Effect of disorder on phases across two-dimensional thermal melting.

We study melting in a two-dimensional system of classical particles with Gaussian-core interactions in disordered environments. The pure system validates the conventional two-step melting with a hexatic phase intervening between the solid and the liquid. This picture is modified in the presence of pinning impurities. A random distribution of pinning centers forces a hexaticlike low-temperature phase that transits into a liquid at a single melting temperature T_{m}^{RP}. In contrast, pinning centers located at randomly chosen sites of a perfect crystal anchor a solid at low temperatures which undergoes a direct transition to the liquid at T_{m}^{CP}. Thus, the two-step melting is lost in either case of disorder. We discuss the characteristics of melting depending on the nature of the impurities.

Universal stress correlations in crystalline and amorphous packings.

We present a universal characterization of stress correlations in athermal systems, across crystalline to amorphous packings. Via numerical analysis of static configurations of particles interacting through harmonic as well as Lennard-Jones potentials, for a variety of preparation protocols and ranges of microscopic disorder, we show that the properties of the stress correlations at large lengthscales are surprisingly universal across all situations, independent of structural correlations, or the correlations in orientational order. In the near-crystalline limit, we present exact results for the stress correlations for both models, which work surprisingly well at large lengthscales, even in the amorphous phase. Finally, we study the differences in stress fluctuations across the amorphization transition, where stress correlations reveal the loss of periodicity in the structure at short lengthscales with increasing disorder.

Onset of glassiness in two-dimensional ring polymers: Interplay of stiffness and crowding.

The effect of ring stiffness and pressure on the glassy dynamics of a thermal assembly of two-dimensional ring polymers is investigated using extensive coarse-grained molecular dynamics simulations. In all cases, dynamical slowing down is observed with increasing pressure, and thereby, a phase space for equilibrium dynamics is identified in the plane of the obtained monomer density and ring stiffness. When the rings are highly flexible, i.e., have low ring stiffness, glassiness sets in via the crowding of crumpled polymers, which take on a globular form. In contrast, at large ring stiffness, when the rings tend to have large asphericity under compaction, we observe the emergence of local domains having orientational ordering at high pressures. Therefore, our simulations highlight how varying the deformability of rings leads to contrasting mechanisms in driving the system toward the glassy regime.

Athermal quasistatic cavitation in amorphous solids: Effect of random pinning.

Amorphous solids are known to fail catastrophically via fracture, and cavitation at nano-metric scales is known to play a significant role in such a failure process. Micro-alloying via inclusions is often used as a means to increase the fracture toughness of amorphous solids. Modeling such inclusions as randomly pinned particles that only move affinely and do not participate in plastic relaxations, we study how the pinning influences the process of cavitation-driven fracture in an amorphous solid. Using extensive numerical simulations and probing in the athermal quasistatic limit, we show that just by pinning a very small fraction of particles, the tensile strength is increased, and also the cavitation is delayed. Furthermore, the cavitation that is expected to be spatially heterogeneous becomes spatially homogeneous by forming a large number of small cavities instead of a dominant cavity. The observed behavior is rationalized in terms of screening of plastic activity via the pinning centers, characterized by a screening length extracted from the plastic-eigenmodes.

iPLA2 inhibition blocks LysoPC-induced TRPC6 externalization and promotes Re-endothelialization of carotid injuries in hypercholesterolemic mice.

Lipid oxidation products, including lysophosphatidylcholine (lysoPC), accumulate at the site of arterial injury after vascular interventions and hinder re-endothelization. LysoPC activates calcium-permeable channels, specifically canonical transient receptor potential 6 (TRPC6) channels that induce a sustained increase in intracellular calcium ion concentration [Ca2+]i and contribute to dysregulation of the endothelial cell (EC) cytoskeleton. Activation of TRPC6 leads to inhibition of EC migration in vitro and delayed re-endothelization of arterial injuries in vivo. Previously, we demonstrated the role of phospholipase A2 (PLA2), specifically calcium-independent PLA2 (iPLA2), in lysoPC-induced TRPC6 externalization and inhibition of EC migration in vitro. The ability of FKGK11, an iPLA2-specific pharmacological inhibitor, to block TRPC6 externalization and preserve EC migration was assessed in vitro and in a mouse model of carotid injury. Our data suggest that FKGK11 prevents lysoPC-induced PLA2 activity, blocks TRPC6 externalization, attenuates calcium influx, and partially preserves EC migration in vitro. Furthermore, FKGK11 promotes re-endothelization of an electrocautery carotid injury in hypercholesterolemic mice. FKGK11 has similar arterial healing effects in male and female mice on a high-fat diet. This study suggests that iPLA2 is a potential therapeutic target to attenuate calcium influx through TRPC6 channels and promote EC healing in cardiovascular patients undergoing angioplasty.

p38 MAPK activation and STIM1-Orai3 association mediate TRPC6 externalization.

