arXiv subjects

Juan J. de Pablo

Publications and source records attributed to Juan J. de Pablo.

At least 55 records · Page 3Linked to original sources

arXiv2021

Poisson's ratio and angle bending in spring networks

The Poisson's ratio of a spring network system has been shown to depend not only on the geometry but also on the relative strength of angle-bending forces in comparison to the bond-compression forces in the system. Here we derive the very simple analytic result that in systems where the spring interaction strength is equal to the bond-reorientation interaction, the Poisson's ratio identically goes to zero and is independent of the network geometry.

cond-mat.soft↗

arXiv2020

Molecular Characterization of Ebselen Binding Activity to SARS-CoV-2 Main Protease

The Coronavirus Disease (COVID-19) pandemic caused by the SARS-coronavirus 2 (SARS-CoV-2) urgently calls for the design of drugs directed against this new virus. Given its essential role in proteolytic processing, the main protease Mpro has been identified as an attractive candidate for drugs against SARS-CoV-2 and similar coronaviruses. Recent high-throughput screening studies have identified a set of existing, small-molecule drugs as potent Mpro inhibitors. Amongst these, Ebselen (2-Phenyl-1,2-benzoselenazol-3-one), a glutathione peroxidase mimetic seleno-organic compound, is particularly attractive. Recent experiments suggest that its effectiveness is higher than that of other molecules that also act at the enzyme catalytic site. By relying on extensive simulations with all-atom models, in this study we examine at a molecular level the potential of Ebselen to decrease Mpro catalytic activity. Our results indicate that Ebselen exhibits a distinct affinity for the catalytic site cavity of Mpro. In addition, our molecular models reveal a second, previously unkown binding site for Ebselen in the dimerization region localized between the II and III domains of the protein. A detailed analysis of the free energy of binding indicates that the affinity of Ebselen to this second binding site is in fact significantly larger than that to the catalytic site. A strain analysis indicates that Ebselen bound between the II-III domains exerts a pronounced allosteric effect that regulates catalytic site access through surface loop interactions, and induces a displacement and reconfiguration of water hotspots, including the catalytic water, which could interfere with normal enzymatic function. Taken together, these findings provide a framework for the future design of more potent and specific Mpro inhibitors, based on the Ebselen scaffold, that could lead to new therapeutic strategies for COVID-19.

q-bio.BM↗

arXiv2020

Structure and dynamics of hydrodynamically interacting finite-size Brownian particles in a spherical cavity: spheres and cylinders

The structure and dynamics of confined suspensions of particles of arbitrary shape is of interest in multiple disciplines, from biology to engineering. Theoretical studies are often limited by the complexity of long-range particle-particle and particle-wall forces, including many-body fluctuating hydrodynamic interactions. Here, we report a computational study on the diffusion of spherical and cylindrical particles confined in a spherical cavity. We rely on an Immersed-Boundary General geometry Ewald-like method to capture lubrication and long-range hydrodynamics, and include appropriate non-slip conditions at the confining walls. A Chebyshev polynomial approximation is used to satisfy the fluctuation-dissipation theorem for the Brownian suspension. We explore how lubrication, long-range hydrodynamics, particle volume fraction and shape affect the equilibrium structure and the diffusion of the particles. It is found that once the particle volume fraction is greater than $10\%$, the particles start to form layered aggregates that greatly influence particle dynamics. Hydrodynamic interactions strongly influence the particle diffusion by inducing spatially dependent short-time diffusion coefficients, stronger wall effects on the particle diffusion towards the walls, and a sub-diffusive regime --caused by crowding-- in the long-time particle mobility. The level of asymmetry of the cylindrical particles considered here is enough to induce an orientational order in the layered structure, decreasing the diffusion rate and facilitating a transition to the crowded mobility regime at low particle concentrations. Our results offer fundamental insights into the diffusion and distribution of globular and fibrillar proteins inside cells.

cond-mat.soft↗

arXiv2020

Shape induced segregation and anomalous particle transport under spherical confinement

