1
|
Adhikari S, Minevich B, Redeker D, Michelson AN, Emamy H, Shen E, Gang O, Kumar SK. Controlling the Self-Assembly of DNA Origami Octahedra via Manipulation of Inter-Vertex Interactions. J Am Chem Soc 2023; 145:19578-19587. [PMID: 37651692 DOI: 10.1021/jacs.3c03181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Recent studies have demonstrated novel strategies for the organization of nanomaterials into three-dimensional (3D) ordered arrays with prescribed lattice symmetries using DNA-based self-assembly strategies. In one approach, the nanomaterial is sequestered into DNA origami frames or "material voxels" and then coordinated into ordered arrays based on the voxel geometry and the corresponding directional interactions based on its valency. While the lattice symmetry is defined by the valency of the bonds, a larger-scale morphological development is affected by assembly processes and differences in energies of anisotropic bonds. To facilely model this assembly process, we investigate the self-assembly behavior of hard particles with six interacting vertices via theory and Monte Carlo simulations and exploration of corresponding experimental systems. We demonstrate that assemblies with different 3D crystalline morphologies but the same lattice symmetry can be formed depending on the relative strength of vertex-to-vertex interactions in orthogonal directions. We observed three distinct assembly morphologies for such systems: cube-like, sheet-like, and cylinder-like. A simple analytical theory inspired by well-established ideas in the areas of protein crystallization, based on calculating the second virial coefficient of patchy hard spheres, captures the simulation results and thus represents a straightforward means of modeling this self-assembly process. To complement the theory and simulations, experimental studies were performed to investigate the assembly of octahedral DNA origami frames with varying binding energies at their vertices. X-ray scattering confirms the robustness of the formed nanoscale lattices for different binding energies, while both optical and electron microscopy imaging validated the theoretical predictions on the dependence of the distinct morphologies of assembled state on the interaction strengths in the three orthogonal directions.
Collapse
Affiliation(s)
- Sabin Adhikari
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Brian Minevich
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Daniel Redeker
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Aaron Noam Michelson
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Hamed Emamy
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Eric Shen
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| | - Oleg Gang
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York 10027, United States
- Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Sanat K Kumar
- Department of Chemical Engineering, Columbia University, New York, New York 10027, United States
| |
Collapse
|
2
|
Gutiérrez AB, Machorro-Martínez BI, Quintana J, Armas-Pérez JC, Mendoza P, Lucero JME, Chapela GA. HIV-1 immature virion and other networks formation with simple patchy disks. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2129759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2022]
Affiliation(s)
- Anthony B. Gutiérrez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, México, México
| | | | - Jaqueline Quintana
- Instituto de Química, Universidad Nacional Autónoma de México, Coyoacán, Ciudad de México
| | - Julio C. Armas-Pérez
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, León, México
| | - Paola Mendoza
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, México, México
| | | | - Gustavo A. Chapela
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, México, México
| |
Collapse
|
3
|
Russo J, Leoni F, Martelli F, Sciortino F. The physics of empty liquids: from patchy particles to water. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:016601. [PMID: 34905739 DOI: 10.1088/1361-6633/ac42d9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Empty liquids represent a wide class of materials whose constituents arrange in a random network through reversible bonds. Many key insights on the physical properties of empty liquids have originated almost independently from the study of colloidal patchy particles on one side, and a large body of theoretical and experimental research on water on the other side. Patchy particles represent a family of coarse-grained potentials that allows for a precise control of both the geometric and the energetic aspects of bonding, while water has arguably the most complex phase diagram of any pure substance, and a puzzling amorphous phase behavior. It was only recently that the exchange of ideas from both fields has made it possible to solve long-standing problems and shed new light on the behavior of empty liquids. Here we highlight the connections between patchy particles and water, focusing on the modelling principles that make an empty liquid behave like water, including the factors that control the appearance of thermodynamic and dynamic anomalies, the possibility of liquid-liquid phase transitions, and the crystallization of open crystalline structures.
