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1
Brampton, Christopher. "Forces in biomolecular systems". Thesis, University of Nottingham, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.429077.
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Shah, Rushina(Rushina Jaidip). "Input-output biomolecular systems". Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/129016.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Mechanical Engineering, 2020Cataloged from student-submitted PDF of thesis.
Includes bibliographical references (pages 194-206).
The ability of cells to sense and respond to their environment is encoded in biomolecular reaction networks, in which information travels through processes such as production, modification, and removal of biomolecules. These reaction networks can be modeled as input-output systems, where the input, state and output variables are concentrations of the biomolecules involved in these reactions. Tools from non-linear dynamics and control theory can be leveraged to analyze and control these systems. In this thesis, we study two key biomolecular networks. In part 1 of this thesis, we study the input-output behavior of signaling systems, which are responsible for the transmission of information both from outside and from within the cells, and are ubiquitous, playing a role in cell cycle progression, survival, growth, differentiation and apoptosis. A signaling pathway transmits information from an upstream system to downstream systems, ideally in a unidirectional fashion.
A key obstacle to unidirectional transmission is retroactivity, the additional reaction flux that affects a system once its species interact with those of downstream systems. In this work, we identify signaling architectures that can overcome retroactivity, allowing unidirectional transmission of signals. These findings can be used to decompose natural signal transduction networks into modules, and at the same time, they establish a library of devices that can be used in synthetic biology to facilitate modular circuit design. In part 2 of this thesis, we design inputs to trigger a transition of cell-fate from one cell type to another. The process of cell-fate decision-making is often modeled by means of multistable gene regulatory networks, where different stable steady states represent distinct cell phenotypes. In this thesis, we provide theoretical results that guide the selection of inputs that trigger a transition, i.e., reprogram the network, to a desired stable steady state.
Our results depend uniquely on the structure of the network and are independent of specific parameter values. We demonstrate these results by means of several examples, including models of the extended network controlling stem-cell maintenance and differentiation.
by Rushina Shah.
Ph. D.
Ph.D. Massachusetts Institute of Technology, Department of Mechanical Engineering
3
Xin, W. (Weidong). "Continuum electrostatics of biomolecular systems". Doctoral thesis, University of Oulu, 2008. http://urn.fi/urn:isbn:9789514287602.
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Abstract
Electrostatic interactions are very important in biomolecular systems. Electrostatic forces have received a great deal of attention due to their long-range nature and the trade-off between desolvation and interaction effects. It remains a challenging task to study and to predict the effects of electrostatic interactions in biomolecular systems. Computer simulation techniques that account for such interactions are an important tool for the study of biomolecular electrostatics.
This study is largely concerned with the role of electrostatic interactions in biomolecular systems and with developing novel models to estimate the strength of such interactions.
First, a novel formulation based upon continuum electrostatics to compute the electrostatic potential in and around two biomolecules in a solvent with ionic strength is presented. Many, if not all, current methods rely on the (non)linear Poisson-Boltzmann equation to include ionic strength. The present formulation, however, describes ionic strength through the inclusion of explicit ions, which considerably extends its applicability and validity range. The method relies on the boundary element method (BEM) and results in two very similar coupled integral equations valid on the dielectric boundaries of two molecules, respectively. This method can be employed to estimate the total electrostatic energy of two protein molecules at a given distance and orientation in an electrolyte solution with zero to moderately high ionic strength.
Secondly, to be able to study interactions between biomolecules and membranes, an alternative model partly based upon the analytical continuum electrostatics (ACE) method has been also formulated. It is desirable to develop a method for calculating the total solvation free energy that includes both electrostatic and non-polar energies. The difference between this model and other continuum methods is that instead of determining the electrostatic potential, the total electrostatic energy of the system is calculated by integrating the energy density of the electrostatic field. This novel approach is employed for the calculation of the total solvation free energy of a system consisting of two solutes, one of which could be an infinite slab representing a membrane surface.
4
Janosi, Lorant. "Multiscale modeling of biomolecular systems". Diss., Columbia, Mo. : University of Missouri-Columbia, 2007. http://hdl.handle.net/10355/4801.
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Thesis (Ph. D.)--University of Missouri-Columbia, 2007.The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file (viewed on February 14, 2008) Vita. Includes bibliographical references.
5
Desai, Amruta. "Design support for biomolecular systems". Cincinnati, Ohio : University of Cincinnati, 2010. http://rave.ohiolink.edu/etdc/view.cgi?acc_num=ucin1265986863.
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Thesis (M.S.)--University of Cincinnati, 2010.Advisor: Carla Purdy. Title from electronic thesis title page (viewed Apr. 19, 2010). Includes abstract. Keywords: Biological pathways; weighted gate; BMDL; pyrimidine. Includes bibliographical references.
6
Diez, Stefan, i Jonathon Howard. "Nanotechnological applications of biomolecular motor systems". Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2008. http://nbn-resolving.de/urn:nbn:de:bsz:14-ds-1223724473713-41365.
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Neuerliche Fortschritte im Verständnis biomolekularer Motoren rücken ihre Anwendung als Nanomaschinen in den Bereich des Möglichen. So könnten sie zum Beispiel als Nanoroboter arbeiten, um in molekularen Fabriken kleine – aber dennoch komplizierte – Strukturen auf winzigen Förderbändern herzustellen, um Netzwerke molekularer Nanodrähte und Transistoren für elektronische Anwendungen zu assemblieren oder sie könnten in adaptiven Materialien patrouillieren und diese, wenn nötig, reparieren. In diesem Sinne besitzen biomolekulare Motoren das Potenzial, die Basis für die Konstruktion, Strukturierung und Wartung nanoskaliger Materialien zu bildenRecent advances in understanding how biomolecular motors work have raised the possibility that they might find applications as nanomachines. For example, they could be used as molecule- sized robots that work in molecular factories where small, but intricate structures are made on tiny assembly lines, that construct networks of molecular conductors and transistors for use as electrical circuits, or that continually patrol inside “adaptive” materials and repair them when necessary. Thus biomolecular motors could form the basis of bottom-up approaches for constructing, active structuring and maintenance at the nanometer scale
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Dey, Abhishek. "Modeling and identification of biomolecular systems". Thesis, IIT Delhi, 2019. http://eprint.iitd.ac.in:80//handle/2074/8121.
