Relevant bibliographies by topics / Moleculor Biophysics

Academic literature on the topic 'Moleculor Biophysics'

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Published: 6 September 2023

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Journal articles on the topic "Moleculor Biophysics"

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Joshi, Prakash, and Partha Pratim Mondal. "Single-Molecule Clustering for Super-Resolution Optical Fluorescence Microscopy." Photonics 9, no. 1 (December 24, 2021): 7. http://dx.doi.org/10.3390/photonics9010007.

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Molecular assembly in a complex cellular environment is vital for understanding underlying biological mechanisms. Biophysical parameters (such as single-molecule cluster density, cluster-area, pairwise distance, and number of molecules per cluster) related to molecular clusters directly associate with the physiological state (healthy/diseased) of a cell. Using super-resolution imaging along with powerful clustering methods (K-means, Gaussian mixture, and point clustering), we estimated these critical biophysical parameters associated with dense and sparse molecular clusters. We investigated Hemaglutinin (HA) molecules in an Influenza type A disease model. Subsequently, clustering parameters were estimated for transfected NIH3T3 cells. Investigations on test sample (randomly generated clusters) and NIH3T3 cells (expressing Dendra2-Hemaglutinin (Dendra2-HA) photoactivable molecules) show a significant disparity among the existing clustering techniques. It is observed that a single method is inadequate for estimating all relevant biophysical parameters accurately. Thus, a multimodel approach is necessary in order to characterize molecular clusters and determine critical parameters. The proposed study involving optical system development, photoactivable sample synthesis, and advanced clustering methods may facilitate a better understanding of single molecular clusters. Potential applications are in the emerging field of cell biology, biophysics, and fluorescence imaging.
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Goñi, Félix M. "Birth and Early Steps of the Organization of Biophysics in Spain." Biophysica 2, no. 4 (November 19, 2022): 498–505. http://dx.doi.org/10.3390/biophysica2040042.

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In the 1960s, Biophysics was an unheard of scientific field in Spain, and even outside Spain, the distinction between Biophysics and Molecular Biology was not clear at the time. This paper describes briefly the developments that led to the foundation of the Spanish National Committee for Biophysics (1981) and of the Spanish Biophysical Society (1987), the incorporation of Spain into IUPAB and EBSA, and the normalized presence of Biophysics as a compulsory subject in undergraduate curricula in Spain.
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Leake, Mark C. "The physics of life: one molecule at a time." Philosophical Transactions of the Royal Society B: Biological Sciences 368, no. 1611 (February 5, 2013): 20120248. http://dx.doi.org/10.1098/rstb.2012.0248.

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The esteemed physicist Erwin Schrödinger, whose name is associated with the most notorious equation of quantum mechanics, also wrote a brief essay entitled ‘What is Life?’, asking: ‘How can the events in space and time which take place within the spatial boundary of a living organism be accounted for by physics and chemistry?’ The 60+ years following this seminal work have seen enormous developments in our understanding of biology on the molecular scale, with physics playing a key role in solving many central problems through the development and application of new physical science techniques, biophysical analysis and rigorous intellectual insight. The early days of single-molecule biophysics research was centred around molecular motors and biopolymers, largely divorced from a real physiological context. The new generation of single-molecule bioscience investigations has much greater scope, involving robust methods for understanding molecular-level details of the most fundamental biological processes in far more realistic, and technically challenging, physiological contexts, emerging into a new field of ‘single-molecule cellular biophysics’. Here, I outline how this new field has evolved, discuss the key active areas of current research and speculate on where this may all lead in the near future.
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Connelly, Patrick R. "Recent drug discovery success signals renaissance in biophysics." Biophysics Reviews 3, no. 2 (June 2022): 020401. http://dx.doi.org/10.1063/5.0099305.

