier. - 0022-4073 .- 1879-1352. ; 277
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Tidskriftsartikel (refereegranskat)abstract
- The HITRAN database is a compilation of molecular spectroscopic parameters. It was established in the early 1970s and is used by various computer codes to predict and simulate the transmission and emission of light in gaseous media (with an emphasis on terrestrial and planetary atmospheres). The HITRAN compilation is composed of five major components: the line-by-line spectroscopic parameters required for high-resolution radiative-transfer codes, experimental infrared absorption cross-sections (for molecules where it is not yet feasible for representation in a line-by-line form), collision-induced absorption data, aerosol indices of refraction, and general tables (including partition sums) that apply globally to the data. This paper describes the contents of the 2020 quadrennial edition of HITRAN. The HITRAN2020 edition takes advantage of recent experimental and theoretical data that were meticulously validated, in particular, against laboratory and atmospheric spectra. The new edition replaces the previous HITRAN edition of 2016 (including its updates during the intervening years). All five components of HITRAN have undergone major updates. In particular, the extent of the updates in the HITRAN2020 edition range from updating a few lines of specific molecules to complete replacements of the lists, and also the introduction of additional isotopologues and new (to HITRAN) molecules: SO, CH3F, GeH4, CS2, CH3I and NF3. Many new vibrational bands were added, extending the spectral coverage and completeness of the line lists. Also, the accuracy of the parameters for major atmospheric absorbers has been increased substantially, often featuring sub-percent uncertainties. Broadening parameters associated with the ambient pressure of water vapor were introduced to HITRAN for the first time and are now available for several molecules. The HITRAN2020 edition continues to take advantage of the relational structure and efficient interface available at www.hitran.org and the HITRAN Application Programming Interface (HAPI). The functionality of both tools has been extended for the new edition.
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| 2. |
- Albert, Damien, et al.
(författare)
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A Decade with VAMDC : Results and Ambitions
- 2020
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Ingår i: Atoms. - : MDPI. - 2218-2004. ; 8:4
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Tidskriftsartikel (refereegranskat)abstract
- This paper presents an overview of the current status of the Virtual Atomic and Molecular Data Centre (VAMDC) e-infrastructure, including the current status of the VAMDC-connected (or to be connected) databases, updates on the latest technological development within the infrastructure and a presentation of some application tools that make use of the VAMDC e-infrastructure. We analyse the past 10 years of VAMDC development and operation, and assess their impact both on the field of atomic and molecular (A&M) physics itself and on heterogeneous data management in international cooperation. The highly sophisticated VAMDC infrastructure and the related databases developed over this long term make them a perfect resource of sustainable data for future applications in many fields of research. However, we also discuss the current limitations that prevent VAMDC from becoming the main publishing platform and the main source of A&M data for user communities, and present possible solutions under investigation by the consortium. Several user application examples are presented, illustrating the benefits of VAMDC in current research applications, which often need the A&M data from more than one database. Finally, we present our vision for the future of VAMDC.
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| 3. |
- Muntean, Stela Andrea, et al.
(författare)
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Dynamics of water near oxidized polystyrene films
- 2012
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Ingår i: Macromolecular Theory and Simulations. - : Wiley-Blackwell. - 1022-1344 .- 1521-3919. ; 21:8, s. 544-552
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Tidskriftsartikel (refereegranskat)abstract
- Atomistic MD simulations of water in the vicinity of oxidized amorphous atactic polystyrene are presented. The changes in the orientational and translational dynamics of water near polymer surfaces with different hydrophilicity are studied. Two main orientational relaxation processes of water molecules are distinguished: a process on a fs timescale, associated with the ballistic motion of water molecules, and a process on a ps timescale, associated with the self-diffusion of water. The fast process is not affected by the presence of the polymeric surface. The second relaxation process differs at the interface from that in the bulk in that the dynamics of water molecules is more heterogeneous in the first. The effect of the representation of polystyrene films on the water dynamics is discussed. MD simulations for the dynamics of water near hydrophilic and hydrophobic polystyrene surfaces are presented. The quantities that characterize the dynamic behavior of water in the first layers near the interface are compared with those in bulk. The influence of the polystyrene model on the dynamic properties of water is studied. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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| 4. |
- Muntean, Stela Andrea
(författare)
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Molecular-dynamics simulations of polymeric surfaces for biomolecular applications
- 2013