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Tyka, Michael. "Absolute free energy calculations for biomolecular systems". Thesis, University of Bristol, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.439666.
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Shu, Wenmiao. "Biomolecular sensing and actuation using microcantilever systems". Thesis, University of Cambridge, 2007. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.612828.
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Lickert, Benjamin [Verfasser], i Gerhard [Akademischer Betreuer] Stock. "Data-based Langevin modeling of biomolecular systems". Freiburg : Universität, 2021. http://d-nb.info/1241962669/34.
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Baker, Nathan Andrew. "Mathematical and computational modeling of biomolecular systems /". Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2001. http://wwwlib.umi.com/cr/ucsd/fullcit?p3007138.
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von, Hansen Yann [Verfasser]. "Stochastic Dynamics in Biomolecular Systems / Yann von Hansen". Berlin : Freie Universität Berlin, 2014. http://d-nb.info/1069165948/34.
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Clark, Kendal W. "STM Study of Molecular and Biomolecular Electronic Systems". Ohio University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1282363151.
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O'Reilly, E. J. "Quantum traits in the dynamics of biomolecular systems". Thesis, University College London (University of London), 2014. http://discovery.ucl.ac.uk/1451070/.
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The majority of biology can be adequately described by classical laws, yet there are suggestions that a variety of organisms may harness non-trivial quantum phenomena to gain a biological advantage. This thesis is concerned with the light induced dynamics in photosynthetic light harvesting antennae. Quantum coherences persisting on picosecond time-scales have been repeatedly observed in a variety of species. This ran contrary to the prevailing theories of energy transfer dynamics in these systems. A consensus has emerged that a delicate competition between electronic and vibrational interactions is responsible for prolonging coherences between electronic states of chromophores. In particular, interactions with specific under-damped vibrational modes are known to play a fundamental role. This thesis demonstrates that room temperature, efficient vibration-assisted energy transfer in a biologically relevant exciton-vibration dimers can manifest and benefit from non-classical fluctuations of collective pigment motions. The inadequacy of a classical description of selected vibrations is further illustrated by identifying features of electronic dynamics that are enhanced by quantum properties. A quan\-tum-thermo\-dynamical form\-alism describing heat and work fluxes between partitions of a closed quan\-tum system is extended to open quan\-tum systems in the non-per\-turb\-ative regime. This reveals non-trivial relations between the electronic interactions among chromophores and the relative contribution of work- and heat-like energy fluxes between electronic and vibrational motions. This in turn highlights relations between structure and energy transformations in photosynthetic complexes. Finally, the thesis investigates energy transfer within and between antennae of purple bacteria acclimated to different illumination conditions. The protein composition is altered depending on the light levels. Consequently, the electronic energy landscape is modified to accelerate intra-complex energy transfer without detriment to inter-complex transfer, thereby promoting or diminishing resonances with specific vibrational motions. This suggests that acclimation may serve to exploit non-trivial quantum phenomena.
15
Mertiri, Alket. "Mid-infrared photothermal hyperspectral imaging of biomolecular systems". Thesis, Boston University, 2014. https://hdl.handle.net/2144/12952.
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Thesis (Ph.D.)--Boston UniversityThe development of novel techniques in spectroscopy and microscopy that are label-free, contactless and accessible is useful among many scientific disciplines, ranging from Materials Science to Biomedical Engineering. Hyperspectral photothermal imaging using vibrational spectroscopy promises to be a new tool in the arsenal for analysis and characterization of materials. This technique can be used for understanding structural composition of a material that is advantageous to the materials scientist. A combination of microscopy and spectroscopy is also beneficial to the biologist or pathologist that analyzes a complex sample with rich morphology. Photothermal hyperspectral microscopy is a label-free nondestructive method that utilizes specific vibrational bands of a molecule giving spectral information to an image. The method is based on changes in the thermal state, and the associated change in the refractive index of the sample as it is irradiated with mid-infrared light. Photothermal microscopy has rapidly emerged as one of the most sensitive label-free optical spectroscopic methods, rivaling current well-established methods based on fluorescence. The method has been used to image single non-fluorescent molecules in room temperature and to directly characterize biological features such as mitochondria and red blood cells. Despite great breakthroughs in the visible regime, the method has not been explored in the mid-infrared regime where most of the biological molecules have characteristic vibrational modes that constitute an intrinsic molecular "fingerprint" . This thesis presents the development of a new technique to measure the linear and nonlinear mid-infrared photothermal response induced by tunable high power lasers such as Quantum Cascade Lasers (QCLs). Photothermal response can be measured in pump-probe heterodyne detection, using short wavelength visible lasers and compact fiber lasers as a probe. This allows for direct detection of the fingerprint mid-infrared vibrational modes through ultrasensitive photodetectors. Integrated into a mid-infrared microscope, the system facilitates the acquisition of spectra and images on condensed phase samples. Photothermal heterodyne mid-infrared hyperspectral vibrational technique is used to image biological samples such as bird brain and other biomolecules First photothermal images on specially designed plasmonic metamaterials, designed to either enhance or suppress a selected mid-infrared vibrational normal mode, are demonstrated. Plasmonic metamaterials can be engineered using electron beam lithography for functional studies on biomolecules enhancing selected vibrational infrared resonances. This study takes advantage of the strong interaction between light and matter and investigates properties of the material that are difficult to detect through conventional spectroscopic methods. The new technique has the ability to advance studies in many fields, as it is applicable to different types of materials, non-destructive, accessible and inexpensive.
