MODELING DYNAMICS OF OZONE AND NITROGEN OXIDES AT SUMMIT, GREENLAND WITH A 1-D PROCESS-SCALE MODEL

This work presents a 1-D process scale model used to investigate the chemical dynamics and temporal variability of nitrogen oxides (NOx) and ozone (O3) within and above snowpack at Summit, Greenland for March-May 2009 and estimates surface exchange of NOx between the snowpack and surface layer in April-May 2009. The model assumes the surface of snowflakes have a Liquid Like Layer (LLL) where aqueous chemistry occurs and interacts with the interstitial air of the snowpack. Model parameters and initialization are physically and chemically representative of snowpack at Summit, Greenland and model results are compared to measurements of NOx and O3 collected by our group at Summit, Greenland from 2008-2010. The model paired with measurements confirmed the main hypothesis in literature that photolysis of nitrate on the surface of snowflakes is responsible for nitrogen dioxide (NO2) production in the top ~50 cm of the snowpack at solar noon for March – May time periods in 2009. Nighttime peaks of NO2 in the snowpack for April and May were reproduced with aqueous formation of peroxynitric acid (HNO4) in the top ~50 cm of the snowpack with subsequent mass transfer to the gas phase, decomposition to form NO2 at nighttime, and transportation of the NO2 to depths of 2 meters. Modeled production of HNO4 was hindered in March 2009 due to the low production of its precursor, hydroperoxy radical, resulting in underestimation of nighttime NO2 in the snowpack for March 2009. The aqueous reaction of O3 with formic acid was the major sync of O3 in the snowpack for March-May, 2009. Nitrogen monoxide (NO) production in the top ~50 cm of the snowpack is related to the photolysis of NO2, which underrepresents NO in May of 2009. Modeled surface exchange of NOx in April and May are on the order of 1011 molecules m-2 s-1. Removal of measured downward fluxes of NO and NO2 in measured fluxes resulted in agreement between measured NOx fluxes and modeled surface exchange in April and an order of magnitude deviation in May. Modeled transport of NOx above the snowpack in May shows an order of magnitude increase of NOx fluxes in the first 50 cm of the snowpack and is attributed to the production of NO2 during the day from the thermal decomposition and photolysis of peroxynitric acid with minor contributions of NO from HONO photolysis in the early morning.

A musculoskeletal shoulder model based on pseudo-inverse and null-space optimization.

The goal of the present work was assess the feasibility of using a pseudo-inverse and null-space optimization approach in the modeling of the shoulder biomechanics. The method was applied to a simplified musculoskeletal shoulder model. The mechanical system consisted in the arm, and the external forces were the arm weight, 6 scapulo-humeral muscles and the reaction at the glenohumeral joint, which was considered as a spherical joint. The muscle wrapping was considered around the humeral head assumed spherical. The dynamical equations were solved in a Lagrangian approach. The mathematical redundancy of the mechanical system was solved in two steps: a pseudo-inverse optimization to minimize the square of the muscle stress and a null-space optimization to restrict the muscle force to physiological limits. Several movements were simulated. The mathematical and numerical aspects of the constrained redundancy problem were efficiently solved by the proposed method. The prediction of muscle moment arms was consistent with cadaveric measurements and the joint reaction force was consistent with in vivo measurements. This preliminary work demonstrated that the developed algorithm has a great potential for more complex musculoskeletal modeling of the shoulder joint. In particular it could be further applied to a non-spherical joint model, allowing for the natural translation of the humeral head in the glenoid fossa.

Siltanosturin mallinnusmenetelmien kehittäminen

Työn tarkoituksena oli selvittää kaupallisen dynamiikan simulointiohjelmiston (Adams) soveltuvuus siltanosturin mallintamiseen. Työn kohteena oli kaksipalkkinen siltanosturi, joka sijaitsi KCI:n tiloissa Hyvinkäällä. Nosturin jänneväli oli noin 19.5 metriä ja nostokyky 16 tonnia. Mallintamisessa keskityttiin nosturin dynamiikkaan sekä ohjausvoimiin nosturin kantopyörissä. Simulointitulokset verifioitiin mittauksin. Koska mallista haluttiin mahdollisimman yksinkertainen, mallinnettiin ainoastaan pääkannattajat ja köydet joustavina. Muut osat mallinnettiin jäykkinä. Yksinkertaisuuteen pyrittiin sen vuoksi, että mallia oli tarkoitus käyttää perustana komponenttikirjaston luomiseksi myöhempää käyttöä varten. Tuloksista todettiin mallin soveltuvan hyvin nosturin dynamiikan mallintamiseen. Mallista saatavat tulokset vastasivat hyvin mitattuja liikkeitä. Ohjausvoimia ei kuitenkaan saatu verifioitua. Käytetty mittausmenetelmä osoittautui sopimattomaksi.

