Relevant bibliographies by topics / Biomolecules Structures

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  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
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Academic literature on the topic 'Biomolecules Structures'

Author: Grafiati
Published: 4 June 2021
Last updated: 17 February 2022

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Journal articles on the topic "Biomolecules Structures"

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Rubach, Paweł, Sebastian Zajac, Borys Jastrzebski, Joanna I. Sulkowska, and Piotr Sułkowski. "Genus for biomolecules." Nucleic Acids Research 48, no. D1 (2019): D1129—D1135. http://dx.doi.org/10.1093/nar/gkz845.

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Abstract The ‘Genus for biomolecules’ database (http://genus.fuw.edu.pl) collects information about topological structure and complexity of proteins and RNA chains, which is captured by the genus of a given chain and its subchains. For each biomolecule, this information is shown in the form of a genus trace plot, as well as a genus matrix diagram. We assemble such information for all and RNA structures deposited in the Protein Data Bank (PDB). This database presents also various statistics and extensive information about the biological function of the analyzed biomolecules. The database is regularly self-updating, once new structures are deposited in the PDB. Moreover, users can analyze their own structures.
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Fujisaki, Hiroshi, Kei Moritsugu, and Yasuhiro Matsunaga. "Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques—Searching for Mechanism and Kinetics of Biomolecular Functions." International Journal of Molecular Sciences 19, no. 10 (2018): 3177. http://dx.doi.org/10.3390/ijms19103177.

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To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics need to be characterized, but its atomistic details are hard to obtain both experimentally and computationally. Here, we review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: one is the Onsager–Machlup action method, and the other is the weighted ensemble method. Some applications of the above methods to biomolecular systems are also discussed and illustrated.
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Wang, Chong, and Min Wang. "Emulsion Electrospinning of Nanofibrous Delivery Vehicles for the Controlled Release of Biomolecules and the In Vitro Release Behaviour of Biomolecules." Advanced Materials Research 410 (November 2011): 98–101. http://dx.doi.org/10.4028/www.scientific.net/amr.410.98.

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Electrospinning is a popular technique for constructing nanofibrous tissue engineering scaffolds. Electrospinning is also amenable to the incorporation of drugs or biomolecules in fibers, which can provide local and sustained delivery of biological signals, such as growth factors, for the seeded cells. Drugs can normally be dissolved in polymer solutions for electrospinning, forming nanofibrous drug delivery systems. However, simply blending biomolecules in polymer solutions can result in denaturation of biomolecules and large initial burst release. Therefore, emulsion electrospinning, which can provide protection for biomolecules during electrospinning, is of great interest. In this investigation, biomolecule-containing scaffolds were emulsion electrospun using bovine serum albumin (BSA) as the model protein. Two polymers, poly (lactic-co-glycolic acid) and poly (D,L-lactic acid), were used due to their different degradation characteristics. Nanofibers with core-shell structures were electrospun from water-in-oil emulsions formulated by polymer solution, BSA-containing deionized water and a surfactant. By changing the polymer concentration and water phase volume, the fiber diameter and core-shell structure were varied. With different polymers and different fiber structures, the in vitro BSA release behaviours from fibrous scaffolds were different.
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Epp, Chris. "Teaching the structures of small biomolecules." Biochemical Education 16, no. 3 (1988): 152–54. http://dx.doi.org/10.1016/0307-4412(88)90190-2.

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Atreya, Hanudatta S. "Structures of biomolecules by NMR spectroscopy." Resonance 20, no. 11 (2015): 1033–39. http://dx.doi.org/10.1007/s12045-015-0271-7.

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Mrozowich, Tyler, Vanessa MeierStephenson, and Trushar R. Patel. "Microscale thermophoresis: warming up to a new biomolecular interaction technique." Biochemist 41, no. 2 (2019): 8–12. http://dx.doi.org/10.1042/bio04102008.

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Biomolecules, such as RNA, DNA, proteins and polysaccharides, are at the heart of fundamental cellular processes. These molecules differ greatly with each other in terms of their structures and functions. However, in the midst of the diversity of biomolecules is the unifying feature that they interact with each other to execute a viable biological system. Interactions of biomolecules are critical for cells to survive and replicate, for food metabolism to produce energy, for antibiotics and vaccines to function, for spreading of diseases and for every other biological process. An improved understanding of these interactions is crucial for studying how cells and organs function, to appreciate how diseases are caused and how infections occur, with infinite implications in medicine and therapy. Many biochemical and biophysical techniques are currently being employed to study biomolecular interactions. Microscale thermophoresis (MST) is a relatively new biophysical technique that can provide powerful insight into the interactions of biomolecules and is quickly being adopted by an increasing number of researchers worldwide. This article provides a brief description of principles underpinning the MST process, in addition to benefits and limitations.
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Ferreiro, Diego U., Elizabeth A. Komives, and Peter G. Wolynes. "Frustration in biomolecules." Quarterly Reviews of Biophysics 47, no. 4 (2014): 285–363. http://dx.doi.org/10.1017/s0033583514000092.

