Superstatistical analysis and modelling of heterogeneous random walks

Neutrophils exhibit distinct migration phenotypes that are regulated by transendothelial migration

The extravasation of polymorphonuclear neutrophils (PMNs) is a critical component of the innate immune response that involves transendothelial migration (TEM) and interstitial migration. TEM-mediated interactions between PMNs and vascular endothelial cells (VECs) trigger a cascade of biochemical and mechanobiological signals whose effects on interstitial migration are currently unclear. To address this question, we cultured human VECs on a fibronectin-treated transwell insert to model the endothelium and basement membrane, loaded PMN-like differentiated HL60 (dHL-60) cells in the upper chamber of the insert, and collected the PMNs that crossed the membrane-supported monolayer from the lower chamber. The 3D chemotactic migration of the TEM-conditioned PMNs through collagen matrices was then quantified. Data collected from over 50,000 trajectories showed two distinct migratory phenotypes, i.e., a high-persistence phenotype and a low-persistence phenotype. These phenotypes were conserved across treatment conditions, and their existence was confirmed in human primary PMNs. The high-persistence phenotype was characterized by more straight trajectories and faster migration speeds, whereas the low-persistence one exhibited more frequent sharp turns and loitering periods. A key finding of our study is that TEM induced a phenotypic shift in PMNs from high-persistence migration to low-persistence migration. Changes in the relative proportion of high-persistence and low-persistence populations correlated with GRK2 expression levels. Inhibiting GRK2 hindered the TEM-induced shift in migratory phenotype and impaired the phagocytic function of PMNs. Overall, our study suggests that TEM-mediated GRK2 signaling primes PMNs for a migration phenotype better suited for spatial exploration and inflammation resolution. These observations provide novel insight into the biophysical impacts of TEM that priming PMNs is essential to conduct sentinel functions.

FMNL1 and mDia1 promote efficient T cell migration through complex environments via distinct mechanisms

Lymphocyte trafficking and migration through tissues is critical for adaptive immune function and, to perform their roles, T cells must be able to navigate through diverse tissue environments that present a range of mechanical challenges. T cells predominantly express two members of the formin family of actin effectors, Formin-like 1 (FMNL1) and mammalian diaphanous-related formin 1 (mDia1). While both FMNL1 and mDia1 have been studied individually, they have not been directly compared to determine functional differences in promoting T cell migration. Through in vivo analysis and the use of in vitro 2D and 3D model environments, we demonstrate that FMNL1 and mDia1 are both required for effective T cell migration, but they have different localization and roles in T cells, with specific environment-dependent functions. We found that mDia1 promotes general motility in 3D environments in conjunction with Myosin-II activity. We also show that, while mDia1 is almost entirely in the cytoplasmic compartment, a portion of FMNL1 physically associates with the nucleus. Furthermore, FMNL1 localizes to the rear of migrating T cells and contributes to efficient migration by promoting deformation of the rigid T cell nucleus in confined environments. Overall, our data indicates that while FMNL1 and mDia1 have similar mechanisms of actin polymerization, they have distinct roles in promoting T cell migration. This suggests that differential modulation of FMNL1 and mDia1 can be an attractive therapeutic route to fine-tune T cell migration behavior.

Cancer cell migration depends on adjacent ASC and adipose spheroids in a 3D bioprinted breast cancer model

Breast cancer develops in close proximity to mammary adipose tissue and interactions with the local adipose environment have been shown to drive tumor progression. The specific role, however, of this complex tumor microenvironment in cancer cell migration still needs to be elucidated. Therefore, in this study, a 3D bioprinted breast cancer model was developed that allows for a comprehensive analysis of individual tumor cell migration parameters in dependence of adjacent adipose stroma. In this co-culture model, a breast cancer compartment with MDA-MB-231 breast cancer cells embedded in collagen is surrounded by an adipose tissue compartment consisting of adipose-derived stromal cell (ASC) or adipose spheroids in a printable bioink based on thiolated hyaluronic acid. Printing parameters were optimized for adipose spheroids to ensure viability and integrity of the fragile lipid-laden cells. Preservation of the adipogenic phenotype after printing was demonstrated by quantification of lipid content, expression of adipogenic marker genes, the presence of a coherent adipo-specific extracellular matrix, and cytokine secretion. The migration of tumor cells as a function of paracrine signaling of the surrounding adipose compartment was then analyzed using live-cell imaging. The presence of ASC or adipose spheroids substantially increased key migration parameters of MDA-MB-231 cells, namely motile fraction, persistence, invasion distance, and speed. These findings shed new light on the role of adipose tissue in cancer cell migration. They highlight the potential of our 3D printed breast cancer-stroma model to elucidate mechanisms of stroma-induced cancer cell migration and to serve as a screening platform for novel anti-cancer drugs targeting cancer cell dissemination.

Data-driven modelling makes quantitative predictions regarding bacteria surface motility

In this work, we quantitatively compare computer simulations and existing cell tracking data of P. aeruginosa surface motility in order to analyse the underlying motility mechanism. We present a three dimensional twitching motility model, that simulates the extension, retraction and surface association of individual Type IV Pili (TFP), and is informed by recent experimental observations of TFP. Sensitivity analysis is implemented to minimise the number of model parameters, and quantitative estimates for the remaining parameters are inferred from tracking data by approximate Bayesian computation. We argue that the motility mechanism is highly sensitive to experimental conditions. We predict a TFP retraction speed for the tracking data we study that is in a good agreement with experimental results obtained under very similar conditions. Furthermore, we examine whether estimates for biologically important parameters, whose direct experimental determination is challenging, can be inferred directly from tracking data. One example is the width of the distribution of TFP on the bacteria body. We predict that the TFP are broadly distributed over the bacteria pole in both walking and crawling motility types. Moreover, we identified specific configurations of TFP that lead to transitions between walking and crawling states.

Learning dynamical models of single and collective cell migration: a review

Single and collective cell migration are fundamental processes critical for physiological phenomena ranging from embryonic development and immune response to wound healing and cancer metastasis. To understand cell migration from a physical perspective, a broad variety of models for the underlying physical mechanisms that govern cell motility have been developed. A key challenge in the development of such models is how to connect them to experimental observations, which often exhibit complex stochastic behaviours. In this review, we discuss recent advances in data-driven theoretical approaches that directly connect with experimental data to infer dynamical models of stochastic cell migration. Leveraging advances in nanofabrication, image analysis, and tracking technology, experimental studies now provide unprecedented large datasets on cellular dynamics. In parallel, theoretical efforts have been directed towards integrating such datasets into physical models from the single cell to the tissue scale with the aim of conceptualising the emergent behaviour of cells. We first review how this inference problem has been addressed in both freely migrating and confined cells. Next, we discuss why these dynamics typically take the form of underdamped stochastic equations of motion, and how such equations can be inferred from data. We then review applications of data-driven inference and machine learning approaches to heterogeneity in cell behaviour, subcellular degrees of freedom, and to the collective dynamics of multicellular systems. Across these applications, we emphasise how data-driven methods can be integrated with physical active matter models of migrating cells, and help reveal how underlying molecular mechanisms control cell behaviour. Together, these data-driven approaches are a promising avenue for building physical models of cell migration directly from experimental data, and for providing conceptual links between different length-scales of description.

