Bottom-up derivation of an effective thermostat for united atoms simulations of water

In this article we derive the effective pairwise interactions in a Langevin type united atoms model of water. The interactions are determined from the trajectories of a detailed molecular dynamics simulation of simple point charge water. A standard method is used for estimating the conservative interaction, whereas a new "bottom-up" method is used to determine the effective dissipative and stochastic interactions. We demonstrate that, when compared to the standard united atoms model, the transport properties of the coarse-grained model is significantly improved by the introduction of the derived dissipative and stochastic interactions. The results are compared to a previous study, where a "top-down" approach was used to obtain transport properties consistent with those of the simple point charge water model.Comment: Submitted to J. Chem. Phy

To measure and compare sustainability : a case study of three Swedish forest companies

Idag publicerar många av de större svenska företagen hållbarhetsrapporter som komplement till de traditionella finansiella rapporterna. En hållbarhetsrapport ska ge information om företagets arbete med hållbarhetsfrågor och dess påverkan på den värld det verkar i. För att ge legitimitet åt sina hållbarhetsrapporter upprättar många företag dessa enligt standardiserade ramverk utvecklade av Global Reporting Initiative (GRI). Dessa ramverk ställer krav på att rapporterna innehåller vissa data och att de ska ta upp ett antal bestämda problemområden gällande hållbarhet. Ramverken tillåter emellertid viss flexibilitet, vilket gör att olika företags hållbarhetsrapporter, trots att de följer samma ramverk, kan redovisa mycket varierande information och data. I uppsatsen presenteras begreppet ekoeffektivitet som ett sätt att mäta och jämföra hållbarhet hos företag genom att kombinera miljömässiga- och ekonomiska data. Genom att analysera den data som redovisas i hållbarhetsrapporter från tre fallföretag inom den svenska skogsindustrin utreds hur väl denna data kan användas för att beräkna, och jämföra hållbarhet i form av ekoeffektivitet. Uppsatsen är genomförd i form av en fallstudie där först en litteraturgenomgång av ämnet ekoeffektivitet görs som sedan ligger till grund för analyser av miljödata publicerad i de valda fallföretagens hållbarhetsrapporter. I analysen testas hur väl denna data kan användas för att beräkna ekoeffektivitet och sedan jämföras mellan fallföretagen. Resultatet av uppsatsen visar att den miljödata som publiceras i fallföretagens hållbarhets-redovsningar är komplicerad att jämföra mellan företagen. Detta beror till stor del på att fallföretagen inte är konsekventa i användandet av enheter och ingående variabler. Av samma anledning visar uppsatsen att det är svårt att jämföra ekoeffektiviteten mellan fallen, även om det är enkelt att beräkna för de enskilda företagen. För att jämföra ekoeffektivitet mellan fallen, visar uppsatsen att det är av större nytta att beräkna utvecklingen av ekoeffektivitet då den inte är enhetsberoende för att bli jämförbar mellan olika fall.In addition to traditional financial reports, many Swedish companies publish sustainability reports. A sustainability report provides information about the work the company is doing in favor of sustainability and the impact the company has on the world around it. To give the sustainability report, it is often developed in accordance with standards established by the Global Reporting Initiative (GRI). These standards ensure that the reports contain certain data and that they address a number of problem areas important for sustainability. However, the GRI standards allow for a certain degree of flexibility when it comes to the information that needs to be reported. This means that the information that is reported can differ a great deal between companies. This essay introduces the concept of eco-efficiency as a way to measure and compare the sustainability of a company by combining environmental- and economical data. By analyzing the data in sustainability reports from three case-companies in the Swedish forest industry, it is investigated if the data is usable for calculating and comparing sustainability in terms of eco-efficiency. The essay is conducted as a case study with a literature review of the topic ecoefficiency as a foundation for the analysis of the data published in the sustainability reports from the case companies. The analysis tests if this data is suited for the calculation of eco-efficiency and if it can be used for comparing the reports of the companies. The results show that it is complicated to compare the environmental data published in the sustainability reports of the case companies. This is largely due to the fact that the companies are not consistent in the methods in which they calculate, nor the units in which they present the data. For the same reason, the results also show that comparing eco-efficiency between the case companies is complicated although it is fairly simple to calculate for the individual case. The essay finds that the most useful way to compare eco-efficiency between cases is to compare the development of eco-efficiency, since that allows for comparisons to be made without being dependent on the unit of measure

