arXiv subjects

Dmitri O. Pushkin

Publications and source records attributed to Dmitri O. Pushkin.

9 recordsLinked to original sources

arXiv2025

Chiral interactions between tropocollagen molecules determine the collagen microfibril structure

Collagen is the most abundant structural protein in animals, forming hierarchically organised fibrils that provide mechanical support to tissues. Despite detailed structural studies, the physical principles that govern the formation of the characteristic axially-periodic collagen microfibril remain poorly understood. Here, we present a theoretical framework that links the amino acid sequence of tropocollagen to its supramolecular organisation. By combining statistical modeling of residue geometry with sequence-informed interaction potentials, we show that the chiral arrangement of outward-facing residues induces directional intermolecular interactions that drive molecular supercoiling. These interactions favour the formation of right-handed, pentameric microfibrils with a staggered axial periodicity of approximately 67 nm. Our simulations reveal that this structure emerges across a wide range of mammalian collagen sequences as a global energy minimum robust to biochemical noise. These findings provide a mechanistic explanation for collagen's supramolecular chirality and offer design principles for engineering synthetic collagen-mimetic materials.

cond-mat.soft↗

arXiv2022

Interfacial activity dynamics of confined active droplets

Active emulsions can spontaneously form self-propelled droplets or phoretic micropumps. It has been predicted that the interaction with their self-generated chemical fields can lead to multistable higher-order flows and chemodynamic phenomena. However, it remains unclear how such reaction-advection-diffusion instabilities can emerge from the interplay between chemical reactions and interfacial hydrodynamics. Here, we simultaneously measure the flow fields and the chemical concentration fields using dual-channel microscopy for oil droplets that dynamically solubilize in a supramicellar aqueous surfactant solution. We developed an experimentally tractable setup with micropumps, droplets that are pinned between the top and bottom surfaces of a microfluidic reservoir, which we compare directly to predictions from a Brinkman squirmer model to account for the confinement. With increasing droplet radius, we observe (i) a migration of vortex flows from the posterior to the anterior of the droplet, analogous to a transition from pusher- to puller-type swimmers, (ii) a bistability between dipolar and quadrupolar flow modes, and, eventually, (iii) a transition to multipolar modes. We also investigate how the dynamics evolve over long time periods. Together, our observations suggest that a local build-up of chemical products leads to a saturation of the surface, which controls the propulsion mechanism. These multistable dynamics can be explained by the competing time scales of slow micellar diffusion governing the chemical buildup and faster molecular diffusion powering the underlying transport mechanism. Our results are directly relevant to phoretic micropumps, but also shed light on the interfacial activity dynamics of self-propelled droplets and other active emulsion systems

cond-mat.soft↗

arXiv2021

Stochastic gel-shatter cycles in coalescence-fragmentation models

We describe a new phenomenon in models of coalescence and fragmentation, that of gel-shatter cycles. These are dynamical, unforced, stochastic cycles in which slow, approximately deterministic coalescence up to and beyond gelation is followed by abrupt random shattering. We describe their appearance in simulations of stochastic models with multiplicative kernels for coalescence and spontaneous fragmentation into monomers (`shattering'). The regime in which such cycles occur is characterized by a cyclicity order parameter, and we provide a simple scaling argument which describes both this regime and those which border it.

math.DS↗

arXiv2019

Confinement enhances the diversity of microbial flow fields

Despite their importance in many biological, ecological and physical processes, microorganismal fluid flows under tight confinement have not been investigated experimentally. Strong screening of Stokelets in this geometry suggests that the flow fields of different microorganisms should be universally dominated by the 2D source dipole from the swimmer's finite-size body. Confinement therefore is poised to collapse differences across microorganisms, that are instead well-established in bulk. Here we combine experiments and theoretical modelling to show that, in general, this is not correct. Our results demonstrate that potentially minute details like microswimmers' spinning and the physical arrangement of the propulsion appendages have in fact a leading role in setting qualitative topological properties of the hydrodynamic flow fields of micro-swimmers under confinement. This is well captured by an effective 2D model, even under relatively weak confinement. These results imply that active confined hydrodynamics is much richer than in bulk, and depends in a subtle manner on size, shape and propulsion mechanisms of the active components.

