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Relevant bibliographies by topics / Mathematical molecular modelling

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Academic literature on the topic 'Mathematical molecular modelling'

Author: Grafiati

Published: 4 June 2021

Last updated: 12 February 2022

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Journal articles on the topic "Mathematical molecular modelling"

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Middleton, A., M. Owen, M. Bennett, and J. King. "Mathematical modelling of gibberellinsignalling." Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 150, no. 3 (July 2008): S46. http://dx.doi.org/10.1016/j.cbpa.2008.04.023.

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Butler, George, Jonathan Rudge, and Philip R. Dash. "Mathematical modelling of cell migration." Essays in Biochemistry 63, no. 5 (October 2019): 631–37. http://dx.doi.org/10.1042/ebc20190020.

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Abstract The complexity of biological systems creates challenges for fully understanding their behaviour. This is particularly true for cell migration which requires the co-ordinated activity of hundreds of individual components within cells. Mathematical modelling can help understand these complex systems by breaking the system into discrete steps which can then be interrogated in silico. In this review, we highlight scenarios in cell migration where mathematical modelling can be applied and discuss what types of modelling are most suited. Almost any aspect of cell migration is amenable to mathematical modelling from the modelling of intracellular processes such as chemokine receptor signalling and actin filament branching to larger scale processes such as the movement of individual cells or populations of cells through their environment. Two common ways of approaching this modelling are the use of models based on differential equations or agent-based modelling. The application of both these approaches to cell migration are discussed with specific examples along with common software tools to facilitate the process for non-mathematicians. We also highlight the challenges of modelling cell migration and the need for rigorous experimental work to effectively parameterise a model.

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Irfan, Sayed Ameenuddin, and Radzuan Razali. "Mathematical modelling of controlled release fertilizer." Malaysian Journal of Fundamental and Applied Sciences 13, no. 4-1 (December 5, 2017): 372–74. http://dx.doi.org/10.11113/mjfas.v13n4-1.878.

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Controlled release fertilizers (CRFs) are essential for sustainable agriculture system. CRFs are designed to maintain the constant optimum release rate of nutrients from the coated granule. This increase the plant uptake of nutrients hence reduces the soil pollution and decreases the crop expenditure. In the literature, the maximum studies have been done by considering the molecular diffusion as the only phenomenon responsible for nutrient release from CRFs. The molecular diffusion model is solved mostly by using the variable separable methods and Laplace transform as well as finite difference methods by different researchers. The release of NPK (nutrient) depends on both molecular diffusions which are expressed by Fick’s second law of diffusion and ionic diffusion, due to the electrolytic behavior of NPK in the soil. In this work, an analytical solution is presented. The obtained solution helps to find the effect of granule coating thickness, nutrient release rate, pH of the soil and temperature of the soil on the nutrient release profiles.

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Leng, G., and D. J. MacGregor. "Mathematical Modelling in Neuroendocrinology." Journal of Neuroendocrinology 20, no. 6 (June 2008): 713–18. http://dx.doi.org/10.1111/j.1365-2826.2008.01722.x.

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Vasieva, Olga, Manan'Iarivo Rasolonjanahary, and Bakhtier Vasiev. "Mathematical modelling in developmental biology." REPRODUCTION 145, no. 6 (June 2013): R175—R184. http://dx.doi.org/10.1530/rep-12-0081.

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In recent decades, molecular and cellular biology has benefited from numerous fascinating developments in experimental technique, generating an overwhelming amount of data on various biological objects and processes. This, in turn, has led biologists to look for appropriate tools to facilitate systematic analysis of data. Thus, the need for mathematical techniques, which can be used to aid the classification and understanding of this ever-growing body of experimental data, is more profound now than ever before. Mathematical modelling is becoming increasingly integrated into biological studies in general and into developmental biology particularly. This review outlines some achievements of mathematics as applied to developmental biology and demonstrates the mathematical formulation of basic principles driving morphogenesis. We begin by describing a mathematical formalism used to analyse the formation and scaling of morphogen gradients. Then we address a problem of interplay between the dynamics of morphogen gradients and movement of cells, referring to mathematical models of gastrulation in the chick embryo. In the last section, we give an overview of various mathematical models used in the study of the developmental cycle of Dictyostelium discoideum, which is probably the best example of successful mathematical modelling in developmental biology.

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MacArthur, B. D., C. P. Please, M. Taylor, and R. O. C. Oreffo. "Mathematical modelling of skeletal repair." Biochemical and Biophysical Research Communications 313, no. 4 (January 2004): 825–33. http://dx.doi.org/10.1016/j.bbrc.2003.11.171.

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Zrcek, František, and Milan Horák. "Mathematical modelling of remote detection of molecular air pollutants." Collection of Czechoslovak Chemical Communications 52, no. 6 (1987): 1397–406. http://dx.doi.org/10.1135/cccc19871397.

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A model of remote detection of molecular air pollutants is devised based on the lidar equation. The various kinds of interaction of radiation with matter, viz. absorption, induced fluorescence, and Raman scattering, are taken into account; detection of either scattered or reflected signal is considered. The reflection is assumed to be either axial, using a retroreflector, or omnidirectional from a field target. Based on this model, an algorithm was set up for simulation of the different variants of the experiment, making allowance for a generally variable concentration of the compound along the optical pathway of the light beam. The basic atmospheric processes, viz. radiation absorption by the backround, heat emission, turbulence, and the effect of atmospheric aerosols, are treated, and the last of them is found to play the major role. Aerosols are looked upon as a source of the Mie scattering and they are described by distribution equations with respect to the particle size and the complex refractive index. The variable concentration of the aerosol along the optical pathway and the simultaneous effect of a higher numberof aerosol types are included.