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With a scope that spans the hierarchy of biological organization from molecules and cells to organisms and populations, the discipline of biophysics has been proven to be particularly well suited for connecting the molecular embodiments of human diseases to the medical conditions experienced by patients. Recently, fundamental biophysical research on aberrant proteins involved in maintaining salt and water balance in our lungs, oxygen transport from our lungs to the rest of the body, and the pumping of blood by our hearts have been successfully translated to the creation of transformational new medicines that are radically changing the lives of patients. With these and other emerging discoveries, the field of applied biophysics is experiencing the beginnings of a veritable renaissance era.
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Kopūstas, Aurimas, Mindaugas Zaremba, and Marijonas Tutkus. "DNA Flow-Stretch Assays for Studies of Protein-DNA Interactions at the Single-Molecule Level." Applied Nano 3, no. 1 (January 11, 2022): 16–41. http://dx.doi.org/10.3390/applnano3010002.

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Protein-DNA interactions are the core of the cell’s molecular machinery. For a long time, conventional biochemical methods served as a powerful investigatory basis of protein-DNA interactions and target search mechanisms. Currently single-molecule (SM) techniques have emerged as a complementary tool for studying these interactions and have revealed plenty of previously obscured mechanistic details. In comparison to the traditional ones, SM methods allow direct monitoring of individual biomolecules. Therefore, SM methods reveal reactions that are otherwise hidden by the ensemble averaging observed in conventional bulk-type methods. SM biophysical techniques employing various nanobiotechnology methods for immobilization of studied molecules grant the possibility to monitor individual reaction trajectories of biomolecules. Next-generation in vitro SM biophysics approaches enabling high-throughput studies are characterized by much greater complexity than the ones developed previously. Currently, several high-throughput DNA flow-stretch assays have been published and have shown many benefits for mechanistic target search studies of various DNA-binding proteins, such as CRISPR-Cas, Argonaute, various ATP-fueled helicases and translocases, and others. This review focuses on SM techniques employing surface-immobilized and relatively long DNA molecules for studying protein-DNA interaction mechanisms.
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Alishahi, Marzieh, and Reza Kamali. "Forced diffusion of water molecules through aquaporin-5 biomembrane; a molecular dynamics study." Biophysics and Physicobiology 15 (2018): 255–62. http://dx.doi.org/10.2142/biophysico.15.0_255.

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Furlan, Aurélien L., Yoann Laurin, Camille Botcazon, Nely Rodríguez-Moraga, Sonia Rippa, Magali Deleu, Laurence Lins, Catherine Sarazin, and Sébastien Buchoux. "Contributions and Limitations of Biophysical Approaches to Study of the Interactions between Amphiphilic Molecules and the Plant Plasma Membrane." Plants 9, no. 5 (May 20, 2020): 648. http://dx.doi.org/10.3390/plants9050648.

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Some amphiphilic molecules are able to interact with the lipid matrix of plant plasma membranes and trigger the immune response in plants. This original mode of perception is not yet fully understood and biophysical approaches could help to obtain molecular insights. In this review, we focus on such membrane-interacting molecules, and present biophysically grounded methods that are used and are particularly interesting in the investigation of this mode of perception. Rather than going into overly technical details, the aim of this review was to provide to readers with a plant biochemistry background a good overview of how biophysics can help to study molecular interactions between bioactive amphiphilic molecules and plant lipid membranes. In particular, we present the biomimetic membrane models typically used, solid-state nuclear magnetic resonance, molecular modeling, and fluorescence approaches, because they are especially suitable for this field of research. For each technique, we provide a brief description, a few case studies, and the inherent limitations, so non-specialists can gain a good grasp on how they could extend their toolbox and/or could apply new techniques to study amphiphilic bioactive compound and lipid interactions.
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Sikosek, Tobias, and Hue Sun Chan. "Biophysics of protein evolution and evolutionary protein biophysics." Journal of The Royal Society Interface 11, no. 100 (November 6, 2014): 20140419. http://dx.doi.org/10.1098/rsif.2014.0419.