Endothelial cell (EC) migration is critical for the repair of monolayer disruption following angioplasties, but migration is inhibited by lipid oxidation products, including lysophosphatidylcholine (lysoPC), which open canonical transient receptor potential 6 (TRPC6) channels. TRPC6 activation requires an increase in intracellular Ca2+ concentration ([Ca2+]i), the source of which is unknown. LysoPC can activate phospholipase A2 to release arachidonic acid (ArA). ArA can activate arachidonic acid-regulated calcium (ARC) channels that are formed by stromal interaction molecule 1 (STIM1) and Orai1 and Orai3 proteins. Both lysoPC and ArA can activate p38 mitogen-activated protein kinase (MAPK) that induces the phosphorylation required for STIM1-Orai3 association. This is accompanied by an increase in [Ca2+]i and TRPC6 externalization. The effect of lysoPC and ArA is not additive, suggesting activation of the same pathway. The increase in [Ca2+]i activates an Src kinase that leads to TRPC6 activation. Downregulation of Orai3 using siRNA blocks the lysoPC- or ArA-induced increase in [Ca2+]i and TRPC6 externalization and preserves EC migration. These data show that lysoPC induces activation of p38 MAPK, which leads to STIM1-Orai3 association and increased [Ca2+]i. This increase in [Ca2+]i activates an Src kinase leading to TRPC6 externalization, which initiates a cascade of events ending in cytoskeletal changes that disrupt EC migration. Blocking this pathway preserves EC migration in the presence of lipid oxidation products.NEW & NOTEWORTHY The major lysophospholipid component in oxidized LDL, lysophosphatidylcholine (lysoPC), can activate p38 MAP kinase, which in turn promotes externalization of Orai3 and STIM1-Orai3 association, suggesting involvement of arachidonic acid-regulated calcium (ARC) channels. The subsequent increase in intracellular calcium activates an Src kinase required for TRPC6 externalization. TRPC6 activation, which has been shown to inhibit endothelial cell migration, is blocked by p38 MAP kinase or Orai3 downregulation, and this partially preserves endothelial migration in lysoPC.

p85α regulatory subunit isoform controls PI3-kinase and TRPC6 membrane translocation.

Activation of phosphatidylinositol 3-kinase (PI3K) by lipid oxidation products, including lysophosphatidylcholine (lysoPC), increases the externalization of canonical transient receptor potential 6 (TRPC6) channels leading to a subsequent increase in intracellular calcium that contributes to cytoskeletal changes which inhibit endothelial cell (EC) migration in vitro and impair EC healing of arterial injuries in vivo. The PI3K p110α and p110δ catalytic subunit isoforms regulate lysoPC-induced TRPC6 externalization in vitro, but have many other functions. The goal of the current study is to identify the PI3K regulatory subunit isoform involved in TRPC6 externalization to potentially identify a more specific treatment regimen to improve EC migration and arterial healing, while minimizing off-target effects. Decreasing the p85α regulatory subunit isoform protein levels, but not the p85ß and p55γ regulatory subunit isoforms, with small interfering RNA inhibits lysoPC-induced translocation of the PI3K catalytic subunit to the plasma membrane, dramatically decreased phosphatidylinositol (3,4,5)-trisphosphate (PIP3) production and TRPC6 externalization, and significantly improves EC migration in the presence of lysoPC. These results identify the important and specific role of p85α in controlling translocation of PI3K from the cytosol to the plasma membrane and PI3K-mediated TRPC externalization by oxidized lipids. Current PI3K inhibitors block the catalytic subunit, but our data suggest that the regulatory subunit is a novel therapeutic target to promote EC migration and healing after arterial injuries that occur with angioplasty.

Universal mechanical instabilities in the energy landscape of amorphous solids: Evidence from athermal quasistatic expansion.

