arXiv subjects

Richard P. Sear

Publications and source records attributed to Richard P. Sear.

At least 19 recordsLinked to original sources

arXiv2025

Simple models for the trapping of charged particles and macromolecules by diffusiophoresis in salt gradients

We study the trapping of charged particles and macromolecules (such as DNA) in salt gradients in aqueous solutions. The source for the salt gradient can be as simple as a dissolving ionic crystal, as shown by McDermott et al. [Langmuir 28, 15491 (2012)]. Trapping is due to a competition between localisation due to diffusiophoresis in the salt gradient, and spreading out by diffusion. The size of the trap is typically 1 to 100 micrometres. We further predict that at steady state, the particle (macromolecule) number density is a power law of the salt concentration, with an exponent that is the ratio of the diffusiophoretic mobility to the diffusion coefficient of the trapped species. This ratio increases with size and typically becomes much greater than 1 for particles or macromolecules with hydrodynamic radii of hundreds of nanometres and above. Thus large particles or macromolecules are easily caught and trapped at steady state by salt gradients.

cond-mat.soft↗

arXiv2024

Salt solutions with two or more salts generate ion currents analogous to magnetic field lines

A gradient of a single salt in a solution generates an electric field, but not a current. Recent theoretical work by one of us [Phys. Rev. Lett. 24, 248004 (2020)] showed that the Nernst-Planck equations imply that crossed gradients of two or more different salts generate ion currents. These currents in solution have associated non-local electric fields. Particle motion driven by these non-local fields has recently been observed in experiment by Williams et al. [Phys. Rev. Fluids 9, 014201 (2024)]; a phenomenon which was dubbed action-at-a-distance diffusiophoresis. Here we use a magnetostatic analogy to show that in the far-field limit, these non-local currents and electric fields both have the functional form of the magnetic field of a magnetic dipole, decaying as r^(-d) in d = 2 and d = 3 dimensions. These long-ranged electric fields are generated entirely within solutions and have potential practical applications since they can drive both electrophoretic motion of particles, and electro-osmotic flows. The magnetostatic analogy also allows us to import tools and ideas from classical electromagnetism, into the study of multicomponent salt solutions.

cond-mat.soft↗

arXiv2024

Estimating the population-level effects of non-pharmaceutical interventions when transmission rates of COVID-19 vary by orders of magnitude from one contact to another

Statistical physicists have long studied systems where the variable of interest spans many orders of magnitude, the classic example is the relaxation times of glassy materials, which are often found to follow power laws. A power-law dependence has been found for the probability of transmission of COVID-19, as a function of length of time a susceptible person is in contact with an infected person. This is in data from the United Kingdom's COVID-19 app. The amount of virus in infected people spans many orders of magnitude. Inspired by this I assume that the power-law behaviour found in COVID-19 transmission, is due to the effective transmission rate varying over orders of magnitude from one contact to another. I then use a model from statistical physics to estimate that if a population all wear FFP2/N95 masks, this reduces the effective reproduction number for COVID-19 transmission by a factor of approximately nine.

physics.soc-ph↗

arXiv2023

Colloidal diffusiophoresis in crossed electrolyte gradients: experimental demonstration of an 'action at a distance' effect predicted by the Nernst-Planck equations

In an externally imposed electrolyte (salt) concentration gradient, charged colloids drift at speeds of order one micrometre per second. This phenomenon is known as diffusiophoresis. In systems with multiple salts and 'crossed' salt gradients, a nonlocal component of the electric field associated with a circulating (solenoidal) ion current can arise. This is in addition to the conventional local component that depends only on the local salt gradients. Here we report experimental observations verifying the existence of this nonlocal contribution. To our knowledge this is the first observation of nonlocal diffusiophoresis. The current develops quasi-instantaneously on the time scale of salt diffusion. Therefore, in systems with multiple salts and crossed salt gradients, one can expect a nonlocal contribution to diffusiophoresis which is dependent on the geometry of the system as a whole and appears as a kind of instantaneous 'action-at-a-distance' effect. The interpretation is aided by a magnetostatic analogy. Our experiments are facilitated by a judicious particle-dependent choice of salt (potassium acetate) for which the two local contributions to diffusiophoresis almost cancel, effectively eliminating conventional diffusiophoresis. This enables us to clearly identify the novel, nonlocal effect and may be useful in other contexts, for example in sorting particle mixtures.

