| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Laurent, Timothée, et al.
(författare)
-
Architecture of the chikungunya virus replication organelle
- 2022
-
Ingår i: eLIFE. - : eLife Sciences Publications. - 2050-084X. ; 11
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Tidskriftsartikel (refereegranskat)abstract
- Alphaviruses are mosquito-borne viruses that cause serious disease in humans and other mammals. Along with its mosquito vector, the Alphavirus chikungunya virus (CHIKV) has spread explosively in the last 20 years, and there is no approved treatment for chikungunya fever. On the plasma membrane of the infected cell, CHIKV generates dedicated organelles for viral RNA replication, so-called spherules. Whereas structures exist for several viral proteins that make up the spherule, the architecture of the full organelle is unknown. Here, we use cryo-electron tomography to image CHIKV spherules in their cellular context. This reveals that the viral protein nsP1 serves as a base for the assembly of a larger protein complex at the neck of the membrane bud. Biochemical assays show that the viral helicase-protease nsP2, while having no membrane affinity on its own, is recruited to membranes by nsP1. The tomograms further reveal that full-sized spherules contain a single copy of the viral genome in double-stranded form. Finally, we present a mathematical model that explains the membrane remodeling of the spherule in terms of the pressure exerted on the membrane by the polymerizing RNA, which provides a good agreement with the experimental data. The energy released by RNA polymerization is found to be sufficient to remodel the membrane to the characteristic spherule shape.
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| 3. |
- Moberg, Christina, et al.
(författare)
-
De unga gör helt rätt när de stämmer staten
- 2022
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Ingår i: Aftonbladet. - 1103-9000.
-
Tidskriftsartikel (populärvet., debatt m.m.)abstract
- 1 620 forskare och lärare i forskarvärlden: Vi ställer oss bakom Auroras klimatkrav
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| 4. |
- Swift, Imogen J, et al.
(författare)
-
A systematic review of progranulin concentrations in biofluids in over 7,000 people-assessing the pathogenicity of GRN mutations and other influencing factors.
- 2024
-
Ingår i: Alzheimer's Research & Therapy. - 1758-9193. ; 16:1
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Tidskriftsartikel (refereegranskat)abstract
- Pathogenic heterozygous mutations in the progranulin gene (GRN) are a key cause of frontotemporal dementia (FTD), leading to significantly reduced biofluid concentrations of the progranulin protein (PGRN). This has led to a number of ongoing therapeutic trials aiming to treat this form of FTD by increasing PGRN levels in mutation carriers. However, we currently lack a complete understanding of factors that affect PGRN levels and potential variation in measurement methods. Here, we aimed to address this gap in knowledge by systematically reviewing published literature on biofluid PGRN concentrations.Published data including biofluid PGRN concentration, age, sex, diagnosis and GRN mutation were collected for 7071 individuals from 75 publications. The majority of analyses (72%) had focused on plasma PGRN concentrations, with many of these (56%) measured with a single assay type (Adipogen) and so the influence of mutation type, age at onset, sex, and diagnosis were investigated in this subset of the data.We established a plasma PGRN concentration cut-off between pathogenic mutation carriers and non-carriers of 74.8ng/mL using the Adipogen assay based on 3301 individuals, with a CSF concentration cut-off of 3.43ng/mL. Plasma PGRN concentration varied by GRN mutation type as well as by clinical diagnosis in those without a GRN mutation. Plasma PGRN concentration was significantly higher in women than men in GRN mutation carriers (p=0.007) with a trend in non-carriers (p=0.062), and there was a significant but weak positive correlation with age in both GRN mutation carriers and non-carriers. No significant association was seen with weight or with TMEM106B rs1990622 genotype. However, higher plasma PGRN levels were seen in those with the GRN rs5848 CC genotype in both GRN mutation carriers and non-carriers.These results further support the usefulness of PGRN concentration for the identification of the large majority of pathogenic mutations in the GRN gene. Furthermore, these results highlight the importance of considering additional factors, such as mutation type, sex and age when interpreting PGRN concentrations. This will be particularly important as we enter the era of trials for progranulin-associated FTD.
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| 5. |
- Andersson, Björn O, 1982, et al.
(författare)
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A Modified TAB Model for Simulation of Atomization in Rotary Bell Spray Painting
- 2013
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Ingår i: Journal of Mechanical Engineering and Automation. - 2163-2413. ; 3:2, s. 54-61
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Tidskriftsartikel (refereegranskat)abstract
- The Rotary bell spray applicator technique is commonly used in the automotive industry for paint application because of its high transfer efficiency and high-quality result. The bell spins rapidly around its axis with a tangential velocity at the edge in the order of 100 m/s. The paint falls off the edge and enters the air with a large relative velocity, driving the atomization into small droplets where the resulting size distribution depends on the process conditions. Especially the rotation speed of the bell is an important parameter governing the size distribution. The main research question in this work is to investigate if the Taylor Analogy Breakup (TAB) model can be used to predict the resulting droplet size distributions in spray painting. As the paint is a viscous fluid a modification of the TAB model taking non-linear effects of large viscosity into account is proposed. The parameters in the breakup model are tuned by optimization to match droplet size distributions obtained in CFD simulations with measured ones. Results are presented for three cases with rotation speeds from 30 to 50 thousand RPM where the full droplet size distributions are compared with measurements. Good results are obtained for all three cases where the simulated size distributions compare well to measurements over a wide range of droplet sizes. The TAB method is able to quantitatively predict the result of the breakup process and can be used in a preprocessing stage of a full spray painting simulation, thereby reducing the need for costly and cumbersome measurements.
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| 6. |
- Andersson, Björn O, 1982, et al.
(författare)
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Modified TAB Model for Viscous Fluids applied to Breakup in Rotary Bell Spray Painting
- 2012
-
Ingår i: ICLASS 2012 - 12th International Conference on Liquid Atomization and Spray Systems.
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Konferensbidrag (refereegranskat)abstract
- The Taylor Analogy Breakup (TAB) model is applied to droplet breakup in rotary bell spray painting commonly used in the automotive industry. The bell spins rapidly around its axis with a tangential velocity at the edge in the order of 100 m/s. The paint falls off the edge and enters the air with a large relative velocity, driving the atomization. The paint is a viscous fluid and a modification of the TAB model taking non-linear effects of large viscosity into account is described. The parameters in the breakup model are tuned to match droplet size distributions obtained in CFD simulations with measured ones. Results are presented for three cases with rotation speeds from 30 to 50 thousand RPM where the full droplet size distributions are compared with measurements. Good results are obtained for all three cases where the simulated size distributions compare well to measurements over a wide range of droplet sizes. The obtained results can be used in a preprocessing stage of a full spray painting simulation thereby reducing the need for costly and cumbersome measurements.
