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Phys Rev E 2021 Dec;104(6-1):064606

Departamento de Ingeniería Física, División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, 37150 León, Guanajuato, Mexico.

During the past decade, there has been a hot debate about the physical mechanisms that determine when a colloidal dispersion approaches the gel transition. However, there is still no consensus on a possible unique route that leads to the conditions for the formation of a gel-like state. Based on gel states identified in experiments, Valadez-Pérez et al. [Phys. Rev. E 88, 060302(R) (2013)PLEEE81539-375510.1103/PhysRevE.88.060302] proposed rigidity percolation as the precursor of colloidal gelation in adhesive hard-sphere dispersions with coordination number 〈n_{b}〉 equal to 2.4. Although this criterion was originally established to describe mechanical transitions in network-forming molecular materials with highly directional interactions, it worked well to explain gel formation in colloidal suspensions with isotropic short-range attractive forces. Recently, this idea has also been used to account for the dynamical arrest experimentally observed in attractive spherocylinders. Then, by assuming that rigidity percolation also drives gelation in spherical colloids interacting with short-ranged and highly directional potentials, we locate the thermodynamic states where gelation seems to occur in dispersions made up of patchy colloids. To check whether the criterion 〈n_{b}〉=2.4 also holds in patchy colloidal systems, we apply the so-called bond-bending analysis to determine the fraction of floppy modes at some percolating clusters. This analysis confirms that the condition 〈n_{b}〉=2.4 is a good approximation to determine those percolating clusters that are either mechanically stable or rigid. Furthermore, our results point out that not all combinations of patches and coverages lead to a gel-like state. Additionally, we systematically study the structure and the cluster size distribution along those thermodynamic states identified as gels. We show that for high coverage values, the structure is very similar for systems that have the same coverage regardless the number or the position of the patches on the particle surface. Finally, by using dynamic Monte Carlo computer simulations, we calculate both the mean-square displacement and the intermediate scattering function at and in the neighborhood of the gel-like states.

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http://dx.doi.org/10.1103/PhysRevE.104.064606 | DOI Listing |

December 2021

J Phys Condens Matter 2022 Jan 13. Epub 2022 Jan 13.

Science and Engineering Division, University of Guanajuato - Leon Campus, Loma del Bosque 103, Leon de los Aldama, Guanajuato, 37150, MEXICO.

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, an intermediate-ranged square-shoulder and a long-ranged square-well. 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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http://dx.doi.org/10.1088/1361-648X/ac4b29 | DOI Listing |

January 2022

Appl Radiat Isot 2022 Feb 15;180:110067. Epub 2021 Dec 15.

Universidad de Guanajuato, División de Ciencias e Ingenierías, Loma del Bosque 103, 37150, León, Gto, Mexico. Electronic address:

The purpose of this work is to develop a material capable of detecting neutrons produced by photodisintegration in a linear accelerator for its medical use. In this study, we have developed a gel-like material doped with fluorescent organic particles. PPO at 1 wt% is used as primary dopant and POPOP as secondary one at 0.03 wt%. A set of four samples is produced, with boric acid concentrations of 0, 400, 800 and 1200 ppm. The viscoelastic properties of the material are characterized with rheological measurements, finding a gel-like behavior, i.e., a material that can keep its original shape if no stresses are applied, but can also be deformed by applying a moderate shear rate. Furthermore, the material was irradiated with gamma, electron, and neutron emission sources from Cs, Na, Co, Po, Sr and AmBe, and its response was measured in two different experimental settings, in two different institutions, for comparative purposes. From these measurements, one can clearly establish that the new material detects neutrons, electrons, and gammas within the MeV regions and below. Thus, our findings show that the developed material and its properties make it a promising technology for its use in a neutron detector.

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http://dx.doi.org/10.1016/j.apradiso.2021.110067 | DOI Listing |

February 2022

J Chem Phys 2021 Jul;155(3):034903

Dipartimento di Chimica and CSGI, Università di Firenze, 50019 Sesto Fiorentino, Italy.

We systematically investigated the structure and aggregate morphology of gel networks formed by colloid-polymer mixtures with a moderate colloid volume fraction and different values of the polymer-colloid size ratio, always in the limit of short-range attraction. Using the coordinates obtained from confocal microscopy experiments, we determined the radial, angular, and nearest-neighbor distribution functions together with the cluster radius of gyration as a function of size ratio and polymer concentration. The analysis of the structural correlations reveals that the network structure becomes increasingly less sensitive to the potential strength with the decreasing polymer-colloid size ratio. For the larger size ratios, compact clusters are formed at the onset of network formation and become progressively more branched and elongated with increasing polymer concentration/attraction strength. For the smallest size ratios, we observe that the aggregate structures forming the gel network are characterized by similar morphological parameters for different values of the size ratio and the polymer concentration, indicating a limited evolution of the gel structure with variations of the parameters that determine the interaction potential between colloids.