cond-mat.soft↗

arXiv2022

Modelling the filtration efficiency of a woven fabric: The role of multiple lengthscales

During the COVID-19 pandemic, many millions have worn masks made of woven fabric, to reduce the risk of transmission of COVID-19. Masks are essentially air filters worn on the face, that should filter out as many of the dangerous particles as possible. Here the dangerous particles are the droplets containing virus that are exhaled by an infected person. Woven fabric is unlike the material used in standard air filters. Woven fabric consists of fibres twisted together into yarns that are then woven into fabric. There are therefore two lengthscales: the diameters of: (i) the fibre and (ii) the yarn. Standard air filters have only (i). To understand how woven fabrics filter, we have used confocal microscopy to take three dimensional images of woven fabric. We then used the image to perform Lattice Boltzmann simulations of the air flow through fabric. With this flow field we calculated the filtration efficiency for particles a micrometre and larger in diameter. In agreement with experimental measurements by others, we find that for particles in this size range, filtration efficiency is low. For particles with a diameter of 1.5 micrometres our estimated efficiency is in the range 2.5 to 10%. The low efficiency is due to most of the air flow being channelled through relatively large (tens of micrometres across) inter-yarn pores. So we conclude that fabric is expected to filter poorly due to the hierarchical structure of woven fabrics.

physics.flu-dyn↗

arXiv2022

How effective are face coverings in reducing transmission of COVID-19?

In the COVID-19 pandemic, billions are wearing face masks, in both health care settings and in public. Which type of mask we should wear in what situation, is therefore important. There are three basic types: cotton, surgical, and respirators (e.g. FFP2, N95 and similar). All are essentially air filters worn on the face. Air filtration is relatively well understood, however, we have almost no direct evidence on the relative role played by aerosol particles of differing sizes in disease transmission. But if the virus concentration is assumed independent of aerosol particle size, then most virus will be in particles > 1 $μ$m. We develop a model that predicts surgical masks are effective at reducing the risk of airborne transmission because the filtering material most surgical masks use is highly effective at filtering particles with diameters > 1 $μ$m. However, surgical masks are significantly less effective than masks of FFP2, N95 and similar standards, mostly due to the poor fit of surgical masks. Earlier work found that ~30% of the air bypasses a surgical mask and is not filtered. This highlights the fact that standards for surgical masks do not specify how well the mask should fit, and so are not adequate for protection against COVID-19.

cond-mat.soft↗

arXiv2021

Efficacy of face coverings in reducing transmission of COVID-19: calculations based on models of droplet capture

In the COVID--19 pandemic, among the more controversial issues is the use of masks and face coverings. Much of the concern boils down to the question -- just how effective are face coverings? One means to address this question is to review our understanding of the physical mechanisms by which masks and coverings operate -- steric interception, inertial impaction, diffusion and electrostatic capture. We enquire as to what extent these can be used to predict the efficacy of coverings. We combine the predictions of the models of these mechanisms which exist in the filtration literature and compare the predictions with recent experiments and lattice Boltzmann simulations, and find reasonable agreement with the former and good agreement with the latter. Building on these results, we explore the parameter space for woven cotton fabrics to show that three-layered cloth masks can be constructed with comparable filtration performance to surgical masks under ideal conditions. Reusable cloth masks thus present an environmentally friendly alternative to surgical masks so long as the face seal is adequate enough to minimise leakage.

cond-mat.soft↗

arXiv2019

Diffusiophoresis in Cells: a General Non-Equilibrium, Non-Motor Mechanism for the Metabolism-Dependent Transport of Particles in Cells

The more we learn about the cytoplasm of cells, the more we realise that the cytoplasm is not uniform but instead is highly inhomogeneous. In any inhomogeneous solution, there are concentration gradients, and particles move either up or down these gradients due to a mechanism called diffusiophoresis. I estimate that inside metabolically active cells, the dynamics of particles can be strongly accelerated by diffusiophoresis, provided that they are at least tens of nanometres across. The dynamics of smaller objects, such as single proteins are largely unaffected.

