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Composed of microscopic layers that stack along one direction while maintaining fluid-like positional disorder within layers, smectics are excellent systems for exploring topology, defects and geometric memory in complex confining geometries. However, the coexistence of crystalline-like characteristics in one direction and fluid-like disorder within layers makes lamellar liquid crystals notoriously difficult to model - especially in the presence of defects and large distortions. Nematic properties of smectics can be comprehensively described by the Q-tensor but to capture the features of the smectic layering alone, we develop a phenomenological Landau theory for a complex-tensor order parameter E, which is capable of describing the local degree of lamellar ordering, layer displacement, and orientation of the layers. This theory can account for both parallel and perpendicular elastic contributions. In addition to resolving the potential ambiguities inherent to complex scalar order parameter models, this model reduces to previous employed models of simple smectics, and opens new possibilities for numerical studies on smectics possessing many defects, within complex geometries and under extreme confinement., Comment: 23 pages, 3 figures

For billions of years, photosynthetic microbes have evolved under the variable exposure to sunlight in diverse ecosystems and microhabitats all over our planet. Their abilities to dynamically respond to alterations of the luminous intensity, including phototaxis, surface association and diurnal cell cycles, are pivotal for their survival. If these strategies fail in the absence of light, the microbes can still sustain essential metabolic functionalities and motility by switching their energy production from photosynthesis to oxygen respiration. For suspensions of motile C. reinhardtii cells above a critical density, we demonstrate that this switch reversibly controls collective microbial aggregation. Aerobic respiration dominates over photosynthesis in conditions of low light, which causes the microbial motility to sensitively depend on the local availability of oxygen. For dense microbial populations in self-generated oxygen gradients, microfluidic experiments and continuum theory based on a reaction–diffusion mechanism show that oxygen-regulated motility enables the collective emergence of highly localized regions of high and low cell densities.

Significance Motile microorganisms commonly live in porous media comprising microhabitats filled with interfaces of complex shape. On such small scales, the interactions with these interfaces, rather than external gradients, dominate their motion in the search for favorable living conditions. We demonstrate with experiments and theory that the geometry of confining interfaces shapes the topology of the most likely, average trajectory, leading to directed fluxes of probability that are not exclusively localized at the near-wall region. Employing this principle allows us to actively shape a microbe’s average direction of movement, which could be of use in the design of topological transport mechanisms for microfluidic environments., When the motion of a motile cell is observed closely, it appears erratic, and yet the combination of nonequilibrium forces and surfaces can produce striking examples of organization in microbial systems. While most of our current understanding is based on bulk systems or idealized geometries, it remains elusive how and at which length scale self-organization emerges in complex geometries. Here, using experiments and analytical and numerical calculations, we study the motion of motile cells under controlled microfluidic conditions and demonstrate that probability flux loops organize active motion, even at the level of a single cell exploring an isolated compartment of nontrivial geometry. By accounting for the interplay of activity and interfacial forces, we find that the boundary’s curvature determines the nonequilibrium probability fluxes of the motion. We theoretically predict a universal relation between fluxes and global geometric properties that is directly confirmed by experiments. Our findings open the possibility to decipher the most probable trajectories of motile cells and may enable the design of geometries guiding their time-averaged motion.

Abstract We study the dynamics of a squirmer in a nematic liquid crystal using the multiparticle collision dynamics (MPCD) method. A recently developed nematic MPCD method [Phys. Rev. E 99, 063319 (2019)] which employs a tensor order parameter to describe the spatial and temporal variations of the nematic order is used to simulate the suspending anisotropic fluid. Considering both nematodynamic effects (anisotropic viscosity and elasticity) and thermal fluctuations, in the present study, we couple the nematic MPCD algorithm with a molecular dynamics (MD) scheme for the squirmer. A unique feature of the proposed method is that the nematic order, the fluid, and the squirmer are all represented in a particle-based framework. To test the applicability of this nematic MPCD-MD method, we simulate the dynamics of a spherical squirmer with homeotropic surface anchoring conditions in a bulk domain. The importance of anisotropic viscosity and elasticity on the squirmer’s speed and orientation is studied for different values of self-propulsion strength and squirmer type (pusher, puller or neutral). In sharp contrast to Newtonian fluids, the speed of the squirmer in a nematic fluid depends on the squirmer type. Interestingly, the speed of a strong pusher is smaller in the nematic fluid than for the Newtonian case. The orientational dynamics of the squirmer in the nematic fluid also shows a non-trivial dependence on the squirmer type. Our results compare well with existing experimental and numerical data. The full particle-based framework could be easily extended to model the dynamics of multiple squirmers in anisotropic fluids. Graphic abstract

We investigate the temperature dependence of the helical pitch of a cholesteric liquid crystal by means of Monte Carlo simulations. We carry out both lattice and off-lattice simulations to assess t...