Using numerical simulations, we study the failure of an amorphous solid under athermal quasistatic expansion starting from a homogeneous high-density state. During the expansion process, plastic instabilities occur, manifested via sudden jumps in pressure and energy, with the largest event happening via cavitation leading to the material's yielding. We demonstrate that all these plastic events are characterized by saddle-node bifurcation, during which the smallest nonzero eigenvalue of the Hessian matrix vanishes via a square-root singularity. We find that after yielding and prior to complete fracture, the statistics of pressure or energy jumps corresponding to the plastic events show subextensive system-size scaling, similar to the case of simple shear but with different exponents. Thus, overall, our paper reveals universal features in the fundamental characteristics during mechanical failure in amorphous solids under any quasistatic deformation protocol.

Modelling the first wave of COVID-19 in India.

Estimating the burden of COVID-19 in India is difficult because the extent to which cases and deaths have been undercounted is hard to assess. Here, we use a 9-component, age-stratified, contact-structured epidemiological compartmental model, which we call the INDSCI-SIM model, to analyse the first wave of COVID-19 spread in India. We use INDSCI-SIM, together with Bayesian methods, to obtain optimal fits to daily reported cases and deaths across the span of the first wave of the Indian pandemic, over the period Jan 30, 2020 to Feb 15, 2021. We account for lock-downs and other non-pharmaceutical interventions (NPIs), an overall increase in testing as a function of time, the under-counting of cases and deaths, and a range of age-specific infection-fatality ratios. We first use our model to describe data from all individual districts of the state of Karnataka, benchmarking our calculations using data from serological surveys. We then extend this approach to aggregated data for Karnataka state. We model the progress of the pandemic across the cities of Delhi, Mumbai, Pune, Bengaluru and Chennai, and then for India as a whole. We estimate that deaths were undercounted by a factor between 2 and 5 across the span of the first wave, converging on 2.2 as a representative multiplier that accounts for the urban-rural gradient. We also estimate an overall under-counting of cases by a factor of between 20 and 25 towards the end of the first wave. Our estimates of the infection fatality ratio (IFR) are in the range 0.05-0.15, broadly consistent with previous estimates but substantially lower than values that have been estimated for other LMIC countries. We find that approximately 35% of India had been infected overall by the end of the first wave, results broadly consistent with those from serosurveys. These results contribute to the understanding of the long-term trajectory of COVID-19 in India.

Residual stress in athermal soft disordered solids: insights from microscopic and mesoscale models.

In soft amorphous materials, shear cessation after large shear deformation leads to configurations having residual shear stress. The origin of these states and the distribution of the local shear stresses within the material is not well understood, despite its importance for the change in material properties and consequent applications. In this work, we use molecular dynamics simulations of a model dense non-Brownian soft amorphous material to probe the non-trivial relaxation process towards a residual stress state. We find that, similar to thermal glasses, an increase in shear rate prior to the shear cessation leads to lower residual stress states. We rationalise our findings using a mesoscopic elasto-plastic description that explicitly includes a long range elastic response to local shear transformations. We find that after flow cessation the initial stress relaxation indeed depends on the pre-sheared stress state, but the final residual stress is majorly determined by newly activated plastic events occurring during the relaxation process, a scenario consistent with the phenomenology of avalanche dynamics in the low shear rate limit of steadily sheared amorphous solids. Our simplified coarse grained description not only allows capturing the phenomenology of residual stress states but also rationalising the altered material properties that are probed using small and large deformation protocols applied to the relaxed material.

Finite-size effects in the diffusion dynamics of a glass-forming binary mixture with large size ratio.

Extensive molecular dynamics computer simulations of an equimolar, glass-forming AB mixture with a large size ratio are presented. While the large A particles show a glass transition around the critical density of mode-coupling theory ρc, the small B particles remain mobile with a relatively weak decrease in their self-diffusion coefficient DB with increasing density. Surprisingly, around ρc, the self-diffusion coefficient of species A, DA, also starts to show a rather weak dependence on density. We show that this is due to finite-size effects that can be understood from the analysis of the collective interdiffusion dynamics.

Rheological response of a glass-forming liquid having large bidispersity.

Using extensive numerical simulations, we investigate the flow behaviour of a model glass-forming binary mixture whose constituent particles have a large size ratio. The rheological response to applied shear is studied in the regime where the larger species are spatially predominant. We demonstrate that the macroscopic rigidity that emerges with increasing density occurs in the regime where the larger species undergo a glass transition while the smaller species continue to be highly diffusive. We analyse the interplay between the timescale imposed by the shear and the quiescent relaxation dynamics of the two species to provide a microscopic insight into the observed rheological response. Finally, by tuning the composition of the mixture, we illustrate that the systematic insertion of the smaller particles affects the rheology by lowering of viscosity of the system.

