Phase field crystal models with applications to laser deposition: A review.

In this article, we address the application of phase field crystal (PFC) theory, a hybrid atomistic-continuum approach, for modeling nanostructure kinetics encountered in laser deposition. We first provide an overview of the PFC methodology, highlighting recent advances to incorporate phononic and heat transport mechanisms. To simulate laser heating, energy is deposited onto a number of polycrystalline, two-dimensional samples through the application of initial stochastic fluctuations. We first demonstrate the ability of the model to simulate plasticity and recrystallization events that follow laser heating in the isothermal limit. Importantly, we also show that sufficient kinetic energy can cause voiding, which serves to suppress shock propagation. We subsequently employ a newly developed thermo-density PFC theory, coined thermal field crystal (TFC), to investigate laser heating of polycrystalline samples under non-isothermal conditions. We observe that the latent heat of transition associated with ordering can lead to long lasting metastable structures and defects, with a healing rate linked to the thermal diffusion. Finally, we illustrate that the lattice temperature simulated by the TFC model is in qualitative agreement with predictions of conventional electron-phonon two-temperature models. We expect that our new TFC formalism can be useful for predicting transient structures that result from rapid laser heating and re-solidification processes.

Kinetic roughening of the urban skyline.

We analyze the morphology of the modern urban skyline in terms of its roughness properties. This is facilitated by a database of 10^{7} building heights in cities throughout the Netherlands which allows us to compute the asymptotic height difference correlation function in each city. We find that in cities for which the height correlations display power-law scaling as a function of distance between the buildings, the corresponding roughness exponents are commensurate to the Edwards-Wilkinson and Kardar-Parisi-Zhang equations for kinetic roughening. Based on analogy to discrete deposition models, we argue that these two limiting classes emerge because of possible height restriction rules for buildings in some cities.

Phase-field crystal for an antiferromagnet with elastic interactions.

We introduce a model which contains the essential elements to formulate and study antiferromagnetism, using the phase-field crystal framework. We focus on the question of how magneto-elastic coupling could lift the frustration in the two-dimensional hexagonal antiferromagnetic phase. Using simulations we observe a rich variety of different phases stable in this model. To characterize different phases we calculate the chiral order parameter and identify the scaling behavior of this order parameter. Furthermore, we observe that vortices appear and are stable close to the nonmagnetic defects. Finally, we studied the ferrimagnetic and spin-flop phase transition in the presence of an external magnetic field.

Sharp interface model for elastic motile cells.

In order to study the effect of cell elastic properties on the behavior of assemblies of motile cells, this paper describes an alternative to the cell phase field (CPF) we have previously proposed. The CPF is a multi-scale approach to simulating many cells which tracked individual cells and allowed for large deformations. Though results were largely in agreement with experiment that focus on the migration of a soft cancer cell in a confluent layer of normal cells, simulations required large computing resources, making a more detailed study unfeasible. In this work we derive a sharp interface limit of CPF, including all interactions and parameters. This new model scales linearly with both system and cell size, compared to our original CPF implementation, which is quadratic in cell size, this gives rise to a considerable speedup, which we discuss in the article. We demonstrate that this model captures a similar behavior and allows us to obtain new results that were previously intractable. We obtain the full velocity distribution for a large range of degrees of confluence, [Formula: see text], and show regimes where its tail is heavier and lighter than a normal distribution. Furthermore, we fully characterize the velocity distribution with a single parameter, and its dependence on [Formula: see text] is fully determined. Finally, cell motility is shown to linearly decrease with increasing [Formula: see text], consistent with previous theoretical results.

Substrate mediated interaction between pairs of keratocytes: Multipole traction force models describe their migratory behavior.

A series of traction force microscopy experiments involving pairs of keratocytes migrating on compliant substrates were analyzed. We observed several instances where keratocytes that are about to collide turn before they touch. We term this phenomenon collision avoidance behavior and we propose that the turning is caused by the substrate mediated elastic interactions between the cells. A multipole analysis of the cell traction reveals that the left-right symmetry of the keratocyte traction pattern is broken during collision avoidance events. The analysis further shows that the cell migration direction reorients before the principal traction dipoles as the cells turn. Linear elasticity theory is used to derive the cell-cell interaction energy between pairs of keratocytes. The traction force applied by each cell is modeled as a two points (dipole) or three points (tripod) force model. We show that both models predict that cells that are about to collide in a head-on manner will turn before touching. The tripod model is further able to account for the quadrupole components of the traction force profile that we observed experimentally. Also, the tripod model proposes a mechanism that may explain why cells tend to scatter with a finite angle after a collision avoidance event. A relationship between the scattering angle and the traction force quadrupole moment is also established. Dynamical simulations of migrating model cells are further used to explain the emergence of other cell pair trajectories that we observed experimentally.

