Interplay of active nematic defects and flow structures

Active nematics are a class of liquid crystals driven out-of-equilibrium by the intrinsic activity of the rod-like constituents. In bulk, global nematic order is destabilised via the coupled feedback between nematic deformations and active flows, facilitating a steady-state population of pairs of half-integer nematic topological defects and chaotic flows (active turbulence). When confined, active nematics can exhibit active turbulence if the activity is sufficient, or more ordered spatiotemporal flow field patterns with a reduced defect count, dependent on the confinement scale. Understanding these complex flow regimes have naturally favoured perspectives centred on the nematic defects, as their emergent steady-state presence is an evident feature of active nematics. Defect orientation, motility and flow generation has been employed to study quasi-particle like descriptions of larger scale flow structures [1]. Within this description, the production of active flows around defects has been studied [2], revealing that the flow-field solution around a +1/2 defect is associated with two vortices and a self-propulsion velocity, while the -1/2 defect is associated with six vortices and active flows tending to zero at their core. However, this viewpoint is necessarily an oversimplification since flows are not simply governed by defects – flows influence the defects in parallel. The reverse viewpoint, ‘how nematic defects respond to the structure of the flow field’, is therefore important for understanding the architecture of active flow patterns but has not received adequate attention. Through experiments of microtubule-kinesin based active nematics [3], and mesoscopic simulations [4], we explore how defects couple to the structure of the velocity field in 2D. We adopt a topological description of the velocity field, identifying the borders between rotationally dominated and strain-rate dominated regions. We establish the importance of these boundaries as paths for defect dynamics and categorize defect behaviours into two regimes associated with +1/2 defects tracing either one boundary or instantaneously traversing intersections. These results demonstrate that the ideal picture of two vortices associated with each of the +1/2 defects is not characteristic of active nematics. Through utilizing topological descriptions of structures in the director field and velocity field, we can provide a complementary perspective on active nematic flows and possible control mechanisms by manipulating either field.

References:
[1] S. Shankar and M. C. Marchetti, Phys Rev. X 9, 041047, (2019)
[2] L. Giomi et al., Phil. Trans. R. Soc. A. 372:20130365, (2014)
[3] J. Hardoüin et al. Nat. Commun. 13 (1), 6675, (2022)
[4] K. Thijssen et al. Soft Matter 16, 2065-2074, (2020)

First passage time statistics of non-Markovian walkers: Onsager’s regression hypothesis approach

How long does it take for a random walker to reach its destination? Such a question on “first passage time” is fundamental in stochastic process, and relevant to many practical applications.
While the problem for the Markovian case (memory free) is well documented in literature, the presence of memory effect makes the standard analysis intractable, leaving many open questions in non-Markovian cases. We propose a method to think about the first passage statistics based on the non-equilibrium statistical mechanics idea, i.e., Onsager’s regression hypothesis, and demonstrate that it enables us to calculate various quantities of interest for non-Markovian systems analytically.

This work is in collaboration with Y. Sakamoto (Aoyama Gakuin University)
Reference: https://arxiv.org/abs/2301.13466

Using movement data to analyze the effect of lockdowns and inform their implementation – the Italian case

While lockdowns are certainly effective in curbing the rise of infections, their imposition severely affects the life and health of citizens. For this reason, the extent of their deployment should be optimized both in time and space to minimize the number of people affected while guaranteeing the safety of the population. At the same time, contact-tracing initiatives can easily violate privacy laws, and are generally difficult to implement for a public administration. It is thus interesting to consider whether anonymized samples of social networks’ datasets still contain enough information to optimize the implementation of lockdowns. Starting from Facebook (FB) users’ movement data from META’s data for good program and publicly available data from the Italian Institute of Statistics (ISTAT), we show how a data-driven meta-population approach can be used to identify a spatial subdivision of a state that maximises movements within communities, while minimizing those outside of them. Specifically, we focus on the level of movements between provinces, administrative entities in between municipalities and regions. After verifying that FB movement data gives reasonable population density in each province, we show that a temporal clustering correctly identifies the first two national lockdowns without any prior information. Finally, by considering the most representative movement networks in both a lockdown and free-movement situation, we identify the optimal communities, i.e. macro regions that minimize the amount of traffic between them. Using two different approaches -modularity and resolution/relevance – gives largely comparable results, supporting the robustness of our findings.