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| 7. |
- Carlson, Andreas, 1981-
(författare)
-
Capillarity and dynamic wetting
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- In this thesis capillary dominated two–phase flow is studied by means of nu- merical simulations and experiments. The theoretical basis for the simulations consists of a phase field model, which is derived from the system’s thermody- namics, and coupled with the Navier Stokes equations. Two types of interfacial flow are investigated, droplet dynamics in a bifurcating channel and sponta- neous capillary driven spreading of drops.Microfluidic and biomedical applications often rely on a precise control of droplets as they traverse through complicated networks of bifurcating channels. Three–dimensional simulations of droplet dynamics in a bifurcating channel are performed for a set of parameters, to describe their influence on the resulting droplet dynamics. Two distinct flow regimes are identified as the droplet in- teracts with the tip of the channel junction, namely, droplet splitting and non- splitting. A flow map based on droplet size and Capillary number is proposed to predict whether the droplet splits or not in such a geometry.A commonly occurring flow is the dynamic wetting of a dry solid substrate. Both experiments and numerical simulations of the spreading of a drop are presented here. A direct comparison of the two identifies a new parameter in the phase field model that is required to accurately predict the experimental spreading behavior. This parameter μf [P a · s], is interpreted as a friction factor at the moving contact line. Comparison of simulations and experiments for different liquids and surface wetting properties enabled a measurement of the contact line friction factor for a wide parameter space. Values for the contact line friction factor from phase field theory are reported here for the first time.To identify the physical mechanism that governs the droplet spreading, the different contributions to the flow are measured from the simulations. An im- portant part of the dissipation may arise from a friction related to the motion of the contact line itself, and this is found to be dominating both inertia and viscous friction adjacent to the contact line. A scaling law based on the con- tact line friction factor collapses the experimental data, whereas a conventional inertial or viscous scaling fails to rationalize the experimental observation, supporting the numerical finding.
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| 8. |
- Carlson, Andreas, et al.
(författare)
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Contact line dissipation in short-time dynamic wetting
- 2012
-
Ingår i: Europhysics letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 97:4
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Tidskriftsartikel (refereegranskat)abstract
- Dynamic wetting of a solid surface is a process that is ubiquitous in Nature, and also of increasing technological importance. The underlying dissipative mechanisms are, however, still unclear. We present here short-time dynamic wetting experiments and numerical simulations, based on a phase field approach, of a droplet on a dry solid surface, where direct comparison of the two allows us to evaluate the different contributions from the numerics. We find that an important part of the dissipation may arise from a friction related to the motion of the contact line itself, and that this may be dominating both inertia and viscous friction in the flow adjacent to the contact line. A contact line friction factor appears in the theoretical formulation that can be distinguished and quantified, also in room temperature where other sources of dissipation are present. Water and glycerin-water mixtures on various surfaces have been investigated where we show the dependency of the friction factor on the nature of the surface, and the viscosity of the liquid.
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| 9. |
- Carlson, Andreas, et al.
(författare)
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Dissipation in rapid dynamic wetting
- 2011
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Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press (CUP). - 0022-1120 .- 1469-7645. ; 682, s. 213-240
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Tidskriftsartikel (refereegranskat)abstract
- In this article, we present a modelling approach for rapid dynamic wetting based on the phase field theory. We show that in order to model this accurately, it is important to allow for a non-equilibrium wetting boundary condition. Using a condition of this type, we obtain a direct match with experimental results reported in the literature for rapid spreading of liquid droplets on dry surfaces. By extracting the dissipation of energy and the rate of change of kinetic energy in the flow simulation, we identify a new wetting regime during the rapid phase of spreading. This is characterized by the main dissipation to be due to a re-organization of molecules at the contact line, in a diffusive or active process. This regime serves as an addition to the other wetting regimes that have previously been reported in the literature.
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| 10. |
- Carlson, Andreas, et al.
(författare)
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Droplet dynamics in a bifurcating channel
- 2010
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Ingår i: International Journal of Multiphase Flow. - : Elsevier BV. - 0301-9322 .- 1879-3533. ; 36:5, s. 397-405
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Tidskriftsartikel (refereegranskat)abstract
- In the present paper we present a phenomenological description of droplet dynamics in a bifurcating channel that is based on three-dimensional numerical experiments using the Phase Field theory. Droplet dynamics is investigated in a junction, which has symmetric outflow conditions in its daughter branches. We identify two different flow regimes as the droplets interact with the tip of the bifurcation, splitting and non-splitting. A distinct criterion for the flow regime transition is found based on the initial droplet volume and the Capillary (Ca) number. The Rayleigh Plateau instability is identified as a driving mechanism for the droplet breakup close to the threshold between the splitting and non-splitting regime.
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| 11. |
- Carlson, Andreas, et al.
(författare)
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Measuring contact line dissipation in dynamic wetting
- 2011
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Dynamic wetting of a solid surface is a process that is ubiquitous in nature, and also of increasing technological importance. The underlying dissipative mechanisms are however still unclear. We present here dynamic wetting experiments of a droplet on a dry surface, showing that an important part of the dissipation may arise from a friction related to the motion of the contact line itself, and that this may be dominating the viscous friction in the flow adjacent to the contact line. By a combination of simulations and experiments, values of a corresponding friction factor are obtained. By this procedure the contact line friction factor can be distinguished and quantified, also in room temperature where other sources of dissipation are present. Water and glycerin-water mixtures on various surfaces have been investigated. We show the dependency of the friction factor on the nature of the surface, and the viscosity of the liquid.
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| 12. |
- Carlson, Andreas, et al.
(författare)
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Modeling of dynamic wetting far from equilibrium
- 2009
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Ingår i: Physics of fluids. - : AIP Publishing. - 1070-6631 .- 1089-7666. ; 21:12
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we present simulations of dynamic wetting far from equilibrium based on phase field theory. In direct simulations of recent experiments [J. C. Bird, S. Mandre, and H. A. Stone, Phys. Rev. Lett. 100, 234501 (2008)], we show that in order to correctly capture the dynamics of rapid wetting, it is crucial to account for nonequilibrium at the contact line, where the gas, liquid, and solid meet. A term in the boundary condition at the solid surface that naturally arises in the phase field theory is interpreted as allowing for the establishment of a local structure in the immediate vicinity of the contact line. A direct qualitative and quantitative match with experimental data of spontaneously wetting liquid droplets is shown.
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| 13. |
- Carlson, Andreas, et al.
(författare)
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Prediction of Two-Phase Flow in Small Tubes : A Systematic Comparison of State-of-The-Art CMFD Codes
- 2008
-
Ingår i: 5th European Thermal-Sciences Conference (EUROTHERM).
-
Konferensbidrag (refereegranskat)abstract
- Multiphase dynamics and its characteristics for two-phase gas-liquid flow have been investigatedby means of advanced numerical simulations. Although important in many engineering applications, methods for robust and accurate simulations for high density and viscosity ratios remainelusive. A comprehensive comparison of two state-of-the-art Computational Multi–Fluid Dynamics (CMFD) codes, Fluent and TransAT, have been performed. The two commonly usedmethods for two–phase flow simulations, namely Volume of Fluid implemented in Fluent andLevel Set implemented in TransAT, could be compared as a result. Significant differences wereobserved between the two flow topologies predicted by the two codes. For the bubbly flow case,a recirculating flow was predicted inside the bubbles by TransAT, meanwhile no significantrecirculation was observed in the solution with Fluent. For the slug flow case a significantdeviation was observed between the results from Fluent and TransAT on the slug formationand frequency. Periodic slug formation was observed with TransAT, in agreement with theexperimental result of Chen et al. [4]. A periodic slug formation was not obtained with Fluent.