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AbstractBiomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their own structures and dynamics using as input seemingly random character strings of their sequence, following which they coalesce and perform integrated cellular functions. In large computational systems with finite interaction-codes, the appearance of conflicting goals is inevitable. Simple conflicting forces can lead to quite complex structures and behaviors, leading to the concept of frustration in condensed matter. We present here some basic ideas about frustration in biomolecules and how the frustration concept leads to a better appreciation of many aspects of the architecture of biomolecules, and especially how biomolecular structure connects to function by means of localized frustration. These ideas are simultaneously both seductively simple and perilously subtle to grasp completely. The energy landscape theory of protein folding provides a framework for quantifying frustration in large systems and has been implemented at many levels of description. We first review the notion of frustration from the areas of abstract logic and its uses in simple condensed matter systems. We discuss then how the frustration concept applies specifically to heteropolymers, testing folding landscape theory in computer simulations of protein models and in experimentally accessible systems. Studying the aspects of frustration averaged over many proteins provides ways to infer energy functions useful for reliable structure prediction. We discuss how frustration affects folding mechanisms. We review here how the biological functions of proteins are related to subtle local physical frustration effects and how frustration influences the appearance of metastable states, the nature of binding processes, catalysis and allosteric transitions. In this review, we also emphasize that frustration, far from being always a bad thing, is an essential feature of biomolecules that allows dynamics to be harnessed for function. In this way, we hope to illustrate how Frustration is a fundamental concept in molecular biology.
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Perale, Giuseppe, Marta Monjo, Joana M. Ramis, et al. "Biomimetic Biomolecules in Next Generation Xeno-Hybrid Bone Graft Material Show Enhanced In Vitro Bone Cells Response." Journal of Clinical Medicine 8, no. 12 (2019): 2159. http://dx.doi.org/10.3390/jcm8122159.

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Bone defects resulting from trauma, disease, surgery or congenital malformations are a significant health problem worldwide. Consequently, bone is the second most transplanted tissue just after blood. Although bone grafts (BGs) have been used for decades to improve bone repairs, none of the currently available BGs possesses all the desirable characteristics. One way to overcome such limitations is to introduce the feature of controlled release of active bone-promoting biomolecules: however, the administration of, e.g., recombinant Bone morphogenetic proteins (BMPs) have been used in concentrations overshooting physiologically occurring concentrations and has thus raised concerns as documented side effects were recorded. Secondly, most such biomolecules are very sensitive to organic solvents and this hinders their use. Here, we present a novel xeno-hybrid bone graft, SmartBonePep®, with a new type of biomolecule (i.e., intrinsically disordered proteins, IDPs) that is both resistant to processing with organic solvent and both triggers bone cells proliferation and differentiation. SmartBonePep® is an advanced and improved modification of SmartBone®, which is a bone substitute produced by combining naturally-derived mineral bone structures with resorbable polymers and collagen fragments. Not only have we demonstrated that Intrinsically Disordered Proteins (IDPs) can be successfully and safely loaded onto a SmartBonePep®, withstanding the hefty manufacturing processes, but also made them bioavailable in a tuneable manner and proved that these biomolecules are a robust and resilient biomolecule family, being a better candidate with respect to other biomolecules for effectively producing the next generation bone grafts. Most other biomolecules which enhances bone formation, e.g., BMP, would not have tolerated the organic solvent used to produce SmartBonePep®.
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Muniyappan, Srinivasan, Yuxi Lin, Young-Ho Lee, and Jin Hae Kim. "17O NMR Spectroscopy: A Novel Probe for Characterizing Protein Structure and Folding." Biology 10, no. 6 (2021): 453. http://dx.doi.org/10.3390/biology10060453.

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Oxygen is a key atom that maintains biomolecular structures, regulates various physiological processes, and mediates various biomolecular interactions. Oxygen-17 (17O), therefore, has been proposed as a useful probe that can provide detailed information about various physicochemical features of proteins. This is attributed to the facts that (1) 17O is an active isotope for nuclear magnetic resonance (NMR) spectroscopic approaches; (2) NMR spectroscopy is one of the most suitable tools for characterizing the structural and dynamical features of biomolecules under native-like conditions; and (3) oxygen atoms are frequently involved in essential hydrogen bonds for the structural and functional integrity of proteins or related biomolecules. Although 17O NMR spectroscopic investigations of biomolecules have been considerably hampered due to low natural abundance and the quadruple characteristics of the 17O nucleus, recent theoretical and technical developments have revolutionized this methodology to be optimally poised as a unique and widely applicable tool for determining protein structure and dynamics. In this review, we recapitulate recent developments in 17O NMR spectroscopy to characterize protein structure and folding. In addition, we discuss the highly promising advantages of this methodology over other techniques and explain why further technical and experimental advancements are highly desired.
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Mersmann, Sophia F., Léonie Strömich, Florian J. Song, et al. "ProteinLens: a web-based application for the analysis of allosteric signalling on atomistic graphs of biomolecules." Nucleic Acids Research 49, W1 (2021): W551—W558. http://dx.doi.org/10.1093/nar/gkab350.

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Abstract The investigation of allosteric effects in biomolecular structures is of great current interest in diverse areas, from fundamental biological enquiry to drug discovery. Here we present ProteinLens, a user-friendly and interactive web application for the investigation of allosteric signalling based on atomistic graph-theoretical methods. Starting from the PDB file of a biomolecule (or a biomolecular complex) ProteinLens obtains an atomistic, energy-weighted graph description of the structure of the biomolecule, and subsequently provides a systematic analysis of allosteric signalling and communication across the structure using two computationally efficient methods: Markov Transients and bond-to-bond propensities. ProteinLens scores and ranks every bond and residue according to the speed and magnitude of the propagation of fluctuations emanating from any site of choice (e.g. the active site). The results are presented through statistical quantile scores visualised with interactive plots and adjustable 3D structure viewers, which can also be downloaded. ProteinLens thus allows the investigation of signalling in biomolecular structures of interest to aid the detection of allosteric sites and pathways. ProteinLens is implemented in Python/SQL and freely available to use at: www.proteinlens.io.
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Dissertations / Theses on the topic "Biomolecules Structures"

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Zhang, Xiaoning. "STRUCTURES AND REACTIONS OF BIOMOLECULES AT INTERFACES." UKnowledge, 2013. http://uknowledge.uky.edu/chemistry_etds/16.

