Добірка наукової літератури з теми "Single polymer biophysics"
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Статті в журналах з теми "Single polymer biophysics"
Qian, Hong, and Elliot L. Elson. "Quantitative Study of Polymer Conformation and Dynamics by Single-Particle Tracking." Biophysical Journal 76, no. 3 (March 1999): 1598–605. http://dx.doi.org/10.1016/s0006-3495(99)77319-4.
Повний текст джерелаLi, Isaac T. S., Matthew Paige, and Gilbert C. Walker. "Solvent Effect on the Unfolding Force of a Single Hydrophobic Polymer." Biophysical Journal 98, no. 3 (January 2010): 592a. http://dx.doi.org/10.1016/j.bpj.2009.12.3220.
Повний текст джерелаWong, Wai Cheng, Jz-Yuan Juo, Chih-Hsiang Lin, Yi-Hung Liao, Ching-Ya Cheng, and Chia-Lung Hsieh. "Single Protein Dynamics in Polymer-Cushioned Lipid Bilayers Derived from Cell Plasma Membranes." Biophysical Journal 118, no. 3 (February 2020): 233a. http://dx.doi.org/10.1016/j.bpj.2019.11.1377.
Повний текст джерелаDeverall, M. A., E. Gindl, E. K. Sinner, H. Besir, J. Ruehe, M. J. Saxton, and C. A. Naumann. "Membrane Lateral Mobility Obstructed by Polymer-Tethered Lipids Studied at the Single Molecule Level." Biophysical Journal 88, no. 3 (March 2005): 1875–86. http://dx.doi.org/10.1529/biophysj.104.050559.
Повний текст джерелаRoder, Friedrich, Dirk Paterok, Sharon Waichman, Oliver Beutel, and Jacob Piehler. "Polymer-Supported Membranes for Probing Transmembrane Protein Diffusion and Interaction by Single-Molecule Techniques." Biophysical Journal 100, no. 3 (February 2011): 257a. http://dx.doi.org/10.1016/j.bpj.2010.12.1619.
Повний текст джерелаBarnes, M. D., K. C. Ng, K. P. McNamara, C. Y. Kung, J. M. Ramsey, and S. C. Hill. "Fluorescence imaging of single molecules in polymer microspheres." Cytometry 36, no. 3 (July 1, 1999): 169–75. http://dx.doi.org/10.1002/(sici)1097-0320(19990701)36:3<169::aid-cyto4>3.0.co;2-i.
Повний текст джерелаKang, Seungtae, and Byung Jun Yoon. "Application of Reptation Model on Brownian Dynamics for Electrophoresis of Single DNA in Polymer Solution." Biophysical Journal 98, no. 3 (January 2010): 43a. http://dx.doi.org/10.1016/j.bpj.2009.12.247.
Повний текст джерелаSiegel, Amanda P., Ann Kimble-Hill, Rainer Jordan, and Christoph A. Naumann. "Raft Recruitment Processes and Oligomerization State of Integrins Studied in Polymer-Tethered Single and Double Bilayer Systems." Biophysical Journal 100, no. 3 (February 2011): 332a. http://dx.doi.org/10.1016/j.bpj.2010.12.2013.
Повний текст джерелаNiu, Qiaoli, Yunhua Xu, Jiaxing Jiang, Junbiao Peng, and Yong Cao. "Efficient polymer white-light-emitting diodes with a single-emission layer of fluorescent polymer blend." Journal of Luminescence 126, no. 2 (October 2007): 531–35. http://dx.doi.org/10.1016/j.jlumin.2006.10.004.
Повний текст джерелаKÖSTER, SARAH, HOLGER STARK, THOMAS PFOHL, and JAN KIERFELD. "FLUCTUATIONS OF SINGLE CONFINED ACTIN FILAMENTS." Biophysical Reviews and Letters 02, no. 02 (April 2007): 155–66. http://dx.doi.org/10.1142/s1793048007000374.
Повний текст джерелаДисертації з теми "Single polymer biophysics"
Quake, Stephen Ronald. "Theory and experiments in polymer physics with single molecules of DNA." Thesis, University of Oxford, 1994. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.386843.
Повний текст джерелаKohram, Maryam. "A Combined Microscopy and Spectroscopy Approach to Study Membrane Biophysics." University of Akron / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=akron1436530389.
Повний текст джерелаViader, Godoy Xavier. "Biophysical properties of single-stranded DNA studied with single-molecule force spectroscopy." Doctoral thesis, Universitat de Barcelona, 2021. http://hdl.handle.net/10803/670920.