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| 14. |
- Carlson, Andreas, et al.
(författare)
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Short and long time drop dynamics on lubricated substrates
- 2013
-
Ingår i: Europhysics letters. - : IOP Publishing. - 0295-5075 .- 1286-4854. ; 104:3, s. 34008-
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Tidskriftsartikel (refereegranskat)abstract
- Liquid infiltrated solids have been proposed as functional solvent-phobic surfaces for handling single and multiphase flows. Implementation of such surfaces alters the interfacial transport phenomenon as compared to a dry substrate. To better understand the interface characteristics in such systems we study experimentally the dynamics of a pendant water drop in air that contacts a substrate coated by thin oil films. At short times the water drop is deformed by the oil that spreads onto the water-air interface, and the dynamics are characterized by inertial and viscous regimes. At late times, the the oil film under the drop relaxes either to a stable thin film or ruptures. In the thin film rupture regime, we measure the waiting time for the rupture as a function of the drop equilibrium contact angle on a dry substrate and the initial film height. The waiting time is rationalized by lubrication theory, which indicates that long-range intermolecular forces destabilize the oil-water interface and is the primary mechanism for the film drainage.
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| 15. |
- Carlson, Andreas, et al.
(författare)
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Universality in dynamic wetting dominated by contact-line friction
- 2012
-
Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 85:4, s. 045302-
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Tidskriftsartikel (refereegranskat)abstract
- We report experiments on the rapid contact-line motion present in the early stages of capillary-driven spreading of drops on dry solid substrates. The spreading data fail to follow a conventional viscous or inertial scaling. By integrating experiments and simulations, we quantify a contact-line friction mu(f) which is seen to limit the speed of the rapid dynamic wetting. A scaling based on this contact-line friction is shown to yield a universal curve for the evolution of the contact-line radius as a function of time, for a range of fluid viscosities, drop sizes, and surface wettabilities.
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| 16. |
- Carlson, Benny, et al.
(författare)
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Lossa bromsen på det etniska företagandet
- 2016
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Ingår i: Expressen. - 1103-923X.
-
Tidskriftsartikel (populärvet., debatt m.m.)abstract
- De samhälleliga och mänskliga kostnaderna för långvarigt utanförskap är förödande.Exemplet med den somaliska integrationen i Minnesota i USA visar att det skulle kunna vara annorlunda – men det kräver att vi gör upp med vår misstänksamhet mot etniskt företagande, skriver Benny Carlsson och Andreas Johansson Heinö.
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| 17. |
- Carlson, Johan E., et al.
(författare)
-
Estimation of dielectric properties of crude oils based on IR spectroscopy
- 2014
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Ingår i: Chemometrics and Intelligent Laboratory Systems. - : Elsevier BV. - 0169-7439 .- 1873-3239. ; 139, s. 1-5
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Tidskriftsartikel (refereegranskat)abstract
- Dielectric properties of crude oils play an important role in characterization and quality control. Measuring permittivity accurately over a wide range of frequencies is, however, a time-consuming task and existing measurement methods are not easily adapted for real-time diagnostics. IR spectroscopy, on the other hand, provides rapid measurements of fundamental molecular properties.In this paper we show that by using multivariate calibration tools such as PLS regression, it is possible to extract dielectric properties of crude oils directly from IR spectra, in addition to conventional interpretation of the spectra, hence reducing the need for direct electrical measurements. Results on 16 different oil samples show that the dielectric parameters obtained with the proposed method agree well with those obtained using direct permittivity measurements. The PLS regression method has also been extended with Monte-Carlo simulation capabilities to account for uncertainties in the data
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| 18. |
- Carlson, Per-Olof, et al.
(författare)
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Systemet Hållbara Byggnader: Bedömningsgrunder för innemiljön
- 2004
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- I föreliggande rapport har krav på byggnaders innemiljö sammanställts som kan användas som funktionskrav eller för att klassa byggnader. Bara sådana komfortrelaterade innemiljöaspekter som har en sådan status att de kan anses vara allmänt accepterade ingår och benämns här innemiljökomfort. Systemet Hållbara Byggnader hanterar utöver innemiljökomfort även energianvändning och miljöpåverkan. Målet med rapporten är att komplettera systemet Hållbara Byggnader med krav på innemiljökomfort, och därigenom täcka in alla miljöaspekter inklusive ohälsa som kan kopplas till mänsklig hälsa. Ohälsa ingår som en del av miljöpåverkan och är en aspekt som man vill minska, medan innemiljökomfort är en aspekt som man försöker förbättra. Visionen är därmed att systemet Hållbara Byggnader på ett heltäckande sätt hanterar de mest betydelsefulla aspekterna som kan relateras till begreppet hållbara byggnader. Innemiljökomfort hanteras med egenskapskrav samt påverkanskrav. Egenskapskrav är sådana (mätbara) egenskaper som kan bestämmas i en befintlig byggnad eller vid projektering. Påverkanskrav för innemiljökomfort baseras på brukarens upplevelse och självskattning och hanteras med hjälp av enkäter.
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| 19. |
- Ceballos, Germán, et al.
(författare)
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Analyzing Graphics Workloads on Tile-based GPUs
- 2017
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Ingår i: Proc. 20th International Symposium on Workload Characterization. - : IEEE. - 9781538612330 ; , s. 108-109
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Konferensbidrag (refereegranskat)
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| 20. |
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| 21. |
- Dahlstedt, Magnus, 1975-, et al.
(författare)
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Systemet med fritt skolval måste bytas ut
- 2018
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Ingår i: Svenska Dagbladet. - Stockholm, Sweden : Svenska Dagbladet AB & Co.. - 1101-2412.
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Tidskriftsartikel (populärvet., debatt m.m.)
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| 22. |
- Edelvik, Fredrik, 1972, et al.
(författare)
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Math-Based Algorithms and Software for Virtual Product Realization Implemented in Automotive Paint Shops
- 2017
-
Ingår i: Math for the Digital Factory. - 2198-3283. ; 27, s. 231-251
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Tidskriftsartikel (refereegranskat)abstract
- We present a simulation framework that makes it possible to accurately simulate spray painting of e.g. a truck cab in only a few hours on a standard computer. This is an extreme improvement compared to earlier approaches that require weeks of simulation time. Unique algorithms for coupled simulations of air flows, electrostatic fields and charged paint particles make this possible. In addition, we demonstrate that the same framework can be used to efficiently simulate the laydown of sealing or adhesive material. In the virtual paint factory the production preparation process can be performed in the computer, which allows the engineers to replace physical prototypes with virtual ones to shorten the lead time in product development, and avoid future unforeseen technological and environmental problems that can be extremely costly if they are discovered at the end of the production line, or even worse by the costumer.
