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1
Ismail, Mohd. "Shock isolation systems incorporating Coulomb friction". Thesis, University of Southampton, 2012. https://eprints.soton.ac.uk/348953/.
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This study investigates a novel approach to the problem of shock isolation. The questions considered are whether friction produces a better performance in terms of reduced response during a shock compared to viscous damping and a lower residual response after the shock. To gain physical insight, a single degree of freedom model with friction applied to the isolated mass is analysed. It serves as a benchmark to the performance of a two degree of freedom model where friction is applied to a secondary mass. The isolation system performance is then quantified. For the two degree of freedom system with an intermediate secondary spring which connects the primary and secondary mass, it is possible to obtain the reduction in the displacement response as good as the single degree of freedom system and at the same time smoother acceleration response compared to the single degree of freedom system. For the purpose of further improvement, a control strategy is introduced to switch on and off friction in both models depending on some response parameters and this is compared to the passive systems. This is the semi active control strategy where friction is changed within a cycle of vibration (discontinuous). The control strategy provides more displacement reduction to ensure the maximum displacement response is much smaller than the base input which cannot be obtained with the passive systems. The practical implementation and experimental validation is presented only for the first stage of the response during the shock. For the practical implementation of the switchable friction, an electromagnet is applied to separate the friction surfaces. Good agreement with the simple theoretical models for both passive and switchable systems is obtained. The reduced displacement and smooth acceleration response were obtained from the experiments with the system used to represent the two degree of freedom model. The issues and limitations in the practical implementation are identified and discussed.
2
Lawrence, Jason William. "Improving motion of systems with coulomb friction". Thesis, Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/16012.
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Altamirano, Gregory L. "Friction Response Approximation Method for Nonlinear Systems". The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu158584450899486.
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Hagler, Lisle Bruce. "Friction induced vibration in disk brake systems /". Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/7119.
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Fan, Peng. "Miniaturised biological diagnostic systems". Thesis, University of Sheffield, 2014. http://etheses.whiterose.ac.uk/6856/.
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Perry, Carole Celia. "Silicification in biological systems". Thesis, University of Oxford, 1985. http://ora.ox.ac.uk/objects/uuid:ae665ac4-63eb-4963-845a-d2db6aea31a6.
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This thesis is concerned with the formation and structure of silicified deposits in biology. The major system studied is silicified macrohairs from the lemma of the grass Phalaris canariensis L. The macrohairs consist of silica and polysaccharides. Chemical and structural studies on the mineral phase utilised electron microscopy (transmission (TEM), scanning (SEM) and ultra high resolution (HRTEM)), energy disoersive X-ray analysis (EDXA), solid state nuclear magnetic resonance ( ᷣ⁹ Si nmr), infrared spectroscopy, birefringence and nitrogen adsorption experiments. Results showed that the silica is chemically 'pure', hydrated, amorphous at a resolution of 1OÅ and a variety of structural morphologies were observed which are related to the maturity of the macrohair. Analytical studies at different times after emergence of the inflorescence utilising EDXA and scanning proton microprob eanalysis (SPM) showed that the inorganic elements Si, K, P, S and Cl are spatially organised within the macrohairs during silicification. It is proposed that the macrohairs are silicified under strict cellular control. The organic matrix in the mature macrohairs was investigated by acid hydrolysis and chromatography. The changing emphasis of polysaccharide synthesis in the macrohairs as mineralisation occurs was followed by in vivo radioactive labelling of inflorescences at different stages using ⁱ⁴C glucose and Harabinose. Analysis o fpolysaccharides synthesised involved acid hydrolysis and enzymic digestions (Amylase and Driselase), followed by paper and thin layer chromatography with scintillation counting of the products. Results showed that at the early stages of mineralisation, arabinoxylans and cellulose are the major polymers synthesised but as the macrohair matures, largely non-cellulosic glucans (as yet unidentified) are synthesised. It is proposed that the change in emphasis of polysaccharide synthesis during wall development is related to the size and ultrastructural arrangements of silica particles observed. The organic matrix was also observed to give additional order to the system, the resulting material being totally impervious. A second system, chosen for comparison, is mineralised teeth from the radula of the common limpet Patella vulgata. The mature teeth contain silica, iron oxide (goethite) and an organic matrix. Investigations on the silicified phase utilising electron microscopy revealed morphological structural variations. Analytical studies involving EDXA and SPM analysis showed that there are complex temporal and spatial variations in the inorganic composition (P, S, Ca, Fe, Si, Cu) in all regions of the teeth. It is proposed that these changes can be correlated with changes in composition of the organic matrix. A comparison is made of the silica from the two systems.
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Satam, Sayali S. "Optimization of Wet Friction Systems Based on Rheological, Adsorption, Lubricant and Friction Material Characterization". University of Akron / OhioLINK, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=akron1503358825451407.
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Baykara, Berkay. "Control Of Systems Under The Effect Of Friction". Master's thesis, METU, 2009. http://etd.lib.metu.edu.tr/upload/12611327/index.pdf.