Generation of 1/f noise from a broken-symmetry model for the arbitrary absolute pitch of musical melodies.

A model is presented to generate power spectrum noise with intensity proportional to 1/f as a function of frequency f. The model arises from a broken-symmetry variable, which corresponds to absolute pitch, where fluctuations occur in an attempt to restore that symmetry, influenced by interactions in the creation of musical melodies.

Wavelet Imaging on Multiple Scales (WIMS) reveals focal adhesion distributions, dynamics and coupling between actomyosin bundle stability.

We introduce and use Wavelet Imaging on Multiple Scales (WIMS) as an improvement to fluorescence correlation spectroscopy to measure physical processes and features that occur across multiple length scales. In this study, wavelet transforms of cell images are used to characterize molecular dynamics at the cellular and subcellular levels (i.e. focal adhesions). We show the usefulness of the technique by applying WIMS to an image time series of a migrating osteosarcoma cell expressing fluorescently labelled adhesion proteins, which allows us to characterize different components of the cell ranging from optical resolution scale through to focal adhesion and whole cell size scales. Using WIMS we measured focal adhesion numbers, orientation and cell boundary velocities for retraction and protrusion. We also determine the internal dynamics of individual focal adhesions undergoing assembly, disassembly or elongation. Thus confirming as previously shown, WIMS reveals that the number of adhesions and the area of the protruding region of the cell are strongly correlated, establishing a correlation between protrusion size and adhesion dynamics. We also apply this technique to characterize the behavior of adhesions, actin and myosin in Chinese hamster ovary cells expressing a mutant form of myosin IIB (1935D) that displays decreased filament stability and impairs front-back cell polarity. We find separate populations of actin and myosin at each adhesion pole for both the mutant and wild type form. However, we find these populations move rapidly inwards toward one another in the mutant case in contrast to the cells that express wild type myosin IIB where those populations remain stationary. Results obtained with these two systems demonstrate how WIMS has the potential to reveal novel correlations between chosen parameters that belong to different scales.

Phase-field model for collective cell migration.

We construct a phase-field model for collective cell migration based on a Ginzburg-Landau free-energy formulation. We model adhesion, surface tension, repulsion, coattraction, and polarization, enabling us to follow the cells' morphologies and the effect of their membranes fluctuations on collective motion. We were able to measure the tissue surface tension as a function of the individual cell cortical tension and adhesion and identify a density threshold for cell-sheet formation.

Very low-carbohydrate diets in the management of diabetes revisited.

Humans can derive energy from carbohydrate, fat, or protein. The metabolism of carbohydrate requires by far the highest secretion of insulin. The central pathology of diabetes is the inability to maintain euglycaemia because of a deficiency in either the action or secretion of insulin. That is, because of either insulin resistance often accompanied by hyperinsulinaemia, or insulin deficiency caused by pancreatic beta cell failure. In individuals dependent on insulin and other hypoglycaemic medication, the difficulty of matching higher intakes of carbohydrates with the higher doses of medication required to maintain euglycaemia increases the risk of adverse events, including potentially fatal hypoglycaemic episodes. Thus, mechanistically it has always made sense to restrict carbohydrate (defined as sugar and starch, but not soluble and insoluble fibre) in the diets of people with diabetes. Randomised clinical trials have confirmed that this action based on first principles is effective. The continued recommendation of higher-carbohydrate, fat-restricted diets has been criticised by some scientists, practitioners and patients. Such protocols when compared with very low-carbohydrate diets provide inferior glycaemic control, and their introduction and subsequent increase in carbohydrate allowances has never been based on strong evidence. The trend towards highercarbohydrate diets for people with diabetes may have played a part in the modern characterisation of type 2 diabetes as a chronic condition with a progressive requirement for multiple medications. Here we will introduce some of the evidence for very low-carbohydrate diets in diabetes management and discuss some of the common objections to their use.