Collapse
Affiliation(s)
- John Russo
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Fabio Leoni
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Fausto Martelli
- IBM Research Europe, Hartree Centre, Daresbury WA4 4AD, United Kingdom
| | - Francesco Sciortino
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| |
Collapse
|
4
|
Howard MP, Sherman ZM, Milliron DJ, Truskett TM. Wertheim’s thermodynamic perturbation theory with double-bond association and its application to colloid–linker mixtures. J Chem Phys 2021; 154:024905. [DOI: 10.1063/5.0033413] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Affiliation(s)
- Michael P. Howard
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Zachary M. Sherman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Delia J. Milliron
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Thomas M. Truskett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
5
|
Malhotra I, Babu SB. Phase diagram of two-patch colloids with competing anisotropic and isotropic interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:355101. [PMID: 32325451 DOI: 10.1088/1361-648x/ab8c8e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Patchy particles are considered to be a good model for protein aggregation. We propose a novel method to generate different structures of glucose isomerase protein such as chains, crystals and bundles by utilising aggregation of two-patch colloidal particles in presence of competing isotropic and anisotropic potential. We calculate the equilibrium phase diagram of two-patch colloidal particles and demonstrates the coexistence of different phases like disordered clusters, chains, crystals and bundles depending on the relative strength of isotropic and anisotropic potential. We also show that the formation of network of bundles is metastable against the formation of thermodynamically favored finite sized bundles along with thermodynamically stable crystals. These bundles appear to be helical in structure similar to that observed in sickle cell hemoglobin. The simulation results show that the method can characterize phase behaviour of glucose isomerase protein, which provides a novel tool to unveil self-assembly mechanism of protein under different conditions.
Collapse
Affiliation(s)
- Isha Malhotra
- Out of Equilibrium Group, Department of physics, Indian Institute of Technology, Delhi-110016, India
| | - Sujin B Babu
- Out of Equilibrium Group, Department of physics, Indian Institute of Technology, Delhi-110016, India
| |
Collapse
|
6
|
Moinuddin M, Biswas P, Tripathy M. The effect of surface roughness on the phase behavior of colloidal particles. J Chem Phys 2020; 152:044902. [PMID: 32007055 DOI: 10.1063/1.5136080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Shape anisotropy of colloidal particles can give rise to complex intermolecular interactions that determine particle packing and phase behavior. The vapor-liquid coexistence curves of attractive rough particles display a shift when compared to attractive smooth spherical particles. We use Integral Equation Theory (IET) to determine the vapor-liquid spinodal phase diagram of smooth and rough colloidal particles interacting through square-well attraction. Additionally, we use Gibbs Ensemble Monte Carlo (GEMC) simulations to locate their vapor-liquid coexistence curves. We model a rough colloidal particle as a spherical core with small beads embedded on its surface. The critical point of smooth spherical particle systems predicted by theory and simulations is in quantitative agreement. An increase in surface roughness due to an increase in either the number of beads or the diameter of the beads has a modest effect on the local structure of the system in the supercritical region. In contrast, increasing surface roughness consistently shifts the vapor-liquid coexistence curves to higher temperatures. The critical temperature is found to be a quadratic function of the number of beads. At a fixed bead size and number of beads, the critical temperature does not vary with the arrangement of beads on the core. Both IET and GEMC simulations predict that unlike critical temperatures, critical packing fractions vary non-monotonically with surface roughness. We find that the feasibility and accuracy of the integral equation theory depend sensitively on the chosen closure combination.