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Precision control under the effect of friction requires an effective compensation of friction. Since friction has a complex and highly nonlinear behaviour, it is generally insufficient to represent the friction in a dynamic control
system only with a linear viscous model, which is mostly valid in high-velocity motions. Especially when the control system moves near zero velocity regions or changes the direction of motion, an accurate modelling of friction including the lowvelocity dynamic behaviour is a prerequisite to obtain a more complete and realistic dynamic model of the system. Furthermore, the parameters of the friction model
should be identified as accurate as possible in order to attain a satisfactory performance. Therefore, the parameters of the friction should be estimated regarding the working conditions. The estimated friction force can then be used to improve the
controlled performance of the dynamic system under consideration.
In this thesis, the modelling, identification and compensation of friction in a rotary mechanical system are studied. The effectiveness of the existing friction models in the literature are investigatednamely the classical Coulomb with viscous friction model, the Stribeck friction model, the LuGre friction model, and the Generalized Maxwell-Slip (GMS) friction model. All friction models are applied to the system together with the same linear, proportional with derivative (PD)-type and proportional with integral and derivative (PID)-type feedback control actions for the sake of being faithful in comparison. The accuracy of the friction compensation methods is examined separately for both the low-velocity and high-velocity motions of the system. The precision of friction estimation is also shown in the case of using both the desired velocity and measured velocity as an input to the friction models. These control studies are verified in simulation environment and the corresponding results are given. Furthermore, an experimental set-up is designed and manufactured as a case study. The parameters of the aforementioned friction models are identified and the control laws with different friction models are applied to the system in order to demonstrate the compensation capabilities of the models. The results of the experiments are evaluated by comparing them among each other and with the simulation results.
9
Sepehri, Ali. "MULTI-SCALE DYNAMICS OF MECHANICAL SYSTEMS WITH FRICTION". OpenSIUC, 2010. https://opensiuc.lib.siu.edu/dissertations/205.
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Contact between rough surfaces occurs in numerous engineering systems and in many instances influences the macro behavior of the system. In many instances, the interaction between rough surfaces, affect the macro behavior of the system. Effective treatment of systems containing rough surface contact requires multiscale modeling and analysis approach. It is the goal of this research to develop simple methods for treating contact of rough surfaces so as to facilitate multiscale analysis of systems containing rough surface contact and friction. This dissertation considers a multi-scale approach that includes interaction at nano-scale, micron-scale and accounting for their cumulative effect as to what we normally perceive to be the influence of contact surfaces and friction. In linking each scale to a higher scale this study employs statistical means to obtain cumulative effect of smaller-scale features. A mixed interactive/optimization technique is used to derive, in approximate closed form, equations for the contact load and real area of contact dependence on approach and parameters of rough surfaces. The equations so derived relate the normal and tangential components of contact load to displacement and surface parameters for three types of contact. The nature of contact interaction that include elastic, elastic-plastic, visco-elastic, and visco-elasto-adhesive behavior are considered and equations relating the normal and tangential contact load to approach and relative sliding are obtained in approximate closed form. The approximate equations provide a tool for efficient calculation of contact force components, especially in surface optimization efforts where repetitive calculation of contact force components may be needed. The approximate equations also facilitate a multi-scale dynamic analysis wherein the effect of contact interaction can be readily included in a mechanical system model. Several dynamical problems involving mechanical systems with friction contact are presented and nonlinear dynamic analyses are employed to link the micron-scale properties of surface to the macro-scale properties of the mechanical system. These lead to, perhaps, the first derivation of contact frequency and damping in rough surface contact.
10
Reichenbach, Tobias. "Dynamic patterns of biological systems". Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-84101.
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Fallon, James Bernard 1975. "Stochastic resonance in biological systems". Monash University, Dept. of Electrical and Computer Systems Engineering, 2001. http://arrow.monash.edu.au/hdl/1959.1/9024.
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Lin, Sijie. "Carbon nanomaterials in biological systems". Connect to this title online, 2007. http://etd.lib.clemson.edu/documents/1193080346/.
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Iannelli, P. "Inertial manifolds in biological systems". Thesis, University College London (University of London), 2009. http://discovery.ucl.ac.uk/16129/.
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The focus of this thesis is biological systems whose dynamics present an interesting feature: only some dimensions drive the whole system. In our examples, the dynamics is expressed as ODEs, such that the ith equation depends on all the variables xi = f (x1,...,xi,xi+1,...), so that they cannot be solved by classical methods. The authors in the literature found that one could express the variable of order bigger than N as a function of the first N variables, thus closing the differential equations; the approximations obtained were exponentially close to the nonapproximated result. In Nonlinear Dynamics, such functions are called Inertial Manifolds. They are defined as manifolds that are invariant under the flow of the dynamical system, and attract all trajectories exponentially. The first example gives rise to a generalisation of a theorem which, in the literature, is proved for the PDE u= -Au + V(u). We prove existence for the most general case u= -A(u)u + V(u) and consider the validity of the results for the biological parameters. We also present a theoretical discussion, by providing examples. The second example arises from Statistics applied to population biology. The infinite number of differential equations for the moments are approximated using a Moment Closure technique, that is expressing moments of order higher than N as a function of the first moments, generally using the function valid for the normal distribution. The example shows exceptional approximation. Though this technique is often used, there is no complete mathematical justification. We examine the relation between the Moment Closure technique and Inertial Manifolds. We prove that the approximated system can be seen as a perturbation of the original system, that it admits an Inertial Manifold, which is close to the original one for \epsilon \rightarrow 0 and t \rightarrow \infty.
