arXiv subjects

Daphne Klotsa

Publications and source records attributed to Daphne Klotsa.

16 recordsLinked to original sources

arXiv2024

Using Activity to Compartmentalize Binary Mixtures

We computationally study suspensions of slow and fast active Brownian particles that have undergone motility induced phase separation and are at steady state. Such mixtures, of varying non-zero activity, remain largely unexplored even though they are relevant for a plethora of systems and applications ranging from cellular biophysics to drone swarms. Our mixtures are modulated by their activity ratios ($\mathrm{Pe}^\mathrm{R}$), which we find to encode information by giving rise to three regimes, each of which display their unique emergent behaviors. Specifically, we found non-monotonic behavior of macroscopic properties, e.g. density and pressure, as a function of activity ratio, microphase separation of fast and slow particle domains, increased fluctuations on the interface and severe avalanche events compared to monodisperse active systems. Our approach of simultaneously varying the two activities of the particle species allowed us to discover these behaviors and explain the microscopic physical mechanisms that drive them.

cond-mat.soft↗

arXiv2022

Reciprocal swimming at intermediate Reynolds number

In Stokes flow, Purcell's scallop theorem forbids objects with time-reversible (reciprocal) swimming strokes from moving. In the presence of inertia, this restriction is eased and reciprocally deforming bodies can swim. A number of recent works have investigated dimer models that swim reciprocally at intermediate Reynolds numbers Re ~ 1-1000. These show interesting results (e.g. switches of the swim direction as a function of inertia) but the results vary and seem to be case-specific. Here, we introduce a general model and investigate the behaviour of an asymmetric spherical dimer of oscillating length for small-amplitude motion at intermediate Re. In our analysis we make the important distinction between particle and fluid inertia, both of which need to be considered separately. We asymptotically expand the Navier-Stokes equations in the small amplitude limit to obtain a system of linear PDEs. Using a combination of numerical (Finite Element) and analytical (reciprocal theorem, method of reflections) methods we solve the system to obtain the dimer's swim speed and show that there are two mechanisms that give rise to motion: boundary conditions (an effective slip velocity) and Reynolds stresses. Each mechanism is driven by two classes of sphere-sphere interactions, between one sphere's motion and 1) the oscillating background flow induced by the other's motion, and 2) a geometric asymmetry induced by the other's presence. We can thus unify and explain behaviours observed in other works. Our results show how sensitive, counter-intuitive and rich motility is in the parameter space of finite inertia of particles and fluid.

physics.flu-dyn↗

arXiv2021

Nonreciprocal model swimmer at intermediate Reynolds numbers

Metachronal swimming, the sequential beating of limbs with a small phase lag, is observed in many organisms at various scales, but has been studied mostly in the limits of high or low Reynolds numbers. Motivated by the swimming of brine shrimp, a mesoscale organism that operates at intermediate Reynolds numbers, we computationally studied a simple nonreciprocal 2D model that performs metachronal swimming. Our swimmer is composed of two pairs of paddles beating with a phase difference that are symmetrically attached to the sides of a flat body. We numerically solved the Navier-Stokes equations and used the immersed boundary method to model the interactions between the fluid and swimmer. To investigate the effect of inertia and geometry, we performed simulations varying the paddle spacing and the Reynolds numbers in the range $Re = 0.05 - 100$. In all cases, we observed back-and-forth motion during the cycle and a finite cycle-averaged swim speed at steady state. Interestingly, we found that the swim speed of the swimmer has nonmonotonic dependence on $Re$, with a maximum around $Re\approx1$, a flat minimum between $Re=20-30$ and an eventual increase for $Re>35$. To get more insight into the mechanism behind this relationship, we first decomposed the swim stroke of the swimmer and each paddle into power and recovery strokes and characterized the forward and backward motion. Unlike for reciprocal swimmers, here, for parts of the cycle there is competition between the two strokes of the paddles - the balance of which leads to net motion. We then studied the cycle-averaged, as well as, power-stroke-averaged and recovery-stroke-averaged fluid flows, and related differences in the fluid field to the nonmonotonic behavior of the swim speed. Our results suggest the existence of distinct motility mechanisms that develop as inertia increases within the intermediate-Re range.

physics.flu-dyn↗

arXiv2021

Dependence of phase behavior and surface tension on particle stiffness for active Brownian particles