Shewanella oneidensis MR-1 are facultative aerobic electroactive bacteria with an appealing potential for sustainable energy production and bioremediation. They gather around air sources, forming aerotactic bands and biofilms. Here, we experimentally follow the evolution of the band around an air bubble, and we find good agreement with the numerical solutions of the pertinent transport equations. Video microscopy reveals a transition between motile and non-motile MR-1 upon oxygen depletion, preventing further development of the biofilm. We discover that MR-1 can alternate between longitudinal fast and sideways slow swimming. The resulting bimodal velocity distributions change in response to different oxygen concentrations and gradients, supporting the biological functions of aerotaxis and confinement.

The structure and degree of order in soft matter and other materials is intimately connected to the nature of the interactions between the particles. One important research goal is to find suitable control mechanisms, to enhance or suppress different structures. Using dynamical density functional theory, we investigate the interplay between external shear and the characteristic length scales in the interparticle correlations of a model system. We show that shear can controllably change the characteristic length scale from one to another quite distinct value. Moreover, with specific small changes in the form of the particle interactions, the applied shear can either selectively enhance or suppress the different characteristic wavelengths of the system, thus showing how to tune these. Our results suggest that the nonlinear response to flow can be harnessed to design different actively responsive materials.

We employ nonequilibrium molecular dynamics simulations to investigate the structure and dynamics of a cholesteric liquid crystal confined between atomically corrugated solid walls. By choosing walls normal to the helical axis, we can study systems with an arbitrary cholesteric pitch without exposing the cholesteric helix to a spurious stress. We investigate the effects of local heating and flow and their joint effects. A steady-state laminar Poiseuille flow is initiated by means of an external body force. Flow alone (i.e., without local heating) in a direction normal to the helical axis does not affect the cholesteric pitch. If the liquid crystal is heated in a small region, the cholesteric helix becomes unstable and melts locally. However, if local heating and flow are combined, a nontrivial synergistic effect is observed in that the helical structure recuperates the better, the higher the speed of the flow is.

We investigate the effect of van der Waals forces on a collection of granular particles by means of molecular dynamics simulations of a vibrated system in three dimensions. The van der Waals interactions introduce two phase coexistences: one between a random close packing and a gas and a second between a polycrystalline dense state and a gas, where the dense, disordered component crystallizes when the driving amplitude exceeds a threshold value. The region of stability of the ordered state in the nonequilibrium phase diagram grows in size as the Hamaker constant increases or the degree of dissipation increases.

The empirical observation of aggregation of dielectric particles under the influence of electrostatic forces lies at the origin of the theory of electricity. The growth of clusters formed of small grains underpins a range of phenomena from the early stages of planetesimal formation to aerosols. However, the collective effects of Coulomb forces on the nonequilibrium dynamics and aggregation process in a granular gas – a model representative of the above physical processes – have so far evaded theoretical scrutiny. Here, we establish a hydrodynamic description of aggregating granular gases that exchange charges upon collisions and interact via the long-ranged Coulomb forces. We analytically derive the governing equations for the evolution of granular temperature, charge variance, and number density for homogeneous and quasi-monodisperse aggregation. We find that, once the aggregates are formed, the granular temperature of the cluster population, the charge variance of the cluster population and the number density of the cluster population evolve in such a way that their non-dimensional combination obeys a physical constraint of nearly constant dimensionless ratio of characteristic electrostatic to kinetic energy. This constraint on the collective evolution of charged clusters is confirmed both by our theory and our detailed molecular dynamics simulations. The inhomogeneous aggregation of monomers and clusters in their mutual electrostatic field proceeds in a fractal manner. Our theoretical framework is extendable to more precise charge exchange mechanisms, a current focus of extensive experimentation. Furthermore, it illustrates the collective role of long-ranged interactions in dissipative gases and can lead to novel designing principles in particulate systems.

