11 research outputs found
Fractional-order susceptible-infected model: definition and applications to the study of COVID-19 main protease
We propose a model for the transmission of perturbations across the amino
acids of a protein represented as an interaction network. The dynamics consists
of a Susceptible-Infected (SI) model based on the Caputo fractional-order
derivative. We find an upper bound to the analytical solution of this model
which represents the worse-case scenario on the propagation of perturbations
across a protein residue network. This upper bound is expressed in terms of
Mittag-Leffler functions of the adjacency matrix of the network of inter-amino
acids interactions. We then apply this model to the analysis of the propagation
of perturbations produced by inhibitors of the main protease of SARS CoV-2. We
find that the perturbations produced by strong inhibitors of the protease are
propagated far away from the binding site, confirming the long-range nature of
intra-protein communication. On the contrary, the weakest inhibitors only
transmit their perturbations across a close environment around the binding
site. These findings may help to the design of drug candidates against this new
coronavirus.Comment: 21 pages, 2 figure
Metaplex networks: influence of the exo-endo structure of complex systems on diffusion
In a complex system the interplay between the internal structure of its
entities and their interconnection may play a fundamental role in the global
functioning of the system. Here, we define the concept of metaplex, which
describes such trade-off between internal structure of entities and their
interconnections. We then define a dynamical system on a metaplex and study
diffusive processes on them. We provide analytical and computational evidences
about the role played by the size of the nodes, the location of the internal
coupling areas, and the strength and range of the coupling between the nodes on
the global dynamics of metaplexes. Finally, we extend our analysis to two
real-world metaplexes: a landscape and a brain metaplex. We corroborate that
the internal structure of the nodes in a metaplex may dominate the global
dynamics (brain metaplex) or play a regulatory role (landscape metaplex) to the
influence of the interconnection between nodes.Comment: 28 pages, 19 figure
Fractional Patlak-Keller-Segel equations for chemotactic superdiffusion
The long range movement of certain organisms in the presence of a
chemoattractant can be governed by long distance runs, according to an
approximate Levy distribution. This article clarifies the form of biologically
relevant model equations: We derive Patlak-Keller-Segel-like equations
involving nonlocal, fractional Laplacians from a microscopic model for cell
movement. Starting from a power-law distribution of run times, we derive a
kinetic equation in which the collision term takes into account the long range
behaviour of the individuals. A fractional chemotactic equation is obtained in
a biologically relevant regime. Apart from chemotaxis, our work has
implications for biological diffusion in numerous processes.Comment: 20 pages, 4 figures, to appear in SIAM Journal on Applied Mathematic
Interacting particles with L\'{e}vy strategies: limits of transport equations for swarm robotic systems
L\'{e}vy robotic systems combine superdiffusive random movement with emergent
collective behaviour from local communication and alignment in order to find
rare targets or track objects. In this article we derive macroscopic fractional
PDE descriptions from the movement strategies of the individual robots.
Starting from a kinetic equation which describes the movement of robots based
on alignment, collisions and occasional long distance runs according to a
L\'{e}vy distribution, we obtain a system of evolution equations for the
fractional diffusion for long times. We show that the system allows efficient
parameter studies for a search problem, addressing basic questions like the
optimal number of robots needed to cover an area in a certain time. For shorter
times, in the hyperbolic limit of the kinetic equation, the PDE model is
dominated by alignment, irrespective of the long range movement. This is in
agreement with previous results in swarming of self-propelled particles. The
article indicates the novel and quantitative modeling opportunities which swarm
robotic systems provide for the study of both emergent collective behaviour and
anomalous diffusion, on the respective time scales.Comment: 23 pages, 3 figures, to appear in SIAM Journal on Applied Mathematic
Macroscopic limit of a kinetic model describing the switch in T cell migration modes via binary interactions
Experimental results on the immune response to cancer indicate that
activation of cytotoxic T lymphocytes (CTLs) through interactions with
dendritic cells (DCs) can trigger a change in CTL migration patterns. In
particular, while CTLs in the pre-activation state move in a non-local search
pattern, the search pattern of activated CTLs is more localised. In this paper,
we develop a kinetic model for such a switch in CTL migration modes. The model
is formulated as a coupled system of balance equations for the one-particle
