Trimers formed by hard spheres, HS, and square well, SW, particles, show a rich structural and phase behaviour. In this work we extend the first-order perturbation theory in order to allow for allosteric effects. The types considered are made of equal-diameter spheres with i) three square wells, ii) two square wells and one hard sphere, and iii) one square well and two hard spheres.
The phase behaviour of some of these systems presents a challenge to standard high-temperature perturbation theory, HTPT; because the phase split occurs at particularly low temperatures. This fact requires a reconsideration of truncated HTPT to incorporate a resummation scheme, which is done here by two alternative approaches. One is the resummation procedure introduced by Ghobadi and Elliot,[1] and the second was proposed by some of the authors of this work [2] based on the work of Sastre et al.[3]
A second difficulty presented by these systems is the need to take into account the allosteric effects due to the screening of one of the spherical sites in one molecule by the presence of the other centres. This effect has been proven to be almost negligible in hard-sphere dimers,[4] but is clearly enhanced when various SW interactions are present. In this case, the allosteric effect depends on the angle distended by the two bonds to the central sphere. The contribution to the free energy due to the formation of chains of three spheres is calculated in the spirit of Wertheim’s PT as is developed in Statistical Associating Fluid Theory, SAFT.[5]
The results of the extended PT are compared with the outcome of Discrete Molecular Dynamics calculations.
Acknowledgement. This work was supported by project Fronteras de la Ciencia FDC 2015-2 1450 of CONACYT, México.
References
[1] A.F. Ghobadi and J.R. Elliot, J. Chem. Phys., 143, 114107 (2015)
[2] F. del Río, O. Guzmán and F. Ordoñez-Martínez, Mol. Phys., 116, 2070-2082 (2018)
[3] F. Sastre, E. Moreno-Hilario, M.G. Sotelo-Serna and A. Gil-Villegas, Mol. Phys., 116, 2070-2082 (2018)
[4] D. Ghonasgi and W.G. Chapman, Mol. Phys., 80, 161-176 (1993)
[5] P. Paricaud, S. Varga and G. Jackson, J. Chem. Phys., 116, 351-360 (2018)
Arrest phenomena of colloidal systems is a very important issue on Soft Condensed Matter Physics. In this work we have systematically studied dynamical behavior and the structural aspects of 3D colloidal gels formed by amphiphilic "Janus" particles. To resolve the dynamics, we studied the Self-Intermediate Scattering Function obtained by Dynamic Light Scattering. Similarly, to resolve the structure, we have analyzed the Static Structure Factor obtained by Static Light Scattering. We discussed the results comparing to Computer Simulation.
The inhomogene over the surface Janus colloids inmerse in liquid cristal, perturbe the host and produce an gradient of concentration, we show with molecular dynamic, the origen of the elastic defect and the activation of Janus particles
The homogeneous cooling instability for granular particles with different shapes and different static and dynamic friction coefficients is explored. To understand the role of friction in the different cases, coefficients of restitution equal and different to zero are considered. In all cases, the total energy falls as the inverse time squared. However, energy equipartition is not held. Rotational kinetic energy falls monotonically, while, in some cases, translational kinetic energy is first slowly transformed into rotational energy and after a transient, it follows the same behavior as the total energy.
The main idea of this work is to persuit the self-assembly of nanoparticles through solutions dynamical equations of conserved and non-conserved fields. However, these equations are non-linear and coupling partial differential equations to both fields and we employed a numerical method to solve them. We made simulations varying the coupling parameter and the relative mobility of nanoparticles in the liquid crystal media. We analyzed the power spectrum as function of time and wave number to identify a linear and non-linear behavior in time and the structure sizes at the end of the simulations.
Consider a collection of independent Brownian particles in a potential. It is assumed that the well is very deep and initially the particles are inside the well. Physically it is expected that the particles will reach a state close to the equilibrium but will escape slowly through the barrier. Now the question is, what is the escape rate that this takes place? This is Kramers' escape rate problem.