Effect of ring stiffness and ambient pressure on the dynamical slowdown in ring polymers.

Using extensive molecular dynamics simulations, we investigate the slowdown of dynamics in a 3D system of ring polymers by varying the ambient pressure and the stiffness of the rings. Our study demonstrates that the stiffness of the rings determines the dynamics of the ring polymers, leading to glassiness at lower pressures for stiffer rings. The threading of the ring polymers, a unique feature that emerges only due to the topological nature of such polymers in three dimensions, is shown to be the determinant feature of dynamical slowdown, albeit only in a certain stiffness range. Our results suggest a possible framework for exploring the phase space spanned by ring stiffness and pressure to obtain spontaneously emerging topologically constrained polymer glasses.

Turbulent route to two-dimensional soft crystals.

We investigate the effect of a two-dimensional, incompressible, turbulent flow on soft granular particles and show the emergence of a crystalline phase due to the interplay of Stokesian drag and short-range interparticle interactions. We quantify this phase through the bond order parameter and local density fluctuations and find a sharp transition between the crystalline and noncrystalline phases as a function of the Stokes number. Furthermore, the nature of preferential concentration, characterized by the correlation dimension, is significantly different from that of particle-laden flows in the absence of repulsive potentials.

Activation of the cytosolic calcium-independent phospholipase A2 ß isoform contributes to TRPC6 externalization via release of arachidonic acid.

During vascular interventions, oxidized low-density lipoprotein and lysophosphatidylcholine (lysoPC) accumulate at the site of arterial injury, inhibiting endothelial cell (EC) migration and arterial healing. LysoPC activates canonical transient receptor potential 6 (TRPC6) channels, leading to a prolonged increase in intracellular calcium ion concentration that inhibits EC migration. However, an initial increase in intracellular calcium ion concentration is required to activate TRPC6, and this mechanism remains elusive. We hypothesized that lysoPC activates the lipid-cleaving enzyme phospholipase A2 (PLA2), which releases arachidonic acid (AA) from the cellular membrane to open arachidonate-regulated calcium channels, allowing calcium influx that promotes externalization and activation of TRPC6 channels. The focus of this study was to identify the roles of calcium-dependent and/or calcium-independent PLA2 in lysoPC-induced TRPC6 externalization. We show that lysoPC induced PLA2 enzymatic activity and caused AA release in bovine aortic ECs. To identify the specific subgroup and the isoform(s) of PLA2 involved in lysoPC-induced TRPC6 activation, transient knockdown studies were performed in the human endothelial cell line EA.hy926 using siRNA to inhibit the expression of genes encoding cPLA2α, cPLA2γ, iPLA2ß, or iPLA2γ. Downregulation of the ß isoform of iPLA2 blocked lysoPC-induced release of AA from EC membranes and TRPC6 externalization, as well as preserved EC migration in the presence of lysoPC. We propose that blocking TRPC6 activation and promoting endothelial healing could improve the outcomes for patients undergoing cardiovascular interventions.

Elastoplastic Approach Based on Microscopic Insights for the Steady State and Transient Dynamics of Sheared Disordered Solids.

We develop a framework to study the mechanical response of athermal amorphous solids via a coupling of mesoscale and microscopic models. Using measurements of coarse-grained quantities from simulations of dense disordered particulate systems, we present a coherent elastoplastic model approach for deformation and flow of yield stress materials. For a given set of parameters, this model allows us to match consistently transient and steady state features of driven disordered systems with diverse preparation histories under both applied shear-rate and creep protocols.

Inhibition of P110α and P110δ catalytic subunits of PI3 kinase reverses impaired arterial healing after injury in hypercholesterolemic male mice.