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This dissertation serves to study a protein's conformation-function relationship since immobilized proteins often behave differently from their solution-state counterparts. Therefore, this study is important to the application of protein-based biodevices. Another aim of this dissertation is to explore a new approach to realize low voltage electrowetting without the help of oil bath. Utilizing this approach, a protein micro-separation was realized. Additionally, the interfacial properties of ionic liquid (IL) solid-like layer, which played a key role in electrowetting, was studied for further developments of IL-based applications. Atomic Force Microscopy (AFM) was utilized in the study and played multiple roles in this dissertation. First, AFM was used as a fabrication tool. In the contact mode, conductive AFM tip was used to conduct the electrochemical oxidation to create a chemical pattern or to conduct an electrowetting experiment. Subsequently, AFM was used as a characterization tool in the tapping mode to characterize the surface structure, the thickness, and the surface potential. Furthermore, AFM in the contact mode was used as a measurement tool to measure the tribological force properties of sample. The results of the study concerning the conformational change in immobilized calmodulin showed that the immobilized CaM retained its activity. Additionally, the immobilization of CaM on a solid support did not interfere with the ability of the protein to bind calcium, as well as CaM kinase binding domain. For the electrowetting experiment, our data suggested that the ultra-high capacitance density of the IL dielectric layer leads to the low voltage electrowetting. We also successfully demonstrated the streptavidin and GFP proteins separation by Electrowetting-on-Dielectric (EWOD) force. The results of the surface properties study indicated that the charge and dipole of the substrate can influence the structures and properties of the IL interfacial layer. Our study would be beneficial in research and assay work involving engineered proteins, as well as the study and development of electrowetting applications.
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Domanova, Olga [Verfasser]. "Automated quantitative analysis methods for translocation of biomolecules in relation to membrane structures / Olga Domanova." Aachen : Hochschulbibliothek der Rheinisch-Westfälischen Technischen Hochschule Aachen, 2013. http://d-nb.info/1046979191/34.

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Marushchak, Denys. "Fluorescence studies of complex systems : organisation of biomolecules." Doctoral thesis, Umeå : Department of Chemistry, Umeå University, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-979.

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Melarkode, Vattekatte Akhila. "3D structures of camelid antibodies : in-silico analyses, prediction and their dynamics." Thesis, La Réunion, 2019. http://www.theses.fr/2019LARE0020.

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Les anticorps sont les nouveaux blockbusters au niveau des médicaments. Les anticorps de camélidés, à savoir les domaines VHH, constituent la prochaine génération de traitements et de diagnostics basés sur les anticorps. Pour améliorer nos connaissances sur ces VHH, il est essentiel d'avoir une meilleure vision de la relation séquence, structure et dynamique de ces protéines, et ceci afin d'améliorer leur affinité et leur stabilité. Dans une première étape, une analyse en profondeur des séquences et de la structure des VHHs est effectuée à l'aide d'approches classiques, mais également d'un alphabet structural appelé Blocs Protéiques. Dans une deuxième étape, la relation séquence-structure de ces domaines est évaluée en examinant le lien entre séquences et structures. Dans une troisième étape, la spécificité et la difficulté d’obtenir des modèles structuraux pertinents sont soulignées avec différentes approches, donnant des résultats inattendus. Ensuite, des simulations dynamiques moléculaires à grande échelle ont été effectuées et ont montré une grande diversité dans les comportements de la dynamique des domaines VHH. Enfin, nous terminons notre thèse en énumérant les principales conclusions des chapitres précédents et des perspectives futures<br>Antibodies are the new blockbusters for drug design. Camelid antibodies, namely VHH domains are projected to be the next generation therapeutics and diagnostics. To improve our knowledge on VHHs, it is essential to have a better view on the sequence, structure and dynamics relationships to improve their affinity and stability. In a first-step a deep analysis of the sequence and the structure of VHHs are done using classical approaches, but also a structural alphabet named Protein Blocks. In a second step, the sequence-structure relationship of these domains is assessed looking at diverse sequence and structures conservations. In a third step, the specificity and difficulty to obtain pertinent structural models are underlined using different approaches, showing unexpected results. Next, the largest scale Molecular dynamic simulations of VHH had been done and shown a large variety in the behaviours of VHH domains dynamics. Finally, the thesis is wrapped up listing significant conclusions from the above chapters and with future perspectives
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Souza, Jairo Cavalcante de. "\"Implementação da técnica de correlações angulares perturbadas no laboratório Pelletron para estudo de estruturas e interações de biomoléculas\"." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-24042007-154751/.