A detailed analysis is made based on the Boltzmann equation of the conditions that specify the energy framework (Landau framework) in contrast to the particle framework (Eckart framework). Using the statistical averages, the relationship between the speed of the Landau frame and the heat flux is obtained in the non-relativistic case.
As a colloidal suspension interacts with an inhomogeneous distribution of light, the dynamics of the colloids is hindered because of the trapping effect associated with the locations of higher intensity. If the energy barrier associated with the external field is not too high, the particle is able to overcome the barrier and thus thermally-driven transitions takes place. In this work I will show the main features of anomalous diffusion of spherical colloids in periodical fields and also of colloidal molecules in random and periodic fields, focusing in the dynamical properties and comparing with a simple yet powerful monte carlo simulation based in the transition probability to overcome the energy barrier.
Kinetic theory and molecular dynamics simulatios are used to study a system of smooth “frozen” Janus-type disks which cannot rotate and are divided by their diameter into two sides of different inelasticities. Taking as a reference a system of colored elastic disks, we find differences in the behavior of the collisions once the anisotropy is included. A homogeneous state, akin to the homogeneous cooling state of granular gases, is seen to arise and the singular behavior of both the collisions and the precollisional correlations are highlighted.
In this work I review, various information theory measures of the approach to equilibrium in biological systems. In particular I studied the classical replicator equation, replicator-mutator equations, and generalized Lotka-Volterra equations. We will relate the parameters of the distribution with the preeminence of the neutral and niche processes. We will discuss these theoretical results and compare them with computational simulations of mathematical models that modulate the presence of one process over the other by the existence of one parameter. Finally, I will discuss an index that is related to the two parameters of the Beta-Cocho, which will allow us to establish the closeness of a transition between the two processes. This index could serve as an early warning signal of changes in an ecosystem.
HIV-1 Gag is a large multidomain poly-protein with flexible unstructured linkers connecting its globular subdomains. It is compact when in solution but assumes an extended conforma- tion when assembled within the immature HIV-1 virion. Here, we use molecular dynamics (MD) simulations to quantitatively characterize the intra-domain interactions of HIV-1 Gag. We find that the matrix (MA) domain and the C-terminal subdomain CActd of the CA capsid domain can form a bound state. The bound state, which is held together primarily by interac- tions between complementary charged and polar residues, stabilizes the compact state of HIV-1 Gag. We calculate the depth of the attractive free energy potential between the MA/ CActd sites and find it to be about three times larger than the dimerization interaction between the CActd domains. Sequence analysis shows high conservation within the newly- found intra-Gag MA/CActd binding site, as well as its spatial proximity to other well known elements of Gag –such as CActd’s SP1 helix region, its inositol hexaphosphate (IP6) binding site and major homology region (MHR), as well as the MA trimerization site. Our results point to a high, but yet undetermined, functional significance of the intra-Gag binding site. Recent biophysical experiments that address the binding specificity of Gag are interpreted in the context of the MA/CActd bound state, suggesting an important role in selective packag- ing of genomic RNA by Gag.
Drug delivery through therapeutic monoclonal (mAb) antibodies in the bloodstream represents a challenge task because these macromolecules deal with capillarity effects and with an increase in the viscosity due to the particle aggregation by means of the active sites of mAb. This is a problem of interest in the pharmaceutical industry and such phenomenon can be understood through the complex protein dynamical landscape and the ways in which the internal domain motion can influence their functionality. We are interested to achieve some signature of this phenomenology by means of a computer simulations through in an all atomistic model.