14
Shim, Sangwoo. "Quantum Dynamics in Biological Systems". Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10125.
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In the first part of this dissertation, recent efforts to understand quantum mechanical effects in biological systems are discussed. Especially, long-lived quantum coherences observed during the electronic energy transfer process in the Fenna-Matthews-Olson complex at physiological condition are studied extensively using theories of open quantum systems. In addition to the usual master equation based approaches, the effect of the protein structure is investigated in atomistic detail through the combined application of quantum chemistry and molecular dynamics simulations. To evaluate the thermalized reduced density matrix, a path-integral Monte Carlo method with a novel importance sampling approach is developed for excitons coupled to an arbitrary phonon bath at a finite temperature. In the second part of the thesis, simulations of molecular systems and applications to vibrational spectra are discussed. First, the quantum dynamics of a molecule is simulated by combining semiclassical initial value representation and density funcitonal theory with analytic derivatives. A computationally-tractable approximation to the sum-of-states formalism of Raman spectra is subsequently discussed.
15
Hidayat, Egi. "On Identification of Biological Systems". Doctoral thesis, Uppsala universitet, Avdelningen för systemteknik, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-215699.
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System identification finds nowadays application in various areas of biological research as a tool of empiric mathematical modeling and model individualization. A fundamental challenge of system identification in biology awaits in the form of response variability. Furthermore, biological systems tend to exhibit high degree of nonlinearity as well as significant time delays. This thesis covers system identification approaches developed for the applications within two particular biomedical fields: neuroscience and endocrinology. The first topic of the thesis is parameter estimation of the classical Elementary Motion Detector (EMD) model in insect vision. There are two important aspects to be taken care of in the identification approach, namely the nonlinear dynamics of the individual EMD and the spatially distributed structure of multiple detectors producing a measurable neural response. Hence, the suggested identification method is comprised of two consecutive stages addressing each of the above aspects. Furthermore, visual stimulus design for high spatial excitation order has been investigated. The second topic is parameter estimation of mathematical model for testosterone regulation in the human male. The main challenges of this application are in the unavailability of input signal measurements and the presence of an unknown pulsatile feedback in the system resulting in a highly nonlinear closed-loop dynamics. Semi-blind identification method has been developed based on a recently proposed pulse-modulated model of pulsatile endocrine regulation. The two system identification problems treated in the thesis bear some resemblance in the sense that both involve measured signals that can be seen as square-integrable functions of time. This property is handled by transforming the signals into the Laguerre domain, i.e. by equivalently representing the functions with their infinite Laguerre series.
16
Norville, Julie Erin 1980. "Modular design of biological systems". Thesis, Massachusetts Institute of Technology, 2011. http://hdl.handle.net/1721.1/71484.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2012."February 2012." Cataloged from PDF version of thesis.
Includes bibliographical references (p. [153]-191).
The focus of my research is the development of technology for building compound biological systems from simpler pieces. I designed BioScaffold parts, a family of variable regions that can be inserted into a DNA sequence so that at a later time another set of pieces can be substituted for each variable. The variable regions are selective so that a particular piece can be targeted to each region. I have used this technique to assemble protein domains, tune the expression levels of proteins and remove BioBrick scars. BioScaffold parts can be used in combination with BioBrick Standard Biological Parts to create and store devices with tunable components. I developed simplified methods to produce and examine SbpA, a protein that can either self associate into two-dimensional crystals or bring together fused enzymes when divalent cations such as calcium are added to the protein monomers. My fast and easy purification protocol allows SbpA to be produced under non-denaturing conditions as well as examination of the native state of the protein monomers before crystallization. The absence of a white precipitate when calcium is added to SbpA monomers concentrated to 1 mg/ml provides a simple visual screen that indicates that the protein has failed to crystallize. I also developed a protocol to embed SbpA crystallized on lipid monolayers in trehalose for electron microscopy, allowing creation of a 7 Å resolution map for SbpA. I created a cells-on-paper system to compose, isolate, and subsequently destack and examine different cell types grown in sheets of ordinary filter paper and maintained in a humidified incubation chamber. I found that E coli diluted in LB broth and then applied to filter paper grew at rates similar to the same culture spotted on agar plates. Track etch membranes could be used to isolate different cell types, while still allowing chemical communication between the layers. Use of plasmids that contain fluorescent proteins allowed the behaviour of cells to be tracked using a scanner after destacking of the layers. The cells-on-paper system can be used both to test and construct modular synthetic systems composed of bacterial ensembles and to create and examine the behavior of compositions of cell types typically found in biofilms.
by Julie Erin Norville.
