A probabilistic algorithm for optimising the steady-state diffusional flux into a partially absorbing body.

Cells in an aqueous environment absorb diffusing nutrient molecules through nanoscale protein channels in their outer membranes. Assuming that there are constraints on the number of such channels a cell can produce, we ask the question: given a nondepleting source of nutrients, what is the optimal distribution of these channels over the cell surface? We coarse-grain this problem, phrasing it as a diffusion problem with position-dependent Robin boundary conditions on the surface. The aim is to maximize the steady-state total flux through the partially absorbing surface under an integral constraint on the local reactivities. We develop an algorithm to tackle this problem that uses the stored and processed results of a particle-based simulation with reflective boundary conditions to a posteriori estimate absorption flux at essentially negligible additional computational cost. We validate the algorithm against a few cases for which analytical or semi-analytical results are available. We apply it to two examples: a spherical cell in the presence of a point source and a spheroidal cell with an isotropic source at infinity. In the former case, there is a significant gain relative to the homogeneous case, while in the latter case the gain is only [Formula: see text].

Microtubule organization and cell geometry.

A characteristic feature of nondividing animal cells is the radial organization of microtubules (MTs), emanating from a single microtubule organizing center (MTOC). As generically these cells are not spherically symmetric, this raises the question of the influence of cell geometry on the orientational distribution of microtubules. We present a systematic study of this question in a simplified setting where MTs are nucleated from a single fixed MTOC in the center of an elliptical cell geometry. Within this context we introduce four models of increasing complexity, each one introducing additional mechanisms that govern the interaction of the MTs with the cell boundary. In order, we consider the cases: MTs that can bind to the boundary with a fixed mean residence time (M0), force-producing MTs that can slide on the boundary towards the cell poles (MS), MTs that interact with a generic polarity factor that is transported and deposited at the boundary, and which in turn stabilizes the MTs at the boundary (MP), and a final model in which both sliding and stabilization by polarity factors is taken into account (MSP). In the baseline model (M0), the exponential length distribution of MTs causes most of the interactions at the cell boundary to occur along the shorter transverse direction in the cell, leading to transverse biaxial order. MT sliding (MS) is able to reorient the main axis of this biaxial order along the longitudinal axis. The polarization mechanism introduced in MP and MSP overrules the geometric bias towards bipolar order observed in M0 and MS, and allows the establishment of unipolar order either along the short (MP) or the long cell axis (MSP). The behavior of the latter two models can be qualitatively reproduced by a very simple toy model with discrete MT orientations.

Modeling the molecular structures and dynamics responsible for the remarkable mechanical properties of a plant cell wall.

The primary plant cell wall is a hydrated meshwork of polysaccharides that is strong enough to withstand large mechanical stresses imposed by turgor while remaining pliant in ways that permit growth. To understand how its macromolecular architecture produces its complex mechanical properties, Zhang et al.1 computationally assembled a realistic network of cellulose microfibrils, hemicellulose, and pectin. The simulated wall responded to computationally applied stress like the real wall on which it was based. The model showed the location and chemical identity of stress-bearing components. It showed that cellulose microfibril interactions and movements dominated the wall's mechanical behavior, while hemicellulose and pectin had surprisingly minor effects.

Frustration-induced complexity in order-disorder transitions of the J_{1}-J_{2}-J_{3} Ising model on the square lattice.

We revisit the field-free Ising model on a square lattice with up to third-neighbor (NNNN) interactions, also known as the J_{1}-J_{2}-J_{3} model, in the mean-field approximation. Using a systematic enumeration procedure, we show that the region of phase space in which the high-temperature disordered phase is stable against all modes representing periodic magnetization patterns up to a given size is a convex polytope that can be obtained by solving a standard vertex enumeration problem. Each face of this polytope corresponds to a set of coupling constants for which a single set of modes, equivalent up to a symmetry of the lattice, bifurcates from the disordered solution. While the structure of this polytope is simple in the half-space J_{3}>0, where the NNNN interaction is ferromagnetic, it becomes increasingly complex in the half-space J_{3}<0, where the antiferromagnetic NNNN interaction induces strong frustration. We then pass to the limit N→∞ giving a closed-form description of the order-disorder surface in the thermodynamic limit, which shows that for J_{3}<0, the emergent ordered phases will have a "devil's surface"-like mode structure. Finally, using Monte Carlo simulations, we show that for small periodic systems, the mean-field analysis correctly predicts the dominant modes of the ordered phases that develop for coupling constants associated with the centroid of the faces of the disorder polytope.

