scholarly journals Conformation of Flexible and Semiflexible Chains Confined in Nanoposts Array of Various Geometries

Polymers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1064 ◽  
Author(s):  
Zuzana Benková ◽  
Lucia Rišpanová ◽  
Peter Cifra
Keyword(s):  
Structure Factor ◽  
Volume Fraction ◽  
Occupation Number ◽  
Chain Extension ◽  
Coarse Grained ◽  
Square Lattice ◽  
Structural Behavior ◽  
Single Chain ◽  
Flexible Chain ◽  
Two Factors

The conformation and distribution of a flexible and semiflexible chain confined in an array of nanoposts arranged in parallel way in a square-lattice projection of their cross-section was investigated using coarse-grained molecular dynamics simulations. The geometry of the nanopost array was varied at the constant post diameter dp and the ensuing modifications of the chain conformation were compared with the structural behavior of the chain in the series of nanopost arrays with the constant post separation Sp as well as with the constant distance between two adjacent post walls (passage width) wp. The free energy arguments based on an approximation of the array of nanopost to a composite of quasi-channels of diameter dc and quasi-slits of height wp provide semiqualitative explanations for the observed structural behavior of both chains. At constant post separation and passage width, the occupation number displays a monotonic decrease with the increasing geometry ratio dc/wp or volume fraction of posts, while a maximum is observed at constant post diameter. The latter finding is attributed to a relaxed conformation of the chains at small dc/wp ratio, which results from a combination of wide interstitial volumes and wide passage apertures. This maximum is approximately positioned at the same dc/wp value for both flexible and semiflexible chains. The chain expansion from a single interstitial volume into more interstitial volumes also starts at the same value of dc/wp ratio for both chains. The dependence of the axial chain extension on the dc/wp ratio turns out to be controlled by the diameter of the interstitial space and by the number of monomers in the individual interstitial volumes. If these two factors act in the same way on the axial extension of chain fragments in interstitial volumes the monotonic increase of the axial chain extension with the dc/wp in the nanopost arrays is observed. At constant wp, however, these two factors act in opposite way and the axial chain extension plotted against the dc/wp ratio exhibits a maximum. In the case of constant post diameter, the characteristic hump in the single chain structure factor whose position correlates with the post separation is found only in the structure factor of the flexible chain confined in the nanopost array of certain value of Sp. The structure factor of the flexible chain contains more information on the monomer organization and mutual correlations than the structure factor of the semiflexible chain. The stiffer chain confined in the nanopost array is composed of low number of statistical segments important for the presence of respective hierarchical regimes in the structure factor.

Multiscale modeling of polymers closely coupled to Broad Q neutron scattering from NIMROD

2013 ◽  
Vol 1524 ◽  
Author(s):  
Thomas Gkourmpis ◽  
Daniel Lopez ◽  
Geoffrey R. Mitchell
Keyword(s):  
Structure Factor ◽  
Chain Structure ◽  
Distribution Functions ◽  
Chain Conformation ◽  
Coarse Grained ◽  
Lamellar Thickness ◽  
Single Chain ◽  
Crystal Unit Cell ◽  
Key Length ◽  
Using Data

ABSTRACTWe use data over an extended Q range from 0.01 to 100Å-1 from the recently commissioned NIMROD instrument at the ISIS pulsed neutron source to develop a multi-scale inverse modeling procedure which will provide insight in to the phase transformations of polymer systems. The first level of our procedure is atomistic and we use internal coordinates (bond length, bond angles and torsion angles) to define the polymer chain in full atomistic detail. Values were assigned to each internal coordinate within the chain using a stochastic Monte Carlo method in which the probabilities were drawn from distributions representing the possible range of values. Using this approach, random chain configurations could be rapidly built and the intrachain structure factor calculated utilizing a small set of parameters and compared with the experimental function. Parameters representing the probability distribution functions were systematically varied using a grid search to find the values which gave the best fit to the structure factor for Q > 3Å-1 in order to determine the details of the chain conformation in the molten phase. This process was repeated for data over the same extended Q range obtained at lower temperatures where the polymer was expected to crystallize. Polymers crystallize via chainfolded thin lamellae crystals. Such crystals give rise to an intense peak at Q ∼ 0.03Å-1. This scattering can be calculated using a lamellar stack model, coarse-grained from the single chain structure. We describe this approach using data obtained on the crystallization from the melt phase of perdeuterated polymers. The objective here is to follow the three key length scales; the chain folded lamellar thickness of ∼ 10nm, the crystal unit cell ∼ 1nm and the detail of the chain conformation is ∼ 0.1nm.