Liquid crystals establish a nearly unique combination of thermodynamic, hydrodynamic, and topological behavior. This poses a challenge to their theoretical understanding and modeling. The arena where these effects come together is the mesoscopic (micron) scale. It is then important to develop models aimed at capturing this variety of dynamics. We have generalized the particle-based multiparticle collision dynamics (MPCD) method to model the dynamics of nematic liquid crystals. Following the Qian-Sheng theory [Phys. Rev. E 58, 7475 (1998)1063-651X10.1103/PhysRevE.58.7475] of nematics, the spatial and temporal variations of the nematic director field and order parameter are described by a tensor order parameter. The key idea is to assign tensorial degrees of freedom to each MPCD particle, whose mesoscopic average is the tensor order parameter. This nematic MPCD method includes backflow effect, velocity-orientation coupling, and thermal fluctuations. We validate the applicability of this method by testing (i) the nematic-isotropic phase transition, (ii) the flow alignment of the director in shear and Poiseuille flows, and (iii) the annihilation dynamics of a pair of line defects. We find excellent agreement with existing literature. We also investigate the flow field around a force dipole in a nematic liquid crystal, which represents the leading-order flow field around a force-free microswimmer. The anisotropy of the medium not only affects the magnitude of velocity field around the force dipole, but can also induce hydrodynamic torques depending on the orientation of dipole axis relative to director field. A force dipole experiences a hydrodynamic torque when the dipole axis is tilted with respect to the far-field director. The direction of hydrodynamic torque is such that the pusher- (or puller-) type force dipole tends to orient along (or perpendicular to) the director field. Our nematic MPCD method can have far-reaching implications not only in modeling of nematic flows, but also to study the motion of colloids and microswimmers immersed in an anisotropic medium.

Shewanella oneidensis MR-1 are facultative aerobic electroactive bacteria, with an appealing potential for sustainable energy production and bioremediation. They gather around air sources, forming aerotactic bands and biofilms. Though accumulation is crucial to technological exploitation, their collective behaviour remains poorly reported. Here we establish a comprehensive framework for the study of aerotaxis, unveiling a novel hybrid locomotion pattern. Despite having only one flagellum, MR-1 combine motility features of mono- and multiflagellate bacteria, alternating longitudinal fast and sideways slow swimming. The adaptive tuning of the resulting bimodal velocity distributions fulfils different biological functions, such as aerotaxis and confinement. Overall, we reveal the mechanisms underlying the aerotactic collective behaviour of MR-1, in the process leading from accumulation to biofilm formation

We investigate the stochastic dynamics of one sedimenting active Brownian particle in three dimensions under the influence of gravity and passive fluctuations in the translational and rotational motion. We present an analytical solution of the Fokker-Planck equation for the stochastic process which allows us to describe the dynamics of one active Brownian particle in three dimensions. We address the time evolution of the density, the polarization, and the steady-state solution. We also perform Brownian dynamics simulations and study the effect of the activity of the particles on their collective motion. These results qualitatively agree with our model. Finally, we compare our results with experiments (J. Palacci et al., Phys. Rev. Lett. 105, 088304 (2010)) and find very good agreement.

Anisotropic fluids (e.g. liquid crystals) offer a remarkable promise as optofluidic materials owing to the directional, tunable, and coupled interactions between the material, flow, and the optical fields. Here we present a comprehensive in silico treatment of this anisotropic interaction by performing nonequilibrium molecular dynamics simulations. We quantify the response of a nematic liquid crystal (NLC) undergoing a Poiseuille flow in the Stokes regime, while being illuminated by a laser beam incident perpendicular to the flow direction. We adopt a minimalistic model to capture the interactions, accounting for two features: first, the laser heats up the NLC locally; and second, the laser polarises the NLC and exerts an optical torque that tends to reorient molecules of the nematic phase. Because of this reorientation the liquid crystal exhibits small regions of biaxiality, where the nematic director is one symmetry axis and the axis of rotation for the reorientation of the molecules is the other one. We find that the relative strength of the viscous and the optical torques mediates the flow-induced response of the biaxial regions, thereby tuning the emergence, shape and location of the regions of enhanced biaxiality. The mechanistic framework presented here promises experimentally tractable routes toward novel optofluidic applications based on material-flow-light interactions.