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Este trabalho de mestrado trata da implementação de um espectrômetro de correlações angulares perturbadas no Laboratório do Acelerador Pelletron do Instituto de Física da Universidade de São Paulo. O espectrômetro é formado por seis detectores cintiladores com cristais de \'BaF IND.2\', de 3 polegadas de diâmetro por 6 de comprimento, com um sistema eletrônico e de aquisição de dados multiparamétrico padrão CAMAC. Diferentemente do usual, os espectros de energia dos raios gama dos núcleos de prova são adquiridos para cada detector, o que permite manter um controle maior sobre todo o experimento. Além disso, um mesmo experimento pode ser revisto com diferentes abordagens por diversas vezes, pois todas as informações sobre ele são armazenadas. Com a configuração eletrônica adotada, os espectros de energia são obtidos por meio de um QDC (charge to digital converter), dispensando o uso de pré-amplificadores. Os espectros de tempo são adquiridos com um TDC (time do digital converter). A seleção dos eventos de coincidência é realizada computacionalmente, procedimento que pode ser realizado durante a aquisição dos dados. Como a motivação para a implementação desse espectrômetro é o estudo de estruturas e interações de biomoléculas por meio da técnica de correlações angulares (PAC), foram realizadas medidas exploratórias, com o uso do espectrômetro do Laboratório de interações Hiperfinas (LIH) do Centro do Reator de Pesquisas (CRPq) no IPEN, paralelamente à implementação do espectrômetro. As primeiras medições foram realizadas com amostras de vesículas lipídicas. Com essas medidas foi possível notar a influência da variação de tamanho das moléculas (diminuição de tamanho em uma ordem de grandeza) no tempo de correlação rotacional à temperatura ambiente, quando adicionado SDS (sodium dodecyl sulfate) na suspensão para formação de um agregado micelar. As duas séries de medidas seguintes foram realizadas com amostras de SDS nas quais variaram-se as concentrações para se tentar verificar alterações na geometria ou na mobilidade das moléculas em função desse parâmetro. Foi possível notar que o comportamento das funções perturbação experimentais variaram com as amostras, porém não foi possível notar sistemática no comportamtento. Outro fator notado foi a influência do meio. O comportamento das moléculas quando na presença de metanol nas amostras era bem diferente das soluções aquosas. Também não foi possível obter uma conclusão clara quanto à concentração micelar crítica para soluções aquosas. Por fim foram realizadas medidas com amostras de proteína calmodulina. Foram feitas medidas à temperatura ambiente e a 77K. Notou-se que essa proteína é passível de ser estudada por meio da técnica PAC. Para confirmar a presença da proteína nas amostras e também tentar verificar um deslocamento na massa devido à presença do íon \'ANTPOT.111 Cd\' \'ANTPOT.2+\' foram realizadas medidas de espectrometria de massas no Laboratório de Espectrometria de Massas na Embrapa em Brasília. Foi possível confirmar a presença da proteína nas amostras, porém não foi possível notar a presença de \'ANTPOT.111 Cd\' devido à baixa concentração de íons utilizados com a técnica PAC.<br>This work is related to the implementation of a perturbed angular correlation (PAC) spectrometer at the University of São Paulo Pelletron Laboratory. The spectrometer consists of 6 cylindrical BaF$_2$ scintillator detectors, with 3 inches diameter and 6 inches length and a multiparameter CAMAC data acquisition system. Different from usual, the gamma ray energy spectra of the cascade nuclei are acquired for each detector, which allows us to have more control of the experiment. Besides, the same experiment can be revised with different approaches at any time. With the adopted electronics configuration, the energy spectra are obtained through a QDC (charge to digital converter) module, which dispenses the use of pre-amplifiers. The time spectra are acquired with a TDC (time to digital converter) module. The selection of coincidence events is performed computationally, and this procedure can be evaluated during the data acquisition. The main motivation for implementing this spectrometer is the study of the structure and interactions of biomolecules through the perturbed angular correlation technique. Test measurements were performed, parallel to the spectrometer construction, with the use of the Hyperfine Interactions Laboratory spectrometer at the Centro do Reator de Pesquisas do Instituto de Pesquisas Energéticas e Nucleares (CRPq-IPEN). The first measurements were performed with lipidic vesicles samples. In this case it was possible to observe the influence of the molecule dimension change (decrease in one order) on the rotational correlation time at room temperature, when SDS (sodium dodecyl sulfate) was added in the suspension to form micellar aggregation. The two following series of measurements were performed with SDS samples in which the concentration was varied in order to verify modifications in the geometry or mobility of the molecules as a function of that parameter. The behavior of the experimental perturbation functions varied with the samples. However, it was not possible to point out any systematics in their behavior. The molecules behavior when in presence of methanol in the samples was very different from the aqueous solutions. Also, it was not possible to obtain a clear conclusion about the critical micellar concentration for the aqueous solutions. Finally, the last measurements were performed with calmodulin protein samples, at room temperature and at 77K. In this case we concluded that this protein can be studied through the PAC technique. In order to confirm the presence of the protein in the samples and at same time to verify if any mass displacement occurred due to the presence of the $^{111}$Cd$^{2+}$, mass spectrometry measurements were performed at the Laboratório de Espectrometria de Massas -- Embrapa in Brasília. It was possible to confirm the presence of the protein in the samples, but it was not possible to observe the mass displacement due to the presence of the $^{111}$Cd, since the ions concentration used with the PAC technique is very low.
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Nigen, Michaël. "Interactions et assemblages entre l'alpha lactalbumine et le lysozyme: mécanismes, structures et stabilité." Phd thesis, Agrocampus - Ecole nationale supérieure d'agronomie de rennes, 2008. http://tel.archives-ouvertes.fr/tel-00438402.

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L'assemblage des protéines est une problématique fondamentale d'intérêt pour différents secteurs (alimentaire, médical, pharmaceutique, etc.). La compréhension des mécanismes à l'origine des interactions initiales et des assemblages protéiques offre la possibilité de contrôler et d'orienter le processus de formation ainsi que la nature et les propriétés fonctionnelles des structures supramoléculaires résultantes. L'objectif de la thèse était d'acquérir de nouvelles connaissances à différentes échelles d'étude sur les mécanismes d'assemblages protéiques et les structures supramoléculaires dans un mélange protéique binaire incluant deux protéines globulaires de charge globale opposée à pH neutre : le lysozyme (LYS) et l'alpha-lactalbumine (alpha-LA). L'utilisation de techniques de fluorescence a permis de caractériser l'interaction moléculaire et la formation d'hétérodimères entre ces deux protéines aussi bien avec les formes chargée (holo alpha-LA) et déplétée (apo alpha-LA) en calcium de l'alpha-LA. La formation de ces hétérodimères s'effectue par la mise en œuvre d'interactions électrostatiques. Les propriétés d'assemblage de ces hétérodimères sont différentes et intimement liées à la stabilité de l'alpha-LA. Les hétérodimères LYS – holo alpha-LA ne semblent pas former de structures supramoléculaires, alors que les hétérodimères LYS – apo alpha-LA s'assemblent en agrégats ou en structures sphériques selon la conformation de l'apo alpha-LA. Une conformation de type « molten globule » de l'apo alpha-LA favorise la formation de microsphères. Ces dernières sont constituées de LYS et d'apo alpha-LA en quantité équimolaire qui sont parfaitement co-localisés au sein de la microstructure. Ce travail souligne le rôle clé joué par la conformation et la flexibilité des protéines dans la formation et l'orientation des assemblages entre protéines alimentaires.
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De, Brevern Alexandre. "Nouvelles stratégies d'analyses et de prédiction des structures tridimensionnelles des protéines." Phd thesis, Université Paris-Diderot - Paris VII, 2001. http://tel.archives-ouvertes.fr/tel-00133819.