We study quasi two-dimensional, monodisperse systems of active Brownian particles (ABPs) for a range of activities, stiffnesses, and densities. We develop a microscopic, analytical method for predicting the dense phase structure formed after motility-induced phase separation (MIPS) has occurred, including the dense cluster's area fraction, interparticle pressure, and radius. Our predictions are in good agreement with our Brownian dynamics simulations. We, then, derive a continuum model to investigate the relationship between the predicted interparticle pressure, the swim pressure, and the macroscopic pressure in the momentum equation. We find that formulating the point-wise macroscopic pressure as the interparticle pressure and modeling the particle activity through a spatially variant body force -- as opposed to a volume-averaged swim pressure -- results in consistent predictions of pressure in both the continuum model and the microscopic theory. This formulation of pressure also results in nearly zero surface tension for the phase separated domains, irrespective of activity, stiffness, and area fraction. Furthermore, using Brownian dynamics simulations and our continuum model, we showed that both the interface width and surface tension, are intrinsic characteristics of the system. On the other hand, if we were to exclude the body force induced by activity, we find that the resulting surface tension values are linearly dependent on the size of the simulation, in contrast to the statistical mechanical definition of surface tension.

cond-mat.soft↗

arXiv2021

Pairwise and collective behavior between model swimmers at intermediate Reynolds numbers

We computationally studied the pair interactions and collective behavior of asymmetric, dumbbell swimmers over a range of intermediate Reynolds numbers and initial configurations. Depending on the initial positions and the Re, we found that two swimmers either repelled and swum away from one another or assembled one of four stable pairs: in-line and in-tandem, both parallel and anti-parallel. When in these stable pairs, swimmers were coordinated, swum together, and generated fluid flows as one. We compared the stable pairs' speeds, swim direction and fluid flows to those of the single swimmer. The in-line stable pairs behaved much like the single swimmer transitioning from puller-like to pusher-like stroke-averaged flow fields. In contrast, for the in-tandem pairs we discovered differences in the swim direction transition, as well as the stroke-averaged fluid flow directions. Notably, the in-tandem V pair switched its swim direction at a higher $\text{Re}$ than the single swimmer while the in-tandem orbiting pair switched at a lower $\text{Re}$. We also studied a system of 122 swimmers and found the collective behavior transitioned from in-line network-like connections to small, transient in-tandem clusters as the Reynolds number increased, consistent with the in-line to in-tandem pairwise behavior. Details in the collective behavior involved the formation of triples and other many-body hydrodynamic interactions that were not captured by either pair or single swimmer behavior. Our findings demonstrate the richness and complexity of the collective behavior of intermediate-$\text{Re}$ swimmers.

physics.flu-dyn↗

arXiv2020

Kinematics of a simple reciprocal model swimmer at intermediate Reynolds numbers

We computationally study the kinematics of a simple model reciprocal swimmer (asymmetric dumbbell) as a function of the Reynolds number (Re) and investigate how the onset and gradual increase of inertia impacts the swimming behavior: a reversal in the swim direction, flow directions, and the swim stroke. We divide the swim stroke into the expansion and compression of the two spheres and relate them to power and recovery strokes. We find that the switch in swim direction also corresponds to a switch in power and recovery strokes. We obtain expressions for the mean swimming velocity by collapsing the net displacement during expansion and compression under power law relationships with respect to Re, the swimmer's amplitude, and the distance between the two spheres. Analyzing the fluid flows, we see the averaged flow field during expansion always resembles a pusher and compression always a puller, but when averaged over the whole cycle, the flow that dominates is the one that occurs during the power stroke. We also relate the power and recovery strokes to the swimming efficiency during times of expansion and compression, and we find that the power stroke is, surprisingly, not always more efficient than the recovery stroke. Our results may have important implications for biology and ultimately the design of artificial swimmers.