Towards a synthetic cell cycle.

Recent developments in synthetic biology may bring the bottom-up generation of a synthetic cell within reach. A key feature of a living synthetic cell is a functional cell cycle, in which DNA replication and segregation as well as cell growth and division are well integrated. Here, we describe different approaches to recreate these processes in a synthetic cell, based on natural systems and/or synthetic alternatives. Although some individual machineries have recently been established, their integration and control in a synthetic cell cycle remain to be addressed. In this Perspective, we discuss potential paths towards an integrated synthetic cell cycle.

A plausible mechanism for longitudinal lock-in of the plant cortical microtubule array after light-induced reorientation.

The light-induced reorientation of the cortical microtubule array in dark-grown Arabidopsis thaliana hypocotyl cells is a striking example of the dynamical plasticity of the microtubule cytoskeleton. A consensus model, based on katanin-mediated severing at microtubule crossovers, has been developed that successfully describes the onset of the observed switch between a transverse and longitudinal array orientation. However, we currently lack an understanding of why the newly populated longitudinal array direction remains stable for longer times and re-equilibration effects would tend to drive the system back to a mixed orientation state. Using both simulations and analytical calculations, we show that the assumption of a small orientation-dependent shift in microtubule dynamics is sufficient to explain the long-term lock-in of the longitudinal array orientation. Furthermore, we show that the natural alternative hypothesis that there is a selective advantage in severing longitudinal microtubules, is neither necessary nor sufficient to achieve cortical array reorientation, but is able to accelerate this process significantly.

What is quantitative plant biology?

Quantitative plant biology is an interdisciplinary field that builds on a long history of biomathematics and biophysics. Today, thanks to high spatiotemporal resolution tools and computational modelling, it sets a new standard in plant science. Acquired data, whether molecular, geometric or mechanical, are quantified, statistically assessed and integrated at multiple scales and across fields. They feed testable predictions that, in turn, guide further experimental tests. Quantitative features such as variability, noise, robustness, delays or feedback loops are included to account for the inner dynamics of plants and their interactions with the environment. Here, we present the main features of this ongoing revolution, through new questions around signalling networks, tissue topology, shape plasticity, biomechanics, bioenergetics, ecology and engineering. In the end, quantitative plant biology allows us to question and better understand our interactions with plants. In turn, this field opens the door to transdisciplinary projects with the society, notably through citizen science.

Critical threshold for microtubule amplification through templated severing.

The cortical microtubule array of dark-grown hypocotyl cells of plant seedlings undergoes a striking, and developmentally significant, reorientation on exposure to light. This process is driven by the exponential amplification of a population of longitudinal microtubules, created by severing events localized at crossovers with the microtubules of the pre-existing transverse array. We present a dynamic one-dimensional model for microtubule amplification through this type of templated severing. We focus on the role of the probability of immediate stabilization-after-severing of the newly created lagging microtubule, observed to be a characteristic feature of the reorientation process. Employing stochastic simulations, we show that in the dynamic regime of unbounded microtubule growth, a finite value of this probability is not required for amplification to occur but does strongly influence the degree of amplification and hence the speed of the reorientation process. In contrast, in the regime of bounded microtubule growth, we show that amplification only occurs above a critical threshold. We construct an approximate analytical theory, based on a priori limiting the number of crossover events considered, which allows us to predict the observed critical value of the stabilization-after-severing probability with reasonable accuracy.

Poroelasticity of (bio)polymer networks during compression: theory and experiment.