A theoretical formalism is presented to analyze and interpret microrheology experiments in anisotropic fluids with nematic order. The predictions of that approach are examined in the context of a simple coarse-grained molecular model which is simulated using nonequilibrium molecular dynamics calculations. The proposed formalism is used to study the effect of confinement, the type of anchoring at the probe-particle surface, and the strength of the nematic field on the rheological response functions obtained from probe-particle active microrheology. As expected, a stronger nematic field leads to increased anisotropy in the rheological response of the material. It is also found that the defect structures that arise around the probe particle, which are determined by the type of anchoring and the particle size, have a significant effect on the rheological response observed in microrheology simulations. Independent estimates of the bulk dynamic modulus of the model nematic fluid considered here are obtained from small-amplitude oscillatory shear simulations with Lees–Edwards boundary conditions. The results of simulations indicate that the dynamic modulus extracted from particle-probe microrheology is different from that obtained in the absence of the particle, but that the differences decrease as the size of the defect also decreases. Importantly, the results of the nematic microrheology theory proposed here are in much closer agreement with simulations than those from earlier formalisms conceived for isotropic fluids. As such, it is anticipated that the theoretical framework advanced in this study could provide a useful tool for interpretation of microrheology experiments in systems such as liquid crystals and confined macromolecular solutions or gels.

Phytoplankton often encounter turbulence in their habitat. As most toxic phytoplankton species are motile, resolving the interplay of motility and turbulence has fundamental repercussions on our understanding of their own ecology and of the entire ecosystems they inhabit. The spatial distribution of motile phytoplankton cells exhibits patchiness at distances of decimeter to millimeter scales for numerous species with different motility strategies. The explanation of this general phenomenon remains challenging. Furthermore, hydrodynamic cell-cell interactions, which grow more relevant as the density in the patches increases, have been so far ignored. Here, we combine particle simulations and continuum theory to study the emergence of patchiness in motile microorganisms in three dimensions. By addressing the combined effects of motility, cell-cell interaction, and turbulent flow conditions, we uncover a general mechanism: The coupling of cell-cell interactions to the turbulent dynamics favors the formation of dense patches. Identification of the important length and time scales, independent from the motility mode, allows us to elucidate a general physical mechanism underpinning the emergence of patchiness. Our results shed light on the dynamical characteristics necessary for the formation of patchiness and complement current efforts to unravel planktonic ecological interactions.

Suspensions of unicellular microswimmers such as flagellated bacteria or motile algae can exhibit spontaneous density heterogeneities at large enough concentrations. We introduce a novel model for biological microswimmers that creates the flow field of the corresponding microswimmers, and takes into account the shape anisotropy of the swimmer's body and stroke-averaged flagella. By employing multiparticle collision dynamics, we directly couple the swimmer's dynamics to the fluid's. We characterize the nonequilibrium phase diagram, as the filling fraction and Peclet number are varied, and find density heterogeneities in the distribution of both pullers and pushers, due to hydrodynamic instabilities. We find a maximum degree of clustering at intermediate filling fractions and at large Peclet numbers resulting from a competition of hydrodynamic and steric interactions between the swimmers. We develop an analytical theory that supports these results. This maximum might represent an optimum for the microorganisms' colonization of their environment.

Disklike molecules with aromatic cores spontaneously stack up in linear columns with high, one-dimensional charge carrier mobilities along the columnar axes making them prominent model systems for functional, self-organized matter. We show by high-resolution optical birefringence and synchrotron-based X-ray diffraction that confining a thermotropic discotic liquid crystal in cylindrical nanopores induces a quantized formation of annular layers consisting of concentric circular bent columns, unknown in the bulk state. Starting from the walls this ring self-assembly propagates layer by layer towards the pore center in the supercooled domain of the bulk isotropic-columnar transition and thus allows one to switch on and off reversibly single, nanosized rings through small temperature variations. By establishing a Gibbs free energy phase diagram we trace the phase transition quantization to the discreteness of the layers' excess bend deformation energies in comparison to the thermal energy, even for this near room-temperature system. Monte Carlo simulations yielding spatially resolved nematic order parameters, density maps and bond-forientational order parameters corroborate the universality and robustness of the confinement-induced columnar ring formation as well as its quantized nature., 7 pages, 5 figures + supplemental material as ancillary file, Physical Review Letters (in press)

