The Experts below are selected from a list of 1467 Experts worldwide ranked by ideXlab platform
Sophie Y. Wong - One of the best experts on this subject based on the ideXlab platform.
-
Entropic Elasticity controls nanomechanics of single tropocollagen molecules.
Biophysical journal, 2007Co-Authors: Markus J Buehler, Sophie Y. WongAbstract:We report molecular modeling of stretching single molecules of tropocollagen, the building block of collagen fibrils and fibers that provide mechanical support in connective tissues. For small deformation, we observe a dominance of Entropic Elasticity. At larger deformation, we find a transition to energetic Elasticity, which is characterized by first stretching and breaking of hydrogen bonds, followed by deformation of covalent bonds in the protein backbone, eventually leading to molecular fracture. Our force-displacement curves at small forces show excellent quantitative agreement with optical tweezer experiments. Our model predicts a persistence length ξp ≈ 16 nm, confirming experimental results suggesting that tropocollagen molecules are very flexible elastic entities. We demonstrate that assembly of single tropocollagen molecules into fibrils significantly decreases their bending flexibility, leading to decreased contributions of Entropic effects during deformation. The molecular simulation results are used to develop a simple continuum model capable of describing an entire deformation range of tropocollagen molecules. Our molecular model is capable of describing different regimes of elastic and permanent deformation, without relying on empirical parameters, including a transition from Entropic to energetic Elasticity.
-
Entropic Elasticity controls nanomechanics of single tropocollagen molecules
MRS Proceedings, 2006Co-Authors: Markus J Buehler, Sophie Y. WongAbstract:We report molecular modeling of stretching single molecules of tropocollagen, the building block of collagen fibrils and fibers that provide mechanical support in connective tissues. For small deformation, we observe a dominance of Entropic Elasticity. At larger deformation, we find a transition to energetic Elasticity, which is characterized by first stretching and breaking of hydrogen bonds, followed by deformation of covalent bonds in the protein backbone, eventually leading to molecular fracture. Our force-displacement curves show excellent quantitative agreement with optical tweezer experiments, suggesting a persistence length of approximately 16 nm. We demonstrate that assembly of single TC molecules into fibrils significantly decreases their flexibility, leading to decreased contributions of Entropic effects during deformation. We develop a simple continuum model capable of describing entire deformation range of TC molecules.
Kohzo Ito - One of the best experts on this subject based on the ideXlab platform.
-
mechanics of slide ring gels novel Entropic Elasticity of a topological network formed by ring and string
Soft Matter, 2012Co-Authors: Koichi Mayumi, Masahiko Tezuka, Akinori Bando, Kohzo ItoAbstract:Slide-ring (SR) gels are polymer networks with movable cross-links that are prepared by cross-linking polyrotaxane (PR) in which many cyclic molecules are threaded into a linear polymer chain. The elastic modulus E of SR gels shows a unique dependence on cross-linking density: at a high cross-linking density, E decreases with increasing cross-linking density. This tendency is not in agreement with conventional rubber Elasticity theory. In order to explain this abnormal dependence, we propose a novel molecular theory for SR gels, which considers the alignment entropy of cyclic molecules on polymer networks. The alignment yields new Entropic Elasticity of the slidable network in SR gels.
-
novel Entropic Elasticity of polymeric materials why is slide ring gel so soft
Polymer Journal, 2012Co-Authors: Kohzo ItoAbstract:Slide-ring gel with freely movable crosslinks shows extremely small Young's modulus and recovers the deformed shape to the original one instantaneously and completely. The small modulus arises from new Entropic Elasticity because of the heterogenous distribution of free cyclic molecules on polyrotaxane. The sliding Elasticity appears in the sliding state, where axis polymer chains and cyclic molecules are sliding actively. In addition, the slide-ring gel should show the sliding transition between the rubber and sliding states. These aspects indicate that the slide-ring gel has its unique dynamics in mechanical properties.
Philip C Nelson - One of the best experts on this subject based on the ideXlab platform.
-
Entropic Elasticity of dna with a permanent kink
Macromolecules, 2006Co-Authors: Philip C Nelson, M D BettertonAbstract:Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the Elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for theories of DNA Elasticity which include helix-deforming proteins. Previous theoretical work on bent DNA has examined a long DNA molecule with many nonspecifically binding proteins. However, recent experiments used relatively short DNA molecules with a single, well-defined bend site. Here we develop a simple, theoretical description of the effect of a single bend. We then include the description of the bend in the finite wormlike chain model (FWLC) of short DNA molecules attached to beads. We predict how the DNA force-extension relation changes due to formation of a single permanent kink, at all values of the applied stretching force. Our predictions suggest that high-resolution single-molecule experiments could determine the bend angle induced upon protein binding.