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The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution.
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Deniz, Ashok A., Samrat Mukhopadhyay, and Edward A. Lemke. "Single-molecule biophysics: at the interface of biology, physics and chemistry." Journal of The Royal Society Interface 5, no. 18 (May 22, 2007): 15–45. http://dx.doi.org/10.1098/rsif.2007.1021.

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Single-molecule methods have matured into powerful and popular tools to probe the complex behaviour of biological molecules, due to their unique abilities to probe molecular structure, dynamics and function, unhindered by the averaging inherent in ensemble experiments. This review presents an overview of the burgeoning field of single-molecule biophysics, discussing key highlights and selected examples from its genesis to our projections for its future. Following brief introductions to a few popular single-molecule fluorescence and manipulation methods, we discuss novel insights gained from single-molecule studies in key biological areas ranging from biological folding to experiments performed in vivo .
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Zhang, Yujia, Jessica Bates, Benoit Gourdet, Louise Birch, Philip Addis, Roland Hjerpe, and Allan M. Jordan. "Abstract 3429: Beyond cereblon IMIDs - biophysics-based discovery of novel molecular glue chemotypes." Cancer Research 83, no. 7_Supplement (April 4, 2023): 3429. http://dx.doi.org/10.1158/1538-7445.am2023-3429.

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Abstract Molecular glue degraders are compact, low molecular weight molecules that can efficiently induce specific and potent degradation of a target protein. This class of degraders function by inducing interactions between a target of interest and a ubiquitin-ligase, either by stabilization of weak pre-existing interactions, or by generation of entirely novel interactions. These molecules offer significant opportunity beyond heterobifunctional degraders such as PROTACs, not least in terms of improved molecular properties. However, beyond the IMID molecular glues, typified by thalidomide, pomalidomide and lenalidomide, novel molecular glue chemotypes remain scarce. To address this need, we have developed biophysics-based molecular glue screening platform, exploiting our internal, high quality fragment library and proximity-based screening platforms to rapidly identify promising new molecular glues for further optimization. A potential advantage of utilizing cell-free biophysical systems is the opportunity to select both the target and the desired ligase, opening up for development of degraders that capitalize upon differential expression of ligases in different tissues. As proof of concept, we have applied this platform to find new molecular glues to degrade CK1α. This Ser/Thr kinase has been found to be over-expressed in metastatic colorectal cancer, and this over-expression correlates with poor overall survival. The kinase has also been implicated as an oncogenic driver in tumors such as B-Cell lymphomas and non-Hodgkin lymphomas, suggesting a potential therapeutic application for novel CK1α molecular glues. Utilizing known IMID-derived molecular glues between CK1α and CRBN as benchmark controls, we identified several non-IMID derived chemotypes as tentative stabilizers of the CRBN/CK1α interaction. Further studies on these novel candidate degrader templates are now underway. Citation Format: Yujia Zhang, Jessica Bates, Benoit Gourdet, Louise Birch, Philip Addis, Roland Hjerpe, Allan M. Jordan. Beyond cereblon IMIDs - biophysics-based discovery of novel molecular glue chemotypes [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3429.
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Dissertations / Theses on the topic "Moleculor Biophysics"

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Huang, Po-Ssu Rees Douglas C. "Biochemistry and molecular biophysics /." Diss., Pasadena, Calif. : California Institute of Technology, 2004. http://resolver.caltech.edu/CaltechETD:etd-06012004-214823.

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Teng, Ching-Ling. "Mapping molecular accessibility and intermolecular interactions between ribonuclease A and paramagnetic small molecules using nuclear magnetic relaxation /." Full text, Acrobat Reader required, 2002. http://viva.lib.virginia.edu/etd/diss/ArtsSci/Biophysics/2002/Teng/TengDiss.pdf.

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Elmlund, Hans. "Protein structure dynamics and interplay : by single-particle electron microscopy." Doctoral thesis, Stockholm : Teknik och hälsa, Technology and Health, Kungliga Tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4669.