Multiple scale model for cell migration in monolayers: Elastic mismatch between cells enhances motility.

We propose a multiscale model for monolayer of motile cells that comprise normal and cancer cells. In the model, the two types of cells have identical properties except for their elasticity; cancer cells are softer and normal cells are stiffer. The goal is to isolate the role of elasticity mismatch on the migration potential of cancer cells in the absence of other contributions that are present in real cells. The methodology is based on a phase-field description where each cell is modeled as a highly-deformable self-propelled droplet. We simulated two types of nearly confluent monolayers. One contains a single cancer cell in a layer of normal cells and the other contains normal cells only. The simulation results demonstrate that elasticity mismatch alone is sufficient to increase the motility of the cancer cell significantly. Further, the trajectory of the cancer cell is decorated by several speed "bursts" where the cancer cell quickly relaxes from a largely deformed shape and consequently increases its translational motion. The increased motility and the amplitude and frequency of the bursts are in qualitative agreement with recent experiments.

Coupling actin dynamics to phase-field in modeling neural growth.

In this paper we model the growth of a neural cell together with the actin dynamics taking place at its growing region by constructing a phase-field model. This is done by assigning auxiliary fields to different constituents of the cell in order to differentiate them. Specifically, the inner and outer regions of the neural cell are described by ϕ = 1 and ϕ = 0 respectively, whereas the inside and outside of its leading edge are portrayed by ψ = 1 and ψ = 0. This formulation inherently locates the boundary, which is required to determine the evolution of the underlying actin dynamics. Therefore, it provides an alternative to boundary tracking algorithms. Then the equations governing the molecular workings of the cell specifically those of actin are modified in order to satisfy their corresponding boundary conditions.

The chaser and the chased: a phase-field model of an immune response.

In this paper we present a model for an immune response to an invading pathogen. Particularly, we follow the motion of a neutrophil as it migrates to the site of infection guided by chemical cues, a mechanism termed chemotaxis, with the ability to reorient itself as the pathogen changes its position. In the process, the cell undergoes morphological alterations, in addition to the structural changes observed at its leading edge. Also, we derive a condition for a successful immune reaction by relating the speed of the neutrophil to that of the pathogen and to the diffusion coefficient of the chemical attractant.

Prediction of the dependence of the line tension on the composition of linactants and the temperature in phase separated membranes.

We calculate the line tension between domains in phase separated, ternary membranes that comprise line active molecules (linactants) that tend to increase the compatibility of the two phase separating species. The predicted line tension, which depends explicitly on the linactant composition and temperature, is shown to decrease significantly as the fraction of linactants in the membrane increases toward a Lifshitz point, above which the membrane phase separates into a modulated phase. We predict regimes of zero line tension at temperatures close to the mixing transition and clarify the two different ways in which the line tension can be reduced: (1) The linactants uniformly distribute in the system and reduce the compositional mismatch between the two bulk domains. (2) The linactants accumulate at the interface with a preferred orientation. Both of these mechanisms have been observed in recent experiments and simulations. The second one is unique to line active molecules, and our work shows that it is increasingly important at large fraction of linactants and is necessary for the emergence of a regime of zero line tension. The methodology is based on the ternary mixture model proposed by Palmieri and Safran [Palmieri, B.; Safran, S. A. Langmuir 2013, 29, 5246], and the line tension is calculated via variationally derived, self-consistent profiles for the local variation of composition and linactant orientation in the interface region.

Phase-field-crystal modeling of glass-forming liquids: spanning time scales during vitrification, aging, and deformation.

Two essential elements required to generate a glass transition within phase-field-crystal (PFC) models are outlined based on observed freezing behaviors in various models of this class. The central dynamic features of glass formation in simple binary liquids are qualitatively reproduced across 12 orders of magnitude in time by applying a physically motivated time scaling to previous PFC simulation results. New aspects of the equilibrium phase behavior of the same binary model system are also outlined, aging behavior is explored in the moderate and deeply supercooled regimes, and aging exponents are extracted. General features of the elastic and plastic responses of amorphous and crystalline PFC solids under deformation are also compared and contrasted.

Microphase separation in comblike liquid-crystalline diblock copolymers.