scholarly journals Block Copolymer of Flexible and Semi-Flexible Block Confined in Nanopost Array

Polymers ◽  
2018 ◽  
Vol 10 (12) ◽  
pp. 1301 ◽  
Author(s):  
Lucia Rišpanová ◽  
Zuzana Benková ◽  
Peter Cifra
Keyword(s):  
Diblock Copolymer ◽  
Size Structure ◽  
Constant Width ◽  
Chain Extension ◽  
Coarse Grained ◽  
Square Lattice ◽  
Filling Fraction ◽  
Competitive Effects ◽  
Interstitial Volume ◽  
Dynamics Simulations

Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated through a comparison of their size, structure, and penetration among nanoposts with the corresponding separate chains. The geometry of a nanopost array was varied at constant post separation or at constant width of the passage between nanoposts. The size of a single interstitial volume was comparable to or smaller than the size of the diblock chain. A comparison of the blocks with their separate analogous chains revealed that the mutual interactions between the blocks were shielded by the nanoposts and, thus, the blocks behaved independently. At constant passage width, competitive effects of the axial chain extension in interstitial volumes and the lateral chain expansion among interstitial volumes led to a nonmonotonic behavior of the axial span. The position of the maximum in the span plotted against the filling fraction for a diblock chain was dictated by the semi-flexible block. The semi-flexible block penetrates among the nanoposts more readily and the expansion of the whole diblock copolymer is governed by the semiflexible block. The main findings were explained using the free energy arguments when an interstitial volume was approximated by a channel geometry and a passage aperture by a slit geometry. Detail knowledge of controlled conformational behavior in a compartmentalized environment can contribute to new processes in the storage and retrieval of information.

scholarly journals Single Chain Dynamic Structure Factor of Linear Polymers in an All-Polymer Nano-Composite

2016 ◽  
Vol 49 (6) ◽  
pp. 2354-2364 ◽  
Author(s):  
Arantxa Arbe ◽  
José A. Pomposo ◽  
Isabel Asenjo-Sanz ◽  
Debsindhu Bhowmik ◽  
Oxana Ivanova ◽  
...  
Keyword(s):  
Structure Factor ◽  
Dynamic Structure ◽  
Dynamic Structure Factor ◽  
Linear Polymers ◽  
Single Chain ◽  
Nano Composite ◽  
Chain Dynamic

scholarly journals A scaled MP-PIC method for bubbling fluidization

2021 ◽  
Author(s):  
Xing Zhao ◽  
Yong Jiang ◽  
Fei Li ◽  
Wei Wang
Keyword(s):  
Fluidized Beds ◽  
Volume Fraction ◽  
Phase Particle ◽  
Scaling Law ◽  
Coarse Graining ◽  
Coarse Grained ◽  
Particle In Cell ◽  
Wide Range ◽  
Pic Method ◽  
Multi Phase

Coarse-grained methods have been widely used in simulations of gas-solid fluidization. However, as a key parameter, the coarse-graining ratio, and its relevant scaling law is still far from reaching a consensus. In this work, a scaling law is developed based on a similarity analysis, and then it is used to scale the multi-phase particle-in-cell (MP-PIC) method, and validated in the simulation of two bubbling fluidized beds. The simulation result shows this scaled MP-PIC can reduce the errors of solids volume fraction and velocity distributions over a wide range of coarse-graining ratios. In future, we expect that a scaling law with consideration of the heterogeneity inside a parcel or numerical particle will further improve the performance of coarse-grained modeling in simulation of fluidized beds.

scholarly journals The Dilatometric Analysis of the High Carbon Alloys from Ni-Ta-Al-M System

2014 ◽  
Vol 59 (3) ◽  
pp. 977-980 ◽  
Author(s):  
P. Bała
Keyword(s):  
Elevated Temperatures ◽  
Volume Fraction ◽  
Intermetallic Phase ◽  
Coarse Grained ◽  
Precipitation Process ◽  
Cast State ◽  
High Carbon ◽  
Chromium Carbides ◽  
Tantalum Carbides ◽  
Co Alloys