Colloid or nanoparticle mobility under confinement is of central importance to a wide range of physical and biological processes. Here, we introduce a minimal model of particles in a hydrodynamic continuum to examine how particle shape and concentration affect the transport of particles in spherical confinement. Specifically, an immersed boundary-General geometry Ewald-like approach is adopted to simulate the dynamics of spheres and cylinders under the influence of short-and long-range fluctuating hydrodynamic interactions with appropriate non-slip conditions at the confining walls. An efficient $\it{O(N)}$ parallel finite element algorithm is used, thereby allowing simulations at high concentrations, while a Chebyshev polynomial approximation is implemented in order to satisfy the fluctuation-dissipation theorem. A concentration-dependent anomalous diffusion is observed for suspended particles. It is found that introducing cylinders in a background of spheres, i.e. particles with a simple degree of anisotropy, has a pronounced influence on the structure and dynamics of the particles. First, increasing the fraction of cylinders induces a particle segregation effect, where spheres are pushed towards the wall and cylinders remain near the center of the cavity. This segregation leads to lower mobility for the spheres relative to that encountered in a system of pure spheres at the same volume fraction. Second, the diffusive-to-anomalous transition and the degree of anomaly--quantified by the power-law exponent in the mean square displacement vs. time relation-both increase as the fraction of cylinders becomes larger. These findings are of relevance for studies of diffusion in the cytoplasm, where proteins exhibit a distribution of size and shapes that could lead to some of the effects identified in the simulations reported here.

cond-mat.soft↗

arXiv2020

Sculpting stable structures in pure liquids

Pure liquids in thermodynamic equilibrium are structurally homogeneous. In liquid crystals, flow and light pulses are used to create reconfigurable domains with polar order. Moreover, through careful engineering of concerted microfluidic flows and localized opto-thermal fields, it is possible to achieve complete control over the nucleation, growth, and shape of such domains. Experiments, theory, and simulations indicate that the resulting structures can be stabilized indefinitely, provided the liquids are maintained in a controlled non-equilibrium state. The resulting sculpted liquids could find applications in microfluidic devices for selective encapsulation of solutes and particles into optically active compartments that interact with external stimuli.

cond-mat.soft↗

arXiv2019

Structuring Stress for Active Materials Control

Active materials are capable of converting free energy into mechanical work to produce autonomous motion, and exhibit striking collective dynamics that biology relies on for essential functions. Controlling those dynamics and transport in synthetic systems has been particularly challenging. Here, we introduce the concept of spatially structured activity as a means to control and manipulate transport in active nematic liquid crystals consisting of actin filaments and light-sensitive myosin motors. Simulations and experiments are used to demonstrate that topological defects can be generated at will, and then constrained to move along specified trajectories, by inducing local stresses in an otherwise passive material. These results provide a foundation for design of autonomous and reconfigurable microfluidic systems where transport is controlled by modulating activity with light.

cond-mat.soft↗

arXiv2019

Ideal isotropic auxetic networks from random networks

Auxetic materials are characterized by a negative Poisson's ratio, $\mathrmν$. As the Poisson's ratio becomes negative and approaches the lower isotropic mechanical limit of $\mathrm{ν= -1}$, materials show enhanced resistance to impact and shear, making them suitable for applications ranging from robotics to impact mitigation. Past experimental efforts aimed at reaching the $\mathrm{ν= -1}$ limit have resulted in highly anisotropic materials, which show a negative Poisson's ratio only when subjected to deformations along specific directions. Isotropic designs have only attained moderately auxetic behavior, or have led to structures that cannot be manufactured in 3D. Here, we present a design strategy to create isotropic structures from disordered networks that leads to Poisson's ratios as low as $\mathrm{ν= -0.98}$. The materials conceived through this approach are successfully fabricated in the laboratory and behave as predicted. The Poisson's ratio $\mathrmν$ is found to depend on network structure and bond strengths; this sheds light on the structural motifs that lead to auxetic behavior. The ideas introduced here can be generalized to 3D, a wide range of materials, and a spectrum of length scales, thereby providing a general platform that could impact technology.

cond-mat.soft↗

arXiv2018

Tunable structure and dynamics of active liquid crystals

Active materials are capable of converting free energy into directional motion, giving rise to striking dynamical phenomena. Developing a general understanding of their structure in relation to the underlying non-equilibrium physics would provide a route towards control of their dynamic behavior and pave the way for potential applications. The active system considered here consists of a quasi-two-dimensional sheet of short ($\approx$ 1 $μ$m) actin filaments driven by myosin-II motors. By adopting a concerted theoretical and experimental strategy, new insights are gained into the non-equilibrium properties of active nematics over a wide range of internal activity levels. In particular, it is shown that topological defect interactions can be led to transition from attractive to repulsive as a function of initial defect separation and relative orientation. Furthermore, by examining the +1/2 defect morphology as a function of activity, it is found that the apparent elastic properties of the system (the ratio of bend-to-splay elastic moduli) are altered considerably by increased activity, leading to an effectively lower bend elasticity. At high levels of activity, the topological defects that decorate the material exhibit a liquid-like structure, and adopt preferred orientations depending on their topological charge. Taken together, these results suggest that it should be possible to tune internal stresses in active nematic systems with the goal of designing out-of-equilibrium structures with engineered dynamic responses.

