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Kalapurakal RAM, Jha PK, Vashisth H. Theory and simulations of light-induced self-assembly in colloids with quantum chemistry derived empirical potentials. SOFT MATTER 2024; 20:7367-7378. [PMID: 39086325 DOI: 10.1039/d4sm00459k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Light-induced self-assembly (LISA) is a non-invasive method for tuning material properties. Photoresponsive ligands coated on the surfaces of nanoparticles are often used to achieve LISA. We report simulation studies for a photoresponsive ligand, azobenzene dithiol (ADT), which switches from a trans-to-cis configuration on exposure to ultraviolet light, allowing self-assembly in ADT-coated gold nanoparticles (NPs). This is attributed to a higher dipole moment of cis-ADT over trans-ADT which leads to a dipole-dipole attraction facilitating self-assembly. Singh and Jha [Comput. Theor. Chem., 2021, 1206, 113492] used quantum-chemistry calculations to quantify the interaction energy of a pair of ADT ligands in their cis and trans conformations. The interaction energy between ligands was fit to a potential energy function of the Lennard-Jones (LJ) form having distinct exponents for attractive and repulsive contributions. Using this generalized equation for the ligand-ligand interaction energy, we calculated the total effective interaction energy between a pair of cis as well as trans ADT-coated NPs. Specifically, we calculated the effective interaction energies between cis/trans-NPs using discrete as well as continuous approaches. Given the limitations of experiments in probing individual ligand conformations, we also studied the effect of varying the functional ligand length on the interaction energy between NPs and identified the optimal functional ligand length to capture the steric and conformational effects. Finally, using the effective interaction energy, we obtained a generalized potential energy function, which was applied in Langevin dynamics simulations to capture self-assembly in NPs.
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Affiliation(s)
| | - Prateek K Jha
- Department of Chemical Engineering, Indian Institute of Technology, Roorkee 247667, India.
| | - Harish Vashisth
- Department of Chemical Engineering and Bioengineering, University of New Hampshire, Durham, NH 03824, USA.
- Department of Chemistry, University of New Hampshire, Durham, NH 03824, USA
- Integrated Applied Mathematics Program, University of New Hampshire, Durham, NH 03824, USA
- Molecular and Cellular Biotechnology Program, University of New Hampshire, Durham, NH 03824, USA
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2
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Tanner CPN, Utterback JK, Portner J, Coropceanu I, Das A, Tassone CJ, Teitelbaum SW, Limmer DT, Talapin DV, Ginsberg NS. In Situ X-ray Scattering Reveals Coarsening Rates of Superlattices Self-Assembled from Electrostatically Stabilized Metal Nanocrystals Depend Nonmonotonically on Driving Force. ACS NANO 2024. [PMID: 38318795 PMCID: PMC10883038 DOI: 10.1021/acsnano.3c12186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
Self-assembly of colloidal nanocrystals (NCs) into superlattices (SLs) is an appealing strategy to design hierarchically organized materials with promising functionalities. Mechanistic studies are still needed to uncover the design principles for SL self-assembly, but such studies have been difficult to perform due to the fast time and short length scales of NC systems. To address this challenge, we developed an apparatus to directly measure the evolving phases in situ and in real time of an electrostatically stabilized Au NC solution before, during, and after it is quenched to form SLs using small-angle X-ray scattering. By developing a quantitative model, we fit the time-dependent scattering patterns to obtain the phase diagram of the system and the kinetics of the colloidal and SL phases as a function of varying quench conditions. The extracted phase diagram is consistent with particles whose interactions are short in range relative to their diameter. We find the degree of SL order is primarily determined by fast (subsecond) initial nucleation and growth kinetics, while coarsening at later times depends nonmonotonically on the driving force for self-assembly. We validate these results by direct comparison with simulations and use them to suggest dynamic design principles to optimize the crystallinity within a finite time window. The combination of this measurement methodology, quantitative analysis, and simulation should be generalizable to elucidate and better control the microscopic self-assembly pathways of a wide range of bottom-up assembled systems and architectures.
