Browsing by Subject "SIMULATIONS"

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  • Liu, Tie; Li, Pak Shing; Juvela, Mika; Kim, Kee-Tae; Evans, Neal J.; Di Francesco, James; Liu, Sheng-Yuan; Yuan, Jinghua; Tatematsu, Ken'ichi; Zhang, Qizhou; Ward-Thompson, Derek; Fuller, Gary; Goldsmith, Paul F.; Koch, P. M.; Sanhueza, Patricio; Ristorcelli, I.; Kang, Sung-ju; Chen, Huei-Ru; Hirano, N.; Wu, Yuefang; Sokolov, Vlas; Lee, Chang Won; White, Glenn J.; Wang, Ke; Eden, David; Li, Di; Thompson, Mark; Pattle, Kate M.; Soam, Archana; Nasedkin, Evert; Kim, Jongsoo; Kim, Gwanjeong; Lai, Shih-Ping; Park, Geumsook; Qiu, Keping; Zhang, Chuan-Peng; Alina, Dana; Eswaraiah, Chakali; Falgarone, Edith; Fich, Michel; Greaves, Jane; Gu, Q. -L.; Kwon, Woojin; Li, Hua-bai; Malinen, Johanna; Montier, Ludovic; Parsons, Harriet; Qin, Sheng-Li; Rawlings, Mark G.; Tang, Y. -W. (2018)
    Magnetic field plays a crucial role in shaping molecular clouds and regulating star formation, yet the complete information on the magnetic field is not well constrained owing to the limitations in observations. We study the magnetic field in the massive infrared dark cloud G035.39-00.33 from dust continuum polarization observations at 850 mu m with SCUBA-2/POL-2 at JCMT for the first time. The magnetic field tends to be perpendicular to the densest part of the main filament (F-M), whereas it has a less defined relative orientation in the rest of the structure, where it tends to be parallel to some diffuse regions. A mean plane-of-the-sky magnetic field strength of similar to 50 mu G for F-M is obtained using the Davis-Chandrasekhar-Fermi method. Based on (CO)-C-13 (1-0) line observations, we suggest a formation scenario of F-M due to large-scale (similar to 10 pc) cloud-cloud collision. Using additional NH3 line data, we estimate that F-M will be gravitationally unstable if it is only supported by thermal pressure and turbulence. The northern part of F-M, however, can be stabilized by a modest additional support from the local magnetic field. The middle and southern parts of F-M are likely unstable even if the magnetic field support is taken into account. We claim that the clumps in F-M may be supported by turbulence and magnetic fields against gravitational collapse. Finally, we identified for the first time a massive (similar to 200 M-circle dot, collapsing starless clump candidate, "c8," in G035.39-00.33. The magnetic field surrounding "c8" is likely pinched, hinting at an accretion flow along the filament.
  • Paton, Mark; Harri, Ari-Matti; Vierkens, Oliver; Savijärvi, Hannu (2019)
    As spacecraft missions return ever more data from Mars, additional tools will be required to explore and analyse these datasets efficiently. To streamline research into the atmosphere of Mars, a user-orientated modelling capability is developed that enables automatic initialisation and running of a column model. As a demonstration we utilise the modelling framework to provide additional verification for the University of Helsinki and Finnish Meteorological Institute Mars column model temperature profiles above the height of typical lander meteorological measurements, i.e. above 2 m. We utilise the framework at landing site locations that are well characterised to understand the model's applicability and to identify future opportunities for modifications to the framework. We do this by using the framework to compare the column model to temperature soundings made by the Mars Reconnaissance Orbiter. We find that the column model, without any modification, is able to reproduce the observed lapse rates and average temperatures closely in most cases except for a 20-60 K increase over the northern hemisphere mid-winter. We can reproduce this discrepancy by incorporating an adiabatic heating term into the column model. Fitting of the modified column model to the observations results in estimated maximum downward vertical wind velocities of similar to 10 cm s(-1) at altitudes of 15-20 km over the winter solstice at the VL-1 and VL-2 sites. The approach developed here may possibly provide a way to independently estimate or observe the vertical motion in the Martian atmosphere. However, even though the magnitude of the vertical wind speed appears reasonable, it is not clear at this point how much the atmospheric heating is due to other mechanisms such as advection. We have introduced new application software that can quickly find and display the requested data and can be immediately analysed using the included tools. We have demonstrated the potential of this type of software application with a glimpse into the upper atmosphere of Mars.