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Caractériser la structure tridimensionnelle des protéines avec les structures secondaires classiques est assez pauvre structurellement. Nous avons donc développé une nouvelle méthodologie pour concevoir des séries de petits prototypes moyens nommés Blocs Protéiques (BPs) qui permettent une bonne approximation des structures protéiques. L'analyse de la spécificité des blocs protéiques a montré leur stabilité et leur spécificité sur le plan structural. Le choix final du nombre de BPs est associé a une prédiction locale correcte.<br />Cette prédiction se base avec une méthode bayésienne qui permet de comprendre l'importance des acides aminés de maniè;re simple. Pour améliorer cette prédiction, nous nous sommes bases sur deux concepts : (i) 1 repliement local -> n séquences et (ii) 1 séquence -> n repliements. Le premier concept signifie que plusieurs types de séquences peuvent être associes a la même structure et le second qu'une séquence peut-être associée a plusieurs type de repliements. Ces deux aspects sont développés en se basant sur la recherche d'un indice de fiabilité lie a la prédiction locale, pour trouver des zones de fortes probabilités. Certains mots, i.e. successions de blocs protéiques apparaissent plus fréquemment que d'autres. Nous avons donc défini au mieux quelle est l'architecture de ces successions, les liens existants entre ces différents mots.<br />Du fait de cette redondance qui peut apparaìtre dans la structure protéique, une méthode de compactage qui permet d'associer des structures structurellement proches sur le plan local a été mise au point. Cette approche appelée "protéine hybride" de conception simple permet de catégoriser en classes "structurellement dépendantes" l'ensemble des structures de la base de données protéiques. Cette approche, en plus du compactage, peut être utilisée dans une optique différente, celle de la recherche d'homologie structurale et de la caractérisation des dépendances entre structures et séquences.
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Chabadel, Anne. "STRUCTURES, STABILITÉ ET FONCTIONS DU CYTOSQUELETTE D'ACTINE DANS LES OSTÉOCLASTES MÂTURES." Phd thesis, Ecole normale supérieure de lyon - ENS LYON, 2007. http://tel.archives-ouvertes.fr/tel-00165656.

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L'ostéoclaste est une cellule spécialisée dans la résorption de la matrice osseuse. Elle présente une organisation différente de l'actine selon les substrats sur lesquels elle est ensemencée. Sur verre ou plastique, l'actine est sous forme de "podosomes", alors que sur un substrat résorbable, elle se ré-organise en une ceinture conttinue, la zone de scellement (SZ). L'étude de cellules déficientes en WIP nous a permis de démontrer qu'un ostéoclaste sur verre forme 2 domaines d'actine distincts: les coeurs de podosomes et le nuage. Ces 2 domaines sont induits par différents récepteurs, CD44 et Beta3, polymérisés par des voies distinctes, et ont pour fonction l'adhérence et la contraction. Ils se ré-organisent en une unique structure, la SZ, quand l'ostéoclaste est transféré sur un substrat résorbable. Nous avons également démontré que le maintien de la ceinture de podosomes dépend d'un réseau de microtubules intact.
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HECKER, Arnaud. "Production, fonction et localisation d'Orchestine: calciprotéine spécifique de la matrice organique des structures minéralisées élaborées par le crustacé terrestre Orchestia cavimana." Phd thesis, Université de Bourgogne, 2002. http://tel.archives-ouvertes.fr/tel-00003662.

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Comme la plupart des Crustacés, Orchestia cavimana possède un exosquelette minéralisé qu'il renouvelle cycliquement. Du fait des mœurs terrestres de cet animal, ces cycles de mue sont associés à des processus de stockage et de résorption de calcium. Le stockage a lieu sous forme de concrétions calcaires au niveau de diverticules de l'intestin moyen appelés cæcums postérieurs. Les concrétions calcaires sont essentiellement constituées de carbonate de calcium amorphe précipité au sein d'une matrice organique comprenant une fraction protéique soluble et une autre insoluble dans un tampon contenant de l'EDTA. Des résultats précédents ont permis de mettre en évidence, parmi les constituants de la fraction soluble, une protéine acide de masse apparente en SDS-PAGE de 23 kDa qui a été appelée Orchestine. Cette protéine, dont le gène a été cloné et séquencé, n'est pas glycosylée et fixe le calcium. Le but de ce travail a été de poursuivre la caractérisation de ce marqueur protéique. Pour ce faire, nous avons montré qu'Orchestine est phosphorylée sur des résidus sérine et tyrosine. Afin d'étudier les relations entre ces phosphorylations et l'aptitude de la protéine à fixer le calcium, nous avons produit une protéine recombinante dépourvue de toute modification post-traductionnelle. La comparaison de l'aptitude à fixer le calcium des protéines native, native déphosphorylée par diverses phosphatases spécifiques, et recombinante nous a permis de conclure à l'importance fondamentale des sérines dans cette aptitude. De plus, Orchestine interfère dans la croissance in vitro de cristaux de carbonate de calcium. D'autre part, la protéine recombinante nous a permis de lever l'ambiguïté de la divergence de masse moléculaire de la protéine observée en SDS-PAGE (de 23 kDa) et de celle déduite de la séquence (de 12,4 kDa) et de conclure à la correspondance gène orchestine-protéine Orchestine. Enfin la protéine recombinante a été utilisée pour la production d'un anticorps polyclonal afin de localiser Orchestine dans les structures biominéralisées élaborées par O. cavimana lors de son cycle de mue. Orchestine semble non seulement localisée dans les couches non minéralisées des concrétions calcaires (structures de réserve du calcium) mais aussi dans celles des sphérules calciques (structures permettant la remobilisation du calcium). Les propriétés ainsi mises en évidence nous conduisent à envisager qu'Orchestine est une molécule-clé dans la formation des structures de stockage et déstockage élaborées de manière cyclique par O. cavimana.
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Gallé, Matthias. "Searching for Compact Hierarchical Structures in DNA by means of the Smallest Grammar Problem." Phd thesis, Université Rennes 1, 2011. http://tel.archives-ouvertes.fr/tel-00595494.