Intermolecular interactions of the malate synthase of Paracoccidioides spp

Background: The fungus Paracoccidioides spp is the agent of paracoccidioidomycosis (PCM), a pulmonary mycosis acquired by the inhalation of fungal propagules. Paracoccidioides malate synthase (PbMLS) is important in the infectious process of Paracoccidioides spp because the transcript is up-regulated during the transition from mycelium to yeast and in yeast cells during phagocytosis by murine macrophages. In addition, PbMLS acts as an adhesin in Paracoccidioides spp. The evidence for the multifunctionality of PbMLS indicates that it could interact with other proteins from the fungus and host. The objective of this study was to identify and analyze proteins that possibly bind to PbMLS (PbMLS-interacting proteins) because protein interactions are intrinsic to cell processes, and it might be possible to infer the function of a protein through the identification of its ligands. Results: The search for interactions was performed using an in vivo assay with a two-hybrid library constructed in S. cerevisiae; the transcripts were sequenced and identified. In addition, an in vitro assay using pull-down GST methodology with different protein extracts (yeast, mycelium, yeast-secreted proteins and macrophage) was performed, and the resulting interactions were identified by mass spectrometry (MS). Some of the protein interactions were confirmed by Far-Western blotting using specific antibodies, and the interaction of PbMLS with macrophages was validated by indirect immunofluorescence and confocal microscopy. In silico analysis using molecular modeling, dynamics and docking identified the amino acids that were involved in the interactions between PbMLS and PbMLS-interacting proteins. Finally, the interactions were visualized graphically using Osprey software. Conclusion: These observations indicate that PbMLS interacts with proteins that are in different functional categories, such as cellular transport, protein biosynthesis, modification and degradation of proteins and signal transduction. These data suggest that PbMLS could play different roles in the fungal cell. © 2013 de Oliveira et al.; licensee BioMed Central Ltd.

Modelagem e controle de posição e orientação de uma Plataforma de Stewart

Este trabalho apresenta o controle de posição e orientação de um modelo não linear de Plataforma de Stewart com seis graus de liberdade construído no ambiente de sistemas multicorpos ADAMS® desenvolvido pela Mechanical Dynamics, Inc. O modelo não linear é exportado para o ambiente SIMULINK® desenvolvido pela MathWorks, Inc., onde o controle de posição e orientação é realizado a partir da linearização do modelo e a aplicação de um sistema seguidor com realimentação de estados. Utililiza-se, também o SIMULINK® para implementar a dinâmica de um sistema servoválvula e cilindro hidráulico com um servocontrole de pressão e assim simular o comportamento dinâmico de um simulador de vôo com acionamento hidráulico. A utilização destes pacotes comerciais visa obter uma economia de tempo e esforço na modelagem de sistemas mecânicos complexos e na programação para obtenção da resposta do sistema no tempo, além de facilitar a análise de várias configurações de Plataformas de Stewart

Modeling soil organic carbon dynamics in Oxisols of Ibiruba (Brazil) with the Century Model

