Modeling transport through an environment crowded by a mixture of obstacles of different shapes and sizes

Many biological environments are crowded by macromolecules, organelles and cells which can impede the transport of other cells and molecules. Previous studies have sought to describe these effects using either random walk models or fractional order diffusion equations. Here we examine the transport of both a single agent and a population of agents through an environment containing obstacles of varying size and shape, whose relative densities are drawn from a specified distribution. Our simulation results for a single agent indicate that smaller obstacles are more effective at retarding transport than larger obstacles; these findings are consistent with our simulations of the collective motion of populations of agents. In an attempt to explore whether these kinds of stochastic random walk simulations can be described using a fractional order diffusion equation framework, we calibrate the solution of such a differential equation to our averaged agent density information. Our approach suggests that these kinds of commonly used differential equation models ought to be used with care since we are unable to match the solution of a fractional order diffusion equation to our data in a consistent fashion over a finite time period.

Calculating the Fickian diffusivity for a lattice-based random walk with agents and obstacles of different shapes and sizes

Random walk models are often used to interpret experimental observations of the motion of biological cells and molecules. A key aim in applying a random walk model to mimic an in vitro experiment is to estimate the Fickian diffusivity (or Fickian diffusion coefficient),D. However, many in vivo experiments are complicated by the fact that the motion of cells and molecules is hindered by the presence of obstacles. Crowded transport processes have been modeled using repeated stochastic simulations in which a motile agent undergoes a random walk on a lattice that is populated by immobile obstacles. Early studies considered the most straightforward case in which the motile agent and the obstacles are the same size. More recent studies considered stochastic random walk simulations describing the motion of an agent through an environment populated by obstacles of different shapes and sizes. Here, we build on previous simulation studies by analyzing a general class of lattice-based random walk models with agents and obstacles of various shapes and sizes. Our analysis provides exact calculations of the Fickian diffusivity, allowing us to draw conclusions about the role of the size, shape and density of the obstacles, as well as examining the role of the size and shape of the motile agent. Since our analysis is exact, we calculateDdirectly without the need for random walk simulations. In summary, we find that the shape, size and density of obstacles has a major influence on the exact Fickian diffusivity. Furthermore, our results indicate that the difference in diffusivity for symmetric and asymmetric obstacles is significant.

Characterizing transport through a crowded environment with different obstacle sizes

Transport through crowded environments is often classified as anomalous, rather than classical, Fickian diffusion. Several studies have sought to describe such transport processes using either a continuous time random walk or fractional order differential equation. For both these models the transport is characterized by a parameter α, where α = 1 is associated with Fickian diffusion and α < 1 is associated with anomalous subdiffusion. Here, we simulate a single agent migrating through a crowded environment populated by impenetrable, immobile obstacles and estimate α from mean squared displacement data. We also simulate the transport of a population of such agents through a similar crowded environment and match averaged agent density profiles to the solution of a related fractional order differential equation to obtain an alternative estimate of α. We examine the relationship between our estimate of α and the properties of the obstacle field for both a single agent and a population of agents; we show that in both cases, α decreases as the obstacle density increases, and that the rate of decrease is greater for smaller obstacles. Our work suggests that it may be inappropriate to model transport through a crowded environment using widely reported approaches including power laws to describe the mean squared displacement and fractional order differential equations to represent the averaged agent density profiles.

A Hopping Mechanism for Cargo Transport by Molecular Motors on Crowded Microtubules

Most models designed to study the bidirectional movement of cargos as they are driven by molecular motors rely on the idea that motors of different polarities can be coordinated by external agents if arranged into a motor-cargo complex to perform the necessary work Gross, Hither and yon: a review of bidirectional microtubule-based transport (Gross in Phys. Biol. 1:R1-R11, 2004). Although these models have provided us with important insights into these phenomena, there are still many unanswered questions regarding the mechanisms through which the movement of the complex takes place on crowded microtubules. For example (i) how does cargo-binding affect motor motility? and in connection with that-(ii) how does the presence of other motors (and also other cargos) on the microtubule affect the motility of the motor-cargo complex? We discuss these questions from a different perspective. The movement of a cargo is conceived here as a hopping process resulting from the transference of cargo between neighboring motors. In the light of this, we examine the conditions under which cargo might display bidirectional movement even if directed by motors of a single polarity. The global properties of the model in the long-time regime are obtained by mapping the dynamics of the collection of interacting motors and cargos into an asymmetric simple exclusion process (ASEP) which can be resolved using the matrix ansatz introduced by Derrida (Derrida and Evans in Nonequilibrium Statistical Mechanics in One Dimension, pp. 277-304, 1997; Derrida et al. in J. Phys. A 26: 1493-1517, 1993).