Microswimmers often exhibit surprising patterns due to the nonequilibrium nature of their dynamics. Collectively, suspensions of microswimmers appear as a liquid whose properties set it apart from its passive counterpart. To understand the impact of hydrodynamic interactions on the basic statistical features of a microswimmer's liquid, we investigate its structure by means of the pair distribution function. We perform particle-based simulations of microswimmers that include steric effects, shape anisotropy, and hydrodynamic interactions. We find that hydrodynamic interactions considerably alter the orientation-dependent pair distribution function compared to purely excluded-volume models like active Brownian particles, and generally decrease the structure of the liquid. Depletion regions are dominant at lower filling fractions, while at larger filling fraction the microswimmer liquid develops a stronger first shell of neighbors in specific directions, while losing structure at larger distances. Our work is a first step towards a statistico-mechanical treatment of the structure of microswimmer suspensions., Comment: 6 pages, 7 figures

We present nonequilibrium molecular dynamics simulations of a spherical colloidal particle with a chemically homogeneous surface immersed in a nematic liquid-crystal host phase. This setup is then placed between planar and atomically structured substrate surfaces that serve to fix the nematic far-field director . The substrates are separated by a sufficiently large distance such that they do not interfere directly with the environment of the colloid. Because of a mismatch between and the local homeotropic anchoring of molecules of the liquid crystal (i.e., mesogens) at the surface of the colloid circular defect (Saturn) rings ℓ arise if the host is in thermodynamic equilibrium (i.e., in the absence of flow). The size of these rings depends on the range of the mesogen–colloid interactions which we model via an attractive Yukawa potential. As Poiseuille flow is initiated, ℓ is deformed. The degree of deformation is analysed quantitatively in terms of characteristic geometric parameters fitted to suitable projections of ℓ. Our results suggest that smaller ℓ are shifted downstream while approximately maintaining their circular shape, whereas larger ones exhibit an elastic deformation in addition. We provide a simple geometric argument to predict the downstream shift of smaller, circular ℓs in excellent agreement with the simulation data over the range of steady-state flows considered.

Neutral grains made of the same dielectric material can attain considerable charges due to collisions and generate long-range interactions. We perform molecular dynamic simulations in three dimensions for a dilute, freely-cooling granular gas of viscoelastic particles that exchange charges during collisions. As compared to the case of clustering of viscoelastic particles solely due to dissipation, we find that the electrostatic interactions due to collisional charging alter the characteristic size, morphology and growth rate of the clusters. The average cluster size grows with time as a power law, whose exponent is relatively larger in the charged gas than the neutral case. The growth of the average cluster size is found to be independent of the ratio of characteristic Coulomb to thermal energy, or equivalently, of the typical Bjerrum length. However, this ratio alters the crossover time of the growth. Both simulations and mean-field calculations based on the Smoluchowski's equation suggest that a suppression of particle diffusion due to the electrostatic interactions helps in the aggregation process.

Cavitation, the nucleation of vapour in liquids, is ubiquitous in fluid dynamics, and is often implicated in a myriad of industrial and biomedical applications. Although extensively studied in isotropic liquids, corresponding investigations in anisotropic liquids are largely lacking. Here, by combining liquid crystal microfluidic experiments, nonequilibrium molecular dynamics simulations and theoretical arguments, we report flow-induced cavitation in an anisotropic fluid. The cavitation domain nucleates due to sudden pressure drop upon flow past a cylindrical obstacle within a microchannel. For an anisotropic fluid, the inception and growth of the cavitation domain ensued in the Stokes regime, while no cavitation was observed in isotropic liquids flowing under similar hydrodynamic parameters. Using simulations we identify a critical value of the Reynolds number for cavitation inception that scales inversely with the order parameter of the fluid. Strikingly, the critical Reynolds number for anisotropic fluids can be 50% lower than that of isotropic fluids., Nature Communications, 8, ISSN:2041-1723

Liquid-crystalline phases are known for their unique properties, i.e., the combination of fluidity and long-range orientational and/or positional order. The presence of a colloidal particle gives rise to perturbations of this order locally. These perturbations are the origin of intercolloidal forces driving the colloidal self-assembly in a directed manner. Hence, the understanding of these perturbations is the first step in understanding and controlling the self-assembly process. Here, we perform Monte Carlo simulations to investigate the perturbations of orientational and positional order in a smectic A phase caused by a spherical colloid. We model the host phase via an interaction potential that reproduces characteristic features of phase behavior, structure, dynamics, and elasticity [S. Püschel-Schlotthauer et al. J. Chem. Phys. 2016, 145, 164903]. For strong homeotropic anchoring conditions, we find a Saturn ring defect and an onion structure in the smectic A phase; the latter has never been reported for colloids so far. For strong planar anchoring conditions, we find Boojum defects that become elongated at low temperature, similar to what is observed in experiments. However, for weak planar anchoring conditions, a double surface ring defect is exhibited in the smectic A phase.