  • Räisänen, Jouni (2017)
    An energy balance decomposition of temperature changes is conducted for idealized transient CO2-only simulations in the fifth phase of the Coupled Model Intercomparison Project. The multimodel global mean warming is dominated by enhanced clear-sky greenhouse effect due to increased CO2 and water vapour, but other components of the energy balance substantially modify the geographical and seasonal patterns of the change. Changes in the net surface energy flux are important over the oceans, being especially crucial for the muted warming over the northern North Atlantic and for the seasonal cycle of warming over the Arctic Ocean. Changes in atmospheric energy flux convergence tend to smooth the gradients of temperature change and reduce its land-sea contrast, but they also amplify the seasonal cycle of warming in northern North America and Eurasia. The three most important terms for intermodel differences in warming are the changes in the clear-sky greenhouse effect, clouds, and the net surface energy flux, making the largest contribution to the standard deviation of annual mean temperature change in 34, 29 and 20 % of the world, respectively. Changes in atmospheric energy flux convergence mostly damp intermodel variations of temperature change especially over the oceans. However, the opposite is true for example in Greenland and Antarctica, where the warming appears to be substantially controlled by heat transport from the surrounding sea areas.
  • Allolio, Christoph; Magarkar, Aniket; Jurkiewicz, Piotr; Baxova, Katarina; Javanainen, Matti; Mason, Philip E.; Sachl, Radek; Cebecauer, Marek; Hof, Martin; Horinek, Dominik; Heinz, Veronika; Rachel, Reinhard; Ziegler, Christine M.; Schröfel, Adam; Jungwirth, Pavel (2018)
    Arginine-rich cell-penetrating peptides do not enter cells by directly passing through a lipid membrane; they instead passively enter vesicles and live cells by inducing membrane multilamellarity and fusion. The molecular picture of this penetration mode, which differs qualitatively from the previously proposed direct mechanism, is provided by molecular dynamics simulations. The kinetics of vesicle agglomeration and fusion by an iconic cell-penetrating peptide-nonaarginine-are documented via real-time fluorescence techniques, while the induction of multilamellar phases in vesicles and live cells is demonstrated by a combination of electron and fluorescence microscopies. This concert of experiments and simulations reveals that the identified passive cell penetration mechanism bears analogy to vesicle fusion induced by calcium ions, indicating that the two processes may share a common mechanistic origin.
  • Holmstrom, E.; Kotakoski, J.; Lechner, L.; Kaiser, U.; Nordlund, K. (2012)
  • Gozaliasl, Ghassem; Finoguenov, Alexis; Tanaka, Masayuki; Dolag, Klaus; Montanari, Francesco; Kirkpatrick, Charles C.; Vardoulaki, Eleni; Khosroshahi, Habib G.; Salvato, Mara; Laigle, Clotilde; McCracken, Henry J.; Ilbert, Olivier; Cappelluti, Nico; Daddi, Emanuele; Hasinger, Guenther; Capak, Peter; Scoville, Nick Z.; Toft, Sune; Civano, Francesca; Griffiths, Richard E.; Balogh, Michael; Li, Yanxia; Ahoranta, Jussi; Mei, Simona; Iovino, Angela; Henriques, Bruno M. B.; Erfanianfar, Ghazaleh (2019)
    We present the results of a search for galaxy clusters and groups in the ∼2 deg2 of the COSMOS field using all available X-ray observations from the XMM-Newton and Chandra observatories.We reach an X-ray flux limit of 3 × 10−16 erg cm−2 s−1 in the 0.5-2 keV range, and identify 247 X-ray groups with M200c = 8 × 1012-3 × 1014M at a redshift range of 0.08 ≤ z < 1.53, using the multiband photometric redshift and the master spectroscopic redshift catalogues of the COSMOS. The X-ray centres of groups are determined using high-resolution Chandra imaging. We investigate the relations between the offset of the brightest group galaxies (BGGs) from halo X-ray centre and group properties and compare with predictions from semi-analytic models and hydrodynamical simulations. We find that BGG offset decreases with both increasing halo mass and decreasing redshift with no strong dependence on the X-ray flux and SNR. We show that the BGG offset decreases as a function of increasing magnitude gap with no considerable redshift-dependent trend. The stellar mass of BGGs in observations extends over a wider dynamic range compared to model predictions. At z < 0.5, the central dominant BGGs become more massive than those with large offsets by up to 0.3 dex, in agreement with model prediction. The observed and predicted log-normal scatter in the stellar mass of both low- and large-offset BGGs at fixed halo mass is ∼0.3 dex.