Low concentrations of perfluoroalkyl acids (PFAAs) in municipal drinking water associated with serum PFAA concentrations in Swedish adolescents

While highly contaminated drinking water (DW) is a major source of exposure to perfluoroalkyl acids (PFAAs), the contribution of low-level contaminated DW (i.e. < 10 ng/L of individual PFAAs) to PFAA body burdens has rarely been studied. To address this knowledge gap, we evaluated the association between concentrations of perflurooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorohexane sulfonic acid (PFHxS) and perfluorooctane sulfonic acid (PFOS), and their sum (& sum;(4)PFAAs) in DW and serum in Swedish adolescents using weighted least squares regression. We paired serum PFAA concentrations in adolescents (age 10-21 years, n = 790) from the dietary survey Riksmaten Adolescents 2016-17 (RMA) with mean PFAA concentrations in water samples collected in 2018 from waterworks (n = 45) supplying DW to the participant residential and school addresses. The median concentrations of individual PFAAs in DW were < 1 ng/L. Median concentrations of PFNA and PFHxS in serum were < 1 ng/g, while those of PFOA and PFOS were 1-2 ng/g. Significant positive associations between PFAA concentrations in DW and serum were found for all four PFAAs and & sum;(4)PFAAs, with estimated serum/DW concentration ratios ranging from 210 (PFOA) to 670 (PFHxS), taking exposure from sources other than DW (background) into consideration. The mean concentrations of PFHxS and & sum;(4)PFAA in DW that would likely cause substantially elevated serum concentrations above background variation were estimated to 0.9 ng/L and 2.4 ng/L, respectively. The European Food Safety Authority has determined a health concern concentration of 6.9 ng & sum;(4)PFAAs/mL serum. This level was to a large degree exceeded by RMA participants with DW & sum;(4)PFAA concentrations above the maximum limits implemented in Denmark (2 ng & sum;(4)PFAAs/L) and Sweden (4 ng & sum;(4)PFAAs/L) than by RMA participants with DW concentrations below the maximum limits. In conclusion, PFAA exposure from low-level contaminated DW must be considered in risk assessment for adolescents

Effects of enrichment on simple aquatic food webs

Simple models, based on Lotka-Volterra types of interactions between predator and prey, predict that enrichment will have a destabilizing effect on populations and that equilibrium population densities will change at the top trophic level and every second level below. We experimentally tested these predictions in three aquatic food web configurations subjected to either high or low nutrient additions. The results were structured by viewing the systems as either food chains or webs and showed that trophic level biomass increased with enrichment, which contradicts food chain theory. However, within each trophic level, food web configuration affected the extent to which different functional groups responded to enrichment. By dividing trophic levels into functional groups, based on vulnerability to consumption, we were able to identify significant effects that were obscured when systems were viewed as food chains. The results support the prediction that invulnerable prey may stabilize trophic-level dynamics by replacing other, more vulnerable prey. Furthermore, the vulnerable prey, such as Daphnia and edible algae, responded as predicted by the paradox of enrichment hypothesis; that is, variability in population density increased with enrichment. Hence, by describing ecosystems as a matrix of food web interactions, and by recognizing the interplay between interspecific competition and predation, a more complete description of the ecosystem function was obtained compared to when species were placed into distinct trophic levels

Using force covariance to derive effective stochastic interactions in dissipative particle dynamics

There exist methods for determining effective conservative interactions in coarse grained particle based mesoscopic simulations. The resulting models can be used to capture thermal equilibrium behavior, but in the model system we study do not correctly represent transport properties. In this article we suggest the use of force covariance to determine the full functional form of dissipative and stochastic interactions. We show that a combination of the radial distribution function and a force covariance function can be used to determine all interactions in dissipative particle dynamics. Furthermore we use the method to test if the effective interactions in dissipative particle dynamics (DPD) can be adjusted to produce a force covariance consistent with a projection of a microscopic Lennard-Jones simulation. The results indicate that the DPD ansatz may not be consistent with the underlying microscopic dynamics. We discuss how this result relates to theoretical studies reported in the literature.Comment: 10 pages, 10 figure

Healthy eating index and diet diversity score as determinants of serum perfluoroalkyl acid (PFAA) concentrations in a national survey of Swedish adolescents