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Affiliation(s)
- Christian P N Tanner
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - James K Utterback
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Joshua Portner
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Igor Coropceanu
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
| | - Avishek Das
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Christopher J Tassone
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Samuel W Teitelbaum
- Department of Physics, Arizona State University, Tempe, Arizona 85287, United States
| | - David T Limmer
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Kavli Energy NanoSciences Institute, University of California, Berkeley, California 94720, United States
| | - Dmitri V Talapin
- Department of Chemistry, James Franck Institute, and Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
- Center for Nanoscale Materials, Argonne National Laboratory, Argonne, Illinois 60517, United States
| | - Naomi S Ginsberg
- Department of Chemistry, University of California, Berkeley, California 94720, United States
- Kavli Energy NanoSciences Institute, University of California, Berkeley, California 94720, United States
- Department of Physics, University of California, Berkeley, California 94720, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- Materials Sciences and Chemical Sciences Divisions, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
- STROBE, NSF Science & Technology Center, Berkeley, California 94720, United States
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3
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Prestipino S, Pini D, Costa D, Malescio G, Munaò G. A density functional theory and simulation study of stripe phases in symmetric colloidal mixtures. J Chem Phys 2023; 159:204902. [PMID: 38010334 DOI: 10.1063/5.0177209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/30/2023] [Indexed: 11/29/2023] Open
Abstract
In a binary mixture, stripes refer to a one-dimensional periodicity of the composition, namely, a regular alternation of layers filled with particles of mostly one species. We have recently introduced [Munaò et al., Phys. Chem. Chem. Phys. 25, 16227 (2023)] a model that possibly provides the simplest binary mixture endowed with stripe order. The model consists of two species of identical hard spheres with equal concentration, which mutually interact through a square-well potential. In that paper, we have numerically shown that stripes are present in both liquid and solid phases when the attraction range is rather long. Here, we study the phase behavior of the model in terms of a density functional theory capable to account for the existence of stripes in the dense mixture. Our theory is accurate in reproducing the phases of the model, at least insofar as the composition inhomogeneities occur on length scales quite larger than the particle size. Then, using Monte Carlo simulations, we prove the existence of solid stripes even when the square well is much thinner than the particle diameter, making our model more similar to a real colloidal mixture. Finally, when the width of the attractive well is equal to the particle diameter, we observe a different and more complex form of compositional order in the solid, where each species of particle forms a regular porous matrix holding in its holes the other species, witnessing a surprising variety of emergent behaviors for a very basic model of interaction.
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Affiliation(s)
- Santi Prestipino
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Davide Pini
- Dipartimento di Fisica "A. Pontremoli," Università di Milano, Via Celoria 16, 20133 Milano, Italy
| | - Dino Costa
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Gianpietro Malescio
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Gianmarco Munaò
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra, Università degli Studi di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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4
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Gurin P, Varga S, Odriozola G. The role of the second virial coefficient in the vapor-liquid phase coexistence of anisotropic square-well particles. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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5
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Munguía-Valadez J, Chávez-Rojo MA, Sambriski EJ, Moreno-Razo JA. The generalized continuous multiple step (GCMS) potential: model systems and benchmarks. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:184002. [PMID: 35090143 DOI: 10.1088/1361-648x/ac4fe8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The generalized continuous multiple step (GCMS) potential is presented in this work. Its flexible form allows forrepulsiveand/orattractivecontributions to be encoded through adjustable energy and length scales. The GCMS interaction provides a continuous representation of square-well, square-shoulder potentials and their variants for implementation in computer simulations. A continuous and differentiable energy representation is required to derive forces in conventional simulation algorithms. Molecular dynamics simulations are of particular interest when considering the dynamic properties of a system. The GCMS potential can mimic other interactions with a judicious choice of parameters due to the versatile sigmoid form. In this study, our benchmarks for the GCMS representation include triangular, Yukawa, Franzese, and Lennard-Jones potentials. Comparisons made with published data on volumetric phase diagrams, liquid structure, and diffusivity from model systems are in excellent agreement.
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Affiliation(s)
- Jorge Munguía-Valadez
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, Avenida San Rafael Atlixco No. 186, Colonia Vicentina, Delegación Iztapalapa, Mexico City 09340 Mexico
| | - Marco Antonio Chávez-Rojo
- Facultad de Ciencias Químicas, Universidad Autónoma de Chihuahua, Circuito Universitario s/n, Campus II, Chihuahua, Chihuahua 31125, Mexico
| | - Edward John Sambriski
- Department of Chemistry, Delaware Valley University, 700 East Butler Avenue, Doylestown, PA 18901 United States of America
| | - José Antonio Moreno-Razo
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, Avenida San Rafael Atlixco No. 186, Colonia Vicentina, Delegación Iztapalapa, Mexico City 09340 Mexico
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6
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Perdomo-Pérez R, Martínez-Rivera J, Palmero-Cruz NC, Sandoval-Puentes MA, Gallegos JAS, Lázaro-Lázaro E, Valadez-Pérez NE, Torres-Carbajal A, Castañeda-Priego R. Thermodynamics, static properties and transport behaviour of fluids with competing interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2022; 34:144005. [PMID: 35026739 DOI: 10.1088/1361-648x/ac4b29] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Competing interaction fluids have become ideal model systems to study a large number of phenomena, for example, the formation of intermediate range order structures, condensed phases not seen in fluids driven by purely attractive or repulsive forces, the onset of particle aggregation under in- and out-of-equilibrium conditions, which results in the birth of reversible and irreversible aggregates or clusters whose topology and morphology depend additionally on the thermodynamic constrictions, and a particle dynamics that has a strong influence on the transport behaviour and rheological properties of the fluid. In this contribution, we study a system of particles interacting through a potential composed by a continuous succession of a short-ranged square-well (SW), an intermediate-ranged square-shoulder and a long-ranged SW. This potential model is chosen to systematically analyse the contribution of every component of the interaction potential on the phase behaviour, the microstructure, the morphology of the resulting aggregates and the transport phenomena of fluids described by competing interactions. Our results indicate that the inclusion of a barrier and a second well leads to new and interesting effects, which in addition result in variations of the physical properties associated to the competition among interactions.