Soft living tissues like cartilage can be considered as biphasic materials comprising a fibrous complex biopolymer network and a viscous background liquid. Here, we show by a combination of experiment and theoretical analysis that both the hydraulic permeability and the elastic properties of (bio)polymer networks can be determined with simple ramp compression experiments in a commercial rheometer. In our approximate closed-form solution of the poroelastic equations of motion, we find the normal force response during compression as a combination of network stress and fluid pressure. Choosing fibrin as a biopolymer model system with controllable pore size, measurements of the full time-dependent normal force during compression are found to be in excellent agreement with the theoretical calculations. The inferred elastic response of large-pore (µm) fibrin networks depends on the strain rate, suggesting a strong interplay between network elasticity and fluid flow. Phenomenologically extending the calculated normal force into the regime of nonlinear elasticity, we find strain-stiffening of small-pore (sub-µm) fibrin networks to occur at an onset average tangential stress at the gel-plate interface that depends on the polymer concentration in a power-law fashion. The inferred permeability of small-pore fibrin networks scales approximately inverse squared with the fibrin concentration, implying with a microscopic cubic lattice model that the number of protofibrils per fibrin fiber cross-section decreases with protein concentration. Our theoretical model provides a new method to obtain the hydraulic permeability and the elastic properties of biopolymer networks and hydrogels with simple compression experiments, and paves the way to study the relation between fluid flow and elasticity in biopolymer networks during dynamical compression.

Microtubule-based actin transport and localization in a spherical cell.

The interaction between actin filaments and microtubules is crucial for many eukaryotic cellular processes, such as, among others, cell polarization, cell motility and cellular wound healing. The importance of this interaction has long been recognized, yet very little is understood about both the underlying mechanisms and the consequences for the spatial (re)organization of the cellular cytoskeleton. At the same time, understanding the causes and the consequences of the interaction between different biomolecular components are key questions for in vitro research involving reconstituted biomolecular systems, especially in the light of current interest in creating minimal synthetic cells. In this light, recent in vitro experiments have shown that the actin-microtubule interaction mediated by the cytolinker TipAct, which binds to actin lattice and microtubule tips, causes the directed transport of actin filaments. We develop an analytical theory of dynamically unstable microtubules, nucleated from the centre of a spherical cell, in interaction with actin filaments. We show that, depending on the balance between the diffusion of unbound actin filaments and propensity to bind microtubules, actin is either concentrated in the centre of the cell, where the density of microtubules is highest, or becomes localized to the cell cortex.

Compression and swelling of hydrogels in polymer solutions: A dominant-mode model.

The swelling and compression of hydrogels in polymer solutions can be understood by considering hydrogel-osmolyte-solvent interactions which determine the osmotic pressure difference between the inside and the outside of a hydrogel particle and the changes in effective solvent quality for the hydrogel network. Using the theory of poroelasticity, we find the exact solution to hydrogel dynamics in a dilute polymer solution, which quantifies the effect of diffusion and partitioning of osmolyte and the related solvent quality change to the volumetric changes of the hydrogel network. By making a dominant-mode assumption, we propose a model for the swelling and compression dynamics of (spherical) hydrogels in concentrated polymer solutions. Osmolyte diffusion induces a biexponential response in the size of the hydrogel radius, whereas osmolyte partitioning and solvent quality effects induce monoexponential responses. Comparison of the dominant-mode model to experiments provides reasonable values for the compressive bulk modulus of a hydrogel particle, the permeability of the hydrogel network, and the diffusion constant of osmolyte molecules inside the hydrogel network. Our model shows that hydrogel-osmolyte interactions can be described in a conceptually simple manner, while still capturing the rich (de)swelling behaviors observed in experiments. We expect our approach to provide a roadmap for further research into and applications of hydrogel dynamics induced by, for example, changes in the temperature and the pH.

Nonmonotonic swelling and compression dynamics of hydrogels in polymer solutions.

Hydrogels are sponge-like materials that can absorb or expel significant amounts of water. Swelling up from a dried state, they can swell up more than a hundredfold in volume, with the kinetics and the degree of swelling depending sensitively on the physicochemical properties of both the polymer network and the aqueous solvent. In particular, the presence of dissolved macromolecules in the background liquid can have a significant effect, as the macromolecules can exert an additional external osmotic pressure on the hydrogel material, thereby reducing the degree of swelling. In this paper, we have submerged dry hydrogel particles in polymer solutions containing large and small macromolecules. Interestingly, for swelling in the presence of large macromolecules we observe a concentration-dependent overshoot behavior, where the particle volume first continuously increases toward a maximum, after which it decreases again, reaching a lower, equilibrium value. In the presence of smaller macromolecules we do not observe this intriguing overshoot behavior, but instead observe a rapid growth followed by a slowed-down growth. To account for the observed overshoot behavior, we realize that the macromolecules entering the hydrogel network not only lead to a reduction of the osmotic pressure difference, but their presence within the network also affects the swelling behavior through a modification of the solvent-polymer interactions. In this physical picture of the swelling process, the net amount of volume change should thus depend on the magnitudes of both the reduction in osmotic pressure and the change in effective solvent quality associated with the macromolecules entering the pores of the hydrogel network. We develop a phenomenological model that incorporates both of these effects. Using this model we are able to account for both the swelling and compression kinetics of hydrogels within aqueous polymer solutions, as a function of the size of the dissolved macromolecules and of their effect on the effective solvent quality.

