Relevant bibliographies by topics / Worm-like chain model

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  1. Journal articles
  2. Dissertations / Theses
  3. Book chapters
  4. Conference papers

Academic literature on the topic 'Worm-like chain model'

Author: Grafiati
Published: 4 June 2021
Last updated: 10 February 2022

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Journal articles on the topic "Worm-like chain model"

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Xu, Xin, and Ying Jiang. "Applications of worm-like chain model in polymer physics." International Journal of Modern Physics B 32, no. 18 (July 15, 2018): 1840006. http://dx.doi.org/10.1142/s0217979218400064.

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Saito, Takahashi and Yunoki developed the continuous version of worm-like chain (WLC) model that is very suitable for description of the polymer conformational properties affected by chain rigidity. By adjusting persistence length directly, the WLC model can depict the extensive range of chain conformations from flexible chains to rigid chains. It is widely accepted that more physical properties of real polymer can be obtained by utilizing coarse-grained model than Gaussian chain (GSC). This paper reviews the applications of the WLC model in the framework based on self-consistent field theory, which is an efficient method of theoretical exploration of phase separation in polymer system. It is noticed that the development of numerical schemes is in favor of solving modified diffusion equation that adjusts the probability distribution of polymers. In addition, we conclude the recent applications of the self-consistent field theory based on the WLC model as the following three points: phase transitions of liquid crystal polymer; the influences of surface curvature on polymer system that involves the chain orientation effects; self-assembly of worm-like block copolymer. These researches have been out of the range of the self-consistent field theory based on GSC model that has been used in a large number of theoretical studies. Finally, we present ideas of theoretical development in field theory simulations based on the WLC model in the future. It is universally acknowledged that chain rigidity is a key factor that influences the properties of structural stabilities in the meso-scale in articles. Theoretical researches determine the key physical mechanisms that play crucial roles in many experimental systems with attractively promising applications in practice, for systems such as liquid crystalline polymers and organic solar cell based on the conjugated polymers.
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Fu, Yi-Ben, Yu-Ru Liu, Peng-Ye Wang, and Ping Xie. "A revised worm-like chain model for elasticity of polypeptide chains." Journal of Polymer Science Part B: Polymer Physics 56, no. 4 (November 4, 2017): 297–307. http://dx.doi.org/10.1002/polb.24541.

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Hillgärtner, Markus, Kevin Linka, and Mikhail Itskov. "Worm-like chain model extensions for highly stretched tropocollagen molecules." Journal of Biomechanics 80 (October 2018): 129–35. http://dx.doi.org/10.1016/j.jbiomech.2018.08.034.

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Ogden, Ray W., Giuseppe Saccomandi, and Ivonne Sgura. "On worm-like chain models within the three-dimensional continuum mechanics framework." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 462, no. 2067 (December 19, 2005): 749–68. http://dx.doi.org/10.1098/rspa.2005.1592.

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In this paper, we review critically some basic models derived from the statistics of long-chain molecules and then discuss the status of such models within the three-dimensional nonlinear theory of elasticity. We draw attention to some deficiencies of certain worm-like chain (WLC) models when viewed within the three-dimensional continuum mechanics framework. Modifications of the WLC models motivated by such considerations and avoiding these deficiencies are then discussed and shown to correspond well with data generated by the exact WLC model.
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Xiao, Hongyi, Xinghua Zhang, and Dadong Yan. "A Local-Exchange Model of Folding Chain Surface of Polymer Crystal Based on Worm-Like Chain Model within Single-Chain in Mean-Field Theory." Polymers 12, no. 11 (October 30, 2020): 2555. http://dx.doi.org/10.3390/polym12112555.