Study of wetting phenomena requires to determine the solid-vapor, liquid-vapor and solid-liquid tensions. Usually the liquid-vapor tension is determined by direct methods as the pendant drop, but the solid-vapor and solid-liquid tensions cannot be determinate directly. The Equation of State Theory and the Surface Tension Components are two approaches that can determine the S-V and S-L tensions based in different thermodynamic postulates. In this work we fabricated polystyrene rough surfaces by the phase separation method and characterized the geometric roughness area by atomic force microscopy (AFM). We proposed the usefulness of the EQS approach to determine effectives S-V and S-L tensions in rough surfaces, and we compare with results of the STC approach.
In this work we study the influence of roughness on solid–liquid interfacial tension measurements through coarse-graining simulations. Using the dissipative particle dynamics (DPD) method, we modeled rough surfaces characterized with an area factor, and three pure liquids: dimethyl–sulfoxide (DMSO), dimethyl–formamide (DMF) and methylene diiodide (MI). The solid–liquid interfacial tension (γ_sl^') is measured for the three interfaces and the effect of the roughness on the γ_sl^' is discussed. Additionally, making use of an equation of state and Young’s equation, solid–vapor surface tension (γ_sv^') and the Young’s contact angle (θ_Y) were calculated as a manner of predictions. Overall, we find two featured trends. At low area factor values, where γ_sl^', γ_sv^', θ_Y slightly varies. And at high area factor values, where the roughness causes an increase on the γ_sl^' and θ_Y, while the γ_sv^' is diminished as the area factor increase.
We study a macroscopic system of magnetic spherical particles under a time-dependent magnetic field. This field provides continuously to the particles of kinetic energy. As a result, the motions of the macroscopic particles present some similarities with the motions of atoms and molecules in glass or crystal forming systems. Early stages of nuclei formation below the critical size when aggregates are unstable are analyzed by determining and comparing different geometric parameters. The phase diagram of the system is also studied.
Different types of gold nanoparticles have been synthesized that great potential in medical applications such as medical imaging, bio-analytical sensing and photothermal therapy. However, their stability, polydispersity and biocompatibility are major issues of concern. For example, the synthesis of gold nanorods, obtained through the elongated micelle process, produce them with a high positive surface charge that is cytotoxic. While gold nanoshells are unstable and within a few weeks they decompose due to Ostwald ripening. In this work, we report the self-assembly of the capsid protein of cowpea chlorotic mottle virus (CCMV) around spherical gold nanoparticles, gold nanorods and gold nanoshells to form virus-like particles (VLPs). All gold nanoparticles were synthesized or treated to give them a negative surface charge, so they can interact with the positive N-terminus of the capsid protein leading to the formation of the VLPs. To induce the protein selfassembly around the negative gold nanoparticles, we use different pH and ionic strength conditions that were determined from the capsid protein phase diagram. The encapsidation with the viral capsid protein confers them better biocompatibility, stability, monodispersity and a new biological substrate on which one can introduce specific ligands towards particular cells, broadening the possibilities of medical application.
La función principal de la respiración es proporcionar oxígeno a los órganos del cuerpo y eliminar el di´oxido de carbono del mismo. La respiración es generada por una red neuronal localizada en el tallo cerebral ventrolateral. Esta región se conoce como el Complejo pre-Bötzinger. Los suspiros son perturbaciones de la respiración espontánea normal que actúan como un restablecedor general del sistema respiratorio, ya que regula varias propiedades mecánicas y químicas. La aplicación local de fármacos al Complejo pre-Bötzinger afecta el ritmo respiratorio. En este proyecto analizaremos registros de respiración in vitro en una rebanada de tallo cerebral que contiene el Complejo pre-Bötzinger, para clasificar los patrones de respiración y ver si el péptido bombesina incrementa de manera estable el ritmo respiratorio.