cond-mat.soft↗

arXiv2018

Simulations of splashing high and low viscosity droplets

In this work simulations are presented of low viscosity ethanol and high viscosity silicone oil droplets impacting on a dry solid surface at atmospheric and reduced ambient pressure. The simulations are able to capture both the effect of the ambient gas pressure and liquid viscosity on droplet impact and breakup. The results suggests that the early time droplet impact and gas film behavior for both low and high viscosity liquids share the same physics. However, for later time liquid sheet formation and breakup high and low viscosity liquids behave differently. These results explain why for both kinds of liquids the pressure effect can be observed, while at the same time different high and low viscosity splashing regimes have been identified experimentally.

physics.flu-dyn↗

arXiv2018

Evolutionary strategy for inverse charge measurements of dielectric particles

We report a computational strategy to obtain the charges of individual dielectric particles from experimental observation of their interactions as a function of time. This strategy uses evolutionary optimization to minimize the difference between trajectories extracted from experiment and simulated trajectories based on many-particle force fields. The force fields include both Coulombic interactions and dielectric polarization effects that arise due to particle-particle charge mismatch and particle-environment dielectric contrast. The strategy was applied to systems of free falling charged granular particles in vacuum, where electrostatic interactions are the only driving forces that influence the particles' motion. We show that when the particles' initial positions and velocities are known, the optimizer requires only an initial and final particle configuration of a short trajectory in order to accurately infer the particles' charges; when the initial velocities are unknown and only the initial positions are given, the optimizer can learn from multiple frames along the trajectory to determine the particles' initial velocities and charges. While the results presented here offer a proof-of-concept demonstration of the proposed ideas, the proposed strategy could be extended to more complex systems of electrostatically charged granular matter.

cond-mat.soft↗

arXiv2018

Drop splashing is independent of substrate wetting

A liquid drop impacting a dry solid surface with sufficient kinetic energy will splash, breaking apart into numerous secondary droplets. This phenomenon shows many similarities to forced wetting, including the entrainment of air at the contact line. Because of these similarities and the fact that forced wetting has been shown to depend on the wetting properties of the surface, existing theories predict splashing to depend on wetting properties as well. However, using high-speed interference imaging we observe that at high capillary numbers wetting properties have no effect on splashing for various liquid-surface combinations. Additionally, by fully resolving the Navier-Stokes equations at length and time scales inaccessible to experiments, we find that the shape and motion of the air-liquid interface at the contact line at the edge of the droplet are independent of wettability. We use these findings to evaluate existing theories and to compare splashing with forced wetting.

physics.flu-dyn↗

arXiv2018

Low-temperature anomalies of a vapor deposited glass

We investigate the low temperature properties of two-dimensional Lennard-Jones glass films, prepared in silico both by liquid cooling and by physical vapor deposition. We identify deep in the solid phase a crossover temperature $T^*$, at which slow dynamics and enhanced heterogeneity emerge. Around $T^*$, localized defects become visible, leading to vibrational anomalies as compared to standard solids. We find that on average, $T^*$ decreases in samples with lower inherent structure energy, suggesting that such anomalies will be suppressed in ultra-stable glass films, prepared both by very slow liquid cooling and vapor deposition.

cond-mat.soft↗

arXiv2017

Interplay of Structure, Elasticity and Dynamics in Actin-Based Nematic Materials

Achieving control and tunability of lyotropic materials has been a long-standing goal of liquid crystal research. Here we show that the elasticity of a liquid crystal system consisting of a dense suspension of semiflexible biopolymers can be manipulated over a relatively wide range of elastic moduli. Specifically, thin films of actin filaments are assembled at an oil-water interface. At sufficiently high concentrations, one observes the formation of a nematic phase riddled with $\pm1/2$ topological defects, characteristic of a two-dimensional nematic system. As the average filament length increases, the defect morphology transitions from a U-shape into a V-shape, indicating the relative increase of the material's bend over splay modulus. Furthermore, through the sparse addition of rigid microtubule filaments, one can further control the liquid crystal elasticity. We show how the material's bend constant can be raised linearly as a function of microtubule filament density, and present a simple means to extract absolute values of the elastic moduli from purely optical observations. Finally, we demonstrate that it is possible to predict not only the static structure of the material, including its topological defects, but also the evolution of the system into dynamically arrested states. Despite the non-equilibrium nature of the material, our continuum model, which couples structure and hydrodynamics, is able to capture the annihilation and movement of defects over long time scales. Thus, we have experimentally realized a lyotropic liquid crystal system that can be truly engineered, with tunable mechanical properties, and a theoretical framework to capture its structure, mechanics, and dynamics.

