Subdiffusion in a system with thin membranes

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.

Lévy Flights Diffusion with Drift in Heterogeneous Membranes

The modelling of diffusion in membranes is essential to understanding transport processes through membranes, especially when it comes to improving process efficiency. The purpose of this study is to understand the relationship between membrane structures, external forces, and the characteristic features of diffusive transport. We investigate Cauchy flight diffusion with drift in heterogeneous membrane-like structures. The study focuses on numerical simulation of particle movement across different membrane structures with differently spaced obstacles. Four studied structures are similar to real polymeric membranes filled with inorganic powder, while the next three structures are designed to show which distribution of obstacles can cause changes in transport. The movement of particles driven by Cauchy flights is compared to a Gaussian random walk both with and without additional drift action. We show that effective diffusion in membranes with an external drift depends on the type of the internal mechanism that causes the movement of particles as well as on the properties of the environment. In general, when movement steps are provided by the long-tailed Cauchy distribution and the drift is sufficiently strong, superdiffusion is observed. On the other hand, strong drift can effectively stop Gaussian diffusion.

Boundary conditions at a thin membrane for the normal diffusion equation which generate subdiffusion

We consider a particle transport process in a one-dimensional system with a thin membrane, described by the normal diffusion equation. We consider two boundary conditions at the membrane that are linear combinations of integral operators, with time-dependent kernels, which act on the functions and their spatial derivatives defined on both membrane surfaces. We show how boundary conditions at the membrane change the temporal evolution of the first and second moments of particle position distribution (the Green's function) which is a solution to the normal diffusion equation. As these moments define the kind of diffusion, an appropriate choice of boundary conditions generates the moments characteristic for subdiffusion. The interpretation of the process is based on a particle random walk model in which the subdiffusion effect is caused by anomalously long stays of the particle in the membrane.

Boundary conditions at a thin membrane that generate non-Markovian normal diffusion

We show that some boundary conditions assumed at a thin membrane may result in normal diffusion not being the stochastic Markov process. We consider boundary conditions defined in terms of the Laplace transform in which there is a linear combination of probabilities and probability fluxes defined on both membrane surfaces. The coefficients of the combination may depend on the Laplace transform parameter. Such boundary conditions are most commonly used when considering diffusion in a membrane system unless collective or nonlocal processes in particles diffusion occur. We find Bachelier-Smoluchowski-Chapmann-Kolmogorov (BSCK) equation in terms of the Laplace transform and we derive the criterion to check whether the boundary conditions lead to fundamental solutions of diffusion equation satisfying this equation. If the BSCK equation is not met, then the Markov property is broken. When a probability flux is continuous at the membrane, the general forms of the boundary conditions for which the fundamental solutions meet the BSCK equation are derived. A measure of broken of semi-group property is also proposed. The relation of this measure to the non-Markovian property measure is discussed.

Model of anomalous diffusion-absorption process in a system consisting of two different media separated by a thin membrane

We present the model of a diffusion-absorption process in a system which consists of two media separated by a thin partially permeable membrane. The kind of diffusion as well as the parameters of the process may be different in both media. Based on a simple model of a particle's random walk in a membrane system we derive the Green's functions, then we find the boundary conditions at the membrane. One of the boundary conditions is rather complicated and takes a relatively simple form in terms of the Laplace transform. Assuming that particles diffuse independently of one another, the obtained boundary conditions can be used to solve differential or differential-integral equations describing the processes in multilayered systems for any initial condition. We consider normal diffusion, subdiffusion, and slow subdiffusion processes, and we also suggest how superdiffusion could be included in this model. The presented method provides the functions in terms of the Laplace transform and some useful methods of calculation of the inverse Laplace transform are shown.

Random walk model of subdiffusion in a system with a thin membrane

We consider in this paper subdiffusion in a system with a thin membrane. The subdiffusion parameters are the same in both parts of the system separated by the membrane. Using the random walk model with discrete time and space variables the probabilities (Green's functions) P(x,t) describing a particle's random walk are found. The membrane, which can be asymmetrical, is characterized by the two probabilities of stopping a random walker by the membrane when it tries to pass through the membrane in both opposite directions. Green's functions are transformed to the system in which the variables are continuous, and then the membrane permeability coefficients are given by special formulas which involve the probabilities mentioned above. From the obtained Green's functions, we derive boundary conditions at the membrane. One of the conditions demands the continuity of a flux at the membrane, but the other one is rather unexpected and contains the Riemann-Liouville fractional time derivative P(x(N)(-),t)=λ(1)P(x(N)(+),t)+λ(2)∂(α/2)P(x(N)(+),t)/∂t(α/2), where λ(1),λ(2) depending on membrane permeability coefficients (λ(1)=1 for a symmetrical membrane), α is a subdiffusion parameter, and x(N) is the position of the membrane. This boundary condition shows that the additional "memory effect," represented by the fractional derivative, is created by the membrane. This effect is also created by the membrane for a normal diffusion case in which α=1.

Subdiffusion-reaction processes with A→B reactions versus subdiffusion-reaction processes with A+B→B reactions

We consider the subdiffusion-reaction process with reactions of a type A+B→B (in which particles A are assumed to be mobile, whereas B are assumed to be static) in comparison to the subdiffusion-reaction process with A→B reactions which was studied by Sokolov, Schmidt, and Sagués [Phys. Rev. E 73, 031102 (2006)]. In both processes a rule that reactions can only occur between particles which continue to exist is taken into account. Although in both processes a probability of the vanishing of particle A due to a reaction is independent of both time and space variables (assuming that in the system with the A+B→B reactions, particles B are distributed homogeneously), we show that subdiffusion-reaction equations describing these processes as well as their Green's functions are qualitatively different. The reason for this difference is as follows. In the case of the former reaction, particles A and B have to meet with some probability before the reaction occurs in contradiction with the case of the latter reaction. For the subdiffusion process with the A+B→B reactions we consider three models which differ in some details concerning a description of the reactions. We base the method considered in this paper on a random walk model in a system with both discrete time and discrete space variables. Then the system with discrete variables is transformed into a system with both continuous time and continuous space variables. Such a method seems to be convenient in analyzing subdiffusion-reaction processes with partially absorbing or partially reflecting walls. The reason is that within this method we can determine Green's functions without a necessity of solving a fractional differential subdiffusion-reaction equation with boundary conditions at the walls. As an example, we use the model to find the Green's functions for a subdiffusive reaction system (with the reactions mentioned above), which is bounded by a partially absorbing wall. This example shows how the model can be used to analyze the subdiffusion-reaction process in a system with partially absorbing or reflecting thin membranes. Employing a simple phenomenological model, we also derive equations related to the reaction parameters used in the considered models.