Ph.D.
17
Luo, Yang. "Stochastic modelling in biological systems". Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610145.
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Whittleston, Christopher Stuart. "Energy landscapes of biological systems". Thesis, University of Cambridge, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.610200.
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Lauback, Stephanie Diane. "Magnetic Actuation of Biological Systems". The Ohio State University, 2017. http://rave.ohiolink.edu/etdc/view?acc_num=osu1494262695434601.
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Billing, Alison Emslie. "Modelling techniques for biological systems". Master's thesis, University of Cape Town, 1987. http://hdl.handle.net/11427/21917.
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The objective of this investigation has been to develop and evaluate techniques which are appropriate to the modelling and simulation of biological reaction system behaviour. The model used as the basis for analysis of modelling and simulation techniques is a reduced version of the biological model proposed by the IAWPRC Task Group for mathematical modell ing in wastewater treatment design. This limited model has the advantage of being easily manageable in terms of analysis and presentation of the simulation techniQues whilst at the same time incorporating a range of features encountered with biological growth applications in general. Because a model may incorporate a number of different components and large number of biological conversion processes, a convenient method of presentation was found to be a matrix format. The matrix representation ensures clarity as to what compounds, processes and react ion terms are to be incorporated and allows easy comparison of different models. In addition, it facilitates transforming the model into a computer program. Simulation of the system response first involves specifying the reactor configuration and flow patterns. With this information fixed, mass balances for each compound in each reactor can be completed. These mass balances constitute a set of simultaneous non-linear differential and algebraic eQuations which, when solved, characterise the system behaviour.
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Santos, Bruno Miguel Ferreira dos. "Bios: Biological input-output systems". Master's thesis, Universidade de Aveiro, 2009. http://hdl.handle.net/10773/2197.
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Mestrado em Engenharia Electrónica e TelecomunicaçõesEste projecto visa a produção de um aparelho portátil para monitorização/análise da actividade cardíaca. Recebendo como entrada o sinal cardíaco (ECG - electrocardiograma), o dispositivo detecta a característica do sinal e, com base nessa característica, averigua se ocorreu alguma anomalia, produzindo um sinal de alarme se tal acontecer. O aparelho em causa tem que ser acessível, ter um baixo consumo energético, e a detecção de anomalias tem de ser efectuada em tempo real. Para que esta ultima condição se verificasse, o software implementado requer o mínimo de computação possível, de forma a efectuar todas as operações de detecção e análise num prazo limite de tempo, mantendo-se um detector fiável. O detector foi optimizado para uma frequência de entrada de 200Hz, e implementado em computador pessoal e num DSP (Digital Signal Processor – processador de sinal digital) desenvolvido pela Microchip. Ambas as implementações foram testadas recorrendo a sinais cardíacos fornecidos pela MIT-BIH Arrhythmia Database. Os testes desenvolvidos têm o propósito de testar a “qualidade” do detector e possíveis limitações do microprocessador usado, particularmente, no que diz respeito à capacidade de executar a detecção de anomalias cardíacas em tempo real. ABSTRACT: This project intends to produce a portable device for monitoring/analysis of cardiac activity. Receiving the cardiac signal (ECG – electrocardiogram) as input, the device detects the signal’s characteristics and, based upon those characteristics, checks whether some anomaly has occurred, producing an alarm signal in such case. The aforementioned device has to be affordable, low-power consumption, and the detection of anomalies has to be done in real-time. For this last condition to be verified, the implemented software requires as little computation as possible, so as to carry out all of the detection and analysis operations in a specified amount of time, while maintaining the characteristics of a reliable detector. The detector has been optimized for an input sampling frequency of 200Hz, and it has been implemented in a personal computer and in a DSP (Digital Signal Processor), developed by Microchip. Both implementations have been tested resorting to cardiac signals supplied by the MIT-BIH Arrhythmia Database. The tests that have been developed are designed to verify the quality of the detector, as well as possible limitations of the microprocessor used, particularly, when it comes to the ability to carry out the detection of cardiac anomalies in real-time.
22
Winter, Matthias. "Concentrated patterns in biological systems". [S.l. : s.n.], 2003. http://www.bsz-bw.de/cgi-bin/xvms.cgi?SWB11163816.
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Zamborszky, Judit. "Compositional Modeling of Biological Systems". Doctoral thesis, Università degli studi di Trento, 2010. https://hdl.handle.net/11572/368785.
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Molecular interactions are wired in a fascinating way resulting in complex behavior of bio-logical systems. Theoretical modeling provides us a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological systems calls for conceptual tools that manage the combinatorial explosion of the set of possible interac-tions. A suitable conceptual tool to attack complexity is compositionality, already success-fully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and si-mulate high-level descriptions of biological circuits. Gillespie’s stochastic simulation algo-rithm applied for BlenX simulations requires the decomposition of phenomenological func-tions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of modeling.