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Neetz, Manuel. "Collective behavior of molecular motors." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-85935.

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Microtubule associated molecular motors are involved in a multitude of fundamental cellular processes such as intracellular transport and spindle positioning. During these movements multiple motor proteins often work together and are, therefore, able to exert high forces. Thus force generation and sensing are common mechanisms for controlling motor driven movement. These mechanisms play a pivotal role when motor proteins antagonize each other, e.g. to facilitate oscillations of the spindle or the nucleus. Single motor proteins have been characterized in depth over the last two decades, our understanding of the collective behavior of molecular motors remains, however, poor. Since motor proteins often cooperate while they walk along microtubules, it is necessary to describe their collective reaction to a load quantitatively in order to understand the mechanism of many motor-driven processes. I studied the antagonistic action of many molecular motors (of one kind) in a gliding geometry. For this purpose I crosslinked two microtubules in an antiparallel fashion, so that they formed \"doublets\". Then I observed the gliding motility of these antiparallel doublets and analyzed the gliding velocity with respect to the relative number of motors pulling or pushing against each other. I observed that the antiparallel doublets gliding on conventional kinesin-1 (from Drosophila melanogaster) as well as cytoplasmic dynein (from Saccharomyces cerevisae) exhibited two distinct modes of movement, slow and fast, which were well separated. Furthermore I found a bistability, meaning, that both kinds of movement, slow and fast, occurred at the same ratio of antagonizing motors. Antiparallel doublets gliding on the non-processive motor protein Ncd (the kinesin-14 from D. melanogaster) showed, however, no bistability. The collective dynamics of all three motor proteins were described with a quantitative theory based on single-motor properties. Furthermore the response of multiple dynein motors towards an external, well-defined load was measured in a gliding geometry by magnetic tweezing. Examples of multi-motor force-velocity relationships are presented and discussed. I established, furthermore, a method for counting single surface immobilized motors to guide the evaluation of the tweezing experiments.
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Shen, Tongye. "Fluctuations and stochastic dynamics in molecular biophysics /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3061634.

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Mukund, Shreyas Ram. "Single molecule biophysics of homologous recombination." Thesis, University of Cambridge, 2015. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708842.

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Tang, Ming. "Atomic-scale biophysics modelling of type I collagen in the extracellular matrix." Thesis, Queensland University of Technology, 2019. https://eprints.qut.edu.au/124650/1/Ming_Tang_Thesis.pdf.

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This thesis explores the biophysics of collagen in the extracellular matrix under external stimuli, by performing cutting edge MD simulations. The obtained results provide significant insights into the design and manufacturing of artificial biomaterials for surgical tissue treatments, of collagen for regenerative medicine applications, and of gold nanoparticles for biomedical applications. The probed biophysical properties consist of the structural properties and the mechanical properties, where the mechanical properties of collagen are regulated by its structure at different levels of hierarchies.
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Klingelhoefer, Jochen W. "Biophysics of nanopores-multiscale molecular dynamics simulation studies." Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540136.

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Bellaiche, Mathias Moussine Jacques. "Molecular mechanisms of protein self-assembly and aggregation." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/277621.

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In this thesis, we investigate the mechanisms driving the self-assembly of peptides and proteins using computational and theoretical tools, always validating our results with experimental measures when possible. In the first part, Chapters 2-5, we focus on the Aβ system, a peptide whose aggregation is intimately linked with the development of Alzheimer's Disease. We begin by simulating the major alloforms of the peptide, Aβ_40 and Aβ_42, demonstrating that the two populate similar disordered ensembles and matching experimental data. Next we investigate how disordered Aβ_42 monomers interact with each other, finding that oligomerisation into amorphous aggregates is driven largely by hydrophobic, non-specific forces. We then move on to probing the aggregation of Aβ_42 into amyloid structures using a native-centric coarse-grained model, and explain the results with a novel Markov state analysis from which we are able to extract structural, kinetic and thermodynamic information on elongation reactions. Finally, we probe the interactions of Aβ_42 monomers with Aβ_42 fibrillar surfaces using a specially designed enhanced sampling scheme, which allows us to obtain enthalpy-driven binding thermodynamics consistent with experiments and to propose major polar binding modes. In the second part of the thesis, Chapters 6 and 7, we model the aggregation of two other self-assembling systems, viruses and a truncated form of the molecular chaperone Hsp70. We first develop a data analysis platform to extract information on the microscopic mechanisms of viral capsid self-assembly from experimental data, synthesising the results from several different systems to draw general evolutionary conclusions about the assembly mechanism. Finally, we model the oligomerisation of Hsp70 thermodynamically and kinetically, showing that its self-assembly is a highly cooperative reaction that is under strong structural constraints.
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King, Paul M. "Application of free energy perturbation calculations to molecular biophysics." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257951.