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Alexander, R. McN. "Modelling approaches in biomechanics." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, no. 1437 (August 6, 2003): 1429–35. http://dx.doi.org/10.1098/rstb.2003.1336.

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Conceptual, physical and mathematical models have all proved useful in biomechanics. Conceptual models, which have been used only occasionally, clarify a point without having to be constructed physically or analysed mathematically. Some physical models are designed to demonstrate a proposed mechanism, for example the folding mechanisms of insect wings. Others have been used to check the conclusions of mathematical modelling. However, others facilitate observations that would be difficult to make on real organisms, for example on the flow of air around the wings of small insects. Mathematical models have been used more often than physical ones. Some of them are predictive, designed for example to calculate the effects of anatomical changes on jumping performance, or the pattern of flow in a 3D assembly of semicircular canals. Others seek an optimum, for example the best possible technique for a high jump. A few have been used in inverse optimization studies, which search for variables that are optimized by observed patterns of behaviour. Mathematical models range from the extreme simplicity of some models of walking and running, to the complexity of models that represent numerous body segments and muscles, or elaborate bone shapes. The simpler the model, the clearer it is which of its features is essential to the calculated effect.

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Head, A. K., S. D. Howison, J. R. Ockendon, and S. P. Tighe. "Mathematical modelling of dislocation plasticity." Physica Scripta T44 (January 1, 1992): 135–36. http://dx.doi.org/10.1088/0031-8949/1992/t44/022.

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McDonald, Andrew G., Keith F. Tipton, and Gavin P. Davey. "Mathematical modelling of metabolism: Summing up." Biochemist 31, no. 3 (June 1, 2009): 24–27. http://dx.doi.org/10.1042/bio03103024.

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Biochemistry is as much a quantitative subject as qualitative. Initial observations of single- or multicellular organisms have given rise to our discipline, which is the discovery and characterization of the chemistry of all living things. We have moved from Lavoisier's seminal observation of respiration as a form of combustion, to a much more detailed knowledge of the associated biochemistry.

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Dissertations / Theses on the topic "Mathematical molecular modelling"

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Wang, Dechao. "Mathematical modelling of plants for facilitating genetic and molecular analysis." Thesis, University of Warwick, 2002. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.396880.

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Montràs, Boet Anna. "Mathematical modelling and molecular analysis of a nitrifying packed bed biofilm reactor." Doctoral thesis, Universitat Autònoma de Barcelona, 2009. http://hdl.handle.net/10803/5327.

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MELiSSA (Micro Ecological Life Support System Alternative) és el sistema desenvolupat per l'Agència Espacial Europea (ESA) i el consorci MELiSSA en el camp del suport de vida durant missions de llarga durada a l'espai. Basat en un ecosistema aquàtic, MELiSSA va ser concebut com una eina per desenvolupar la tecnologia necessària per a un sistema de suport de vida biològic que en un futur ha de permetre la producció d'aliment, aigua i oxigen a partir dels residus orgànics generats per una tripulació.
Per assolir aquest objectiu, el concepte MELiSSA compta amb l'activitat combinada de cinc compartiments colonitzats per diferents microorganismes i plantes superiors, interconnectats entre ells. Aquesta tesi es centra en el tercer compartiment del bucle MELiSSA, en el qual l'amoni és convertit a nitrat, que és la font de nitrogen més adequada per al creixement dels cianobacteris i plantes superiors que colonitzen els compartiments fotosintètics.
L'oxidació biològica d'amoni a nitrat té lloc en dues etapes successives que porten a terme dos tipus de soques bacterianes. En el projecte MELiSSA aquest procés es porta a terme en una columna de llit fix mitjançant Nitrosomonas europaea i Nitrobacter winogradkyi immobilitzats sobre un suport polimèric, i amb aportació d'aire en el mateix sentit de circulació que el medi líquid. El reactor pilot del tercer compartiment ha estat operant a la planta pilot del projecte MELiSSA durant períodes prolongats de temps abans de l'inici del treball realitzat en aquesta tesi.
La principal aportació d'aquesta tesi es troba en l'obtenció de nova informació sobre el funcionament del reactor a través d'un estudi detallat de la biopel·lícula i també mitjançant el desenvolupament d'un model matemàtic que ens permetrà estudiar els efectes de diferents paràmetres d'operació sobre el procés i l'estructura de la biopel·lícula. S'implementaran també els aparells de mesura necessaris per millorar la qualitat de la monitorització de les diferents espècies de nitrogen a la fase líquida. Els coneixements adquirits en la realització d'aquest treball seran utilitzats per portar a terme el re-disseny del reactor per tal de millorar-ne el funcionament dins de la planta pilot del projecte MELiSSA.
MELiSSA (Micro Ecological Life Support System Alternative) is the system developed by the European Space Agency (ESA) and the MELiSSA consortium in the field of life support for long term manned missions in Space. Based on the principle of an aquatic ecosystem, MELiSSA was conceived as a tool to develop the required technology for a future biological life support system. Its final aim is the production of food, fresh water and oxygen from the organic wastes of a crew.
To achieve this goal, the MELiSSA concept is based on the use of five interconnected compartments colonised by several microorganisms and higher plants. This thesis is focused on the third compartment of the MELiSSA loop, in which ammonium is converted to nitrate, the most suitable nitrogen source for the growth of the bacteria and higher plants colonising the photosynthetic compartment. The biological oxidation of ammonium to nitrate, which consists of two successive reactions carried out by two different bacterial strains, takes place in a packed bed biofilm reactor. Nitrosomonas europaea and Nitrobacter winogradskyi are immobilised on a polymeric support, with air flowing cocurrently with the feed medium. The pilot-scale reactor of compartment III (CIII) had been in operation in the MELiSSA pilot plant for several years before the start of the present work.
The main contributions of this thesis are in increasing the understanding of the reactor performance by studying the nitrifying biofilm in depth, and by developing a mathematical model that allows the effects of different operational parameters on the process and on the biofilm structure, to be studied. Moreover, continuous monitoring of the nitrifying efficiency will be improved by installing the necessary on-line equipment to experimentally measure the concentrations of all the nitrogen species in the liquid phase. The additional knowledge achieved on the reactor performance via this work will finally lead to re-design the reactor hardware for optimal performance in the MELiSSA pilot plant.
The knowledge acquired in this thesis was finally used to define the main features of the re-design of the pilot reactor of the MELiSSA compartment III.

