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On the nature of self-assembly in low-density condensed matter: A classical molecular dynamics approach
Stockholm University, Faculty of Science, Department of Materials and Environmental Chemistry (MMK).ORCID iD: 0000-0003-0237-7250
2015 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The study of the physics of self-assembly in low-density condensed matter is an extremely interesting, mostly unexplored field of scientific research. The contribution reported in this thesis explains how this problem can be addressed using molecular dynamics simulation of 3D systems composed by simple, identical particles, interacting via a spherically symmetric pair potential, which belongs to the class of Dzugutov potentials. Such approach resulted in four, self-assembled archetypal structures, which are reported in the included papers I, II, III, IV. In order to produce the reported results, a major effort of software development has been done by the author, both in the simulation and the analysis programs used. This thesis will start with a brief introduction to the field, highlighting the important aspects needed to have a more complete, general understanding of the reported scientific results. Some conclusions will be drawn, together with some possible future endeavors.

Place, publisher, year, edition, pages
Stockholm: Department of Materials and Environmental Chemistry (MMK), Stockholm University , 2015. , 96 p.
National Category
Condensed Matter Physics Physical Chemistry
Research subject
Physical Chemistry
Identifiers
URN: urn:nbn:se:su:diva-115849ISBN: 978-91-7649-149-2 (print)OAI: oai:DiVA.org:su-115849DiVA: diva2:800395
Public defence
2015-05-12, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Submitted. Paper 4: Submitted. Paper 5: Submitted.

Available from: 2015-04-20 Created: 2015-04-03 Last updated: 2015-04-23Bibliographically approved
List of papers
1. Formation of the smectic-B crystal from a simple monatomic liquid
Open this publication in new window or tab >>Formation of the smectic-B crystal from a simple monatomic liquid
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2013 (English)In: Physical Review E. Statistical, Nonlinear, and Soft Matter Physics, ISSN 1539-3755, E-ISSN 1550-2376, Vol. 88, no 6, 062502Article in journal (Refereed) Published
Abstract [en]

We report a molecular dynamics simulation demonstrating that the smectic-B crystalline phase (Cry-B), commonly observed in mesogenic systems of anisotropic molecules, can be formed by a system of identical particles interacting via a spherically symmetric potential. The Cry-B phase forms as a result of a first-order transition from an isotropic liquid phase upon isochoric cooling at appropriate number density. Its structure, determined by the design of the pair potential, corresponds to the Cry-B structure formed by elongated particles with the aspect ratio 1.8. The diffraction pattern and the real-space structure inspection demonstrate dominance of the ABC-type of axial layer stacking. This result opens a general possibility of producing smectic phases using isotropic interparticle interaction both in simulations and in colloidal systems.

National Category
Physical Sciences
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-99892 (URN)10.1103/PhysRevE.88.062502 (DOI)000328605400003 ()
Funder
Swedish Research Council
Note

AuthorCount:5;

Available from: 2014-01-23 Created: 2014-01-20 Last updated: 2017-12-06Bibliographically approved
2. Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid
Open this publication in new window or tab >>Formation of a new archetypal Metal-Organic Framework from a simple monatomic liquid
2014 (English)In: Journal of Chemical Physics, ISSN 0021-9606, E-ISSN 1089-7690, Vol. 141, no 23, 234503Article in journal (Refereed) Published
Abstract [en]

We report a molecular-dynamics simulation of a single-component system of particles interacting via a spherically symmetric potential that is found to form, upon cooling from a liquid state, a low-density porous crystalline phase. Its structure analysis demonstrates that the crystal can be described by a net with a topology that belongs to the class of topologies characteristic of the Metal-Organic Frameworks (MOFs). The observed net is new, and it is now included in the Reticular Chemistry Structure Resource database. The observation that a net topology characteristic of MOF crystals, which are known to be formed by a coordination-driven self-assembly process, can be reproduced by a thermodynamically stable configuration of a simple single-component system of particles opens a possibility of using these models in studies of MOF nets. It also indicates that structures with MOF topology, as well as other low-density porous crystalline structures can possibly be produced in colloidal systems of spherical particles, with an appropriate tuning of interparticle interaction.