Collapse
Affiliation(s)
- Md Moinuddin
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Prithwish Biswas
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| | - Mukta Tripathy
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai 400076, Maharashtra, India
| |
Collapse
|
7
|
Febra SA, Aasen A, Adjiman CS, Jackson G, Galindo A. Intramolecular bonding in a statistical associating fluid theory of ring aggregates. Mol Phys 2019. [DOI: 10.1080/00268976.2019.1671619] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- S. A. Febra
- Department of Chemical Engineering, Centre for Process Systems Engineering, Institute for Molecular Science and Engineering, Imperial College London, London, UK
| | - A. Aasen
- Department of Energy and Process Engineering, Norwegian University of Science and Technology, Trondheim, Norway
| | - C. S. Adjiman
- Department of Chemical Engineering, Centre for Process Systems Engineering, Institute for Molecular Science and Engineering, Imperial College London, London, UK
| | - G. Jackson
- Department of Chemical Engineering, Centre for Process Systems Engineering, Institute for Molecular Science and Engineering, Imperial College London, London, UK
| | - A. Galindo
- Department of Chemical Engineering, Centre for Process Systems Engineering, Institute for Molecular Science and Engineering, Imperial College London, London, UK
| |
Collapse
|
8
|
Bansal A, Asthagiri D, Chapman WG. A cluster size distribution theory to study the thermodynamics and phase behavior of multi-bonding single site solutes in patchy colloidal mixtures. SOFT MATTER 2018; 14:7469-7482. [PMID: 30182119 DOI: 10.1039/c8sm01487f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We study binary mixtures of multi-bonding single site solute particles in a solvent comprising patchy colloid particles. The particles in the mixture interact by very short-ranged attraction and hard-sphere repulsion. The attractive patch on the solute can bond with multiple solvent particles, whereas the patch on the solvent is restricted to bond only once. From a quasi-chemical analysis of association, in the hard-sphere reference we develop an accurate multi-body correlation information for the distribution of solvent particles over the patch region of the solute. We use this information within Wertheim's multi-density formalism to develop a cluster size distribution theory that is capable of capturing the physics of multi-body association for any geometry of association sites on the solute. We use this general framework to study a mixture containing Janus solutes and one- or two-patch solvent particles over a range of concentration of the solute and association strengths. We find that a mixture of two-patch solvent (with both patches of the same kind) and multi-bonding solutes with different patch geometries can have a vapor-liquid equilibrium, although the pure components themselves cannot phase separate. The liquid state occurs at very low densities, forming a so-called empty liquid. For the relative association strengths studied in this work, we observe that the vapor-liquid coexistence curve broadens as the concentration of the patchy solvent particles in the liquid phase is increased. The pressure-composition phase equilibrium curves show negative azeotropes for these mixtures. We also observe that, for these mixtures, as the size of the patch on the solute particles is decreased, the critical temperature and the critical packing fraction decreases.
Collapse
Affiliation(s)
- Artee Bansal
- Chemical and Biomolecular Engineering, Rice University, Houston, TX, USA.
| | | | | |
Collapse
|
9
|
Marenda M, Orlandini E, Micheletti C. Discovering privileged topologies of molecular knots with self-assembling models. Nat Commun 2018; 9:3051. [PMID: 30076306 PMCID: PMC6076300 DOI: 10.1038/s41467-018-05413-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Accepted: 07/03/2018] [Indexed: 11/09/2022] Open
Abstract
Despite the several available strategies to build complex supramolecular constructs, only a handful of different molecular knots have been synthesised so far. Here, in response to the quest for further designable topologies, we use Monte Carlo sampling and molecular dynamics simulations, informed by general principles of supramolecular assembly, as a discovery tool for thermodynamically and kinetically accessible knot types made of helical templates. By combining this approach with the exhaustive enumeration of molecular braiding patterns applicable to more general template geometries, we find that only few selected shapes have the closed, symmetric and quasi-planar character typical of synthetic knots. The corresponding collection of admissible topologies is extremely restricted. It covers all known molecular knots but it especially includes a limited set of novel complex ones that have not yet been obtained experimentally, such as 10124 and 15n41185, making them privileged targets for future self-assembling experiments.