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Nguyen, Lan K. "Dynamical modelling of feedback gene regulatory networks." Diss., Lincoln University, 2009. http://hdl.handle.net/10182/1340.

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Living cells are made up of networks of interacting genes, proteins and other bio-molecules. Simple interactions between network components in forms of feedback regulations can lead to complex collective dynamics. A key task in cell biology is to gain a thorough understanding of the dynamics of intracellular systems and processes. In this thesis, a combined approach of mathematical modelling, computational simulation and analytical techniques, has been used to obtain a deeper insight into the dynamical aspects of a variety of feedback systems commonly encountered in cells. These systems range from model system with detailed available molecular knowledge to general regulatory motifs with varying network structures. Deterministic as well as stochastic modelling techniques have been employed, depending primarily on the specific questions asked. The first part of the thesis focuses on dissecting the principles behind the regulatory design of the Tryptophan Operon system in Escherichia coli. It has evolved three negative feedback loops, namely repression, attenuation and enzyme inhibition, as core regulator mechanisms to control the intracellular level of tryptophan amino acid, which is taken up for protein synthesis. Despite extensive experimental knowledge, the roles of these seemingly redundant loops remain unclear from a dynamical point of view. We aim to understand why three loops, rather than one, have evolved. Using a large-scale perturbation/response analysis through modelling and simulations and novel metrics for transient dynamics quantification, it has been revealed that the multiple negative feedback loops employed by the tryptophan operon are not redundant. In fact, they have evolved to concertedly give rise to a much more efficient, adaptive and stable system, than any single mechanism would provide. Since even the full topology of feedback interactions within a network is insufficient to determine its behavioural dynamics, other factors underlying feedback loops must be characterised to better predict system dynamics. In the second part of the thesis, we aim to derive these factors and explore how they shape system dynamics. We develop an analytical approach for stability and bifurcation analysis and apply it to class of feedback systems commonly encountered in cells. Our analysis showed that the strength and the Hill coefficient of a feedback loop play key role in determining the dynamics of the system carrying the loop. Not only that, the position of the loop was also found to be crucial in this decision. The analytical method we developed also facilitates parameter sensitivity analysis in which we investigate how the production and degradation rates affect system dynamics. We find that these rates are quite different in the way they shape up system behaviour, with the degradation rates exhibiting a more intricate manner. We demonstrated that coupled-loop systems display greater complexity and a richer repertoire of behaviours in comparison with single-loop ones. Different combinations of the feedback strengths of individual loops give rise to different dynamical regimes. The final part of the thesis aims to understand the effects of molecular noise on dynamics of specific systems, in this case the Tryptophan Operon. We developed two stochastic models for the system and compared their predictions to those given by the deterministic model. By means of simulations, we have shown that noise can induce oscillatory behaviour. On the other hand, incorporating noise in an oscillatory system can alter the characteristics of oscillation by shifting the bifurcation point of certain parameters by a substantial amount. Measurement of fluctuations reveals that that noise at the transcript level is most significant while noise at the enzyme level is smallest. This study highlights that noise should not be neglected if we want to obtain a complete understanding of the dynamic behaviour of cells.

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Dekoninck, Sophie. "Defining the molecular and cellular mechanisms underlying wound repair and postnatal growth in the mouse epidermis." Doctoral thesis, Universite Libre de Bruxelles, 2020. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/303112.