introduction of conservation practices in degraded agricultural land will generally recuperate soil quality, especially by increasing soil organic matter. This aspect of soil organic C (SOC) dynamics under distinct cropping and management systems can be conveniently analyzed with ecosystem models such as the Century Model. In this study, Century was used to simulate SOC stocks in farm fields of the Ibiruba region of north central Rio Grande do Sul state in Southern Brazil. The region, where soils are predominantly Oxisols, was originally covered with subtropical woodlands and grasslands. SOC dynamics was simulated with a general scenario developed with historical data on soil management and cropping systems beginning with the onset of agriculture in 1900. From 1993 to 2050, two contrasting scenarios based on no-tillage soil management were established: the status quo scenario, with crops and agricultural inputs as currently practiced in the region and the high biomass scenario with increased frequency of corn in the cropping system, resulting in about 80% higher biomass addition to soils. Century simulations were in close agreement with SOC stocks measured in 2005 in the Oxisols with finer texture surface horizon originally under woodlands. However, simulations in the Oxisols with loamy surface horizon under woodlands and in the grassland soils were not as accurate. SOC stock decreased from 44% to 50% in fields originally under woodland and from 20% to 27% in fields under grasslands with the introduction of intensive annual grain crops with intensive tillage and harrowing operations. The adoption of conservation practices in the 1980s led to a stabilization of SOC stocks followed by a partial recovery of native stocks. Simulations to 2050 indicate that maintaining status quo would allow SOC stocks to recover from 81% to 86% of the native stocks under woodland and from 80% to 91 % of the native stocks under grasslands. Adoption of a high biomass scenario would result in stocks from 75% to 95% of the original stocks under woodlands and from 89% to 102% in the grasslands by 2050. These simulations outcomes underline the importance of cropping system yielding higher biomass to further increase SOC content in these Oxisols. This application of the Century Model could reproduce general trends of SOC loss and recovery in the Oxisols of the Ibiruba region. Additional calibration and validation should be conducted before extensive usage of Century as a support tool for soil carbon sequestration projects in this and other regions can be recommended. (C) 2009 Elsevier B.V. All rights reserved.

Modeling the Dynamics of Viral Evolution Considering Competition Within Individual Hosts and at Population Level: The Effects of Treatment

We consider two viral strains competing against each other within individual hosts (at cellular level) and at population level (for infecting hosts) by studying two cases. In the first case, the strains do not mutate into each other. In this case, we found that each individual in the population can be infected by only one strain and that co-existence in the population is possible only when the strain that has the greater basic intracellular reproduction number, R (0c) , has the smaller population number R (0p) . Treatment against the one strain shifts the population equilibrium toward the other strain in a complicated way (see Appendix B). In the second case, we assume that the strain that has the greater intracellular number R (0c) can mutate into the other strain. In this case, individual hosts can be simultaneously infected by both strains (co-existence within the host). Treatment shifts the prevalence of the two strains within the hosts, depending on the mortality induced by the treatment, which is, in turn, dependent upon the doses given to each individual. The relative proportions of the strains at the population level, under treatment, depend both on the relative proportions within the hosts (which is determined by the dosage of treatment) and on the number of individuals treated per unit time, that is, the rate of treatment. Implications for cases of real diseases are briefly discussed.

Comments on ‘‘Modeling fractional stochastic systems as non-random fractional dynamics driven Brownian motions

Applied Mathematical Modelling, Vol.33

Urban land cover change detection analysis and modeling spatio-temporal Growth dynamics using Remote Sensing and GIS Techniques: A case study of Dhaka, Bangladesh

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Population Dynamics Modeling of Arapaima gigas

Pirarucu (Arapaima gigas) has been of the most important natural fishing resources of the Amazon region. Due to its economic importance, and the necessity to preserve the species hand, field research concerning the habits and behavior of the pirarucu has been increasing for the last 20 years. The aim of this paper is to present a mathematical model for the pirarucu population dynamics considering the species peculiarities, particularly the male parental care over the offspring. The solution of the dynamical systems indicates three possible equilibrium points for the population. The first corresponds to extinction; the third corresponds to a stable population close to the environmental carrying capacity. The second corresponds to an unstable equilibrium located between extinction and full use of the carrying capacity. It is shown that lack of males’ parental care closes the gap between the point corresponding to the unstable equilibrium and the point of stable non-trivial equilibrium. If guarding failure reaches a critical point the two points coincide and the population tends irreversibly to extinction. If some event tends to destabilize the population equilibrium, as for instance inadequate parental care, the model responds in such a way as to restore the trajectory towards the stable equilibrium point avoiding the route to extinction. The parameters introduced to solve the system of equations are partially derived from limited but reliable field data collected at the Mamirauá Sustainable Development Reserve (MSDR) in the Brazilian Amazonian Region.

Dynamics in growth and metabolism of adherent MDCK cells unraveled by an integrated modeling approach

Otto-von-Guericke-Universität Magdeburg, Fakultät für Verfahrens- und Systemtechnik, Univ., Dissertation, 2015

Ab initio modeling and molecular dynamics simulation of the alpha 1b-adrenergic receptor activation.