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Motivé par la découverte automatique de la structure hiérarchique de séquences d'ADN, nous nous intéressons au probléme classique de la recherche de la plus petite grammaire algébrique générant exactement une séquence donnée. Ce probléme NP-dur a été largement étudié pour des applications comme la compression de données, la découverte de structure et la théorie algorithmique de l'information. Nous proposons de décomposer ce probléme en deux problémes d'optimisation complémentaires. Le premier consiste á choisir les chaînes de la séquence qui seront les constituants de la grammaire finale alors que le second, que nous appelons ''analyse grammaticale minimale'', consiste á trouver une grammaire de taille minimale permettant l'analyse syntaxique de ces constituants. Nous donnons une solution polynomiale au probléme d' ''analyse grammaticale minimale'' et montrons que cette décomposition permet de définir un espace de recherche complet pour le probléme de la plus petite grammaire algébrique. Nous nous intéressons aux algorithmes praticables permettant de retourner une approximation du probléme en un temps suffisamment raisonnable pour être appliqués á de grandes séquences telles que les séquences génomiques. Nous analysons l'impact de l'utilisation de classes différentes de maximalité de répétitions pour le choix des constituants et le compromis entre l'efficacité et la taille de la grammaire finale. Nous présentons des avancées algorithmiques pour une meilleure efficacité des algorithmes hors-ligne existants, dont notamment la mise á jour incrémentale de tableaux de suffixes en cours de recodage. Enfin, la nouvelle décomposition du probléme nous permet de proposer de nouveaux algorithmes génériques permettant de trouver des grammaires 10\% plus petites que l'état de l'art. Enfin, nous nous intéressons á l'impact de ces idées sur les applications. En ce qui concerne la découverte de structures, nous étudions le nombre de grammaires minimales et montrons que ce nombre peut être exponentiel dans le pire cas. Nos expérimentations sur des jeux de séquences permettent cependant de montrer une certaine stabilité de structure au sein des grammaires minimales obtenues á partir d'un ensemble de constituants. En ce qui concerne la compression des données, nous contribuons dans chacune des trois étapes de la compression á base de grammaires. Nous définissons alors un nouvel algorithme qui optimise la taille de la chaine de bits finale au lieu de la taille de la grammaire. En l'appliquant sur les séquences d'ADN, nos expérimentations montrent que cet algorithme surpasse tout autre compresseur spécifique d'ADN á base de grammaire. Nous améliorons ce résultat en utilisant des répétitions inexactes et arrivons á améliorer les taux de compression de 25\% par rapport aux meilleurs compresseurs d'ADN á base de grammaire. Outre l'obtention de taux de compression plus performants, cette approche permet également envisager des généralisations intéressantes de ces grammaires.
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Books on the topic "Biomolecules Structures"

1

Soumpasis, D. M. Computation of Biomolecular Structures: Achievements, Problems, and Perspectives. Springer Berlin Heidelberg, 1993.

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Wolfram, Saenger, ed. Hydrogen bonding in biological structures. Springer-Verlag, 1991.

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Jeffrey, George A. Hydrogen bonding in biological structures. Springer-Verlag, 1994.

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Chen, Luonan. Modeling biomolecular networks in cells: Structures and dynamics. Springer, 2010.

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Liwo, Adam, ed. Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-28554-7.

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Liwo, Adam, ed. Computational Methods to Study the Structure and Dynamics of Biomolecules and Biomolecular Processes. Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-319-95843-9.

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Soumpasis, Dikeos Mario, and Thomas M. Jovin, eds. Computation of Biomolecular Structures. Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-77798-1.

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Ehrenberg, Anders, Rudolf Rigler, Astrid Gräslund, and Lennart Nilsson, eds. Structure, Dynamics and Function of Biomolecules. Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-71705-5.

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Vergoten, Gérard, and Theophile Theophanides, eds. Biomolecular Structure and Dynamics. Springer Netherlands, 1997. http://dx.doi.org/10.1007/978-94-011-5484-0.

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Vergoten, Gérard. Biomolecular Structure and Dynamics. Springer Netherlands, 1997.

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Book chapters on the topic "Biomolecules Structures"

1

Ahlström, Peter, Jukka Lausmaa, Patrik Löfgren, and Herman J. C. Berendsen. "Biomolecules at Phase Boundaries." In Modelling of Biomolecular Structures and Mechanisms. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0497-5_29.

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Hoang, T. X., N. T. T. Nhung, J. R. Banavar, and A. Maritan. "Symmetry and Folded Structures of Biomolecules." In IFMBE Proceedings. Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-32183-2_90.

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Clore, G. Marius, and Angela M. Gronenborn. "Determination of 3D-Structures of Macromolecules by Restrained Molecular Dynamics on the Basis of Interproton Distances." In Structure, Dynamics and Function of Biomolecules. Springer Berlin Heidelberg, 1987. http://dx.doi.org/10.1007/978-3-642-71705-5_23.