  • Magarkar, Aniket; Dhawan, Vivek; Kallinteri, Paraskevi; Viitala, Tapani; Elmowafy, Mohammed; Rog, Tomasz; Bunker, Alex (2014)
  • Owen, Michael C.; Kulig, Waldemar; Rog, Tomasz; Vattulainen, Ilpo; Strodel, Birgit (2018)
    In an effort to delineate how cholesterol protects membrane structure under oxidative stress conditions, we monitored the changes to the structure of lipid bilayers comprising 30 mol% cholesterol and an increasing concentration of Class B oxidized 1-palmitoyl-2-oleoylphosphatidylcholine (POPC) glycerophospholipids, namely, 1-palmitoyl-2-(9'-oxo-nonanoyl)-sn-glycero-3-phosphocholine (PoxnoPC), and 1-palmitoyl-2-azelaoyl-sn-glycero-3-phosphocholine (PazePC), using atomistic molecular dynamics simulations. Increasing the content of oxidized phospholipids (oxPLs) from 0 to 60 mol% oxPL resulted in a characteristic reduction in bilayer thickness and increase in area per lipid, thereby increasing the exposure of the membrane hydrophobic region to water. However, cholesterol was observed to help reduce water injury by moving into the bilayer core and forming more hydrogen bonds with the oxPLs. Cholesterol also resists altering its tilt angle, helping to maintain membrane integrity. Water that enters the 1-nm-thick core region remains part of the bulk water on either side of the bilayer, with relatively few water molecules able to traverse through the bilayer. In cholesterol-rich membranes, the bilayer does not form pores at concentrations of 60 mol% oxPL as was shown in previous simulations in the absence of cholesterol.
  • Poojari, Chetan; Zak, Agata; Dzieciuch-Rojek, Monika; Bunker, Alex; Kepczynski, Mariusz; Rog, Tomasz (2020)
    Cholesterol plays a crucial role in modulating the physicochemical properties of biomembranes, both increasing mechanical strength and decreasing permeability. Cholesterol is also a common component of vesicle-based delivery systems, including liposome-based drug delivery systems (LDSs). However, its effect on the partitioning of drug molecules to lipid membranes is very poorly recognized. Herein, we performed a combined experimental/computational study of the potential for the use of the LDS formulation for the delivery of the antifungal drug itraconazole (ITZ). We consider the addition of cholesterol to the lipid membrane. Since ITZ is only weakly soluble in water, its bioavailability is limited. Use of an LDS has thus been proposed. We studied lipid membranes composed of cholesterol, 1-palmitoyl-2-oleoyl-sn-glycerol-3-phosphocholine (POPC), and ITZ using a combination of computational molecular dynamics (MD) simulations of lipid bilayers and Brewster angle microscopy (BAM) experiments of monolayers. Both experimental and computational results show separation of cholesterol and ITZ. Cholesterol has a strong preference to orient parallel to the bilayer normal. However, ITZ, a long and relatively rigid molecule with weakly hydrophilic groups along the backbone, predominantly locates below the interface between the hydrocarbon chain region and the polar region of the membrane, with its backbone oriented parallel to the membrane surface; the orthogonal orientation in the membrane could be the cause of the observed separation. In addition, fluorescence measurements demonstrated that the affinity of ITZ for the lipid membrane is decreased by the presence of cholesterol, which is thus probably not a suitable formulation component of an LDS designed for ITZ delivery.