Effect of bacterial diet on bacteriophage infection

Bacteria play a huge role in the human and natural world, for richer and for poorer. Their most well-known role being a pathogen. With the gradual reduction in antimicrobial efficacy, the promise of phage as a potential solution has gathered attention.
Bacteria are also able to rapidly develop resistances to bacteriophage through numerous pathways. Here I have investigated how the bacteria-bacteriophage system dynamics depends on environmental conditions. Escherichia coli, grown in a range of media with various carbon sources, were exposed to T1 bacteriophage. In all cases the bacteria developed a resistance to the phage at long times. However, the population dynamics of the system both post and during infection varied with both carbon source and the number of phage added. Long-read and short-read sequencing of surviving mutant bacteria was undertaken. These results suggest a coupling between carbon source and the progression of a bacterial populations response. These results contribute to the understanding of the dominant factors in the growth of phage which could result in significant differences between the rates of death and resistance development in vivo and in vitro due to differing environmental conditions.

Soft matter lubrication

Friction between sliding surfaces has a great economic and environmental cost, with it leading to a third of a car’s fuel use and wasting 23% of global energy production. This has spurred development of highly loaded contacts with liquid lubricants. Lightly loaded surfaces, with a thick liquid film are considered inefficient, and even trivial. This situation is common in soft matter, from swallowing food, or applying skin cream, to ceramic extrusion and even in synovial joints. However, there are additional complexities such as texture (tongue papillae), a non-Newtonian fluid (skin cream), deformability or a combination of sliding and squeezing.

In this talk, I will explore how scaling theories, alongside experiments, can disentangle soft matter lubrication. For a textured surface, the delicate balance between shear and pressure-driven flows is highlighted, while squeeze flow beneath a flexible surface isolates the coupling between pressure-driven flow and deformation. Finally, I will touch upon how such approaches lead to the design of optimised non-Newtonian fluids.

Time-dependent dynamics of 3D states in viscoelastic pressure-driven channel flow

Dilute polymer solutions do not flow like Newtonian fluids. Their flows exhibit in- stabilities at very low Reynolds numbers that are driven not by inertia, but rather by anisotropic elastic stresses. Further increase of the flow rate results in a chaotic flow, often referred to as purely elastic turbulence. The mechanism of this new type of chaotic motion is poorly understood.
In this talk we present the first coherent state in purely elastic parallel shear flows. We consider a model shear-thinning viscoelastic fluid driven by an applied pressure gradient through two- and three-dimensional channels. By starting from a linearly unstable mode recently discovered by Khalid et al.1 at very large flow rates and very low polymer dilution, we demonstrate that this instability sub-critically connects to significantly higher values of polymer concentration and lower flow rates2, rendering these structures experimentally relevant The dynamics becomes unsteady upon embedding the 2D coherent state in a 3D domain, see Fig. 1 for an instantaneous snapshot, and the time-dependent dynamics is discussed. The characterisation of those 3D states suggests their strong connection to purely elastic turbulence.

To the Centre of Titan and Beyond: 30 Years of Neutron Diffraction with The Paris-Edinburgh Cell

From Membrane Binding to Function: Investigating the Importance of Anionic Lipids in Alpha-Synuclein Biology

Alpha-synuclein, a protein that is abundant in the brain, has been linked to several neurodegenerative disorders, including Parkinson’s disease. Lipids are crucial to the normal function of alpha-synuclein, as well as to the development of disease. In my research, I have investigated the initial interaction between alpha-synuclein and model lipid membranes, which involves membrane remodeling activity, with amyloid fibril formation occurring during longer incubation periods. I have examined the impact of various factors, such as the composition of model lipid membranes, protein variants, and the presence of molecules that remain bound to neuronal membranes under physiological conditions, on the outcome of this reaction. Using a combination of methods, including spectroscopy and microscopy, I have studied the interaction between alpha-synuclein and model lipid membranes. The results of these studies provide new insights into the role of lipids in the biology of alpha-synuclein and may contribute to the development of novel therapies for neurodegenerative disorders.