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http://dx.doi.org/10.1063/5.0052273 | DOI Listing |

July 2021

J Chem Phys 2021 Jul;155(2):024901

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Guanajuato, Mexico.

Depletion interactions between colloidal particles surrounded by smaller depletants are typically characterized by a strong attraction at contact and a moderately repulsive barrier in front of it that extends at distances similar to the size of the depletants; the appearance and height of the barrier basically depend on the concentration and, therefore, the correlation between depletants. From a thermodynamic point of view, the former can drive the system to phase separation or toward non-equilibrium states, such as gel-like states, but its effects on both local and global properties may be controlled by the latter, which acts as a kind of entropic gate. However, the latter has not been entirely analyzed and understood within the context of colloidal mixtures mainly driven by entropy. In this contribution, we present a systematic study of depletion forces in ternary mixtures of hard spherical particles with two species of depletants, in two and three dimensions. We focus the discussion on how the composition of the depletants becomes the main physical parameter that drives the competition between the attractive well and the repulsive barrier. Our results are obtained by means of the integral equation theory of depletion forces and techniques of contraction of the description adapted to molecular dynamics computer simulations.

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http://dx.doi.org/10.1063/5.0052369 | DOI Listing |

July 2021

J Chem Phys 2021 Feb;154(8):084902

Departamento de Ingeniería Física, División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico.

In this work, a new parameterization for the Statistical Association Fluid Theory for potentials of Variable Range (SAFT-VR) is coupled to the discrete potential theory to represent the thermodynamic properties of several fluids, ranging from molecular liquids to colloidal-like dispersions. In this way, this version of the SAFT-VR approach can be straightforwardly applied to any kind of either simple or complex fluid. In particular, two interaction potentials, namely, the Lennard-Jones and the hard-core attractive Yukawa potentials, are discretized to study the vapor-liquid equilibrium properties of both molecular and complex liquids, respectively. Our results are assessed with Monte Carlo computer simulations and available and accurate theoretical results based on the self-consistent Ornstein-Zernike approximation.

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http://dx.doi.org/10.1063/5.0037630 | DOI Listing |

February 2021

Phys Chem Chem Phys 2021 Feb;23(7):4404-4412

Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA. and Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, USA.

Critical Casimir force (CCF) is a solvent fluctuation introduced interaction between particles dispersed in a binary solvent. Recently, it has been demonstrated that the CCF induced attraction between particles can trigger particle size-sensitive aggregation, and has thus been used as an efficient way to purify nanoparticles by size. Here, combining small angle neutron scattering and dynamic light scattering, we investigate the effects of size and concentration on this particle size separation method. Increasing the particle concentration does not significantly affect the purification method, but the solvent composition needs to be adjusted for an optimized efficiency. This purification method is further demonstrated to work also very efficiently for systems with particle size ranging from 15 nm to about 50 nm with a very large size polydispersity. These results indicate that for both short-ranged and long-ranged attraction relative to the particle diameter, the CCF introduced particle aggregation is always size sensitive. This implies that particle aggregation is strongly affected by size polydispersity for many colloidal systems. We further propose a method to use light scattering to help identify the temperature range within which this particle purification method can work efficiently instead of using neutron scattering.

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http://dx.doi.org/10.1039/d0cp06136k | DOI Listing |

February 2021

J Chem Phys 2020 Dec;153(23):234901

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Mexico.

The Ewald method has been the cornerstone in molecular simulations for modeling electrostatic interactions of charge-stabilized many-body systems. In the late 1990s, Wolf and collaborators developed an alternative route to describe the long-range nature of electrostatic interactions; from a computational perspective, this method provides a more efficient and straightforward way to implement long-range electrostatic interactions than the Ewald method. Despite these advantages, the validity of the Wolf potential to account for the electrostatic contribution in charged fluids remains controversial. To alleviate this situation, in this contribution, we implement the Wolf summation method to both electrolyte solutions and charged colloids with moderate size and charge asymmetries in order to assess the accuracy and validity of the method. To this end, we verify that the proper selection of parameters within the Wolf method leads to results that are in good agreement with those obtained through the standard Ewald method and the theory of integral equations of simple liquids within the so-called hypernetted chain approximation. Furthermore, we show that the results obtained with the original Wolf method do satisfy the moment conditions described by the Stillinger-Lovett sum rules, which are directly related to the local electroneutrality condition and the electrostatic screening in the Debye-Hückel regime. Hence, the fact that the solution provided by the Wolf method satisfies the first and second moments of Stillinger-Lovett proves, for the first time, the reliability of the method to correctly incorporate the electrostatic contribution in charge-stabilized fluids. This makes the Wolf method a powerful alternative compared to more demanding computational approaches.