Повний текст джерелаEn aquesta tesi hem realitzat experiments fent servir pinces òptiques per tal d’extreure informació precisa sobre les propietats termodinàmiques i cinètiques de diferents sistemes moleculars, posant especial èmfasi en les propietats elàstiques de la cadena simple d’ADN (ssDNA, pel seu acrònim en anglès). La tesi es troba dividida en tres parts. A la primera part s’introdueix de forma general el camp de recerca dels experiments de molècula única, així com s’expliquen els conceptes més bàsics que es desenvoluparan en les parts II i III. La configuració experimental emprada al llarg de tota la tesi, les pinces òptiques, s’introdueix al capítol 2. Per a fer-ho, s’expliquen els principis físics de funcionament de les pinces, que es basen en l’atrapament òptic. Breument, la focalització d’un feix de llum d’alta intensitat permet atrapar i exercir forces en micropartícules dielèctriques (pilotes fetes de plàstic de la mida d’un bacteri), que són recobertes químicament de manera que la molècula d’estudi pot estirar-se, de forma individual, repetides vegades. El capítol 3 conté una breu introducció a les biomolècules que apareixen en aquesta tesi, amb una breu explicació de la seva descoberta, així com la seva estructura i funció (íntimament relacionades). Ens centrem en la descripció de la ssDNA que és el principal objecte d’estudi de la tesi. Al capítol 4 s’introdueixen els models de polímers que s’empren habitualment per a descriure l’elasticitat d’àcids nucleics i proteïnes. En concret, es descriuen els models de la Freely-Jointed Chain i la Worm-Like Chain. La Part II tracta de l’elasticitat de la ssDNA, i inclou els capítols 5, 6 i 7. El capítol 5 es basa en la caracterització de l’elasticitat de la cadena ideal de ssDNA, és a dir, aquella que pot ser modelitzada pels polímers ideals introduïts en el capítol 4. S’estudia l’elasticitat de diferents seqüències de ssDNA, introduint un nou mètode experimental, blocking-splint oligo, per tal d’ampliar el rang de forces estudiat habitualment en molècules curtes (d’una longitud de desenes de bases) de ssDNA. L’estudi mostra la necessitat d’emprar models elàstics extensibles per a la correcte caracterització de l’elasticitat de ssDNA, que explica les discrepàncies existents entre els paràmetres elàstics trobats a la literatura. També hipotetitzem que l’extensibilitat del model pot ser explicada gràcies a la transició experimentada a nivell de nucleòtids: el canvi que experimenta la distància interfosfat de l’ADN es veu modificada segons quina sigui la configuració de l’anell de desoxiribosa. Tot i que és un fenomen molt més conegut en la cadena doble d’ADN, l’apilament-desapilament de bases també s’ha observat en certes seqüències de ssDNA (especialment les que són riques en contingut de purines). Al capítol 6 s’estudien quatre molècules amb un grau d’apilament diferent a partir de les seves corbes força-extensió (FECs). Es desenvolupa un model helix-coil (hèlix-cabdell) per tal d’ajustar les FECs, fet que permet d’obtenir, indirectament, les propietats elàstiques de la cadena apilada. També s’estudia la dependència d’aquesta transició variant la concentració de sal dels experiments en més de dos ordres de magnitud. A través d’aquests experiments, trobem una dependència amb la concentració de sal de l’energia lliure de formació de l’apilament de la ssDNA, fet que ens permet explicar, parcialment, la dependència que es troba en la literatura per la hibridació de la cadena doble d’ADN. El capítol 7 tracta de la formació d’estructures no específiques que apareixen a forces baixes i a concentració de sal alta per a molècules de ssDNA de més de ~100bases. Es proposa un model helix-coil amb cooperativitat per tal de caracteritzar propietats de camp mitjà de les estructures estudiades. S’estudien vuit seqüències diferents, entre 120 i ~14000 bases, i es caracteritza el seu desviament respecte de la corba elàstica ideal amb el model. També s’estudia la dependència de l’estructura secundària de la ssDNA en funció de la concentració de la sal. Analitzant experiments variant la concentració de MgCl2 i NaCl, aconseguim reproduir les FECs a partir de fer dependre els paràmetres del model amb la sal. Finalment, el model desenvolupat ens permet predir la formació d’estructura secundària a força zero (fet que no podem detectar directament a partir d’experiments d’espectroscopia de forces). Es comparen les previsions del model amb les trobades per Mfold, trobant una compatibilitat per als resultats per a molècules de de menys de 1000 bases. La darrera part se centra en col·laboracions que he fet durant a tesi i que necessiten una determinació precisa de les propietats elàstiques de la ssDNA. Al capítol 8 s’estudia la interacció entre l’helicasa del bacteri E. coli i l’ADN, que s’encarrega d’obrir la cadena doble d’ADN, alliberant ssDNA. S’extreuen les seves propietats cinètiques, com la velocitat de translocació – obtenim, independentment de la força aplicada, d’uns 50bp/s, d’acord amb la literatura –. També n’estudiem les seves propietats termodinàmiques, a partir del Teorema de Fluctuació. Finalment, al capítol 9 s’estudien els efectes de certs defectes en molècules d’ADN. A partir d’experiments fora de l’equilibri s’extrau la penalització que suposa per a la hibridització d’ADN la presència d’aquestes bases no complementàries (és a dir, que no són enllaços de A-T o G-C).
