Dynamic Nanofishing of Single Polymer Chains

2009 ◽  
Vol 82 (2) ◽  
pp. 271-282
Author(s):  
Ken Nakajima ◽  
Toshio Nishi
Keyword(s):  
Polymer Chain ◽  
Single Molecule ◽  
Structural Information ◽  
Persistence Length ◽  
Frictional Coefficient ◽  
Polymer Chains ◽  
Contour Length ◽  
Single Polymer Chain ◽  
Afm Cantilever ◽  
Solvent Molecules

Abstract Single molecule force spectroscopy (SMFS) realized by atomic force microscope (AFM) on a single polymer chain (static nanofishing), where a polymer chain is picked up and pulled at its chemically modified terminals, only gives structural information such as persistence length and contour length. Beyond this technique, dynamic nanofishing, where an AFM cantilever is imposed on the forced oscillation at its resonant frequency (∼10 kHz), enables us to investigate more fruitful information. The method gave extension-dependent changes of entropic elasticity and frictional coefficient with solvent molecules for mono-disperse living-polymerized polystyrene (PS). The solvent temperature dependence revealed that the frictional coefficient could be correlated with macroscopic “intrinsic viscosity.” Another novel technique, nanofishing at fast pulling rate (fast nanofishing), exhibited internal entanglement of a single PS chain and its subsequent relaxation.

Electroelasticity of dielectric elastomers based on molecular chain statistics

2018 ◽  
Vol 24 (3) ◽  
pp. 862-873 ◽  
Author(s):  
Mikhail Itskov ◽  
Vu Ngoc Khiêm ◽  
Sugeng Waluyo
Keyword(s):  
Constitutive Model ◽  
Polymer Chain ◽  
Mechanical Response ◽  
Three Dimensional ◽  
Polymer Chains ◽  
Molecular Chain ◽  
Dielectric Elastomers ◽  
Finite Extensibility ◽  
Single Polymer Chain ◽  
Non Gaussian

The mechanical response of dielectric elastomers can be influenced or even controlled by an imposed electric field. It can, for example, cause mechanical stress or strain without any applied load; this phenomenon is referred to as electrostriction. There are many purely phenomenological hyperelastic models describing this electroactive response of dielectric elastomers. In this contribution, we propose an electromechanical constitutive model based on molecular chain statistics. The model considers polarization of single polymer chain segments and takes into account their directional distribution. The latter results from non-Gaussian chain statistics, taking finite extensibility of polymer chains into account. The resulting (one-dimensional) electric potential of a single polymer chain is further generalized to the (three-dimensional) network potential. To this end, we apply directional averaging on the basis of numerical integration over a unit sphere. In a special case of the eight-direction (Arruda–Boyce) model, directional averaging is obtained analytically. This results in an invariant-based electroelastic constitutive model of dielectric elastomers. The model includes a small number of physically interpretable material constants and demonstrates good agreement with experimental data, with respect to the electroactive response and electrostriction of dielectric elastomers.

scholarly journals Direct observation of morphological transition for an adsorbed single polymer chain

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yukari Oda ◽  
Daisuke Kawaguchi ◽  
Yuma Morimitsu ◽  
Satoru Yamamoto ◽  
Keiji Tanaka
Keyword(s):  
Polymer Chain ◽  
Synthetic Polymer ◽  
Polymer Chains ◽  
Dynamics Simulation ◽  
Morphological Transition ◽  
Nano Composite ◽  
Force Microscopy ◽  
Local Conformation ◽  
Atomic Force ◽  
Single Polymer Chain

AbstractA better understanding of the structure of polymers at solid interfaces is crucial for designing various polymer nano-composite materials from structural materials to nanomaterials for use in industry. To this end, the first step is to obtain information on how synthetic polymer chains adsorb onto a solid surface. We closely followed the trajectory of a single polymer chain on the surface as a function of temperature using atomic force microscopy. Combining the results with a full-atomistic molecular dynamics simulation revealed that the chain became more rigid on the way to reaching a pseudo-equilibrium state, accompanied by a change in its local conformation from mainly loops to trains. This information will be useful for regulating the physical properties of polymers at the interface.

scholarly journals Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 687
Author(s):  
Amna Abdalla Mohammed Khalid ◽  
Pietro Parisse ◽  
Barbara Medagli ◽  
Silvia Onesti ◽  
Loredana Casalis
Keyword(s):  
Atomic Force Microscopy ◽  
Nucleic Acid ◽  
Single Molecule ◽  
Protein Complex ◽  
The Other ◽  
Contour Length ◽  
Force Microscopy ◽  
Atomic Force ◽  
Mcm Complex ◽  
Dna Double Helix

The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.

scholarly journals Optimal Relabeling of Water Molecules and Single-Molecule Entropy Estimation

Biophysica ◽  
2021 ◽  
Vol 1 (3) ◽  
pp. 279-296
Author(s):  
Federico Fogolari ◽  
Gennaro Esposito
Keyword(s):  
Single Molecule ◽  
Degrees Of Freedom ◽  
Water Molecules ◽  
Maximum Information ◽  
Nearest Neighbours ◽  
Biomolecular Simulations ◽  
Solvent Molecules ◽  
Solvation Entropy ◽  
Dynamics Simulations ◽  
Internal Degrees Of Freedom

Estimation of solvent entropy from equilibrium molecular dynamics simulations is a long-standing problem in statistical mechanics. In recent years, methods that estimate entropy using k-th nearest neighbours (kNN) have been applied to internal degrees of freedom in biomolecular simulations, and for the rigorous computation of positional-orientational entropy of one and two molecules. The mutual information expansion (MIE) and the maximum information spanning tree (MIST) methods were proposed and used to deal with a large number of non-independent degrees of freedom, providing estimates or bounds on the global entropy, thus complementing the kNN method. The application of the combination of such methods to solvent molecules appears problematic because of the indistinguishability of molecules and of their symmetric parts. All indistiguishable molecules span the same global conformational volume, making application of MIE and MIST methods difficult. Here, we address the problem of indistinguishability by relabeling water molecules in such a way that each water molecule spans only a local region throughout the simulation. Then, we work out approximations and show how to compute the single-molecule entropy for the system of relabeled molecules. The results suggest that relabeling water molecules is promising for computation of solvation entropy.

