1,058 research outputs found
Multiscale modeling in biology
The 1966 science-fction film Fantastic Voyage captured the public imagination with a clever idea: what fantastic things might we see and do if we could minaturize ourselves and travel through the bloodstream as corpuscles do? (This being Hollywood, the answer was that we'd save a fellow scientist from evildoers.
A Novel Stochastic Multi-Scale Model of Francisella tularensis Infection to Predict Risk of Infection in a Laboratory
We present a multi-scale model of the within-phagocyte, within-host and population-level infection dynamics of Francisella tularensis, which extends the mechanistic one proposed by Wood et al. (2014). Our multi-scale model incorporates key aspects of the interaction between host phagocytes and extracellular bacteria, accounts for inter-phagocyte variability in the number of bacteria released upon phagocyte rupture, and allows one to compute the probability of response, and mean time until response, of an infected individual as a function of the initial infection dose. A Bayesian approach is applied to parameterize both the within-phagocyte and within-host models using infection data. Finally, we show how dose response probabilities at the individual level can be used to estimate the airborne propagation of Francisella tularensis in indoor settings (such as a microbiology laboratory) at the population level, by means of a deterministic zonal ventilation model
Constructing universal Phenomenology for biological cellular systems: An idiosyncratic review on evolutionary dimensional reduction
Possibility to establish macroscopic phenomenological theory for biological
systems, akin to the akin to the well-established framework of thermodynamics,
is briefly reviewed. We introduce the concept of an evolutionary
fluctuation-response relationship, which highlights the need for a tight
correlation between the variance in phenotypic traits caused by genetic
mutations and by internal noise. We provide a distribution theory that allows
us to derive these relationships, which suggests that the changes in traits
resulting from adaptation and evolution are considerably constrained within a
lower-dimensional space. We explore the reasons behind this dimensional
reduction, focusing on the constraints posed by the requirements for steady
growth and robustness achieved through the evolutionary process. We draw
support from recent laboratory and numerical experiments to substantiate our
claims. Universality of evolutionary dimensional reduction is presented,
whereas potential theoretical formulations for it are discussed. We conclude by
briefly considering the prospects of establishing a macroscopic framework that
characterizes biological robustness and irreversibility in cell
differentiation, as well as an ideal cell model.Comment: 22pages,2 figures, proceeding paper for STATPHYS28, submitted to
JSTA
Quantitative modelling of bacterial growth physiology, cell size and shape control
Bacteria are highly adaptive microorganisms that proliferate in a wide range of environmental conditions via changes in cell size, shape and molecular composition. How bacterial cell size, shapes and physiological properties are regulated in diverse environmental conditions are questions of longstanding interest. Regulation of cell size and shape imply cellular control mechanisms that couple bacterial growth and division processes to their cellular environment and molecular composition. Studies in the past decades have revealed many fundamental principles of bacterial growth physiology, in particular the relationship between cellular growth rate, proteome composition and the nutrient environment. However, the quantitative relations defining the interdependence of cell growth and morphology, together with the molecular mechanisms underlying the control of bacterial cell morphology remain poorly understood. In this thesis I develop quantitative theory and models for bacterial growth dynamics that link cellular proteome with cell size and division control (Chapter 2), cell shape control (Chapter 3), regulation of bacterial growth and morphology in the presence of antibiotic stress (Chapter 4), and energy allocation strategies for cellular growth and shape control (Chapter 5). My work reveals that cell size maintenance under nutrient perturbations requires a balanced trade-off between ribosomes and division protein synthesis. Deviations from this tradeoff relationship are predicted under translation inhibition, leading to distinct modes of cell morphological changes, in agreement with single-cell data on Escherichia coli growth and cell morphology. Using the particular example of ribosome-targeting antibiotics, I present a systems-level model for the regulation of cell shape and growth physiology under antibiotic stress, and uncover various feedback mechanisms that bacteria can harness to increase their fitness in the presence of antibiotics
Cytoskeleton and Cell Motility
The present article is an invited contribution to the Encyclopedia of
Complexity and System Science, Robert A. Meyers Ed., Springer New York (2009).
It is a review of the biophysical mechanisms that underly cell motility. It
mainly focuses on the eukaryotic cytoskeleton and cell-motility mechanisms.
Bacterial motility as well as the composition of the prokaryotic cytoskeleton
is only briefly mentioned. The article is organized as follows. In Section III,
I first present an overview of the diversity of cellular motility mechanisms,
which might at first glance be categorized into two different types of
behaviors, namely "swimming" and "crawling". Intracellular transport, mitosis -
or cell division - as well as other extensions of cell motility that rely on
the same essential machinery are briefly sketched. In Section IV, I introduce
the molecular machinery that underlies cell motility - the cytoskeleton - as
well as its interactions with the external environment of the cell and its main
regulatory pathways. Sections IV D to IV F are more detailed in their
biochemical presentations; readers primarily interested in the theoretical
modeling of cell motility might want to skip these sections in a first reading.
I then describe the motility mechanisms that rely essentially on
polymerization-depolymerization dynamics of cytoskeleton filaments in Section
V, and the ones that rely essentially on the activity of motor proteins in
Section VI. Finally, Section VII is devoted to the description of the
integrated approaches that have been developed recently to try to understand
the cooperative phenomena that underly self-organization of the cell
cytoskeleton as a whole.Comment: 31 pages, 16 figures, 295 reference
Towards a non-equilibrium thermodynamic theory of ecosystem assembly and development
Non-equilibrium thermodynamics has had a significant historic influence on the development
of theoretical ecology, even informing the very concept of an ecosystem. Much of this influence
has manifested as proposed extremal principles. These principles hold that systems will tend
to maximise certain thermodynamic quantities, subject to the other constraints they operate
under. A particularly notable extremal principle is the maximum entropy production principle
(MaxEPP); that systems maximise their rate of entropy production. However, these principles
are not robustly based in physical theory, and suffer from treating complex ecosystems in
an extremely coarse manner. To address this gap, this thesis derives a limited but physically
justified extremal principle, as well as carrying out a detailed investigation of the impact of
non-equilibrium thermodynamic constraints on the assembly of microbial communities. The extremal
principle we obtain pertains to the switching between states in simple bistable systems,
with switching paths that generate more entropy being favoured. Our detailed investigation
into microbial communities involved developing a novel thermodynamic microbial community
model, using which we found the rate of ecosystem development to be set by the availability
of free-energy. Further investigation was carried out using this model, demonstrating the way
that trade-offs emerging from fundamental thermodynamic constraints impact the dynamics of
assembling microbial communities. Taken together our results demonstrate that theory can be
developed from non-equilibrium thermodynamics, that is both ecologically relevant and physically
well grounded. We find that broad extremal principles are unlikely to be obtained, absent
significant advances in the field of stochastic thermodynamics, limiting their applicability to
ecology. However, we find that detailed consideration of the non-equilibrium thermodynamic
mechanisms that impact microbial communities can broaden our understanding of their assembly
and functioning.Open Acces
An introduction to the maximum entropy approach and its application to inference problems in biology
A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data
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