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Affiliation(s)
- Román Perdomo-Pérez
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Jaime Martínez-Rivera
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Norma C Palmero-Cruz
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Miguel A Sandoval-Puentes
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Javier A S Gallegos
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Edilio Lázaro-Lázaro
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
| | - Néstor E Valadez-Pérez
- Facultad de Ciencias en Física y Matemáticas, Universidad Autónoma de Chiapas, Carretera Emiliano Zapata km 8, 29050 Tuxtla Gutiérrez, Mexico
| | - Alexis Torres-Carbajal
- Unidad Profesional Interdisciplinaria de Ingeniería, Campus Tlaxcala, Instituto Politécnico Nacional. Plaza Bicentenario, Guillermo Valle 11, Centro, 9000 Tlaxcala de Xicohténcatl, Tlaxcala, México
| | - Ramón Castañeda-Priego
- Departamento de Ingeniería Física, División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico
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7
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Gómez de Santiago M, Gurin P, Varga S, Odriozola G. Extended law of corresponding states: square-well oblates. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:104002. [PMID: 34874295 DOI: 10.1088/1361-648x/ac3fd8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 12/03/2021] [Indexed: 06/13/2023]
Abstract
The vapour-liquid coexistence collapse in the reduced temperature,Tr=T/Tc, reduced density,ρr=ρ/ρc, plane is known as a principle of corresponding states, and Noro and Frenkel have extended it for pair potentials of variable range. Here, we provide a theoretical basis supporting this extension, and show that it can also be applied to short-range pair potentials where both repulsive and attractive parts can be anisotropic. We observe that the binodals of oblate hard ellipsoids for a given aspect ratio (κ= 1/3) with varying short-range square-well interactions collapse into a single master curve in theΔB2*-ρrplane, whereΔB2*=(B2(T)-B2(Tc))/v0,B2is the second virial coefficient, andv0is the volume of the hard body. This finding is confirmed by both REMC simulation and second virial perturbation theory for varying square-well shells, mimicking uniform, equator, and pole attractions. Our simulation results reveal that the extended law of corresponding states is not related to the local structure of the fluid.
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Affiliation(s)
- Miguel Gómez de Santiago
- Área de Física de Procesos Irreversibles, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, 02200 Ciudad de México, Mexico
| | - Péter Gurin
- Physics Department, Center for Natural Sciences, Faculty of Engineering, University of Pannonia, PO Box 158, Veszprém H-8201, Hungary
| | - Szabolcs Varga
- Physics Department, Center for Natural Sciences, Faculty of Engineering, University of Pannonia, PO Box 158, Veszprém H-8201, Hungary
| | - Gerardo Odriozola
- Área de Física de Procesos Irreversibles, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, 02200 Ciudad de México, Mexico
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8
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Marín-Aguilar S, Smallenburg F, Sciortino F, Foffi G. Monodisperse patchy particle glass former. J Chem Phys 2021; 154:174501. [PMID: 34241071 DOI: 10.1063/5.0036963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Glass formers are characterized by their ability to avoid crystallization. As monodisperse systems tend to rapidly crystallize, the most common glass formers in simulations are systems composed of mixtures of particles with different sizes. Here, we make use of the ability of patchy particles to change their local structure to propose them as monodisperse glass formers. We explore monodisperse systems with two patch geometries: a 12-patch geometry that enhances the formation of icosahedral clusters and an 8-patch geometry that does not appear to strongly favor any particular local structure. We show that both geometries avoid crystallization and present glassy features at low temperatures. However, the 8-patch geometry better preserves the structure of a simple liquid at a wide range of temperatures and packing fractions, making it a good candidate for a monodisperse glass former.
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Affiliation(s)
- Susana Marín-Aguilar
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Frank Smallenburg
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
| | - Francesco Sciortino
- Department of Physics, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Rome, Italy
| | - Giuseppe Foffi
- Université Paris-Saclay, CNRS, Laboratoire de Physique des Solides, 91405 Orsay, France
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9
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Sastre F, Sotelo-Serna MG, Moreno-Hilario E, Benavides AL. Helmholtz free-energy high-temperature perturbation expansion for square-well and square-shoulder potentials. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1887527] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Francisco Sastre
- Departamento de Ingeniería Física, División de Ciencias e Ingenierías, Campus León de la Universidad de Guanajuato, León, Guanajuato, Mexico
| | | | | | - Ana Laura Benavides
- Departamento de Ingeniería Física, División de Ciencias e Ingenierías, Campus León de la Universidad de Guanajuato, León, Guanajuato, Mexico
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10
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Gutiérrez AB, Chapela GA. Effect of shape on liquid-vapor coexistence and surface properties of parallelepiped molecules. J Chem Phys 2020; 152:134501. [PMID: 32268761 DOI: 10.1063/1.5141352] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Liquid-vapor coexistence is calculated via molecular dynamics for a variety of parallelepiped shaped molecules. Models are constructed as an array of tangential hard spheres interacting with an attractive square-well potential. Each shape is formed by varying the number of spheres in their three sides. The initial density of the system is chosen close to the critical density of a SW fluid to obtain an equilibrated liquid-vapor coexistence curve by the process of spinodal decomposition. A pattern that relates the geometry of the molecular models and the existence or non-existence of a liquid-vapor orthobaric curve is shown.