Endothelial cell (EC) migration is critical for healing arterial injuries, such as those that occur with angioplasty. Impaired re-endothelialization following arterial injury contributes to vessel thrombogenicity, intimal hyperplasia, and restenosis. Oxidized lipid products, including lysophosphatidylcholine (lysoPC), induce canonical transient receptor potential 6 (TRPC6) externalization leading to increased [Ca2+]i, activation of calpains, and alterations of the EC cytoskeletal structure that inhibit migration. The p110α and p110δ catalytic subunit isoforms of phosphatidylinositol 3-kinase (PI3K) regulate lysoPC-induced TRPC6 externalization in vitro. The goal of this study was to assess the in vivo relevance of those in vitro findings to arterial healing following a denuding injury in hypercholesterolemic mice treated with pharmacologic inhibitors of the p110α and p110δ isoforms of PI3K and a general PI3K inhibitor. Pharmacologic inhibition of the p110α or the p110δ isoform of PI3K partially preserves healing in hypercholesterolemic male mice, similar to a general PI3K inhibitor. Interestingly, the p110α, p110δ, and the general PI3K inhibitor do not improve arterial healing after injury in hypercholesterolemic female mice. These results indicate a potential new role for isoform-specific PI3K inhibitors in male patients following arterial injury/intervention. The results also identify significant sex differences in the response to PI3K inhibition in the cardiovascular system, where female sex generally has a cardioprotective effect. This study provides a foundation to investigate the mechanism for the sex differences in response to PI3K inhibition to develop a more generally applicable treatment option.

P110α and P110δ catalytic subunits of PI3 kinase regulate lysophosphatidylcholine-induced TRPC6 externalization.

Lipid oxidation products, including lysophosphatidylcholine (lysoPC) inhibit endothelial cell (EC) migration in vitro and impair EC healing of arterial injuries in vivo, in part by activating phosphatidylinositol 3-kinase (PI3K), which increases the externalization of canonical transient receptor potential 6 (TRPC6) channels and the subsequent increase in intracellular calcium. Inhibition of PI3K is a potential method to decrease TRPC6 activation and restore migration, but PI3K is involved in multiple intracellular signaling pathways and has multiple downstream effectors. The goal of this study is to identify the specific p110 catalytic subunit isoforms responsible for lysoPC-induced TRPC6 externalization to identify a target for intervention while minimizing impact on alternative signaling pathways. Down-regulation of the p110α and p110δ isoforms, but not the p110ß or p110γ isoforms, with small interfering RNA significantly decreased phosphatidylinositol (3,4,5)-trisphosphate production and TRPC6 externalization, and significantly improved EC migration in the presence of lysoPC. These results identify an additional role of p110α in EC and reveal for the first time a specific role of p110δ in EC, providing a foundation for subsequent in vivo studies to investigate the impact of p110 isoform inhibition on arterial healing after injury.

Flow heterogeneities in supercooled liquids and glasses under shear.

Using extensive nonequilibrium molecular dynamics simulations, we investigate a glass-forming binary Lennard-Jones mixture under shear. Both supercooled liquids and glasses are considered. Our focus is on the characterization of inhomogeneous flow patterns such as shear bands that appear as a transient response to the external shear. For the supercooled liquids, we analyze the crossover from Newtonian to non-Newtonian behavior with increasing shear rate γ[over ̇]. Above a critical shear rate γ[over ̇]_{c} where a non-Newtonian response sets in, the transient dynamics are associated with the occurrence of short-lived vertical shear bands, i.e., bands of high mobility that form perpendicular to the flow direction. In the glass states, long-lived horizontal shear bands, i.e., bands of high mobility parallel to the flow direction, are observed in addition to vertical ones. The systems with shear bands are characterized in terms of mobility maps, stress-strain relations, mean-squared displacements, and (local) potential energies. The initial formation of a horizontal shear band provides an efficient stress release, corresponds to a local minimum of the potential energy, and is followed by a slow broadening of the band towards the homogeneously flowing fluid in the steady state. Whether a horizontal or a vertical shear band forms cannot be predicted from the initial undeformed sample. Furthermore, we show that with increasing system size, the probability for the occurrence of horizontal shear bands increases.

Dense hard disk ordering: influence of bidispersity and quenched disorder.

Using Monte Carlo simulations, the impact on structural ordering in two-dimensional systems via the interplay of size bidispersity and quenched disorder in the form of an externally applied spatially random potential, is studied for a system of hard disks. By scanning across a wide range of dense packing fractions, size ratios and roughness of the applied potential, the phase diagram is constructed, which demonstrates that both quenched and size disorders shift the onset of translational order to higher packings, while maintaining the presence of the intermediate hexatic phase. At larger disorder strengths, the signatures of structural order are absent within the range of investigated packing fractions. Further, the dynamics with increasing potential strength is analysed for the mono-component system to obtain a spatio-temporal description of the melting process. Finally, the influence of the externally rough field on the Mermin-Wagner fluctuations, characteristic to two-dimensional systems, is investigated.