Food is an important source of perfluoroalkyl acid (PFAA) exposure for the general adult population, but few data exist for adolescents. Healthy food habits established during adolescence may positively influence health later in life. Associations between serum PFAA concentrations and a healthy eating index (SHEIA15), as well as a diet diversity score (RADDS), were determined in a nationally representative adolescent population from Sweden (Riksmaten Adolescents 2016–2017, RMA). Using consumption data from food registrations and frequency questionnaires, we additionally analyzed associations with commonly consumed food groups. Associations were analyzed by fitting a cumulative probability model using ordinal regression. Among the seven PFAAs detected in ≥70% of the 1098 participants (age 10–21 years), median concentrations ranged fro

Determining interaction rules in animal swarms

In this paper we introduce a method for determining local interaction rules in animal swarms. The method is based on the assumption that the behavior of individuals in a swarm can be treated as a set of mechanistic rules. The principal idea behind the technique is to vary parameters that define a set of hypothetical interactions to minimize the deviation between the forces estimated from observed animal trajectories and the forces resulting from the assumed rule set. We demonstrate the method by reconstructing the interaction rules from the trajectories produced by a computer simulation.Comment: v3: text revisions to make the article more comprehensibl

Demographic, life-style and physiological determinants of serum per- and polyfluoroalkyl substance (PFAS) concentrations in a national cross-sectional survey of Swedish adolescents

Per: and polyfluoroalkyl substances (PFAS) may affect adolescent health, yet factors related to PFAS concentrations in serum are poorly understood. We studied demographic, life-style and physiological determinants of serum PFAS concentrations in Swedish adolescents from a nation-wide survey, Riksmaten Adolescents 2016-17 (RMA, age 10-21 years, n = 1098). Serum samples were analyzed for 42 PFAS, using liquid chromatography-tandem mass spectrometry. The cumulative probability model was used to estimate associations between serum PFAS and determinants, using ordinal logistic regression. Legacy linear (lin-) perfluorooctanoic acid (PFOA), perfluorononaoic acid (PFNA), perfluorodecanoic acid (PFDA), perfluoroundecanoic acid (PFUnDA), lin-perfluorohexanesulfonic acid (PFHxS) and lin-/branched (br-) perfluorooctanesulfonic acid (PFOS) were quantifiable in >= 70% of the samples. The emerging PFAS 9-chlorohexanedecafluoro-3-oxanone-1-sulfonic acid (9Cl-PF3ONS) was quantified in 5.4% of the samples, suggesting initiation of long-range transport far from production sites. Median concentrations of all legacy PFAS were 100 ng/g serum) lin-PFHxS and lin-/br-PFOS concentrations due to previous high exposure from PFAS-contaminated drinking water. Legacy PFAS exposure was strongly associated with birth country of the participants and their mothers. 2-fold higher estimated adjusted mean (EAM) concentrations were seen among high income country participants with mothers from high income countries than among low/lower-middle income country participants with mothers from the same category. Menstruating females had lower lin-PFOA and br-PFOS EAM concentrations than those who were not. Iron status (plasma ferritin) among females may be a marker of intensity of menstrual bleeding, but it was not significantly associated with legacy PFAS concentrations among females. Further studies are needed to determine how physiological changes occurring around menstruation affect the toxicokinetics of PFAS in females. In conclusion, PFAS are pollutants of the industrialized world and some of the identified determinants may be overlooked confounders/effect modifiers that should be included in future PFAS/health studies among adolescents

Exit of pediatric pre-B acute lymphoblastic leukaemia cells from the bone marrow to the peripheral blood is not associated with cell maturation or alterations in gene expression

<p>Abstract</p> <p>Background</p> <p>Childhood pre-B acute lymphoblastic leukemia (ALL) is a bone marrow (BM) derived disease, which often disseminates out of the BM cavity, where malignant cells to a variable degree can be found circulating in the peripheral blood (PB). Normal pre-B cells are absolutely dependent on BM stroma for survival and differentiation. It is not known whether transformed pre-B ALL cells retain any of this dependence, which possibly could impact on drug sensitivity or MRD measurements.</p> <p>Results</p> <p>Pre-B ALL cells, highly purified by a novel method using surface expression of CD19 and immunoglobulin light chains, from BM and PB show a very high degree of similarity in gene expression patterns, with differential expression of vascular endothelial growth factor (VEGF) as a notable exception. In addition, the cell sorting procedure revealed that in 2 out of five investigated patients, a significant fraction of the malignant cells had matured beyond the pre-B cell stage.</p> <p>Conclusion</p> <p>The transition of ALL cells from the BM into the circulation does not demand, or result in, major changes of gene expression pattern. This might indicate an independence of BM stroma on the part of transformed pre-B cells, which contrasts with that of their normal counterparts.</p