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Viveca, Lindahl. "Optimizing sampling of important events in complex biomolecular systems". Doctoral thesis, KTH, Fysik, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-217837.
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Proteins and DNA are large, complex molecules that carry out biological functions essential to all life. Their successful operation relies on adopting specific structures, stabilized by intra-molecular interactions between atoms. The spatial and temporal resolution required to study the mechanics of these molecules in full detail can only be obtained using computer simulations of molecular models. In a molecular dynamics simulation, a trajectory of the system is generated, which allows mapping out the states and dynamics of the molecule. However, the time and length scales characteristic of biological events are many orders of magnitude larger than the resolution needed to accurately describe the microscopic processes of the atoms. To overcome this problem, sampling methods have been developed that enhance the occurrence of rare but important events, which improves the statistics of simulation data. This thesis summarizes my work on developing the AWH method, an algorithm that adaptively optimizes sampling toward a target function and simultaneously finds and assigns probabilities to states of the simulated system. I have adapted AWH for use in molecular dynamics simulations. In doing so, I investigated the convergence of the method as a function of its input parameters and improved the robustness of the method. I have also worked on a generally applicable approach for calculating the target function in an automatic and non-arbitrary way. Traditionally, the target is set in an ad hoc way, while now sampling can be improved by 50% or more without extra effort. I have also used AWH to improve sampling in two biologically relevant applications. In one paper, we study the opening of a DNA base pair, which due to the stability of the DNA double helix only very rarely occurs spontaneously. We show that the probability of opening depends on both nearest-neighbor and longer-range sequence effect and furthermore structurally characterize the open states. In the second application the permeability and ammonia selectivity of the membrane protein aquaporin is investigated and we show that these functions are sensitive to specific mutations.QC 20171117
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Prévot, Martine. "Biomolecular simulations: structure, thermodynamics and dynamics of biological systems". Doctoral thesis, Universite Libre de Bruxelles, 2002. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/211440.
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Alapan, Yunus. "MICROFABRICATED SYSTEMS INTEGRATED WITH BIOMOLECULAR PROBES FOR CELL MECHANICS". Case Western Reserve University School of Graduate Studies / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=case1466014738.
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VanMetre, Holly Sue Morris. "Individual submicrometer particles and biomolecular systems studied on the nanoscale". Diss., University of Iowa, 2016. https://ir.uiowa.edu/etd/3207.
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The necessity to explore nanoscopic systems is ever increasing in the world of science and technology. This evolving need to study such physically small systems demands new experimental techniques and methodologies. Atomic force microscopy (AFM) is a versatile technique that can overcome many nanoscopic size limitations. AFM has been utilized in the world of nanotechnology to study physiochemical properties of particles, materials, and biomolecules through characterization of morphology, electrical and mechanical properties, binding interactions, and surface tension, among others. The work discussed herein is largely a report of several novel AFM methodologies that were developed to allow new characterization techniques of individual submicrometer particles and single biomolecular interactions.
The effects of atmospheric aerosols on the radiative budget of the earth and climate are largely unknown. For this reason, characterizing the physiochemical properties of aerosols is vital. Since the particles that have relatively long lifetimes in the atmosphere are smaller than one micrometer in size, high resolution microscopy techniques are required to study them. AFM is a suitable technique for single particle studies because it has nanometer spatial resolution, can perform experiments under ambient pressure and variable relative humidity and temperature. These advantages were utilized here and AFM was used to study morphology, organic volume fraction, water uptake, and surface tension of nascent sea spray aerosol (SSA) particles as well as laboratory generated aerosols composed of relevant chemical model systems. The morphology of SSA was found, often times, to be composed of core-shell structure. With complementary microscopy techniques, the composition of the core and the shell was found to be inorganic and organic in nature, respectively. Novel methodology to measure water uptake and surface tension of single substrate deposited particles with AFM was established using chemical model systems. Furthermore, these methodologies were employed on nascent chemically complex SSA particles collected from a biologically active oceanic waveflume experiment. Finally, phase imaging was used to measure organic volume fraction on a single particle basis and was correlated with biological activity. Overall, this suite of single (submicrometer) particle AFM analysis techniques have been established, allowing future systematic studies of increasing complexity aimed at bridging the gap between the simplicity of laboratory generated particles and the complexity of nature.
Another nanotechnology topic of interest is studying single biomolecular interactions. Virtually every biological process involves some amount of minute forces that are required for the biomolecular system to function properly. For example, there are picoNewton forces associated with enzymatic motions that are important for enzyme catalysis. The AFM studies reported here use a model enzyme/drug system to measure the forces associated with single molecule adhesion events. Escherichia Dihydrofolate Reductase (DHFR) is a target of cancer therapeutic studies because it can be inhibited by drugs like methotrexate (MTX) that are structurally similar to the natural folate binder but have much higher binding affinity. One of the obstacles of single molecular recognition force spectroscopy (MRFS) studies is the contribution of non-specific forces that create a source of uncertainty. In this study, DHFR and MTX are bound to the surface and the AFM tip, respectively, using several different linking molecules. These linking molecules included polyethylene glycol (PEG) and double stranded DNA (dsDNA) and the distribution of forces was compared to scenarios were a linker was not employed. We discovered that dsDNA and PEG both allow identification and removal of non-specific interaction forces from specific forces of interest, which increases the accuracy of the measurement compared to directly bound constructs. Traditionally, the linker of choice in the MRFS community is PEG. Here, we introduce dsDNA as a viable linker that offers more rigidity than PEG, which may be desirable in future molecular constructs.