Within the context of micromagnetic theory, different types of mechanical and magnetic angular momentum couplings have been observed. In particular, Barnett demonstrated that a mechanical rotation of a demagnetized ferromagnet produces a net magnetization along the rotation axis, whereas Einstein and de Haas showed that the magnetic moment change of a ferromagnetic wire induces a mechanical torque, this magnetomechanical coupling is studied by the standard model of magnetic domain--wall (Landau--Lifshitz--Gilbert formalism). From the point of view of Linear Irreversible Thermodynamics (Onsager phenomenological relations), a unified description of the Barnett and Einstein--de Hass effects can be performed. In addition, by using a set of objective functions, we described the influence of some operation modes on the domain--wall motion.
In this work, we propose using a granular system as an alternative model to study active systems such as those formed by microorganisms, for example paramecium. Paramecium is a protozoan commonly used for the study of ciliate organisms. These have a swimming mechanism characterized by a random motion produced by small flagella in their body, which change the swimming direction according to the host-fluid temperature. We study the motion of Paramecium by analyzing their swimming in a quasi-two-dimensional system. The mean squared displacement and the diffusion coefficient at different temperatures and concentrations are determined. These observations are compared with the results obtained in a two-dimensional non-vibrating granular system. The dynamical and structural similarities found between both systems suggest that the granular system could be a good model of active matter.
The hard-sphere potential is widely used to study the physical properties, in and out of equilibrium [1], of many-body systems with competing time and length scales, such as the multicomponent colloidal hard-sphere dispersions. However, from simulation point view, the study of the dynamics of such systems possesses a challenge since the force at contact cannot be correctly treated in those conventional algorithms employed to investigate the (slow) transport properties of colloids. However, in a recent contribution [1], using the second virial coefficient it was possible to map the hard-sphere potential onto a continuous potential. The latter one can be then used in, for example, the standard Ermak-McCammon algorithm to describe the diffusive properties of colloidal particles. As it was shown in Ref. [1], this soft potential reproduces the thermodynamic properties of monocomponent colloidal hard-spheres. Moreover, colloids are susceptible to external potentials. This susceptibility has important consequences for the arrangement and dynamics of colloids; the behavior of the system will depend on the competing between the particle-particle and particle-potential interactions. There are several computer simulations and experimental contributions about the effect of a periodic external potential over the behavior of binary mixtures of hard spheres. However, most of them are related to the structural properties of the dispersion; the dynamical properties have only been studied from an experimental point of view.
Using a similar approach as in Ref. [1], in this work, the second virial coefficient is determined for multicomponent colloidal systems in order to obtain the potential parameters of a continuous potential that accurately describes the equation of state of several types of colloidal dispersions, namely, asymmetric binary mixtures of hard-spheres and polydisperse hard-spheres. Our results are compared with some well-known equations of state for multicomponent hard-spheres. Results for the statics and dynamics are also presented and discussed. Additionally, using the continuous potential the structure and dynamics of two-dimensional hard spheres subjected to a periodic external potential have been studied through Brownian dynamics computer simulations. Our results are compared with experimental data already reported in Ref. [2].
Bibliography:
[1] C. A. Báez, A. Torres-Carbajal, A. Villada Balbuena, J. Méndez Alcaraz, S. Herrera-Velarde, R. Castañeda-Priego. Using the second virial coefficient as a physical criterion to map the hard-sphere potential onto a continuous potential. J. Chem. Phys. 149, 164907 (2018).
[2] R. F. Capellmann, A. Khisameeva, F. Platten, S. U. Egelhaaf. Dense colloidal mixtures in an external sinusoidal potential. J. Chem. Phys. 148, 114903(2018).
Transport of colloids in crowded and disordered media has relevance in many fields, including transport in porous media, gels and motion of particles in biological systems for applications in drug release, filtration and transport in biological membranes. In this work, we investigate the transport of colloids moving through the void space of fractal-like structures fixed in space. We obtain colloid-colloid pair correlation functions and calculate the effective interactions between them. The resulting effective potential is attractive and long-range even when the real interaction between colloids and colloid-fractal is hard-core. Also, we perform Brownian Dynamics simulations and obtain long-time diffusion coeffcients as a function of both the colloid concentration and the fractal dimension of the aggregate. Those results show a fluid-solid transition when the diffusion coeffcient is 0.1, according to the Löwen criterion for freezing transition. On the other hand, the behavior of the intermediate scattering function shows a power law decay a long-times indicating a possible dynamical arrest.