  • Kulig, Waldemar; Korolainen, Hanna; Zatorska, Maria; Kwolek, Urszula; Wydro, Pawel; Kepczynski, Mariusz; Rog, Tomasz (2019)
    Phosphatidic acids (PAs) have many biological functions in biomembranes, e.g., they are involved in the proliferation, differentiation, and transformation of cells. Despite decades of research, the molecular understanding of how PAs affect the properties of biomembranes remains elusive. In this study, we explored the properties of lipid bilayers and monolayers composed of PAs and phosphatidylcholines (PCs) with various acyl chains. For this purpose, the Langmuir monolayer technique and atomistic molecular dynamics (MD) simulations were used to study the miscibility of PA and PC lipids and the molecular organization of mixed bilayers. The monolayer experiments demonstrated that the miscibility of membrane components strongly depends on the structure of the hydrocarbon chains and thus on the overall lipid shape. Interactions between PA and PC molecules vary from repulsive, for systems containing lipids with saturated and unsaturated acyl tails (strongly positive values of the excess free energy of mixing), to attractive, for systems in which all lipid tails are saturated (negative values of the excess free energy of mixing). The MD simulations provided atomistic insight into polar interactions (formation of hydrogen bonds and charge pairs) in PC-PA systems. H-bonding between PA monoanions and PCs in mixed bilayers is infrequent, and the lipid molecules interact mainly via electrostatic interactions. However, the number of charge pairs significantly decreases with the number of unsaturated lipid chains in the PA-PC system. The PA dianions weakly interact with the zwitterionic lipids, but their headgroups are more hydrated as compared to the monoanionic form. The acyl chains in all PC-PA bilayers are more ordered compared to single-component PC systems. In addition, depending on the combination of lipids, we observed a deeper location of the PA phosphate groups compared to the PC phosphate groups, which can alter the presentation of PAs for the peripheral membrane proteins, affecting their accessibility for binding.
  • Lyashenko, A.; Safi, E.; Polvi, J.; Djurabekova, F.; Nordlund, K. (2020)
    Gaseous nitrogen is planned to be used as a seeding species to control the power flux in future fusion reactors with ITER-like divertors. Nitrogen interacts with the first wall materials, particularly with tungsten, leading to sputtering and changes of chemical composition of the material. We use the molecular dynamics methods with a recently developed WN potential to analyze the mechanisms leading to these modifications. We performed the simulations of cumulative nitrogen irradiation runs of tungsten surface. The sputtering yields obtained in our cumulative runs are in good agreement with experimental data. We observe the decrease of the tungsten sputtering yield with nitrogen accumulation and determine the reasons for the observed trend. The cluster analysis reveals the composition of the sputtered particles, suggesting the swift chemical sputtering process that occurs under the prolonged nitrogen irradiation of tungsten. We also observe and analyze the nitrogen saturation in the temperature range below the thermal stability limit. (C) 2020 Elsevier B.V. All rights reserved.
  • Hari, Pertti Kaarlo Juhani; Petäjä, Tuukka Taneli; Bäck, Jaana Kaarina; Kerminen, Veli-Matti; Lappalainen, Hanna K; Vihma, Timo; Laurila, Tuomas; Viisanen, Yrjö; Vesala, Timo Veikko; Kulmala, Markku Tapio (2016)
    The global environment is changing rapidly due to anthropogenic emissions and actions. Such activities modify aerosol and greenhouse gas concentrations in the atmosphere, leading to regional and global climate change and affecting, e.g., food and fresh-water security, sustainable use of natural resources and even demography. Here we present a conceptual design of a global, hierarchical observation network that can provide tools and increased understanding to tackle the inter-connected environmental and societal challenges that we will face in the coming decades. The philosophy behind the conceptual design relies on physical conservation laws of mass, energy and momentum, as well as on concentration gradients that act as driving forces for the atmosphere-biosphere exchange. The network is composed of standard, flux and/or advanced and flagship stations, each of which having specific and identified tasks. Each ecosystem type on the globe has its own characteristic features that have to be taken into consideration. The hierarchical network as a whole is able to tackle problems related to large spatial scales, heterogeneity of ecosystems and their complexity. The most comprehensive observations are envisioned to occur in flagship stations, with which the process-level understanding can be expanded to continental and global scales together with advanced data analysis, Earth system modelling and satellite remote sensing. The denser network of the flux and standard stations allows application and up-scaling of the results obtained from flagship stations to the global level.