-
Entropic Elasticity of dna with a permanent kink
arXiv: Biological Physics, 2006Co-Authors: Philip C Nelson, M D BettertonAbstract:Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the Elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for theories of DNA Elasticity which include helix-deforming proteins. Previous theoretical work on bent DNA has examined a long DNA molecule with many nonspecifically binding proteins. However, recent experiments used relatively short DNA molecules with a single, well-defined bend site. Here we develop a simple theoretical description of the effect of a single bend. We then include the description of the bend in the finite worm like chain model (FWLC) of short DNA molecules attached to beads. We predict how the DNA force-extension relation changes due to formation of a single permanent kink, at all values of the applied stretching force. Our predictions show that high-resolution single-molecule experiments could determine the bend angle induced upon protein binding.
-
dna Entropic Elasticity for short molecules attached to beads
arXiv: Biological Physics, 2006Co-Authors: M D Betterton, Philip C NelsonAbstract:Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer force-extension behavior to calibrate the experiments; typically the experiments use the worm-like chain (WLC) theory for double-stranded DNA and RNA. This theory agrees well with experiments for long molecules. Recent single-molecule experiments have used shorter molecules, with contour lengths in the range of 1-10 persistence lengths. Most WLC theory calculations to date have assumed infinite molecule lengths, and do not agree well with experiments on shorter chains. Key physical effects that become important when shorter molecules are used include (i) boundary conditions which constrain the allowed fluctuations at the ends of the molecule and (ii) rotational fluctuations of the bead to which the polymer is attached, which change the apparent extension of the molecule. We describe the finite worm-like chain (FWLC) theory, which takes into account these effects. We show the FWLC predictions diverge from the classic WLC solution for molecules with contour lengths a few times the persistence length. Thus the FWLC will allow more accurate experimental calibration for relatively short molecules, facilitating future discoveries in single-molecule force microscopy.
-
Entropic Elasticity of twist storing polymers
Macromolecules, 1998Co-Authors: David J Moroz, Philip C NelsonAbstract:We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness AkBT and twist stiffness CkBT. In such a model, thermal bend fluctuations couple geometrically to an applied torque through the relation Lk = Tw + Wr. We explore this coupling and find agreement between the predictions of our model and recent experimental results on single λ-DNA molecules. This analysis affords an experimental determination of the microscopic twist stiffness (averaged over a helix repeat). Quantitative agreement between theory and experiment is obtained using C = 109 nm (i.e., twist rigidity CkBT = 4.5 × 10-19 erg cm). The theory further predicts a thermal reduction of the effective twist rigidity induced by bend fluctuations. Finally, we find a small reflection of molecular chirality in the experimental data and interpret it in terms of a twist−stretch coupling of the DNA duplex.
-
sequence disorder effects on dna Entropic Elasticity
Physical Review Letters, 1998Co-Authors: Philip C NelsonAbstract:DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by this method is a combination of bend stiffness and intrinsic bend effects reflecting sequence information, just as at zero stretching force. This observation resolves the discrepancy between the value of A measured in these experiments and the larger ``dynamic persistence length'' measured by other means. On the other hand, the twist persistence length deduced from torsionally-constrained stretching experiments suffers no such correction. Our calculation is very simple and analytic; it applies to DNA and other polymers with weak intrinsic disorder.
Yacov Kantor - One of the best experts on this subject based on the ideXlab platform.
-
Entropic Elasticity at the sol gel transition
EPL, 2002Co-Authors: Oded Farago, Yacov KantorAbstract:The sol-gel transition is studied in two purely Entropic models consisting of hard spheres in continuous three-dimensional space, with a fraction p of nearest-neighbor spheres tethered by inextensible bonds. When all the tethers are present (p = 1) the two systems have connectivities of simple cubic and face-centered cubic lattices. For all p above the percolation threshold pc, the Elasticity has a cubic symmetry characterized by two distinct shear moduli. When p approaches pc, both shear moduli decay as (p − pc)f, where f 2 for each type of connectivity. This result is similar to the behavior of the conductivity in random resistor networks, and is consistent with many experimental studies of gel Elasticity. The difference between the shear moduli that measures the deviation from isotropy decays as (p − pc)h, with h 4.