The emergence of patterns and phase separation in many-body systems far from thermal equilibrium is discussed using the example of driven granular gases. It is shown that phase separation follows a similar mechanism as in the systems of active Brownian particles. Depending on the quantities chosen for observation, it may or may not be easy to find functionals analogous to the free energy in equilibrium statistical physics. We argue that although such functionals can always be derived from the dynamics, it is of only limited value for predicting relevant aspects of the nonequilibrium steady state of the system. Consequently, although there is indeed a ‘principle’ governing the selection of collective nonequilibrium steady states (and the corresponding large deviation functional can be identified), it is not generally useful for predicting the behaviour of the system.

In irreversible aggregation processes droplets or polymers of microscopic size successively coalesce until a large cluster of macroscopic scale forms. This gelation transition is widely believed to be self-averaging, meaning that the order parameter (the relative size of the largest connected cluster) attains well-defined values upon ensemble averaging with no sample-to-sample fluctuations in the thermodynamic limit. Here, we report on anomalous gelation transition types. Depending on the growth rate of the largest clusters, the gelation transition can show very diverse patterns as a function of the control parameter, which includes multiple stochastic discontinuous transitions, genuine non-self-averaging and ultra-slow convergence of the transition point. Our framework may be helpful in understanding and controlling gelation., 8 pages, 10 figures

Trophallaxis, the regurgitation and mouth to mouth transfer of liquid food between members of eusocial insect societies, is an important process that allows the fast and efficient dissemination of food in the colony. Trophallactic systems are typically treated as a network of agent interactions. This approach, though valuable, does not easily lend itself to analytic predictions. In this work we consider a simple trophallactic system of randomly interacting agents with finite carrying capacity, and calculate analytically and via a series of simulations the global food intake rate for the whole colony as well as observables describing how uniformly the food is distributed within the nest. Our model and predictions provide a useful benchmark to assess to what level the observed food uptake rates and efficiency in food distribution is due to stochastic effects or specific trophallactic strategies by the ant colony. Our work also serves as a stepping stone to describing the collective properties of more complex trophallactic systems, such as those including division of labor between foragers and workers.

Biofilms are complex, self-organized consortia of microorganisms that produce a functional, protective matrix of biomolecules. Physically, the structure of a biofilm can be described as an entangled polymer network which grows and changes under the effect of gradients of nutrients, cell differentiation, quorum sensing, bacterial motion, and interaction with the environment. Its development is complex, and constantly adapting to environmental stimuli. Here, we review the fundamental physical processes the govern the inception, growth and development of a biofilm. Two important mechanisms guide the initial phase in a biofilm life cycle: (\emph{i}) the cell motility near or at a solid interface, and (\emph{ii}) the cellular adhesion. Both processes are crucial for initiating the colony and for ensuring its stability. A mature biofilm behaves as a viscoelastic fluid with a complex, history-dependent dynamics. We discuss progress and challenges in the determination of its physical properties. Experimental and theoretical methods are now available that aim at integrating the biofilm's hierarchy of interactions, and the heterogeneity of composition and spatial structures. We also discuss important directions in which future work should be directed.

The complex interplay of molecular scale effects, nonlinearities in the orientational field and long-range elastic forces makes liquid-crystal physics very challenging. A consistent way to extract information from the microscopic, molecular scale up to the meso- and macroscopic scale is still missing. Here, we develop a hybrid procedure that bridges this gap by combining extensive Monte Carlo (MC) simulations, a local Landau-de Gennes theory, classical density functional theory, and finite-size scaling theory. As a test case to demonstrate the power and validity of our novel approach we study the effective interaction among colloids with Boojum defect topology immersed in a nematic liquid crystal. In particular, at sufficiently small separations colloids attract each other if the angle between their center-of-mass distance vector and the far-field nematic director is about 30 degrees. Using the effective potential in coarse-grained two-dimensional MC simulations we show that self-assembled structures formed by the colloids are in excellent agreement with experimental data.