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Affiliation(s)
- Anthony B Gutiérrez
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, 09340 México D.F., Mexico
| | - Gustavo A Chapela
- Departamento de Física, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Col. Vicentina, 09340 México D.F., Mexico
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11
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Abstract
In this chapter we describe numerical procedures to evaluate the phase behavior of coarse-grained models for globular proteins. Specifically we focus on models based on hard spheres complemented with "patchy-like" anisotropic interactions that mimic the attractive regions on the surface of the proteins. We introduce the basic elements of grand canonical Monte Carlo simulations for these types of models in which rotational and translational moves need to be accounted for. We describe the techniques for the estimation of the fluid-fluid critical point, coexistence curve, and fluid-crystal boundaries. We also discuss an efficient method for the evaluation of the fluid-fluid phase diagram: the successive umbrella sampling technique. Finally we briefly describe how to exploit the same tools for the calculation of the phase behavior of protein binary mixtures.
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Affiliation(s)
| | - Francesco Sciortino
- Dipartimento di Fisica, "Sapienza" Università di Roma, Piazzale A. Moro 2, Roma, Italy
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12
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Zerón IM, Vega C, Benavides AL. Continuous version of a square-well potential of variable range and its application in molecular dynamics simulations. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1481232] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- I. M. Zerón
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Guanajuato, México
| | - C. Vega
- Depto. Química Física I, Fac. Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - A. L. Benavides
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Guanajuato, México
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13
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Tasios N, Dijkstra M. From 2D to 3D: Critical Casimir interactions and phase behavior of colloidal hard spheres in a near-critical solvent. J Chem Phys 2017; 146:134903. [DOI: 10.1063/1.4979518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nikos Tasios
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - Marjolein Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
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14
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Sun G, Wang Y, Lomakin A, Benedek GB, Stanley HE, Xu L, Buldyrev SV. The phase behavior study of human antibody solution using multi-scale modeling. J Chem Phys 2017; 145:194901. [PMID: 27875860 DOI: 10.1063/1.4966972] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Phase transformation in antibody solutions is of growing interest in both academia and the pharmaceutical industry. Recent experimental studies have shown that, as in near-spherical proteins, antibodies can undergo a liquid-liquid phase separation under conditions metastable with respect to crystallization. However, the phase diagram of the Y-shaped antibodies exhibits unique features that differ substantially from those of spherical proteins. Specifically, antibody solutions have an exceptionally low critical volume fraction (CVF) and a broader and more asymmetric liquid-liquid coexistence curve than those of spherical proteins. Using molecular dynamics simulation on a series of trimetric Y-shaped coarse-grained models, we investigate the phase behavior of antibody solutions and compare the results with the experimental phase diagram of human immunoglobulin G (IgG), one of the most common Y-shape typical of antibody molecules. With the fitted size of spheres, our simulation reproduces both the low CVF and the asymmetric shape of the experimental coexistence curve of IgG antibodies. The broadness of the coexistence curve can be attributed to the anisotropic nature of the inter-protein interaction. In addition, the repulsion between the inner parts of the spherical domains of IgG dramatically expands the coexistence region in the scaled phase diagram, while the hinge length has only a minor effect on the CVF and the overall shape of the coexistence curve. We thus propose a seven-site model with empirical parameters characterizing the exclusion volume and the hinge length of the IgG molecules, which provides a base for simulation studies of the phase behavior of IgG antibodies.
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Affiliation(s)
- Gang Sun
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, China
| | - Ying Wang
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - Aleksey Lomakin
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - George B Benedek
- Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
| | - H Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| | - Limei Xu
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, China
| | - Sergey V Buldyrev
- Department of Physics, Yeshiva University, 500 West 185th Street, New York, New York 10033, USA
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15
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Tasios N, Edison JR, van Roij R, Evans R, Dijkstra M. Critical Casimir interactions and colloidal self-assembly in near-critical solvents. J Chem Phys 2016; 145:084902. [DOI: 10.1063/1.4961437] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nikos Tasios
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
| | - John R. Edison
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, USA
| | - René van Roij
- Institute for Theoretical Physics, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - Robert Evans
- H. H. Wills Physics Laboratory, University of Bristol, Bristol BS8 1TL, United Kingdom
| | - Marjolein Dijkstra
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584 CC Utrecht, The Netherlands
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16
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Preisler Z, Vissers T, Smallenburg F, Sciortino F. Crystals of Janus colloids at various interaction ranges. J Chem Phys 2016. [DOI: 10.1063/1.4960423] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- Z. Preisler
- Dipartimento di Fisica, Università di Roma “Sapienza,” Piazzale Aldo Moro 5, 00185 Roma, Italy
- Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht, The Netherlands
| | - T. Vissers
- Dipartimento di Fisica, Università di Roma “Sapienza,” Piazzale Aldo Moro 5, 00185 Roma, Italy
- SUPA and School of Physics and Astronomy, The University of Edinburgh, James Clerk Maxwell Building, Peter Guthrie Tait Road, Edinburgh EH9 3FD, United Kingdom
| | - F. Smallenburg
- Dipartimento di Fisica, Università di Roma “Sapienza,” Piazzale Aldo Moro 5, 00185 Roma, Italy
- Institut für Theoretische Physik II: Weiche Materie, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - F. Sciortino
- Dipartimento di Fisica, Università di Roma “Sapienza,” Piazzale Aldo Moro 5, 00185 Roma, Italy
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17
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Škrbić T, Badasyan A, Hoang TX, Podgornik R, Giacometti A. From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang-Landau approach. SOFT MATTER 2016; 12:4783-4793. [PMID: 27137225 DOI: 10.1039/c6sm00542j] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We use a micro-canonical Wang-Landau technique to study the equilibrium properties of a single flexible homopolymer where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well potential. To mimic the characteristics of a protein-like system, the model is then refined in two different directions. Firstly, by allowing partial overlap between consecutive beads, we break the spherical symmetry and thus provide a severe constraint on the possible conformations of the chain. Alternatively, we introduce additional spherical beads at specific positions in the direction normal to the backbone, to represent the steric hindrance of the side chains in real proteins. Finally, we consider also a combination of these two ingredients. In all three systems, we obtain the full phase diagram in the temperature-interaction range plane and find the presence of helicoidal structures at low temperatures in the intermediate range of interactions. The effect of the range of the square-well attraction is highlighted, and shown to play a role similar to that found in simple liquids and polymers. Perspectives in terms of protein folding are finally discussed.