An entropy-based approach for assessing the directional persistence of cell migration

Cell migration, which is primarily characterized by directional persistence, is essential for the development of normal tissues and organs, as well as for numerous pathological processes. However, there is a lack of simple and efficient tools to analyze the systematic properties of persistence based on cellular trajectory data. Here, we present a novel approach, the entropy of angular distribution , which combines cellular turning dynamics and Shannon entropy to explore the statistical and time-varying properties of persistence that strongly correlate with cellular migration modes. Our results reveal the changes in the persistence of multiple cell lines that are tightly regulated by both intra- and extracellular cues, including Arpin protein, collagen gel/substrate, and physical constraints. Significantly, some previously unreported distinctive details of persistence have also been captured, helping to elucidate how directional persistence is distributed and evolves in different cell populations. The analysis suggests that the entropy of angular distribution-based approach provides a powerful metric for evaluating directional persistence and enables us to better understand the relationships between cellular behaviors and multiscale cues, which also provides some insights into the migration dynamics of cell populations, such as collective cell invasion.

Morphological entropy encodes cellular migration strategies on multiple length scales

Cell migration is crucial for numerous physiological and pathological processes. A cell adapts its morphology, including the overall and nuclear morphology, in response to various cues in complex microenvironments, such as topotaxis and chemotaxis during migration. Thus, the dynamics of cellular morphology can encode migration strategies, from which diverse migration mechanisms can be inferred. However, deciphering the mechanisms behind cell migration encoded in morphology dynamics remains a challenging problem. Here, we present a powerful universal metric, the Cell Morphological Entropy (CME), developed by combining parametric morphological analysis with Shannon entropy. The utility of CME, which accurately quantifies the complex cellular morphology at multiple length scales through the deviation from a perfectly circular shape, is illustrated using a variety of normal and tumor cell lines in different in vitro microenvironments. Our results show how geometric constraints affect the MDA-MB-231 cell nucleus, the emerging interactions of MCF-10A cells migrating on collagen gel, and the critical transition from proliferation to invasion in tumor spheroids. The analysis demonstrates that the CME-based approach provides an effective and physically interpretable tool to measure morphology in real-time across multiple length scales. It provides deeper insight into cell migration and contributes to the understanding of different behavioral modes and collective cell motility in more complex microenvironments.

Cellular subpopulations identified using an ensemble average of multiple dielectrophoresis measurements

While the average value measurement approach can successfully analyze and predict the general behavior and biophysical properties of an isogenic cell population, it fails when significant differences among individual cells are generated in the population by intracellular changes such as the cell cycle, or different cellular responses to certain stimuli. Detecting such single-cell differences in a cell population has remained elusive. Here, we describe an easy-to-implement and generalizable platform that measures the dielectrophoretic cross-over frequency of individual cells by decreasing measurement noise with a stochastic method and computing ensemble average statistics. This platform enables multiple, real-time, label-free detection of individual cells with significant dielectric variations over time within an isogenic cell population. Using a stochastic method in combination with the platform, we distinguished cell subpopulations from a mixture of drug-untreated and -treated isogenic cells. Furthermore, we demonstrate that our platform can identify drug-treated isogenic cells with different recovery rates.

Extract latent features of single-particle trajectories with historical experience learning

Single-particle tracking has enabled real-time, in situ quantitative studies of complex systems. However, inferring dynamic state changes from noisy and undersampling trajectories encounters challenges. Here, we introduce a data-driven method for extracting features of subtrajectories with historical experience learning (Deep-SEES), where a single-particle tracking analysis pipeline based on a self-supervised architecture automatically searches for the latent space, allowing effective segmentation of the underlying states from noisy trajectories without prior knowledge on the particle dynamics. We validated our method on a variety of noisy simulated and experimental data. Our results showed that the method can faithfully capture both stable states and their dynamic switch. In highly random systems, our method outperformed commonly used unsupervised methods in inferring motion states, which is important for understanding nanoparticles interacting with living cell membranes, active enzymes, and liquid-liquid phase separation. Self-generating latent features of trajectories could potentially improve the understanding, estimation, and prediction of many complex systems.

Heterogeneous anomalous transport in cellular and molecular biology

It is well established that a wide variety of phenomena in cellular and molecular biology involve anomalous transport e.g. the statistics for the motility of cells and molecules are fractional and do not conform to the archetypes of simple diffusion or ballistic transport. Recent research demonstrates that anomalous transport is in many cases heterogeneous in both time and space. Thus single anomalous exponents and single generalised diffusion coefficients are unable to satisfactorily describe many crucial phenomena in cellular and molecular biology. We consider advances in the field ofheterogeneous anomalous transport(HAT) highlighting: experimental techniques (single molecule methods, microscopy, image analysis, fluorescence correlation spectroscopy, inelastic neutron scattering, and nuclear magnetic resonance), theoretical tools for data analysis (robust statistical methods such as first passage probabilities, survival analysis, different varieties of mean square displacements, etc), analytic theory and generative theoretical models based on simulations. Special emphasis is made on high throughput analysis techniques based on machine learning and neural networks. Furthermore, we consider anomalous transport in the context of microrheology and the heterogeneous viscoelasticity of complex fluids. HAT in the wavefronts of reaction-diffusion systems is also considered since it plays an important role in morphogenesis and signalling. In addition, we present specific examples from cellular biology including embryonic cells, leucocytes, cancer cells, bacterial cells, bacterial biofilms, and eukaryotic microorganisms. Case studies from molecular biology include DNA, membranes, endosomal transport, endoplasmic reticula, mucins, globular proteins, and amyloids.

Whole-genome screens reveal regulators of differentiation state and context-dependent migration in human neutrophils

Neutrophils are the most abundant leukocyte in humans and provide a critical early line of defense as part of our innate immune system. We perform a comprehensive, genome-wide assessment of the molecular factors critical to proliferation, differentiation, and cell migration in a neutrophil-like cell line. Through the development of multiple migration screen strategies, we specifically probe directed (chemotaxis), undirected (chemokinesis), and 3D amoeboid cell migration in these fast-moving cells. We identify a role for mTORC1 signaling in cell differentiation, which influences neutrophil abundance, survival, and migratory behavior. Across our individual migration screens, we identify genes involved in adhesion-dependent and adhesion-independent cell migration, protein trafficking, and regulation of the actomyosin cytoskeleton. This genome-wide screening strategy, therefore, provides an invaluable approach to the study of neutrophils and provides a resource that will inform future studies of cell migration in these and other rapidly migrating cells.