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http://dx.doi.org/10.1063/5.0033561 | DOI Listing |

December 2020

J Phys Condens Matter 2020 Nov 5;33(5). Epub 2020 Nov 5.

División de Ciencias e Ingenierías, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Mexico.

Condensed matter physics (CMP) seeks to understand the microscopic interactions of matter at the quantum and atomistic levels, and describes how these interactions result in both mesoscopic and macroscopic properties. CMP overlaps with many other important branches of science, such as chemistry, materials science, statistical physics, and high-performance computing. With the advancements in modern machine learning (ML) technology, a keen interest in applying these algorithms to further CMP research has created a compelling new area of research at the intersection of both fields. In this review, we aim to explore the main areas within CMP, which have successfully applied ML techniques to further research, such as the description and use of ML schemes for potential energy surfaces, the characterization of topological phases of matter in lattice systems, the prediction of phase transitions in off-lattice and atomistic simulations, the interpretation of ML theories with physics-inspired frameworks and the enhancement of simulation methods with ML algorithms. We also discuss in detail the main challenges and drawbacks of using ML methods on CMP problems, as well as some perspectives for future developments.

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http://dx.doi.org/10.1088/1361-648X/abb895 | DOI Listing |

November 2020

J Chem Phys 2020 May;152(20):204501

Departamento de Física Aplicada, CINVESTAV del IPN, A. P. 73 "Cordemex", 97310 Mérida, Yucatán, Mexico.

We investigate the static correlations of a dipolar fluid in terms of the irreducible coefficients of the spherical harmonic expansion of the static structure factor. To this end, we develop a theoretical framework based on a soft-core version of Wertheim's solution of the mean spherical approximation (MSA), which renders the analytical determination of such coefficients possible. The accuracy of this approximation is tested by a comparison against the results obtained with the assistance of extensive molecular dynamics simulations at different regimes of concentration and temperature. Crucial aspects for the comparison of the results provided by the two methods are carefully discussed, concerning the different reference frames used in theory and simulations to describe rotations and orientations, and leading to important differences in the behavior of correlation functions with the same combination of spherical harmonic indices. We find a remarkable agreement between the two approaches in the fluid regime, thus providing a first stringent comparison of the irreducible coefficients of the spherical harmonic expansion of the dipolar fluid's static structure factor, provided by the MSA theory and molecular dynamics simulations.

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http://dx.doi.org/10.1063/5.0004200 | DOI Listing |

May 2020

Soft Matter 2020 Jan 27;16(1):170-190. Epub 2019 Nov 27.

Departamento de Física Aplicada, CINVESTAV del IPN, A. P. 73 "Cordemex", 97310 Mérida, Yucatán, Mexico.

We report the combined results of molecular dynamics simulations and theoretical calculations concerning various dynamical arrest transitions in a model system representing a dipolar fluid, namely, N (soft core) rigid spheres interacting through a truncated dipole-dipole potential. By exploring different regimes of concentration and temperature, we find three distinct scenarios for the slowing down of the dynamics of the translational and orientational degrees of freedom: at low (η = 0.2) and intermediate (η = 0.4) volume fractions, both dynamics are strongly coupled and become simultaneously arrested upon cooling. At high concentrations (η≥ 0.6), the translational dynamics shows the features of an ordinary glass transition, either by compressing or cooling down the system, but with the orientations remaining ergodic, thus indicating the existence of partially arrested states. In this density regime, but at lower temperatures, the relaxation of the orientational dynamics also freezes. The physical scenario provided by the simulations is discussed and compared against results obtained with the self-consistent generalized Langevin equation theory, and both provide a consistent description of the dynamical arrest transitions in the system. Our results are summarized in an arrested states diagram which qualitatively organizes the simulation data and provides a generic picture of the glass transitions of a dipolar fluid.

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http://dx.doi.org/10.1039/c9sm00687g | DOI Listing |

January 2020

Phys Rev E 2019 Apr;99(4-1):042603

Institut für Materialphysik im Weltraum, Deutsches Zentrum für Luft-und Raumfahrt (DLR), Linder Höhe 51170, Köln, Germany.

We perform a systematic and detailed study of the glass transition in highly asymmetric binary mixtures of colloidal hard spheres, combining differential dynamic microscopy experiments, event-driven molecular dynamics simulations, and theoretical calculations, exploring the whole state diagram and determining the self-dynamics and collective dynamics of both species. Two distinct glassy states involving different dynamical arrest transitions are consistently described, namely, a double glass with the simultaneous arrest of the self-dynamics and collective dynamics of both species, and a single glass of large particles in which the self-dynamics of the small species remains ergodic. In the single-glass scenario, spatial modulations in the collective dynamics of both species occur due to the structure of the large spheres, a feature not observed in the double-glass domain. The theoretical results, obtained within the self-consistent generalized Langevin equation formalism, are in agreement with both simulations and experimental data, thus providing a stringent validation of this theoretical framework in the description of dynamical arrest in highly asymmetric mixtures. Our findings are summarized in a state diagram that classifies the various amorphous states of highly asymmetric mixtures by their dynamical arrest mechanisms.