physics.bio-ph↗

arXiv2017

A solvable model of axisymmetric and non-axisymmetric droplet bouncing

We introduce a solvable Lagrangian model for droplet bouncing. The model predicts that, for an axisymmetric drop, the contact time decreases to a constant value with increasing Weber number, in qualitative agreement with experiments, because the system is well approximated as a simple harmonic oscillator. We introduce asymmetries in the velocity, initial droplet shape, and contact line drag acting on the droplet and show that asymmetry can often lead to a reduced contact time and lift-off in an elongated shape. The model allows us to explain the mechanisms behind non-axisymmetric bouncing in terms of surface tension forces. Once the drop has an elliptical footprint the surface tension force acting on the longer sides is greater. Therefore the shorter axis retracts faster and, due to the incompressibility constraints, pumps fluid along the more extended droplet axis. This leads to a positive feedback, allowing the drop to jump in an elongated configuration, and more quickly.

physics.flu-dyn↗

arXiv2014

Stirring by swimmers in confined microenvironments

We consider the tracer diffusion $D_{rr}$ that arises from the run-and-tumble motion of low Reynolds number swimmers, such as bacteria. In unbounded dilute suspensions, where the dipole swimmers move in uncorrelated runs of length $λ$, an exact solution showed that $D_{rr}$ is independent of $λ$. Here we verify this result in numerical simulations for a particular model swimmer, the spherical squirmer. We also note that in confined microenvironments, such as microscopic droplets, microfluidic devices and bacterial microzones in marine ecosystems, the size of the system can be comparable to $λ$. We show that this effect alone reduces the value of $D_{rr}$ in comparison to its bulk value, and predict a scaling form for its relative decrease.

cond-mat.soft↗

arXiv2013

Fluid mixing by curved trajectories of microswimmers

We consider the tracer diffusion $D_{rr}$ that arises from the run-and-tumble motion of low Reynolds number swimmers, such as bacteria. Assuming a dilute suspension, where the bacteria move in uncorrelated runs of length $λ$, we obtain an exact expression for $D_{rr}$ for dipolar swimmers in three dimensions, hence explaining the surprising result that this is independent of $λ$. We compare $D_{rr}$ to the contribution to tracer diffusion from entrainment.

cond-mat.soft↗

arXiv2012

Fluid transport by individual microswimmers

We discuss the path of a tracer particle as a microswimmer moves past on an infinite straight trajectory. If the tracer is sufficiently far from the path of the swimmer it moves in a closed loop. As the initial distance between the tracer and the path of the swimmer $ρ$ decreases, the tracer is displaced a small distance backwards (relative to the direction of the swimmer velocity). For much smaller tracer-swimmer separations, however, the tracer displacement becomes positive and diverges as $ρ\to 0$. To quantify this behaviour we calculate the Darwin drift, the total volume swept out by a material sheet of tracers, initially perpendicular to the swimmer path, during the swimmer motion. We find that the drift can be written as the sum of a {\em universal} term which depends on the quadrupolar flow field of the swimmer, together with a non-universal contribution given by the sum of the volumes of the swimmer and its wake. The formula is compared to exact results for the squirmer model and to numerical calculations for a more realistic model swimmer.

physics.flu-dyn↗

arXiv2004

Scale-free nonlinear conservative cascades and their stationary spectra

We show that a variety of complex processes can be viewed from the unified standpoint of scale-free nonlinear conservative cascades. Examples include certain turbulence models, percolation, cluster coagulation (aggregation) and fragmentation, `coarse-grained' forest fire model of self-organized criticality, and scale-free network growth. We classify such cascades by the values of three indices, and show how power-law steady spectra may arise. The power-law exponent is proven to depend only on the values of the three indices by a simple algebraic formula.

cond-mat.dis-nn↗