From plasmodesma geometry to effective symplasmic permeability through biophysical modelling.

Regulation of molecular transport via intercellular channels called plasmodesmata (PDs) is important for both coordinating developmental and environmental responses among neighbouring cells, and isolating (groups of) cells to execute distinct programs. Cell-to-cell mobility of fluorescent molecules and PD dimensions (measured from electron micrographs) are both used as methods to predict PD transport capacity (i.e., effective symplasmic permeability), but often yield very different values. Here, we build a theoretical bridge between both experimental approaches by calculating the effective symplasmic permeability from a geometrical description of individual PDs and considering the flow towards them. We find that a dilated central region has the strongest impact in thick cell walls and that clustering of PDs into pit fields strongly reduces predicted permeabilities. Moreover, our open source multi-level model allows to predict PD dimensions matching measured permeabilities and add a functional interpretation to structural differences observed between PDs in different cell walls.

Gravity-driven syneresis in model low-fat mayonnaise.

Low-fat food products often contain natural, edible polymers to retain the desired mouth feel and elasticity of their full-fat counterparts. This type of product, however, can suffer from syneresis: densification due to the expulsion of fluid. Gaining insight into the physical principles governing syneresis in such soft hybrid dispersions remains a challenge from a theoretical perspective, as experimental data are needed to establish a basis. We record non-accelerated syneresis in a model system for low-fat mayonnaise: a colloid polymer mixture, consisting of oil in water emulsion with starch in the aqueous phase. We find the flow rate of expelled fluid to be proportional to the difference in hydrostatic pressure over the system. The osmotic pressure of the added starch, while being higher than the hydrostatic pressure, does not prevent syneresis because the soluble starch is lost to the expelled fluid. From these findings, we conclude that forced syneresis in these systems can be described as a gravity-driven porous flow through the densely packed emulsion, explainable with a model based on Darcy's law.

Confinement and crowding control the morphology and dynamics of a model bacterial chromosome.

Motivated by recent experiments probing the shape, size and dynamics of bacterial chromosomes in growing cells, we consider a polymer model consisting of a circular backbone to which side-loops are attached, confined to a cylindrical cell. Such a model chromosome spontaneously adopts a helical shape, which is further compacted by molecular crowders to occupy a nucleoid-like sub-volume of the cell. With increasing cell length, the longitudinal size of the chromosome increases in a non-linear fashion until finally saturating, its morphology gradually opening up while displaying a changing number of helical turns. For shorter cells, the chromosome extension varies non-monotonically with cell size, which we show is associated with a radial to longitudinal spatial reordering of the crowders. Confinement and crowders constrain chain dynamics leading to anomalous diffusion. While the scaling exponent for the mean squared displacement of center of mass grows and saturates with cell length, that of individual loci displays a broad distribution with a sharp maximum.

CLASP stabilization of plus ends created by severing promotes microtubule creation and reorientation.

Central to the building and reorganizing cytoskeletal arrays is creation of new polymers. Although nucleation has been the major focus of study for microtubule generation, severing has been proposed as an alternative mechanism to create new polymers, a mechanism recently shown to drive the reorientation of cortical arrays of higher plants in response to blue light perception. Severing produces new plus ends behind the stabilizing GTP-cap. An important and unanswered question is how these ends are stabilized in vivo to promote net microtubule generation. Here we identify the conserved protein CLASP as a potent stabilizer of new plus ends created by katanin severing in plant cells. Clasp mutants are defective in cortical array reorientation. In these mutants, both rescue of shrinking plus ends and the stabilization of plus ends immediately after severing are reduced. Computational modeling reveals that it is the specific stabilization of severed ends that best explains CLASP's function in promoting microtubule amplification by severing and array reorientation.