Modeling three-dimensional T-cell motility using clustering and hidden Markov models

Recent advances in imaging technologies now allow for real-time tracking of fast-moving immune cells as they search for targets such as pathogens and tumor cells through complex three-dimensional tissues. Cytotoxic T cells are specialized immune cells that continually scan tissues for such targets to engage and kill, and have emerged as the principle mediators of breakthrough immunotherapies against cancers. Modeling the way these T cells move is of great value in furthering our understanding of their collective search efficiency. T-cell motility is characterized by heterogeneity at two levels: (a) Individual cells display different distributions of translational speeds and turning angles, and (b) each cell can during a given track, its motility, switch between local search and directional motion. Despite a likely considerable influence on a motile population's search performance, statistical models that accurately capture both such heterogeneities in a distinguishing manner are lacking. Here, we model three-dimensional T-cell trajectories through a spherical representation of their incremental steps and compare model outputs to real-world motility data from primary T cells navigating physiological environments. T cells in a population are clustered based on their directional persistence and characteristic "step lengths" therein capturing between-cell heterogeneity. The motility dynamics of cells within each cluster are individually modeled through hidden Markov model to capture within-cell transitions between local and more extensive search patterns. We explore the importance of explicitly capturing altered motility patterns when cells lie in close proximity to one another, through a non-homogenous hidden Markov model.

Classification at the accuracy limit: facing the problem of data ambiguity

Data classification, the process of analyzing data and organizing it into categories or clusters, is a fundamental computing task of natural and artificial information processing systems. Both supervised classification and unsupervised clustering work best when the input vectors are distributed over the data space in a highly non-uniform way. These tasks become however challenging in weakly structured data sets, where a significant fraction of data points is located in between the regions of high point density. We derive the theoretical limit for classification accuracy that arises from this overlap of data categories. By using a surrogate data generation model with adjustable statistical properties, we show that sufficiently powerful classifiers based on completely different principles, such as perceptrons and Bayesian models, all perform at this universal accuracy limit under ideal training conditions. Remarkably, the accuracy limit is not affected by certain non-linear transformations of the data, even if these transformations are non-reversible and drastically reduce the information content of the input data. We further compare the data embeddings that emerge by supervised and unsupervised training, using the MNIST data set and human EEG recordings during sleep. We find for MNIST that categories are significantly separated not only after supervised training with back-propagation, but also after unsupervised dimensionality reduction. A qualitatively similar cluster enhancement by unsupervised compression is observed for the EEG sleep data, but with a very small overall degree of cluster separation. We conclude that the handwritten letters in MNIST can be considered as 'natural kinds', whereas EEG sleep recordings are a relatively weakly structured data set, so that unsupervised clustering will not necessarily re-cover the human-defined sleep stages.

Distributed medium viscosity yields quasi-exponential step-size probability distributions in heterogeneous media

The analysis of the statistics of random walks undertaken by passive particles in complex media has important implications in a number of areas including pathogen transport and drug delivery. In several systems in which heterogeneity is important, the distribution of particle step-sizes has been found to be exponential in nature, as opposed to the Gaussian distribution associated with Brownian motion. Here, we first develop a theoretical framework to study a simplified version of this problem: the motion of passive tracers in a range of sub-environments with different viscosity. We show that in the limit of a large number of equi-distributed sub-environments spanning a broad viscosity range, an exact analytical expression for the underlying particle step-size distribution can be derived, which approaches an exponential distribution when step sizes are small. We then validate this using a simple experimental system of glycerol-water mixtures, in which the volume fraction of glycerol is systematically varied. Overall, the assumption of exponentially distributed step sizes may substantially over-estimate the incidence of large steps in heterogeneous systems, with important implications in the analysis of various biophysical processes.

Distinct Dynamics of Migratory Response to PD-1 and CTLA-4 Blockade Reveals New Mechanistic Insights for Potential T-Cell Reinvigoration following Immune Checkpoint Blockade

Cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death protein 1 (PD-1), two clinically relevant targets for the immunotherapy of cancer, are negative regulators of T-cell activation and migration. Optimizing the therapeutic response to CTLA-4 and PD-1 blockade calls for a more comprehensive insight into the coordinated function of these immune regulators. Mathematical modeling can be used to elucidate nonlinear tumor-immune interactions and highlight the underlying mechanisms to tackle the problem. Here, we investigated and statistically characterized the dynamics of T-cell migration as a measure of the functional response to these pathways. We used a previously developed three-dimensional organotypic culture of patient-derived tumor spheroids treated with anti-CTLA-4 and anti-PD-1 antibodies for this purpose. Experiment-based dynamical modeling revealed the delayed kinetics of PD-1 activation, which originates from the distinct characteristics of PD-1 and CTLA-4 regulation, and followed through with the modification of their contributions to immune modulation. The simulation results show good agreement with the tumor cell reduction and active immune cell count in each experiment. Our findings demonstrate that while PD-1 activation provokes a more exhaustive intracellular cascade within a mature tumor environment, the time-delayed kinetics of PD-1 activation outweighs its preeminence at the individual cell level and consequently confers a functional dominance to the CTLA-4 checkpoint. The proposed model explains the distinct immunostimulatory pattern of PD-1 and CTLA-4 blockade based on mechanisms involved in the regulation of their expression and may be useful for planning effective treatment schemes targeting PD-1 and CTLA-4 functions.

Heterogeneous run-and-tumble motion accounts for transient non-Gaussian super-diffusion in haematopoietic multi-potent progenitor cells

Multi-potent progenitor (MPP) cells act as a key intermediary step between haematopoietic stem cells and the entirety of the mature blood cell system. Their eventual fate determination is thought to be achieved through migration in and out of spatially distinct niches. Here we first analyze statistically MPP cell trajectory data obtained from a series of long time-course 3D in vivo imaging experiments on irradiated mouse calvaria, and report that MPPs display transient super-diffusion with apparent non-Gaussian displacement distributions. Second, we explain these experimental findings using a run-and-tumble model of cell motion which incorporates the observed dynamical heterogeneity of the MPPs. Third, we use our model to extrapolate the dynamics to time-periods currently inaccessible experimentally, which enables us to quantitatively estimate the time and length scales at which super-diffusion transitions to Fickian diffusion. Our work sheds light on the potential importance of motility in early haematopoietic progenitor function.

T cell morphodynamics reveal periodic shape oscillations in three-dimensional migration

T cells use sophisticated shape dynamics (morphodynamics) to migrate towards and neutralize infected and cancerous cells. However, there is limited quantitative understanding of the migration process in three-dimensional extracellular matrices (ECMs) and across timescales. Here, we leveraged recent advances in lattice light-sheet microscopy to quantitatively explore the three-dimensional morphodynamics of migrating T cells at high spatio-temporal resolution. We first developed a new shape descriptor based on spherical harmonics, incorporating key polarization information of the uropod. We found that the shape space of T cells is low-dimensional. At the behavioural level, run-and-stop migration modes emerge at approximately 150 s, and we mapped the morphodynamic composition of each mode using multiscale wavelet analysis, finding 'stereotyped' motifs. Focusing on the run mode, we found morphodynamics oscillating periodically (every approx. 100 s) that can be broken down into a biphasic process: front-widening with retraction of the uropod, followed by a rearward surface motion and forward extension, where intercalation with the ECM in both of these steps likely facilitates forward motion. Further application of these methods may enable the comparison of T cell migration across different conditions (e.g. differentiation, activation, tissues and drug treatments) and improve the precision of immunotherapeutic development.