Functionalization of boundaries in active nematics: inclusions and confinement.

Active fluids and their spontaneous flows promise exciting new paths toward efficient transport phenomena and new autonomous materials. However, the fulfillment of this promise pends on finding effective ways to control them. In this regard, an auspicious avenue is the use of inclusions and confinement, which, in its simplest form, has led to the emergence of long-lived coordinated flows. Here we extend these efforts in two different ways: First, we show how combining custom anchoring conditions within nematic colloidal inclusions can lead to an effective self-propulsion. In particular, we show how the steering dynamics of such self-propulsion is intimately linked to the dynamics of a companion -1/2 topological defect. Second, by expanding to 3D channels, we show how confinement can lead to spontaneous helical flows that break chiral symmetry both locally and globally. As such, this work demonstrates the potential of confinement geometry to unravel complex but organized spatiotemporal structures in active liquid crystals, thus showing that they may present a path to functionality.

Single-Molecule Structure and Topology of Kinetoplast DNA Networks

The Kinetoplast DNA (kDNA) is a 2D network of mutually inter-linked DNA minicircles found in Trypanosomes that heavily resembles an “Olympic gel”. Understanding the self-assembly and replication of this structure are not only major open questions in biology but can also inform the design of synthetic topological materials such as polycatenanes, dubbed as “the Holy Grail of Polymer Chemistry” by Nobel laureate Sir Fraser Stoddart.
In this talk I will present the first high-resolution, single-molecule study of kDNA network topology using AFM and steered molecular dynamics simulations. We accurately measure the spatial distribution of DNA in the network and quantify the distribution of valence of the minicircles. Additionally, we use sub-isostatic network theory to characterise the elastic Young modulus and bending stiffness of the network, and discover that they are 10^6 and 10^3 times smaller than the ones in typical 2D materials such as lipid membranes, thus rendering the kDNA the first example of a “ultra-soft” topological gel.
Our findings explain outstanding questions in the biology of kDNA and offer single-molecule insights into the properties of a unique topological material.

Producing the Ultimate High Energy Density Material

Nitrogen is a truly unique element. As a diatomic molecule, N2, is extremely stable and features the strongest homoatomic bond. However, under the application of extreme pressures and temperatures, the N2 molecule breaks apart and nitrogen transforms into a 3D polymeric solid called cubic gauche polymeric nitrogen (cg-N). This solid, comprised solely of single-bonded nitrogen atoms, is the ultimate high energy density material. It can store and release about 10x more energy than the best compounds and is 100% environmentally friendly. A small problem remains: cg-N cannot be recovered to ambient conditions.

In this talk, we will explore a variety of experimental high-pressure high-temperature paths to produce alternatives to cg-N. An unexpectedly large zoology of nitrogen species is discovered, with many exotic and exciting properties, including materials highly energetic and fully recoverable to ambient conditions.

Room 2511 JCMB

Interfacial rheology – measuring mechanical properties of complex-liquid interfaces

In this presentation, I will introduce colloidal, micron-sized particles at liquid interfaces. These are interesting 2D model systems, but they are also interesting for (potential) applications e.g. particle-stabilized aka Pickering emulsions and bijels (bicontinuous Pickering emulsions). The mechanical properties of the particle-laden interfaces are challenging to measure, but they are important, for example to explain Pickering-emulsion stability. I will summarize some of our past and recent work on measuring and interpreting the mechanical properties of particle-laden liquid interfaces, including our recent development of ‘contactless’ interfacial rheology.

Today at 4:00 pm, back in JCMB room 2511.