Reiter-Scherer, Valentin D. "Multivalency in the interaction of biological polymers." Doctoral thesis, Humboldt-Universität zu Berlin, 2020. http://dx.doi.org/10.18452/21711.
Повний текст джерелаThis thesis focuses on studying multivalent interactions between influenza virus hemagglutinin (HA) as well as neuraminidase (NA) of two viral strains (H1N1 and H3N2) and the cellular ligand sialic acid (SA) by using scanning force microscopy and single molecule force spectroscopy (SMFS). Unbinding forces as well as dissociation and association kinetics together with the free energy landscapes were, to the best knowledge for the first time, individually quantified on the single molecule level using SMFS. To this extent, designed synthetic monovalent (SAPEGLA) and multivalent (dPGSA) SA displaying ligands were employed. Surprisingly, the experimental force spectra did not show the log-linear trend predicted by the classical Kramers-Bell-Evans model, but rather follow the more recent Friddle-Noy-De Yoreo model. NA of both viral strains forms a more stable bond with SA than HA, and dissociates 3 to 7 times slower. It is reasoned that the higher stability compensates for the lesser amount of NA compared to HA that is typically found on the viral envelope. The unbinding forces of the cluster of SAPEGLA increased gradually with the number of bonds in the cluster and the dissociation kinetics follow the theoretically predicted trend. The dissociation rate of NA was found to be about 6 times higher than its catalytic rate, indicating that multiple bonds are needed for cleavage of SA. The dissociation rate of N1 is on the same order as that of H3, suggesting that these similarities between the two strains favor transmissibility. The thermal stability of the HA-dPGSA bond is higher than the HA-SAPEGLA reaching that of three to four single bonds, proving specificity and cooperativity. Such an enhancement could not be observed for the binding of NA. This thesis also shows that SMFS could be used as a tool to screen antiviral inhibitors in competitive binding assays, which may contribute insight into the design of antiviral inhibitors on the single molecule level.
Matek, Christian C. A. "Statistical mechanics of nucleic acids under mechanical stress." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:ce44cf50-2001-4f54-8e57-d1757f709fd6.
Повний текст джерелаRickard, Deborah. "Multiphase, Multicomponent Systems: Divalent Ionic Surfactant Phases and Single-Particle Engineering of Protein and Polymer Glasses." Diss., 2011. http://hdl.handle.net/10161/3934.
Повний текст джерелаThis thesis presents an analysis of the material properties and phase behavior of divalent ionic surfactant salts, and protein and polymer glasses. There has been extensive interest in understanding the phase behavior of divalent ionic surfactants due to the many applications of ionic surfactants in which they come into contact with divalent ions, such as detergency, oil recovery, and surfactant separation processes. One goal of determining the phase boundaries was to explore the option of incorporating a hydrophobic molecule into the solid phase through the micelle-to-crystal bilayer transition, either for drug delivery applications (with a biologically compatible surfactant) or for the purpose of studying the hydrophobic molecule itself. The liquid micellar and solid crystal phases of the alkaline earth metal dodecyl sulfates were investigated using calorimetry, visual inspection, solubilization of a fluorescent probe, and x-ray diffraction. The Krafft temperature and dissolution enthalpy were determined for each surfactant, and partial composition-temperature phase diagrams of magnesium dodecyl sulfate-water, calcium dodecyl sulfate-water, as well as sodium dodecyl sulfate with MgCl2 and CaCl2 are presented. As a proof of concept, fluorescence microscopy images showed that it is, in fact, possible to incorporate a small hydrophobic molecule, diphenylhexatriene, into the solid phase.