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| 23. |
- Egan, Allyson C, et al.
(författare)
-
The Sound of Interconnectivity; The European Vasculitis Society 2022 Report
- 2022
-
Ingår i: Kidney International Reports. - : Elsevier BV. - 2468-0249. ; 7:8, s. 1745-1757
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Tidskriftsartikel (refereegranskat)abstract
- The first European Vasculitis Society (EUVAS) meeting report was published in 2017. Herein, we report on developments in the past 5 years which were greatly influenced by the pandemic. The adaptability to engage virtually, at this critical time in society, embodies the importance of networks and underscores the role of global collaborations. We outline state-of-the-art webinar topics, updates on developments in the last 5 years, and proposals for agendas going forward. A host of newly reported clinical trials is shaping practice on steroid minimization, maintenance strategies, and the role of newer therapies. To guide longer-term strategies, a longitudinal 10-year study investigating relapse, comorbidity, malignancy, and survival rates is at an advanced stage. Disease assessment studies are refining classification criteria to differentiate forms of vasculitis more fully. A large international validation study on the histologic classification of anti-neutrophil cytoplasmic antibody (ANCA) glomerulonephritis, recruiting new multicenter sites and comparing results with the Kidney Risk Score, has been conducted. Eosinophilic granulomatosis with polyangiitis (EGPA) genomics offers potential pathogenic subset and therapeutic insights. Among biomarkers, ANCA testing is favoring immunoassay as the preferred method for diagnostic evaluation. Consolidated development of European registries is progressing with an integrated framework to analyze large clinical data sets on an unprecedented scale.
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| 24. |
- Feneuil, Blandine, et al.
(författare)
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Experimental and numerical investigation of bubble migration in shear flow : Deformability-driven chaining and repulsion
- 2023
-
Ingår i: Physical Review Fluids. - : American Physical Society (APS). - 2469-990X. ; 8:6
-
Tidskriftsartikel (refereegranskat)abstract
- We study the interaction-induced migration of bubbles in shear flow and observe that bubbles suspended in elastoviscoplastic emulsions organize into chains aligned in the flow direction, similarly to particles in viscoelastic fluids. To investigate the driving mechanism, we perform experiments and simulations on bubble pairs, using suspending fluids with different rheological properties. First, we notice that, for all fluids, the interaction type depends on the relative position of the bubbles. If they are aligned in the vorticity direction, then they repel, if not, then they attract each other. The simulations show a similar behavior in Newtonian fluids as in viscoelastic and elastoviscoplastic fluids, as long as the capillary number is sufficiently large. This shows that the interaction-related migration of the bubbles is strongly affected by the bubble deformation. We suggest that the cause of migration is the interaction between the heterogeneous pressure fields around the deformed bubbles, due to capillary pressure.
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| 25. |
- Ferrara, Giovanni, et al.
(författare)
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Idiopathic pulmonary fibrosis in Sweden : report from the first year of activity of the Swedish IPF-Registry.
- 2016
-
Ingår i: European Clinical Respiratory Journal. - : Informa UK Limited. - 2001-8525. ; 3
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Idiopathic pulmonary fibrosis (IPF) is an emerging problem in the western world, being related to increasing age and implying significant costs for the diagnosis and management of affected patients. The epidemiology of IPF is not well understood.METHODS: To allow estimates of the problem and eventually to evaluate quality of the care of IPF patients in Sweden, a national IPF Registry was started in the autumn of 2014. Data on criteria used to diagnose IPF, demographics, lung function, and quality of life (measured with the King's Brief Interstitial Lung Disease Questionnaire, K-BILD) were reported directly to the registry, based at the coordinating centre (Karolinska University Hospital, Stockholm, Sweden) via a web-based platform.RESULTS: During the first year, the registry was implemented in 11 (33%) of the 33 respiratory units in the country. Seventy-one patients were registered between October 2014 and October 2015, 50 (70.4%) males and 21 (29.6%) females. Median age was 70 (range 47-86). The mean K-BILD score at the first inclusion in the registry was 54.3+9.5.CONCLUSIONS: The main features of IPF patients in this first Swedish cohort were consistent with data published in the literature in main multinational randomized controlled trials. The K-BILD questionnaire showed that quality of life of patients with IPF and their perception of the disease are quite poor at the time of inclusion in the registry.
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| 26. |
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| 27. |
- Galván, Ignacio Fdez., et al.
(författare)
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OpenMolcas : From Source Code to Insight
- 2019
-
Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 15:11, s. 5925-5964
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Tidskriftsartikel (refereegranskat)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.
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| 28. |
- Hashemi, Helya, et al.
(författare)
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Localized IgG4-related disease manifested on the tongue : a case report
- 2021
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Ingår i: Upsala Journal of Medical Sciences. - : Upsala Medical Society. - 0300-9734 .- 2000-1967. ; 126:1
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Tidskriftsartikel (refereegranskat)abstract
- Immunoglobulin G4-related disease (IgG4-RD) is an immune-mediated fibroinflammatory condition that can affect multiple organs. IgG4-RD may show a variety of initial symptoms. In the oral mucosa, lesions present as inflammatory fibrosis with a large number of IgG4-positive plasma cells. Evaluating treatment is a well-known problem in IgG4-RD due to the absence of an established assessment system. There are difficulties in defining the severity of the disease, which is why treatment is primarily based on its clinical manifestations. We present a case report of localized IgG4-RD with ulcerative and proliferative manifestations on the tongue, which clinically mimicked oral squamous cell carcinoma. A tumor-like lesion on the tongue can indicate something else other than the malignant or reactive changes commonly found in the oral mucosa. Multiple differential diagnoses of these atypical oral lesions, including localized IgG4-RD, should be considered.
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| 29. |
- Herum, Kate M., et al.
(författare)
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Syndecan-4 Protects the Heart From the Profibrotic Effects of Thrombin-Cleaved Osteopontin
- 2020
-
Ingår i: Journal of the American Heart Association. - 2047-9980. ; 9:3, s. 013518-013518
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Pressure overload of the heart occurs in patients with hypertension or valvular stenosis and induces cardiac fibrosis because of excessive production of extracellular matrix by activated cardiac fibroblasts. This initially provides essential mechanical support to the heart, but eventually compromises function. Osteopontin is associated with fibrosis; however, the underlying signaling mechanisms are not well understood. Herein, we examine the effect of thrombin-cleaved osteopontin on fibrosis in the heart and explore the role of syndecan-4 in regulating cleavage of osteopontin. Methods and Results: Osteopontin was upregulated and cleaved by thrombin in the pressure-overloaded heart of mice subjected to aortic banding. Cleaved osteopontin was higher in plasma from patients with aortic stenosis receiving crystalloid compared with blood cardioplegia, likely because of less heparin-induced inhibition of thrombin. Cleaved osteopontin and the specific osteopontin peptide sequence RGDSLAYGLR that is exposed after thrombin cleavage both induced collagen production in cardiac fibroblasts. Like osteopontin, the heparan sulfate proteoglycan syndecan-4 was upregulated after aortic banding. Consistent with a heparan sulfate binding domain in the osteopontin cleavage site, syndecan-4 was found to bind to osteopontin in left ventricles and cardiac fibroblasts and protected osteopontin from cleavage by thrombin. Shedding of the extracellular part of syndecan-4 was more prominent at later remodeling phases, at which time levels of cleaved osteopontin were increased. Conclusions: Thrombin-cleaved osteopontin induces collagen production by cardiac fibroblasts. Syndecan-4 protects osteopontin from cleavage by thrombin, but this protection is lost when syndecan-4 is shed in later phases of remodeling, contributing to progression of cardiac fibrosis.