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http://dx.doi.org/10.1103/PhysRevE.99.042603 | DOI Listing |

April 2019

J Chem Phys 2018 Oct;149(16):164907

Subdirección de Postgrado e Investigación, Instituto Tecnológico Superior de Xalapa, Sección 5A Reserva Territorial s/n, 91096 Xalapa, Veracruz, Mexico.

In the same sense as in the extended law of corresponding states [M. Noro and D. Frenkel, J. Chem. Phys. , 2941 (2000)], we propose the use of the second virial coefficient to map the hard-sphere potential onto a continuous potential. We show that this criterion provides accurate results when the continuous potential is used, for example, in computer simulations to reproduce the physical properties of systems with hard-core interactions. We also demonstrate that this route is straightforwardly applicable to any spatial dimension, does not depend on the particle density and, from a numerical point of view, is easy to implement.

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http://dx.doi.org/10.1063/1.5049568 | DOI Listing |

October 2018

Phys Rev Lett 2018 Jun;120(24):248004

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Guanajuato, Mexico.

Cluster morphology of spherical particles interacting with a short-range attraction has been extensively studied due to its relevance to many applications, such as the large-scale structure in amorphous materials, phase separation, protein aggregation, and organelle formation in cells. Although it was widely accepted that the range of the attraction solely controls the fractal dimension of clusters, recent experimental results challenged this concept by also showing the importance of the strength of attraction. Using Monte Carlo simulations, we conclusively demonstrate that it is possible to reduce the dependence of the cluster morphology to a single variable, namely, the reduced second virial coefficient, B_{2}^{*}, linking the local properties of colloidal systems to the extended law of corresponding states. Furthermore, the cluster size distribution exhibits two well-defined regimes: one identified for small clusters, whose fractal dimension, d_{f}, does not depend on the details of the attraction, i.e., small clusters have the same d_{f}, and another related to large clusters, whose morphology depends exclusively on B_{2}^{*}, i.e., d_{f} of large aggregates follows a master curve, which is only a function of B_{2}^{*}. This physical scenario is confirmed with the reanalysis of experimental results on colloidal-polymer mixtures.

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http://dx.doi.org/10.1103/PhysRevLett.120.248004 | DOI Listing |

June 2018

Phys Chem Chem Phys 2018 Mar;20(10):6917-6928

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico.

We report on the friction and diffusion of a single mobile nano-colloidal disk, whose size and mass are one and two orders of magnitude, respectively, greater than the molecules of the host solvent; all particles are restricted to move in a two-dimensional space. Using molecular dynamics simulations, the variation of the transport coefficients as a function of the thermodynamic state of the supporting fluid, in particular, around those states in the neighbourhood of the liquid-liquid phase coexistence, is investigated. The diffusion coefficient is determined through the fit of the mean-square displacement at long times and with the Green-Kubo relationship for the velocity autocorrelation function, whereas the friction coefficient is computed from the correlation of the fluctuating force. From the determination of the transport properties, the applicability of the Stokes-Einstein relation in two dimensions around the second critical point is discussed.

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http://dx.doi.org/10.1039/c7cp08302e | DOI Listing |

March 2018

J Chem Phys 2017 Apr;146(16):164902

Division of Sciences and Engineering, Campus León, University of Guanajuato, Loma del Bosque 103, 37150 León, Mexico.

The study of the effects associated with the electrostatic properties of DNA is of fundamental importance to understand both its molecular properties at the single molecule level, like the rigidity of the chain, and its interaction with other charged bio-molecules, including other DNA molecules; such interactions are crucial to maintain the thermodynamic stability of the intra-cellular medium. In the present work, we combine the Poisson-Boltzmann mean-field theory with an irreversible thermodynamic approximation to analyze the effects of counterion accumulation inside DNA on both the denaturation profile of the chain and the equation of state of the suspension. To this end, we model the DNA molecule as a porous charged cylinder immersed in an aqueous solution. These thermo-electrostatic effects are explicitly studied in the particular case of some genes for which damage in their sequence is associated with diffuse large B-cell lymphoma.

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http://dx.doi.org/10.1063/1.4981208 | DOI Listing |

April 2017

Soft Matter 2017 Feb;13(6):1096-1106

Dipartimento di Fisica, Universitá di Camerino, I-62032 Camerino, Italy.