The second, and main, part of this thesis expands on work done previously in the lab by using the micropipette technique to study two-phase microsystems. These microsystems consist of a liquid droplet suspended in a second, immiscible liquid medium, and can serve as direct single-particle studies of drug delivery systems that are formed using solvent extraction (e.g., protein encapsulated in a biodegradable polymer), and as model systems with which to study the materials and principles that govern particle formation. The assumptions of the Epstein-Plesset model, which predicts the rate of droplet dissolution, are examined in the context of the micropipette technique. A modification to the model is presented that accounts for the effect a solute has on the dissolution rate. The modification is based on the assumption that the droplet interface is in local thermodynamic equilibrium, and that the water activity in a solution droplet can be used to determine its dissolution (or dehydration) rate. The model successfully predicts the dissolution rates of NaCl solutions into octanol and butyl acetate up to the point of NaCl crystallization. The dehydration of protein solutions (lysozyme or bovine serum albumin) results in glassified microbeads with less than a monolayer of water coverage per protein molecule, which can be controlled by the water activity of the surrounding organic medium. The kinetics of dehydration match the prediction of the activity-based model, and it is shown how the micropipette technique can be used to study the effect of dissolution rate on final particle morphology. By using a stable protein with a simple geometry (lyosyzme), this technique was be used to determine the distance dependence of protein-protein interactions in the range of 2-25 Å, providing the first calculation of the hydration pressure decay length for globular proteins. The distance-dependence of the interaction potential at distances less than 9 Å was found to have a decay length of 1.7 Å, which is consistent with the known decay length of hydration pressure between other biological materials. Biodegradable polyesters, such as poly(lactide-co-glycolide) (PLGA), are some of the most common materials used for the encapsulation of therapeutics in microspheres for long-term drug release. Since they degrade by hydrolysis, release rates depend on water uptake, which can be affected by processing parameters and the material properties of the encapsulated drug. The micropipette technique allows observations not possible on any bulk preparation method. Single-particle observations of microsphere formation (organic solvent extraction into a surrounding aqueous phase) show that as solvent leaves the microsphere and the water concentration in the polymer matrix becomes supersaturated, water phase separates and inclusions initially grow quickly. Once the concentration in the polymer matrix equilibrates with the surrounding aqueous medium, the water inclusions continue to grow due to dissolved impurities, solvent, and/or water-soluble polymer fragments resulting from hydrolysis, all of which locally lower the water activity in the inclusion. Experiments are also presented in which glassified protein microbeads were suspended in PLGA solution prior to forming the single microspheres. This technique allowed the concentration of protein in a single microbead/inclusion to be determined as a function of time.
Dissertation
Ge, Yifan. "Investigating spatial distribution and dynamics of membrane proteins in polymer-tethered lipid bilayer systems using single molecule-sensitive imaging techniques." Thesis, 2016. https://doi.org/10.7912/C2765K.
Повний текст джерелаPlasma membranes are complex supramolecular assemblies comprised of lipids and membrane proteins. Both types of membrane constituents are organized in highly dynamic patches with profound impact on membrane functionality, illustrating the functional importance of plasma membrane fluidity. Exemplary, dynamic processes of membrane protein oligomerization and distribution are of physiological and pathological importance. However, due to the complexity of the plasma membrane, the underlying regulatory mechanisms of membrane protein organization and distribution remain elusive. To address this shortcoming, in this thesis work, different mechanisms of dynamic membrane protein assembly and distribution are examined in a polymer-tethered lipid bilayer system using comple-mentary confocal optical detection techniques, including 2D confocal imaging and single molecule-sensitive confocal fluorescence intensity analysis methods [fluorescence correlation spectroscopy (FCS) autocorrelation analysis and photon counting histogram (PCH) method]. Specifically, this complementary methodology was applied to investigate mechanisms of membrane protein assembly and distribution, which are of significance in the areas of membrane biophysics and cellular mechanics. From the membrane biophysics perspective, the role of lipid heterogeneities in the distribution and function of membrane proteins in the plasma membrane has been a long-standing problem. One of the most well-known membrane heterogeneities are known as lipid rafts, which are domains enriched in sphingolipids and cholesterol (CHOL). A hallmark of lipid rafts is that they are important regulators of membrane protein distribution and function in the plasma membrane. Unfortunately, progress