The majority of the work and data presented in this dissertation supports the establishment of new AFM methodologies that can be used to better explore single biomolecular interactions and individual submicrometer particles on the nanoscale.
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Melli, Mauro. "Mechanical resonating devices and their applications in biomolecular studies". Doctoral thesis, SISSA, 2010. http://hdl.handle.net/20.500.11767/4646.
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To introduce the reader in the subjects of the thesis, Chapter 1 provides an overview on the
different aspects of the mechanical sensors. After a brief introduction to NEMS/MEMS, the
different approaches of mechanical sensing are provided and the main actuation and detection
schemes are described. The chapter ends with an introduction to microfabrication.
Chapter 2 deals with experimental details. In first paragraph the advantages of using a pillar
instead of common horizontal cantilever are illustrated. Then, the fabrication procedures and the
experimental setup for resonance frequencies measurement are described. The concluding
paragraph illustrates the technique, known as dip and dry, I used for coupling mechanical
detection with biological problems.
In Chapter 3, DNA kinetics of adsorption and hybridization efficiency, measured by means of pillar
approach, are reported.
Chapter 4 gives an overview of the preliminary results of two novel applications of pillar approach.
They are the development of a protein chip technology based on pillars and the second is the
combination of pillars and nanografting, an AFM based nanolithography.
Chapter 5 starts with an introduction about the twin cantilever approach and of the mechanically
induced functionalization. Fabrication procedure is described in the second paragraph. Then the
chemical functionalizations are described and proved. Cleaved surface analyses and the
spectroscopic studies of the mechanically induced functionalization are reported.
In Appendix A there is an overview of the physical models that are used in this thesis.
21
Torun, Hamdi. "Micromachined membrane-based active probes for biomolecular force spectroscopy". Diss., Georgia Institute of Technology, 2010. http://hdl.handle.net/1853/39638.
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Atomic force microscope (AFM) is an invaluable tool for measurement of pico-Newton to nano-Newton levels of interaction forces in liquid. As such, it is widely used to measure single-molecular interaction forces through dynamic force spectroscopy. In this technique, the interaction force spectra between a specimen on the sharp tip of the cantilever and another specimen on the substrate is measured by repeatedly moving the cantilever in and out of contact with the substrate. By varying the loading rate and measuring the bond rupture force or bond lifetime give researchers information about the strength and dissociation rates of non-covalent bonds, which in turn determines the energy barriers to overcome. Commercially available cantilevers can resolve interaction forces as low as 5 pN with 1 kHz bandwidth in fluid. This resolution can be improved to 1 pN by using smaller cantilevers at the expense of microfabrication constraints and sophisticated detection systems. The pulling speed of the cantilever, which determines the loading rate of the bonds, is limited to the point where the hydrodynamic drag force becomes comparable to the level of the molecular interaction force. This level is around 10 um/s for most cantilevers while higher pulling speeds are required for complete understanding of force spectra. Thus, novel actuators that allow higher loading rates with minimal hydrodynamic drag forces on the cantilevers, and fast, sensitive force sensors with simple detection systems are highly desirable.
This dissertation presents the research efforts for the development of membrane-based active probe structures with electrostatic actuation and integrated diffraction-based optical interferometric force detection for single-molecular force measurements. Design, microfabrication and characterization of the probes are explained in detail. A setup including optics and electronics for experimental characterization and biological experiments with the probes membranes is also presented. Finally, biological experiments are included in this dissertation.
The "active" nature of the probe is because of the integrated, parallel-plate type electrostatic actuator. The actuation range of the membrane is controlled with the gap height between the membrane and the substrate. Within this range it is possible to actuate the membrane fast, with a speed limited by the membrane dynamics with negligible hydrodynamic drag. Actuating these membrane probes and using a cantilever coupled to the membrane, fast pulling experiments with an order of magnitude faster than achieved by regular AFM systems are demonstrated.
The displacement noise spectral density for the probe was measured to be below 10 fm/rtHz for frequencies as low as 3 Hz with differential readout scheme. This noise floor provides a force sensitivity of 0.3 - 3 pN with 1 kHz bandwidth using membranes with spring constants of 1 - 10 N/m. This low inherent noise has a potential to probe wide range of biomolecules. The probes have been demonstrated for fast-pulling and high-resolution force sensing. Feasibility for high throughput parallel operation has been explored. Unique capabilities of the probes such as electrostatic spring constant tuning and thermal drift cancellation in AFM are also presented in this dissertation.
22
Kummer, Kurt. "Investigation of structural properties in biomolecular systems using synchrotron-based spectroscopies". Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-39506.