q-bio.SC↗

arXiv2017

Diffusiophoresis in non-adsorbing polymer solutions: the Asakura-Oosawa model and stratification in drying films

A colloidal particle placed in an inhomogeneous solution of smaller non-adsorbing polymers will move towards regions of lower polymer concentration, in order to reduce the free energy of the interface between the surface of the particle and the solution. This phenomenon is known as diffusiophoresis. Treating the polymer as penetrable hard spheres, as in the Asakura-Oosawa model, a simple analytic expression for the diffusiophoretic drift velocity can be obtained. In the context of drying films we show that diffusiophoresis by this mechanism can lead to stratification under easily accessible experimental conditions. By stratification we mean spontaneous formation of a layer of polymer on top of a layer of the colloid. Transposed to the case of binary colloidal mixtures, this offers an explanation for the stratification observed recently in these systems [A. Fortini et al, Phys. Rev. Lett. 116, 118301 (2016)]. Our results emphasise the importance of treating solvent dynamics explicitly in these problems, and caution against the neglect of hydrodynamic interactions or the use of implicit solvent models in which the absence of solvent backflow results in an unbalanced osmotic force which gives rise to large but unphysical effects.

cond-mat.soft↗

arXiv2017

Controlling the crystal polymorph by exploiting the time dependence of nucleation rates

Most substances can crystallise into two or more different crystal lattices, called polymorphs. Despite this, there are no systems in which we can quantitatively predict the probability of one competing polymorph forming, instead of the other. We address this problem using large scale (hundreds of events) studies of the competing nucleation of the alpha and gamma polymorphs of glycine. In situ Raman spectroscopy is used to identify the polymorph of each crystal. We find that the nucleation kinetics of the two polymorphs is very different. Nucleation of the alpha polymorph starts off slowly but accelerates, while nucleation of the gamma polymorph starts off fast but then slows. We exploit this difference to increase the purity with which we obtain the gamma polymorph by a factor of ten. The statistics of the nucleation of crystals is analogous to that of human mortality, and using a result from medical statistics we show that conventional nucleation data can say nothing about what, if any, are the correlations between competing nucleation processes. Thus we can show that, with data of our form, it is impossible to disentangle the competing nucleation processes. We also find that the growth rate and the shape of a crystal depends on when it nucleated. This is new evidence that nucleation and growth are linked.

cond-mat.soft↗

arXiv2016

Dynamic stratification in drying films of colloidal mixtures

In simulations and experiments, we study the drying of films containing mixtures of large and small colloidal particles in water. During drying, the mixture stratifies into a layer of the larger particles at the bottom with a layer of the smaller particles on top. We developed a model to show that a gradient in osmotic pressure, which develops dynamically during drying, is responsible for the segregation mechanism behind stratification.

cond-mat.soft↗

arXiv2015

Liquids that form due to dynamics of the molecules that depend on the local density

RNA molecules in living cells form what look like liquid droplets formed by liquid/liquid phase separation. But unlike the molecules in conventional phase separating mixtures, RNA molecules are transported by molecular motors that consume energy and so are out of equilibrium. Motivated by this we consider what sort of simple rules for the dynamics of model mRNA molecules lead to liquid/liquid phase separation. We find that dynamics that slow as the local density of molecules increases, drive the formation of liquids. We also look at the analogous separation of the two blocks of a block copolymer, in which the monomers of one block have dynamics that depend on the local density of monomers of that block. We find that this block condenses and separates from the monomers of the other block. This is a simple model of the out-of-equilibrium domain formation found in the chromatin in the nucleus of cells.

cond-mat.soft↗

arXiv2014

Nucleation of a new phase on a surface that is changing irreversibly with time

Nucleation of a new phase almost always starts at a surface. This surface is almost always assumed not to change with time. However, surfaces can roughen, partially dissolve and change chemically with time. Each of these irreversible changes will change the nucleation rate at the surface, resulting in a time-dependent nucleation rate. Here we use a simple model to show that partial surface dissolution can qualitatively change the nucleation process, in a way that is testable in experiment. The changing surface means that the nucleation rate is increasing with time. There is an initial period during which no nucleation occurs, followed by relatively rapid nucleation.