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Simmerling, Carlos, Ron Elber, and Jing Zhang. "MOIL-View — A Program for Visualization of Structure and Dynamics of Biomolecules and STO — A Program for Computing Stochastic Paths." In Modelling of Biomolecular Structures and Mechanisms. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0497-5_20.

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Messaoudi, Hamza, Susanta Kumar Das, Janine Lange, et al. "Femtosecond-Laser Induced Periodic Surface Structures for Surface Enhanced Raman Spectroscopy of Biomolecules." In Progress in Nonlinear Nano-Optics. Springer International Publishing, 2014. http://dx.doi.org/10.1007/978-3-319-12217-5_12.

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Pizziconi, Vincent B., Darren L. Page, Catherine T. Connolly, and Pamela A. Diamond. "Scanning Probe Microscopy Imaging and Characterization of Biological Structures from Biomolecules to Living Cells." In Atomic Force Microscopy/Scanning Tunneling Microscopy. Springer US, 1994. http://dx.doi.org/10.1007/978-1-4757-9322-2_3.

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Glick, M., and Amiram Goldblum. "A Stochastic Method for the Positioning of Protons in X-ray Structures of Biomolecules." In Molecular Modeling and Prediction of Bioactivity. Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4141-7_117.

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Pangule, Ravindra C., Shyam Sundhar Bale, Dhiral A. Shah, et al. "Biomolecule-Nanomaterial Interactions: Effect on Biomolecular Structure, Function, and Stability." In Biological Interactions on Materials Surfaces. Springer US, 2009. http://dx.doi.org/10.1007/978-0-387-98161-1_5.

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Banci, Lucia, Francesca Cantini, Mirko Cevec, et al. "Structure of Biomolecules: Fundamentals." In NMR of Biomolecules. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644506.ch2.

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Guerry, Paul, and Torsten Herrmann. "Automated Protein Structure Determination Methods." In NMR of Biomolecules. Wiley-VCH Verlag GmbH & Co. KGaA, 2012. http://dx.doi.org/10.1002/9783527644506.ch33.

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Conference papers on the topic "Biomolecules Structures"

1

Goddard, Gregory, and Jennifer E. Whittier. "Biomolecules as nanomaterials: interface characterization for sensor development." In Smart Structures and Materials, edited by Vijay K. Varadan. SPIE, 2006. http://dx.doi.org/10.1117/12.658771.

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Nguyen, Mary-Anne, and Andy Sarles. "Microfabrication for Packaged Biomolecular Unit Cells." In ASME 2013 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/smasis2013-3068.

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This paper focuses on developing a closed fluidic environment for packaging biomolecular unit cells, which consists of a synthetic lipid bilayer and other biomolecules contained in a near solid-state material with two regions that contain hydrophobic oil (i.e. nonpolar solvent) surrounding aqueous droplets. This research provides a stepping-stone towards an autonomic biomolecular material system, whereby a packaged system will allow for precise droplet interface bilayer (DIB) formation without the interference of outside contamination for long-term applications. Also, substrate materials need to maintain droplets and preserve the self-assembly and stimuli-responsive properties of biomolecules within the unit cell. A critical feature of an encapsulating material is that it does not absorb either of the liquid phases required to form DIBs. Oil depletion tests within sealed, polymeric substrates show that polydimethylsiloxane (PDMS) absorbs full volume of injected hexadecane in approximately 27 hours. However, polyurethane substrates maintain the original amount of oil injected even after several weeks. Bilayer lifetime is also monitored within an environment in which the oil is also depleting. The results of this test show the longevity of a DIB to be shorter than oil lifetime. The lipid-encased droplets disconnect after approximately 10 hours, when there is only approximately &lt;60% amount of oil present. In addition, an initial microfluidic substrate is designed such that a single T-junction intersection can be used to form monodisperse droplets within a primary oil-filled channel and a downstream increase in channel width can be used to connect droplets to form DIBs.
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Kim, Jae-Woo, Sang H. Choi, Peter T. Lillehei, et al. "Electrochemical reconstitution of biomolecules for applications as electrocatalysts for the bionanofuel cell." In Smart Structures and Materials, edited by Vijay K. Varadan. SPIE, 2004. http://dx.doi.org/10.1117/12.539268.

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Khoo, E. H., Y. Li Hor, Eunice S. P. Leong, and Y. J. Liu. "Effect of layered composite meta-structures on the optical activity and ellipticity of structural biomolecules." In SPIE NanoScience + Engineering, edited by Nader Engheta, Mikhail A. Noginov, and Nikolay I. Zheludev. SPIE, 2014. http://dx.doi.org/10.1117/12.2061492.

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Shinohara, Hiroaki. "Nanospace interface for the electrochemical communication between redox-active biomolecules and metal oxide electrodes." In 1996 Symposium on Smart Structures and Materials, edited by Andrew Crowson. SPIE, 1996. http://dx.doi.org/10.1117/12.232138.

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Veliyeva, L. I. "Study of structures of biomolecules of drostatin family by means of computer modelling." In 2009 International Conference on Application of Information and Communication Technologies (AICT). IEEE, 2009. http://dx.doi.org/10.1109/icaict.2009.5372592.

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Helenius, Vesa M., P. H. Hynninen, and Jouko E. Korppi-Tommola. "Molecular structures of chlorophyll a aggregates: spectroscopic and molecular modeling study." In Laser Spectroscopy of Biomolecules: 4th International Conference on Laser Applications in Life Sciences, edited by Jouko E. Korppi-Tommola. SPIE, 1993. http://dx.doi.org/10.1117/12.146105.

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El-Beyrouthy, Joyce, and Eric C. Freeman. "Rapid and Real-Time Measurement of Membrane Potential Through Intramembrane Field Compensation." In ASME 2020 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/smasis2020-2352.

