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Virus symmetry-breaking, elasticity and self-assembly
Spherical crystals are elementary models of geometric frustration in materials, with important realizations in a range of systems from viral shells and fullerenes to particle- and molecular-coated droplets. Using continuum elasticity theory, we study the structure and elastic energy of ground states of crystalline caps conforming to a spherical surface. We find that the ground states with icosahedral subgroup symmetries in caps arise across a range of curvatures, even far from the closure point of complete shells. Furthermore, we use Monte Carlo simulations to investigate the kinetic pathway of the formation of viral shells (capsids) and find that the key to the formation of perfect icosahedral capsids is in the strength of elastic energy compared to the protein-protein interactions and the chemical potential of free subunits.
At the end of the talk, I discuss our efforts to understand the formation of SARS-CoV-2 particles in their host cells. In contrast to icosahedral viruses, the structures of coronaviruses are heterogeneous both in morphology and size, significantly complicating any theory of their formation.
SERS substrates based on plasmonic nano and superstructures for health and environmental applications
There is currently a high demand for ultrasensitive sensors for both health and environmental applications, and both areas are closely related. The detection of contaminants in food, water, and in general in the environment is essential since many of these contaminants are usually harmful to health, even at trace levels. On the other hand, the detection of cancer biomarkers and cancer cells in early stages of the disease is essential to have greater chances of success in eradicating it in the patient; and for this it is necessary to be able to detect biomarkers and cells at trace levels. In recent years, plasmonic nano and superstructures have played an important role in the development of new sensors with high detection capacity. This type of material can be used as Surface Enhanced Raman Spectroscopy (SERS) substrates. In this contribution, several strategies for the synthesis of plasmonic nano and superstructures will be presented, as well as evaluation of their performance as SERS substrates for the sensing of model molecules, contaminants, drugs, and prostate cancer cells. 1-5 Various synthetic strategies were used: chemical synthesis (including synthesis bicontinuous microemulsions), electrodeposition, electrophoresis and galvanic replacement reaction. Varied nanostructures and superstructures such as nanostars, nanodendrites decorated with nanoparticles, and hollow nanostructured polyhedrons, based on Au, Ag, or Cu and their combinations were synthesized. Some of the molecules sensed were: model molecules (rhodamine 6G, 4-aminothiophenol, crystal violet), emerging contaminants (bisphenol A and triclosan), antibiotics (tetracycline and vancomycin), and drugs (tramadol). In addition, by means of proper functionalization, prostate cancer cells (LNCaP) were also sensed. The obtained results demonstrate the high potential of plasmonic hierarchical nanostructures and superstructures for the development of ultrasensitive SERS-based sensors.
Materials Science and Nanofluidics Devices
The rise of physical research in nanofluidics is slowly moving towards applications in water desalination and purification, chemical separation, pharmaceutical processing, dialysis, biotechnology, food processing, fuel cells, energy harvesting, healthcare, among others. Transport across nanoporous membranes is governed by the solution diffusion mechanism, while selectivity arises from differences in the solubility and diffusivity of the permeating species. Important factors for effective separation are the thickness of the membrane, the shape of the pores, and the porosity of the membrane. An ideal membrane should combine an ultra-thin selective layer with high-density pores of the correct size to reduce energy consumption and thus, the final cost of separation processes.
2D materials, as graphene, graphene oxide, transition metal dichalcogenides, MXenes, etc., hold great promise for advancing nanofluidics research into applications. The properties of 2D materials, such as impermeability towards gases as He, high surface area, high mechanical and chemical stability, high heat, electrical, and charge transport, among others, made 2D materials the ideal platform for the construction of nanofluidic devices. Furthermore, stable colloidal dispersions of 2D materials allow the fabrication of membranes by simple vacuum filtration. In this talk, I will present the preparation of stable colloidal dispersions of 2D materials, the fabrication of pristine, combined, and functionalized membranes, and their performance in power, sensing, and separation applications. Membranes of 2D materials have the advantage that can be directly used as nanofluidic device avoiding the use of nanolithography technologies. Unfortunately, different problems must be faced, selectivity, clogging, and fouling in pores, are some of them. Materials science could contribute to solve these and other problems through the implementation of molecular strategies.
The effective force of synthetic microswimmers
Active colloids are force- and torque-free microparticles that move forward in a liquid medium because of self-generated slip flows near their surface. Despite the absence of real forces, it is common practice to assume that a spherical microswimmer behaves as if it is ‘pulled’ by an external force proportional to the self-propulsion velocity and known as the effective swimming force. However, active colloids are smarter than that, because the direction of the velocity vector changes as the particle rotates.