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In-vitro diagnostics plays a very important role in the present healthcare system. It consists of a large variety of medical devices designed to diagnose a medical condition by measuring a target molecule in a sample, such as blood or urine. In vitro is the latin term for in glass and refers here to the fact that the samples are investigated outside the living organism. The range of target molecules is very broad, spanning from salts to small molecules, proteins, nucleic acids and cells. An important segment in this range is the measurement of macromolecules, such as biomarker proteins or nucleic acids, in biological samples. Biosensors are compact systems for rapid detection of biological molecules. The first commercial biosensor was introduced in 1975 for glucose analysis by the Yellow Springs Instrument Company, based on the pioneering work of Clark and Lyons. Since that time, biosensors are becoming more integrated, more sensitive, smaller, faster and cheaper and are becoming available for more and more classes of biomarkers. The immunoassays can be performed nowadays in devices with very different formats, from the high-throughput parallel analysis on well-plates to integrated point-of-care biosensors using lab-on-a-chip technology. The solid phase in these devices is very often a polymeric glass. Polymeric glasses, such as polystyrene, are easy to process and can be produced at low costs, which makes them suitable for disposable cartridges in lab-on-a-chip devices. An important process in the immunoassays is the physisorption of the macromolecules to the polymeric solid phase, such as the non-specific binding of molecules from the biological sample onto the polymeric carrier. This process plays a very important role in the limit of detection, which is given by specific binding (signal) over non-specific binding (background). Therefore, the understanding of the non-specific binding of macromolecules to polymeric surfaces is crucial for the improvement of the sensitivity in these devices. The scope of this thesis is to gain fundamental knowledge on the physisorption of proteins onto polymeric surfaces and to understand how to model this process in atomistic details. The goal of this work is to model the interaction between myoglobin and polystyrene surfaces, within a clean buffer. Computer simulations provide detailed informations about the nature of the non-specific interactions between the biomolecule and the polymeric substrate, at molecular and atomic scales. The high level of detail obtained from simulations on a smaller scale is complementary to the experimental results obtained at a larger scale. The polymeric substrate is in our case modeled by an atactic amorphous polystyrene thin film. We would like to explore the possibility of changing the properties of the polymeric substrate, to prevent non-specific interaction, by chemical modification induced by oxidation. Pure polystyrene is a hydrophobic material. We tune the hydrophilicity of its surface by adding oxygen atoms to the phenyl rings of the polystyrene chain. This addition of oxygen is a way to mimic the oxidation of polystyrene surfaces that is performed in experiments. We represent the buffer solution in simulations by explicit water molecules described at atomistic level, to which we add Na+ and Cl- ions to reproduce the salt concentration in the experimentally used buffer solution. We chose myoglobin as model biomolecule because it is a relatively small globular protein, well studied in the past and represents a good candidate for practical applications. The first question we intend to answer is to which extent the model used to represent the polystyrene chains is important for the macroscopic properties of the polystyrene films and in particular to their interaction with the water molecules. To tackle this issue, we chose two representations of the polystyrene chains: the united atoms representations on one hand, in which only the heavy atoms are modeled explicitly and the hydrogen atoms are collapsed on the carbon atoms to which they are covalently bonded, and the dummy-hydrogens atoms representation on the other hand, in which the hydrogen atoms are modeled as interaction sites with no mass and with a positive partial electrical charge. The results of these simulations are presented in Chapter 3. We begin our systematic study on the interacting species in a biomedical device by characterizing the atactic amorphous polystyrene substrate. In Chapter 4 we present the results of molecular-dynamics simulations of polystyrene surfaces with controlled degree of oxidation. The variations in degree of oxidation at the surface, ranging from 0% to 24%, correspond to different degrees of hydrophilicity of the polystyrene surface, from hydrophobic to hydrophilic. We study the influence of the oxidation on the roughness of the film, both in vacuum and in water environment. We compare our results with experimental results from AFM measurements obtained by our collaborators. We also analyze the ordering of the molecular segments in non-oxidized and oxidized polystyrene at the interface with vacuum and with water. The structure of the water interface near polystyrene surfaces with different hydrophilicity is analyzed as well. Since the interaction between proteins and polymeric surfaces is a water-mediated process, it is very important to know how water behaves near these surfaces. In Chapter 5 we discuss the dynamics of water near non-oxidized (hydrophobic) and oxidized (hydrophilic) polystyrene surfaces, both in united-atoms and dummy-hydrogen atoms representations. We discuss the orientational dynamics of water molecules and its dependence on the distance from the interface. Furthermore, the translational diffusion of water molecules is briefly discussed. In Chapter 6 we study the nature of non-specific adsorption of myoglobin, as model protein, to hydrophobic and hydrophilic polystyrene surfaces. We investigate the importance of the orientation of the protein in the process of adsorption. We also discuss the influence of the hydrophilicity of the surface on the strength of adsorption of the protein. We conclude this thesis by Chapter 7, in which our main results are summarized. In addition, we give there an outlook on further interesting questions.