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Zámborszky, Judit. "Compositional Modeling of Biological Systems". Doctoral thesis, University of Trento, 2010. http://eprints-phd.biblio.unitn.it/565/1/PhD-Thesis_final.pdf.
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Molecular interactions are wired in a fascinating way resulting in complex behavior of bio-logical systems. Theoretical modeling provides us a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological systems calls for conceptual tools that manage the combinatorial explosion of the set of possible interac-tions. A suitable conceptual tool to attack complexity is compositionality, already success-fully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and si-mulate high-level descriptions of biological circuits. Gillespie’s stochastic simulation algo-rithm applied for BlenX simulations requires the decomposition of phenomenological func-tions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of modeling.
25
Battisti, Anna. "Computer Simulation of Biological Systems". Doctoral thesis, Università degli studi di Trento, 2012. https://hdl.handle.net/11572/368453.
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This thesis investigates two biological systems using atomistic modelling and molecular dynamics simulation.
The work is focused on: (a) the study of the interaction between a segment of a DNA molecule and a functionalized surface; (b) the dynamical modelling of protein tau, an intrinsically disordered protein.
We briefly describe here the two problems; for their detailed introduction we refer respectively to chapter DNA and chapter TAU.
The interest in the study of the adsorption of DNA on functionalized surfaces is related to the considerable effort that in recent years has been devoted in developing technologies for faster and cheaper genome sequencing.
In order to sequence a DNA molecule, it has to be extracted from the cell where it is stored (e.g. the blood cells). As a consequence any genomic analysis requires a purification process in order to remove from the DNA molecule proteins,
lipids and any other contaminants. The extraction and purification of DNA from biological samples is hence the first step towards an efficient and cheap genome sequencing.
Using the chemical and physical properties of DNA it is possible to generate an attractive interaction between this macromolecule and a properly treated surface. Once positioned on the surface, the DNA can be more easily purified.
In this work we set up a detailed molecular model of DNA interacting with a surface functionalized with amino silanes. The intent is to investigate the free energy of adsorption of small DNA oligomers as a function of the pH and ionic strength of the solution.
The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state do not have an average stable structure and fluctuate between many conformations.
In its physiological state, tau protein helps nucleating and stabilizing the microtubules in the axons of the neurons. On the other hand, the same tau - in a pathological aggregation - is involved in
the development of the Alzheimer disease.
IDPs do not have a definite 3D structure, therefore their dynamical simulation cannot start from a known list of atomistic positions, like a protein data bank file.
We first introduce a procedure to find an initial dynamical state for a generic IDP, and we apply it to the tau protein.
We then analyze the dynamical properties of tau, like the propensity of residues to form temporary secondary structures like beta-sheets or alpha-helices.
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Battisti, Anna. "Computer Simulation of Biological Systems". Doctoral thesis, University of Trento, 2012. http://eprints-phd.biblio.unitn.it/689/1/Tesi-PhD.pdf.
Pełny tekst źródłaStreszczenie:
This thesis investigates two biological systems using atomistic modelling and molecular dynamics simulation.
The work is focused on: (a) the study of the interaction between a segment of a DNA molecule and a functionalized surface; (b) the dynamical modelling of protein tau, an intrinsically disordered protein.
We briefly describe here the two problems; for their detailed introduction we refer respectively to chapter DNA and chapter TAU.
The interest in the study of the adsorption of DNA on functionalized surfaces is related to the considerable effort that in recent years has been devoted in developing technologies for faster and cheaper genome sequencing.
In order to sequence a DNA molecule, it has to be extracted from the cell where it is stored (e.g. the blood cells). As a consequence any genomic analysis requires a purification process in order to remove from the DNA molecule proteins,
lipids and any other contaminants. The extraction and purification of DNA from biological samples is hence the first step towards an efficient and cheap genome sequencing.
Using the chemical and physical properties of DNA it is possible to generate an attractive interaction between this macromolecule and a properly treated surface. Once positioned on the surface, the DNA can be more easily purified.
In this work we set up a detailed molecular model of DNA interacting with a surface functionalized with amino silanes. The intent is to investigate the free energy of adsorption of small DNA oligomers as a function of the pH and ionic strength of the solution.
The tau protein belongs to the category of Intrinsically Disordered Proteins (IDP), which in their native state do not have an average stable structure and fluctuate between many conformations.
In its physiological state, tau protein helps nucleating and stabilizing the microtubules in the axons of the neurons. On the other hand, the same tau - in a pathological aggregation - is involved in
the development of the Alzheimer disease.
IDPs do not have a definite 3D structure, therefore their dynamical simulation cannot start from a known list of atomistic positions, like a protein data bank file.
We first introduce a procedure to find an initial dynamical state for a generic IDP, and we apply it to the tau protein.
