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Marienhagen P, Wagner J. Reexamining equations of state of oblate hard ellipsoids of revolution: Numerical simulation utilizing a cluster Monte Carlo algorithm and comparison to virial theory. Phys Rev E 2022; 105:014125. [PMID: 35193301 DOI: 10.1103/physreve.105.014125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/05/2022] [Indexed: 06/14/2023]
Abstract
We provide highly accurate equation-of-state data determined by means of cluster Monte Carlo simulations for the isotropic phase of oblate hard ellipsoids of revolution. Both equation-of-state data and phase boundaries of the isotropic phase are obtained from relatively large ensembles with typically 1000 particles. The comparison of simulation data with a virial approach gives evidence for the importance of high-order so-far-unknown virial coefficients and therewith many-particle interactions in dense, isotropic systems of anisotropic particles. While a virial approach with a rescaled Carnahan-Starling correction for the unknown, higher-order virial coefficients reproduces the simulation data of moderately anisotropic particles with high accuracy, we suggest for highly anisotropic shapes a simple, heuristic equation of state as a suitable approach.
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Affiliation(s)
| | - Joachim Wagner
- Institut für Chemie, Universität Rostock, 18059 Rostock, Germany
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2
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Kumari S, Ye F, Podgornik R. Ordering of adsorbed rigid rods mediated by the Boussinesq interaction on a soft substrate. J Chem Phys 2020; 153:144905. [PMID: 33086810 DOI: 10.1063/5.0022556] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Orientational ordering driven by mechanical distortion of soft substrates plays a major role in material transformation processes such as elastocapillarity and surface anchoring. We present a theoretical model of the orientational response of anisotropic rods deposited onto a surface of a soft, elastic substrate of finite thickness. We show that anisotropic rods exhibit a continuous isotropic-nematic phase transition, driven by orientational interactions between surface deposited rods. This interaction is mediated by the deformation of the underlying elastic substrate and is quantified by the Boussinesq solution adapted to the case of slender, surface deposited rods. From the microscopic rod-rod interactions, we derive the appropriate Maier-Saupe mean-field description, which includes the Boussinesq elastic free energy contribution due to the substrate elasticity, derive the conditions for the existence of a continuous orientational ordering transition, and discuss the implication of results in the soft (bio)system context.
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Affiliation(s)
- Sunita Kumari
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangfu Ye
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Rudolf Podgornik
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
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Bores C, Pettitt BM. Structure and the role of filling rate on model dsDNA packed in a phage capsid. Phys Rev E 2020; 101:012406. [PMID: 32069548 DOI: 10.1103/physreve.101.012406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Indexed: 06/10/2023]
Abstract
The conformation of DNA inside bacteriophages is of paramount importance for understanding packaging and ejection mechanisms. Models describing the structure of the confined macromolecule have depicted highly ordered conformations, such as spooled or toroidal arrangements that focus on reproducing experimental results obtained by averaging over thousands of configurations. However, it has been seen that more disordered states, including DNA kinking and the presence of domains with different DNA orientation can also accurately reproduce many of the structural experiments. In this work we have compared the results obtained through different simulated filling rates. We find a rate dependence for the resulting constrained states showing different anisotropic configurations. We present a quantitative analysis of the density distribution and the DNA orientation across the capsid showing excellent agreement with structural experiments. Second, we have analyzed the correlations within the capsid, finding evidence of the presence of domains characterized by aligned segments of DNA characterized by the structure factor. Finally, we have measured the number and distribution of DNA defects such as the emergence of bubbles and kinks as function of the filling rate. We find the slower the rate the fewer kink defects that appear and they would be unlikely at experimental filling rates with our model parameters. DNA domains of various orientation get larger with slower rates.
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Affiliation(s)
- Cecilia Bores
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston Tx, 77555, USA
| | - B Montgomery Pettitt
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston Tx, 77555, USA
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Noya EG, Almarza NG, Lomba E. Assembly of trivalent particles under confinement: from an exotic solid phase to a liquid phase at low temperature. SOFT MATTER 2017; 13:3221-3229. [PMID: 28398440 DOI: 10.1039/c7sm00217c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Using computer simulations, we study the phase diagram of a two-dimensional system of disk particles with three patches distributed symmetrically along the particle equator. The geometry of the particles is compatible with a honey-comb lattice at moderately low temperature and pressure, whereas it is expected that the system forms a close-packed triangular lattice at high temperature and pressure. The effect of patch size within the single bond per patch regime was investigated, and it was found that the topology of the phase diagram changes drastically with patch size. Interestingly, in particles with small patches (with a half opening angle of 10°), the fluid transforms upon increasing the pressure into a rather exotic phase that can be understood as a honey-comb lattice whose voids are filled continuously with additional particles that remain, on average, unbound. Eventually, all the voids are occupied so that particles are located at the positions of a triangular lattice, but only two thirds of the particles are orientationally ordered whereas the remaining one third can rotate almost freely as in a plastic crystal. At moderately low temperature, the fluid transforms into a nearly empty honey-comb lattice, whereas at high temperature it transforms directly into the almost filled lattice. Interestingly, for particles with big patches (with a half opening angle of 20°), the honey-comb and triangular lattices are separated by a liquid phase that remains stable down to fairly low temperatures. Less surprisingly, only particles with big patches exhibit an equilibrium gas-liquid separation.