Collapse
Affiliation(s)
- Mattia Marenda
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136, Trieste, Italy
| | - Enzo Orlandini
- Dipartimento di Fisica e Astronomia "Galileo Galilei", sezione INFN, Università degli Studi di Padova, via Marzolo 8, I-35131, Padova, Italy
| | - Cristian Micheletti
- SISSA, International School for Advanced Studies, via Bonomea 265, I-34136, Trieste, Italy.
| |
Collapse
|
10
|
Malhotra I, Babu SB. Aggregation kinetics of irreversible patches coupled with reversible isotropic interaction leading to chains, bundles and globules. PURE APPL CHEM 2018. [DOI: 10.1515/pac-2017-0910] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Abstract
In the present study we are performing simulation of simple model of two patch colloidal particles undergoing irreversible diffusion limited cluster aggregation using patchy Brownian cluster dynamics. In addition to the irreversible aggregation of patches, the spheres are coupled with isotropic reversible aggregation through the Kern–Frenkel potential. Due to the presence of anisotropic and isotropic potential we have also defined three different kinds of clusters formed due to anisotropic potential and isotropic potential only as well as both the potentials together. We have investigated the effect of patch size on self-assembly under different solvent qualities for various volume fractions. We will show that at low volume fractions during aggregation process, we end up in a chain conformation for smaller patch size while in a globular conformation for bigger patch size. We also observed a chain to bundle transformation depending on the attractive interaction strength between the chains or in other words depending on the quality of the solvent. We will also show that bundling process is very similar to nucleation and growth phenomena observed in colloidal system with short range attraction. We have also studied the bond angle distribution for this system, where for small patches only two angles are more probable indicating chain formation, while for bundling at very low volume fraction a tail is developed in the distribution. While for the case of higher patch angle this distribution is broad compared to the case of low patch angles showing we have a more globular conformation. We are also proposing a model for the formation of bundles which are similar to amyloid fibers using two patch colloidal particles.
Collapse
Affiliation(s)
- Isha Malhotra
- Department of Physics , Indian Institute of Technology , Hauz Khas, New Delhi-110016 , India
| | - Sujin B. Babu
- Department of Physics , Indian Institute of Technology , Hauz Khas, New Delhi-110016 , India
| |
Collapse
|
11
|
Porter CL, Crocker JC. Directed assembly of particles using directional DNA interactions. Curr Opin Colloid Interface Sci 2017. [DOI: 10.1016/j.cocis.2017.04.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
12
|
|
13
|
Duguet É, Hubert C, Chomette C, Perro A, Ravaine S. Patchy colloidal particles for programmed self-assembly. CR CHIM 2016. [DOI: 10.1016/j.crci.2015.11.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
14
|
Tavares JM, Almarza NG, Telo da Gama MM. Generalization of Wertheim's theory for the assembly of various types of rings. SOFT MATTER 2015; 11:5828-5838. [PMID: 26098611 DOI: 10.1039/c5sm00559k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We generalize Wertheim's first order perturbation theory to account for the effect in the thermodynamics of the self-assembly of rings characterized by two energy scales. The theory is applied to a lattice model of patchy particles and tested against Monte Carlo simulations on a fcc lattice. These particles have 2 patches of type A and 10 patches of type B, which may form bonds AA or AB that decrease the energy by εAA and by εAB ≡ rεAA, respectively. The angle θ between the 2 A-patches on each particle is fixed at 60°, 90° or 120°. For values of r below 1/2 and above a threshold rth(θ) the models exhibit a phase diagram with two critical points. Both theory and simulation predict that rth increases when θ decreases. We show that the mechanism that prevents phase separation for models with decreasing values of θ is related to the formation of loops containing AB bonds. Moreover, we show that by including the free energy of B-rings (loops containing one AB bond), the theory describes the trends observed in the simulation results, but that for the lowest values of θ, the theoretical description deteriorates due to the increasing number of loops containing more than one AB bond.