We then analyze the dynamical properties of tau, like the propensity of residues to form temporary secondary structures like beta-sheets or alpha-helices.
27
Trebbi, Bruno <1977>. "Theoretical study of biological systems". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2007. http://amsdottorato.unibo.it/513/1/TesiBrunoTrebbi.pdf.
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Trebbi, Bruno <1977>. "Theoretical study of biological systems". Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2007. http://amsdottorato.unibo.it/513/.
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Shih, Yu-Keng. "Identifying Protein Functions and Biological Systems through Exploring Biological Networks". The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1388676152.
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Unal, Fuat Gokhan. "Development Of A Computer Program For Friction Winding Systems". Master's thesis, METU, 2011. http://etd.lib.metu.edu.tr/upload/12613744/index.pdf.
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ABSTRACT
DEVELOPMENT OF A COMPUTER PROGRAM FOR FRICTION WINDING SYSTEM DESIGN
Ünal, Fuat Gö
khan M.Sc., Department of Mining Engineering Supervisor: Prof. Dr. Naci Bö
lü
kbasi September 2011, 99 pages As the trend to deeper mines continues, mine hoists and associated equipment will become more sophisticated, complex, large and expensive. Correct selection of the right type of hoist is imperative. In this vital link between underground and surface, crude estimates of hoist capacity are not good enough, and the mining engineer must design and select the right hoisting system to meet the design specifications and establish the most suitable operating parameters. This study aims to constitute a software model, which results all required design parameters of friction type winding system on minimum required power. The computer program has been structured on Microsoft Visual Basic programming language. The program requires user inputs (winding depth, hourly hoisting capacity) and selections (type and number of motors, type of friction wheel mounting) to run macros and equations so that the operating parameters such as skip capacity, rope type and diameter, hoisting speed, acceleration, cycle period, friction wheel diameter are determined to give the minimum motor power requirement.
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Tariku, Fitsum. "Simulation of dynamic mechanical systems with stick-slip friction". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1998. http://www.collectionscanada.ca/obj/s4/f2/dsk2/tape17/PQDD_0011/MQ38415.pdf.
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Lane, Jeffrey Scott. "Control of dynamic systems using semi-active friction damping". Diss., Georgia Institute of Technology, 1993. http://hdl.handle.net/1853/16020.
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KONDEPUDI, RAMABALARAJENDRASESH. "NUMERICAL ANALYSIS OF LUMPED PARAMETER DYNAMIC SYSTEMS WITH FRICTION". University of Cincinnati / OhioLINK, 2004. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1083622496.
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Remez, Vinogradov Nikita 1985. "Drug design at biological systems level". Doctoral thesis, Universitat Pompeu Fabra, 2016. http://hdl.handle.net/10803/396352.
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The explosion of reductionist approaches at the end of the XXth
century allowed for fast and high-throughput data collection in
pharmaceutical industry, but did not deliver the expected gain in
drug discovery performance. Omics methodologies were able to
provide large amounts of information on one-to-one cause-effect
relationships, but could not explain some of the complex effects in
living organisms and biological systems in general. This Thesis,
performed in the premises of an emerging biotech company,
represents an attempt to explore the impact of an integrative
systems approach to drug discovery. On the one hand, in silico
prediction of drug-target interactions developed at Chemotargets
was applied to the identifcation of cancer-relevant targets, the
design of a biologically diverse chemical library, and the
implementation of a novel methodology for predictive drug safety.
On the other hand, major efforts were devoted to develop and
carefully validate a new approach to anticipating in vivo organ
toxicities from in vitro pharmacological profles and gene expression
datas. This novel methodology was designed to complement and
assist the expert toxicologist by providing insights at the anatomical
level . Last but no least, key contributions have been made to develop
a brand new platform-independent version of the company’s flagship
software, CT-link, allowing for easy distribution and
commercializationA les darreries del segle XX, l'auge de les aproximacions reduccionistes van permetre a la industria farmacèutica la recopilació de gran quantitat de informació, pero l’impacte en el rendiment de la producció de nous fàrmacs no va ser l’esperat. Encara que es van extreure moltes dades sobre les relacions un-a-un entre entitats sistèmiques els efectes complexos causats als sistemes biològics no es van poder adreçar adequadament. Aquesta tesi, desenvolupada en el marc d’una empresa biotecnolòica emergent, intenta introduir un marc de referència integral per l’aproximació sistèmica al disseny de fàrmacs. D'una banda, s’ha aplicat la predicció in silico de xarxes fàrmac-diana per identifcar les proteïnes relacionades amb càncer, per la construcció d’una biblioteca química d’amplia cobertura biològica i per anticipar la toxicitat relacionada amb dianes secundàries. D'altra banda, es va ampliar l’aproximació de biologia de sistemes per abastar les connexions anatòmiques. Aquesta nova metodologia fou dissenyada per complementar i assistir al toxicòleg expert en la identificació de toxicitats a nivell anatòmic. Finalment, durant aquests anys s’ha contribuit de manera important al desenvolupament d’una nova versió independent de la plataforma del programari estrella de l’empresa, CT-link, que n’ha facilitat enormement la seva distribució i comercialització.