Biomimetic crystallization of biomorphs and chemical gardens: Understanding their formation and studying their self-motion

Abiotic crystallization is typically described by classical models to form geometric shapes with flat faces, sharp edges, and well defined angles. This is in stark contrast to crystallization routes used by living systems which instead grows smoothly curved shapes such as teeth, bone, and nacre. Such morphological distinctions have been applied to determine the biogenicity of structures found in ancient rocks. However, laboratory experiments in far-from-equilibrium systems are able to precipitate similar curvilinear morphologies previously only prescribed to living organisms thus blurring the line between structures derived from biotic and abiotic origins. The first example I will discuss is the crystallization of metal carbonate and silica microstructures known as “biomorphs”. They are composed of thousands of coaligned nanorods that self-organize into larger life-like shapes such as leaf-like sheets, helices, funnels, and flowers. At the nanoscale, the growing crystallization front forms from the addition of smaller nanodot building units that merge into the elongated rod shape. At the microscale, the pseudo two-dimensional sheet shape can be simulated using reaction-diffusion equations. Finally, the hierarchical ordering is extended into the centimeter scale with the merging of neighbouring biomorphs at the air-solution interface. The second example is chemical gardens. Formed from steep chemical gradients between a metal salt and a solution of silicate, the final result is hollow tubes which resemble filaments found in many geological settings. This quick and easy production process for generating tubes can be exploited by controlling the composition of the final material to create self-moving chemical gardens.

“Polymer physics of cancer genomes”

While every cell in our bodies contains the same genome, different sets of genes are active in different types of cell, and the “switching on and off” of specific genes must be tightly controlled as cells develop. Gene regulation is tightly related to the spatial organisation of the chromosomes within the cell nucleus. A number of physical mechanisms through which this organisation is controlled have been identified, and polymer physics models have proved extremely useful for understanding these. I will present recent work in which polymer models were used to understand genome rearrangements in cancer. There are several methods which the cell employs to repair the genome should the DNA get broken, however these sometimes do not work correctly, and genome rearrangements can arise. For example, two different broken chromosomes could get joined together; this changes the spatial organisation, disrupts gene regulation, and can give rise to disease. Our polymer simulations were able to predict the changes in gene expression which result from genome rearrangements commonly found in B-cell cancers, shedding light on this poorly understood process. The results also allowed us to identify specific sites on the DNA which drive oncogene overexpression after the rearrangement. We are now performing genome editing experiments which target these sites with a view to reversing the over-expression; this will provide new understanding which could eventually lead to new therapies.

First principles crystal structure prediction

The last 15 years have established crystal structure prediction from electronic structure calculations as a genuine tool for materials discovery, which can interpret, guide, and sometimes correct experimental findings. In this talk I will review how this came about, how and why structure prediction works, how and why it fails, and discuss some of the ongoing efforts to increase the method’s capabilities.

How We Measure Pressure: Pressure Determination in Static High-Pressure Experiments

Advances in experimental design over the past few decades have dramatically increased the pressures accessible both with static and dynamic compression techniques. In tandem, techniques for measuring the pressure induced in a sample have evolved and continue to be developed to overcome the challenges faced when pushing matter into the ultra-high-pressure domain. I will provide a brief overview of the history of pressure measurement, explore current state of the art methods, and discuss the challenges involved in determining the pressure in diamond anvil cells at multi-megabar conditions.

How to give a talk

Intranuclear phase separation, and its role in transcription and gene regulation

Microscopy studies suggest that chromatin and its associated proteins often form phase separated droplets within the nucleus of eukaryotic organisms. I will discuss some possible biophysical mechanisms, suggested by coarse-grained molecular dynamics simulations and theory, underlying such intranuclear phase separation and microphase separation (arrested phase separation resulting in the formation of droplets of self-limiting size). I will also discuss potential functional roles of phase separation in transcription and gene regulation. We will see that these phenomena provide a way to quantitatively understand the elusive link between the 3D structure of a gene and its expression level,  and to predict the transcriptional activity of, in principle, any human gene.

Statistics and dynamics of plectonemes in braided structures

Braids composed by two intertwined filaments naturally arise in biological systems, such as during DNA replication [1] and in amyloid fibrils [2]. Interestingly, braids subject to a pulling force display a phase transition [3]: when the linking number between the two strands exceeds a critical number, the braid, initially straight, writhes in 3D forming structures known as plectonemes. Nowadays, single molecule experiments can easily investigate the physics behind such a transition and plectonemes diffusion along the braided structure [4].

In the last few years, we developed a polymer model which, combined with a stochastic field theory, allows to visualise plectonemes as structures interacting through phenomena typical of liquid-gas systems [5]. Moreover, a further application of the polymer model has allowed investigation into site-selection mechanisms of retroviruses into DNA braids revealing spatio-temporal correlations between consecutive integration events [6].