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The structure of amorphous layer of folding surface controls the properties of the polymer lamellar crystal, which consists of chains with a loop conformation. The surface tension depends on the length and the distance between two injection points of the loop which involving the reptation motion and lateral exchange motion of the stems. In the present work, a local-exchange motion model based on the worm-like chain model is developed to investigate the effects of lateral motion of stems on the release the surface tension. The optimal distance between two injection points is determined by the balance of chain bending energy and conformational entropy. The numerical results provide evidences to the adjacent re-entry model for various loop lengths. A possible explanation involving density of injection points is proposed to interpret the mechanism.
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Ou, C. R. "WORM LIKE CHAIN MODEL - PROPOGATIONS OF THE DOMAIN WALLS AND THE STABILITIES ISSUES." Journal of Biomechanics 40 (January 2007): S734. http://dx.doi.org/10.1016/s0021-9290(07)70722-4.

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Chan, Yue, Richard G. Haverkamp, and James M. Hill. "Force-extension formula for the worm-like chain model from a variational principle." Journal of Theoretical Biology 262, no. 3 (February 2010): 498–504. http://dx.doi.org/10.1016/j.jtbi.2009.10.009.

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Liao, Xinyu, Prashant K. Purohit, and Arvind Gopinath. "Extensions of the worm-like-chain model to tethered active filaments under tension." Journal of Chemical Physics 153, no. 19 (November 21, 2020): 194901. http://dx.doi.org/10.1063/5.0025200.

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DING, YAN, and TIEJUN LI. "A NOTE ON THE ANALYSIS OF A HETEROGENEOUS ROD-LIKE CHAIN IN DNA MODELING." International Journal of Modern Physics B 22, no. 14 (June 10, 2008): 2213–24. http://dx.doi.org/10.1142/s0217979208039460.

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Two different results concerning the elastic behavior of the heterogeneous worm-like chain (WLC) [D. Bensimon et al., Europhys. Lett.42, 97 (1998)] and rod-like chain (RLC) [P. Nelson, Phys. Rev. Lett.80, 5810 (1998)] are compared. We argue that the RLC is a more suitable model for double-stranded (ds-) DNA. As the hetero-RLC is the basic model for studying sequence-dependent ds-DNA, a rigorous path integral analysis for the effective bending persistence length is performed in the weak disorder limit. The novelty of the paper is in analyzing a path integral on the Lie group SO(3) with random forcing, which supplies a rigorous basis for the analysis of RLC type models.
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Hsu, Hsiao-Ping, Wolfgang Paul, and Kurt Binder. "Polymer chain stiffness vs. excluded volume: A Monte Carlo study of the crossover towards the worm-like chain model." EPL (Europhysics Letters) 92, no. 2 (October 1, 2010): 28003. http://dx.doi.org/10.1209/0295-5075/92/28003.

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Dissertations / Theses on the topic "Worm-like chain model"

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Bagheri, Mehran. "Intrinsically Disordered Proteins: Mechanics, Assemblies, and Structural Transitions." Thesis, Université d'Ottawa / University of Ottawa, 2017. http://hdl.handle.net/10393/36576.