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Books on the topic "Moleculor Biophysics"

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Kostyukov, Viktor. Molecular mechanics of biopolymers. ru: INFRA-M Academic Publishing LLC., 2020. http://dx.doi.org/10.12737/1010677.

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The monograph is devoted to molecular mechanics simulations of biologically important polymers like proteins and nucleic acids. It is shown that the algorithms based on the classical laws of motion of Newton, with high-quality parameterization and sufficient computing resources is able to correctly reproduce and predict the structure and dynamics of macromolecules in aqueous solution. Summarized the development path of biopolymers molecular mechanics, its theoretical basis, current status and prospects for further progress. It may be useful to researchers specializing in molecular Biophysics and molecular biology, as well as students of senior courses of higher educational institutions, studying the biophysical and related areas of training.
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Scherer, Philipp, and Sighart F. Fischer. Theoretical Molecular Biophysics. Berlin, Heidelberg: Springer Berlin Heidelberg, 2010. http://dx.doi.org/10.1007/978-3-540-85610-8.

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Scherer, Philipp O. J., and Sighart F. Fischer. Theoretical Molecular Biophysics. Berlin, Heidelberg: Springer Berlin Heidelberg, 2017. http://dx.doi.org/10.1007/978-3-662-55671-9.

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F, Fischer Sighart, ed. Theoretical molecular biophysics. Berlin: Springer, 2008.

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1938-, Beveridge David L., and Lavery Richard, eds. Theoretical biochemistry & molecular biophysics. Schenectady, NY: Adenine Press, 1991.

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Harold, Lecar, ed. Molecular and cell biophysics. Redwood City, Calif: Addison-Wesley Pub. Co., the Advanced Book Program, 1991.

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Nossal, Ralph J. Molecular and cell biophysics. Redwood City, Calif: Addison-Wesley, 1991.

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Tuszynski, J. A. Molecular and cellular biophysics. Boca Raton: Chapman & Hall/CRC, 2008.

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Dewey, Thomas Gregory. Fractals in molecular biophysics. Oxford: Oxford University Press, 1997.

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Komatsuzaki, Tamiki, Masaru Kawakami, Satoshi Takahashi, Haw Yang, and Robert J. Silbey, eds. Single-Molecule Biophysics. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2011. http://dx.doi.org/10.1002/9781118131374.

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Book chapters on the topic "Moleculor Biophysics"

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Glaser, Roland. "Molecular Structure of Biological Systems." In Biophysics, 5–103. Berlin, Heidelberg: Springer Berlin Heidelberg, 2005. http://dx.doi.org/10.1007/978-3-662-04494-0_2.

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Glaser, Roland. "Molecular Structure of Biological Systems." In Biophysics, 5–93. Berlin, Heidelberg: Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-662-45845-7_2.

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Pilizota, Teuta, Yoshiyuki Sowa, and Richard M. Berry. "Single-Molecule Studies of Rotary Molecular Motors." In Handbook of Single-Molecule Biophysics, 183–216. New York, NY: Springer US, 2009. http://dx.doi.org/10.1007/978-0-387-76497-9_7.