In this talk I will summarise our main results providing insights about polymer braids, their applications and possible future research areas.

[1] A. Mariezcurrena and F. Uhlmann. Genes & Development 31, 2151 (2017).

[2] C. Ionescu-Zanetti, R. Khurana, J. R. Gillespie, J. S. Petrick, L. C. Trabachino, L. J. Minert, S. A. Carter, and A. L. Fink. Proceedings of the National Academy of Sciences 96, 13175 (1999).

[3] G. Charvin, A. Vologodskii, D. Bensimon, and V. Croquette. Biophysical Journal 88, 4124 (2005).

[4] M. T. J. van Loenhout, M. V. de Grunt, and C. Dekker. Science 338, 94 (2012).

[5] G. Forte, M. Caraglio, D. Marenduzzo, and E. Orlandini. Physical Review E 99, 052503 (2019).

[6] G. Forte, D. Michieletto, D. Marenduzzo, and E. Orlandini. Journal of the Royal Society Interface 18, 20210229 (2021).

Buckling instabilities in chaining bacterial colonies

Bacteria in the natural environment frequently grow as structured communities known as bacterial biofilms. The morphology of the colony is an emergent property, driven in part by the growth and activity of the constituents. Here, we are interested in the effect of pole-pole adhesion between constituents on the resulting colony dynamics and properties, in an effort to understand more about colonies of chaining bacteria such as \textit{Bacillus subtilis}. In this work, we investigate a 2D discrete element simulation of a growing bacterial colony composed of non-motile rod-shaped bacteria where daughter cells are able to `chain’ together with springs. We find that despite the simplicity of the model, the emergent dynamics and morphology of the colony are drastically altered. At small chain lengths, the classic mosaic of micro-domains is recovered where the colony is isotropic on large length-scales but locally is heterogeneous and composed of domains of aligned cells. As we increase the chain length, there is a crossover to a regime where the colony is able to collectively buckle, characterised by an oscillatory-type morphology and a peak in observable properties e.g. colony aspect ratio, density, micro-domain area etc.. Continuing to increase the chain length gives rise to the possibility of individual chains buckling due to active stresses within the chain overcoming the restoring elastic force of the links, leading to a winding, ribbon-like appearance of the colony and a collapse in the observable properties.

Supercritical Fluids – Not Quite So Indistinguishable

While the gaseous and solid states of matter are relatively well understood, and clearly distinguished by their lack of or presence of long-range order, a complete characterisation of the liquid state is still being debated. Generally, liquids have been thought of by analogy to gases, as an extreme case of non-ideal gases. The problem with this approach is that one can compress a fluid to reach densities comparable to those of the solid, which cannot be tackled by analogy to gases. Midway through the last century, Yakov Frenkel proposed a ‘Kinetic Theory of Liquids’, where he aimed to describe liquids by analogy to solids, leading to a more realistic but also significantly conceptually denser theory than traditional gas analogies. Due to the latter fact his theory was largely ignored by researchers without a particular interest in very high densities, i.e. the canonical liquids community. However, in 2012, a crossover was proposed to occur in supercritical and near-supercritical fluids (Brazhkin, PRL) between a non-rigid ‘gas’-like state and a rigid ‘liquid’-like state. This crossover, called a ‘Frenkel line’, was originally characterised by the onset of oscillations in the velocity autocorrelation function of fluids as density is increased. In this talk I will present our efforts concerning this topic, first finding a structural marker associated with the Frenkel line crossover, identifying correlated changes in the evolution of the nearest neighbour coordination number and diffusion constant and the use of a machine-learned interatomic forcefield positing this crossover to originate at the triple point and formulate an analytic criterion for it. I will talk about how a fluid state crossover can be coherently identified in both traditional fluids (Krypton, Nitrogen) as well as colloidal/micellar systems, and discuss whether this is related to the Frenkel line, the recently found ‘c’-transition (Brazhkin, PRE 2021) or if we can even call a continuous crossover a ‘line’.