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Affiliation(s)
- Tatjana Škrbić
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.
| | - Artem Badasyan
- Material Research Laboratory, University of Nova Gorica, SI-5270 Ajdovscina, Slovenia.
| | - Trinh Xuan Hoang
- Center for Computational Physics Institute of Physics, Vietnam Academy of Science and Technology, 10 Dao Tan St., Hanoi, Vietnam.
| | - Rudolf Podgornik
- Department of Theoretical Physics, J. Stefan Institute and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, SI-1000 Ljubljana, Slovenia.
| | - Achille Giacometti
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia, Campus Scientifico, Edificio Alfa, via Torino 155, 30170 Venezia Mestre, Italy.
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18
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Hansen J, Platten F, Wagner D, Egelhaaf SU. Tuning protein-protein interactions using cosolvents: specific effects of ionic and non-ionic additives on protein phase behavior. Phys Chem Chem Phys 2016; 18:10270-80. [PMID: 27020538 DOI: 10.1039/c5cp07285a] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cosolvents are routinely used to modulate the (thermal) stability of proteins and, hence, their interactions with proteins have been studied intensely. However, less is known about their specific effects on protein-protein interactions, which we characterize in terms of the protein phase behavior. We analyze the phase behavior of lysozyme solutions in the presence of sodium chloride (NaCl), guanidine hydrochloride (GuHCl), glycerol, and dimethyl sulfoxide (DMSO). We experimentally determined the crystallization boundary (XB) and, in combination with data on the cloud-point temperatures (CPTs), the crystallization gap. In agreement with other studies, our data indicate that the additives might affect the protein phase behavior through electrostatic screening and additive-specific contributions. At high salt concentrations, where electrostatic interactions are screened, both the CPT and the XB are found to be linear functions of the additive concentration. Their slopes quantify the additive-specific changes of the phase behavior and thus of the protein-protein interactions. While the specific effect of NaCl is to induce attractions between proteins, DMSO, glycerol and GuHCl (with increasing strength) weaken attractions and/or induce repulsions. Except for DMSO, changes of the CPT are stronger than those of the XB. Furthermore, the crystallization gap widens in the case of GuHCl and glycerol and narrows in the case of NaCl. We relate these changes to colloidal interaction models, namely square-well and patchy interactions.
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Affiliation(s)
- Jan Hansen
- Condensed Matter Physics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany.
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19
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Fusco D, Charbonneau P. Soft matter perspective on protein crystal assembly. Colloids Surf B Biointerfaces 2016; 137:22-31. [DOI: 10.1016/j.colsurfb.2015.07.023] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/07/2015] [Accepted: 07/09/2015] [Indexed: 01/24/2023]
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20
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Haxton TK, Hedges LO, Whitelam S. Crystallization and arrest mechanisms of model colloids. SOFT MATTER 2015; 11:9307-9320. [PMID: 26428696 DOI: 10.1039/c5sm01833a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
We performed dynamic simulations of spheres with short-range attractive interactions for many values of interaction strength and range. Fast crystallization occurs in a localized region of this parameter space, but the character of crystallization pathways is not uniform within this region. Pathways range from one-step, in which a crystal nucleates directly from a gas, to two-step, in which substantial liquid-like clusters form and only subsequently become crystalline. Crystallization can fail because of slow nucleation from either gas or liquid, or because of dynamic arrest caused by strong interactions. Arrested states are characterized by the formation of networks of face-sharing tetrahedra that can be detected by a local common neighbor analysis.