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The epidermis is the first barrier of protection of living organisms against external attacks. It is constantly renewed throughout life, through a process called "homeostasis", which ensures that every cell lost on its surface is replaced by new ones. Recent studies have shown that this balance is ensured by a hierarchy of stem cells (SC) and progenitors that perform 3 types of cell divisions, each having a fixed probability. Although the epidermis has been extensively studied during homeostasis, little is known about the cellular dynamics taking place when the epidermis must expand its surface. Are these probabilities of division immutable or can they change? In this project, we focused on two conditions of epidermal expansion: postnatal growth and wound healing. Using the mouse tail epidermis as a model, we show that the re-epithelialization after a wound is achieved via the formation of two transient compartments that are spatially and molecularly distinct :a leading edge and a proliferative hub. We show that the leading edge cells have a specific transcriptional signature that is independent of their quiescent state and we propose new markers not previously described. Using the technique of "lineage tracing", coupled with clonal analysis and mathematical modeling, we highlight the proliferation dynamics of SCs and progenitors during healing. We show that different populations of cells residing in different compartments, the hair follicle infundibulum and the interfollicular epidermis, acquire a similar dynamics and re-activate their SC while the progenitors increase their rate of proliferation without changing their division probabilities. This similar proliferation dynamics in two compartments of the epidermis suggests that division probabilities are not dictated by the cell of origin. Interestingly, cell dynamics is different during postnatal growth. Using lineage tracing, clonal analysis and single-cell transcriptional analysis, we demonstrate that the post-natal epidermis is composed of a homogeneous population of equipotent progenitors which ensure a harmonious tissue growth through a constant imbalance towards self-renewing divisions and an ever decreasing proliferation rate. On the other hand, we show that basal cells in the adult epidermis display a greater molecular heterogeneity and that this heterogeneity is acquired progressively at the end of growth. Finally, by coupling in vivo measurements and in vitro micro-patterning experiments, we show that the orientation of cell division of equipotent progenitors is locally influenced by the alignment of the collagen fibers of the underlying dermis. These data suggest that SC specification occurs late in postnatal development and that proliferation dynamics are not immutable and could therefore be influenced by extrinsic factors.
L’épiderme est la première barrière de protection des organismes vivants contre des attaques extérieures. Il est constamment renouvelé au cours de la vie, via un processus appelé « homeostasie », qui assure que chaque cellule perdue à sa surface soit remplacée par de nouvelles. Des études récentes ont montré que cet équilibre était assuré par une hiérarchie de cellules souches (CS) et de progéniteurs qui réalisent 3 types de divisions cellulaires, chaque type de division ayant une probabilité fixe. Bien que l’épiderme ait été intensivement étudié durant l’homeostasie, peu de choses sont connues concernant la dynamique cellulaire prenant place lors de phénomènes où l’épiderme doit grandir. Ces probabilités de division sont-elles immuables ou peuvent-elles au contraire changer ?Dans ce projet, nous nous sommes intéressés à deux conditions d’expansion de l’épiderme :la croissance post-natale et la cicatrisation des plaies. En utilisant l’épiderme de la queue de souris comme modèle, nous montrons que la ré-épithélialisation d’une plaie est réalisée via la formation de deux compartiments cellulaires transitoires distincts spatialement et du point de vue moléculaire :un front de migration et un centre prolifératif. Nous montrons que les cellules du front de migration ont une signature transcriptionnelle spécifique qui est indépendante de leur état de quiescence et proposons de nouveaux marqueurs non décrits auparavant. En utilisant la technique du « lineage tracing », couplée à une analyse clonale et à de la modélisation mathématique, nous mettons en évidence la dynamique de prolifération des CS et des progéniteurs lors de la cicatrisation. Nous montrons que différentes populations de cellules résidant dans des compartiments différents, l’infundibulum du follicule pileux et l’épiderme interfolliculaire, acquièrent une dynamique similaire et ré-activent leur CS tandis que les progéniteurs augmentent leur taux de prolifération sans changer leur probabilité de division. Cette dynamique de prolifération similaire dans deux compartiments de l’épiderme suggère que les probabilités de divisions ne sont pas dictées par la cellule d’origine. De façon intéressante, la dynamique cellulaire est par contre différente durant la croissance post-natale. En utilisant le lineage tracing, l’analyse clonale et des analyses transcriptionnelles sur cellule unique, nous démontrons que l’épiderme post-natal est composé d’une population homogène de progéniteurs équipotents qui présentent un constant déséquilibre envers des divisions d’auto-renouvèlement et un taux de prolifération décroissant, assurant une croissance harmonieuse de l’épiderme. En revanche, les cellules basales de l’épiderme adulte montrent une plus grande hétérogénéité moléculaire et cet hétérogénéité est acquise progressivement à la fin de la croissance. Enfin, en couplant des mesures in vivo et des expériences de micro-patterning in vitro, nous montrons que l’orientation de la division cellulaire des progéniteurs équipotents est localement influencée par l’alignement des fibres de collagène du derme sous-jacent. Ces données suggèrent que la spécification des CS survient tardivement au cours du développement post-natal et que la dynamique de prolifération n’est pas immuable et pourraient donc être influencée par des facteurs extrinsèques.
Doctorat en Sciences biomédicales et pharmaceutiques (Pharmacie)
info:eu-repo/semantics/nonPublished

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Xie, Zhi. "Modelling genetic regulatory networks: a new model for circadian rhythms in Drosophila and investigation of genetic noise in a viral infection process." Phd thesis, Lincoln University. Agriculture and Life Sciences Division, 2007. http://theses.lincoln.ac.nz/public/adt-NZLIU20070712.144258/.