Learning the rules of collective cell migration using deep attention networks

Collective, coordinated cellular motions underpin key processes in all multicellular organisms, yet it has been difficult to simultaneously express the ‘rules’ behind these motions in clear, interpretable forms that effectively capture high-dimensional cell-cell interaction dynamics in a manner that is intuitive to the researcher. Here we apply deep attention networks to analyze several canonical living tissues systems and present the underlying collective migration rules for each tissue type using only cell migration trajectory data. We use these networks to learn the behaviors of key tissue types with distinct collective behaviors—epithelial, endothelial, and metastatic breast cancer cells—and show how the results complement traditional biophysical approaches. In particular, we present attention maps indicating the relative influence of neighboring cells to the learned turning decisions of a ‘focal cell’–the primary cell of interest in a collective setting. Colloquially, we refer to this learned relative influence as ‘attention’, as it serves as a proxy for the physical parameters modifying the focal cell’s future motion as a function of each neighbor cell. These attention networks reveal distinct patterns of influence and attention unique to each model tissue. Endothelial cells exhibit tightly focused attention on their immediate forward-most neighbors, while cells in more expansile epithelial tissues are more broadly influenced by neighbors in a relatively large forward sector. Attention maps of ensembles of more mesenchymal, metastatic cells reveal completely symmetric attention patterns, indicating the lack of any particular coordination or direction of interest. Moreover, we show how attention networks are capable of detecting and learning how these rules change based on biophysical context, such as location within the tissue and cellular crowding. That these results require only cellular trajectories and no modeling assumptions highlights the potential of attention networks for providing further biological insights into complex cellular systems.

Collective behaviors are crucial to the function of multicellular life, with large-scale, coordinated cell migration enabling processes spanning organ formation to coordinated skin healing. However, we lack effective tools to discover and cleanly express collective rules at the level of an individual cell. Here, we employ a carefully structured neural network to extract collective information directly from cell trajectory data. The network is trained on data from various systems, including canonical collective cell systems (HUVEC and MDCK cells) which display visually distinct forms of collective motion, and metastatic cancer cells (MDA-MB-231) which are highly uncoordinated. Using these trained networks, we can produce attention maps for each system, which indicate how a cell within a tissue takes in information from its surrounding neighbors, as a function of weights assigned to those neighbors. Thus for a cell type in which cells tend to follow the path of the cell in front, the attention maps will display high weights for cells spatially forward of the focal cell. We present results in terms of additional metrics, such as accuracy plots and number of interacting cells, and encourage future development of improved metrics.

Exact solution for the Anisotropic Ornstein-Uhlenbeck process

Active-Matter models commonly consider particles with overdamped dynamics subject to a force (speed) with constant modulus and random direction. Some models also include random noise in particle displacement (a Wiener process), resulting in diffusive motion at short time scales. On the other hand, Ornstein-Uhlenbeck processes apply Langevin dynamics to the particles' velocity and predict motion that is not diffusive at short time scales. Experiments show that migrating cells have gradually varying speeds at intermediate and long time scales, with short-time diffusive behavior. While Ornstein-Uhlenbeck processes can describe the moderate-and long-time speed variation, Active-Matter models for over-damped particles can explain the short-time diffusive behavior. Isotropic models cannot explain both regimes, because short-time diffusion renders instantaneous velocity ill-defined, and prevents the use of dynamical equations that require velocity time-derivatives. On the other hand, both models correctly describe some of the different temporal regimes seen in migrating biological cells and must, in the appropriate limit, yield the same observable predictions. Here we propose and solve analytically an Anisotropic Ornstein-Uhlenbeck process for polarized particles, with Langevin dynamics governing the particle's movement in the polarization direction and a Wiener process governing displacement in the orthogonal direction. Our characterization provides a theoretically robust way to compare movement in dimensionless simulations to movement in experiments in which measurements have meaningful space and time units. We also propose an approach to deal with inevitable finite-precision effects in experiments and simulations.

Disentangling cadherin-mediated cell-cell interactions in collective cancer cell migration

Cell dispersion from a confined area is fundamental in a number of biological processes, including cancer metastasis. To date, a quantitative understanding of the interplay of single-cell motility, cell proliferation, and intercellular contacts remains elusive. In particular, the role of E- and N-cadherin junctions, central components of intercellular contacts, is still controversial. Combining theoretical modeling with in vitro observations, we investigate the collective spreading behavior of colonies of human cancer cells (T24). The spreading of these colonies is driven by stochastic single-cell migration with frequent transient cell-cell contacts. We find that inhibition of E- and N-cadherin junctions decreases colony spreading and average spreading velocities, without affecting the strength of correlations in spreading velocities of neighboring cells. Based on a biophysical simulation model for cell migration, we show that the behavioral changes upon disruption of these junctions can be explained by reduced repulsive excluded volume interactions between cells. This suggests that in cancer cell migration, cadherin-based intercellular contacts sharpen cell boundaries leading to repulsive rather than cohesive interactions between cells, thereby promoting efficient cell spreading during collective migration.

Anomalous diffusion, aging, and nonergodicity of scaled Brownian motion with fractional Gaussian noise: overview of related experimental observations and models

How does a systematic time-dependence of the diffusion coefficient $D (t)$ affect the ergodic and statistical characteristics of fractional Brownian motion (FBM)? Here, we examine how the behavior of the...

Sleep as a random walk: a super-statistical analysis of EEG data across sleep stages

In clinical practice, human sleep is classified into stages, each associated with different levels of muscular activity and marked by characteristic patterns in the EEG signals. It is however unclear whether this subdivision into discrete stages with sharply defined boundaries is truly reflecting the dynamics of human sleep. To address this question, we consider one-channel EEG signals as heterogeneous random walks: stochastic processes controlled by hyper-parameters that are themselves time-dependent. We first demonstrate the heterogeneity of the random process by showing that each sleep stage has a characteristic distribution and temporal correlation function of the raw EEG signals. Next, we perform a super-statistical analysis by computing hyper-parameters, such as the standard deviation, kurtosis, and skewness of the raw signal distributions, within subsequent 30-second epochs. It turns out that also the hyper-parameters have characteristic, sleep-stage-dependent distributions, which can be exploited for a simple Bayesian sleep stage detection. Moreover, we find that the hyper-parameters are not piece-wise constant, as the traditional hypnograms would suggest, but show rising or falling trends within and across sleep stages, pointing to an underlying continuous rather than sub-divided process that controls human sleep. Based on the hyper-parameters, we finally perform a pairwise similarity analysis between the different sleep stages, using a quantitative measure for the separability of data clusters in multi-dimensional spaces.

