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 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.

Self-assembly and structural manipulation of diblock-copolymer grafted nanoparticles in a homopolymer matrix

2019 ◽  
Vol 21 (22) ◽  
pp. 11785-11796 ◽  
Author(s):  
Sai Li ◽  
Zhiyu Zhang ◽  
Guanyi Hou ◽  
Jun Liu ◽  
Yangyang Gao ◽  
...  
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Diblock Copolymer ◽  
Self Assembly ◽  
Coarse Grained ◽  
Grafted Nanoparticles ◽  
Structural Manipulation ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

Detailed coarse-grained molecular dynamics simulations are performed to investigate the structural and mechanical properties of nanoparticles (NPs) grafted with an amphiphilic AB diblock copolymer, with the A-block being compatible with NPs and the B-block being miscible with a homopolymer matrix.

Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

2020 ◽  
Author(s):  
Julian Keupp ◽  
Johannes P. Dürholt ◽  
Rochus Schmid
Keyword(s):  
First Principles ◽  
Good Accuracy ◽  
Field Investigation ◽  
Square Lattice ◽  
Side Chain ◽  
Second Step ◽  
Side Chains ◽  
Dynamics Simulations ◽  
Complex Phenomena ◽  
Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle-<br>wheel units and connected by dinitrogen pillars, can undergo a breathing phase<br>transition by a “wine-rack” type motion of the square lattice. We studied this not<br>yet fully understood behavior using an accurate first principles parameterized force<br>field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:<br>benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-<br>cations for an interface between a closed and an open pore phase traveling through<br>the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In<br>conventional simulations in small supercells this mechanism is prevented by periodic<br>boundary conditions (PBC), enforcing a synchronous transformation of the entire<br>crystal. Here, we extend this investigation to pillared layer MOFs with flexible<br>side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-<br>tally known to have different properties with the side-chains acting as fixed guest<br>molecules. First, in order to extend the parameterization for such flexible groups,<br>1a new parametrization strategy for MOF-FF had to be developed, using a multi-<br>structure force based fit method. The resulting parametrization for a library of<br>fu-MOFs is then validated with respect to a set of reference systems and shows very<br>good accuracy. In the second step, a series of fu-MOFs with increasing side-chain<br>length is studied with respect to the influence of the side-chains on the breathing<br>behavior. For small supercells in PBC a systematic trend of the closed pore volume<br>with the chain length is observed. However, for a nanocrystallite model a distinct<br>interface between a closed and an open pore phase is visible only for the short chain<br>length, whereas for longer chains the interface broadens and a nearly concerted trans-<br>formation is observed. Only by molecular dynamics simulations using accurate force<br>fields such complex phenomena can be studied on a molecular level.

Parameterization of Divalent Cations for Coarse-Grained Simulations

2020 ◽  
Author(s):  
Florencia Klein ◽  
Daniela Cáceres-Rojas ◽  
Monica Carrasco ◽  
Juan Carlos Tapia ◽  
Julio Caballero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Metal Ions ◽  
Molecular Dynamics Simulations ◽  
Divalent Cations ◽  
Computational Cost ◽  
Data Bank ◽  
Coarse Grained ◽  
Interaction Parameters ◽  
Dynamics Simulations ◽  
Dynamical Description

<p>Although molecular dynamics simulations allow for the study of interactions among virtually all biomolecular entities, metal ions still pose significant challenges to achieve an accurate structural and dynamical description of many biological assemblies. This is particularly the case for coarse-grained (CG) models. Although the reduced computational cost of CG methods often makes them the technique of choice for the study of large biomolecular systems, the parameterization of metal ions is still very crude or simply not available for the vast majority of CG- force fields. Here, we show that incorporating statistical data retrieved from the Protein Data Bank (PDB) to set specific Lennard-Jones interactions can produce structurally accurate CG molecular dynamics simulations. Using this simple approach, we provide a set of interaction parameters for Calcium, Magnesium, and Zinc ions, which cover more than 80% of the metal-bound structures reported on the PDB. Simulations performed using the SIRAH force field on several proteins and DNA systems show that using the present approach it is possible to obtain non-bonded interaction parameters that obviate the use of topological constraints. </p>

scholarly journals Variation of Interaction Zone Size For The Target Design of 2D Supramolecular Networks

2021 ◽  
Author(s):  
Łukasz Piotr Baran ◽  
Wojciech Rżysko ◽  
Dariusz Tarasewicz
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Coarse Grained ◽  
Zone Size ◽  
Interaction Zone ◽  
Supramolecular Networks ◽  
Dynamics Simulations ◽  
Target Design

In this study we have performed extensive coarse-grained molecular dynamics simulations of the self-assembly of tetra-substituted molecules. We have found that such molecules are able to form a variety of...

Molecular Dynamics Simulations of Shock-Defect Interactions in Two-Dimensional Nonreactive Crystals

1992 ◽  
Vol 296 ◽  
Author(s):  
Robert S. Sinkovits ◽  
Lee Phillips ◽  
Elaine S. Oran ◽  
Jay P. Boris
Keyword(s):  
Molecular Dynamics ◽  
Hexagonal Lattice ◽  
Square Lattice ◽  
Two Dimensional ◽  
Connection Machine ◽  
Defect Sites ◽  
Principal Axes ◽  
Shock Motion ◽  
Defect Interactions ◽  
Dynamics Simulations

AbstractThe interactions of shocks with defects in two-dimensional square and hexagonal lattices of particles interacting through Lennard-Jones potentials are studied using molecular dynamics. In perfect lattices at zero temperature, shocks directed along one of the principal axes propagate through the crystal causing no permanent disruption. Vacancies, interstitials, and to a lesser degree, massive defects are all effective at converting directed shock motion into thermalized two-dimensional motion. Measures of lattice disruption quantitatively describe the effects of the different defects. The square lattice is unstable at nonzero temperatures, as shown by its tendency upon impact to reorganize into the lower-energy hexagonal state. This transition also occurs in the disordered region associated with the shock-defect interaction. The hexagonal lattice can be made arbitrarily stable even for shock-vacancy interactions through appropriate choice of potential parameters. In reactive crystals, these defect sites may be responsible for the onset of detonation. All calculations are performed using a program optimized for the massively parallel Connection Machine.

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