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Li, Weiwei. "Optimal control for biological movement systems". Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3205051.
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Thesis (Ph. D.)--University of California, San Diego, 2006.Title from first page of PDF file (viewed April 4, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 131-146).
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Brenner, Sibylle. "Mechanistic Control of Biological Redox Systems". Thesis, University of Manchester, 2009. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.518447.
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Harish, Arun Mysore. "Nanomechanical cantilever systems for biological sensing". Thesis, University of Newcastle Upon Tyne, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.507138.
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Robinson, Alexander Joseph. "Magnetic field effects on biological systems". Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.543006.
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Tessmer, Ingrid. "Single molecule interactions in biological systems". Thesis, University of Nottingham, 2003. http://eprints.nottingham.ac.uk/10023/.
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The interactions of biological molecules are traditionally investigated using ensemble techniques. These provide information on the molecular behaviour based on averaged data resulting from collective ensemble properties. While this has enabled the resolution of structure and function of many proteins and other biomolecules, an understanding of how and why the molecules go about structural changes and modulate inter- and intra-molecular interactions is difficult to gain using these approaches. More recently, single molecule techniques have evolved. These allow us to follow the behaviour of the individual molecules over time and/or under changing conditions. From such data, subtle molecular changes can be resolved without the need to synchronise the system. Further, variations within a biological system can be detected which would be lost using the ensemble techniques, due to the concomitant averaging procedures. This is exploited to help understand the molecular procedures involved. In this thesis, the application and comparison of two of the main single molecule techniques, optical tweezers and AFM, are described. With these, a range of systems was investigated; namely drug-DNA, protein-DNA, and cell adhesive interactions. The presented results provide new and complementary information on the different biological systems, demonstrating the diversity of single molecule applications. The combination of different experimental approaches was further exploited to gain a more complete picture of the observed processes.
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Humphreys, Paul Nigel. "Biological denitrification in activated sludge systems". Thesis, London South Bank University, 1991. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.303974.
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Bell, Alexander Charlton. "Formal computational models of biological systems". Thesis, University of Sheffield, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.301423.
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Fryer, M. J. "Light-induced damage to biological systems". Thesis, University of Essex, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.238538.
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Lewis, Randy Stewart. "Nitric oxide kinetics in biological systems". Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/36947.
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Preto, Jordane. "Long-range interactions in biological systems". Thesis, Aix-Marseille, 2012. http://www.theses.fr/2012AIXM4053.
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L'auto-organisation des organismes vivants est d'une complexité et d'une efficacité étonnantes. Plus précisément, les systèmes biologiques abritent un nombre gigantesque de réactions très spécifiques qui nécessitent que la bonne biomolécule se retrouve à la bonne place, dans le bon ordre et en un temps suffisamment court pour permettre le fonctionnement cellulaire, et au-delà la vie cellulaire. D'un point de vue dynamique, cela pose la question fondamentale de savoir comment les biomolécules trouvent efficacement leur(s) cible(s) spécifique(s), ou encore, quels types de forces rassemblent tous ces partenaires de réaction spécifiques dans un environnement aussi dense et ionisé que les micro-environnements cellulaires. Dans cette thèse, nous explorons la possibilité que des biomolécules puissent interagir à travers des interactions électromagnétiques de longue-portée telles que ces dernières sont prédites à partir des premiers principes de la physique; ''longue-portée'' signifiant que les interactionsen question sont actives sur des distances bien plus larges que les dimensions typiques des molécules mises en jeu (i.e., plus grandes qu'environ 50 angströms dans les systèmes biologiques). Après avoir posé les fondements théoriques concernant les interactionsde longue-portée potentiellement actives sur de longue distances dans un contexte biologique, nous étudions la posssibilité de détecter leur éventuelle contribution à partir de dispositifs expérimentaux qui sont accessibles de nos jours. Sur ce dernier point, des résultats préliminaires encourageants tant sur le plan théorique qu'expérimental sont présentésSelf-organization of living organisms is of an astonishing complexity and efficiency. More specifically, biological systems are the site of a huge number of very specific reactions thatrequire the right biomolecule to be at the right place, in the right order and in a reasonably short time to sustain cellular function and ultimately cellular life. From the dynamic point of view, this raises the fundamental question of how biomolecules effectively find their target(s); in other words, what kinds of forces bring all these specific cognate partners together in an environment as dense and ionized as cellular micro-environments. In the present thesis, we explore the possibility that biomolecules interact through long-range electromagnetic interactions as they are predicted from the first principles of physics; "long-range" meaning that the mentioned interactions are effective over distances much larger than the typical dimensions of the molecules involved (i.e., larger than about 50 angströms in biological systems).After laying the theoretical foundations about interactions that are potentially active over long distances in a biological context, we investigate the possibility of detecting their contribution from experimental devices which are nowadays available. On the latter point, encouraging preliminary results both at the theoretical and experimental levels are exposed
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Sudağıtan, Mert Güneş Hatice. "Test of biomaterials in biological systems/". [s.l.]: [s.n.], 2001. http://library.iyte.edu.tr/tezler/master/biyoloji/T000021.pdf.