The term single file (SF) dynamics refers to the motion of an assembly of particles through a channel with cross-sections comparable to the particles' diameter. Single file diffusion (SFD) is then the diffusion of a tagged particle in a single file, i.e., under the condition that particle passing is not allowed. SFD accounts for a large variety of processes in nature, including diffusion of colloids in synthetic and natural channels, biological motors along molecular chains, electrons in proteins and liquid helium, ions through membranes, just to mention a few examples. Albeit introduced in 1965s, over the last decade the classical notion of SF dynamics has been generalised to account for a more realistic modelling of the particle properties, file geometry, particle-particle and channel-particle interactions, which paves the way to remarkable applications of the SF model, for instance, in the technology of bio-integrated nanodevices. We provide here a comprehensive review of the recent advances in the theory of SF dynamics with the purpose of spurring further experimental work.

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http://dx.doi.org/10.1039/c6sm02570f | DOI Listing |

February 2017

Soft Matter 2016 Nov;12(46):9303-9313

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico.

Colloidal gels formed by colloid-polymer mixtures with an intermediate volume fraction (ϕ ≈ 0.4) are investigated by confocal microscopy. In addition, we have performed Monte Carlo simulations based on a simple effective pair potential that includes a short-range attractive contribution representing depletion interactions, and a longer-range repulsive contribution describing the electrostatic interactions due to the presence of residual charges. Despite neglecting non-equilibrium effects, experiments and simulations yield similar gel structures, characterised by, e.g., the pair, angular and bond distribution functions. We find that the structure hardly depends on the strength of the attraction if the electrostatic contribution is fixed, but changes significantly if the electrostatic screening is changed. This delicate balance between attractions and repulsions, which we quantify by the second virial coefficient, also determines the location of the gelation boundary.

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http://dx.doi.org/10.1039/c6sm01822j | DOI Listing |

November 2016

Soft Matter 2016 Nov;12(44):9047-9057

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, Mexico.

The peculiarity of a bounded pair potential in combination with strong confinement brings some quite interesting new phenomenology in the structure and dynamics of one-dimensional colloidal systems. Such behaviour is atypical in comparison with colloidal systems interacting with potentials that diverge at the origin. In this contribution, by means of molecular dynamics simulations, a confined one-dimensional model of particles interacting via a Gaussian-core pair potential is studied. We explore the effects of confinement, density and temperature on the structural and dynamical correlation functions. Our findings indicate that the static and dynamic liquid-state anomalies already reported in open systems are also present in this 1D model system. Using the radial distribution function and the static structure factor to characterise the spatial ordering, it is observed that the system remains fluid at all densities. However, when the reduced temperature is above 0.03, it displays typical features of a liquid regime, i.e., there exist short-range spatial correlations among particles. In contrast, at lower temperatures and densities, where the particle-particle interaction dominates, the system behaves structurally and dynamically similar to a hard-core repulsive system. In such a region, interestingly, there is a crossover from a liquid to a solid-like regime. At any given temperature, the system undergoes a sort of reentrant structural behaviour as the density increases. At either high densities or temperatures, particle correlations vanish, thus, the system exhibits structural and dynamical properties similar to those of an ideal gas. To examine a possible correlation between the structural anomalies and the diffusive behaviour, the mean-square displacement and the self-intermediate scattering function are also computed. From these observables, we establish the thermodynamic phase-space points where the dynamical behaviour is non-monotonic. In conjunction with the observed anomalous diffusion, we have found a dynamical crossover from single-file diffusion, which is characteristic of one-dimensional systems with a well-defined hard-core, to the ordinary Fickian diffusion present in open systems.

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http://dx.doi.org/10.1039/c6sm01558a | DOI Listing |

November 2016

J Chem Phys 2016 Sep;145(10):104905

División de Ciencias e Ingenierías, University of Guanajuato, Loma del Bosque 103, 37150 León, Mexico.

Depletion forces are a particular class of effective interactions that have been mainly investigated in binary mixtures of hard-spheres in bulk. Although there are a few contributions that point toward the effects of confinement on the depletion potential, little is known about such entropic potentials in two-dimensional colloidal systems. From theoretical point of view, the problem resides in the fact that there is no general formulation of depletion forces in arbitrary dimensions and, typically, any approach that works well in three dimensions has to be reformulated for lower dimensionality. However, we have proposed a theoretical framework, based on the formalism of contraction of the description within the integral equations theory of simple liquids, to account for effective interactions in colloidal liquids, whose main feature is that it does not need to be readapted to the problem under consideration. We have also shown that such an approach allows one to determine the depletion pair potential in three-dimensional colloidal mixtures even near to the demixing transition, provided the bridge functions are sufficiently accurate to correctly describe the spatial correlation between colloids [E. López-Sánchez et al., J. Chem. Phys. 139, 104908 (2013)]. We here report an extensive analysis of the structure and the entropic potentials in binary mixtures of additive hard-disks. In particular, we show that the same functional form of the modified-Verlet closure relation used in three dimensions can be straightforwardly employed to obtain an accurate solution for two-dimensional colloidal mixtures in a wide range of packing fractions, molar fractions, and size asymmetries. Our theoretical results are explicitly compared with the ones obtained by means of event-driven molecular dynamics simulations and recent experimental results. Furthermore, to assess the accuracy of our predictions, the depletion potentials are used in an effective one-component model to reproduce the structure of either the big or the small disks. This demonstrates the robustness of our theoretical scheme even in two dimensions.