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In spite of remarkable progress in molecular biology, our understanding of the dynamics and functions of intra- and inter-cellular biological networks has been hampered by their complexity. Kinetics modelling, an important type of mathematical modelling, provides a rigorous and reliable way to reveal the complexity of biological networks. In this thesis, two genetic regulatory networks have been investigated via kinetic models. In the first part of the study, a model is developed to represent the transcriptional regulatory network essential for the circadian rhythms in Drosophila. The model incorporates the transcriptional feedback loops revealed so far in the network of the circadian clock (PER/TIM and VRI/PDP1 loops). Conventional Hill functions are not used to describe the regulation of genes, instead the explicit reactions of binding and unbinding processes of transcription factors to promoters are modelled. The model is described by a set of ordinary differential equations and the parameters are estimated from the in vitro experimental data of the clocks components. The simulation results show that the model reproduces sustained circadian oscillations in mRNA and protein concentrations that are in agreement with experimental observations. It also simulates the entrainment by light-dark cycles, the disappearance of the rhythmicity in constant light and the shape of phase response curves resembling that of experimental results. The model is robust over a wide range of parameter variations. In addition, the simulated E-box mutation, perS and perL mutants are similar to that observed in the experiments. The deficiency between the simulated mRNA levels and experimental observations in per01, tim01 and clkJrk mutants suggests some differences in the model from reality. Finally, a possible function of VRI/PDP1 loops is proposed to increase the robustness of the clock. In the second part of the study, the sources of intrinsic noise and the influence of extrinsic noise are investigated on an intracellular viral infection system. The contribution of the intrinsic noise from each reaction is measured by means of a special form of stochastic differential equation, the chemical Langevin equation. The intrinsic noise of the system is the linear sum of the noise in each of the reactions. The intrinsic noise arises mainly from the degradation of mRNA and the transcription processes. Then, the effects of extrinsic noise are studied by means of a general form of stochastic differential equation. It is found that the noise of the viral components grows logarithmically with increasing noise intensities. The system is most susceptible to noise in the virus assembly process. A high level of noise in this process can even inhibit the replication of the viruses. In summary, the success of this thesis demonstrates the usefulness of models for interpreting experimental data, developing hypotheses, as well as for understanding the design principles of genetic regulatory networks.

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Mouawad, Charbel. "Transfert de matière dans un système solide/liquide "ions/eau/pectine" : interactions, partage ionique et simulation par dynamique moléculaire." Thesis, Vandoeuvre-les-Nancy, INPL, 2007. http://www.theses.fr/2007INPL072N/document.

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Mass transfer intervening during the process of immersion influences the final composition of the product. These transfers primarily depend on the size of the immersed products, as well as temperature, the concentration and the nature of the solution of immersion. The main objective of this work is to study the mass transfer phenomena (water loss and solid gain) in solid/liquid system constituted of vegetable product (eggplant) immerged in salt solution. We determined the kinetic studies of eggplant in different salts solutions with two concentrations (saturation and 20%) at 3°C. The physicochemical properties of solution and salt such as molar concentration, molecular weight and ionic type affected the mechanism of water loss and solid gain. Knowledge about interaction ions/vegetable pectin is important for new product formulation. Determination of partition coefficient of ion in equilibrium system showed that the main physicochemical properties of ions and solution are ionic radius, electronegativity, ionic force and molar concentration. Mathematical predictive model was developed to predict the partition coefficient of ions in food/ solution system. Molecular dynamics simulations using a dynamic force field have been carried out to investigate the absorption of ions (K+, Na+, Ca2+, Mg2+, Cl-) in pectin/water/ion/aqueous solution system. Four systems were used. The results showed that the ionic type (cation and anion) influence the type and number of interactions between pectin-ion and water-ion and then offered an explicit description transfer phenomena and distribution of ions in the system solid/liquid
Les transferts de matière intervenant au cours du procédé d’immersion dépendent essentiellement de la taille des produits immergés, la température, la concentration et la nature de la solution d'immersion. L’objectif principal de ce travail porte sur l’étude des transferts dans un système solide/liquide constitué d’un produit végétal (aubergine) et d’une solution saline. Afin de parvenir à une bonne maîtrise de ces paramètres, les études cinétiques ont été conduites à 3°C sur des aubergines immergées dans des solutions salines avec deux concentrations. Les propriétés des solutions et des sels telles que la concentration molaire, la masse molaire et surtout la nature ionique influencent le mécanisme de perte et de gain. Les connaissances sur les interactions ions/pectines végétaux sont importants pour la formulation de nouveaux produits La détermination du coefficient de partage des ions à l’équilibre dans le système aubergine/solution ont montré que les principales propriétés des ions et des solutions influençant le coefficient de partage sont le rayon ionique, l’électronégativité, la force ionique et la concentration molaire. Un modèle mathématique a permis de prédire le coefficient de partage des ions dans ce système. Dans le but d’expliquer l’absorption des ions par la phase solide, une simulation par dynamique moléculaire a été menée sur un système pectine-eau-sels. Quatre systèmes ont été utilisés. Les résultats obtenus ont montré que la nature ionique influencent la nature et le nombre d’interaction entre pectine-ion et eau-ion et donc offrent une description explicite des phénomènes de transferts et distribution des ions dans le système solide/liquide

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Thompson, Duncan. "Modeling of Molecular Weight Distributions in Ziegler-Natta Catalyzed Ethylene Copolymerizations." Thesis, 2009. http://hdl.handle.net/1974/1896.