To improve our understand of how EEG activity reflects the dynamics of human sleep, Metzner et al. use human EEG data and superstatistical analysis to demonstrate that each sleep stage has a characteristic distribution and temporal correlation function of raw EEG signals. They also show that the hyper-parameters controlling the EEG signals have characteristic, sleep-stage-dependent distributions, which can be exploited for a simple Bayesian sleep stage detection.

Detecting long-range interactions between migrating cells

Chemotaxis enables cells to systematically approach distant targets that emit a diffusible guiding substance. However, the visual observation of an encounter between a cell and a target does not necessarily indicate the presence of a chemotactic approach mechanism, as even a blindly migrating cell can come across a target by chance. To distinguish between the chemotactic approach and blind migration, we present an objective method that is based on the analysis of time-lapse recorded cell migration trajectories: For each movement step of a cell relative to the position of a potential target, we compute a p value that quantifies the likelihood of the movement direction under the null-hypothesis of blind migration. The resulting distribution of p values, pooled over all recorded cell trajectories, is then compared to an ensemble of reference distributions in which the positions of targets are randomized. First, we validate our method with simulated data, demonstrating that it reliably detects the presence or absence of remote cell-cell interactions. In a second step, we apply the method to data from three-dimensional collagen gels, interspersed with highly migratory natural killer (NK) cells that were derived from two different human donors. We find for one of the donors an attractive interaction between the NK cells, pointing to a cooperative behavior of these immune cells. When adding nearly stationary K562 tumor cells to the system, we find a repulsive interaction between K562 and NK cells for one of the donors. By contrast, we find attractive interactions between NK cells and an IL-15-secreting variant of K562 tumor cells. We therefore speculate that NK cells find wild-type tumor cells only by chance, but are programmed to leave a target quickly after a close encounter. We provide a freely available Python implementation of our p value method that can serve as a general tool for detecting long-range interactions in collective systems of self-driven agents.

Cell migration guided by long-lived spatial memory

Living cells actively migrate in their environment to perform key biological functions-from unicellular organisms looking for food to single cells such as fibroblasts, leukocytes or cancer cells that can shape, patrol or invade tissues. Cell migration results from complex intracellular processes that enable cell self-propulsion, and has been shown to also integrate various chemical or physical extracellular signals. While it is established that cells can modify their environment by depositing biochemical signals or mechanically remodelling the extracellular matrix, the impact of such self-induced environmental perturbations on cell trajectories at various scales remains unexplored. Here, we show that cells can retrieve their path: by confining motile cells on 1D and 2D micropatterned surfaces, we demonstrate that they leave long-lived physicochemical footprints along their way, which determine their future path. On this basis, we argue that cell trajectories belong to the general class of self-interacting random walks, and show that self-interactions can rule large scale exploration by inducing long-lived ageing, subdiffusion and anomalous first-passage statistics. Altogether, our joint experimental and theoretical approach points to a generic coupling between motile cells and their environment, which endows cells with a spatial memory of their path and can dramatically change their space exploration.

A mathematical framework for modelling 3D cell motility: applications to glioblastoma cell migration

The collection of 3D cell tracking data from live images of micro-tissues is a recent innovation made possible due to advances in imaging techniques. As such there is increased interest in studying cell motility in 3D in vitro model systems but a lack of rigorous methodology for analysing the resulting data sets. One such instance of the use of these in vitro models is in the study of cancerous tumours. Growing multicellular tumour spheroids in vitro allows for modelling of the tumour microenvironment and the study of tumour cell behaviours, such as migration, which improves understanding of these cells and in turn could potentially improve cancer treatments. In this paper, we present a workflow for the rigorous analysis of 3D cell tracking data, based on the persistent random walk model, but adaptable to other biologically informed mathematical models. We use statistical measures to assess the fit of the model to the motility data and to estimate model parameters and provide confidence intervals for those parameters, to allow for parametrization of the model taking correlation in the data into account. We use in silico simulations to validate the workflow in 3D before testing our method on cell tracking data taken from in vitro experiments on glioblastoma tumour cells, a brain cancer with a very poor prognosis. The presented approach is intended to be accessible to both modellers and experimentalists alike in that it provides tools for uncovering features of the data set that may suggest amendments to future experiments or modelling attempts.

Deriving time-varying cellular motility parameters via wavelet analysis

Cell migration, which is regulated by intracellular signaling pathways (ICSP) and extracellular matrix (ECM), plays an indispensable role in many physiological and pathological process such as normal tissue development and cancer metastasis. However, there is a lack of rigorous and quantitative tools for analyzing the time-varying characteristics of cell migration in heterogeneous microenvironment, resulted from, e.g. the time-dependent local stiffness due to microstructural remodeling by migrating cells. Here, we develop a wavelet-analysis approach to derive the time-dependent motility parameters from cell migration trajectories, based on the time-varying persistent random walk model. In particular, the wavelet denoising and wavelet transform are employed to analyze migration velocities and obtain the wavelet power spectrum. Subsequently, the time-dependent motility parameters are derived via Lorentzian power spectrum. Our results based on synthetic data indicate the superiority of the method for estimating the intrinsic transient motility parameters, robust against a variety of stochastic noises. We also carry out a systematic parameter study and elaborate the effects of parameter selection on the performance of the method. Moreover, we demonstrate the utility of our approach via analyzing experimental data ofin vitrocell migration in distinct microenvironments, including the migration of MDA-MB-231 cells in confined micro-channel arrays and correlated migration of MCF-10A cells due to ECM-mediated mechanical coupling. Our analysis shows that our approach can be as a powerful tool to accurately derive the time-dependent motility parameters, and further analyze the time-dependent characteristics of cell migration regulated by complex microenvironment.

Analysis and visualization of sleep stages based on deep neural networks

Automatic sleep stage scoring based on deep neural networks has come into focus of sleep researchers and physicians, as a reliable method able to objectively classify sleep stages would save human resources and simplify clinical routines. Due to novel open-source software libraries for machine learning, in combination with enormous recent progress in hardware development, a paradigm shift in the field of sleep research towards automatic diagnostics might be imminent. We argue that modern machine learning techniques are not just a tool to perform automatic sleep stage classification, but are also a creative approach to find hidden properties of sleep physiology. We have already developed and established algorithms to visualize and cluster EEG data, facilitating first assessments on sleep health in terms of sleep-apnea and consequently reduced daytime vigilance. In the following study, we further analyze cortical activity during sleep by determining the probabilities of momentary sleep stages, represented as hypnodensity graphs and then computing vectorial cross-correlations of different EEG channels. We can show that this measure serves to estimate the period length of sleep cycles and thus can help to find disturbances due to pathological conditions.