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Proteins are essential parts of living organisms that initiate and control almost all cellular processes. Despite the widely accepted belief that all functional proteins fold into stable and well-defined three-dimensional (3D) structures mandatory for protein activity, the existence of biologically functional disordered proteins has been increasingly recognized during past two decades. Proteins with inherent structural disorder, commonly known as intrinsically disordered proteins (IDPs), play many roles in a biological context. However, in contrast to their folded counterparts, they are dynamically unstructured and typically fluctuate among many conformations even while performing biological functions. In fact, it is this dynamical structural heterogeneity that that allows for IDPs to interact with other biological macromolecules in unique ways. Moreover, while a majority of proteins in eukaryotic proteomes have been found to have intrinsically disordered regions (IDR), the mechanisms by which protein disorder fives rise to biological functionality is still not well understood. Through a series of simulation studies on specific systems, this thesis probes several aspects of the emerging structure-function paradygm of IDPs, namely the mechanics, intermolecular assembly, and structural transitions occurring in these proteins. The lack of well-defined 3D structure in IDPs gives rise to distinct mechanical properties, the subject of the first study in the thesis on the elasticity of a elastomeric gluten-mimetic polypeptide with an intrinsically disordered character. This disordered polypeptide was shown to exhibit distinctively variable elastic response to a wide range of tensions, which a classical worm-like chain model failed to accurately describe, thus requiring a molecular-level analysis. IDPs frequently are frequently involved in protein-protein interactions, the focus of the second study on the propensity of an IDR, the B domain in dynamin-related protein 1 (Dpr1), to self-assemble into dimer structures while remaining disordered in all solution conditions. Despite a hypothesized auto-inhibitory role for this domain in Dpr1 that was assumed to be triggered by an disordered-to-order transition, the B domains in solution showed no tendency to form ordered structures even in the presence of order promoting osmolytes. Instead, self-association in the presence of osmolyte was found to occur by favorable intermolecular intereactions between specific region on the surface of the B-domains. Other IDPs do undergo a disorder-to-order transition in response to environmental cues, in ways that are unique disordered proteins, the focus of the last study on intermolecular ordering transitions in silk-like proteins. Factors such as protein sequence and physical tension were investigated, and results suggested that tyrosine residues in the key silk sequence motifs promote templating of beta structure from disordered precursors and that elongational stresses preferentialy stabilize antiparallel beta-sheet order. Together, these three computational studies provide insight into the nature of the structure-function mechanisms of IDPs.
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Le, Treut Guillaume. "Models of chromosome architecture and connection with the regulation of genetic expression." Thesis, Université Paris-Saclay (ComUE), 2016. http://www.theses.fr/2016SACLS411/document.

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Plusieurs indices suggèrent que le repliement du chromosome et la régulation de l’expression génétique sont étroitement liés. Par exemple, la co-expression d’un grand nombre de gènes est favorisée par leur rapprochement dans l’espace cellulaire. En outre, le repliement du chromosome permet de faire émerger des structures fonctionnelles. Celles-ci peuvent être des amas condensés et fibrillaires, interdisant l’accès à l’ADN, ou au contraire des configurations plus ouvertes de l’ADN avec quelques amas globulaires, comme c’est le cas avec les usines de transcription. Bien que dissemblables au premier abord, de telles structures sont rendues possibles par l’existence de protéines bivalentes, capable d’apparier des régions parfois très éloignées sur la séquence d’ADN. Le système physique ainsi constitué du chromosome et de protéines bivalentes peut être très complexe. C’est pourquoi les mécanismes régissant le repliement du chromosome sont restés majoritairement incompris.Nous avons étudié des modèles d’architecture du chromosome en utilisant le formalisme de la physique statistique. Notre point de départ est la représentation du chromosome sous la forme d’un polymère rigide, pouvant interagir avec une solution de protéines liantes. Les structures résultant de ces interactions ont été caractérisées à l’équilibre thermodynamique. De plus, nous avons utilisé des simulations de dynamique Brownienne en complément des méthodes théoriques, car elles permettent de prendre en considération une plus grande complexité dans les phénomènes biologiques étudiés.Les principaux aboutissements de cette thèse ont été : (i) de fournir un modèle pour l’existence des usines de transcriptions caractérisées in vivo à l’aide de microscopie par fluorescence ; (ii) de proposer une explication physique pour une conjecture portant sur un mécanisme de régulation de la transcription impliquant la formation de boucles d’ADN en tête d’épingle sous l’effet de la protéine H-NS, qui a été émise suite à l’observation de ces boucles au microscope à force atomique ; (iii) de proposer un modèle du chromosome qui reproduise les contacts mesurés à l’aide des techniques Hi-C. Les conséquences de ces mécanismes sur la régulation de la transcription ont été systématiquement discutées
Increasing evidences suggest that chromosome folding and genetic expression are intimately connected. For example, the co-expression of a large number of genes can benefit from their spatial co-localization in the cellular space. Furthermore, functional structures can result from the particular folding of the chromosome. These can be rather compact bundle-like aggregates that prevent the access to DNA, or in contrast, open coil configurations with several (presumably) globular clusters like transcription factories. Such phenomena have in common to result from the binding of divalent proteins that can bridge regions sometimes far away on the DNA sequence. The physical system consisting of the chromosome interacting with divalent proteins can be very complex. As such, most of the mechanisms responsible for chromosome folding and for the formation of functional structures have remained elusive.Using methods from statistical physics, we investigated models of chromosome architecture. A common denominator of our approach has been to represent the chromosome as a polymer with bending rigidity and consider its interaction with a solution of DNA-binding proteins. Structures entailed by the binding of such proteins were then characterized at the thermodynamical equilibrium. Furthermore, we complemented theoretical results with Brownian dynamics simulations, allowing to reproduce more of the biological complexity.The main contributions of this thesis have been: (i) to provide a model for the existence of transcrip- tion factories characterized in vivo with fluorescence microscopy; (ii) to propose a physical basis for a conjectured regulatory mechanism of the transcription involving the formation of DNA hairpin loops by the H-NS protein as characterized with atomic-force microscopy experiments; (iii) to propose a physical model of the chromosome that reproduces contacts measured in chromosome conformation capture (CCC) experiments. Consequences on the regulation of transcription are discussed in each of these studies
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Book chapters on the topic "Worm-like chain model"