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Affiliation(s)
- Thomas K Haxton
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
| | - Lester O Hedges
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. and Department of Physics, University of Bath, Bath, BA2 7AY, UK
| | - Stephen Whitelam
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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21
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Avvisati G, Dijkstra M. Phase separation and self-assembly in a fluid of Mickey Mouse particles. SOFT MATTER 2015; 11:8432-8440. [PMID: 26358691 DOI: 10.1039/c5sm02076j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Recent developments in the synthesis of colloidal particles allow for control over shape and inter-particle interaction. One example, among others, is the so-called "Mickey Mouse" (MM) particle for which the self-assembly properties have been previously studied yielding a stable cluster phase together with elongated, tube-like structures. Here, we investigate under which conditions a fluid of Mickey Mouse particles can yield phase separation and how the self-assembly behaviour affects the gas-liquid coexistence. We vary the distance between the repulsive and the attractive lobes (bond length), and the interaction range, and follow the evolution of the gas-liquid (GL) coexistence curve. We find that upon increasing the bond length distance the binodal line shifts to lower temperatures, and that the interaction range controls the transition between phase separation and self-assembly of clusters. Upon further reduction of the interaction range and temperature, the clusters assume an increasingly ordered tube-like shape, ultimately matching the one previously reported in literature. These results are of interest when designing particle shape and particle-particle interaction for self-assembly processes.
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Affiliation(s)
- Guido Avvisati
- Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584CC Utrecht, The Netherlands.
| | - Marjolein Dijkstra
- Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 1, 3584CC Utrecht, The Netherlands.
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22
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Platten F, Hansen J, Milius J, Wagner D, Egelhaaf SU. Additivity of the Specific Effects of Additives on Protein Phase Behavior. J Phys Chem B 2015; 119:14986-93. [DOI: 10.1021/acs.jpcb.5b08078] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Florian Platten
- Condensed Matter Physics
Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Jan Hansen
- Condensed Matter Physics
Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Johanna Milius
- Condensed Matter Physics
Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Dana Wagner
- Condensed Matter Physics
Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | - Stefan U. Egelhaaf
- Condensed Matter Physics
Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
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23
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Rżysko W, Sokołowski S, Staszewski T. Monte Carlo simulations of a model two-dimensional, two-patch colloidal particles. J Chem Phys 2015; 143:064509. [DOI: 10.1063/1.4928507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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24
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Paganini IE, Pastorino C, Urrutia I. Structure, thermodynamic properties, and phase diagrams of few colloids confined in a spherical pore. J Chem Phys 2015; 142:244707. [PMID: 26133449 DOI: 10.1063/1.4923164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We study a system of few colloids confined in a small spherical cavity with event driven molecular dynamics simulations in the canonical ensemble. The colloidal particles interact through a short range square-well potential that takes into account the basic elements of attraction and excluded-volume repulsion of the interaction among colloids. We analyze the structural and thermodynamic properties of this few-body confined system in the framework of inhomogeneous fluids theory. Pair correlation function and density profile are used to determine the structure and the spatial characteristics of the system. Pressure on the walls, internal energy, and surface quantities such as surface tension and adsorption are also analyzed for a wide range of densities and temperatures. We have characterized systems from 2 to 6 confined particles, identifying distinctive qualitative behavior over the thermodynamic plane T - ρ, in a few-particle equivalent to phase diagrams of macroscopic systems. Applying the extended law of corresponding states, the square well interaction is mapped to the Asakura-Oosawa model for colloid-polymer mixtures. We link explicitly the temperature of the confined square-well fluid to the equivalent packing fraction of polymers in the Asakura-Oosawa model. Using this approach, we study the confined system of few colloids in a colloid-polymer mixture.
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Affiliation(s)
- Iván E Paganini
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, CNEA, Av.Gral. Paz 1499, 1650 Pcia. de Buenos Aires, Argentina
| | - Claudio Pastorino
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, CNEA, Av.Gral. Paz 1499, 1650 Pcia. de Buenos Aires, Argentina
| | - Ignacio Urrutia
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, CNEA, Av.Gral. Paz 1499, 1650 Pcia. de Buenos Aires, Argentina
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25
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Platten F, Valadez-Pérez NE, Castañeda-Priego R, Egelhaaf SU. Extended law of corresponding states for protein solutions. J Chem Phys 2015; 142:174905. [DOI: 10.1063/1.4919127] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Florian Platten
- Condensed Matter Physics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
| | | | | | - Stefan U. Egelhaaf
- Condensed Matter Physics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany
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26
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Méndez-Maldonado GA, Chapela GA, Martínez-González JA, Moreno JA, Díaz-Herrera E, Alejandre J. Fluid-solid coexistence from two-phase simulations: Binary colloidal mixtures and square well systems. J Chem Phys 2015; 142:054501. [DOI: 10.1063/1.4906424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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27
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Wei J, Xu L, Song F. Range effect on percolation threshold and structural properties for short-range attractive spheres. J Chem Phys 2015; 142:034504. [PMID: 25612717 DOI: 10.1063/1.4906084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Percolation or aggregation in colloidal system is important in many fields of science and technology. Using molecular dynamics simulations, we study the percolation behavior for systems consisting of spheres interacting with short-range square-well (SRSW) which mimic colloidal particles, with different interaction ranges. We specifically focus on how the interaction range affects the percolation thresholds in the supercritical region. We find that the contact percolation boundaries are strongly dependent on the interaction ranges of SRSW, especially away from the liquid-liquid critical point. However, varying the interaction ranges of SRSW does not affect much the structure along percolation boundaries especially for low packing fractions. For instance, along the percolation boundary, distributions of coordination number show convergence, and distributions of cluster size are universal for different interaction ranges considered. In addition, either the bond percolation boundaries or isolines of average bond coordination number collapse to those for Baxter sticky model on phase diagram, which confirms the extended law of corresponding states.