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Abstract Synthetic lipid membranes are self-assembled biomolecular double layers designed to approximate the properties of living cell membranes. These membranes are employed as model systems for studying the interactions of cellular envelopes with the surrounding environment in a controlled platform. They are constructed by dispersing amphiphilic lipids into a combination of immiscible fluids enabling the biomolecules to self-assemble into ordered sheets, or monolayers at the oil-water interface. The adhesion of two opposing monolayer sheets forms the membrane, or the double layer. The mechanical properties of these synthetic membranes often differ from biological ones mainly due to the presence of residual solvent in between the leaflets. In fact, the double layer compresses in response to externally applied electrical field with an intensity that varies depending on the solvent present. While typically viewed as a drawback associated with their assembly, in this work the elasticity of the double layer is utilized to further quantify complex biophysical phenomena. The adsorption of charged molecules on the surface of a lipid bilayer is a key property to decipher biomolecule interactions at the interface of the cell membrane, as well as to develop effective antimicrobial peptides and similar membrane-active molecules. This adsorption generates a difference in the boundary potentials on either side of the membrane which may be tracked through electrophysiology. The soft synthetic membranes produced in the laboratory compress when exposed to an electric field. Tracking the minimum membrane capacitance allows for quantifying when the intrinsic electric field produced by the asymmetry is properly compensated by the supplied transmembrane voltage. The technique adopted in this work is the intramembrane field compensation (IFC). This technique focuses on the current generated by the bilayer in response to a sinusoidal voltage with a DC component, VDC. Briefly, the output sinusoidal current is divided into its harmonics and the second harmonic equals zero when VDC compensates the internal electric field. In this work, we apply the IFC technique to droplet interface bilayers (DIB) enabling the development of a biological sensor. A certain membrane elasticity is needed for accurate measurements and is tuned through the solvent selection. The asymmetric DIBs are formed, and an automated PID-controlled IFC design is implemented to rapidly track and compensate the membrane asymmetry. The closed loop system continuously reads the current and generates the corresponding voltage until the second harmonic is abated. This research describes the development and optimization of a biological sensor and examines how varying the structure of the synthetic membrane influences its capabilities for detecting membrane-environment interactions. This platform may be applied towards studying the interactions of membrane-active molecules and developing models for the associated phenomena to enhance their design.
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Arbon, Robert E., Alex J. Jones, Lars A. Bratholm, Tom Mitchell, and David R. Glowacki. "Sonifying Stochastic Walks on Biomolecular Energy Landscapes." In The 24th International Conference on Auditory Display. The International Community for Auditory Display, 2018. http://dx.doi.org/10.21785/icad2018.032.

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Translating the complex, multi-dimensional data produced by simulations of biomolecules into an intelligible form is a major challenge in computational chemistry and biology. The so-called “free energy landscape” is amongst the most fundamental concepts used by scientists to understand both static and dynamic properties of biomolecular systems. In this paper we use Markov models to design a strategy for mapping features of this landscape to sonic parameters, for use in conjunction with visual display techniques such as structural animations and free energy diagrams. This allows for concurrent visual display of the physical configuration of a biomolecule and auditory display of characteristics of the corresponding free energy landscape. The resulting sonification provides information about the relative free energy features of a given configuration including its stability.
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Aubrey, Kelly L., Stacy A. Towse, and George J. Thomas, Jr. "Viruses and Raman spectroscopy: determination of secondary structures of viral capsids and chromosomes by difference methods." In Laser Spectroscopy of Biomolecules: 4th International Conference on Laser Applications in Life Sciences, edited by Jouko E. Korppi-Tommola. SPIE, 1993. http://dx.doi.org/10.1117/12.146127.

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Reports on the topic "Biomolecules Structures"

1

Frauenfelder, H., J. R. Berendzen, A. Garcia, et al. Structure, dynamics, and function of biomolecules. Office of Scientific and Technical Information (OSTI), 1998. http://dx.doi.org/10.2172/674922.

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Turner, J. E., R. N. Hamm, R. H. Ritchie, and W. E. Bolch. Monte Carlo track-structure calculations for aqueous solutions containing biomolecules. Office of Scientific and Technical Information (OSTI), 1993. http://dx.doi.org/10.2172/10192405.

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Garcia, A. E., J. Berendzen, and P. ,. Chen, X. Catasti. Computational and theoretical aspects of biomolecular structure and dynamics. Office of Scientific and Technical Information (OSTI), 1996. http://dx.doi.org/10.2172/378935.

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Belcher, Angela M. Biomolecular Recognition of Semiconductor and Magnetic Materials to Pattern Quantum Confined and Magnetoelectronic Structures. Defense Technical Information Center, 2003. http://dx.doi.org/10.21236/ada415861.

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Hupp, J. T. Dynamic structural effects and ultrafast biomolecular kinetics in photoinduced charge transfer reactions. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/5714156.

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Hummer, G., A. E. Garcia, and D. M. Soumpasis. Potential-of-mean-force description of ionic interactions and structural hydration in biomolecular systems. Office of Scientific and Technical Information (OSTI), 1994. http://dx.doi.org/10.2172/10186924.

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Hupp, J. T. Dynamic structural effects and ultrafast biomolecular kinetics in photoinduced charge transfer reactions. Progress report, September 15, 1990--March 14, 1992. Office of Scientific and Technical Information (OSTI), 1992. http://dx.doi.org/10.2172/10121185.

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Hupp, J. T. Dynamic structural effects and ultrafast biomolecular kinetics in photoinduced charge transfer reactions. Three year progress report, March 15, 1991--May 14, 1994. Office of Scientific and Technical Information (OSTI), 1994. http://dx.doi.org/10.2172/10144260.

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