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Milstein, Joshua N., and Jens-Christian Meiners. "Worm-Like Chain (WLC) Model." In Encyclopedia of Biophysics, 2757–60. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_502.

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"Worm-Like Chain Model." In Encyclopedia of Biophysics, 2760. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_101124.

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"Kratky-Porod Worm-Like Chain Model." In Encyclopedia of Biophysics, 1223. Berlin, Heidelberg: Springer Berlin Heidelberg, 2013. http://dx.doi.org/10.1007/978-3-642-16712-6_100509.

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Bensimon, David, Vincent Croquette, Jean-François Allemand, Xavier Michalet, and Terence Strick. "The Mechanical Properties of Nucleic Acids." In Single-Molecule Studies of Nucleic Acids and Their Proteins, 67–104. Oxford University Press, 2018. http://dx.doi.org/10.1093/oso/9780198530923.003.0004.

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This chapter reviews models which describe the elastic properties of stretched polymers—the Kratky–Porod, Freely Jointed Chain (FJC), and Worm-Like Chain (WLC) models—and the effect of self-avoidance on results derived from these. The models are compared with double-stranded DNA (dsDNA) stretching experiments. Dynamics of a single polymer in the presence (Zimm model) or absence (Rouse model) of hydrodynamic interactions between its segments is described, and results on the dynamics of dsDNA and ssDNA of various lengths are discussed. Theoretical and experimental behaviour of twisted DNA is described, deducing the molecule’s torsional modulus and its coupling between stretching and twisting. After discussing the braiding of two DNA molecules and simulation of the twisting and stretching of DNA molecules, this chapter describes the results of stretching experiments on ssDNA and RNA, where self-avoiding and base-pairing interactions contribute to elastic behaviour.
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Conference papers on the topic "Worm-like chain model"

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Ou, Chung-Jen, Chung-Ming Ou, Chien-Han Lin, and Hong-Syuan Lin. "Domain switching mechanism for ferroelectric moleculars and the comparision to the biomolecular worm like chain(WLC) model." In 2011 IEEE 4th International Nanoelectronics Conference (INEC). IEEE, 2011. http://dx.doi.org/10.1109/inec.2011.5991681.

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Raj, Ritwik, and Prashant K. Purohit. "Role of the Kinetic Relation in a Phase Transition-Based Model for Mechanical Unfolding in Macromolecules." In ASME 2010 International Mechanical Engineering Congress and Exposition. ASMEDC, 2010. http://dx.doi.org/10.1115/imece2010-40760.