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http://dx.doi.org/10.1063/1.4962423 | DOI Listing |

September 2016

Phys Rev E 2016 Jul 11;94(1-1):012608. Epub 2016 Jul 11.

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, México.

We report on the short-time dynamics in colloidal mixtures made up of monomers and dimers highly confined between two glass plates. At low concentrations, the experimental measurements of colloidal motion agree well with the solution of the Navier-Stokes equation at low Reynolds numbers; the latter takes into account the increase in the drag force on a colloidal particle due to wall-particle hydrodynamic forces. More importantly, we find that the ratio of the short-time diffusion coefficient of the monomer and that of the center of mass of the dimmer is almost independent of both the dimer molar fraction, x_{d}, and the total packing fraction, ϕ, up to ϕ≈0.5. At higher concentrations, this ratio displays a small but systematic increase. A similar physical scenario is observed for the ratio between the parallel and the perpendicular components of the short-time diffusion coefficients of the dimer. This dynamical behavior is corroborated by means of molecular dynamics computer simulations that include explicitly the particle-particle hydrodynamic forces induced by the solvent. Our results suggest that the effects of colloid-colloid hydrodynamic interactions on the short-time diffusion coefficients are almost identical and factorable in both species.

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http://dx.doi.org/10.1103/PhysRevE.94.012608 | DOI Listing |

July 2016

Phys Chem Chem Phys 2016 Jul 27;18(26):17335-40. Epub 2016 May 27.

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, Lomas del Campestre, 37150 León, Guanajuato, México.

The physical properties of colloidal particles suspended in an aqueous environment are well-understood when the latter is considered to be a continuum and a structureless medium. However, this approach fails to explain complex phenomena, for example, the critical Casimir forces among colloids and the colloidal self-assembly near critical solvents, and the inertial contribution of the solvent molecules on the diffusion of non-spherical Brownian particles. Therefore, the role played by the solvent on the physical properties of colloidal dispersions is of paramount relevance. Recently, there has been an interest in the (non-trivial) diffusion mechanisms of a nano-colloidal particle in a solvent that undergoes a vapour-liquid transition. Nonetheless, the models typically used to incorporate the solvent details do not capture quantitatively the thermodynamic properties of real substances. It is then important to study the Brownian motion of colloids in more realistic models. To reach such goal, one first has to characterise the thermodynamic states and the microscopic features of the solvent. Hence, in this contribution, we have investigated the coexistence densities of a core-softened potential in two- and three-dimensions, whose potential parameters are able to capture some anomalies of water. We show that in the two-dimensional case, the potential model exhibits, besides the normal vapour-liquid coexistence region, additional liquid-liquid coexistence densities. We particularly focus our attention to the structural properties and the dynamical behaviour of the solvent around the liquid-liquid critical point and assess the differences with the three-dimensional case.

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http://dx.doi.org/10.1039/c6cp01565d | DOI Listing |

July 2016

Phys Chem Chem Phys 2015 Jul;17(29):19557-68

Brownian motion is a feature of colloidal particles immersed in a liquid-like environment. Usually, it can be described by means of the generalised Langevin equation (GLE) within the framework of the Mori theory. In principle, all quantities that appear in the GLE can be calculated from the molecular information of the whole system, i.e., colloids and solvent molecules. In this work, by means of extensive Molecular Dynamics simulations, we study the effects of the microscopic details and the thermodynamic state of the solvent on the movement of a single nano-colloid. In particular, we consider a two-dimensional model system in which the mass and size of the colloid are two and one orders of magnitude, respectively, larger than the ones associated with the solvent molecules. The latter ones interact via a Lennard-Jones-type potential to tune the nature of the solvent, i.e., it can be either repulsive or attractive. We choose the linear momentum of the Brownian particle as the observable of interest in order to fully describe the Brownian motion within the Mori framework. We particularly focus on the colloid diffusion at different solvent densities and two temperature regimes: high and low (near the critical point) temperatures. To reach our goal, we have rewritten the GLE as a second kind Volterra integral in order to compute the memory kernel in real space. With this kernel, we evaluate the momentum-fluctuating force correlation function, which is of particular relevance since it allows us to establish when the stationarity condition has been reached. Our findings show that even at high temperatures, the details of the attractive interaction potential among solvent molecules induce important changes in the colloid dynamics. Additionally, near the critical point, the dynamical scenario becomes more complex; all the correlation functions decay slowly in an extended time window, however, the memory kernel seems to be only a function of the solvent density. Thus, the explicit inclusion of the solvent in the description of Brownian motion allows us to better understand the behaviour of the memory kernel at those thermodynamic states near the critical region without any further approximation. This information is useful to elaborate more realistic descriptions of Brownian motion that take into account the particular details of the host medium.