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Solid state approaches to structural properties like diffraction or microscopy techniques often cannot be applied to biomolecular systems, at least not without special postpreparation which often corrupts the desired properties of the pristine systems. In this work the capabilities of synchrotron-based, soft X-ray spectroscopies as an alternative way to unravel structural properties of such systems are tested. To this end, three exemplary systems were investigated each with the focus on another facet and characteristic length scale. The first example are DNA-alkanethiol self-assembled monolayers, also known as DNA microarrays or DNA chips, for which a way to monitor and controllably tune the structural composition on the mesoscopic scale of many thousands of molecules was sought for. The second example focuses on the single-molecule and submolecular scale in metalprotein hybrid compounds with the aim to identify the binding site of metal atoms or ions within protein molecules and the underlying interaction mechanisms. The most fundamental structural scale, the level of single bonds and molecular orbitals, is addressed in the last example where it was tried to elaborate an approach to map the topology of molecular orbitals based upon X-ray absorption properties. This approach was put to the practical test for the characteristic pi*peptide orbitals in protein backbones. For all three investigated examples, spectroscopies using soft X-ray synchrotron radiation were able to extract the desired information, thus confirming that they may grant alternative access to structural properties of soft-matter systems in cases where standard approaches failKlassische Festkörpertechniken zur Strukturuntersuchung, wie Streu- oder Mikroskopiemethoden, können häufig nicht auf Biomolekülsysteme angewandt werden, zumindest nicht ohne spezielle Postpräparation, die die ursprünglichen Eigenschaften dieser Systeme oft verfälscht. In dieser Arbeit soll untersucht werden, inwieweit Röntgenspektroskopien basierend auf Synchrotronstrahlung einen alternativen Zugang zu Struktureigenschaften solcher Systeme bieten. Dazu wurden drei Systeme exemplarisch untersucht, jeweils mit Schwerpunkt auf einen anderen Aspekt und charakteristischen Längenbereich. Für selbstorganisierende DNA-Alkanthiol-Schichten, sogenannte DNA-Chips, wurde nach eine Weg gesucht, ihre strukturelle Zusammensetzung auf der mesoskopischen Ebene vieler tausend Moleküle zu bestimmen und kontrolliert zu modifizieren. Metallisierte Proteinstrukturen wurden auf Einzelmolekül- bzw. submolekularer Ebene untersucht, mit dem Ziel, die Orte der Metallanlagerung innerhalb des Proteins und die zugrundeliegenden Wechselwirkungsmechanismen zu identifizieren. Die unterste strukturelle Ebene, der Bereich einzelne Bindungen und Molekülorbitale, wurde adressiert am Beispiel der pi*peptide Orbitale des Proteinrückrats. Dafür wurde eine Methode zur Kartographierung einzelner Orbitale anhand von Röntgenabsorptionseigentschaften herausgearbeitet und praktisch getestet. In allen drei Fällen konnten Röntgenspektroskopien die nötigen Informationen liefern und damit ihr Potential für Strukturuntersuchungen in weicher Materie unter Beweis stellen
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Nakajima, Nobuyuki. "A multicanonical molecular dynamics method and its applications to biomolecular systems". 京都大学 (Kyoto University), 2000. http://hdl.handle.net/2433/181460.
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Schaudinnus, Norbert [Verfasser], i Gerhard [Akademischer Betreuer] Stock. "Stochastic modeling of biomolecular systems using the data-driven Langevin equation". Freiburg : Universität, 2015. http://d-nb.info/1122646887/34.
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Smart, Jason. "The application of contimuum electrostatics and diffusional models to biomolecular systems /". Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC IP addresses, 1998. http://wwwlib.umi.com/cr/ucsd/fullcit?p9906489.
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Börjesson, Ulf Börjesson Ulf Erik. "Electrostatic interactions in computer simulations of biomolecular systems : influence of system size, solvation, and titration /". [S.l.] : [s.n.], 2004. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=15454.
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Weggler, Sophie [Verfasser], i Andreas [Akademischer Betreuer] Hildebrandt. "Correlation induced electrostatic effects in biomolecular systems / Sophie Weggler. Betreuer: Andreas Hildebrandt". Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2011. http://d-nb.info/105109514X/34.
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Seibert, Johann Jakob [Verfasser]. "Computation of Electronic Excitation Spectra of Large Biomolecular Systems / Johann Jakob Seibert". Bonn : Universitäts- und Landesbibliothek Bonn, 2020. http://d-nb.info/1224270584/34.
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Herath, Narmada Kumari. "Model order reduction for stochastic models of biomolecular systems with time-scale separation". Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/118083.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 177-183).
Biomolecular systems often involve reactions that take place on different time-scales, giving rise to 'slow' and 'fast' system variables. This property is widely used in the analysis of systems to obtain dynamical models with reduced dimensions. In deterministic systems, methods to obtain such reduced-order models are well defined by the singular perturbation or averaging techniques. However, model reduction of stochastic systems remains an ongoing area of research. In particular, existing model reduction methods for stochastic models of biomolecular systems lack rigorous error quantifications between the full and reduced dynamics. Furthermore, they only provide approximations for the slow variable dynamics, making the application of such methods to biomolecular systems difficult since the variables of interest are typically mixed (i.e., they encompass both fast and slow variables). In this thesis, we consider biomolecular systems modeled using the chemical Langevin equation (CLE) and the Linear Noise Approximation (LNA). Specifically, we consider biomolecular systems with linear propensity functions modeled by the CLE and systems with arbitrary propensity functions modeled by the LNA. For these systems, we obtain reduced-order models that approximate both the slow and fast variables under time-scale separation conditions. In particular, with suitable assumptions, we prove that the moments of the reduced-order models converge to those of the full systems as the time-scale separation becomes large. Our results further provide a rigorous justification for the accuracy of the stochastic total quasi-steady state approximation (tQSSA). We then consider two applications of these reduced-order models. In the first application, we analyze the trade-offs between modularity and signal noise in biomolecular networks. In the second application, we consider the application of the reduced-order LNA developed in this work to obtain reduced-order stochastic models for gene-regulatory networks.
by Narmada Kumari Herath.
Ph. D.
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Zanoli, Laura Maria. "Ultrasensitive methods for the detection of biomolecular systems at the micro/nano scale". Doctoral thesis, Università di Catania, 2012. http://hdl.handle.net/10761/976.
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A great effort has been devoted, during the past decade, to the development of new devices for specific DNA sequences detection, due to the relevance of nucleic acid analysis in many areas, including clinical diagnostics, environmental monitoring and food-quality control. However, diagnostic tools used for the detection of nucleic acids need to fulfil specific requirements in term of sensitivity, selectivity and high-throughput in order to expand their applicability and to minimize the cost of the assay. In fact, very small amount of DNA is typically available for the analysis and a detection scheme capable of directly transducing the hybridization events with a proper sensitivity is required. In addition, the sequence to be targeted is often present in a complex environment such as the whole genomic DNA and the use of very specific and highly efficient probes is required in order to build highly selective detection scheme.