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The objective of this work is to develop mathematical models to predict molecular weight distributions (MWDs) of ethylene copolymers produced in an industrial gas-phase reactor using a Ziegler-Natta (Z-N) catalyst. Because of the multi-site nature of Z-N catalysts, models of Z-N catalyzed copolymerization tend to be very large and have many parameters that need to be estimated. It is important that the data that are available for parameter estimation be used effectively, and that a suitable balance is achieved between modeling rigour and simplification. In the thesis, deconvolution analysis is used to gain an understanding of how the polymer produced by various types of active sites on the Z-N catalyst responds to changes in the reactor operating conditions. This analysis reveals which reactions are important in determining the MWD and also shows that some types of active sites share similar behavior and can therefore share some kinetic parameters. With this knowledge, a simplified model is developed to predict MWDs of ethylene/hexene copolymers produced at 90 °C. Estimates of the parameters in this isothermal model provide good initial guesses for parameter estimation in a subsequent more complex model. The isothermal model is extended to account for the effects of butene and temperature. Estimability analysis and cross-validation are used to determine which parameters should be estimated from the available industrial data set. Twenty model parameters are estimated so that the model provides good predictions of MWD and comonomer incorporation. Finally, D-, A-,and V-optimal experimental designs for improving the quality of the model predictions are determined. Difficulties with local minima are addressed and a comparison of the optimality criteria is presented.
Thesis (Ph.D, Chemical Engineering) -- Queen's University, 2009-05-28 20:43:58.37

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Owusu, Frank K. "Mathematical modelling of low HIV viral load within Ghanaian population." Thesis, 2020. http://hdl.handle.net/10500/26903.

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Comparatively, HIV like most viruses is very minute, unadorned organism which cannot reproduce unaided. It remains the most deadly disease which has ever hit the planet since the last three decades. The spread of HIV has been very explosive and mercilessly on human population. It has tainted over 60 million people, with almost half of the human population suffering from AIDS related illnesses and death finally. Recent theoretical and computational breakthroughs in delay differential equations declare that, delay differential equations are proficient in yielding rich and plausible dynamics with reasonable parametric estimates. This paper seeks to unveil the niche of delay differential equation in harmonizing low HIV viral haul and thereby articulating the adopted model, to delve into structured treatment interruptions. Therefore, an ordinary differential equation is schemed to consist of three components such as untainted CD4+ T-cells, tainted CD4+ T-cells (HIV) and CTL. A discrete time delay is ushered to the formulated model in order to account for vital components, such as intracellular delay and HIV latency which were missing in previous works, but have been advocated for future research. It was divested that when the reproductive number was less than unity, the disease free equilibrium of the model was asymptotically stable. Hence the adopted model with or without the delay component articulates less production of virions, as per the decline rate. Therefore CD4+ T-cells in the blood remains constant at 𝛿1/𝛿3, hence declining the virions level in the blood. As per the adopted model, the best STI practice is intimated for compliance.
Mathematical Sciences
Ph.D. (Applied Mathematics)

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Ivan, Matúš. "Modelování představ žáků o chemických principech s využitím matematiky." Doctoral thesis, 2018. http://www.nusl.cz/ntk/nusl-388766.

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Key words mathematical modelling, chemical principles, shape and structure of the molecules, visualisation of chemical structures, chemistry and mathematics interdisciplinarity Ivan, Matúš: Modelling students' conceptions on chemical principles using mathematics. (Ph.D. Thesis). Prague: Faculty of Science, Charles University, 2018. Abstract The primary aims of the dissertation project is identification of "contact areas" of subjects of chemistry and mathematics and creation of interventions to solve the problems of chosen areas. At first, it was necessary to analyse available literature by the authors from the field, that have mentioned the problematics of interdisciplinarity between mathematics and chemistry. A part of literature research was dedicated to a search for the expected outcomes in curricular documents in Czech Republic and in Slovak Republic. In Czech Republic these were Framework Educational Programmes (RVP ZV, 2017 a RVP G, 2007). In Slovak Republic thee documents are State Educational programme ISCED 2 - lower secondary education (2015) and State Educational programme ISCED 3A - upper secondary education (2015). After that the analysis of a sample of School educational programmes of chosen schools in Czech Republic was conducted. The sample was chosen through proportional stratified...

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Books on the topic "Mathematical molecular modelling"

1

Hinchliffe, Alan. Molecular Modelling for Beginners. New York: John Wiley & Sons, Ltd., 2006.

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Molecular modelling for beginners. 2nd ed. Hoboken, NJ: Wiley, 2008.

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Molecular and particle modelling of laminar and turbulent flows. Hackensack, N.J: World Scientific, 2005.

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Molecular Modelling für Anwender: Anwendung von Kraftfeld- und MO-Methoden in der organischen Chemie. Stuttgart: Teubner, 1991.

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Comba, P. Molecular modeling of inorganic compounds. Weinheim: VCH, 1995.

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Comba, Peter. Molecular modeling of inorganic compounds. 2nd ed. Weinheim: Wiley-VCH, 2001.

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Applied Pulp and Paper Molecular Modelling Symposium (1st 2005 Montreal, Canada). The proceedings of the first applied pulp and paper molecular modelling symposium: August 24-26, 2005, McCord Museum, McGill University, Montreal, Canada. Montreal: Cascades Inc., 2006.

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Applied Pulp and Paper Molecular Modelling Symposium (1st 2005 Montreal, Canada). The proceedings of the first applied pulp and paper molecular modelling symposium: August 24-26, 2005, McCord Museum, McGill University, Montreal, Canada. Montreal: Cascades Inc., 2006.