Collapse
Affiliation(s)
- J M Tavares
- Centro de Física Teórica e Computacional, Universidade de Lisboa, Campo Grande, P-1749-016 Lisbon, Portugal.
| | | | | |
Collapse
|
15
|
Fantoni R, Pastore G. Wertheim perturbation theory: thermodynamics and structure of patchy colloids. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1061150] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Riccardo Fantoni
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca’ Foscari Venezia , Venezia, Italy
| | - Giorgio Pastore
- Dipartimento di Fisica, Università di Trieste , Trieste, Italy
| |
Collapse
|
16
|
Dufal S, Lafitte T, Haslam AJ, Galindo A, Clark GN, Vega C, Jackson G. The A in SAFT: developing the contribution of association to the Helmholtz free energy within a Wertheim TPT1 treatment of generic Mie fluids. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1029027] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
17
|
Fantoni R, Pastore G. Wertheim and Bjerrum-Tani-Henderson theories for associating fluids: A critical assessment. J Chem Phys 2014; 141:074108. [DOI: 10.1063/1.4892878] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
18
|
Nekrasov VM, Polshchitsin AA, Yurkin MA, Yakovleva GE, Maltsev VP, Chernyshev AV. Brownian aggregation rate of colloid particles with several active sites. J Chem Phys 2014; 141:064309. [DOI: 10.1063/1.4892163] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Vyacheslav M. Nekrasov
- Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090 Novosibirsk, Russia
- Physics Department, Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | - Alexey A. Polshchitsin
- Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090 Novosibirsk, Russia
- JSC “VECTOR-BEST”, PO BOX 492, Novosibirsk 630117 Russia
| | - Maxim A. Yurkin
- Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090 Novosibirsk, Russia
- Physics Department, Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | | | - Valeri P. Maltsev
- Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090 Novosibirsk, Russia
- Physics Department, Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
- Department of Preventive Medicine, Novosibirsk State Medical University, Krasny Prospect 52, 630091 Novosibirsk, Russia
| | - Andrei V. Chernyshev
- Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090 Novosibirsk, Russia
- Physics Department, Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| |
Collapse
|
19
|
Prabhu A, Babu SB, Dolado JS, Gimel JC. Brownian cluster dynamics with short range patchy interactions: its application to polymers and step-growth polymerization. J Chem Phys 2014; 141:024904. [PMID: 25028043 DOI: 10.1063/1.4886585] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a novel simulation technique derived from Brownian cluster dynamics used so far to study the isotropic colloidal aggregation. It now implements the classical Kern-Frenkel potential to describe patchy interactions between particles. This technique gives access to static properties, dynamics and kinetics of the system, even far from the equilibrium. Particle thermal motions are modeled using billions of independent small random translations and rotations, constrained by the excluded volume and the connectivity. This algorithm, applied to a single polymer chain leads to correct static and dynamic properties, in the framework where hydrodynamic interactions are ignored. By varying patch angles, various local chain flexibilities can be obtained. We have used this new algorithm to model step-growth polymerization under various solvent qualities. The polymerization reaction is modeled by an irreversible aggregation between patches while an isotropic finite square-well potential is superimposed to mimic the solvent quality. In bad solvent conditions, a competition between a phase separation (due to the isotropic interaction) and polymerization (due to patches) occurs. Surprisingly, an arrested network with a very peculiar structure appears. It is made of strands and nodes. Strands gather few stretched chains that dip into entangled globular nodes. These nodes act as reticulation points between the strands. The system is kinetically driven and we observe a trapped arrested structure. That demonstrates one of the strengths of this new simulation technique. It can give valuable insights about mechanisms that could be involved in the formation of stranded gels.