Microorganisms, such as bacteria and microalgae, often live in habitats consisting of a liquid phase and a plethora of interfaces. The precise ways in which these motile microbes behave in their confined environment remain unclear. Using experiments, Brownian dynamics simulations, and analytical theory, we study the motility of a single Chlamydomonas microalga in an isolated microhabitat with controlled geometric properties. We demonstrate how the geometry of the habitat controls the cell's navigation in confinement. The probability of finding the cell swimming near the boundary scales linearly with the wall curvature, as seen for both circular and elliptical chambers. The theory, utilizing an asymmetric dumbbell model of the cell and steric wall interactions, captures this curvature-guided navigation quantitatively with no free parameters., Comment: 9 pages, 5 figures, revised text

We report molecular dynamics simulations of confined liquid crystals using the Gay–Berne–Kihara model. Upon isobaric cooling, the standard sequence of isotropic–nematic–smectic A phase transitions is found. Upon further cooling a reentrant nematic phase occurs. We investigate the temperature dependence of the self-diffusion coefficient of the fluid in the nematic, smectic and reentrant nematic phases. We find a maximum in diffusivity upon isobaric cooling. Diffusion increases dramatically in the reentrant phase due to the high orientational molecular order. As the temperature is lowered, the diffusion coefficient follows an Arrhenius behavior. The activation energy of the reentrant phase is found in reasonable agreement with the reported experimental data. We discuss how repulsive interactions may be the underlying mechanism that could explain the occurrence of reentrant nematic behavior for polar and non-polar molecules.

We welcome the commentary by L. Egghe (Scientometrics, this issue) stimulating discussion on our recent article "Natural selection of academic papers" (NSAP) (Scientometrics, 85(2):553---559, 2010) that focuses on an important modern issue at the heart of the scientific enterprise--the open and continuous evaluation and evolution of research. We are also grateful to the editor of Scientometrics for giving us the opportunity to respond to some of the arguments by L. Egghe that we believe are inaccurate or require further comment.

We discuss some recent progress in understanding the anomalous behavior of liquid water, by combining information provided by recent experiments and simulations on water in bulk, nanoconfined, and biological environments. We interpret evidence from recent experiments designed to test the hypothesis that liquid water may display “polymorphism” in that it can exist in two different phases — and discuss recent work on water's transport anomalies as well as the unusual behavior of water in biological environments. Finally, we will discuss how the general concept of liquid polymorphism may prove useful in understanding anomalies in other liquids, such as silicon, silica, and carbon, as well as metallic glasses which have in common that they are characterized by two characteristic length scales in their interactions.

Academic papers, like genes, code for ideas or technological innovations that structure and transform the scientific organism and consequently the society at large. Genes are subject to the process of natural selection which ensures that only the fittest survive and contribute to the phenotype of the organism. The process of selection of academic papers, however, is far from natural. Commercial for-profit publishing houses have taken control over the evaluation and access to scientific information with serious consequences for the dissemination and advancement of knowledge. Academic authors and librarians are reacting by developing an alternative publishing system based on free-access journals and self-archiving in institutional repositories and global disciplinary libraries. Despite the emergence of such trends, the journal monopoly, rather than the scientific community, is still in control of selecting papers and setting academic standards. Here we propose a dynamical and transparent peer review process, which we believe will accelerate the transition to a fully open and free-for-all science that will allow the natural selection of the fittest ideas.

Four scenarios have been proposed for the low--temperature phase behavior of liquid water, each predicting different thermodynamics. The physical mechanism which leads to each is debated. Moreover, it is still unclear which of the scenarios best describes water, as there is no definitive experimental test. Here we address both open issues within the framework of a microscopic cell model by performing a study combining mean field calculations and Monte Carlo simulations. We show that a common physical mechanism underlies each of the four scenarios, and that two key physical quantities determine which of the four scenarios describes water: (i) the strength of the directional component of the hydrogen bond and (ii) the strength of the cooperative component of the hydrogen bond. The four scenarios may be mapped in the space of these two quantities. We argue that our conclusions are model-independent. Using estimates from experimental data for H bond properties the model predicts that the low-temperature phase diagram of water exhibits a liquid--liquid critical point at positive pressure., Comment: 18 pages, 3 figures