The purpose of my research activity was the identification of new methodologies useful for DNA detection with the principal aim to perform the analysis with a very small amount of samples. In this perspective, interesting results were obtained by using microfluidic systems, characterized by the presence of one or more microchannels where fluid reagents are easily and carefully manipulated. In particular, the combined use of a droplet-based microfluidics, PNA-MBs and fluorescence microscopy enabled the selective and sensitive detection of DNA in an innovative and efficient platform. The experiments were carried out by using both oligonucleotides and PCR amplification products and were aimed at detecting DNA sequences of different olive cultivar.
The ultrasensitive detection of DNA was also investigated by coupling microfluidic devices with the SPRi apparatus. A similar approach allowed a real time label-free detection of specific genomic DNA sequences carrying the â°39 thalassemia mutation. The capacity in term of selectivity and sensitivity was investigated by employing surface-immobilized PNA probes in combination with gold nanoparticle-enhanced SPRi detection. The DNA concentrations measured by this method are in a range suitable for detecting DNA samples without amplification.
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Doro, F. "COMPUTATIONAL MODELLING OF BIOMOLECULAR SYSTEMS: APPLICATIONS TO THE STUDY OF MOLECULAR RECOGNITION PROCESSES". Doctoral thesis, Università degli Studi di Milano, 2014. http://hdl.handle.net/2434/229385.
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In this thesis a broad range of computational modelling techniques has been used to study biomolecular systems. In particular two main topics have been addressed: (i) the conformational analysis of unnatural glycopeptides, in which Monte Carlo methods have been used to sample different molecule conformations in order to analyze and characterize their structural, dynamical and functional properties and (ii) the analysis of protein-protein interactions (PPIs) in classical cadherins and the design of small peptidomimetic inhibitors. Here, molecular dynamics techniques (both biased and unbiased) together with computer-aided drug design were used to study the structural properties and the mechanism of the cadherin homophilic binding and to design the first class of small molecule inhibitors of their interaction.
The conformational studies performed on a series of α-N-linked glycopeptides revealed their preference for an extended conformation, a feature which was later confirmed by NMR data, thus demonstrating the predictive ability of the calculations. PPIs studies on classical cadherins led to the development of the first rationally designed inhibitors of the homophilic cadherin-cadherin interaction and also allowed to gain more insight into the cadherin binding mechanism.
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Börjesson, Ulf [Verfasser]. "Electrostatic interactions in computer simulations of biomolecular systems: influence of system size, solvation, and titration / Ulf Börjesson". Aachen : Shaker, 2004. http://d-nb.info/1170529933/34.
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Quantrill, Nigel Stuart Michael. "Optical fluoroassays based on substrate induced quenching". Thesis, Cranfield University, 1995. http://dspace.lib.cranfield.ac.uk/handle/1826/10428.
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The
recently proposed bioassay procedure that is based on the substrate induced
quenching (SIQ) of an indicator fluorescence for the measurement of analyte
concentrations is evaluated. In this type of assay a enzynatic reaction and a
fluorescence
quenching interaction are coupled together. Typically, an appropriate
dehydrogenase enzyme reduces or oxidises the nicotinamide adenine dinucleotide
cofactor. The
change in the concentration of NADH results in variations in the excited
fluorophore population as observed through fluorescence intensity. This latter aspect is
used to monitor substrate (analyte) concentrations.
Results on the
investigation of the substrate induced quenching bioassay method and
possibilities of using it as the basis of (i) a novel enzyme bioassay technique and (ii) a
novel
bioprobe format are presented. Ethanol was chosen as the model analyte, and a
new
assay procedure for its measurement was developed.
A
generic theoretical relation is discussed for the observed assay kinetics of substrate
induced
quenching (SIQ) and a model is described that includes the effects due to
dynamic/static quenching of the fluorophore by either the enzyme substrate or product.
The
validity of the derived model is shown by comparison with experimental results for a
SIQ based ethanol assay. The option of running the dehydrogenase reaction so as to
consume NADH rather than
generate it is also investigated. In order to demonstrate this
approach acetaldehyde was chosen as the model analyte, and a assay procedure for its
measurement was
developed.
The
potential of the SIQ technique for incorporation into biosensor based upon a
'reservoir' format was demonstrated through the development of custom optical
instrumentation and resevoir flowcell. Applicability of the SIQ technique to other
biosensor formats such as flow-injection analysis and 'dry reagent' technology is
discussed.
The overall
applicability of the SIQ technique is assessed through the generation of a
number of SIQ assays on the following substrates: ethanol, glucose, glucose-6-
phosphate, L-glutamic acid, isocitric acid, acetaldehyde, pyruvic acid, ot-ketoglutaric
acid, and oxalacetic acid.
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Markthaler, Daniel [Verfasser], i Niels [Akademischer Betreuer] Hansen. "Disentangling force field and sampling issues in biomolecular systems / Daniel Markthaler ; Betreuer: Niels Hansen". Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2020. http://d-nb.info/1233737767/34.
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Lenive, Oleg. "The role of extrinsic noise in biomolecular information processing systems : an in silico analysis". Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/31575.