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Affiliation(s)
- Eva G Noya
- Instituto de Química Física Rocasolano, Consejo Superior de Investigaciones Cientficas, CSIC, Calle Serrano 119, 28026 Madrid, Spain.
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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: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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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: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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: 0.8] [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.
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Affiliation(s)
- N G Almarza
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain
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Almarza NG, Tavares JM, Simões M, Telo da Gama MM. The condensation and ordering of models of empty liquids. J Chem Phys 2011; 135:174903. [DOI: 10.1063/1.3657406] [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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Almarza N, Noya E. Phase transitions of a lattice model for patchy particles with tetrahedral symmetry. Mol Phys 2011. [DOI: 10.1080/00268976.2010.523521] [Citation(s) in RCA: 9] [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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Almarza NG, Martín C, Lomba E. Phase behavior of the confined Lebwohl-Lasher model. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2010; 82:011140. [PMID: 20866598 DOI: 10.1103/physreve.82.011140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2009] [Revised: 04/19/2010] [Indexed: 05/29/2023]
Abstract
The phase behavior of confined nematogens is studied using the Lebwohl-Lasher model. For three-dimensional systems the model is known to exhibit a discontinuous nematic-isotropic phase transition, whereas the corresponding two-dimensional systems apparently show a continuous Berezinskii-Kosterlitz-Thouless-like transition. In this paper, we study the phase transitions of the Lebwohl-Lasher model when confined between planar slits of different widths in order to establish the behavior of intermediate situations between the pure planar model and the three-dimensional system, and compare with previous estimates for the critical thickness, i.e., the slit width at which the transition switches from continuous to discontinuous.
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Affiliation(s)
- N G Almarza
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain
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Almarza NG, Gallardo A, Martín C, Guil JM, Lomba E. Topological considerations on microporous adsorption processes in simple models for pillared interlayered clays. J Chem Phys 2009; 131:244701. [PMID: 20059093 DOI: 10.1063/1.3273209] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The microporous structure of pillared interlayered clays is determined by their interlayer separation and the distribution of the pillars that separate their layers. The pillars provide stability to these quasi-two-dimensional high surface area materials. In this work we present a topological analysis of available and accessible volumes within various simple models of pillared interlayered clays. Each model is characterized by a distribution of pillars. Both fully ordered structures and disordered pillar distributions with either attractive or repulsive interpillar correlations are considered. Particular attention is paid to the problem of accessibility. In systems with similar degrees of porosity, even when cavities within each model might be able to host the same adsorbate molecules, their accessibility will strongly depend on the pillar distribution. The theoretical analysis presented in this work may facilitate the interpretation of experimental results, pointing out those quantities that are key to describe the texture of the porous material.
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Affiliation(s)
- N G Almarza
- Instituto de Química-Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain.
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Almarza NG, Capitán JA, Cuesta JA, Lomba E. Phase diagram of a two-dimensional lattice gas model of a ramp system. J Chem Phys 2009; 131:124506. [DOI: 10.1063/1.3223999] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Almarza NG, Martín C, Lomba E. Phase behavior of the hard-sphere Maier-Saupe fluid under spatial confinement. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009; 80:031501. [PMID: 19905114 DOI: 10.1103/physreve.80.031501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2009] [Indexed: 05/28/2023]
Abstract
The Maier-Saupe hard-sphere fluid is one of the simplest models that accounts for the isotropic-nematic transition characteristic of liquid crystal phases. At low temperatures the model is known to present a gas-liquid-like transition with a large difference between the densities of the coexistence phases, whereas at higher temperature the transition becomes a weak first-order transition resembling the typical order-disorder (nematic-isotropic) phase change of liquid crystals. Spatial dimensionality directly conditions the character of the orientational phase change (i.e., the high temperature transition), that goes from a first-order transition in the purely three-dimensional case, to a Berezinskii-Kosterlitz-Thouless-like continuous transition which occurs when the three dimensional Maier-Saupe spins are constrained to lie on a plane. In the latter instance, the ordered phase is not endowed with true long-range order. In this work we investigate how the continuous transition transforms into a true first-order phase change, by analyzing the phase behavior of a system of three dimensional Maier-Saupe hard spheres confined between two parallel plates, with separations ranging from the quasi-two-dimensional regime to the bulk three-dimensional limit. Our results indicate that spatial confinement in one direction induces the change from first order to a continuous transition with a corresponding decrease of the transition temperatures. As to the gas-liquid transition, the estimated "critical" temperatures and densities also decrease as the fluid is confined, in agreement with previous results for other simple systems.