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Alberte, Pullman, Jortner Joshua, and Pullman Bernard 1919-, eds. Modelling of biomolecular structures and mechanisms: Proceedings of the Twenty-seventh Jerusalem Symposium on Quantum Chemistry and Biochemistry held in Jerusalem, Israel, May 23-26, 1994. Dordrecht: Kluwer Academic Publishers, 1995.

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1960-, Rhodes John A., ed. Mathematical models in biology: An introduction. Cambridge, UK: Cambridge University Press, 2004.

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Book chapters on the topic "Mathematical molecular modelling"

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Suzuki, Takashi. "Molecular Dynamics." In Lecture Notes on Mathematical Modelling in the Life Sciences, 1–11. Singapore: Springer Singapore, 2017. http://dx.doi.org/10.1007/978-981-10-3671-2_1.

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Getto, Philipp, and Anna Marciniak-Czochra. "Mathematical Modelling as a Tool to Understand Cell Self-renewal and Differentiation." In Methods in Molecular Biology, 247–66. New York, NY: Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2519-3_15.

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Varfolomeev, Sergey, Viktor Bykov, and Svetlana Tsybenova. "Kinetic modelling of processes in the cholinergic synapse. Mechanisms of functioning and control methods." In ORGANOPHOSPHORUS NEUROTOXINS, 127–39. ru: Publishing Center RIOR, 2020. http://dx.doi.org/10.29039/22_127-139.

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The kinetic model describing the dynamics of synaptic “discharge” taking into account the kinetics of the injection of the neurotransmitter into the synaptic cleft, the pH-dependence of catalytic activity of the enzyme and diffusion withdrawal of protons is proposed and studied. In the framework of the kinetic model, the functioning of the cholinergic synapse is considered. The results of mathematical modeling of changes in the level of acetylcholine, induced pH impulse, the influence of the frequency of impulse transfer and inhibition of acetylcholinesterase are presented. Physico-chemical explanation for a number of important physiological phenomena, such as neuromuscular paralysis, the molecular mechanism of neurological memory, actions of nerve poisons and toxins and Alzheimer’s disease is given.

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Varfolomeev, Sergey, Viktor Bykov, and Svetlana Tsybenova. "Kinetic modelling of processes in the cholinergic synapse. Mechanisms of functioning and control methods." In Organophosphorous Neurotoxins, 121–33. ru: Publishing Center RIOR, 2020. http://dx.doi.org/10.29039/chapter_5e4132b600e1c6.27895580.

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The kinetic model describing the dynamics of synaptic “discharge” taking into account the kinetics of the injection of the neurotransmitter into the synaptic cleft, the pH-dependence of catalytic activity of the enzyme and diffusion withdrawal of protons is proposed and studied. In the framework of the kinetic model, the functioning of the cholinergic synapse is considered. The results of mathematical modeling of changes in the level of acetylcholine, induced pH impulse, the influence of the frequency of impulse transfer and inhibition of acetylcholinesterase are presented. Physico-chemical explanation for a number of important physiological phenomena, such as neuromuscular paralysis, the molecular mechanism of neurological memory, actions of nerve poisons and toxins and Alzheimer’s disease is given.

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Chan, Yue. "CHAPTER 9. Mathematical Modelling and Simulations for Using Nanotubes and Graphene for Ultrafiltration and Molecular and Charge Transport." In Ambipolar Materials and Devices, 214–25. Cambridge: Royal Society of Chemistry, 2020. http://dx.doi.org/10.1039/9781788019279-00214.

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Carvalho, S. A., and M. L. Martins. "Biochemical Warfare Between Living Organisms for Survival: Mathematical Modelling." In Bioactive Molecules in Food, 1–38. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-76887-8_52-1.

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Antkowiak, Michał. "Parallel Exact Diagonalization Approach to Large Molecular Nanomagnets Modelling." In Parallel Processing and Applied Mathematics, 351–58. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-78054-2_33.

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Santillán, Moisés. "Molecule Synthesis and Degradation." In Lecture Notes on Mathematical Modelling in the Life Sciences, 29–49. Cham: Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-06689-9_4.

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Antkowiak, Michał, Łukasz Kucharski, and Grzegorz Kamieniarz. "Genetic Algorithm and Exact Diagonalization Approach for Molecular Nanomagnets Modelling." In Parallel Processing and Applied Mathematics, 312–20. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-32152-3_29.

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Antkowiak, Michał, Łukasz Kucharski, and Monika Haglauer. "clique: A Parallel Tool for the Molecular Nanomagnets Simulation and Modelling." In Parallel Processing and Applied Mathematics, 312–22. Cham: Springer International Publishing, 2020. http://dx.doi.org/10.1007/978-3-030-43222-5_27.

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Conference papers on the topic "Mathematical molecular modelling"

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Groll, Rodion. "Mathematical Modeling of Binary Nano Scale Diffusion of Molecular Gas Suspensions in Liquid Media." In ASME 2007 5th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2007. http://dx.doi.org/10.1115/icnmm2007-30092.