Novel binary hydrides synthesized under high pressure

Metal hydrides are important materials for hydrogen and energy storage. High pressure is an effective tool for the synthesis of new hydrides, because it dramatically increases the Gibbs free energy of molecular H2, thus increasing its reactivity. With the discovery of superconductivity in H3S with a critical temperature of 203K at 150GPa considerable efforts of the high-pressure community were concentrated on the search of novel hydrogen-rich materials under high pressure. In this talk I will give a short overview of the ongoing progress, with a focus on the Zr-H, Ta-H, Gd-H, Rb-H and Cs-H systems.

Discovery of charge density wave order in 3D metallic U₂Ti

We consider thermodynamic, transport and x-ray diffraction measurements supporting the formation of a previously unidentified charge density wave (CDW) phase of U₂Ti. The CDW is incommensurate, forming at 71 K, and undergoes a commensurate transition at 46 K. This doubles the unit cell along the hexagonal c-axis in a Peierls-like transition as predicted from DFT calculations [1]. This is compared to the unusual CDW in α-U and motivates U₂Ti as a simpler system to explore 3D metallic CDW formation.   Additionally, our measurements suggest that U₂Ti is not bulk superconductor at ambient pressure in contrast to a previous study [2].

[1] Kaur, G., Jaya, S. M., & Panigrahi, B. K. (2018). Phonon instability and charge density wave in U2Ti. Journal of Alloys and Compounds, 730, 36-41.

[2] Maple, M. B., Torikachvili, M. S., Rossel, C., Chen, J. W., & Hake, R. R. (1985). Four new uranium compound superconductors. Physica B+ C, 135(1-3), 430-433.

Investigating the role of SMC proteins and CTCF in gene expression by HiP-HoP simulations of degron experiments

The three-dimensional organization of chromatin within the nucleus is highly interconnected with gene expression and crucial for cell function. It has been observed that SMC complexes play a key role in organizing the genome. Indeed, cohesin is able to extrude loops that stop at convergent occupied CTCF binding sites. However, the effect of cohesin and other loop extrusion regulatory factors on the transcriptional regulatory network of the cell has not yet been completely understood. 

In this work, we used simulations to investigate the roles played by loop extrusion driven by SMC proteins and regulatory factors such as CTCF and WAPL in shaping chromatin architecture. We also studied their effects on gene expression on a chromosomal scale. To obtain the results, we employed the highly predictive heteromorphic polymer (HiP-HoP) framework, which integrates polymer physics with bioinformatic data, to predict the effect of degrading each of these proteins in turn. 

Consistently with previous experimental results, we observe that the average transcriptional activity is not strongly impacted by loop extrusion by SMC proteins. Strikingly, the transcriptional noise (measuring the variability of gene expression in the cell population) is instead strongly affected by the removal of these regulatory factors. From our simulations, we are also able to relate these changes in the transcriptional pattern to the ones in 3D chromosomal and gene structure. 

The role of pH in detection of bacterial biofilms

The Effect of Coagulation on Drying Blood Droplets

Blood is a mixture of biological colloids and polymers, the drying of which has been examined for some time. These experiments have all used anticoagulants such as EDTA and tri-sodium citrate to extend the lifetime and transportability of the blood by preventing coagulation, making it easier to perform laboratory experiments. While experiments using anticoagulated blood produce useful information for personalised medicine, they may be of limited relevance for the typical crime scene. To extend the usefulness of blood droplet research to real-life crime scenes where coagulation naturally occurs, this research explores the viability of reintroducing a coagulation-like process to samples containing anticoagulant via the addition of calcium chloride in order to examine how the process affects a change in droplet evaporation.

What can Differential Dynamic Microscopy do for you?

The dynamics of soft matter systems are key to their understanding, the dynamics themselves are of interest but can also provide information on the underlying physics and characterisation of the system. Differential Dynamic Microscopy (DDM) is a relatively new technique for studying these dynamics over a range of time- and length-scales. DDM has been applied to a wide range of systems in the literature with more published each week, however most experimentalists are not familiar with the technique. In this talk I will introduce DDM and provide an intuitive overview of how it works, before discussing several examples of DDM which highlight its strengths and concluding with an overview of other applications selected to align with interests of others in the school.