Abstract In the following work presents results of high carbon alloys from the Ni-Ta-Al-M system are presented. The alloys have been designed to have a good tribological properties at elevated temperatures. Despite availability of numerous hot work tool materials there is still a growing need for new alloys showing unique properties, which could be used under heavy duty conditions, i.e. at high temperatures, in a chemically aggressive environment and under heavy wear conditions. A characteristic, coarse-grained dendritic microstructure occurs in the investigated alloys in the as-cast condition. Primary dendrites with secondary branches can be observed. Tantalum carbides of MC type and graphite precipitations are distributed in interdendritic spaces in the Ni-Ta-Al-C and Ni-Ta-Al-C-Co alloys, while Tantalum carbides of MC type and Chromium carbides of M7C3 type appeared in the Ni-Ta-Al-C-Co-Cr and Ni-Ta-Al-C-Cr alloys. In all alloys g’ phase is present, however, its volume fraction in the Ni-Ta-Al-C and Ni-Ta-Al-C-Co alloys is small.During heating from as-cast state in Ni-Ta-Al-C and Ni-Ta-Al-C-Co alloys, the beginning of the tantalum carbides precipitation process (MC type) followed (or simultaneous) by the intermetallic phase precipitation (g’ – Ni3(AlTa)) was stated, while in Ni-Ta-Al-C-Co-Cr and Ni-Ta-Al-C-Cr alloys, besides Tantalum carbides also the Chromium carbides precipitation occurred. It means that the investigated alloys were partially supersaturated in as-cast state. Above 1050°C in all investigated alloys the g’ phase is dissolving. In addition, the precipitation of secondary carbides during slow cooling was occured.

UNRES-Dock—protein–protein and peptide–protein docking by coarse-grained replica-exchange MD simulations

2020 ◽  
Author(s):  
Paweł Krupa ◽  
Agnieszka S Karczyńska ◽  
Magdalena A Mozolewska ◽  
Adam Liwo ◽  
Cezary Czaplewski
Keyword(s):  
Protein Complexes ◽  
Md Simulations ◽  
Protein Docking ◽  
Conformational Space ◽  
Coarse Grained ◽  
Supplementary Information ◽  
Replica Exchange ◽  
Variable Degree ◽  
Single Chain ◽  
Simulation Speed

Abstract Motivation The majority of the proteins in living organisms occur as homo- or hetero-multimeric structures. Although there are many tools to predict the structures of single-chain proteins or protein complexes with small ligands, peptide–protein and protein–protein docking is more challenging. In this work, we utilized multiplexed replica-exchange molecular dynamics (MREMD) simulations with the physics-based heavily coarse-grained UNRES model, which provides more than a 1000-fold simulation speed-up compared with all-atom approaches to predict structures of protein complexes. Results We present a new protein–protein and peptide–protein docking functionality of the UNRES package, which includes a variable degree of conformational flexibility. UNRES-Dock protocol was tested on a set of 55 complexes with size from 43 to 587 amino-acid residues, showing that structures of the complexes can be predicted with good quality, if the sampling of the conformational space is sufficient, especially for flexible peptide–protein systems. The developed automatized protocol has been implemented in the standalone UNRES package and in the UNRES server. Availability and implementation UNRES server: http://unres-server.chem.ug.edu.pl; UNRES package and data used in testing of UNRES-Dock: http://unres.pl. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Modelling and Experimental Validation of the Porosity Effect on the Behaviour of Nano-Crystalline Materials

Metals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 821
Author(s):  
Panagiotis Bazios ◽  
Konstantinos Tserpes ◽  
Spiros Pantelakis
Keyword(s):  
Numerical Model ◽  
Volume Fraction ◽  
Coarse Grained ◽  
Compression Tests ◽  
X Ray Diffraction ◽  
Static Compression ◽  
Crystalline Materials ◽  
Nano Crystalline ◽  
Porosity Effect ◽  
Grain Diameter

Nano-crystalline metals have attracted considerable attention over the past two decades due to their increased mechanical properties as compared to their microcrystalline counterparts. However, the behaviour of nano-crystalline metals is influenced by imperfections introduced during synthesis or heat treatment. These imperfections include pores, which are mostly located in the area of grain boundaries. To study the behaviour of multiphase nano-crystalline materials, a novel fully parametric algorithm was developed. The data required for implementing the developed numerical model were the volume fraction of the alloying elements and their basic properties as well as the density and the size of randomly distributed pores. To validate the developed algorithm, the alloy composition 75 wt% tungsten and 25 wt% copper was examined experimentally under compression tests. For the investigation, two batches of specimens were used; a batch having a coarse-grained microstructure with an average grain diameter of 150 nm and a nanocrystalline batch having a grain diameter of 100 nm, respectively. The porosity of both batches was derived to range between 9% and 10% based on X-ray diffraction analyses. The results of quasi-static compression testing revealed that the nanocrystalline W-Cu material exhibited brittle behaviour which was characterised by an elastic deformation that led to fracture without remarkable plasticity. A compressive strength of about 1100 MPa was derived which was more than double compared to conventional W-Cu samples. Finite element simulations of the behaviour of porous nano-crystalline materials were performed and compared with the respective experimental compression tests. The numerical model and experimental observations were in good agreement.