This work describes the ab initio procedure employed to build an activation model for the alpha 1b-adrenergic receptor (alpha 1b-AR). The first version of the model was progressively modified and complicated by means of a many-step iterative procedure characterized by the employment of experimental validations of the model in each upgrading step. A combined simulated (molecular dynamics) and experimental mutagenesis approach was used to determine the structural and dynamic features characterizing the inactive and active states of alpha 1b-AR. The latest version of the model has been successfully challenged with respect to its ability to interpret and predict the functional properties of a large number of mutants. The iterative approach employed to describe alpha 1b-AR activation in terms of molecular structure and dynamics allows further complications of the model to allow prediction and interpretation of an ever-increasing number of experimental data.

Modeling U.S. Inflation Dynamics: A Bayesian Nonparametric Approach

This paper uses an infinite hidden Markov model (IIHMM) to analyze U.S. inflation dynamics with a particular focus on the persistence of inflation. The IHMM is a Bayesian nonparametric approach to modeling structural breaks. It allows for an unknown number of breakpoints and is a flexible and attractive alternative to existing methods. We found a clear structural break during the recent financial crisis. Prior to that, inflation persistence was high and fairly constant.

Lifelong dynamics of human CD4+CD25+ regulatory T cells: insights from in vivo data and mathematical modeling.

Despite their limited proliferation capacity, regulatory T cells (T(regs)) constitute a population maintained over the entire lifetime of a human organism. The means by which T(regs) sustain a stable pool in vivo are controversial. Using a mathematical model, we address this issue by evaluating several biological scenarios of the origins and the proliferation capacity of two subsets of T(regs): precursor CD4(+)CD25(+)CD45RO(-) and mature CD4(+)CD25(+)CD45RO(+) cells. The lifelong dynamics of T(regs) are described by a set of ordinary differential equations, driven by a stochastic process representing the major immune reactions involving these cells. The model dynamics are validated using data from human donors of different ages. Analysis of the data led to the identification of two properties of the dynamics: (1) the equilibrium in the CD4(+)CD25(+)FoxP3(+)T(regs) population is maintained over both precursor and mature T(regs) pools together, and (2) the ratio between precursor and mature T(regs) is inverted in the early years of adulthood. Then, using the model, we identified three biologically relevant scenarios that have the above properties: (1) the unique source of mature T(regs) is the antigen-driven differentiation of precursors that acquire the mature profile in the periphery and the proliferation of T(regs) is essential for the development and the maintenance of the pool; there exist other sources of mature T(regs), such as (2) a homeostatic density-dependent regulation or (3) thymus- or effector-derived T(regs), and in both cases, antigen-induced proliferation is not necessary for the development of a stable pool of T(regs). This is the first time that a mathematical model built to describe the in vivo dynamics of regulatory T cells is validated using human data. The application of this model provides an invaluable tool in estimating the amount of regulatory T cells as a function of time in the blood of patients that received a solid organ transplant or are suffering from an autoimmune disease.

Estimating dormant and active hematopoietic stem cell kinetics through extensive modeling of bromodeoxyuridine label-retaining cell dynamics.

Bone marrow hematopoietic stem cells (HSCs) are responsible for both lifelong daily maintenance of all blood cells and for repair after cell loss. Until recently the cellular mechanisms by which HSCs accomplish these two very different tasks remained an open question. Biological evidence has now been found for the existence of two related mouse HSC populations. First, a dormant HSC (d-HSC) population which harbors the highest self-renewal potential of all blood cells but is only induced into active self-renewal in response to hematopoietic stress. And second, an active HSC (a-HSC) subset that by and large produces the progenitors and mature cells required for maintenance of day-to-day hematopoiesis. Here we present computational analyses further supporting the d-HSC concept through extensive modeling of experimental DNA label-retaining cell (LRC) data. Our conclusion that the presence of a slowly dividing subpopulation of HSCs is the most likely explanation (amongst the various possible causes including stochastic cellular variation) of the observed long term Bromodeoxyuridine (BrdU) retention, is confirmed by the deterministic and stochastic models presented here. Moreover, modeling both HSC BrdU uptake and dilution in three stages and careful treatment of the BrdU detection sensitivity permitted improved estimates of HSC turnover rates. This analysis predicts that d-HSCs cycle about once every 149-193 days and a-HSCs about once every 28-36 days. We further predict that, using LRC assays, a 75%-92.5% purification of d-HSCs can be achieved after 59-130 days of chase. Interestingly, the d-HSC proportion is now estimated to be around 30-45% of total HSCs - more than twice that of our previous estimate.