National Category
Chemical Sciences
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-113567 (URN)10.1063/1.4903925 (DOI)000346662700033 ()
Note

AuthorCount:4;

Available from: 2015-02-05 Created: 2015-02-04 Last updated: 2017-12-05Bibliographically approved
3. Formation of a Columnar Liquid Crystal in a Simple One-Component System of Particles
Open this publication in new window or tab >>Formation of a Columnar Liquid Crystal in a Simple One-Component System of Particles
2015 (English)In: Soft Matter, ISSN 1744-683X, E-ISSN 1744-6848, Vol. 11, no 23, 4606-4613 p.Article in journal (Refereed) Published
Abstract [en]

We report a molecular dynamics simulation demonstrating that a columnar liquid crystal, commonly formed by disc-shaped molecules, can be formed by identical particles interacting via a spherically symmetric potential. Upon isochoric cooling from a low-density isotropic liquid state the simulated system performed a weak first order phase transition which produced a liquid crystal phase composed of parallel particle columns arranged in a hexagonal pattern in the plane perpendicular to the column axis. The particles within columns formed a liquid structure and demonstrated a significant intracolumn diffusion. Further cooling resulted in another first-order transition whereby the column structure became periodically ordered in three dimensions transforming the liquid-crystal phase into a crystal. This result is the first observation of a liquid crystal formation in a simple one-component system of particles. Its conceptual significance is in that it demonstrated that liquid crystals that have so far only been produced in systems of anisometric molecules, can also be formed by mesoscopic soft-matter and colloidal systems of spherical particles with appropriately tuned interatomic potential.

Keyword
columnar phase, liquid crystal, soft matter, molecular dynamics
National Category
Condensed Matter Physics
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-115847 (URN)10.1039/c5sm00570a (DOI)000355735900007 ()
Available from: 2015-04-03 Created: 2015-04-03 Last updated: 2017-12-04Bibliographically approved
4. A new kind of soft-matter quasicrystal
Open this publication in new window or tab >>A new kind of soft-matter quasicrystal
(English)In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723Article in journal (Refereed) Submitted
Abstract [en]

Quasiperiodic order in mesoscopic soft-matter systems is now a new research frontier of rapidly growing interest \cite{DUB}. Here, we report a novel kind of soft-matter quasicrystal that has so far never been observed, nor theoretically predicted. It represents a structure composed of hexagonally densely packed particle layers axially stacked in a $ABA...$ order, resembling smectic-$B$ crystal \cite{CHANDR}. In contrast to the latter, $A$ and $B$ layers in this structure are rotated by $30^{\circ}$ with respect to each other, in the layer plane, which induces 12-fold global rotational symmetry. So far, the only kind of quasiperiodic order observed in smectic phases \cite{CHANDR} has been twist grain boundaries (TGB) structure induced by commensurate helical rotation of the smectic slabs around the axis parallel to the layer plane \cite{LUB, GOOD}. The quasicrystal we report was produced in a molecular-dynamics simulation of a single-component system of particles interacting via a spherically-symmetric potential, as a result of a first-order phase transition from a liquid phase under constant-density cooling. This finding implies that a similarly structured quasicrystal can possibly be produced by the mesogens of the kind that produce smectic-B crystals. The simple isotropic form of the pair potential used in this simulation makes it possible to expect that this type of quasicrystal can also be produced in a system of spherically-shaped colloidal particles with appropriately tuned force field.

Keyword
smectic-b, quasicrystal, soft matter, condensed matter, molecular dynamics
National Category
Condensed Matter Physics
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-115848 (URN)
Available from: 2015-04-03 Created: 2015-04-03 Last updated: 2017-12-04
5. A new computer program for topological, visual analysis of 3D particle configurations based on visual representation of radial distribution function peaks as bonds
Open this publication in new window or tab >>A new computer program for topological, visual analysis of 3D particle configurations based on visual representation of radial distribution function peaks as bonds
(English)In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944Article in journal (Refereed) Submitted
Abstract [en]

We present a new program able to perform unique visual analysis on generic particle systems: PASYVAT (PArticle SYstem Visual Analysis Tool). More specifically, it can perform a selection of multiple interparticle distance ranges from a radial distribution function (RDF) plot and display them in 3D as bonds. This software can be used with any data set representing a system of particles in 3D. In this manuscript the reader will find a description of the program and its internal structure, with emphasis on its applicability in the study of certain particle configurations, obtained from classical molecular dynamics simulation in condensed matter physics.

Keyword
radial distribution function, molecular dynamics, visual analysis, bonding, topology
National Category
Condensed Matter Physics Software Engineering
Research subject
Physical Chemistry
Identifiers
urn:nbn:se:su:diva-115845 (URN)
Available from: 2015-04-03 Created: 2015-04-03 Last updated: 2017-12-04

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