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McCoy, Airlie J. "Molecular Replacement." In Encyclopedia of Biophysics, 1588–89. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_657.

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Monticelli, Luca, and D. Peter Tieleman. "Molecular Dynamics Simulations." In Encyclopedia of Biophysics, 1–7. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-642-35943-9_570-1.

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Kamp, Marc Willem. "Car-Parrinello Molecular Dynamics." In Encyclopedia of Biophysics, 244. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_276.

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Kunji, Edmund R. S. "Mitochondrial Transporters: Molecular Mechanism." In Encyclopedia of Biophysics, 1554–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_669.

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Van Wijk, Roeland. "Cellular and Molecular Aspects of Integrative Biophysics." In Integrative Biophysics, 179–201. Dordrecht: Springer Netherlands, 2003. http://dx.doi.org/10.1007/978-94-017-0373-4_4.

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Pietropaolo, Adriana, and Concetta Cozza. "Molecular Simulations of Biological Nanoswitches." In Encyclopedia of Biophysics, 1–5. Berlin, Heidelberg: Springer Berlin Heidelberg, 2020. http://dx.doi.org/10.1007/978-3-642-35943-9_10092-1.

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Towse, Clare-Louise, and Valerie Daggett. "Protein Folding: Molecular Dynamics Simulations." In Encyclopedia of Biophysics, 1–9. Berlin, Heidelberg: Springer Berlin Heidelberg, 2018. http://dx.doi.org/10.1007/978-3-642-35943-9_607-1.

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Conference papers on the topic "Moleculor Biophysics"

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Bao, Gang. "Single-Molecule Biomechanics: DNA and Protein Deformation." In ASME 2000 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2000. http://dx.doi.org/10.1115/imece2000-1918.

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Abstract With the advent of molecular biology and biophysics during the past decade, single-molecule biomechanics has emerged as a new field. Different techniques have been used to study the mechanical properties of DNA and protein molecules; various models have been developed to quantify the deformation of biomolecules under force. Here we review some of these advances, explore the connection between mechanics and biochemistry, and discuss the concepts, issues and challenges in developing molecular biomechanics.
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Taddei-Ferretti, C. "Biophysics of Photoreception; Molecular and Phototransductive Events." In Proceedings of the International School of Biophysics. WORLD SCIENTIFIC, 1998. http://dx.doi.org/10.1142/9789814529372.

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Mofrad, Mohammad R. K. "Molecular Mechanosensors and Focal Adhesion Mechanotransduction." In ASME 2010 Summer Bioengineering Conference. American Society of Mechanical Engineers, 2010. http://dx.doi.org/10.1115/sbc2010-19707.

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Cellular response to mechanical stimulation is mediated by both biochemical mechanisms via changes in gene expression and by biophysical mechanisms via mechanically induced changes in specific molecules’ structure and function. These mechanically responsive molecules can be described as the cell’s mechanosensors and can function to initiate processes such as focal adhesion formation. A series of molecular dynamics investigations explore the mechanosensor function of key molecules involved in focal adhesion formation and cytoskeletal dynamics.
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Erickson, David. "Single-Molecule Biophysics with Optofluidic Trapping." In Frontiers in Optics. Washington, D.C.: OSA, 2011. http://dx.doi.org/10.1364/fio.2011.fma2.

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SHALAEVA, D. N., D. A. CHEREPANOV, M. Y. GALPERIN, and A. Y. MULKIDJANIAN. "EVOLUTIONARY BIOPHYSICS OF P-LOOP NUCLEOSIDE TRIPHOSPHATASES." In 5TH MOSCOW INTERNATIONAL CONFERENCE "MOLECULAR PHYLOGENETICSAND BIODIVERSITY BIOBANKING". TORUS PRESS, 2018. http://dx.doi.org/10.30826/molphy2018-09.