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http://dx.doi.org/10.1039/c5cp02777b | DOI Listing |

July 2015

J Chem Phys 2015 May;142(17):174905

Condensed Matter Physics Laboratory, Heinrich Heine University, 40225 Düsseldorf, Germany.

The so-called extended law of corresponding states, as proposed by Noro and Frenkel [J. Chem. Phys. 113, 2941 (2000)], involves a mapping of the phase behaviors of systems with short-range attractive interactions. While it has already extensively been applied to various model potentials, here we test its applicability to protein solutions with their complex interactions. We successfully map their experimentally determined metastable gas-liquid binodals, as available in the literature, to the binodals of short-range square-well fluids, as determined by previous as well as new Monte Carlo simulations. This is achieved by representing the binodals as a function of the temperature scaled with the critical temperature (or as a function of the reduced second virial coefficient) and the concentration scaled by the cube of an effective particle diameter, where the scalings take into account the attractive and repulsive contributions to the interaction potential, respectively. The scaled binodals of the protein solutions coincide with simulation data of the adhesive hard-sphere fluid. Furthermore, once the repulsive contributions are taken into account by the effective particle diameter, the temperature dependence of the reduced second virial coefficients follows a master curve that corresponds to a linear temperature dependence of the depth of the square-well potential. We moreover demonstrate that, based on this approach and cloud-point measurements only, second virial coefficients can be estimated, which we show to agree with values determined by light scattering or by Derjaguin-Landau-Verwey-Overbeek (DLVO)-based calculations.

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http://dx.doi.org/10.1063/1.4919127 | DOI Listing |

May 2015

J Chem Phys 2015 Jan;142(2):024902

Division of Sciences and Engineering, Campus Leon, University of Guanajuato, Loma del Bosque 103, 37150 Leon, Mexico.

We report on the ordering and dynamics of interacting colloidal particles confined by a parabolic potential. By means of Brownian dynamics simulations, we find that by varying the magnitude of the trap stiffness, it is possible to control the dimension of the system and, thus, explore both the structural transitions and the long-time self-diffusion coefficient as a function of the degree of confinement. We particularly study the structural ordering in the directions perpendicular and parallel to the confinement. Further analysis of the local distribution of the first-neighbors layer allows us to identify the different structural phases induced by the parabolic potential. These results are summarized in a structural state diagram that describes the way in which the colloidal suspension undergoes a structural re-ordering while increasing the confinement. To fully understand the particle dynamics, we take into account hydrodynamic interactions between colloids; the parabolic potential constricts the available space for the colloids, but it does not act on the solvent. Our findings show a non-linear behavior of the long-time self-diffusion coefficient that is associated to the structural transitions induced by the external field.

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http://dx.doi.org/10.1063/1.4905215 | DOI Listing |

January 2015

Soft Matter 2014 Nov;10(42):8475-81

UPIIG-IPN, Mineral de Valenciana 200, 36275 Silao de la Victoria, Guanajuato, Mexico.

Interactions between membranes and molecules are important for many biological processes, e.g., transport of molecules across cell membranes. However, the detailed physical description of the membrane-biomolecule system remains a challenge and simplified schemes allow capturing its main intrinsic features. In this work, by means of Monte Carlo computer simulations, we systematically study the distribution of uncharged spherical molecules in contact with a flexible surface. Our results show that the distribution for finite size particles has the same simple functional form as the one obtained for point-like particles and depends only on the ratio of the lateral correlation length of the membrane and the radius of the molecules.