Shannon entropy for time-varying persistence of cell migration

Cell migration, which can be significantly affected by intracellular signaling pathways and extracellular matrix, plays a crucial role in many physiological and pathological processes. Cell migration is typically modeled as a persistent random walk, which depends on two critical motility parameters, i.e., migration speed and persistence time. It is generally very challenging to efficiently and accurately quantify the migration dynamics from noisy experimental data. Here, we introduce the normalized Shannon entropy (SE) based on the FPS of cellular velocity autocovariance function to quantify migration dynamics. The SE introduced here possesses a similar physical interpretation as the Gibbs entropy for thermal systems in that SE naturally reflects the degree of order or randomness of cellular migration, attaining the maximal value of unity for purely diffusive migration (i.e., SE = 1 for the most "random" dynamics) and the minimal value of 0 for purely ballistic dynamics (i.e., SE = 0 for the most "ordered" dynamics). We also find that SE is strongly correlated with the migration persistence but is less sensitive to the migration speed. Moreover, we introduce the time-varying SE based on the WPS of cellular dynamics and demonstrate its superior utility to characterize the time-dependent persistence of cell migration, which typically results from complex and time-varying intra- or extracellular mechanisms. We employ our approach to analyze experimental data of in vitro cell migration regulated by distinct intracellular and extracellular mechanisms, exhibiting a rich spectrum of dynamic characteristics. Our analysis indicates that the SE and wavelet transform (i.e., SE-based approach) offers a simple and efficient tool to quantify cell migration dynamics in complex microenvironment.

Enhanced persistence and collective migration in cooperatively aligning cell clusters

Most cells possess the capacity to locomote. Alone or collectively, this allows them to adapt, to rearrange, and to explore their surroundings. The biophysical characterization of such motile processes, in health and in disease, has so far focused mostly on two limiting cases: single-cell motility on the one hand and the dynamics of confluent tissues such as the epithelium on the other. The in-between regime of clusters, composed of relatively few cells moving as a coherent unit, has received less attention. Such small clusters are, however, deeply relevant in development but also in cancer metastasis. In this work, we use cellular Potts models and analytical active matter theory to understand how the motility of small cell clusters changes with N, the number of cells in the cluster. Modeling and theory reveal our two main findings: cluster persistence time increases with N, whereas the intrinsic diffusivity decreases with N. We discuss a number of settings in which the motile properties of more complex clusters can be analytically understood, revealing that the focusing effects of small-scale cooperation and cell-cell alignment can overcome the increased bulkiness and internal disorder of multicellular clusters to enhance overall migrational efficacy. We demonstrate this enhancement for small-cluster collective durotaxis, which is shown to proceed more effectively than for single cells. Our results may provide some novel, to our knowledge, insights into the connection between single-cell and large-scale collective motion and may point the way to the biophysical origins of the enhanced metastatic potential of small tumor cell clusters.

Non-Markovian data-driven modeling of single-cell motility

Trajectories of human breast cancer cells moving on one-dimensional circular tracks are modeled by the non-Markovian version of the Langevin equation that includes an arbitrary memory function. When averaged over cells, the velocity distribution exhibits spurious non-Gaussian behavior, while single cells are characterized by Gaussian velocity distributions. Accordingly, the data are described by a linear memory model which includes different random walk models that were previously used to account for various aspects of cell motility such as migratory persistence, non-Markovian effects, colored noise, and anomalous diffusion. The memory function is extracted from the trajectory data without restrictions or assumptions, thus making our approach truly data driven, and is used for unbiased single-cell comparison. The cell memory displays time-delayed single-exponential negative friction, which clearly distinguishes cell motion from the simple persistent random walk model and suggests a regulatory feedback mechanism that controls cell migration. Based on the extracted memory function we formulate a generalized exactly solvable cell migration model which indicates that negative friction generates cell persistence over long timescales. The nonequilibrium character of cell motion is investigated by mapping the non-Markovian Langevin equation with memory onto a Markovian model that involves a hidden degree of freedom and is equivalent to the underdamped active Ornstein-Uhlenbeck process.

CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates

Mesenchymal cell crawling is a critical process in normal development, in tissue function, and in many diseases. Quantitatively predictive numerical simulations of cell crawling thus have multiple scientific, medical, and technological applications. However, we still lack a low-computational-cost approach to simulate mesenchymal three-dimensional (3D) cell crawling. Here, we develop a computationally tractable 3D model (implemented as a simulation in the CompuCell3D simulation environment) of mesenchymal cells crawling on a two-dimensional substrate. The Fürth equation, the usual characterization of mean-squared displacement (MSD) curves for migrating cells, describes a motion in which, for increasing time intervals, cell movement transitions from a ballistic to a diffusive regime. Recent experiments have shown that for very short time intervals, cells exhibit an additional fast diffusive regime. Our simulations' MSD curves reproduce the three experimentally observed temporal regimes, with fast diffusion for short time intervals, slow diffusion for long time intervals, and intermediate time -interval-ballistic motion. The resulting parameterization of the trajectories for both experiments and simulations allows the definition of time- and length scales that translate between computational and laboratory units. Rescaling by these scales allows direct quantitative comparisons among MSD curves and between velocity autocorrelation functions from experiments and simulations. Although our simulations replicate experimentally observed spontaneous symmetry breaking, short-timescale diffusive motion, and spontaneous cell-motion reorientation, their computational cost is low, allowing their use in multiscale virtual-tissue simulations. Comparisons between experimental and simulated cell motion support the hypothesis that short-time actomyosin dynamics affects longer-time cell motility. The success of the base cell-migration simulation model suggests its future application in more complex situations, including chemotaxis, migration through complex 3D matrices, and collective cell motion.

Neutrophil-like HL-60 cells expressing only GFP-tagged β-actin exhibit nearly normal motility

Observations of actin dynamics in living cells using fluorescence microscopy have been foundational in the exploration of the mechanisms underlying cell migration. We used CRISPR/Cas9 gene editing to generate neutrophil‐like HL‐60 cell lines expressing GFP‐β‐actin from the endogenous locus (ACTB). In light of many previous reports outlining functional deficiencies of labeled actin, we anticipated that HL‐60 cells would only tolerate a monoallelic edit, as biallelic edited cells would produce no normal β‐actin. Surprisingly, we recovered viable monoallelic GFP‐β‐actin cells as well as biallelic edited GFP‐β‐actin cells, in which one copy of the ACTB gene is silenced and the other contains the GFP tag. Furthermore, the edited cells migrate with similar speeds and persistence as unmodified cells in a variety of motility assays, and have nearly normal cell shapes. These results might partially be explained by our observation that GFP‐β‐actin incorporates into the F‐actin network in biallelic edited cells at similar efficiencies as normal β‐actin in unedited cells. Additionally, the edited cells significantly upregulate γ‐actin, perhaps helping to compensate for the loss of normal β‐actin. Interestingly, biallelic edited cells have only modest changes in global gene expression relative to the monoallelic line, as measured by RNA sequencing. While monoallelic edited cells downregulate expression of the tagged allele and are thus only weakly fluorescent, biallelic edited cells are quite bright and well‐suited for live cell microscopy. The nondisruptive phenotype and direct interpretability of this fluorescent tagging approach make it a promising tool for studying actin dynamics in these rapidly migrating and highly phagocytic cells.