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| 30. |
- Huo, Yan, et al.
(författare)
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Effects of baseline P-wave duration and choice of atrial septal pacing site on shortening atrial activation time during pacing.
- 2012
-
Ingår i: Europace. - : Oxford University Press (OUP). - 1532-2092 .- 1099-5129. ; 14:9, s. 1294-1301
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Atrial septal pacing (ASP) has been shown to shorten P-wave duration (PWD) and reduce recurrence of atrial fibrillation (AF) in patients with bradyarrhythmias. However, variability of interatrial connections and atrial conduction properties may explain ASP's modest clinical benefit. The aim of this study was to assess the effect of ASP site on the duration of the paced P wave. METHODS AND RESULTS: Atrial septal pacing at high atrial septum (HAS), posterior septum behind the fossa ovalis (PSFO), and coronary sinus ostium (CSo) was performed in 69 patients admitted for electrophysiological study (52 ± 16 years, 41 men). Twelve-lead electrocardiogram was recorded at baseline and during pacing, signal-averaged for analysis of PWD and P-wave shortening achieved by ASP (ΔPWD = paced PWD-baseline PWD). Baseline PWD was 128 ± 15 ms. The shortest PWD during pacing was achieved at CSo (112 ± 15 ms) followed by HAS (122 ± 14 ms, P< 0.001 vs. CSo) and PSFO (124 ± 21 ms, P< 0.001 vs. CSo). P wave was shortened during pacing in patients with baseline PWD of > 120 ms (n= 50), whereas those with PWD of ≤ 120 ms showed PWD lengthening (n= 19) when paced at HAS (8 ± 17 vs. -12 ± 15 ms, P< 0.001), PSFO (15 ± 17 vs. -12 ± 26 ms, P< 0.001) and CSo (6 ± 16 vs. -25 ± 18 ms, P< 0.001). CONCLUSION: Pacing at CSo is associated with the shortest PWD. P-wave shortening is greatest in patients with baseline PWD of > 120 ms regardless of the pacing site. The results may have implications on the selection of candidates for ASP and the placement of the atrial septal lead, and warrant further evaluation in cases of permanent pacing in patients with paroxysmal AF.
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| 31. |
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| 32. |
- Johansson, Petter, et al.
(författare)
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Water-substrate physico-chemistry in wetting dynamics
- 2015
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Ingår i: Journal of Fluid Mechanics. - : Cambridge University Press. - 0022-1120 .- 1469-7645. ; 781, s. 695-711
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Tidskriftsartikel (refereegranskat)abstract
- We consider the wetting of water droplets on substrates with different chemical composition and molecular spacing, but with an identical equilibrium contact angle. A combined approach of large-scale molecular dynamics simulations and a continuum phase field model allows us to identify and quantify the influence of the microscopic physics at the contact line on the macroscopic droplet dynamics. We show that the substrate physico-chemistry, in particular hydrogen bonding, can significantly alter the flow. Since the material parameters are systematically derived from the atomistic simulations, our continuum model has only one adjustable parameter, which appears as a friction factor at the contact line. The continuum model approaches the atomistic wetting rate only when we adjust this contact line friction factor. However, the flow appears to he qualitatively different when comparing the atomistic and continuum models, highlighting that non-trivial continuum effects can come into play near the interface of the wetting front.
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| 33. |
- Kirkinen, Tita, et al.
(författare)
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Accuracy of the Swedish quality registry for caries and periodontal diseases (SKaPa) – evaluation in 6- and 12-year-olds in the region of Värmland, Sweden
- 2023
-
Ingår i: Acta Odontologica Scandinavica. - : Taylor & Francis. - 0001-6357 .- 1502-3850. ; 81:8, s. 615-621
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Tidskriftsartikel (refereegranskat)abstract
- Objectives This study evaluates the agreement of data on dental caries between electronic dental records and data retrieved from the national SKaPa-registry (Swedish Quality Registry for caries and periodontal disease), with special reference to e/M in deft/DMFT.Methods In a random sample of 500 6- and 12-year-old children having received dental care in 2014 in the county region of Värmland, Sweden, the diagnostic accuracy of data in electronic dental records with corresponding data obtained from the SKaPa-registry was compared by using Cohen’s Kappa and Intraclass correlation coefficient (ICC).Results For dft/DFT the Kappa was 0.95, and ICC 0.98 (total population). For deft/DMFT in the total population the Kappa was 0.80 and ICC 0.96. For 6-year-olds (deft) the Kappa was 0.89 and ICC 0.99 and for 12-year-olds (DMFT) the Kappa was 0.70, and ICC 0.83. The corresponding figures for Kappa and ICC when excluding individuals without caries (deft/DMFT = 0) were: Total population 0.63 and 0.94; 6-year-olds 0.79 and 0.99; 12-year-olds 0.42 and 0.68.Conclusion Agreement between data in the dental records and SKaPa was very high for dft/DFT confirming that transfer from the dental records to the SKaPa-registry is safe and correct. As the accuracy of deft/DMFT was considerably lower than for dft/DFT we advise against using deft/DMFT data from SKaPa for research purposes at this point.
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| 34. |
- Krueger, Martin W., et al.
(författare)
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In-silico modeling of atrial repolarization in normal and atrial fibrillation remodeled state
- 2013
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Ingår i: Medical & Biological Engineering & Computing. - : Springer Science and Business Media LLC. - 0140-0118 .- 1741-0444. ; 51:10, s. 1105-1119
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Tidskriftsartikel (refereegranskat)abstract
- Atrial fibrillation (AF) is the most common cardiac arrhythmia, and the total number of AF patients is constantly increasing. The mechanisms leading to and sustaining AF are not completely understood yet. Heterogeneities in atrial electrophysiology seem to play an important role in this context. Although some heterogeneities have been used in in-silico human atrial modeling studies, they have not been thoroughly investigated. In this study, the original electrophysiological (EP) models of Courtemanche et al., Nygren et al. and Maleckar et al. were adjusted to reproduce action potentials in 13 atrial regions. The parameter sets were validated against experimental action potential duration data and ECG data from patients with AV block. The use of the heterogeneous EP model led to a more synchronized repolarization sequence in a variety of 3D atrial anatomical models. Combination of the heterogeneous EP model with a model of persistent AF-remodeled electrophysiology led to a drastic change in cell electrophysiology. Simulated Ta-waves were significantly shorter under the remodeling. The heterogeneities in cell electrophysiology explain the previously observed Ta-wave effects. The results mark an important step toward the reliable simulation of the atrial repolarization sequence, give a deeper understanding of the mechanism of atrial repolarization and enable further clinical investigations.