Slow Expansion of a Single Polymer Chain from the Knotted Globule

2004 ◽  
Vol 37 (13) ◽  
pp. 4917-4921 ◽  
Author(s):  
Mitsuo Nakata ◽  
Yoshiki Nakamura ◽  
Yasuyuki Maki ◽  
Naoki Sasaki
Keyword(s):  
Polymer Chain ◽  
Slow Expansion ◽  
Single Polymer Chain

Conformation and segmental mobility of a diluted single polymer chain simulated with bond fluctuation model

2012 ◽  
Vol 358 (12-13) ◽  
pp. 1452-1458 ◽  
Author(s):  
R. Sabater i Serra ◽  
C. Torregrosa-Cabanilles ◽  
J.M. Meseguer-Dueñas ◽  
J.L. Gómez Ribelles ◽  
J. Molina-Mateo
Keyword(s):  
Polymer Chain ◽  
Segmental Mobility ◽  
Single Polymer Chain ◽  
Bond Fluctuation ◽  
Fluctuation Model

scholarly journals Anharmonicity and Spectra–Structure Correlations in MIR and NIR Spectra of Crystalline Menadione (Vitamin K3)

Molecules ◽  
2021 ◽  
Vol 26 (22) ◽  
pp. 6779
Author(s):  
Krzysztof B. Beć ◽  
Justyna Grabska ◽  
Christian W. Huck ◽  
Sylwester Mazurek ◽  
Mirosław A. Czarnecki
Keyword(s):  
Single Molecule ◽  
Near Infrared ◽  
Structural Information ◽  
Molecular System ◽  
Theoretical Calculations ◽  
Vitamin K3 ◽  
Structure Correlations ◽  
Mir Spectra ◽  
Combination Bands ◽  
The Relationship

Mid-infrared (MIR) and near-infrared (NIR) spectra of crystalline menadione (vitamin K3) were measured and analyzed with aid of quantum chemical calculations. The calculations were carried out using the harmonic approach for the periodic model of crystal lattice and the anharmonic DVPT2 calculations applied for the single molecule model. The theoretical spectra accurately reconstructed the experimental ones permitting for reliable assignment of the MIR and NIR bands. For the first time, a detailed analysis of the NIR spectrum of a molecular system based on a naphthoquinone moiety was performed to elucidate the relationship between the chemical structure of menadione and the origin of the overtones and combination bands. In addition, the importance of these bands during interpretation of the MIR spectrum was demonstrated. The overtones and combination bands contribute to 46.4% of the total intensity of menadione in the range of 3600–2600 cm−1. Evidently, these bands play a key role in shaping of the C-H stretching region of MIR spectrum. We have shown also that the spectral regions without fundamentals may provide valuable structural information. For example, the theoretical calculations reliably reconstructed numerous overtones and combination bands in the 4000–3600 and 2800–1800 cm−1 ranges. These results, provide a comprehensive origin of the fundamentals, overtones and combination bands in the NIR and MIR spectra of menadione, and the relationship of these spectral features with the molecular structure.

scholarly journals Hierarchical coupling between ATP hydrolysis and Hsp90’s client binding site

2020 ◽  
Author(s):  
Steffen Wolf ◽  
Benedikt Sohmen ◽  
Björn Hellenkamp ◽  
Johann Thurn ◽  
Gerhard Stock ◽  
...  
Keyword(s):  
Binding Site ◽  
Single Molecule ◽  
Information Transfer ◽  
Atp Hydrolysis ◽  
Structural Information ◽  
Substrate Binding ◽  
Signal Propagation ◽  
Nonequilibrium Molecular Dynamics ◽  
Time Resolved ◽  
Substrate Binding Site

I.ABSTRACTSeveral indicators for a signal propagation from a binding site to a distant functional site have been found in the Hsp90 dimer. Here we determined a time-resolved pathway from ATP hydrolysis to changes in a distant folding substrate binding site. This was possible by combining single-molecule fluorescence-based methods with extensive atomistic nonequilibrium molecular dynamics simulations. We find that hydrolysis of one ATP effects a structural asymmetry in the full Hsp90 dimer that leads to the collapse of a central folding substrate binding site. Arg380 is the major mediator in transferring structural information from the nucleotide to the substrate binding site. This allosteric process occurs via hierarchical dynamics that involve timescales from picoto milliseconds and length scales from Ångstroms to several nanometers. We presume that similar hierarchical mechanisms are fundamental for information transfer through many other proteins.

scholarly journals Collapse of a polymer chain in a melt of incompatible polymer chains

1981 ◽  
Vol 42 (8) ◽  
pp. 1145-1150 ◽  
Author(s):  
J.F. Joanny ◽  
F. Brochard
Keyword(s):  
Polymer Chain ◽  
Polymer Chains
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