cond-mat.soft↗

arXiv2019

Active binary mixtures of fast and slow hard spheres

We computationally studied the phase behavior and dynamics of binary mixtures of active particles, where each 'species' had distinct activities leading to distinct velocities, fast and slow. We obtained phase diagrams demonstrating motility-induced phase separation (MIPS) upon varying the activity and concentration of each species, and extended current kinetic theory of active/passive mixtures to active/active mixtures. We discovered two regimes of behavior quantified through the participation of each species in the dense phase compared to their monodisperse counterparts. In regime I (active/passive and active/weakly-active), we found that the dense phase was segregated by particle type into domains of fast and slow particles. Moreover, fast particles were suppressed from entering the dense phase while slow particles were enhanced entering the dense phase, compared to monodisperse systems of all-fast or all-slow particles. These effects decayed asymptotically as the activity of the slow species increased, approaching the activity of the fast species until they were negligible (regime II). In regime II, the dense phase was homogeneously mixed and each species participated in the dense phase as if it were it a monodisperse system; each species behaved as if it weren't mixed at all. Finally, we collapsed our data defining two quantities that measure the total activity of the system. We thus found expressions that predict, a priori, the percentage of each particle type that participates in the dense phase through MIPS.

cond-mat.soft↗

arXiv2018

Transition in swimming direction in a model self-propelled inertial swimmer

We propose a reciprocal, self-propelled model swimmer at intermediate Reynolds numbers ($Re$). Our swimmer consists of two unequal spheres that oscillate in antiphase generating nonlinear steady streaming (SS) flows. We show computationally that the SS flows enable the swimmer to propel itself, and also switch direction as $Re$ increases. We quantify the transition in the swimming direction by collapsing our data on a critical $Re$ and show that the transition in swimming directions corresponds to the reversal of the SS flows. Based on our findings, we propose that SS can be an important physical mechanism for motility at intermediate $Re$.

physics.flu-dyn↗

arXiv2016

Propulsion of a two-sphere swimmer

We describe experiments and simulations demonstrating the propulsion of a neutrally-buoyant swimmer that consists of a pair of spheres attached by a spring, immersed in a vibrating fluid. The vibration of the fluid induces relative motion of the spheres which, for sufficiently large amplitudes, can lead to motion of the center of mass of the two spheres. We find that the swimming speed obtained from both experiment and simulation agree and collapse onto a single curve if plotted as a function of the streaming Reynolds number, suggesting that the propulsion is related to streaming flows. There appears to be a critical onset value of the streaming Reynolds number for swimming to occur. We observe a change in the streaming flows as the Reynolds number increases, from that generated by two independent oscillating spheres to a collective flow pattern around the swimmer as a whole. The mechanism for swimming is traced to a strengthening of a jet of fluid in the wake of the swimmer.

physics.flu-dyn↗

arXiv2016

Digital Alchemy for Materials Design: Colloids and Beyond

Starting with the early alchemists, a holy grail of science has been to make desired materials by modifying the attributes of basic building blocks. Building blocks that show promise for assembling new complex materials can be synthesized at the nanoscale with attributes that would astonish the ancient alchemists in their versatility. However, this versatility means that making direct connection between building block attributes and bulk behavior is both necessary for rationally engineering materials, and difficult because building block attributes can be altered in many ways. Here we show how to exploit the malleability of the valence of colloidal nanoparticle "elements" to directly and quantitatively link building block attributes to bulk behavior through a statistical thermodynamic framework we term "digital alchemy". We use this framework to optimize building blocks for a given target structure, and to determine which building block attributes are most important to control for self assembly, through a set of novel thermodynamic response functions, moduli and susceptibilities. We thereby establish direct links between the attributes of colloidal building blocks and the bulk structures they form. Moreover, our results give concrete solutions to the more general conceptual challenge of optimizing emergent behaviors in nature, and can be applied to other types of matter. As examples, we apply digital alchemy to systems of truncated tetrahedra, rhombic dodecahedra, and isotropically interacting spheres that self assemble diamond, FCC, and icosahedral quasicrystal structures, respectively.

cond-mat.soft↗

arXiv2014

Understanding shape entropy through local dense packing

Entropy drives the phase behavior of colloids ranging from dense suspensions of hard spheres or rods to dilute suspensions of hard spheres and depletants. Entropic ordering of anisotropic shapes into complex crystals, liquid crystals, and even quasicrystals has been demonstrated recently in computer simulations and experiments. The ordering of shapes appears to arise from the emergence of directional entropic forces (DEFs) that align neighboring particles, but these forces have been neither rigorously defined nor quantified in generic systems. Here, we show quantitatively that shape drives the phase behavior of systems of anisotropic particles upon crowding through DEFs. We define DEFs in generic systems, and compute them for several hard particle systems. We show that they are on the order of a few kT at the onset of ordering, placing DEFs on par with traditional depletion, van der Waals, and other intrinsic interactions. In experimental systems with these other interactions, we provide direct quantitative evidence that entropic effects of shape also contribute to self-assembly. We use DEFs to draw a distinction between self-assembly and packing behavior. We show that the mechanism that generates directional entropic forces is the maximization of entropy by optimizing local particle packing. We show that this mechanism occurs in a wide class of systems, and we treat, in a unified way, the entropy-driven phase behavior of arbitrary shapes incorporating the well-known works of Kirkwood, Onsager, and Asakura and Oosawa.