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The intrinsic stochasticity of biomolecular systems is a well studied phe- nomenon. Less attention has been paied to other sources of variability, so called extrinsic noise. While the precise definition of extrinsic noise de- pends on the system in question, it affects all cells and its significance has been demonstrated experimentally. Information theory provides a rigorous mathematical framework for quan- tifying both the amount of information available to a signalling system and its ability to transmit this information. Intracellular signal transduction re- mains a relatively unexplored frontier for the application of information theory. In this thesis, we rely on a metric called mutual information to quantify in- formation flow in models of biochemical signalling systems. After briefly discussing the theoretical background and some of the practical difficulties of estimating mutual information in Chapter 2, we apply it in the context of simplified models of intracellular signalling, referred to as motifs. Using a comprehensive set of two-node motifs we explore the effects of extrinsic noise, model parameters and various combinations of interaction, on the system's ability to transmit information about an input signal, repre- sented by a telegraph process. Our results illustrate the importance of the system's response time and demonstrate a trade-off in transmitting infor- mation about the current state of the input or its average intensity over a period of time. In Chapter 4, we address the problem of determining the magnitude of ex- trinsic noise in the presence of intrinsic stochasticity. Using the Approximate Bayesian Computation - sequential Monte Carlo algorithm, together with published experimental data, we infer parameters describing extrinsic noise in a model of E. coli gene expression. Lastly, in Chapter 5, we construct and analyse models of bacterial two- component signalling, bringing together insights gleaned from earlier work. The results show how the abundances of different molecular species in the system may transmit information about the input signal despite its stochas-tic nature and considerable variation in the numbers of protein molecules present.
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Tauer, Anthony Philip. "Theoretical Investigations of Pi-Pi and Sulfur-Pi Interactions and their Roles in Biomolecular Systems". Thesis, Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/7573.
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The study of noncovalent interactions between aromatic rings and various functional groups is a very popular topic in current computational chemistry. The research presented in this thesis takes steps to bridge the gap between theoretical prototypes and real-world systems.
The non-additive contributions to the interaction energy in stacked aromatic systems are measured by expanding the prototype benzene dimer into trimeric and tetrameric systems. We show that the three- and four-body interaction terms generally do not contribute significantly to the overall interaction energy, and that the two-body terms are essentially the same as in the isolated dimer.
The sulfur-pi interaction is then studied by using the hydrogen sufide-benzene dimer as a prototype system for theoretical predictions. We obtain higly-accurate potential energy curves, as well as an interaction energy extrapolated to the complete basis set limit. Energy decomposition analysis using symmetry-adapted perturbation theory shows that the sulfur-pi interaction is primarily electrostatic in nature.
These theoretical results are then compared to an analysis of real sulfur-pi contacts found by searching protein structures in the Brookhaven Protein DataBank. We find that the most frequently seen configuration does not correspond to the theoretically predicted equilibrium for sydrogen sulfide-benzene, but instead to a configuration that suggests an alkyl-pi interaction involving the carbon adjacent to the sulfur atom. We believe our findings indicate that environmental effects within proteins are altering the energetics of the sulfur-pi interaction so that other functional groups are preferred for interacting with the aromatic ring.
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Fowler, Philip William. "Qualitative and quantitative aspects of biomolecular systems revealed by large scale and grid computing methods". Thesis, University College London (University of London), 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.430877.
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Monti, Susanna. "Molecular Dynamics Studies of the Adsorption of Biomolecular Systems on Metal and Metal Oxide Surfaces". Doctoral thesis, KTH, Teoretisk kemi och biologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-198489.
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Kenning, Nicole Lynn. "Spatial and temporal evolution of the photoinitiation rate in thick polymer systems". Diss., University of Iowa, 2006. http://ir.uiowa.edu/etd/76.
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Beutler, Thomas Christian. "Thermodynamic properties derived from molecular dynamics computer simulations : improved methods for the application to biomolecular systems /". [S.l.] : [s.n.], 1994. http://e-collection.ethbib.ethz.ch/show?type=diss&nr=10915.
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Schneider, Violetta Franziska Roswitha [Verfasser], i M. [Akademischer Betreuer] Elstner. "Structural Studies of Biomolecular Systems with Molecular Dynamics Simulations / Violetta Franziska Roswitha Schneider ; Betreuer: M. Elstner". Karlsruhe : KIT-Bibliothek, 2018. http://d-nb.info/1168325587/34.
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Crompton, D. L. "Decoding the picosecond dynamics of aqueous biomolecular systems : through novel terahertz instrumentation and molecular dynamic simulations". Thesis, University of Essex, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.617016.
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This thesis explores the picosecond dynamics of aqueous solvent and the low frequency modes of biomolecular systems. These dynamics are probed with a combination of experimental THz spectroscopy and theoretical models from molecular dynamic simulations. The dynamics of the water are first measured in a polar liquid concentration series, with an attenuated total reflectance method to reduce absorption from the highly absorbing solvent. Reverse micelle systems are also investigated using a transmission method to reduce the non-essential bulk water around the sugar trehalose. The THz spectrum and molecular dynamic simulations of both these experiments show increasingly sterically hindered waters in the presence of a perturbed hydrogen bond network. Classical computational models of condensed phased water do not reproduce a broad spectral feature at 200 cm-l (6 THz). A region associated with the bending and stretching motions of hydrogen bonding. Three methods of explicit polarisation are tested on classical water models to improve modelling of this bending and stretching dynamic, but each method fails to replicate a 200 cm-l peak. It was concluded quantum mechanical effects of the hydrogen bond are not adequately accounted for, which may significantly impact the 200 cm-l frequency region. The low frequency modes of proteins are also investigated using the Gprotein coupled receptor bovine rhodopsin . Rhodopsin is activated by light illumination, which causes a conformational shift in the protein structure. This was detected as a change in the proteins low frequency dynamics that were stabilised by the presence of membrane. Normal mode analysis of the inactive and active bovine rhodopsin crystal structure confirmed these results. Furthermore, part of this thesis explores a novel THz spectrometer design, based on the principles of polarisation modulation infrared reflection absorption spectroscopy. This spectrometer has advantages over traditional methods, principally being able to perform real time referencing without the need of a separate optical path.