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| 35. |
- Köksal, Elif Senem, et al.
(författare)
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Nanotube-Mediated Path to Protocell Formation
- 2019
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Ingår i: ACS Nano. - : American Chemical Society (ACS). - 1936-086X .- 1936-0851.
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Tidskriftsartikel (refereegranskat)abstract
- Cellular compartments are membrane-enclosed, spatially distinct microenvironments that confine and protect biochemical reactions in the biological cell. On the early Earth, the autonomous formation of compartments is thought to have led to the encapsulation of nucleotides, thereby satisfying a starting condition for the emergence of life. Recently, surfaces have come into focus as potential platforms for the self-assembly of prebiotic compartments, as significantly enhanced vesicle formation was reported in the presence of solid interfaces. The detailed mechanism of such formation at the mesoscale is still under discussion. We report here on the spontaneous transformation of solid-surface-adhered lipid deposits to unilamellar membrane compartments through a straightforward sequence of topological changes, proceeding via a network of interconnected lipid nanotubes. We show that this transformation is entirely driven by surface-free energy minimization and does not require hydrolysis of organic molecules or external stimuli such as electrical currents or mechanical agitation. The vesicular structures take up and encapsulate their external environment during formation and can subsequently separate and migrate upon exposure to hydrodynamic flow. This may link the self-directed transition from weakly organized bioamphiphile assemblies on solid surfaces to protocells with secluded internal contents.
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| 36. |
- Köksal, Elif Senem, et al.
(författare)
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Rapid Growth and Fusion of Protocells in Surface-Adhered Membrane Networks
- 2020
-
Ingår i: Small. - : Wiley. - 1613-6810 .- 1613-6829. ; 16:38
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Tidskriftsartikel (refereegranskat)abstract
- Elevated temperatures might have promoted the nucleation, growth, and replication of protocells on the early Earth. Recent reports have shown evidence that moderately high temperatures not only permit protocell assembly at the origin of life, but can have actively supported it. Here, the fast nucleation and growth of vesicular compartments from autonomously formed lipid networks on solid surfaces, induced by a moderate increase in temperature, are shown. Branches of the networks, initially consisting of self-assembled interconnected nanotubes, rapidly swell into microcompartments which can spontaneously encapsulate RNA fragments. The increase in temperature further causes fusion of adjacent network-connected compartments, resulting in the redistribution of the RNA. The experimental observations and the mathematical model indicate that the presence of nanotubular interconnections between protocells facilitates the fusion process.
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| 37. |
- Laurila, T., et al.
(författare)
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Thermohydrodynamics of boiling in a van der Waals fluid
- 2012
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Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 85:2, s. 026320-
-
Tidskriftsartikel (refereegranskat)abstract
- We present a modeling approach that enables numerical simulations of a boiling Van der Waals fluid based on the diffuse interface description. A boundary condition is implemented that allows in and out flux of mass at constant external pressure. In addition, a boundary condition for controlled wetting properties of the boiling surface is also proposed. We present isothermal verification cases for each element of our modeling approach. By using these two boundary conditions we are able to numerically access a system that contains the essential physics of the boiling process at microscopic scales. Evolution of bubbles under film boiling and nucleate boiling conditions are observed by varying boiling surface wettability. We observe flow patters around the three-phase contact line where the phase change is greatest. For a hydrophilic boiling surface, a complex flow pattern consistent with vapor recoil theory is observed.
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| 38. |
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| 39. |
- Lin, Yuan, et al.
(författare)
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A phase field model for multiphase electro-hydrodynamic flow
- 2012
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Ingår i: International Journal of Multiphase Flow. - : Elsevier BV. - 0301-9322 .- 1879-3533. ; 45, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- The principles of electro-hydrodynamics have been known for more than a century and extensive experimental studies have been carried out. Insight about such types of flows have been widely adopted for industrial applications, e.g. fluid mixing and de-mixing, but analytical solutions only exist in a limited number of cases, e.g. small deformation of a single droplet in a uniform and steady electric field. Numerical modeling of such phenomena can provide significant insights into electro-hydrodynamic multi-phase flows. In the present paper we propose a phase field model for studying two-phase electro-hydrodynamic flow generated by an electric field. The proposed model is validated and found to be in good agreement with existing analytical solutions and numerical studies in the literature. We also investigate the influence of viscosity ratio and surface tension in binary coalescence of drops in an immiscible fluid.
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| 40. |
- Mark, Andreas, 1980, et al.
(författare)
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Optimisation of Robotised Sealing Stations in Paint Shops by Process Simulation and Automatic Path Planning
- 2014
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Ingår i: International Journal of Manufacturing Research. - 1750-0591 .- 1750-0605. ; 9:1, s. 4-26
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Tidskriftsartikel (refereegranskat)abstract
- Application of sealing materials is done in order to prevent water leakage into cavities of the car body, and to reduce noise. The complexity of the sealing spray process is characterised by multi-phase and free surface flows,multi-scale phenomena, and large moving geometries, which poses great challenges for mathematical modelling and simulation. The aim of this paper is to present a novel framework that includes detailed process simulation andautomatic generation of collision free robot paths. To verify the simulations, the resulting width, thickness and shape of applied material on test plates as a function of time and spraying distance have been compared to experiments. The agreement is in general very good. The efficient implementation makes it possible to simulate application of one meter of sealing material in less than anhour on a standard computer, and it is therefore feasible to include such detailed simulations in the production preparation process and off-line programming of the sealing robots.
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| 41. |
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| 42. |
- Mark, Andreas, 1980, et al.
(författare)
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Simulation of Electrostatic Rotary Bell Spray Painting in Automotive PAint Shops
- 2013
-
Ingår i: Atomization and Sprays. - 1044-5110 .- 1936-2684. ; 23:1, s. 25-45
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Tidskriftsartikel (refereegranskat)abstract
- A new framework for simulation of electrostatic spray painting is proposed based on novel algorithms for coupled simulations of air flow, electromagnetic fields, and paint droplets. Particularly important for the computational efficiency is the Navier-Stokes solver. The incompressible solver is based on a finite volume discretization on a dynamic Cartesian octree grid and unique immersed boundary methods are used to model the presence of objects in the fluid. This enables modeling of moving objects at virtually no additional computational cost and greatly simplifies preprocessing by avoiding the cumbersome generation of a body-conforming mesh. To validate the simulation framework an extensive measurement campaign has been performed. Several test plates and car fenders were painted with different process conditions and robot paths. The same cases were then simulated and overall the agreement between simulations and experiments are remarkably good. The very efficient implementation gives a major improvement of computational speed compared to other approaches and makes it possible to simulate spray painting of a full car in just a few hours on a standard computer.
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| 43. |
- Mark, Andreas, 1980, et al.