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Affiliation(s)
- Jiachen Wei
- State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, No. 15 Beisihuanxi Road, Beijing 100190, China
| | - Limei Xu
- International Center for Quantum Materials and School of Physics, Peking University, No. 5 Yiheyuan Road, Beijing 100871, China
| | - Fan Song
- State Key Laboratory of Nonlinear Mechanics (LNM), Institute of Mechanics, Chinese Academy of Sciences, No. 15 Beisihuanxi Road, Beijing 100190, China
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28
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Williamson JJ, Evans RML. Measuring local volume fraction, long-wavelength correlations, and fractionation in a phase-separating polydisperse fluid. J Chem Phys 2014; 141:164901. [PMID: 25362335 DOI: 10.1063/1.4897560] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Affiliation(s)
- J. J. Williamson
- Department of Physics, Institute for Soft Matter Synthesis and Metrology, Georgetown University, 37th and O Streets, N.W., Washington, D.C. 20057, USA
| | - R. M. L. Evans
- School of Mathematics, University of Leeds, Leeds LS2 9JT, United Kingdom
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29
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Quang LJ, Sandler SI, Lenhoff AM. Anisotropic Contributions to Protein–Protein Interactions. J Chem Theory Comput 2014; 10:835-45. [DOI: 10.1021/ct4006695] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Leigh J. Quang
- Department of Chemical and
Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States of America
| | - Stanley I. Sandler
- Department of Chemical and
Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States of America
| | - Abraham M. Lenhoff
- Department of Chemical and
Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States of America
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30
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Hoppe T. Singular value decomposition of the radial distribution function for hard sphere and square well potentials. PLoS One 2013; 8:e75792. [PMID: 24143174 PMCID: PMC3797047 DOI: 10.1371/journal.pone.0075792] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 08/20/2013] [Indexed: 11/18/2022] Open
Abstract
We compute the singular value decomposition of the radial distribution function g(r) for hard sphere, and square well solutions. We find that g(r) decomposes into a small set of basis vectors allowing for an extremely accurate representation at all interpolated densities and potential strengths. In addition, we find that the coefficient vectors describing the magnitude of each basis vector are well described by a low-order polynomial. We provide a program to calculate g(r) in this compact representation for the investigated parameter range.
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Affiliation(s)
- Travis Hoppe
- National Institutes of Health, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland, United States of America
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31
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Rivera-Torres S, del Río F, Espíndola-Heredia R, Kolafa J, Malijevský A. Molecular dynamics simulation of the free-energy expansion of the square-well fluid of short ranges. J Mol Liq 2013. [DOI: 10.1016/j.molliq.2012.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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32
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Shin H, Schweizer KS. Self-consistent phonon theory of the crystallization and elasticity of attractive hard spheres. J Chem Phys 2013; 138:084510. [DOI: 10.1063/1.4792440] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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33
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Valadez-Pérez NE, Benavides AL, Schöll-Paschinger E, Castañeda-Priego R. Phase behavior of colloids and proteins in aqueous suspensions: Theory and computer simulations. J Chem Phys 2012; 137:084905. [PMID: 22938263 DOI: 10.1063/1.4747193] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Affiliation(s)
- Néstor E Valadez-Pérez
- División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico
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34
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Almudallal AM, Buldyrev SV, Saika-Voivod I. Phase diagram of a two-dimensional system with anomalous liquid properties. J Chem Phys 2012; 137:034507. [DOI: 10.1063/1.4735093] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
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35
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Williamson JJ, Evans RML. Spinodal fractionation in a polydisperse square-well fluid. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:011405. [PMID: 23005415 DOI: 10.1103/physreve.86.011405] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2012] [Indexed: 06/01/2023]
Abstract
Using kinetic Monte Carlo simulation, we model gas-liquid spinodal decomposition in a size-polydisperse square well fluid, representing a "near-monodisperse" colloidal dispersion. We find that fractionation (demixing) of particle sizes between the phases begins asserting itself shortly after the onset of phase ordering. Strikingly, the direction of size fractionation can be reversed by a seemingly trivial choice between two interparticle potentials which, in the monodisperse case, are identical--we rationalize this in terms of a perturbative, equilibrium theory of polydispersity. Furthermore, our quantitative results show that kinetic Monte Carlo simulation can provide detailed insight into the role of fractionation in real colloidal systems.