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PAULSEN, R., M. BÄHNER, A. HUBER, M. SCHILLO, S. SCHULZ, R. WOTTRICH, and J. BENTROP. "THE MOLECULAR DESIGN OF A VISUAL CASCADE: MOLECULAR STAGES OF PHOTOTRANSDUCTION IN DROSOPHILA." In Proceedings of the International School of Biophysics. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799975_0004.

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Galpayage Dona, Kalpani Nisansala Udeni, Jia Liu, Yuhao Qiang, E. Du, and A. W. C. Lau. "Electrical Equivalent Circuit Model of Sickle Cell." In ASME 2017 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2017. http://dx.doi.org/10.1115/imece2017-70677.

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Mature red blood cell (RBC) consists of cytoplasm, mainly normal hemoglobin (HbA) within a plasma membrane. In sickle cell disease, abnormal sickle hemoglobin (HbS) molecule polymerizes and forms into rigid fibers at low oxygen tension, which contributes to variation in the biophysical properties of sickle cells from healthy RBCs. This paper presents an electrical equivalent circuit (EEC) model of sickle cell that considers the phase transition of oxy-HbS solution to deoxy-HbS polymers. Briefly, we model the oxy-HbS solution following healthy RBCs using a resistor and deoxy-HbS fibers as a capacitor. To validate the model, electrical impedance measurements of cell suspensions for normal RBCs and sickle cells are performed, using a multi-channel lock in amplifier in the frequency range of 1 kHz to 10 MHz in a customized microfluidic chamber. Quantitative measurements of the classical components of EEC model are extracted using the developed EEC sickle cell model, allowing us to better understand the biophysics of cell sickling event in sickle cell disease.
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Shepard, Ken. "Solid-state electronics and single-molecule biophysics." In 2012 70th Annual Device Research Conference (DRC). IEEE, 2012. http://dx.doi.org/10.1109/drc.2012.6256965.

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MOYA, KENNETH L., ALVIN W. LYCKMAN, and ANNAMARIA CONFALONI. "MOLECULAR CHANGES DURING PRIMARY VISUAL PATHWAY DEVELOPMENT." In Proceedings of the International School of Biophysics. WORLD SCIENTIFIC, 2001. http://dx.doi.org/10.1142/9789812799975_0006.

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Nikjoo, Hooshang. "Application of Radiation Track in Radiation Biophysics and Dosimetry." In ATOMIC AND MOLECULAR DATA AND THEIR APPLICATIONS: 3rd International Conference on Atomic and Molecular Data and Their Applications ICAMDATA. AIP, 2002. http://dx.doi.org/10.1063/1.1516320.

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Reports on the topic "Moleculor Biophysics"

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Ha, Ji Won. Single Molecule and Nanoparticle Imaging in Biophysical, Surface, and Photocatalysis Studies. Office of Scientific and Technical Information (OSTI), January 2013. http://dx.doi.org/10.2172/1116723.

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del Rincon, Sonia. Elucidating the Role of CKS Proteins in Breast Cancer by Combining the Disciplines of Molecular Biology, Pathology, and Biophysics. Fort Belvoir, VA: Defense Technical Information Center, March 2007. http://dx.doi.org/10.21236/ada472330.

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Azem, Abdussalam, George Lorimer, and Adina Breiman. Molecular and in vivo Functions of the Chloroplast Chaperonins. United States Department of Agriculture, June 2011. http://dx.doi.org/10.32747/2011.7697111.bard.