Non-motorized public transport : a global review and analysis of trends and issues

Over recent decades there has been growing interest in the role of non-motorized modes in the overall transport system (especially walking and cycling for private purposes) and many government initiatives have been taken to encourage these active modes. However there has been relatively little research attention given to the paid form of non-motorized travel which can be called non-motorized public transport (NMPT). This involves cycle-powered vehicles which can carry several passengers (plus the driver) and a small amount of goods; and which provide flexible hail-and-ride services. Effectively they are non-motorized taxis. Common forms include cycle-rickshaw (Bangladesh, India), becak (Indonesia), cyclos (Vietnam, Cambodia), bicitaxi (Columbia, Cuba), velo-taxi (Germany, Netherland), and pedicabs (UK, Japan, USA). --------- The popularity of NMPT is widespread in developing countries, where it caters for a wide range of mobility needs. For instance in Dhaka, Bangladesh, rickshaws are the preferred mode for non-walk trips and have a higher mode share than cars or buses. Factors that underlie the continued existence and popularity of NMPT in many developing countries include positive contribution to social equity, micro-macro economic significance, employment creation, and suitability for narrow and crowded streets. Although top speeds are lower than motorized modes, NMPT is competitive and cost-effective for short distance door-to-door trips that make up the bulk of travel in many developing cities. In addition, NMPT is often the preferred mode for vulnerable groups such as females, children and elderly people. NMPT is more prominent in developing countries but its popularity and significance is also gradually increasing in several developed countries of Asia, Europe and parts of North America, where there is a trend for the NMPT usage pattern to broaden from tourism to public transport. This shift is due to a number of factors including the eco-sustainable nature of NMPT; its operating flexibility (such as in areas where motorized vehicle access is restricted or discouraged through pricing); and the dynamics that it adds to the urban fabric. Whereas NMPT may have been seen as a “dying” mode, in many cities it is maintaining or increasing its significance and with potential for further growth. --------- This paper will examine and analyze global trends in NMPT incorporating both developing and developed country contexts and issues such as usage patterns; NMPT policy and management practices; technological development; and operational integration of NMPT into the overall transport system. It will look at how NMPT policies, practices and usage have changed over time and the differing trends in developing and developed countries. In particular, it will use Dhaka, Bangladesh as a case study in recognition of its standing as the major NMPT city in the world. The aim is to highlight NMPT issues and trends and their significance for shaping future policy towards NMPT in developing and developed countries. The paper will be of interest to transport planners, traffic engineers, urban and regional planners, environmentalists, economists and policy makers.

Enhancing public transport passenger experience via mobile-mediated applications and services

Despite the rapidly urbanising population, public transport usage in metropolitan areas is not growing at a level that corresponds to the trend. Many people are reluctant to travel using public transport, as it is commonly associated with unpleasant experiences such as limited services, long wait time, and crowded spaces. This study aims to explore the use of mobile spatial interactions and services, and investigate their potential to increase the enjoyment of our everyday commuting experience. The main goal is to develop and evaluate mobile-mediated design interventions to foster interactions for and among passengers, as well as between passengers and public transport infrastructures, with the aim to positively influence the experience of commuting. Ultimately, this study hopes to generate findings and knowledge towards creating a more enjoyable public transport experience, as well as to explore innovative uses of mobile technologies and context-aware services for the urban lifestyle.

Control of material transport through pulse shape manipulation-a development toward designer pulses

The variety of laser systems available to industrial laser users is growing and the choice of the correct laser for a material target application is often based on an empirical assessment. Industrial master oscillator power amplifier systems with tuneable temporal pulse shapes have now entered the market, providing enormous pulse parameter flexibility in an already crowded parameter space. In this paper, an approach is developed to design interaction parameters based on observations of material responses. Energy and material transport mechanisms are studied using pulsed digital holography, post process analysis techniques and finite-difference modelling to understand the key response mechanisms for a variety of temporal pulse envelopes incident on a silicon (1/1/1) substrate. The temporal envelope is shown to be the primary control parameter of the source term that determines the subsequent material response and the resulting surface morphology. A double peak energy-bridged temporal pulse shape designed through direct application of holographic imaging data is shown to substantially improve surface quality. © 2014 IEEE.