Colloidal Liquid Crystals Confined to Synthetic Tactoids.

When a liquid crystal forming particles are confined to a spatial volume with dimensions comparable to that of their own size, they face a complex trade-off between their global tendency to align and the local constraints imposed by the boundary conditions. This interplay may lead to a non-trivial orientational patterns that strongly depend on the geometry of the confining volume. This novel regime of liquid crystalline behavior can be probed with colloidal particles that are macro-aggregates of biomolecules. Here we study director fields of filamentous fd-viruses in quasi-2D lens-shaped chambers that mimic the shape of tactoids, the nematic droplets that form during isotropic-nematic phase separation. By varying the size and aspect ratio of the chambers we force these particles into confinements that vary from circular to extremely spindle-like shapes and observe the director field using fluorescence microscopy. In the resulting phase diagram, next to configurations predicted earlier for 3D tactoids, we find a number of novel configurations. Using Monte Carlo Simulations, we show that these novel states are metastable, yet long-lived. Their multiplicity can be explained by the co-existence of multiple dynamic relaxation pathways leading to the final stable states.

Molecular Dynamics Simulation of a Feather-Boa Model of a Bacterial Chromosome.

The chromosome of a bacterium consists of a mega-base pair long circular DNA, which self-organizes within the micron-sized bacterial cell volume, compacting itself by three orders of magnitude. Unlike in eukaryotes, it lacks a nuclear membrane, and freely floats in the cytosol confined by the cell membrane. It is believed that strong confinement, cross-linking by associated proteins, and molecular crowding all contribute to determine chromosome size and morphology. Modeling the chromosome simply as a circular polymer decorated with closed side-loops in a cylindrical confining volume, has been shown to already recapture some of the salient properties observed experimentally. Here, we describe how a computer simulation can be set up to study structure and dynamics of bacterial chromosomes using this model.

A computational framework for cortical microtubule dynamics in realistically shaped plant cells.

Plant morphogenesis is strongly dependent on the directional growth and the subsequent oriented division of individual cells. It has been shown that the plant cortical microtubule array plays a key role in controlling both these processes. This ordered structure emerges as the collective result of stochastic interactions between large numbers of dynamic microtubules. To elucidate this complex self-organization process a number of analytical and computational approaches to study the dynamics of cortical microtubules have been proposed. To date, however, these models have been restricted to two dimensional planes or geometrically simple surfaces in three dimensions, which strongly limits their applicability as plant cells display a wide variety of shapes. This limitation is even more acute, as both local as well as global geometrical features of cells are expected to influence the overall organization of the array. Here we describe a framework for efficiently simulating microtubule dynamics on triangulated approximations of arbitrary three dimensional surfaces. This allows the study of microtubule array organization on realistic cell surfaces obtained by segmentation of microscopic images. We validate the framework against expected or known results for the spherical and cubical geometry. We then use it to systematically study the individual contributions of global geometry, cell-edge induced catastrophes and cell-face induced stability to array organization in a cuboidal geometry. Finally, we apply our framework to analyze the highly non-trivial geometry of leaf pavement cells of Arabidopsis thaliana, Nicotiana benthamiana and Hedera helix. We show that our simulations can predict multiple features of the microtubule array structure in these cells, revealing, among others, strong constraints on the orientation of division planes.

SPR2 protects minus ends to promote severing and reorientation of plant cortical microtubule arrays.

The cortical microtubule arrays of higher plants are organized without centrosomes and feature treadmilling polymers that are dynamic at both ends. The control of polymer end stability is fundamental for the assembly and organization of cytoskeletal arrays, yet relatively little is understood about how microtubule minus ends are controlled in acentrosomal microtubule arrays, and no factors have been identified that act at the treadmilling minus ends in higher plants. Here, we identify Arabidopsis thaliana SPIRAL2 (SPR2) as a protein that tracks minus ends and protects them against subunit loss. SPR2 function is required to facilitate the rapid reorientation of plant cortical arrays as stimulated by light perception, a process that is driven by microtubule severing to create a new population of microtubules. Quantitative live-cell imaging and computer simulations reveal that minus protection by SPR2 acts by an unexpected mechanism to promote the lifetime of potential SPR2 severing sites, increasing the likelihood of severing and thus the rapid amplification of the new microtubule array.