(författare)
-
Simulation of Electrostatic Rotary Bell Spray Painting in Automotive Paint Shops
- 2012
-
Ingår i: Proceedings of 12th International Conference on Liquid Atomization and Spray Systems.
-
Konferensbidrag (refereegranskat)abstract
- A new framework for simulation of electrostatic spray painting is proposed based on novel algorithms for coupled simulations of air flow, electromagnetic fields and paint droplets. Particularly important for the computational efficiency is the Navier-Stokes solver. The incompressible solver is based on a finite volume discretization on a dynamic Cartesian octree grid and unique immersed boundary methods are used to model the presence of objects in the fluid. This enables modeling of moving objects at virtually no additional computational cost, and greatly simplifies preprocessing by avoiding the cumbersome generation of a body conforming mesh. To validate the simulation framework an extensive measurement campaign has been performed. Several test plates and car fenders were painted with different process conditions and robot paths. The same cases were then simulated and overall the agreement between simulations and experiments are remarkably good. The very efficient implementation gives a major improvement of computational speed compared to other approaches and makes it possible to simulate spray painting of a full car in just a few hours on a standard computer.
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| 44. |
- Mathsson, Linda, et al.
(författare)
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Cryoglobulin-induced cytokine production via FcgammaRIIa: inverse effects of complement blockade on the production of TNF-alpha and IL-10. Implications for the growth of malignant B-cell clones.
- 2005
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Ingår i: British Journal of Haematology. ; 129:6, s. 830-838
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Tidskriftsartikel (refereegranskat)abstract
- Monoclonal antibodies produced by patients with lymphoproliferative diseases sometimes appear as cryoglobulins (CG), immunoglobulins (Ig) that reversibly agglutinate and form immune complexes (IC) when cooled below normal body temperature or through variation in pH and ionic strength. In accordance with our findings of IC-induced cytokine production from peripheral blood mononuclear cells (PBMC) in systemic lupus erythematosus, we investigated whether CG can also induce cytokine production. One IgG and one IgM type I CG from two patients with multiple myeloma and Waldenstrom's macroglobulinaemia were individually purified and added to PBMC cultures. In separate experiments temperature and ionic strength were varied, or FcgammaRIIa, FcgammaRIII and complement activation were blocked; supernatant cytokine levels were then determined by enzyme-linked immunosorbent assay. CG-induced cytokine production from monocytes varied with precipitation induced by changes in temperature and ionic strength and was mediated via FcRIIa- and complement-dependent mechanisms. Complement blockade resulted in increased IgG CG-induced interleukin (IL)-10 production that was inversely correlated with decreased production of tumour necrosis factor-alpha. CG-induced IL-10 might be a growth factor for malignant B-lymphocytes in CG-associated lymphoproliferative diseases with constant complement consumption. Knowledge of mechanisms underlying CG-induced cytokine production can be useful for designing treatments for type I CG-associated pathology in lymphoproliferative diseases.
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| 45. |
- Nakamura, Yoshinori, et al.
(författare)
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Dynamic wetting at the nanoscale
- 2013
-
Ingår i: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics. - 1539-3755 .- 1550-2376. ; 88:3, s. 033010-
-
Tidskriftsartikel (refereegranskat)abstract
- Although the capillary spreading of a drop on a dry substrate is well studied, understanding and describing the physical mechanisms that govern the dynamics remain challenging. Here we study the dynamics of spreading of partially wetting nanodroplets by combining molecular dynamics simulations and continuum phase field simulations. The phase field simulations account for all the relevant hydrodynamics, i.e., capillarity, inertia, and viscous stresses. By coordinated continuum and molecular dynamics simulations, the macroscopic model parameters are extracted. For a Lennard-Jones fluid spreading on a planar surface, the liquid slip at the solid substrate is found to be significant, in fact crucial for the motion of the contact line. Evaluation of the different contributions to the energy transfer shows that the liquid slip generates dissipation of the same order as the bulk viscous dissipation or the energy transfer to kinetic energy. We also study the dynamics of spreading on a substrate with a periodic nanostructure. Here it is found that a nanostructure with a length scale commensurate with molecular size completely inhibits the liquid slip. The dynamic spreading is thus about 30% slower on a nanostructured surface compared to one that is atomically smooth.
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| 46. |
- Neudecker, Denise, et al.
(författare)
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Templates of expected measurement uncertainties
- 2023
-
Ingår i: EPJ NUCLEAR SCIENCES & TECHNOLOGIES. - : EDP Sciences. - 2491-9292. ; 9
-
Tidskriftsartikel (refereegranskat)abstract
- The covariance committee of CSEWG (Cross Section Evaluation Working Group) established templates of expected measurement uncertainties for neutron-induced total, (n,gamma), neutron-induced charged-particle, and (n,xn) reaction cross sections as well as prompt fission neutron spectra, average prompt and total fission neutron multiplicities, and fission yields. Templates provide a list of what uncertainty sources are expected for each measurement type and observable, and suggest typical ranges of these uncertainties and correlations based on a survey of experimental data, associated literature, and feedback from experimenters. Information needed to faithfully include the experimental data in the nuclear-data evaluation process is also provided. These templates could assist (a) experimenters and EXFOR compilers in delivering more complete uncertainties and measurement information relevant for evaluations of new experimental data, and (b) evaluators in achieving a more comprehensive uncertainty quantification for evaluation purposes. This effort might ultimately lead to more realistic evaluated covariances for nuclear-data applications. In this topical issue, we cover the templates coming out of this CSEWG effort-typically, one observable per paper. This paper here prefaces this topical issue by introducing the concept and mathematical framework of templates, discussing potential use cases, and giving an example of how they can be applied (estimating missing experimental uncertainties of 235U(n,f) average prompt fission neutron multiplicities), and their impact on nuclear-data evaluations.
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| 47. |
- Nikoleris, Nikos, et al.
(författare)
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CoolSim : Eliminating Traditional Cache Warming with Fast, Virtualized Profiling
- 2016
-
Ingår i: 2016 IEEE International Symposium On Performance Analysis Of Systems And Software ISPASS 2016. - 9781509019533 ; , s. 149-150
-
Konferensbidrag (refereegranskat)abstract
- Sampling (e.g., SMARTS and SimPoint) improves simulation performance by an order of magnitude or more through the reduction of large workloads into a small but representative sample. Virtualized fast-forwarding (e.g., FSA) speeds up simulation further by advancing execution at near-native speed between simulation points, making cache warming the critical limiting factor for simulation performance. CoolSim is an efficient simulation framework that eliminates cache warming. It collects sparse memory reuse information (MRI) while advancing between simulation points using virtualized fast-forwarding. During detailed simulation, a statistical cache model uses the previously acquired MRI to estimate the performance of the caches. CoolSim builds upon KVM and gem5 and runs 19x faster than the state-of-the-art sampled simulation. It estimates the CPI of the SPEC CPU2006 bench-marks with 3.62% error on average, across a wide range of cache sizes.
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| 48. |
- Nikoleris, Nikos, et al.