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Affiliation(s)
- N G Almarza
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain
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Almarza NG, Lomba E, Martín C, Gallardo A. Demixing in binary mixtures of apolar and dipolar hard spheres. J Chem Phys 2008; 129:234504. [DOI: 10.1063/1.3039512] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Chamati H, Romano S. Topological transitions in two-dimensional lattice models of liquid crystals. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008; 77:051704. [PMID: 18643084 DOI: 10.1103/physreve.77.051704] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/29/2008] [Indexed: 05/26/2023]
Abstract
The phase diagram of hard-core nematogenic models in three-dimensional space can be studied by means of Onsager's theory, and, on the other hand, the critical properties of continuous interaction potentials can be investigated using the molecular field approach pioneered by Maier and Saupe. Comparison between these treatments shows a certain formal similarity, reflecting their common variational root; on this basis, hard-core potential models can be mapped onto continuous ones, via their excluded volume. Some years ago, this line of reasoning had been applied to hard spherocylinders, hence the continuous potential G(tau)=a+bsqrt[1-tau{2}], b>0 had been used to define a mesogenic model on a three-dimensional lattice [S. Romano, Int. J. Mod. Phys. B 9, 85 (1995)]; in the formula, tau denotes the scalar product between the two unit vectors defining particle orientations. Here we went on by addressing the same interaction potential on a two-dimensional lattice. Our analysis based on extensive Monte Carlo simulations found evidence of a topological transition, and the critical behavior in its vicinity was studied in detail. Results obtained for the present model were compared with those already obtained in the literature for interaction potentials defined by Legendre polynomials of second and fourth orders in the scalar product tau.
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Affiliation(s)
- H Chamati
- Institute of Solid State Physics, Bulgarian Academy of Sciences, 72 Tzarigradsko Chaussée, 1784 Sofia, Bulgaria
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Lomba E, Almarza NG, Martín C. Phase behavior of a family of continuous two-dimensional n -vector models with n=2, 3, and 4. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 76:061107. [PMID: 18233814 DOI: 10.1103/physreve.76.061107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2007] [Indexed: 05/25/2023]
Abstract
In this work we investigate the phase behavior of a family of continuous bidimensional n -vector models (with n=2, 3, and 4) using Monte Carlo simulation. In all cases we detect the presence of a defect mediated order-disorder transition of the Berezinskii-Kosterlitz-Thouless type with critical temperatures that decrease with the spin dimensionality. Coupled with the order-disorder transition a gas-liquid equilibrium is found at low temperatures. Here one observes that the stability region of the liquid phase shrinks with the growing spin dimensionality, in parallel with a decrease in magnitude of the angular averaged spin-spin interaction.
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Affiliation(s)
- E Lomba
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, Madrid, Spain
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Lomba E, Almarza NG, Martín C, McBride C. Phase behavior of attractive and repulsive ramp fluids: Integral equation and computer simulation studies. J Chem Phys 2007; 126:244510. [PMID: 17614567 DOI: 10.1063/1.2748043] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Using computer simulations and a thermodynamically self-consistent integral equation we investigate the phase behavior and thermodynamic anomalies of a fluid composed of spherical particles interacting via a two-scale ramp potential (a hard core plus a repulsive and an attractive ramp) and the corresponding purely repulsive model. Both simulation and integral equation results predict a liquid-liquid demixing when attractive forces are present, in addition to a gas-liquid transition. Furthermore, a fluid-solid transition emerges in the neighborhood of the liquid-liquid transition region, leading to a phase diagram with a somewhat complicated topology. This solidification at moderate densities is also present in the repulsive ramp fluid, but in this case inhibits the fluid-fluid separation.
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Affiliation(s)
- E Lomba
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain
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Lomba E, Martín C, Almarza NG, Lado F. Phase behavior of a hard sphere Maier-Saupe nematogenic system in three dimensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2006; 74:021503. [PMID: 17025433 DOI: 10.1103/physreve.74.021503] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Indexed: 05/12/2023]
Abstract
We present a detailed computer simulation and integral equation study of the phase behavior of a nematogenic system composed of hard spheres with embedded three-dimensional Maier-Saupe spins. For this well-known system, we map the gas-liquid equilibrium, which is coupled to a first-order isotropic-nematic transition. The anisotropic integral equation theory is found to yield excellent agreement with the simulation data within the fluid regime. Additionally, we determine the fluid-solid equilibrium transition by means of computer simulation.
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Affiliation(s)
- E Lomba
- Instituto de Química Física Rocasolano, CSIC, Serrano 119, E-28006 Madrid, Spain
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