In this talk, I will show how the combination of effective swimming force and reorientation allows active Brownian particles to swim in complex environment, break free from confinements and counteract external fields. As examples, I will consider three situations: (1) active microbeads confined in optical traps, (2) microswimmers under gravity, and (3) active colloids in crowded two-dimensional environments. In (1), we prepare patchy colloids with homogeneous refractive index, actuate them under vertical AC fields, and look at their motion in harmonic laser potentials. In (2), we disperse catalytic microswimmers in fuel-enriched solutions of various density to tune their buoyant weight and observe their behaviour in bulk and near flat walls. In (3), we confine active particles in monolayers made of colloids with tuneable inter-particle interactions. Our results highlight that synthetic microswimmers can be viewed as driven Brownian particles with an additional degree of freedom.
Adhesion modulates cell migration, erythrocyte morphology and endothelial cell dynamics
One of the most fundamental abilities required for the sustainability of complex life forms is active cell migration, being essential in diverse processes from morphogenesis to leukocyte chemotaxis in immune response. The movement of a cell is the result of intricate mechanisms, that involve the coordination between mechanical forces, biochemical regulatory pathways, and environmental cues. We will present how adhesion can influence cell migration and cell morphology in different contexts. We start by exploring how adhesion and spatial restriction affect migration of a self-propelled droplet in dense fibrous media Implementing a phase-field model, we have measured in our simulation the cell's velocity and quantified its morphology as a function of the fibre density and of its adhesiveness to thematrix fibres. We then apply the model to tackle epithelial cell basal extrusion in the contextof hereditary diffuse gastric cancer. In this disease, E-cadherin-defective cells can be detectedinvading the adjacent stroma since very early stages. We have demonstrated that, aside fromloss of cell-cell adhesion, increased matrix attachment further improves cell extrusionefficiency. Importantly, we were able to show that the cylindrical structure of gastric glands is a major factor in the cell’s ability to disseminate, and that cell migration is as effective as tissue curvature allows. We then use this model to explore polarization and dynamics ofendothelial cells in a blood vessel. We show that we can simulate the endothelial cellpolarization and shape in a vessel by assuming that endothelial cells migrate in the bloodflow direction with variable velocities. We further explore cell morphology during spoutingangiogenesis. Finally, we present the alterations in red blood cell morphology resultant from erythrocyte-erythrocyte adhesion forces in the presence of fibrinogen. These forces were quantified and matched with experimental data. The changes observed on erythrocyte- erythrocyte interactions may give important insights about the pathophysiological relevance of fibrinogen and erythrocyte aggregation, since an increment on both may induce an impairment in microcirculatory blood flow.
Model of the human liver circulatory system
The liver is the largest organ within the body. It performs many important functions such as food digestion, energy storage and toxin removal. To perform these functions, the liver hasa peculiar circulatory system composed of two blood supply vascular networks, the microcirculation, and the drainage vascular network. The understanding of hemodynamics and hepatic vasculature is fundamental to study the affectations that liver diseases cause on them. We develop a model of the entire human liver circulatory system, from macrocirculation to microcirculation. We use physiological values on the dimensions and hemodynamics of the hepatic vascular system as model inputs, and we obtain results within the physiological range as well. We are able to obtain the blood flow and pressure at different key points of the vasculature. We emulate some liver vascular alterations and successfully reproduce their affectation on the hemodynamics, obtaining results according to those clinically observed.
Quantum Molecular Thermodynamics
In recent years there has been an increasing interest in mesoscopic and macroscopic systems that can exhibit quantum effects within a wide range of temperatures. In this talk we shall be concerned with recent advances on models for real substances where quantum effects are relevant in bulk and confined phases. A review will be presented on molecular simulation and quantum thermodynamic perturbation theory based on the path integral approach, that have been applied to the prediction of phase diagrams of quantum fluids, including the cases of associating behaviour due to hydrogen bonding and drop formation
Mobility dynamics of social insects
There is a growing interest in the study of mobility both in biology and physics that includes the dynamics of random and deterministic walkers that obey Levy statistics (LS) and superdiffusive transport. It has been found that animal mobility such as spider monkeys, humans, birds, fish, insects and many more are described by LS. The list of biological examples also includes individual cells (cancer), eye movements or even genetic mutations. In this presentation I will discuss recent results of experiments and models of mobility and interacting networks in termites to show how sociality influences mobility patterns and the emergence of LS in these insects
Decoupling of rotational and translational tracer diffusion in entangled polymeric matrices
Passive microrheology is a technique based on tracking the diffusion of a probe particle in a viscoelastic medium. In a homogeneous medium, the translation and rotation of a spherical particle are coupled, so that the ratio of the corresponding mean-square displacements is constant. However, if the particle is trapped within the matrix so that its diffusion is significantly hindered, the rotation may decouple from translation. As a result, the viscoelastic responses obtained from the two types of motion might not coincide. In the present contribution, we will discuss a gradual decoupling of rotational and translational tracer diffusion observed experimentally under restrained tracer dynamics conditions and non-zero matrix compressibility. A simple-model theory is suggested to explain the observed discrepancies in the microscopic viscoelasticity as provide by the two types of tracer diffusion.