(författare)
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CoolSim : Statistical Techniques to Replace Cache Warming with Efficient, Virtualized Profiling
- 2016
-
Ingår i: Proceedings Of 2016 International Conference On Embedded Computer Systems. - : IEEE. - 9781509030767 ; , s. 106-115
-
Konferensbidrag (refereegranskat)abstract
- Simulation is an important part of the evaluation of next-generation computing systems. Detailed, cycle-accurate simulation, however, can be very slow when evaluating realistic workloads on modern microarchitectures. Sampled simulation (e.g., SMARTS and SimPoint) improves simulation performance by an order of magnitude or more through the reduction of large workloads into a small but representative sample. Additionally, the execution state just prior to a simulation sample can be stored into checkpoints, allowing for fast restoration and evaluation. Unfortunately, changes in software, architecture or fundamental pieces of the microarchitecture (e.g., hardware-software co-design) require checkpoint regeneration. The end result for co-design degenerates to creating checkpoints for each modification, a task checkpointing was designed to eliminate. Therefore, a solution is needed that allows for fast and accurate simulation, without the need for checkpoints. Virtualized fast-forwarding (VFF), an alternative to using checkpoints, allows for execution at near-native speed between simulation points. Warming the micro-architectural state prior to each simulation point, however, requires functional simulation, a costly operation for large caches (e.g., 8 M B). Simulating future systems with caches of many MBs can require warming of billions of instructions, dominating simulation time. This paper proposes CoolSim, an efficient simulation framework that eliminates cache warming. CoolSim uses VFF to advance between simulation points collecting at the same time sparse memory reuse information (MRI). The MRI is collected more than an order of magnitude faster than functional simulation. At the simulation point, detailed simulation with a statistical cache model is used to evaluate the design. The previously acquired MRI is used to estimate whether each memory request hits in the cache. The MRI is an architecturally independent metric and a single profile can be used in simulations of any size cache. We describe a prototype implementation of CoolSim based on KVM and gem5 running 19 x faster than the state-of-the-art sampled simulation, while it estimates the CPI of the SPEC CPU2006 benchmarks with 3.62% error on average, across a wide range of cache sizes.
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| 49. |
- Nikoleris, Nikos, et al.
(författare)
-
Implementing Fast, Virtualized Profiling to Eliminate Cache Warming
- 2016
-
Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Simulation is an important part of the evaluation of next-generation computing systems. Detailed, cycle-level simulation, however, can be very slow when evaluating realistic workloads on modern microarchitectures. Sampled simulation (e.g., SMARTS and SimPoint) improves simulation performance by an order of magnitude or more through the reduction of large workloads into a small but representative sample. Additionally, the execution state just prior to a simulation sample can be stored into checkpoints, allowing for fast restoration and evaluation. Unfortunately, changes in software, architecture or fundamental pieces of the microarchitecture (e.g., hardware-software co-design) require checkpoint regeneration. The end result for co-design degenerates to creating checkpoints for each modification, a task checkpointing was designed to eliminate. Therefore, a solution is needed that allows for fast and accurate simulation, without the need for checkpoints. Virtualized fast-forwarding proposals, like FSA, are an alternative to checkpoints that speed up sampled simulation by advancing the execution at near-native speed between simulation points. They rely, however, on functional simulation to warm the architectural state prior to each simulation point, a costly operation for moderately-sized last-level caches (e.g., above 8MB). Simulating future systems with DRAM caches of many GBs can require warming of billions of instructions, dominating the time for simulation and negating the benefit of virtualized fast-forwarding. This paper proposes CoolSim, an efficient simulation framework that eliminates cache warming. CoolSim advances between simulation points using virtualized fast-forwarding, while collecting sparse memory reuse information (MRI). The MRI is collected more than an order of magnitude faster than functional warming. At the simulation point, detailed simulation is used to evaluate the design while a statistical cache model uses the previously acquired MRI to estimate whether each memory request hits in the cache. The MRI is an architecturally independent metric and therefore a single profile can be used in simulations of any size cache. We describe a prototype implementation of CoolSim based on KVM and gem5 running 19x faster than the state-of-the-art sampled simulation, while it estimates the CPI of the SPEC CPU2006 benchmarks with 3.62% error on average, across a wide range of cache sizes.
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| 50. |
- Rundqvist, Robert, 1974, et al.
(författare)
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Modeling and Simulation of Sealing Spray Application Using Smoothed Particle Hydrodynamics
- 2011
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Ingår i: Fluid Dynamics and Materials Processing. - 1555-2578 .- 1555-256X. ; 7:3, s. 259-278
-
Tidskriftsartikel (refereegranskat)abstract
- Multiphase flow simulation using Smoothed Particle Hydrodynamics (SPH)has gained interest during recent years, mostly due to the inherentflexibility of the method and the physically rather intuitiveformulation of extra constitutive equations needed when dealing withfor instance non-Newtonian flows. In the work presented here,simulations based on an SPH model implemented in the flow solverIBOFlow has been used for simulation of robotic application of sealingmaterial on a car body. Application of sealing materials is done inorder to prevent water leakage into cavities of the body, and toreduce noise. In off-line programming of the robots in the automotivepaintshop it is of great interest to predict shape and appearance ofsealing material without having to resort to trial and errorprocedures.The flow of sealing material in the air between applicator and target(car body) is relatively uncomplicated, as the material mostly movesat constant velocity until impact on target. The flow of the materialon the target is however more complex, applied material flows at thetarget surface due to inertia, gravity and pressure and in order topredict the appearance of the applied material, flow equations for anon-Newtonian fluid with an open surface needs to be solved. Thesealing material is both thixotropic and viscoelastic; the material isshear thinning but needs to be sheared for some time before thestructure of the material is broken down. Conversely, the regain ofstructure of the material, and thereby also the increase of viscositywhen shearing is stopped or reduced, is also connected to a delaytime. In the model used, the local viscosity is considered obeying afirst order differential equation where the stationary limit isdetermined by a Bingham relation.The simulation model was built by comparing simulations andexperiments at three different stages of complexity. In the mostfundamental stage the material properties were determined. Using arotational rheometer, yield stress, plastic viscosity and thixotropytime constant was determined and implemented in the simulation model.To verify the numerical behaviour of the rheology, simulated rheometerexperiments were carried out and compared with the physicalexperiments. In the second stage, simulation of application of sealingmaterial with a stationary hollowcone nozzle was carried out. Toverify the simulations, the resulting thickness, width and shape ofapplied material as a function of time were compared to experiments.In the third stage a moving applicator of the same type wasconsidered, here thickness width and shape of applied material as afunction of applicator to target distances were compared betweenexperiments and simulation. At all three stages the number of SPHparticles, /i.e./ grid points, in the simulations was varied in orderto verify that the simulations were resolution independent.Results of the simulations show good agreement between experiments andsimulations in all stages using no artificial tuning of the models,that is, all parameters used in the models are based on physicalconsiderations. Furthermore, simulation time on a desktop computerindicate that computational power required for industrially relevantcases is not prohibitively large, for the most complex cases in thiswork simulation time did not exceed six hours.
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