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Schneider, Violetta [Verfasser], i M. [Akademischer Betreuer] Elstner. "Structural Studies of Biomolecular Systems with Molecular Dynamics Simulations / Violetta Franziska Roswitha Schneider ; Betreuer: M. Elstner". Karlsruhe : KIT-Bibliothek, 2018. http://d-nb.info/1168325587/34.
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Hahn, Jaeseung. "Programmable biomolecular integration and dynamic behavior of DNA-based systems for development of biomedical nano-devices". Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122213.
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Thesis: Ph. D. in Medical Engineering and Medical Physics, Harvard-MIT Program in Health Sciences and Technology, 2019Cataloged from PDF version of thesis.
Includes bibliographical references.
Departing from the traditional role as a carrier of genetic information, DNA has emerged as an engineering material for construction of nano-devices. The advances in the field of DNA nanotechnology have enabled design and synthesis of DNA nanostructures of arbitrary shapes and manipulation of the nanostructures' conformations in a programmable way. DNA-based systems offer potential applications in medicine by manipulating the biological components and processes that occur at the nanometer scale. To accelerate the translation of DNA-based systems for medical applications, we identified some of the challenges that are hindering our ability to construct biomedical nano-devices and addressed these challenges through advances in both structural and dynamic DNA nanotechnology. First, we tested the stability of DNA nanostructures in biological environments to highlight the necessity of and path towards protection strategies for prolonged integrity of biomedical nano-devices. Then, we constructed a platform for robust 3D molecular integration using DNA origami technique and implemented the platform for a nanofactory capable of production of therapeutic RNA to overcome the challenges in RNA delivery. Moreover, we established a mechanism to drive DNA devices by changing temperature with prolonged dynamic behavior that was previously challenging to accomplish without special modification of DNA and/or equipment not readily available in a typical lab setting. Together, the progress made in this thesis bring us another step closer to realization of medical applications of DNA nanotechnology by focusing on the challenges in both structural and dynamic aspects of the technology.
by Jaeseung Hahn.
Ph. D. in Medical Engineering and Medical Physics
Ph.D.inMedicalEngineeringandMedicalPhysics Harvard-MIT Program in Health Sciences and Technology
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FARROTTI, ANDREA. "Molecular dynamics approaches in the study of biomolecular systems of increasing complexity: peptides, proteins and membranes". Doctoral thesis, Università degli Studi di Roma "Tor Vergata", 2013. http://hdl.handle.net/2108/203357.
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Molecular dynamics (MD) simulations are a powerful tool to study biochemical processes at the atomic level and to complement experiments by providing otherwise unattainable structural and dynamic information. In this thesis, different simulative approaches were applied to two classes of problems. The first regards the mechanism of lipid bilayer perturbation by antimicrobial peptides (AMPs), which kill bacteria by disrupting their membranes. Our computational results on peptides temporin L, LAH4, trichogin GAIV and PMAP-23 clarified several aspects of the mechanism of action of AMPs, illustrating how peptide sequence modulates aggregation and insertion in the lipid bilayer, and showing several facets of membrane disruption by AMPs, such as formation of bilayer defects, membrane thinning and perturbation of lipid dynamics. Overall, these data indicate that AMPs activity is regulated by several complex equilibria that should be taken into account in the rational design of new antibiotic drugs. Other studies focused on RRAS and SHP-2, two proteins involved in the MAPK pathway and in a family of disorders called RASopathies. We analyzed an RRAS mutation, isolated in a patient affected by Noonan syndrome, causing an enhancement in the rate of GDP dissociation. MD simulations revealed that this effect is related to the perturbation of the conformational transitions of the RRAS molecular switch. Similarly, simulations showed that the motions of an α-helix resulted to be essential in the function of SHP-2, thus providing new indications on the possible molecular effects of several pathogenic mutations. These studies underline once more the importance of conformational fluctuations in the physiological and aberrant function of proteins. All MD simulations reported in this thesis were consistent with the available experimental data, thus confirming the reliability of in silico approaches in obtaining novel insights in the characterization of complex biomolecular systems.
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Mujica, Martinez Cesar Augusto [Verfasser], i Michael [Akademischer Betreuer] Thorwart. "Quantum dissipative dynamics of electrons in tailored molecular systems and of excitons in biomolecular systems / Cesar Augusto Mujica Martinez. Betreuer: Michael Thorwart". Hamburg : Staats- und Universitätsbibliothek Hamburg, 2014. http://d-nb.info/1059238004/34.
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Lemke, Oliver [Verfasser]. "Theoretical Analysis of Biomolecular Systems: Computational Simulations, Core-set Markov State Models, Clustering, Molecular Docking / Oliver Lemke". Berlin : Freie Universität Berlin, 2020. http://d-nb.info/1205735461/34.
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Andrejić, Milica. "Development of Hybrid QM/QM Local Correlation Methods for the Study of Metal Sites in Biomolecular Catalysis". Doctoral thesis, Niedersächsische Staats- und Universitätsbibliothek Göttingen, 2015. http://hdl.handle.net/11858/00-1735-0000-0022-6011-C.
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Benson, Sven P. [Verfasser], i Jürgen [Akademischer Betreuer] Pleiss. "Molecular modeling of hydrophobic effects in complex biomolecular systems : from simple mixtures to protein-interface aggregation / Sven P. Benson. Betreuer: Jürgen Pleiss". Stuttgart : Universitätsbibliothek der Universität Stuttgart, 2015. http://d-nb.info/1066646015/34.
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Nydén, Magnus. "NMR diffusion studies of microheterogeneous systems surfactant solutions, polymers solutions and gels /". Lund : University of Lund, 1998. http://catalog.hathitrust.org/api/volumes/oclc/68945132.html.
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