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| 5. |
- Muntean, Stela Andrea, et al.
(författare)
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Myoglobin interactions with polystyrene surfaces of different hydrophobicity
- 2014
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Ingår i: Macromolecular Theory and Simulations. - : Wiley-Blackwell. - 1022-1344 .- 1521-3919. ; 23:2, s. 63-75
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Tidskriftsartikel (refereegranskat)abstract
- The atomistic molecular-dynamics simulations of the initial stage of myoglobin adsorption on amorphous polystyrene surfaces with varying hydrophobicity are presented. The polystyrene surfaces as non-oxidized (hydrophobic) and oxidized (hydrophilic) films, both in united-atoms and dummy-hydrogen atoms representations are modeled. The protein is placed initially at different distances and orientations from the polymer. We monitor the interactions between the protein and the polystyrene surface for the same polystyrene surface in contact with the protein in different initial orientations and for one initial orientation of the protein in contact with different polystyrene surfaces. By comparing the stability and the number of myoglobin-polystyrene atomic contacts and the interaction energies, it is found that the initial contact of the protein with the hydrophobic polystyrene surfaces is stronger than with the hydrophilic ones. The orientations of the myoglobin in which the more rigid protein parts face the polymer exhibit stronger initial contact with the polymeric surface. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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| 6. |
- Muntean, Stela Andrea, et al.
(författare)
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Representation of hydrogen atoms in molecular dynamics simulations : The influence on the computed properties of thin polystyrene films
- 2012
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Ingår i: Macromolecular Theory and Simulations. - : Wiley-Blackwell. - 1022-1344 .- 1521-3919. ; 21:2, s. 90-97
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Tidskriftsartikel (refereegranskat)abstract
- The united atoms (UA) and dummy hydrogen atom (DHA) approaches for molecular dynamics simulations of the interface between oxidized atactic polystyrene (aPS) thin films and water are compared. For both oxidized and non-oxidized aPS films the polymer density profile decays steepest when using the UA model. The surface roughness of the aPS film and the ordering of the phenyl rings near the surface decrease upon changing from vacuum to water for the UA, but not for the DHA model. This also supports the fact that the non-oxidized aPS films modeled in DHA representation become less hydrophobic. The water structure close to the interface also suggests that the aPS films modeled using UA are more hydrophobic compared to the aPS films modeled with DHA in the phenyl rings. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
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| 7. |
- Muntean, Stela Andrea, et al.
(författare)
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Roughness and ordering at the interface of oxidized polystyrene and water
- 2011
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 27:14, s. 8678-8686
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Tidskriftsartikel (refereegranskat)abstract
- For the first time, atomistically detailed molecular dynamics calculations revealed molecular ordering of the water-oxidized atactic polystyrene (aPS) interface. Both ordering of the water molecules and the phenyl rings occur. In addition, the natural roughness of the surface has been simulated and compared to experimental values. The composition of the simulated aPS films is based on spin-coated aPS films that have been oxidized and characterized experimentally. The aPS surfaces are oxidized with ultraviolet-ozone radiation and have been characterized by XPS, AFM, and water contact angle measurements. XPS measurements show that the oxygen content in the sample increases rapidly with exposure and reaches saturation near 24 at. % of oxygen. The molecular dynamics simulations show smoothening of an hydrophobic aPS surface upon transition from vacuum to water. The smoothening decreases with increasing hydrophilicity. The calculations reveal ordering of oxidized phenyl rings for aPS surfaces in water. The order increases with increasing hydrophilicity. Additionally, we investigated the water structure near the aPS-water interface as a function of the surface hydrophilicity. With increasing hydrophilicity, the density of water at the aPS-water interface increases. The water density profile is steeper in the presence of hydrophobic aPS. The water shows an ordered layer near both the hydrophobic and hydrophilic surfaces; the position of this layer shifts toward the interface with increasing hydrophilicity. © 2011 American Chemical Society.
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