Disentangling the behavioural variability of confined cell migration

Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows under identical conditions. Here, we observe the migration of single human breast cancer cells (MDA-MB-231) in confining two-state micropatterns. To describe the stochastic dynamics of this confined migration, we employ a dynamical systems approach. We identify statistics to measure the behavioural variance of the migration, which significantly exceeds that predicted by a population-averaged stochastic model. This additional variance can be explained by the combination of an ‘ageing’ process and population heterogeneity. To quantify population heterogeneity, we decompose the cells into subpopulations of slow and fast cells, revealing the presence of distinct classes of dynamical systems describing the migration, ranging from bistable to limit cycle behaviour. Our findings highlight the breadth of migration behaviours present in cell populations.

Glassy dynamics in models of confluent tissue with mitosis and apoptosis

Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy dynamics in some epithelial layers despite continued cell cycling. To address this discrepancy, we quantify the role of cell birth and death on glassy states in confluent tissues using simulations of an active vertex model that includes cell motility, cell division, and cell death. Our simulation data is consistent with a simple ansatz in which the rate of cell-life cycling and the rate of relaxation of the tissue in the absence of cell cycling contribute independently and additively to the overall rate of cell motion. Specifically, we find that a glass-like regime with caging behavior indicated by subdiffusive cell displacements can be achieved in systems with sufficiently low rates of cell cycling.

Stochastic and Heterogeneous Cancer Cell Migration: Experiment and Theory

Cell migration, an essential process for normal cell development and cancer metastasis, differs from a simple random walk: the mean-square displacement (〈(Δr)²(t)〉) of cells sometimes shows non-Fickian behavior, and the spatiotemporal correlation function (G(r, t)) of cells is often non-Gaussian. We find that this intriguing cell migration should be attributed to heterogeneity in a cell population, even one with a homogeneous genetic background. There are two limiting types of heterogeneity in a cell population: cellular heterogeneity and temporal heterogeneity. Cellular heterogeneity accounts for the cell-to-cell variation in migration capacity, while temporal heterogeneity arises from the temporal noise in the migration capacity of single cells. We illustrate that both cellular and temporal heterogeneity need to be taken into account simultaneously to elucidate cell migration. We investigate the two-dimensional migration of A549 lung cancer cells using time-lapse microscopy and find that the migration of A549 cells is Fickian but has a non-Gaussian spatiotemporal correlation. We find that when a theoretical model considers both cellular and temporal heterogeneity, the model reproduces all of the anomalous behaviors of cancer cell migration.

Crosshatch nanofiber networks of tunable interfiber spacing induce plasticity in cell migration and cytoskeletal response

Biomechanical cues within tissue microenvironments are critical for maintaining homeostasis, and their disruption can contribute to malignant transformation and metastasis. Once transformed, metastatic cancer cells can migrate persistently by adapting (plasticity) to changes in the local fibrous extracellular matrix, and current strategies to recapitulate persistent migration rely exclusively on the use of aligned geometries. Here, the controlled interfiber spacing in suspended crosshatch networks of nanofibers induces cells to exhibit plasticity in migratory behavior (persistent and random) and the associated cytoskeletal arrangement. At dense spacing (3 and 6 µm), unexpectedly, elongated cells migrate persistently (in 1 dimension) at high speeds in 3-dimensional shapes with thick nuclei, and short focal adhesion cluster (FAC) lengths. With increased spacing (18 and 36 µm), cells attain 2-dimensional morphologies, have flattened nuclei and longer FACs, and migrate randomly by rapidly detaching their trailing edges that strain the nuclei by ∼35%. At 54-µm spacing, kite-shaped cells become near stationary. Poorly developed filamentous actin stress fibers are found only in cells on 3-µm networks. Gene-expression profiling shows a decrease in transcriptional potential and a differential up-regulation of metabolic pathways. The consistency in observed phenotypes across cell lines supports using this platform to dissect hallmarks of plasticity in migration in vitro.-Jana, A., Nookaew, I., Singh, J., Behkam, B., Franco, A. T., Nain, A. S. Crosshatch nanofiber networks of tunable interfiber spacing induce plasticity in cell migration and cytoskeletal response.

On the efficiency of chemotactic pursuit - Comparing blind search with temporal and spatial gradient sensing

In chemotaxis, cells are modulating their migration patterns in response to concentration gradients of a guiding substance. Immune cells are believed to use such chemotactic sensing for remotely detecting and homing in on pathogens. Considering that immune cells may encounter a multitude of targets with vastly different migration properties, ranging from immobile to highly mobile, it is not clear which strategies of chemotactic pursuit are simultaneously efficient and versatile. We tackle this problem theoretically and define a tunable response function that maps temporal or spatial concentration gradients to migration behavior. The seven free parameters of this response function are optimized numerically with the objective of maximizing search efficiency against a wide spectrum of target cell properties. Finally, we reverse-engineer the best-performing parameter sets to uncover strategies of chemotactic pursuit that are efficient under different biologically realistic boundary conditions. Although strategies based on the temporal or spatial sensing of chemotactic gradients are significantly more efficient than unguided migration, such ‘blind search’ turns out to work surprisingly well, in particular if the immune cells are fast and directionally persistent. The resulting simulated data can be used for the design of chemotaxis experiments and for the development of algorithms that automatically detect and quantify goal oriented behavior in measured immune cell trajectories.

Collective regulation of cell motility using an accurate density-sensing system

The capacity of living cells to sense their population density and to migrate accordingly is essential for the regulation of many physiological processes. However, the mechanisms used to achieve such functions are poorly known. Here, based on the analysis of multiple trajectories of vegetative Dictyostelium discoideum cells, we investigate such a system extensively. We show that the cells secrete a high-molecular-weight quorum-sensing factor (QSF) in their medium. This extracellular signal induces, in turn, a reduction of the cell movements, in particular, through the downregulation of a mode of motility with high persistence time. This response appears independent of cAMP and involves a G-protein-dependent pathway. Using a mathematical analysis of the cells' response function, we evidence a negative feedback on the QSF secretion, which unveils a powerful generic mechanism for the cells to detect when they exceed a density threshold. Altogether, our results provide a comprehensive and dynamical view of this system enabling cells in a scattered population to adapt their motion to their neighbours without physical contact.

Non-Gaussian, non-ergodic, and non-Fickian diffusion of tracers in mucin hydrogels

Native mucus is polymer-based soft-matter material of paramount biological importance. How non-Gaussian and non-ergodic is the diffusive spreading of pathogens in mucus? We study the passive, thermally driven motion of micron-sized tracers in hydrogels of mucins, the main polymeric component of mucus. We report the results of the Bayesian analysis for ranking several diffusion models for a set of tracer trajectories [C. E. Wagner et al., Biomacromolecules, 2017, 18, 3654]. The models with "diffusing diffusivity", fractional and standard Brownian motion are used. The likelihood functions and evidences of each model are computed, ranking the significance of each model for individual traces. We find that viscoelastic anomalous diffusion is often most probable, followed by Brownian motion, while the model with a diffusing diffusion coefficient is only realised rarely. Our analysis also clarifies the distribution of time-averaged displacements, correlations of scaling exponents and diffusion coefficients, and the degree of non-Gaussianity of displacements at varying pH levels. Weak ergodicity breaking is also quantified. We conclude that-consistent with the original study-diffusion of tracers in the mucin gels is most non-Gaussian and non-ergodic at low pH that corresponds to the most heterogeneous networks. Using the Bayesian approach with the nested-sampling algorithm, together with the quantitative analysis of multiple statistical measures, we report new insights into possible physical mechanisms of diffusion in mucin gels.