Rigidity and Nonlocality in Dense Granular Materials
Rigidity is the ability of a system to resist imposed stresses before ultimately undergoing failure, and real granular materials exhibit a range of behaviors from local creep to bulk flow. Disordered materials often contain both rigid and floppy regions that complicate the utility of taking system-wide averages, and make continuum modeling challenging to achieve. I will talk about several frameworks (network science, rigidity percolation, vibrational modes) capable of connecting the internal structure of disordered materials to their rigidity and/or failure under loading, and describe how we apply these ideas to laboratory data on both disordered lattices and granular materials.
Numerical Evaluation of Depletion Forces.
Being effective interactions, depletion forces are not easy to measure in experimental or simulational settings. We show a consistent way of evaluating depletion forces in bidisperse or, in general, polydisperse colloidal mixtures, for any values of the densities of the components. The method works without confining the kinematics of the system, and therefore obtains the depletion forces in equilibrium and without needing the usual diluted limit. The forces obtained are Effective Pair Interactions, dependent therefore on density and temperature, and incorporate three- and many-body effects as averaged corrections. We validate the results obtained for these forces via Dynamical Simulation of the effective systems, and show how the Pair Distribution Functions agree up to numerical error. We show also the differences between these forces and the Mean Forces, as evaluated directly from Pair Distribution Functions.
Trapping active particles up to the limiting case: bacteria enclosed in a biofilm
Active matter systems are composed of constituents, each one in nonequilibrium, that consume energy in order to move [1]. A characteristic feature of active matter is collective motion leading to nonequilibrium phase transitions or large scale directed motion [2]. A number of recent works have featured active particles interacting with obstacles, either moving or fixed [3,4,5]. When an active particle encounters an asymmetric obstacle, different behaviours are detected depending on the nature of its active motion. On the one side, rectification effects arise in a suspension of run-and-tumble particles interacting with a wall of funnelled-shaped openings, caused by particles persistence length [6]. The same trapping mechanism could be responsible for the intake of microorganisms in the underground leaves [7] of Carnivorous plants [8]. On the other side, for aligning particles [9] interacting with a wall of funnelled-shaped openings, trapping happens on the (opposite) wider opening side of the funnels [10,11]. Interestingly, when funnels are located on a circular array, trapping is more localised and depends on the nature of the Vicsek model.
Active particles can be synthetic (such as synthetic active colloids) or alive (such as living bacteria). A prototypical model to study living microswimmers is P. fluorescens, a rod shaped and biofilm forming bacterium. Biofilms are microbial communities self-assembled onto external interfaces. Biofilms can be described within the Soft Matter physics framework [12] as a viscoelastic material consisting of colloids (bacterial cells) embedded in a cross-linked polymer gel (polysaccharides cross-linked via proteins/multivalent cations), whose water content vary depending on the environmental conditions. Bacteria embedded in the polymeric matrix control biofilm structure and mechanical properties by regulating its matrix composition. We have recently monitored structural features of Pseudomonas fluorescens biofilms grown with and without hydrodynamic stress [13,14]. We have demonstrated that bacteria are capable of self-adapting to hostile hydrodynamic stress by tailoring the biofilm chemical composition, thus affecting both the mesoscale structure of the matrix and its viscoelastic properties that ultimately regulate the bacteria-polymer interactions.