in deciphering the mechanisms of raft-mediated regulation of membrane protein distribution has been sluggish, largely due to the small size and transient nature of raft domains in cellular membranes. To overcome this challenge, the current thesis explored the distribution and oligomerization of membrane proteins in raft-mimicking lipid mixtures, which form stable coexisting CHOL-enriched and CHOL-deficient lipid domains of micron-size, which can easily be visualized using optical microscopy techniques. In particular, model membrane experiments were designed, which provided insight into the role of membrane CHOL level versus binding of native ligands on the oligomerization state and distribution of GPI-anchored urokinase plasminogen activator receptor (uPAR) and the transmembrane protein αvβ3 integrin. Experiments on uPAR showed that receptor oligomerization and raft sequestration are predominantly influenced by the binding of natural ligands, but are largely independent of CHOL level changes. In contrast, through a presumably different mechanism, the sequestration of αvβ3 integrin in raft-mimicking lipid mixtures is dependent on both ligand binding and CHOL content changes without altering protein oligomerization state. In addition, the significance of membrane-embedded ligands as regulators of integrin sequestration in raft-mimicking lipid mixtures was explored. One set of experiments showed that ganglioside GM3 induces dimerization of α5β1 integrins in a CHOL-free lipid bilayer, while addition of CHOL suppresses such a dimerization process. Furthermore, GM3 was found to recruit α5β1 integrin into CHOL-enriched domains, illustrating the potential sig-nificance of GM3 as a membrane-associated ligand of α5β1 integrin. Similarly, uPAR was observed to form complexes with αvβ3 integrin in a CHOL dependent manner, thereby causing the translocation of the complex into CHOL-enriched domains. Moreover, using a newly developed dual color FCS and PCH assay, the composition of uPAR and integrin within complexes was determined for the first time. From the perspective of cell mechanics, the characterization of the dynamic assembly of membrane proteins during formation of cell adhesions represents an important scientific problem. Cell adhesions play an important role as force transducers of cellular contractile forces. They may be formed between cell and extracellular matrix, through integrin-based focal adhesions, as well as between different cells, through cadherin-based adherens junctions (AJs). Importantly, both types of cell adhesions act as sensitive force sensors, which change their size and shape in response to external mechanical signals. Traditionally, the correlation between adhesion linker assembly and external mechanical cues was investigated by employing polymeric substrates of adjustable substrate stiffness containing covalently attached linkers. Such systems are well suited to mimic the mechanosensitive assembly of focal adhesions (FAs), but fail to replicate the rich dynamics of cell-cell linkages, such as treadmilling of adherens junctions, during cellular force sensing. To overcome this limitation, the 2D confocal imaging methodology was applied to investigate the dynamic assembly of N-cadherin-chimera on the surface of a polymer-tethered lipid multi-bilayer in the presence of plated cells. Here, the N-cadherin chimera-functionalized polymer-tethered lipid bilayer acts as a cell surface-mimicking cell substrate, which: (i) allows the adjustment of substrate stiffness by changing the degree of bilayer stacking and (ii) enables the free assembly of N-cadherin chimera linkers into clusters underneath migrating cells, thereby forming highly dynamic cell-substrate linkages with remarkable parallels to adherens junctions. By applying the confocal methodology, the dynamic assembly of dye-labeled N-cadherin chimera into clusters was monitored underneath adhered cells. Moreover, the long-range mobility of N-cadherin chimera clusters was analyzed by tracking the cluster positions over time using a MATLAB-based multiple-particle tracking method. Disruption of the cytoskeleton organization of plated cells confirmed the disassembly of N-cadherin chimera clusters, emphasizing the important role of the cytoskeleton of migrating cells during formation of cadherin-based cell-substrate linkages. Size and dynamics of N-cadherin chimera clusters were also analyzed as a function of substrate stiffness.
Mühle, Steffen. "Nanoscale Brownian Dynamics of Semiflexible Biopolymers." Doctoral thesis, 2020. http://hdl.handle.net/21.11130/00-1735-0000-0005-1433-B.
Повний текст джерелаKöster, Sarah Friederike. "Biological Matter in Microfluidic Environment - from Single Molecules to Self-Assembly." Doctoral thesis, 2006. http://hdl.handle.net/11858/00-1735-0000-0006-B59C-F.
Повний текст джерелаЧастини книг з теми "Single polymer biophysics"
Drickamer, H. G. "Pressure-Tuning Spectroscopy: A Tool for Investigating Molecular Interactions." In High Pressure Effects in Molecular Biophysics and Enzymology. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195097221.003.0005.
Повний текст джерелаMacgregor Jr, Robert B., and John Q. Wu. "Sequence, Salt, Charge, and the Stability of DNA at High Pressure." In High Pressure Effects in Molecular Biophysics and Enzymology. Oxford University Press, 1996. http://dx.doi.org/10.1093/oso/9780195097221.003.0014.
Повний текст джерела