cond-mat.soft↗

arXiv2013

Complexity in surfaces of densest packings for families of polyhedra

Packings of hard polyhedra have been studied for centuries due to their mathematical aesthetic and more recently for their applications in fields such as nanoscience, granular and colloidal matter, and biology. In all these fields, particle shape is important for structure and properties, especially upon crowding. Here, we explore packing as a function of shape. By combining simulations and analytic calculations, we study three 2-parameter families of hard polyhedra and report an extensive and systematic analysis of the densest packings of more than 55,000 convex shapes. The three families have the symmetries of triangle groups (icosahedral, octahedral, tetrahedral) and interpolate between various symmetric solids (Platonic, Archimedean, Catalan). We find that optimal (maximum) packing density surfaces that reveal unexpected richness and complexity, containing as many as 130 different structures within a single family. Our results demonstrate the utility of thinking of shape not as a static property of an object in the context of packings, but rather as but one point in a higher dimensional shape space whose neighbors in that space may have identical or markedly different packings. Finally, we present and interpret our packing results in a consistent and generally applicable way by proposing a method to distinguish regions of packings and classify types of transitions between them.

cond-mat.soft↗

arXiv2013

Emergent collective phenomena in a mixture of hard shapes through active rotation

We investigate collective phenomena with rotationally driven spinners of concave shape. Each spinner experiences a constant internal torque in either a clockwise or counterclockwise direction. Although the spinners are modeled as hard, otherwise non-interacting rigid bodies, we find that their active motion induces an effective interaction that favors rotation in the same direction. With increasing density and activity, phase separation occurs via spinodal decomposition, as well as self-organization into rotating crystals. We observe the emergence of cooperative, super-diffusive motion along interfaces, which can transport inactive test particles. Our results demonstrate novel phase behavior of actively rotated particles that is not possible with linear propulsion or in non-driven, equilibrium systems of identical hard particles.

cond-mat.soft↗

arXiv2013

Controlling crystal self-assembly using a real-time feedback scheme

We simulate crystallisation of hard spheres with short-ranged attractive potentials, as a model self-assembling system. We show how measurements of correlation and response functions during assembly can be used to tune the interaction parameters as assembly proceeds, in order to obtain high-quality crystals. The method we use is independent of details of the interaction potential and of the structure of the final crystal - we propose that it could be applied to a wide range of self-assembling systems.

cond-mat.soft↗

arXiv2011

Predicting the self-assembly of a model colloidal crystal

We investigate the self-assembly (crystallisation) of particles with hard cores and isotropic, square-well interactions, using a Monte Carlo scheme to simulate overdamped Langevin dynamics. We measure correlation and response functions during the early stages of assembly, and we analyse the results using fluctuation-dissipation theorems, aiming to predict which systems will self-assemble successfully and which will get stuck in disordered states. The early-time correlation and response measurements are made before significant crystallisation has taken place, indicating that dynamical measurements are valuable in measuring a system's propensity for kinetic trapping.

cond-mat.soft↗

arXiv2005

Electronic Transport in DNA

We study the electronic properties of DNA by way of a tight-binding model applied to four particular DNA sequences. The charge transfer properties are presented in terms of localisation lengths, crudely speaking the length over which electrons travel. Various types of disorder, including random potentials, are employed to account for different real environments. We have performed calculations on poly(dG)-poly(dC), telomeric-DNA, random-ATGC DNA and lambda-DNA. We find that random and lambda-DNA have localisation lengths allowing for electron motion among a few dozen base pairs only. A novel enhancement of localisation lengths is observed at particular energies for an increasing binary backbone disorder. We comment on the possible biological relevance of sequence dependent charge transfer in DNA.

q-bio.GN↗