[1] C. Bechinger et al. Rev. Mod. Phys. 88, 045006 (2016) [2] T. Vicsek, A. Zafeiris Phys. Rep. 517, 71 (2012) [3] C. Bechinger, R. Di Leonardo, H. Lowen, C. Reichhardt, G. Volpe, and G. Volpe, Reviews of Modern Physics 88, 045006 (2016) [4] R Martinez, F Alarcon, DR Rodriguez, JL Aragones, C Valeriani The European Physical Journal E 41, 1 (2018) [5] DR Rodriguez, F Alarcon, R Martinez, J Ramírez, C Valeriani, Soft matter 16 (5), 1162 (2020) [6] C. O. Reichhardt and C. Reichhardt, Annual Review of Condensed Matter Physics 8, 51 (2017) [7] W Barthlott, S Porembski, E Fischer, B Gemmel Nature 392, 447 (1998) [8] C B. Giuliano, R Zhang, R.Martinez Fernandez, C.Valeriani and L.Wilson (in preparation, 2021) [9] R Martinez, F Alarcon, JL Aragones, C Valeriani Soft matter 16 (20), 4739 (2020) [10] P. Galajada, J. Keymer, P. Chaikin and R.Austin, Journal of bacteriology, 189, 8704 (2007). [11] M. Wan, C.O. Reichhardt, Z. Nussinov, and C. Reichhardt, Physical Review Letters 101, 018102 (2008). [12] J N. Wilking , T E. Angelini , A Seminara , M P. Brenner , and D A. Weitz MRS Bulletin 36, 385 (2011) [13]J Jara, F Alarcón, A K Monnappa, J Ignacio Santos, V Bianco, P Nie, M Pica Ciamarra, A Canales, L Dinis, I López-Montero, C Valeriani, B Orgaz, Frontiers in microbiology 11, 3460 (2021) [14] P Nie, F Alarcon, I López-Montero, B Orgaz, C Valeriani, M Pica Ciamarra Soft Material, 0, 1 (2021)
Effective temperatures, bridging the adiabatic limit far from equilibrium
Understanding and managing the influence that either external forces or non-equilibrated environments may have on physicochemical processes is one of the central questions to solve in order to generalize the transition state theory and, therefore, of central importance in chemical kinetics and transport theory. Here, we describe recent works allowing us to generalize Eyring’s equation based on the definition of an effective thermal energy (temperature) emerging from the coupling of both fast and slow dynamic variables analyzed within the generalized Langevin and the Fokker-Planck schemes. The introduction of the effective thermal energy enables one to restore an effective adiabatic separation of timescales leading to a renormalization of the generalized fluctuation–dissipation theorem. This procedure opens the possibility to deal with systems far away from equilibrium and has the significant consequence that Eyring’s equation may be used to treat systems under the influence of strong external forces.
New Dewetting Mechanisms Followed by Ostwald Ripening During Crystal Growth Observed in Ultrathin Organic films on Mica
Langmuir–Blodgett films have been proposed as the building blocks for many interesting applications, such as biological membranes models, as biosensors and passive layers in metal-insulator-semiconductor, among other. The high-surface-pressure mesophases in Langmuir monolayers of single chain surfactants are known to develop three-dimensional crystal-like structures from moderate to high surface pressure. Monolayers of single chain fatty acids form mesophases known as condensed solid (CS), solid (S) and super liquid (LS) at high surface pressure. However, little is known of their stability as transferred films. We transferred monolayers from these phases onto mica, and observe that these transferred monolayers start dewetting the solid substrate leading to the formation of three-dimensional crystallites. We report new dewetting mechanisms that depend on the molecular order of the precursor monolayer, which for each monolayer phase shows different dewetting patterns and crystal growth power laws. Furthermore, an Ostwald ripening process sets in when dewetting patterns of neighboring crystals merge in all cases. We also propose the minimum thickness of transferred film that can be thermodynamically stable. Our study points out to the importance in our understanding of the stability of these kinds of ultrathin organic films, in order to take advantage in new technological developments base on these films.
Lorena Romero, UAEMEX
Lorena Romero, UAEMEX
Technological applications of statistical thermodynamics for scaffolds in tissue engineering
Organ recovery and transplant are a very important issue nowadays. There have been different approaches to solve such an issue, from donners list to technological devices that con substitute, for a given time a certain organ. In our research group, our contributions have investigated about understanding and obtaining scaffolds for future applications. Our first incursion was in cornea scaffolds and now in pulmonary heart valves. Some of our results have shed light on bio-micromechanical properties that are important for the mechanic-transduction process for cellular growth. In addition, we have proposed a device that under controlled flux and thermodynamic parameters can incorporate thermophoretic traps to decellularize, or separate biomolecules in microfluidic devices and/or efficient transport phenomenon accounting the entropy generation for efficient biotechnological applications.
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