Collapse
Affiliation(s)
- A Prabhu
- Département Polymères Colloïdes Interfaces, LUNAM Université, Université du Maine, IMMM-UMR CNRS 6283, av. O. Messiaen, 72085 Le Mans Cedex 9, France
| | - S B Babu
- Department of Physics, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - J S Dolado
- Tecnalia Research and Innovation, Derio, Spain
| | - J-C Gimel
- Département Polymères Colloïdes Interfaces, LUNAM Université, Université du Maine, IMMM-UMR CNRS 6283, av. O. Messiaen, 72085 Le Mans Cedex 9, France
| |
Collapse
|
20
|
Tavares JM, Almarza NG, Telo da Gama MM. Three-dimensional patchy lattice model: Ring formation and phase separation. J Chem Phys 2014; 140:044905. [DOI: 10.1063/1.4863135] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
21
|
Marshall BD, Chapman WG. Resummed thermodynamic perturbation theory for bond cooperativity in associating fluids. J Chem Phys 2013; 139:214106. [DOI: 10.1063/1.4834637] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
22
|
Rovigatti L, Tavares JM, Sciortino F. Self-assembly in chains, rings, and branches: a single component system with two critical points. PHYSICAL REVIEW LETTERS 2013; 111:168302. [PMID: 24182307 DOI: 10.1103/physrevlett.111.168302] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Indexed: 06/02/2023]
Abstract
We study the interplay between phase separation and self-assembly in chains, rings, and branched structures in a model of particles with dissimilar patches. We extend Wertheim's first order perturbation theory to include the effects of ring formation and to theoretically investigate the thermodynamics of the model. We find a peculiar shape for the vapor-liquid coexistence, featuring reentrant behavior in both phases and two critical points, despite the single-component nature of the system. The emergence of the lower critical point is caused by the self-assembly of rings taking place in the vapor, generating a phase with lower energy and lower entropy than the liquid. Monte Carlo simulations of the same model fully support these unconventional theoretical predictions.
Collapse
Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | | | | |
Collapse
|
23
|
Rovigatti L, Kantorovich S, Ivanov AO, Tavares JM, Sciortino F. Branching points in the low-temperature dipolar hard sphere fluid. J Chem Phys 2013; 139:134901. [PMID: 24116579 DOI: 10.1063/1.4821935] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Lorenzo Rovigatti
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale A. Moro 2, 00185 Roma, Italy
| | | | | | | | | |
Collapse
|
24
|
Marshall BD, Chapman WG. Molecular theory for self assembling mixtures of patchy colloids and colloids with spherically symmetric attractions: The single patch case. J Chem Phys 2013; 139:104904. [DOI: 10.1063/1.4820417] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
25
|
Marshall BD, Chapman WG. Molecular theory for the phase equilibria and cluster distribution of associating fluids with small bond angles. J Chem Phys 2013; 139:054902. [DOI: 10.1063/1.4816665] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
26
|
López LG, Linares DH, Ramirez-Pastor AJ, Stariolo DA, Cannas SA. Critical behavior of self-assembled rigid rods on two-dimensional lattices: Bethe-Peierls approximation and Monte Carlo simulations. J Chem Phys 2013; 138:234706. [PMID: 23802975 DOI: 10.1063/1.4809987] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The critical behavior of adsorbed monomers that reversibly polymerize into linear chains with restricted orientations relative to the substrate has been studied. In the model considered here, which is known as self-assembled rigid rods (SARRs) model, the surface is represented by a two-dimensional lattice and a continuous orientational transition occurs as a function of temperature and coverage. The phase diagrams were obtained for the square, triangular, and honeycomb lattices by means of Monte Carlo simulations and finite-size scaling analysis. The numerical results were compared with Bethe-Peierls analytical predictions about the orientational transition for the square and triangular lattices. The analysis of the phase diagrams, along with the behavior of the critical average rod lengths, showed that the critical properties of the model do not depend on the structure of the lattice at low temperatures (coverage), revealing a quasi-one-dimensional behavior in this regime. Finally, the universality class of the SARRs model, which has been subject of controversy, has been revisited.