We study a macroscopic system of magnetic spherical particles under a time-dependent magnetic field. This field provides continuously to the particles of kinetic energy. As a result, the motions of the macroscopic particles present some similarities with the motions of atoms and molecules in glass or crystal forming systems. Early stages of nuclei formation below the critical size when aggregates are unstable are analyzed by determining and comparing different geometric parameters. The phase diagram of the system is also studied.
One of the known routes to the gel formation consist in an instant quench inside the spinodal region. The computer simulation or theoretical studies requires the knowledge of the molecular interaction potential. Due to the great diversity and complexity of the gel formation systems is of interest to establish a description in terms of an isotropic pair potential, that allow us to qualitatively describes the gel phenomenology. In this work, we analyse the thermodynamic, structural and dynamical behaviour of fluids instantly quenched that are characterised by different model potentials. We identify that the fluid properties characterised by an interaction potential with a short attractive range and a long repulsive range reproduce the phenomenology observed in gels obtained trough non-equilibrium route.
The growing interest in anomalous thermodynamic properties of isotropic fluids has been followed by several attempts to implement an accurate and simple theoretical description of these phenomena. Here, we have performed an extensive Monte Carlo exploration of the thermodynamic properties and vapor-liquid equilibrium of the Lennard-Jones core softened potential with variable gaussian tail strengths $\lambda$ spanning fluids with short range attraction and long range repulsion to those with short range repulsion and long range attraction. The results have been compared with the theoretical framework provided by the Barker and Henderson perturbation theory evaluated at longer ranges than those usually employed in the literature. The correlation in close shells particles is also incorporated in an empirical way. The agreement between the theoretical approach and the simulation results are in quantitative agreement in most cases, but worsens when the gaussian tail is deep enough to provoke substantial modifications in the fluid structure. These structured radial distribution functions differ from those of typical atomic fluids in the liquid state and are the main responsible of the inaccuracy of the perturbative approach for quantitative purposes. Despite this drawback, we have successfully applied the theoretical treatment for predicting anomalies in fluid models that are in agreement with those reported in the literature. These results open the door for a wide use of perturbative treatments for predicting fluid anomalies if care is taken of the range of the perturbative approach and of the particle correlation within neighboring shells.
The hard-sphere potential is widely used to study the physical properties, in and out of equilibrium [1], of many-body systems with competing time and length scales, such as the multicomponent colloidal hard-sphere dispersions. However, from simulation point view, the study of the dynamics of such systems possesses a challenge since the force at contact cannot be correctly treated in those conventional algorithms employed to investigate the (slow) transport properties of colloids. However, in a recent contribution [1], using the second virial coefficient it was possible to map the hard-sphere potential onto a continuous potential. The latter one can be then used in, for example, the standard Ermak-McCammon algorithm to describe the diffusive properties of colloidal particles. As it was shown in Ref. [1], this soft potential reproduces the thermodynamic properties of monocomponent colloidal hard-spheres. Moreover, colloids are susceptible to external potentials. This susceptibility has important consequences for the arrangement and dynamics of colloids; the behavior of the system will depend on the competing between the particle-particle and particle-potential interactions. There are several computer simulations and experimental contributions about the effect of a periodic external potential over the behavior of binary mixtures of hard spheres. However, most of them are related to the structural properties of the dispersion; the dynamical properties have only been studied from an experimental point of view.