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We present here the final report for our research project entitled "The molecular and in vivo functions of the chloroplast chaperonins”. Over the past few decades, intensive investigation of the bacterial GroELS system has led to a basic understanding of how chaperonins refold denatured proteins. However, the parallel is limited in its relevance to plant chaperonins, since the plant system differs from GroEL in genetic complexity, physiological roles of the chaperonins and precise molecular structure. Due to the importance of plant chaperonins for chloroplast biogenesis and Rubisco assembly, research on this topic will have implications for many vital applicative fields such as crop hardiness and efficiency of plant growth as well as the production of alternative energy sources. In this study, we set out to investigate the structure and function of chloroplast chaperonins from A. thaliana. Most plants harbor multiple genes for chaperonin proteins, making analysis of plant chaperonin systems more complicated than the GroEL-GroES system. We decided to focus on the chaperonins from A. thaliana since the genome of this plant has been well defined and many materials are available which can help facilitate studies using this system. Our proposal put forward a number of goals including cloning, purification, and characterization of the chloroplast cpn60 subunits, antibody preparation, gene expression patterns, in vivo analysis of oligomer composition, preparation and characterization of plant deletion mutants, identification of substrate proteins and biophysical studies. In this report, we describe the progress we have made in understanding the structure and function of chloroplast chaperonins in each of these categories.
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Gorbunov, Maxim Y., and Paul G. Falkowski. Analysis of Biophysical, Optical and Genetic Diversity of DoD Coral Reef Communities Using Advanced Fluorescence and Molecular Biology Techniques (Addendum). Fort Belvoir, VA: Defense Technical Information Center, August 2011. http://dx.doi.org/10.21236/ada551908.

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Tzfira, Tzvi, Michael Elbaum, and Sharon Wolf. DNA transfer by Agrobacterium: a cooperative interaction of ssDNA, virulence proteins, and plant host factors. United States Department of Agriculture, December 2005. http://dx.doi.org/10.32747/2005.7695881.bard.

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Agrobacteriumtumefaciensmediates genetic transformation of plants. The possibility of exchanging the natural genes for other DNA has led to Agrobacterium’s emergence as the primary vector for genetic modification of plants. The similarity among eukaryotic mechanisms of nuclear import also suggests use of its active elements as media for non-viral genetic therapy in animals. These considerations motivate the present study of the process that carries DNA of bacterial origin into the host nucleus. The infective pathway of Agrobacterium involves excision of a single-stranded DNA molecule (T-strand) from the bacterial tumor-inducing plasmid. This transferred DNA (T-DNA) travels to the host cell cytoplasm along with two virulence proteins, VirD2 and VirE2, through a specific bacteriumplant channel(s). Little is known about the precise structure and composition of the resulting complex within the host cell and even less is known about the mechanism of its nuclear import and integration into the host cell genome. In the present proposal we combined the expertise of the US and Israeli labs and revealed many of the biophysical and biological properties of the genetic transformation process, thus enhancing our understanding of the processes leading to nuclear import and integration of the Agrobacterium T-DNA. Specifically, we sought to: I. Elucidate the interaction of the T-strand with its chaperones. II. Analyzing the three-dimensional structure of the T-complex and its chaperones in vitro. III. Analyze kinetics of T-complex formation and T-complex nuclear import. During the past three years we accomplished our goals and made the following major discoveries: (1) Resolved the VirE2-ssDNA three-dimensional structure. (2) Characterized VirE2-ssDNA assembly and aggregation, along with regulation by VirE1. (3) Studied VirE2-ssDNA nuclear import by electron tomography. (4) Showed that T-DNA integrates via double-stranded (ds) intermediates. (5) Identified that Arabidopsis Ku80 interacts with dsT-DNA intermediates and is essential for T-DNA integration. (6) Found a role of targeted proteolysis in T-DNA uncoating. Our research provide significant physical, molecular, and structural insights into the Tcomplex structure and composition, the effect of host receptors on its nuclear import, the mechanism of T-DNA nuclear import, proteolysis and integration in host cells. Understanding the mechanical and molecular basis for T-DNA nuclear import and integration is an essential key for the development of new strategies for genetic transformation of recalcitrant plant species. Thus, the knowledge gained in this study can potentially be applied to enhance the transformation process by interfering with key steps of the transformation process (i.e. nuclear import, proteolysis and integration). Finally, in addition to the study of Agrobacterium-host interaction, our research also revealed some fundamental insights into basic cellular mechanisms of nuclear import, targeted proteolysis, protein-DNA interactions and DNA repair.
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