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Affiliation(s)
- J J Williamson
- Soft Matter Group, School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, England, United Kingdom
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36
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Jadrich R, Schweizer KS. Percolation, phase separation, and gelation in fluids and mixtures of spheres and rods. J Chem Phys 2012; 135:234902. [PMID: 22191900 DOI: 10.1063/1.3669649] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The relationship between kinetic arrest, connectivity percolation, structure and phase separation in protein, nanoparticle, and colloidal suspensions is a rich and complex problem. Using a combination of integral equation theory, connectivity percolation methods, naïve mode coupling theory, and the activated dynamics nonlinear Langevin equation approach, we study this problem for isotropic one-component fluids of spheres and variable aspect ratio rigid rods, and also percolation in rod-sphere mixtures. The key control parameters are interparticle attraction strength and its (short) spatial range, total packing fraction, and mixture composition. For spherical particles, formation of a homogeneous one-phase kinetically stable and percolated physical gel is predicted to be possible, but depends on non-universal factors. On the other hand, the dynamic crossover to activated dynamics and physical bond formation, which signals discrete cluster formation below the percolation threshold, almost always occurs in the one phase region. Rods more easily gel in the homogeneous isotropic regime, but whether a percolation or kinetic arrest boundary is reached first upon increasing interparticle attraction depends sensitively on packing fraction, rod aspect ratio and attraction range. Overall, the connectivity percolation threshold is much more sensitive to attraction range than either the kinetic arrest or phase separation boundaries. Our results appear to be qualitatively consistent with recent experiments on polymer-colloid depletion systems and brush mediated attractive nanoparticle suspensions.
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Affiliation(s)
- Ryan Jadrich
- Department of Chemistry, University of Illinois, Urbana, Illinois 61801, USA
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38
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Romano F, De Michele C, Marenduzzo D, Sanz E. Monte Carlo and event-driven dynamics of Brownian particles with orientational degrees of freedom. J Chem Phys 2011; 135:124106. [DOI: 10.1063/1.3629452] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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39
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Pini D, Parola A, Colombo J, Reatto L. An investigation of the SCOZA for narrow square-well potentials and in the sticky limit. Mol Phys 2011. [DOI: 10.1080/00268976.2011.558028] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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40
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41
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42
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Bannerman MN, Lue L. Exact on-event expressions for discrete potential systems. J Chem Phys 2010; 133:124506. [DOI: 10.1063/1.3486567] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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43
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Orkoulas G. Communication: Tracing phase boundaries via molecular simulation: An alternative to the Gibbs–Duhem integration method. J Chem Phys 2010; 133:111104. [DOI: 10.1063/1.3486090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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44
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Huang HC, Chen WW, Singh JK, Kwak SK. Direct determination of fluid-solid coexistence of square-well fluids confined in narrow cylindrical hard pores. J Chem Phys 2010; 132:224504. [DOI: 10.1063/1.3429741] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Orkoulas G. Spatial updating Monte Carlo algorithms in particle simulations. MOLECULAR SIMULATION 2010. [DOI: 10.1080/08927022.2010.496785] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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46
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Romano F, Sanz E, Sciortino F. Phase diagram of a tetrahedral patchy particle model for different interaction ranges. J Chem Phys 2010. [DOI: 10.1063/1.3393777] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Giacometti A, Lado F, Largo J, Pastore G, Sciortino F. Effects of patch size and number within a simple model of patchy colloids. J Chem Phys 2010; 132:174110. [DOI: 10.1063/1.3415490] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Rżysko W, Patrykiejew A, Sokołowski S, Pizio O. Phase behavior of a two-dimensional and confined in slitlike pores square-shoulder, square-well fluid. J Chem Phys 2010; 132:164702. [DOI: 10.1063/1.3392744] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Taylor MP, Paul W, Binder K. Phase transitions of a single polymer chain: A Wang-Landau simulation study. J Chem Phys 2010; 131:114907. [PMID: 19778149 DOI: 10.1063/1.3227751] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A single flexible homopolymer chain can assume a variety of conformations which can be broadly classified as expanded coil, collapsed globule, and compact crystallite. Here we study transitions between these conformational states for an interaction-site polymer chain comprised of N=128 square-well-sphere monomers with hard-sphere diameter sigma and square-well diameter lambdasigma. Wang-Landau sampling with bond-rebridging Monte Carlo moves is used to compute the density of states for this chain and both canonical and microcanonical analyses are used to identify and characterize phase transitions in this finite size system. The temperature-interaction range (i.e., T-lambda) phase diagram is constructed for lambda<or=1.30. Chains assume an expanded coil conformation at high temperatures and a crystallite structure at low temperatures. For lambda>1.06 these two states are separated by an intervening collapsed globule phase and thus, with decreasing temperature a chain undergoes a continuous coil-globule (collapse) transition followed by a discontinuous globule-crystal (freezing) transition. For well diameters lambda<1.06 the collapse transition is pre-empted by the freezing transition and thus there is a direct first-order coil-crystal phase transition. These results confirm the recent prediction, based on a lattice polymer model, that a collapsed globule state is unstable with respect to a solid phase for flexible polymers with sufficiently short-range monomer-monomer interactions.
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Affiliation(s)
- Mark P Taylor
- Department of Physics, Hiram College, Hiram, Ohio 44234, USA.
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50
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