scholarly journals Self-assembly in mixtures with competing interactions

Soft Matter ◽  
2021 ◽  
Author(s):  
Oksana Patsahan ◽  
Marek Litniewski ◽  
Alina Ciach

Coexistence lines between gas and ordered phases in binary microsegregating mixtures are studied theoretically and by MD simulations.

2015 ◽  
Vol 51 (21) ◽  
pp. 4402-4405 ◽  
Author(s):  
Åge A. Skjevik ◽  
Benjamin D. Madej ◽  
Callum J. Dickson ◽  
Knut Teigen ◽  
Ross C. Walker ◽  
...  

In this work we report the first example of spontaneous lipid bilayer formation in unbiased all-atom molecular dynamics (MD) simulations.


2015 ◽  
Vol 17 (7) ◽  
pp. 5413-5420 ◽  
Author(s):  
Susan James ◽  
Michelle K. Quinn ◽  
Jennifer J. McManus

Anisotropy is central to protein self-assembly. The kinetic and thermodynamic properties of proteins in which competing interactions exist due to the anisotropic or patchy nature of the protein surface have been explored using a phase diagram approach.


Structure ◽  
2008 ◽  
Vol 16 (4) ◽  
pp. 621-630 ◽  
Author(s):  
Kathryn A. Scott ◽  
Peter J. Bond ◽  
Anthony Ivetac ◽  
Alan P. Chetwynd ◽  
Syma Khalid ◽  
...  

Author(s):  
I. Novak ◽  
L. Truskinovsky

The complexity of fracture-induced segmentation in elastically constrained cohesive (fragile) systems originates from the presence of competing interactions. The role of discreteness in such phenomena is of interest in a variety of fields, from hierarchical self-assembly to developmental morphogenesis. In this paper, we study the analytically solvable example of segmentation in a breakable mass–spring chain elastically linked to a deformable lattice structure. We explicitly construct the complete set of local minima of the energy in this prototypical problem and identify among them the states corresponding to the global energy minima. We show that, even in the continuum limit, the dependence of the segmentation topology on the stretching/pre-stress parameter in this problem takes the form of a devil's type staircase. The peculiar nature of this staircase, characterized by locking in rational microstructures, is of particular importance for biological applications, where its structure may serve as an explanation of the robustness of stress-driven segmentation. This article is part of the themed issue ‘Patterning through instabilities in complex media: theory and applications.’


2016 ◽  
Vol 18 (15) ◽  
pp. 10573-10584 ◽  
Author(s):  
Åge A. Skjevik ◽  
Benjamin D. Madej ◽  
Callum J. Dickson ◽  
Charles Lin ◽  
Knut Teigen ◽  
...  

Spontaneous bilayer self-assembly of zwitterionic and anionic phospholipids probed by unbiased all-atom molecular dynamics (MD) simulations with three major lipid force fields.


2013 ◽  
Vol 117 (38) ◽  
pp. 19426-19435 ◽  
Author(s):  
Chris R. L. Chapman ◽  
Elvis C.M. Ting ◽  
Ashley Kereszti ◽  
Irina Paci

Soft Matter ◽  
2017 ◽  
Vol 13 (44) ◽  
pp. 8055-8063 ◽  
Author(s):  
Andrew P. Santos ◽  
Jakub Pȩkalski ◽  
Athanassios Z. Panagiotopoulos

Colloidal clustering driven by isotropic competing interactions can resemble surfactant micellization or exhibit novel, non-pressure-affecting clustering, depending on conditions.


2006 ◽  
Vol 947 ◽  
Author(s):  
Kai de lang Kristiansen ◽  
Eldrid Svåsand ◽  
Geir Helgesen ◽  
Arne T. Skjeltorp

ABSTRACTNonmagnetic microspheres dispersed in a ferrofluid are denoted magnetic holes. When the spheres are confined to a monolayer between two plane, parallel plates and subjected to AC magnetic fields, they show a variety of dynamical behaviors and assemblages. The magnetic interactions between the particles and their dynamical behavior are influenced by the boundaries and the degree of confinement. We have derived analytical results for the pair-wise competing interactions, and these compare favorably with experimental results.It is also possible to characterize the self-assembly and dynamics of the spheres by the theory of braids. It involves classifying different ways of tracing curves in space. The essentially two-dimensional motion of a sphere can be represented as a curve in a three-dimensional space-time diagram, and so several spheres in motion produce a set of braided curves. The dynamical modes can then be described in terms of braid-words. We also present a few other examples on how this system can be used to study dynamical processes.


2021 ◽  
Vol 11 (5) ◽  
pp. 2357
Author(s):  
Ruixin Li ◽  
Haorong Chen ◽  
Hyeongwoon Lee ◽  
Jong Hyun Choi

DNA origami has emerged as a versatile method to synthesize nanostructures with high precision. This bottom-up self-assembly approach can produce not only complex static architectures, but also dynamic reconfigurable structures with tunable properties. While DNA origami has been explored increasingly for diverse applications, such as biomedical and biophysical tools, related mechanics are also under active investigation. Here we studied the structural properties of DNA origami and investigated the energy needed to deform the DNA structures. We used a single-layer rectangular DNA origami tile as a model system and studied its cyclization process. This origami tile was designed with an inherent twist by placing crossovers every 16 base-pairs (bp), corresponding to a helical pitch of 10.67 bp/turn, which is slightly different from that of native B-form DNA (~10.5 bp/turn). We used molecular dynamics (MD) simulations based on a coarse-grained model on an open-source computational platform, oxDNA. We calculated the energies needed to overcome the initial curvature and induce mechanical deformation by applying linear spring forces. We found that the initial curvature may be overcome gradually during cyclization and a total of ~33.1 kcal/mol is required to complete the deformation. These results provide insights into the DNA origami mechanics and should be useful for diverse applications such as adaptive reconfiguration and energy absorption.


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