Identifying the mechanism for superdiffusivity in mouse fibroblast motility

We seek to characterize the motility of mouse fibroblasts on 2D substrates. Utilizing automated tracking techniques, we find that cell trajectories are super-diffusive, where displacements scale faster than t1/2 in all directions. Two mechanisms have been proposed to explain such statistics in other cell types: run and tumble behavior with Lévy-distributed run times, and ensembles of cells with heterogeneous speed and rotational noise. We develop an automated toolkit that directly compares cell trajectories to the predictions of each model and demonstrate that ensemble-averaged quantities such as the mean-squared displacements and velocity autocorrelation functions are equally well-fit by either model. However, neither model correctly captures the short-timescale behavior quantified by the displacement probability distribution or the turning angle distribution. We develop a hybrid model that includes both run and tumble behavior and heterogeneous noise during the runs, which correctly matches the short-timescale behaviors and indicates that the run times are not Lévy distributed. The analysis tools developed here should be broadly useful for distinguishing between mechanisms for superdiffusivity in other cells types and environments.

Bayesian analysis of single-particle tracking data using the nested-sampling algorithm: maximum-likelihood model selection applied to stochastic-diffusivity data

We employ Bayesian statistics using the nested-sampling algorithm to compare and rank multiple models of ergodic diffusion (including anomalous diffusion) as well as to assess their optimal parameters for in silico-generated and real time-series. We focus on the recently-introduced model of Brownian motion with "diffusing diffusivity"-giving rise to widely-observed non-Gaussian displacement statistics-and its comparison to Brownian and fractional Brownian motion, also for the time-series with some measurement noise. We conduct this model-assessment analysis using Bayesian statistics and the nested-sampling algorithm on the level of individual particle trajectories. We evaluate relative model probabilities and compute best-parameter sets for each diffusion model, comparing the estimated parameters to the true ones. We test the performance of the nested-sampling algorithm and its predictive power both for computer-generated (idealised) trajectories as well as for real single-particle-tracking trajectories. Our approach delivers new important insight into the objective selection of the most suitable stochastic model for a given time-series. We also present first model-ranking results in application to experimental data of tracer diffusion in polymer-based hydrogels.

Estimation of diffusive states from single-particle trajectory in heterogeneous medium using machine-learning methods

We propose a novel approach to analyze random walks in heterogeneous medium using a hybrid machine-learning method based on a gamma mixture and a hidden Markov model. A gamma mixture and a hidden Markov model respectively provide the number and the most probable sequence of diffusive states from the time series position data of particles/molecules obtained by single-particle/molecule tracking (SPT/SMT) method. We evaluate the performance of our proposed method for numerically generated trajectories. It is shown that our proposed method can correctly extract the number of diffusive states when each trajectory is long enough to be frame averaged. We also indicate that our method can provide an indicator whether the assumption of a medium consisting of discrete diffusive states is appropriate or not based on the available amount of trajectory data. Then, we demonstrate an application of our method to the analysis of experimentally obtained SPT data.

The Biophysics of 3D Cell Migration

Three-dimensional (3D) cell culture systems have gained increasing interest not only for 3D migration studies but also for their use in drug screening, tissue engineering, and ex vivo modeling of metastatic behavior in the field of cancer biology and morphogenesis in the field of developmental biology. The goal of studying cells in a 3D context is to attempt to more faithfully recapitulate the physiological microenvironment of tissues, including mechanical and structural parameters that we envision will reveal more predictive data for development programs and disease states. In this review, we discuss the pros and cons of several well-characterized 3D cell culture systems for performing 3D migration studies. We discuss the intracellular and extracellular signaling mechanisms that govern cell migration. We also describe the mathematical models and relevant assumptions that can be used to describe 3D cell movement.

Bayesian model selection for complex dynamic systems

Time series generated by complex systems like financial markets and the earth’s atmosphere often represent superstatistical random walks: on short time scales, the data follow a simple low-level model, but the model parameters are not constant and can fluctuate on longer time scales according to a high-level model. While the low-level model is often dictated by the type of the data, the high-level model, which describes how the parameters change, is unknown in most cases. Here we present a computationally efficient method to infer the time course of the parameter variations from time-series with short-range correlations. Importantly, this method evaluates the model evidence to objectively select between competing high-level models. We apply this method to detect anomalous price movements in financial markets, characterize cancer cell invasiveness, identify historical policies relevant for working safety in coal mines, and compare different climate change scenarios to forecast global warming.

Systematic changes in stock market prices or in the migration behaviour of cancer cells may be hidden behind random fluctuations. Here, Mark et al. describe an empirical approach to identify when and how such real-world systems undergo systematic changes.

Persistent random deformation model of cells crawling on a gel surface

In general, cells move on a substrate through extension and contraction of the cell body. Though cell movement should be explained by taking into account the effect of such shape fluctuations, past approaches to formulate cell-crawling have not sufficiently quantified the relationship between cell movement (velocity and trajectory) and shape fluctuations based on experimental data regarding actual shaping dynamics. To clarify this relationship, we experimentally characterized cell-crawling in terms of shape fluctuations, especially extension and contraction, by using an elasticity-tunable gel substrate to modulate cell shape. As a result, an amoeboid swimmer-like relation was found to arise between the cell velocity and cell-shape dynamics. To formulate this experimentally-obtained relationship between cell movement and shaping dynamics, we established a persistent random deformation (PRD) model based on equations of a deformable self-propelled particle adopting an amoeboid swimmer-like velocity-shape relationship. The PRD model successfully explains the statistical properties of velocity, trajectory and shaping dynamics of the cells including back-and-forth motion, because the velocity equation exhibits time-reverse symmetry, which is essentially different from previous models. We discuss the possible application of this model to classify the phenotype of cell migration based on the characteristic relation between movement and shaping dynamics.

First-passage time for superstatistical Fokker-Planck models

The first-passage-time (FPT) problem is studied for superstatistical models assuming that the mesoscopic system dynamics is described by a Fokker-Planck equation. We show that all moments of the random intensive parameter associated to the superstatistical approach can be put in one-to-one correspondence with the moments of the FPT. For systems subjected to an additional uncorrelated external force, the same statistical information is obtained from the dependence of the FPT moments on the external force. These results provide an alternative technique for checking the validity of superstatistical models. As an example, we characterize the mean FPT for a forced Brownian particle.