distribution functions of CTLs in the pre-activation state, activated CTLs and
DCs. CTL activation is modelled via binary interactions between CTLs in the
pre-activation state and DCs. Moreover, cell motion is represented as a
velocity-jump process, with the running time of CTLs in the pre-activation
state following a long-tailed distribution, which is consistent with a L\'evy
walk, and the running time of activated CTLs following a Poisson distribution,
which corresponds to Brownian motion. We formally show that the macroscopic
limit of the model comprises a coupled system of balance equations for the cell
densities whereby activated CTL movement is described via a classical diffusion
term, whilst a fractional diffusion term describes the movement of CTLs in the
pre-activation state. The modelling approach presented here and its possible
generalisations are expected to find applications in the study of the immune
response to cancer and in other biological contexts in which switch from
non-local to localised migration patterns occurs.Comment: 21 pages, 1 figur
Asymptotic preserving schemes for nonlinear kinetic equations leading to volume-exclusion chemotaxis in the diffusive limit
In this work we first prove, by formal arguments, that the diffusion limit of
nonlinear kinetic equations, where both the transport term and the turning
operator are density-dependent, leads to volume-exclusion chemotactic
equations. We generalise an asymptotic preserving scheme for such nonlinear
kinetic equations based on a micro-macro decomposition. By properly
discretizing the nonlinear term implicitly-explicitly in an upwind manner, the
scheme produces accurate approximations also in the case of strong
chemosensitivity. We show, via detailed calculations, that the scheme presents
the following properties: asymptotic preserving, positivity preserving and
energy dissipation, which are essential for practical applications. We extend
this scheme to two dimensional kinetic models and we validate its efficiency by
means of 1D and 2D numerical experiments of pattern formation in biological
systems.Comment: 30 pages, 8 figure
Space-time fractional diffusion in cell movement models with delay
The movement of organisms and cells can be governed by occasional long
distance runs, according to an approximate L\'evy walk. For T cells migrating
through chronically-infected brain tissue, runs are further interrupted by long
pauses, and the aim here is to clarify the form of continuous model equations
which describe such movements. Starting from a microscopic velocity-jump model
based on experimental observations, we include power-law distributions of run
and waiting times and investigate the relevant parabolic limit from a kinetic
equation for resting and moving individuals. In biologically relevant regimes
we derive nonlocal diffusion equations, including fractional Laplacians in
space and fractional time derivatives. Its analysis and numerical experiments
shed light on how the searching strategy, and the impact from chemokinesis
responses to chemokines, shorten the average time taken to find rare targets in
the absence of direct guidance information such as chemotaxis.Comment: 25 pages, 8 figures, Mathematical Models and Methods in Applied
Sciences (2019
Asymptotic preserving schemes for nonlinear kinetic equations leading to volume-exclusion chemotaxis in the diffusive limit
In this work we first prove, by formal arguments, that the diffusion limit of nonlinear kinetic equations, where both the transport term and the turning operator are density-dependent, leads to volume-exclusion chemotactic equations. We generalise an asymptotic preserving scheme for such nonlinear kinetic equations based on a micromacro decomposition. By properly discretizing the nonlinear term implicitly-explicitly in an upwind manner, the scheme produces accurate approximations also in the case of strong chemosensitivity. We show, via detailed calculations, that the scheme presentsthe following properties: asymptotic preserving, positivity preserving and energy dissipation, which are essential for practical applications. We extend this scheme to two dimensional kinetic models and we validate its efficiency by means of 1D and 2D numerical experiments of pattern formation in biological systems
Macroscopic descriptions of follower-leader systems
The fundamental derivation of macroscopic model equations to describe swarms
based on microscopic movement laws and mathematical analyses into their
self-organisation capabilities remains a challenge from the perspective of both
modelling and analysis. In this paper we clarify relevant continuous
macroscopic model equations that describe follower-leader interactions for a
swarm where these two populations are fixed. We study the behaviour of the
swarm over long and short time scales to shed light on the number of leaders
needed to initiate swarm movement, according to the homogeneous or
inhomogeneous nature of the interaction (alignment) kernel. The results
indicate the crucial role played by the interaction kernel to model transient
behaviour.Comment: 22 pages, accepted for publication in Kinetic and Related Model