  • Enkavi, Giray; Mikkolainen, Heikki; Gungor, Burcin; Ikonen, Elina; Vattulainen, Ilpo (2017)
    Niemann-Pick Protein C2 (NPC2) is a small soluble protein critical for cholesterol transport within and from the lysosome and the late endosome. Intriguingly, NPC2-mediated cholesterol transport has been shown to be modulated by lipids, yet the molecular mechanism of NPC2-membrane interactions has remained elusive. Here, based on an extensive set of atomistic simulations and free energy calculations, we clarify the mechanism and energetics of NPC2-membrane binding and characterize the roles of physiologically relevant key lipids associated with the binding process. Our results capture in atomistic detail two competitively favorable membrane binding orientations of NPC2 with a low interconversion barrier. The first binding mode (Prone) places the cholesterol binding pocket in direct contact with the membrane and is characterized by membrane insertion of a loop (V59-M60-G61-I62-P63-V64P65). This mode is associated with cholesterol uptake and release. On the other hand, the second mode (Supine) places the cholesterol binding pocket away from the membrane surface, but has overall higher membrane binding affinity. We determined that bis(monoacylglycero) phosphate (BMP) is specifically required for strong membrane binding in Prone mode, and that it cannot be substituted by other anionic lipids. Meanwhile, sphingomyelin counteracts BMP by hindering Prone mode without affecting Supine mode. Our results provide concrete evidence that lipids modulate NPC2-mediated cholesterol transport either by favoring or disfavoring Prone mode and that they impose this by modulating the accessibility of BMP for interacting with NPC2. Overall, we provide a mechanism by which NPC2-mediated cholesterol transport is controlled by the membrane composition and how NPC2-lipid interactions can regulate the transport rate.
  • Farahi, Arya; Mulroy, Sarah L.; Evrard, August E.; Smith, Graham P.; Finoguenov, Alexis; Bourdin, Herve; Carlstrom, John E.; Haines, Chris P.; Marrone, Daniel P.; Martino, Rossella; Mazzotta, Pasquale; O'Donnell, Christine; Okabe, Nobuhiro (2019)
    The largest clusters of galaxies in the Universe contain vast amounts of dark matter, plus baryonic matter in two principal phases, a majority hot gas component and a minority cold stellar phase comprising stars, compact objects, and low-temperature gas. Hydrodynamic simulations indicate that the highest-mass systems retain the cosmic fraction of baryons, a natural consequence of which is anti-correlation between the masses of hot gas and stars within dark matter halos of fixed total mass. We report observational detection of this anti-correlation based on 4 elements of a 9 x 9-element covariance matrix for nine cluster properties, measured from multi-wavelength observations of 41 clusters from the Local Cluster Substructure Survey. These clusters were selected using explicit and quantitative selection rules that were then encoded in our hierarchical Bayesian model. Our detection of anti-correlation is consistent with predictions from contemporary hydrodynamic cosmological simulations that were not tuned to reproduce this signal.
  • Rodriguez-Becerra, Jorge; Cáceres-Jensen, Lizethly; Díaz, Tatiana; Druker, Sofía; Bahamonde Padilla, Victor; Pernaa, Johannes; Aksela, Maija (2020)
    The purpose of this descriptive case study was to develop pre-service chemistry teachers’ Technological Pedagogical Science Knowledge (TPASK) through novel computational chemistry modules. The study consisted of two phases starting with designing a computational chemistry based learning environment followed by a case study where students’ perceptions towards educational computational chemistry were explored. First, we designed an authentic research-based chemistry learning module that supported problem-based learning through the utilization of computational chemistry methods suitable for pre-service chemistry education. The objective of the learning module was to promote learning of specific chemistry knowledge and development of scientific skills. Systematic design decisions were made through the TPASK framework. The learning module was designed for a third-year physical chemistry course taken by pre-service chemistry teachers in Chile. After the design phase, the learning module was implemented in a course and students’ perceptions were gathered using semi-structured group interviews. The sample consisted of 22 pre-service chemistry teachers. Data were analyzed through qualitative content analysis using the same TPASK framework employed in the learning module design. Based on our findings, pre-service chemistry teachers first acquired Technological Scientific Knowledge (TSK) and then developed some elements of their TPASK. In addition, they highly appreciated the combination of student-centred problem-based learning and the use of computational chemistry tools. Students felt the educational computational learning environment supported their own knowledge acquisition and expressed an interest in applying similar learning environments in their future teaching careers. This case study demonstrates that learning through authentic real-world problems using educational computational methods offers great potential in supporting pre-service teachers’ instruction in the science of chemistry and pedagogy. For further research in the TPASK framework, we propose there would be significant benefit from developing additional learning environments of this nature and evaluating their utility in pre-service and in-service chemistry teacher’s education.