-
Entropic Elasticity at the sol gel transition
arXiv: Statistical Mechanics, 2001Co-Authors: Oded Farago, Yacov KantorAbstract:The sol-gel transition is studied in two purely Entropic models consisting of hard spheres in continuous three-dimensional space, with a fraction $p$ of nearest neighbor spheres tethered by inextensible bonds. When all the tethers are present ($p=1$) the two systems have connectivities of simple cubic and face-centered cubic lattices. For all $p$ above the percolation threshold $p_c$, the Elasticity has a cubic symmetry characterized by two distinct shear moduli. When $p$ approaches $p_c$, both shear moduli decay as $(p-p_c)^f$, where $f\simeq 2$ for each type of the connectivity. This result is similar to the behavior of the conductivity in random resistor networks, and is consistent with many experimental studies of gel Elasticity. The difference between the shear moduli that measures the deviation from isotropy decays as $(p-p_c)^h$, with $h\simeq 4$.
-
Entropic Elasticity of two dimensional self avoiding percolation systems
Physical Review Letters, 2000Co-Authors: Oded Farago, Yacov KantorAbstract:The sol-gel transition is studied on a purely Entropic two-dimensional model system consisting of hard spheres (disks) in which a fraction $p$ of neighbors are tethered by inextensible bonds. We use a new method to measure directly the elastic properties of the system. We find that over a broad range of hard sphere diameters $a$ the rigidity threshold is insensitive to $a$ and indistinguishable from the percolation threshold ${p}_{c}$. Close to ${p}_{c}$, the shear modulus behaves as $({p\ensuremath{-}p}_{c}{)}^{f}$, where the exponent $f\ensuremath{\simeq}1.3$ is independent of $a$ and is similar to the conductivity exponent in random resistor networks.
-
Entropic Elasticity of phantom percolation networks
arXiv: Statistical Mechanics, 2000Co-Authors: Oded Farago, Yacov KantorAbstract:A new method is used to measure the stress and elastic constants of purely Entropic phantom networks, in which a fraction $p$ of neighbors are tethered by inextensible bonds. We find that close to the percolation threshold $p_c$ the shear modulus behaves as $(p-p_c)^f$, where the exponent $f\approx 1.35$ in two dimensions, and $f\approx 1.95$ in three dimensions, close to the corresponding values of the conductivity exponent in random resistor networks. The components of the stiffness tensor (elastic constants) of the spanning cluster follow a power law $\sim(p-p_c)^g$, with an exponent $g\approx 2.0$ and 2.6 in two and three dimensions, respectively.
Markus J Buehler - One of the best experts on this subject based on the ideXlab platform.
-
comparative analysis of nanomechanics of protein filaments under lateral loading
Nanoscale, 2012Co-Authors: Max Solar, Markus J BuehlerAbstract:Using a combination of explicit solvent atomistic simulation and continuum theory, here we study the lateral deformation mechanics of three distinct protein structures: an amyloid fibril, a beta helix, and an alpha helix. We find that the two β-sheet rich structures – amyloid fibril and beta helix, with persistence lengths on the order of μm – are well described by continuum mechanical theory, but differ in the degree to which shear deformation affects the overall bending behavior. The alpha helical protein structure, however, with a persistence length on the order of one nanometer, does not conform to the continuum theory and its deformation is dominated by Entropic Elasticity due to significant fluctuations. This study provides fundamental insight into the nanomechanics of widely found protein motifs and insight into molecular-scale deformation mechanisms, as well as quantitative estimates of Young's modulus and shear modulus in agreement with experimental results.
-
Strength limit of Entropic Elasticity in beta-sheet protein domains.
Physical Review E, 2008Co-Authors: Sinan Keten, Markus J BuehlerAbstract:Elasticity and strength of individual beta-sheet protein domains govern key biological functions and the mechanical properties of biopolymers including spider silk, amyloids, and muscle fibers. The worm-like-chain (WLC) model is commonly used to describe the Entropic Elasticity of polypeptides and other biomolecules. However, force spectroscopy experiments have shown pronounced deviations from the ideal WLC behavior, leading to controversial views about the appropriate elastic description of proteins at nanoscale. Here we report a simple model that explains the physical mechanism that leads to the breakdown of the WLC idealization in experiments by using only two generic parameters of the protein domain, the H-bond energy and the protein backbone's persistence length. We show that a rupture initiation condition characterized by the free energy release rate of H-bonds characterizes the limit of WLC Entropic Elasticity of beta-sheet protein domains and the onset of rupture. Our findings reveal that strength and Elasticity are coupled and cannot be treated separately. The predictions of the model are compared with atomic force microscopy experiments of protein rupture.