cond-mat.soft↗

arXiv2016

Controlling mechanical properties of a polymeric glass

In this work we use molecular simulations to examine methods of controlling mechanical properties of polymeric glass materials such as elastic moduli, mechanical heterogeneity as well as their glass transition temperature. We study filled and unfilled polymers and examine the effect of particle size, volume fraction and polymer-particle interactions. We identify a relationship between mobility and dynamic heterogeneity with elastic moduli and glass transition temperature.

cond-mat.soft↗

arXiv2016

Mesoscale Structure of Chiral Nematic Shells

There is considerable interest in understanding and controlling topological defects in nematic liquid crystals (LCs). Confinement, in the form of droplets, has been particularly effective in that regard. Here, we employ the Landau-de Gennes method to explore the geometrical frustration of nematic order in shell geometries, and focus on chiral materials. By varying the chirality and thickness in uniform shells, we construct a phase diagram that includes tetravalent structures, bipolar structures (BS), bent structures and radial spherical structures (RSS). It is found that, in uniform shells, the BS-to-RSS structural transition, in response to both chirality and shell geometry, is accompanied by an abrupt change of defect positions, implying a potential use for chiral nematic shells as sensors. Moreover, we investigate thickness heterogeneity in shells and demonstrate that non-chiral and chiral nematic shells exhibit distinct equilibrium positions of their inner core that are governed by shell chirality c.

cond-mat.soft↗

arXiv2016

Tension-dependent Free Energies of Nucleosome Unwrapping

Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome, and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails are crucial for stabilizing the outer turn of nucleosomal DNA.

physics.bio-ph↗

arXiv2016

Nanoscopic Characterization of DNA within Hydrophobic Pores:Thermodynamics and Kinetics

The energetic and transport properties of a double-stranded DNA dodecamer encapsulated in hydrophobic carbon nanotubes are probed employing two limiting nanotube diameters, D=4 nm and D=3 nm, corresponding to (51,0) and (40,0) zig-zag topologies, respectively. It is observed that the thermodynamically spontaneous encapsulation in the 4 nm nanopore (40 kJ/mol) is annihilated when the solid diameter narrows down to 3 nm, and that the confined DNA termini directly contact the hydrophobic walls with no solvent slab in-between. During the initial moments after confinement (2-3 ns),the biomolecule translocates along the nano pore's inner volume according to Fick's law (t) with a self-diffusion coefficient D=1.713 x 10-9m2/s, after which molecular diffusion assumes a single-file type mechanism (t1/2). As expected, diffusion is anisotropic, with the pore main axis as the preferred direction, but an in-depth analysis shows that the instantaneous velocity probabilities are essentially identical along the x, y and z directions. The 3D velocity histogram shows a maximum probability located at v=30.8 m/s, twice the observed velocity for a single-stranded three nucleotide DNA encapsulated in comparable armchair geometries (v=16.7 m/s, D=1.36-1.89 nm). Because precise physiological conditions (310 K, [NaCl] = 134 mM) are employed throughout, the present study establishes a landmark for the development of next generation in vivo drug delivery technologies based on carbon nanotubes as encapsulation agents.

physics.bio-ph↗

arXiv2016

Endohedral confinement of a DNA dodecamer onto pristine carbon nanotubes and the stability of the canonical B form

Although carbon nanotubes are potential candidates for DNA encapsulation and subsequent delivery of biological payloads to living cells, the thermodynamical spontaneity of DNA encapsulation under physiological conditions is still a matter of debate. Using enhanced sampling techniques, we show for the first time that, given a sufficiently large carbon nanotube, the confinement of a double-stranded DNA segment, 5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3', is thermodynamically favourable under physiological environments (134 mM, 310 K, 1 bar), leading to DNA-nanotube hybrids with lower free energy than the unconfined biomolecule. A diameter threshold of 3 nm is established below which encapsulation is inhibited. The confined DNA segment maintains its translational mobility and exhibits the main geometrical features of the canonical B form. To accommodate itself within the nanopore, the DNA end-to-end length increases from 3.85 nm up to approximately 4.1 nm, due to a 0.3 nm elastic expansion of the strand termini. The canonical Watson-Crick H-bond network is essentially conserved throughout encapsulation, showing that the contact between the DNA segment and the hydrophobic carbon walls results in minor rearrangements of the nucleotides H-bonding. The results obtained here are paramount to the usage of carbon nanotubes as encapsulation media for next generation drug delivery technologies.

physics.bio-ph↗