Mesoscale Simulation of the Structure of Star Acrylated Poly(ethylene glycol-co-lactide) Hydrogels

2012 ◽  
Vol 1418 ◽  
Author(s):  
Seyed Sina Moeinzadeh ◽  
Esmaiel Jabbari
Keyword(s):  
Ethylene Glycol ◽  
Volume Fraction ◽  
Equations Of Motion ◽  
Dissipative Particle Dynamics ◽  
Random Force ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Poly Ethylene Glycol ◽  
The Core ◽  
Poly Ethylene

ABSTRACTIn this work the microstructures of star acrylated poly(ethylene glycol-co-lactide) (SPELA) with different LA:EG ratios in the aqueous solution have been simulated via Dissipative Particle Dynamics (DPD) approach at the mesoscale. The system components were coarse-grained into different beads (set of atoms) which moved according to the Newton’s equations of motion integrated via a modified Velocity-Verlet algorithm. The force acting on each bead, in a specific cutoff distance (rc), was divided into a conservative force (FC), random force (FR), dissipative force (FD), bond force (FS) and bond angle force (FE). The repulsion parameters of the conservative force (αij) were calculated from the solubility parameter of the beads, each of which were extracted from an atomistic molecular dynamics simulation (MD). Simulations showed the formation of micelles with lactide and acrylate beads occupied the core and hydrophilic ethylene oxide segments extending through the water to form the corona. The micelles showed an increasing trend in size and decreasing trend in number density with increase in LA:EG ratio. Results showed that the acrylate density decreased from the center of the micelles to the core surface although the overall amount of acrylates increased due to the increase in volume. Furthermore, the running integration number of acrylate-water beads showed decreasing accessibility of acrylates to water with increasing PLA volume fraction.

Investigating the Relationship between Network Mechanics and Single-Chain Extension Using Biomimetic Polysaccharide Gels

2012 ◽  
Vol 45 (11) ◽  
pp. 4863-4869 ◽  
Author(s):  
Erich Schuster ◽  
Leif Lundin ◽  
Martin A. K. Williams
Keyword(s):  
Chain Extension ◽  
Single Chain ◽  
The Relationship

scholarly journals Cyclic deformation behaviour and stability of grain-refined 301LN austenitic stainless structure

2018 ◽  
Vol 165 ◽  
pp. 06005 ◽  
Author(s):  
Jiří Man ◽  
Antti Järvenpää ◽  
Matias Jaskari ◽  
Ivo Kuběna ◽  
Stanislava Fintová ◽  
...  
Keyword(s):  
Strain Rate ◽  
Volume Fraction ◽  
Early Stage ◽  
Low Cycle Fatigue ◽  
Deformation Behaviour ◽  
Polarized Light ◽  
Constant Strain Rate ◽  
Coarse Grained ◽  
Grain Sizes ◽  
Cyclic Straining

Low cycle fatigue (LCF) behaviour of metastable austenitic 301LN stainless steel with different grain sizes – coarse-grained (13 μm), fine-grained (1.4 μm) and ultrafine-grained (0.6 μm) – produced by reversion annealing after prior cold rolling was investigated. Fully symmetrical LCF tests with constant total strain amplitudes of 0.5% and 0.6% were performed at room temperature with a low constant strain rate of 2×10-3 s-1. Microstructural changes in different positions within the gauge part of the specimens were examined by optical microscopy (polarized light) and electron backscatter diffraction (EBSD) technique; for quantitative assessment of the volume fraction of deformation induced martensite (DIM) a Feritscope FMP 30 was adopted. The cyclic stress-strain response and specific changes of hysteresis loop shapes in the very early stage of cycling are confronted with the character of DIM formation and its distribution in the whole volume of the material. A possible effect of strain rate (frequency of cycling) on the destabilization of austenitic structure during cyclic straining of materials with different grain sizes is highlighted.

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