Using a similar approach as in Ref. [1], in this work, the second virial coefficient is determined for multicomponent colloidal systems in order to obtain the potential parameters of a continuous potential that accurately describes the equation of state of several types of colloidal dispersions, namely, asymmetric binary mixtures of hard-spheres and polydisperse hard-spheres. Our results are compared with some well-known equations of state for multicomponent hard-spheres. Results for the statics and dynamics are also presented and discussed. Additionally, using the continuous potential the structure and dynamics of two-dimensional hard spheres subjected to a periodic external potential have been studied through Brownian dynamics computer simulations. Our results are compared with experimental data already reported in Ref. [2].
References
[1] C. A. Báez, A. Torres-Carbajal, A. Villada Balbuena, J. Méndez Alcaraz, S. Herrera-Velarde, R. Castañeda-Priego. Using the second virial coefficient as a physical criterion to map the hard-sphere potential onto a continuous potential. J. Chem. Phys. 149, 164907 (2018).
[2] R. F. Capellmann, A. Khisameeva, F. Platten, S. U. Egelhaaf. Dense colloidal mixtures in an external sinusoidal potential. J. Chem. Phys. 148, 114903(2018).
In the inference and analysis of network models in the natural and social sciences, a lot of emphasis is given to the way in which we determine what are the most relevant interactions or links between the nodes or vertices in a graph. Several approaches for network reconstruction states very clearly why and how system components are related to form the (sometimes quite complex) structures in a network.
Little is discussed however regarding what (if any) is the possible role of the "missing links", those relations (edges in the graph) that our intuition on the system's phenomenology or the structure of the network dictate that should exist, but they are not present. Here we will discuss what kind of information we can derive about our model systems, and how to use it, in the context of a class of probabilistic networks known as Markov Random Fields by looking at those missing links as conditional independence conditions and developing an asymptotic theory based on Crámer functions and large deviations theory. We will show how to use such conditional independence relations as graphs to generate feature selection schemas in the analysis of large datasets.
A functional, H(f), that in equilibrium is the entropy is obtained by means of a variational procedure. This is inspired by the Hamilton principle and the Tolman's proposal. The out of equilibrium distribution functions is obtained. The equilibrium one is recovered in the appropriate conditions. Restrictions for an insulated system with inhomogeneities are imposed on the functional H in terms on the Lagrange multipliers. On these bases, a theoretical scheme to describe relaxation processes for discrete spectra systems is discussed.
By means of Monte Carlo computer simulations, we study the structure and the coordination number in colloidal dispersions composed of particles interacting with the Kern-Frenkel interaction potential. We mainly focus on the mechanisms of gelation in patchy colloidal systems and, in particular, we study the relationship between physical gelation and rigidity percolation, which here is assumed to occur when the coordination number takes the value of 2.4
Alzheimer's disease is a neurodegenerative disorder and the most common form of dementia. The etiology of AD remains unclear; researchers have focus in two possible answers, the aggregation of: a) amyloid beta peptide (which accumulate forming senile plaques) and b) tau proteins, located on the chromosome 17. Tau stabilizes the microtubules neurons, but in the hyper phosphorylation state, it lost this function and aggregation process begins. Tau protein is an intrinsically disordered protein, it means, that a well-defined structure has not been found, instead, they present a multitude of conformational states. This behavior makes difficult to obtain a description of the aggregates during the different phases of the aggregation process. Computational simulation using atomistic molecular dynamics (MD) can provide information of the aggregation dynamics, and thereby help in the interpretation of experimental results. In this work, we performed atomistic MD to analyze the structural properties of a tau protein and investigate the aggregation process of two tau proteins.
Aggregation of amyloid b peptides (AβP) forming fibrils and senile plaques is associated to numerous neurodegenerative disorders such as Alzheimer ́s diseases (AD). C60 fullerene derivatives are promising molecules to be used as inhibitors AβP aggregation. A series of C60 fullerene adducts were analyzed by means of molecular dynamics, to understand their behavior in water and their interactions with AβP. Tools such as density profiles and pair correlation functions are used to show its behavior in water. Dynamic Light Scattering experiments were also used to help us to better understand the phenomena.