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Gibson, Michael Andrew Bruck Jehoshua. "Computational methods for stochastic biological systems /". Diss., Pasadena, Calif. : California Institute of Technology, 2000. http://resolver.caltech.edu/CaltechETD:etd-05132005-154222.
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Ackerman, Joseph J. H. "Diffusion sensitive MR in biological systems". Universitätsbibliothek Leipzig, 2015. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-184533.
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Scano, Paola. "Theoretical investigations on some biological systems". Thesis, University of St Andrews, 1997. http://hdl.handle.net/10023/15455.
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In this thesis molecular properties of different biological systems are studied by means of Quantum Mechanical methods. After a brief introduction, the basic theory of the methods here used is presented in Chapter 1. In Chapter 2 the heats of formation and the ionization potentials of some carcinogenic compounds such as Polycyclic Aromatic Hydrocarbons are studied and compared with experimental data. The methods used are the semiempirical methods with the AM1 and PM3 Hamiltonians. The results show that the experimental heats of formation are better reproduced by PM3, while as far as the ionization potentials are concerned AM1 is slightly better than PM3. In Chapter 3, the Lipid Peroxidation mechanism has been studied at the molecular level. The energetic details of the pathway proposed by Porter have been studied using the semiempirical AM1 and PM3 Hamiltonians. Six model compounds, which retain the same functional characteristics as the physiological fatty acid, have been used. The results are in good agreement with the experimental observations. Characteristics and metabolism of the anticancer drug NMF (N-Methylformide) have been studied in detail in Chapter 4. Accurate ab initio calculations have been carried out and the effect of the solvent has been taken into account. The results represent a good example of the high quality of information that the application of ab initio methods can give when properties of molecules and energetic details of pathways are examined.
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West, H. K. "Competing divalent cations in biological systems". Thesis, University of Worcester, 2001. http://eprints.worc.ac.uk/7188/.
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Heil, Katharina Friedlinde. "Systems biological approach to Parkinson's disease". Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/31043.
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Parkinson’s Disease (PD) is the second most common neurodegenerative disease in the Western world. It shows a high degree of genetic and phenotypic complexity with many implicated factors, various disease manifestations but few clear causal links. Ongoing research has identified a growing number of molecular alterations linked to the disease. Dopaminergic neurons in the substantia nigra, specifically their synapses, are the key-affected region in PD. Therefore, this work focuses on understanding the disease effects on the synapse, aiming to identify potential genetic triggers and synaptic PD associated mechanisms. Currently, one of the main challenges in this area is data quality and accessibility. In order to study PD, publicly available data were systematically retrieved and analysed. 418 PD associated genes could be identified, based on mutations and curated annotations. I curated an up-to-date and complete synaptic proteome map containing a total of 6,706 proteins. Region specific datasets describing the presynapse, postsynapse and synaptosome were also delimited. These datasets were analysed, investigating similarities and differences, including reproducibility and functional interpretations. The use of Protein-Protein-Interaction Network (PPIN) analysis was chosen to gain deeper knowledge regarding specific effects of PD on the synapse. Thus I generated a customised, filtered, human specific Protein-Protein Interaction (PPI) dataset, containing 211,824 direct interactions, from four public databases. Proteomics data and PPI information allowed the construction of PPINs. These were analysed and a set of low level statistics, including modularity, clustering coefficient and node degree, explaining the network’s topology from a mathematical point of view were obtained. Apart from low-level network statistics, high-level topology of the PPINs was studied. To identify functional network subgroups, different clustering algorithms were investigated. In the context of biological networks, the underlying hypothesis is that proteins in a structural community are more likely to share common functions. Therefore I attempted to identify PD enriched communities of synaptic proteins. Once identified, they were compared amongst each other. Three community clusters could be identified as containing largely overlapping gene sets. These contain 24 PD associated genes. Apart from the known disease associated genes in these communities, a total of 322 genes was identified. Each of the three clusters is specifically enriched for specific biological processes and cellular components, which include neurotransmitter secretion, positive regulation of synapse assembly, pre- and post-synaptic membrane, scaffolding proteins, neuromuscular junction development and complement activation (classical pathway) amongst others. The presented approach combined a curated set of PD associated genes, filtered PPI information and synaptic proteomes. Various small- and large-scale analytical approaches, including PPIN topology analysis, clustering algorithms and enrichment studies identified highly PD affected synaptic proteins and subregions. Specific disease associated functions confirmed known research insights and allowed me to propose a new list of so far unknown potential disease associated genes. Due to the open design, this approach can be used to answer similar research questions regarding other complex diseases amongst others.