The interplay between liquid crystallinity and microphase separation in comblike liquid-crystalline diblock copolymers is examined via a Brazovskii-type phenomenological model using both analytical and numerical calculations. For symmetric diblock copolymers we determine a critical electric field that is required to tilt the orientation of the constituent liquid crystals of the polymer side chains in the microphase-separated lamellar state. Such electrically induced reorientation of the liquid-crystal molecules can lead to substantially large changes of lamellar periodicity. Our numerical results show that highly aligned polymer lamellar domains can self-assemble when the liquid-crystal ordering precedes microphase separation, and that weak electric fields can be used to direct the self-assembly process due to the dielectric anisotropy of the liquid-crystal side chains. We also find that phase separation of asymmetric diblock copolymers can coexist with a network of liquid-crystal nematic orientations, with domain morphology depending on the details of copolymer and liquid-crystal coupling.

Phase-field-crystal model for magnetocrystalline interactions in isotropic ferromagnetic solids.

An isotropic magnetoelastic phase-field-crystal model to study the relation between morphological structure and magnetic properties of pure ferromagnetic solids is introduced. Analytic calculations in two dimensions were used to determine the phase diagram and obtain the relationship between elastic strains and magnetization. Time-dependent numerical simulations in two dimensions were used to demonstrate the effect of grain boundaries on the formation of magnetic domains. It was shown that the grain boundaries act as nucleating sites for domains of reverse magnetization. Finally, we derive a relation for coercivity versus grain misorientation in the isotropic limit.

Phase-field approach to chemotactic driving of neutrophil morphodynamics.

To simulate the motion of neutrophils and their morphodynamics in response to chemical cues, we construct a model based on the phase-field method utilizing a description with a free-energy functional and associated dynamics which captures the basic features of the phenomenon. We additionally incorporate spatial sensing by introducing an auxiliary field which depicts the polymerization of the region of the cell facing the highest concentration of the chemical attractant.

Micromechanics of emergent patterns in plastic flows.

Crystalline solids undergo plastic deformation and subsequently flow when subjected to stresses beyond their elastic limit. In nature most crystalline solids exist in polycrystalline form. Simulating plastic flows in polycrystalline solids has wide ranging applications, from material processing to understanding intermittency of earthquake dynamics. Using phase field crystal (PFC) model we show that in sheared polycrystalline solids the atomic displacement field shows spatio-temporal heterogeneity spanning over several orders of length and time scales, similar to that in amorphous solids. The displacement field also exhibits localized quadrupolar patterns, characteristic of two dislocations of the opposite sign approaching each other. This is a signature of crystallinity at microscopic scale. Polycrystals being halfway between single crystals and amorphous solids, in terms of the degree of structural order, descriptions of solid mechanics at two widely different scales, namely continuum plastic flow and discrete dislocation dynamics turns out to be necessary here.

Modeling multiple time scales during glass formation with phase-field crystals.

The dynamics of glass formation in monatomic and binary liquids are studied numerically using a microscopic field theory for the evolution of the time-averaged atomic number density. A stochastic framework combining phase-field crystal free energies and dynamic density functional theory is shown to successfully describe several aspects of glass formation over multiple time scales. Agreement with mode coupling theory is demonstrated for underdamped liquids at moderate supercoolings, and a rapidly growing dynamic correlation length is found to be associated with fragile behavior.

Positive interactions and the emergence of community structure in metacommunities.

The significant role of space in maintaining species coexistence and determining community structure and function is well established. However, community ecology studies have mainly focused on simple competition and predation systems, and the relative impact of positive interspecific interactions in shaping communities in a spatial context is not well understood. Here we employ a spatially explicit metacommunity model to investigate the effect of local dispersal on the structure and function of communities in which species are linked through an interaction web comprising mutualism, competition and exploitation. Our results show that function, diversity and interspecific interactions of locally linked communities undergo a phase transition with changes in the rate of species dispersal. We find that low spatial interconnectedness favors the spontaneous emergence of strongly mutualistic communities which are more stable but less productive and diverse. On the other hand, high spatial interconnectedness promotes local biodiversity at the expense of local stability and supports communities with a wide range of interspecific interactions. We argue that investigations of the relationship between spatial processes and the self-organization of complex interaction webs are critical to understanding the geographic structure of interactions in real landscapes.