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http://dx.doi.org/10.1039/c4sm01550a | DOI Listing |

November 2014

J R Soc Interface 2014 Nov;11(100):20140827

Department of Computational Genomics, National Institute of Genomic Medicine, Mexico City, Mexico Complexity in Systems Biology, Center for Complexity Sciences, National Autonomous University of México, Mexico City, Mexico

DNA damage is one of the mechanisms of mutagenesis. Sequence integrity may be affected by the action of thermal changes, chemical agents, both endogenous and exogenous, and other environmental issues. Abnormally high mutation rates are referred to as genomic instability: a phenomenon closely related to the onset of cancer. Mutant genotypes may be able to confer some kind of selective advantage on subclonal cell populations, leading them to multiply until dominance in a localized tissue environment that later becomes the tumour. Cellular stress, especially that of oxidative and ionic nature, is a recognized trigger for DNA-damaging processes. A physico-chemical model has shown that high hysteresis rates in DNA denaturation curves may be indicative of dissipative processes inducing DNA damage, thus potentially leading to uncontrolled mutagenesis and genome instability. We here study selectively to what extent this phenomenon may occur by analysing the sequence length and composition effects on the thermodynamic behaviour and the presence of hysteresis in pressure-driven DNA denaturation; pronounced hysteresis in the denaturation/renaturation curves may indicate thermal susceptibility to DNA damage. In particular, we consider highly mutated regions of the genome characterized in diffuse large B-cell lymphoma on a recent whole exome next-generation sequencing effort.

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http://dx.doi.org/10.1098/rsif.2014.0785 | DOI Listing |

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4191112 | PMC |

November 2014

J Chem Phys 2014 Jun;140(24):244116

División de Ciencias e Ingenierías, Campus León, Universidad de Guanajuato, Loma del Bosque 103, 37150 León, Guanajuato, Mexico.

The long-time self-diffusion coefficient, D(L), of charged spherical colloidal particles in parallel planar layers is studied by means of Brownian dynamics computer simulations and mode-coupling theory. All particles (regardless which layer they are located on) interact with each other via the screened Coulomb potential and there is no particle transfer between layers. As a result of the geometrical constraint on particle positions, the simulation results show that D(L) is strongly controlled by the separation between layers. On the basis of the so-called contraction of the description formalism [C. Contreras-Aburto, J. M. Méndez-Alcaraz, and R. Castañeda-Priego, J. Chem. Phys. 132, 174111 (2010)], the effective potential between particles in a layer (the so-called observed layer) is obtained from integrating out the degrees of freedom of particles in the remaining layers. We have shown in a previous work that the effective potential performs well in describing the static structure of the observed layer (loc. cit.). In this work, we find that the D(L) values determined from the simulations of the observed layer, where the particles interact via the effective potential, do not agree with the exact values of D(L). Our findings confirm that even when an effective potential can perform well in describing the static properties, there is no guarantee that it will correctly describe the dynamic properties of colloidal systems.

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http://dx.doi.org/10.1063/1.4884822 | DOI Listing |

June 2014

J Chem Phys 2014 Jun;140(21):214115

Centro de Estudios en Física y Matemáticas Básicas y Aplicadas, Universidad Autónoma de Chiapas, Carretera Emiliano Zapata, Km. 8, Rancho San Francisco, C. P. 29050, Tuxtla Gutiérrez, Chiapas, México.

The many-particle Langevin equation, written in local coordinates, is used to derive a Brownian dynamics simulation algorithm to study the dynamics of colloids moving on curved manifolds. The predictions of the resulting algorithm for the particular case of free particles diffusing along a circle and on a sphere are tested against analytical results, as well as with simulation data obtained by means of the standard Brownian dynamics algorithm developed by Ermak and McCammon [J. Chem. Phys. 69, 1352 (1978)] using explicitly a confining external field. The latter method allows constraining the particles to move in regions very tightly, emulating the diffusion on the manifold. Additionally, the proposed algorithm is applied to strong correlated systems, namely, paramagnetic colloids along a circle and soft colloids on a sphere, to illustrate its applicability to systems made up of interacting particles.

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http://dx.doi.org/10.1063/1.4881060 | DOI Listing |

June 2014

Soft Matter 2014 Jul;10(28):5061-71

Center for Neutron Science, Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St, Newark, DE 19716, USA.

Colloidal liquids interacting with short range attraction and long range repulsion, such as proposed for some protein solutions, have been found to exhibit novel states consisting of equilibrium particle clusters. Monte Carlo simulations are performed for two physically meaningful inter-particle potentials across a broad range of interaction parameters, temperatures and volume fractions to locate the conditions where clustered states are found. A corresponding states phase behavior is identified when normalized by the critical point of an appropriately selected reference attractive fluid. Clustered fluid states and cluster percolated states are found exclusively within the two phase region of the state diagram for a reference attractive fluid, confirming the underlying intrinsic relation between clustered states and bulk phase separation. Clustered and cluster percolated states consistently exhibit an intermediate range order peak in their structure factors with a magnitude above 2.7, leading to a semi-empirical rule for identifying clustered fluids in scattering experiments.

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http://dx.doi.org/10.1039/c3sm53220h | DOI Listing |

July 2014

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