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A model describing the suspension diffusion process of gas molecules in liquid media is presented in this paper. This process is not yet solved by a satisfactory model for micro-scale applications at this time. The new model allows the simulation of diffusion processes in continuous media considering the molecular mass flux in a suspension/carrier phase mixture. Modelling the diffusion of gas suspensions in liquid media the saturation mass ratio is reached near the liquid/gas surface very quickly. The increase of gas concentration in the liquid domain depends on the elapsed time and the physical properties of gas and liquid media. The molecular gas velocity is described by a Maxwell probability density function. Based on this spectral method macroscopic physical values are modelled to describe time-dependent global concentration changes. Modelling the gas species diffusion the molecular convection is considered. Modelling the mass flux of the molecular gas suspension characteristic time scales are developed describing the completion level of the saturation progress based on non-dimensional formulations of the molecular convection equation. The present model is implemented in a CFD code and validated by a family of parametric simulation results depending on the saturation mass ratio of the suspended gas phase. This simulation result array shows the dependency of saturation time and saturation mass ratio of the suspended gas molecules. Based on this relation macroscopic diffusion processes in micromixers and microchannels are described with this model and without an extra solution of molecule trajectories or spectral fields of molecule velocity.

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NABIEVICH, H. B., S. MAHRUY, H. M. BAHROMOVNA, and A. B. RAHIMBERDIEVICH. "MATHEMATICAL AND COMPUTER MODELLING CONTROL MECHANISMS OF HIERARCHICAL MOLECULAR-GENETIC SYSTEMS." In International Symposium on Mathematical and Computational Biology. WORLD SCIENTIFIC, 2010. http://dx.doi.org/10.1142/9789814304900_0005.

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Stepanova, Larisa V., and Oksana N. Belova. "A molecular dynamics simulation analysis of mixed mode crack growth." In 29TH RUSSIAN CONFERENCE ON MATHEMATICAL MODELLING IN NATURAL SCIENCES. AIP Publishing, 2021. http://dx.doi.org/10.1063/5.0059574.

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Nikolaev, G. I., N. A. Shuldov, I. P. Bosko, A. I. Anischenko, A. V. Tuzikov, and A. M. Andrianov. "Application of Deep Learning and Molecular Modelling Methods to Identify Potential HIV-1 Entry Inhibitors." In Mathematical Biology and Bioinformatics. Pushchino: IMPB RAS - Branch of KIAM RAS, 2020. http://dx.doi.org/10.17537/icmbb20.6.

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Gerasimov, Roman M., and Pavel S. Volegov. "Modeling of interaction of edge dislocations and microvoids using molecular dynamic approach." In 28TH RUSSIAN CONFERENCE ON MATHEMATICAL MODELLING IN NATURAL SCIENCES. AIP Publishing, 2020. http://dx.doi.org/10.1063/5.0003484.

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Ryzhkov, Alexandr, and Yuriy Raikher. "Field-induced response of non-spherical magnetopolymersomes: Coarse-grained molecular dynamics model." In 29TH RUSSIAN CONFERENCE ON MATHEMATICAL MODELLING IN NATURAL SCIENCES. AIP Publishing, 2021. http://dx.doi.org/10.1063/5.0059529.

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Barker, R. S., M. R. Russell, and L. R. Whitmer. "Mathematical Modelling of a Four-Bed Molecular Sieve with CO2 and H2O Collection." In International Conference On Environmental Systems. 400 Commonwealth Drive, Warrendale, PA, United States: SAE International, 1991. http://dx.doi.org/10.4271/911470.

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Sutrisno, Galo Ayu Megga Nanda, and Hayuni Retno Widarti. "The effectiveness of inquiry based learning with OE3R strategy for conceptual understanding of molecular shape of high school students’." In 28TH RUSSIAN CONFERENCE ON MATHEMATICAL MODELLING IN NATURAL SCIENCES. AIP Publishing, 2020. http://dx.doi.org/10.1063/5.0000620.

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Pyatkov, M. I., A. Y. Zaytsev, M. M. Olshevets, and N. S. Fialko. "Implementation of partially automated calculations on hybrid supercomputers in the modelling of charge transfer in quasi-one-dimensional molecular chains." In Mathematical Biology and Bioinformatics. Pushchino: IMPB RAS - Branch of KIAM RAS, 2018. http://dx.doi.org/10.17537/icmbb18.66.

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Zucca, Alessandro, Daniele L. Marchisio, Antonello A. Barresi, and Giancarlo Baldi. "Mathematical Modelling of Particle Formation in Combustion Processes." In ASME 8th Biennial Conference on Engineering Systems Design and Analysis. ASMEDC, 2006. http://dx.doi.org/10.1115/esda2006-95407.

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In recent years the problem of studying particle formation and evolution in turbulent flames has become increasingly important, for both environmental and technological reasons. Information on particle size and morphology is often required, since these characteristics largely influence the effects of particulate matter on human health and global climate in the case of soot. A mathematical model able to describe the evolution of these particulate systems must solve the population balance equation within a Computational Fluid Dynamics (CFD) code that predicts the temperature, composition and velocity fields of the flame. In this work, the recently proposed Direct Quadrature Method of Moments (DQMOM) is applied to the study of soot formation in turbulent non-premixed flames. The model takes into account nucleation, molecular growth, oxidation and aggregation of soot particles; simplified kinetic rates are employed, while velocity and scalar fields are computed by simulations based on the solution of the Reynolds Averaged Navier Stokes (RANS) equations. Different population balance formulations are implemented and compared and results show that DQMOM is a suitable modelling tool; comparison of predictions with experimental data shows that the model accurately describes the morphological properties of soot aggregates.

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