Collapse
Affiliation(s)
- L G López
- Departamento de Física, Instituto de Física Aplicada, Universidad Nacional de San Luis, CONICET, 5700 San Luis, Argentina
| | | | | | | | | |
Collapse
|
27
|
Marshall BD, Chapman WG. Thermodynamic perturbation theory for associating fluids with small bond angles: effects of steric hindrance, ring formation, and double bonding. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2013; 87:052307. [PMID: 23767540 DOI: 10.1103/physreve.87.052307] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 04/17/2013] [Indexed: 06/02/2023]
Abstract
We develop a comprehensive approach to model associating fluids with small bond angles using Wertheim's perturbation theory. We show theoretically and through Monte Carlo simulations that as bond angle is varied various modes of association become dominant. The theory is shown to be in excellent agreement with Monte Carlo simulation for the prediction of the internal energy, pressure, and fractions in rings and chains, double bonded over the full range of bond angles.
Collapse
Affiliation(s)
- Bennett D Marshall
- Department of Chemical and Biomolecular Engineering, Rice University, 6100 S. Main, Houston, Texas 77005, USA
| | | |
Collapse
|
28
|
Kantorovich S, Ivanov AO, Rovigatti L, Tavares JM, Sciortino F. Nonmonotonic magnetic susceptibility of dipolar hard-spheres at low temperature and density. PHYSICAL REVIEW LETTERS 2013; 110:148306. [PMID: 25167048 DOI: 10.1103/physrevlett.110.148306] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Indexed: 05/15/2023]
Abstract
We investigate, via numerical simulations, mean field, and density functional theories, the magnetic response of a dipolar hard sphere fluid at low temperatures and densities, in the region of strong association. The proposed parameter-free theory is able to capture both the density and temperature dependence of the ring-chain equilibrium and the contribution to the susceptibility of a chain of generic length. The theory predicts a nonmonotonic temperature dependence of the initial (zero field) magnetic susceptibility, arising from the competition between magnetically inert particle rings and magnetically active chains. Monte Carlo simulation results closely agree with the theoretical findings.
Collapse
Affiliation(s)
- Sofia Kantorovich
- Ural Federal University, Lenin Avenue 51, 620083, Ekaterinburg, Russia and Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - Alexey O Ivanov
- Ural Federal University, Lenin Avenue 51, 620083, Ekaterinburg, Russia
| | - Lorenzo Rovigatti
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, 00185 Roma, Italy
| | - José Maria Tavares
- Instituto Superior de Engenharia de Lisboa-ISEL, Rua Conselheiro Emídio Navarro 1, P-1950-062 Lisbon, Portugal and Centro de Física Teórica e Computacional, Avenida Professor Gama Pinto 2, P-1649-003 Lisbon, Portugal
| | - Francesco Sciortino
- Dipartimento di Fisica, Università di Roma La Sapienza, Piazzale Aldo Moro 2, 00185 Roma, Italy and CNR-ISC, Università di Roma La Sapienza, Piazzale A. Moro 2, 00185 Roma, Italy
| |
Collapse
|
29
|
Almarza NG, Tavares JM, Noya EG, Telo da Gama MM. Three-dimensional patchy lattice model for empty fluids. J Chem Phys 2012; 137:244902. [DOI: 10.1063/1.4771591] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
30
|
Almarza NG. Closed-loop liquid-vapor equilibrium in a one-component system. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:030101. [PMID: 23030851 DOI: 10.1103/physreve.86.030101] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Indexed: 06/01/2023]
Abstract
We report Monte Carlo simulations that show a closed-loop liquid-vapor equilibrium in a pure substance. This finding has been achieved on a two-dimensional lattice model for patchy particles that can form network fluids. We have considered related models with a slightly different patch distribution in order to understand the features of the distribution of patches on the surface of the particles that make possible the presence of the closed-loop liquid-vapor equilibrium, and its relation to the phase diagram containing so-called empty liquids. Finally we discuss the likelihood of finding the closed-loop liquid-vapor equilibria on related models for three-dimensional models of patchy particles in the continuum, and speculate on the possible relationship between the mechanism behind the closed-loop liquid-vapor equilibrium of our simple lattice model and the salt-induced reentrant condensation found in complex systems.
Collapse
Affiliation(s)
- N G Almarza
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain
| |
Collapse
|