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We present applications of a model developed to describe unfolding in macromolecules under an axial force. We show how different experimentally observed force-extension behaviors can be reproduced within a common theoretical framework. We propose that the unfolding occurs via the motion of a folded/unfolded interface along the length of the molecule. The molecules are modeled as one-dimensional continua capable of existing in two metastable states under an applied tension. The interface separates these two metastable states and represents a jump in stretch, which is related to applied force by the worm-like-chain relation. The mechanics of the interface are governed by the Abeyaratne-Knowles theory of phase transitions. The thermodynamic driving force controls the motion of the interface via an equation called the kinetic relation. By choosing an appropriate kinetic relation for the unfolding conditions and the macro-molecule under consideration, we have been able to generate a variety of unfolding processes in macromolecules.
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Lee, Byung Chul, Chanmin Kang, Jinsik Kim, Ji Yoon Kang, Hyun-Joon Shin, and Sang-Youp Lee. "Electrically Tethered DNA Stretching in Nanochannels." In ASME 2009 International Mechanical Engineering Congress and Exposition. ASMEDC, 2009. http://dx.doi.org/10.1115/imece2009-10986.

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In present study, stretching dynamics of electrically tethered λ-DNA (48.5kbp) in SiO2 nanochannels has been investigated. At high electrical fields (above 20kV/m), elongations of electrically tethered DNA molecules were observed. At high E-fields, DNAs were tethered in nanochannels and were spontaneously elongated along the nanochannels up to about 90 percent of its contour length. With E-field turned off, the measured relaxation time was about 10 sec from stretching with 20kV/m. In current study, observed behaviors of DNA molecules in nanochannels were explained by field-induced dielectrophoretic DNA trap due to the particular cross-sectional geometry of nanochannels. Also the elongation ratio between 20kV/m and 60kV/m cases and the effect of E-field distribution in the transverse plane on field-induced dielectrophoretic tethering force are discussed based on “worm-like chain” model. The FEM simulation was done to verify induced dielectrophoretic tethering force into the nanohorn.
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Yun, Zhong, Chuang Xiang, and Liang Wang. "A hybird red blood cell model based on the linear spring network model and worm-like-chains model." In 2017 10th International Congress on Image and Signal Processing, BioMedical Engineering and Informatics (CISP-BMEI). IEEE, 2017. http://dx.doi.org/10.1109/cisp-bmei.2017.8302241.

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Lykotrafitis, George, and He Li. "Two-Component Coarse-Grain Model for Erythrocyte Membrane." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-62133.

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Biological membranes are vital components of living cells as they function to maintain the structural integrity of the cells. Red blood cell (RBC) membrane comprises the lipid bilayer and the cytoskeleton network. The lipid bilayer consists of phospholipids, integral membrane proteins, peripheral proteins and cholesterol. It behaves as a 2D fluid. The cytoskeleton is a network of spectrin tetramers linked at the actin junctions. It is connected to the lipid bilayer primarily via Band-3 and ankyrin proteins. In this paper, we introduce a coarse-grained model with high computational efficiency for simulating a variety of dynamic and topological problems involving erythrocyte membranes. Coarse-grained agents are used to represent a cluster of lipid molecules and proteins with a diameter on the order of lipid bilayer thickness and carry both translational and rotational freedom. The membrane cytoskeleton is modeled as a canonical exagonal network of entropic springs that behave as Worm-Like-Chains (WLC). By simultaneously invoking these characteristics, the proposed model facilitates simulations that span large length-scales (∼ μm) and time-scales (∼ ms). The behavior of the model under shearing at different rates is studied. At low strain rates, the resulted shear stress is mainly due to the spectrin network and it shows the characteristic non-linear behavior of entropic networks, while the viscosity of the fluid-like lipid bilayer contributes to the resulting shear stress at higher strain rates. The apparent ease of this model in combining the spectrin network with the lipid bilayer presents a major advantage over conventional continuum methods such as finite element or finite difference methods for cell membranes.
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