  • Kaurola, Petri; Sharma, Vivek; Vonk, Amanda; Vattulainen, Ilpo; Rog, Tomasz (2016)
    Quinone and its analogues (Q) constitute an important class of compounds that perform key electron transfer reactions in oxidative- and photo-phosphorylation. In the inner membrane of mitochondria, ubiquinone molecules undergo continuous redox transitions enabling electron transfer between the respiratory complexes. In such a dynamic system undergoing continuous turnover for ATP synthesis, an uninterrupted supply of substrate molecules is absolutely necessary. In the current work, we have performed atomistic molecular dynamics simulations and free energy calculations to assess the structure, dynamics, and localization of quinone and its analogues in a lipid bilayer, whose composition mimics the one in the inner mitochondrial membrane. The results show that there is a strong tendency of both quinone and quinol molecules to localize in the vicinity of the lipids' acyl groups, right under the lipid head group region. Additionally, we observe a second location in the middle of the bilayer where quinone molecules tend to stabilize. Translocation of quinone through a lipid bilayer is very fast and occurs in 10-100 ns time scale, whereas the translocation of quinol is at least an order of magnitude slower. We suggest that this has important mechanistic implications given that the localization of Q ensures maximal occupancy of the Q-binding sites or Q-entry points in electron transport chain complexes, thereby maintaining an optimal turnover rate for ATP synthesis. (C) 2016 Elsevier B.V. All rights reserved.
  • Warnecke, Jörn; Käpylä, Petri J.; Mantere, Maarit J.; Brandenburg, Axel (2012)
  • Neuvonen, Maarit; Manna, Moutusi; Mokkila, Sini; Javanainen, Matti; Rog, Tomasz; Liu, Zheng; Bittman, Robert; Vattulainen, Ilpo; Ikonen, Elina (2014)
  • Euclid Collaboration; Knabenhans, Mischa; Stadel, Joachim; Marelli, Stefano; Potter, Doug; Teyssier, Romain; Legrand, Laurent; Schneider, Aurel; Sudret, Bruno; Blot, Linda; Awan, Saeeda; Burigana, Carlo; Carvalho, Carla Sofia; Kurki-Suonio, Hannu; Sirri, Gabriele (2019)
    We present a new power spectrum emulator named EuclidEmulator that estimates the nonlinear correction to the linear dark matter power spectrum depending on the six cosmological parameters ωb, ωm, ns, h, w0, and σ8. It is constructed using the uncertainty quantification software UQLab using a spectral decomposition method called polynomial chaos expansion. All steps in its construction have been tested and optimized: the large highresolution N-body simulations carried out with PKDGRAV3 were validated using a simulation from the Euclid Flagship campaign and demonstrated to have converged up to wavenumbers k ≈ 5 h Mpc−1 for redshifts z ≤ 5. The emulator is based on 100 input cosmologies simulated in boxes of (1250 Mpc/h)3 using 20483 particles. We show that by creating mock emulators it is possible to successfully predict and optimize the performance of the final emulator prior to performing any N-body simulations. The absolute accuracy of the final nonlinear power spectrum is as good as one obtained with N-body simulations, conservatively, ∼1 per cent for k 1 h Mpc−1 and z 1. This enables efficient forward modelling in the nonlinear regime, allowing for estimation of cosmological parameters using Markov ChainMonteCarlo methods. EuclidEmulator has been compared to HALOFIT, CosmicEmu, and NGenHalofit, and shown to be more accurate than these other approaches. This work paves a new way for optimal construction of future emulators that also consider other cosmological observables, use higher resolution input simulations, and investigate higher dimensional cosmological parameter spaces.