-
hierarchical chemo nanomechanics of proteins Entropic Elasticity protein unfolding and molecular fracture
Journal of Mechanics of Materials and Structures, 2007Co-Authors: Markus J BuehlerAbstract:Proteins are an integral part of nature’s material design. Here we apply multiscale modeling capable of providing a bottom-up description of the nanomechanics of chemically complex protein materials under large deformation and fracture. To describe the formation and breaking of chemical bonds of different character, we use a new reactive force field approach that enables us to describe the unfolding dynamics while considering the breaking and formation of chemical bonds in systems that are comprised of several thousand atoms. We particularly focus on the relationship between secondary and tertiary protein structures and the mechanical properties of molecules under large deformation and fracture. Our research strategy is to systematically investigate the nanomechanics of three protein structures with increasing complexity, involving alpha helices, random coils and beta sheets. The model systems include an alpha helical protein from human vimentin, a small protein -conotoxin PnIB from conus pennaceus, and lysozyme, an enzyme that catalyzes breaking of glycosidic bonds. We find that globular proteins can feature extremely long unfolding paths of several tens of nanometers, displaying a characteristic sawtooth shape of the force-displacement curve. Our results suggest that the presence of disulfide crosslinks can significantly influence the mechanics of unfolding. Fibrillar proteins show shorter unfolding paths and continuous increase of forces until molecular rupture occurs. In the last part of the article we outline how a mesoscale representation of the alpha helical protein structure can be developed within the framework of hierarchical multiscale modeling, utilizing the results of atomistic modeling, without relying on empirical parameters. We apply this model to describe the competition between Entropic and energetic Elasticity in the mechanics of a single alpha helical protein molecule, at long time scales reaching several microseconds. We conclude with a discussion of hybrid reactive-nonreactive modeling that could help to overcome some of the computational limitations of reactive force fields.
-
Entropic Elasticity controls nanomechanics of single tropocollagen molecules.
Biophysical journal, 2007Co-Authors: Markus J Buehler, Sophie Y. WongAbstract:We report molecular modeling of stretching single molecules of tropocollagen, the building block of collagen fibrils and fibers that provide mechanical support in connective tissues. For small deformation, we observe a dominance of Entropic Elasticity. At larger deformation, we find a transition to energetic Elasticity, which is characterized by first stretching and breaking of hydrogen bonds, followed by deformation of covalent bonds in the protein backbone, eventually leading to molecular fracture. Our force-displacement curves at small forces show excellent quantitative agreement with optical tweezer experiments. Our model predicts a persistence length ξp ≈ 16 nm, confirming experimental results suggesting that tropocollagen molecules are very flexible elastic entities. We demonstrate that assembly of single tropocollagen molecules into fibrils significantly decreases their bending flexibility, leading to decreased contributions of Entropic effects during deformation. The molecular simulation results are used to develop a simple continuum model capable of describing an entire deformation range of tropocollagen molecules. Our molecular model is capable of describing different regimes of elastic and permanent deformation, without relying on empirical parameters, including a transition from Entropic to energetic Elasticity.
-
Entropic Elasticity controls nanomechanics of single tropocollagen molecules
MRS Proceedings, 2006Co-Authors: Markus J Buehler, Sophie Y. WongAbstract:We report molecular modeling of stretching single molecules of tropocollagen, the building block of collagen fibrils and fibers that provide mechanical support in connective tissues. For small deformation, we observe a dominance of Entropic Elasticity. At larger deformation, we find a transition to energetic Elasticity, which is characterized by first stretching and breaking of hydrogen bonds, followed by deformation of covalent bonds in the protein backbone, eventually leading to molecular fracture. Our force-displacement curves show excellent quantitative agreement with optical tweezer experiments, suggesting a persistence length of approximately 16 nm. We demonstrate that assembly of single TC molecules into fibrils significantly decreases their flexibility, leading to decreased contributions of Entropic effects during deformation. We develop a simple continuum model capable of describing entire deformation range of TC molecules.