cond-mat.soft↗

arXiv2013

Generalisation of Levine's prediction for the distribution of freezing temperatures of droplets: A general singular model for ice nucleation

Models without an explicit time dependence, called singular models, are widely used for fitting the distribution of temperatures at which water droplets freeze. In 1950 Levine developed the original singular model. His key assumption was that each droplet contained many nucleation sites, and that freezing occurred due to the nucleation site with the highest freezing temperature. The fact that freezing occurs due to the maximum value out of large number of nucleation temperatures, means that we can apply the results of what is called extreme-value statistics. This is the statistics of the extreme, i.e., maximum or minimum, value of a large number of random variables. Here we use the results of extreme-value statistics to show that we can generalise Levine's model to produce the most general singular model possible. We show that when a singular model is a good approximation, the distribution of freezing temperatures should always be given by what is called the generalised extreme-value distribution. In addition, we also show that the distribution of freezing temperatures for droplets of onesize, can be used to make predictions for the scaling of the median nucleation temperature with droplet size, and vice versa.

physics.ao-ph↗

arXiv2006

Modeling Dual Pathways for the Metazoan Spindle Assembly Checkpoint

Using computational modelling, we investigate mechanisms of signal transduction focusing on the spindle assembly checkpoint where a single unattached kinetochore is able to signal to prevent cell cycle progression. This inhibitory signal switches off rapidly once spindle microtubules have attached to all kinetochores. This requirement tightly constrains the possible mechanisms. Here we investigate two possible mechanisms for spindle checkpoint operation in metazoan cells, both supported by recent experiments. The first involves the free diffusion and sequestration of cell-cycle regulators. This mechanism is severely constrained both by experimental fluorescence recovery data and also by the large volumes involved in open mitosis in metazoan cells. Using a simple mathematical analysis and computer simulation, we find that this mechanism can generate the inhibition found in experiment but likely requires a two stage signal amplification cascade. The second mechanism involves spatial gradients of a short-lived inhibitory signal that propagates first by diffusion but then primarily via active transport along spindle microtubules. We propose that both mechanisms may be operative in the metazoan spindle assembly checkpoint, with either able to trigger anaphase onset even without support from the other pathway.

q-bio.SC↗

arXiv2005

The cytoplasm of living cells: A functional mixture of thousands of components

Inside every living cell is the cytoplasm: a fluid mixture of thousands of different macromolecules, predominantly proteins. This mixture is where most of the biochemistry occurs that enables living cells to function, and it is perhaps the most complex liquid on earth. Here we take an inventory of what is actually in this mixture. Recent genome-sequencing work has given us for the first time at least some information on all of these thousands of components. Having done so we consider two physical phenomena in the cytoplasm: diffusion and possible phase separation. Diffusion is slower in the highly crowded cytoplasm than in dilute solution. Reasonable estimates of this slowdown can be obtained and their consequences explored, for example, monomer-dimer equilibria are established approximately twenty times slower than in a dilute solution. Phase separation in all except exceptional cells appears not to be a problem, despite the high density and so strong protein-protein interactions present. We suggest that this may be partially a byproduct of the evolution of other properties, and partially a result of the huge number of components present.

cond-mat.soft↗

arXiv2005

Formation of a metastable phase due to the presence of impurities

Phase transitions into a new phase that is itself metastable are common; instead of the equilibrium phase nucleating a metastable phase does so. When this occurs the system is sometimes said to be obeying Ostwald's rule. We show how this can happen when there are impurities present that reduce the barrier to heterogeneous nucleation of the metastable phase. We do so by studying a Potts lattice model using Monte Carlo simulation. Thus, which phase forms depends not only on the properties of the different phases but also on the impurities present. Understanding why systems obey Ostwald's rule may therefore require a study of the impurities present.

cond-mat.stat-mech↗

arXiv2004

A model for the accidental catalysis of protein unfolding in vivo

Activated processes such as protein unfolding are highly sensitive to heterogeneity in the environment. We study a highly simplified model of a protein in a random heterogeneous environment, a model of the in vivo environment. It is found that if the heterogeneity is sufficiently large the total rate of the process is essentially a random variable; this may be the cause of the species-to-species variability in the rate of prion protein conversion found by Deleault et al. [Nature, 425 (2003) 717].

q-bio.BM↗