arXiv subjects

C. V. Giuraniuc

Publications and source records attributed to C. V. Giuraniuc.

6 recordsLinked to original sources

arXiv2009

On the equilibria of the MAPK cascade: cooperativity, modularity and bistability

In this paper we present a discussion of a phenomenological model of the MAPK cascade which was originally proposed by Angeli et al. (PNAS 101, 1822 (2004)). The model and its solution are extended in several respects: a) an analytical solution is given for the cascade equilibria, exploiting a parameter-based symmetry of the rate equations; b) we discuss the cooperativity (Hill coefficients) of the cascade and show that a feedforward loop within the cascade increases its cooperativity. The relevance of this result for the notion of modularity is discussed; c) the feedback model for cascade bistability by Angeli et al. is reconsidered. We argue that care must be taken in modeling the interactions and a biologically realistic phenomenological model cannot be too reductionist. The inclusion of a time-dependent degradation rate is needed to account for a switching of the cascade.

q-bio.MN↗

arXiv2008

Mean-field vs. stochastic models for transcriptional regulation

We introduce a minimal model description for the dynamics of transcriptional regulatory networks. It is studied within a mean-field approximation, i.e., by deterministic ode's representing the reaction kinetics, and by stochastic simulations employing the Gillespie algorithm. We elucidate the different results both approaches can deliver, depending on the network under study, and in particular depending on the level of detail retained in the respective description. Two examples are addressed in detail: the repressilator, a transcriptional clock based on a three-gene network realized experimentally in E. coli, and a bistable two-gene circuit under external driving, a transcriptional network motif recently proposed to play a role in cellular development.

q-bio.MN↗

arXiv2007

Evidence for nonmonotonic magnetic field penetration in a type-I superconductor

Polarized neutron reflectometry (PNR) provides evidence that nonlocal electrodynamics governs the magnetic field penetration in an extreme low-k superconductor. The sample is an indium film with a large elastic mean free path (11 mkm) deposited on a silicon oxide wafer. It is shown that PNR can resolve the difference between the reflected neutron spin asymmetries predicted by the local and nonlocal theories of superconductivity. The experimental data support the nonlocal theory, which predicts a nonmonotonic decay of the magnetic field.

cond-mat.supr-con↗

arXiv2006

Criticality on networks with topology-dependent interactions

Weighted scale-free networks with topology-dependent interactions are studied. It is shown that the possible universality classes of critical behaviour, which are known to depend on topology, can also be explored by tuning the form of the interactions at fixed topology. For a model of opinion formation, simple mean field and scaling arguments show that a mapping $γ'=(γ-μ)/(1-μ)$ describes how a shift of the standard exponent $γ$ of the degree distribution can absorb the effect of degree-dependent pair interactions $J_{ij} \propto (k_ik_j)^{-μ}$, where $k_i$ stands for the degree of vertex $i$. This prediction is verified by extensive numerical investigations using the cavity method and Monte Carlo simulations. The critical temperature of the model is obtained through the Bethe-Peierls approximation and with the replica technique. The mapping can be extended to nonequilibrium models such as those describing the spreading of a disease on a network.

cond-mat.stat-mech↗

arXiv2005

Trading interactions for topology in scale-free networks

Scale-free networks with topology-dependent interactions are studied. It is shown that the universality classes of critical behavior, which conventionally depend only on topology, can also be explored by tuning the interactions. A mapping, $γ' = (γ- μ)/(1-μ)$, describes how a shift of the standard exponent $γ$ of the degree distribution $P(q)$ can absorb the effect of degree-dependent pair interactions $J_{ij} \propto (q_iq_j)^{-μ}$. Replica technique, cavity method and Monte Carlo simulation support the physical picture suggested by Landau theory for the critical exponents and by the Bethe-Peierls approximation for the critical temperature. The equivalence of topology and interaction holds for equilibrium and non-equilibrium systems, and is illustrated with interdisciplinary applications.

cond-mat.dis-nn↗

arXiv2003

Cellular automaton for bacterial towers

A simulation approach to the stochastic growth of bacterial towers is presented, in which a non-uniform and finite nutrient supply essentially determines the emerging structure through elementary chemotaxis. The method is based on cellular automata and we use simple, microscopic, local rules for bacterial division in nutrient-rich surroundings. Stochastic nutrient diffusion, while not crucial to the dynamics of the total population, is influential in determining the porosity of the bacterial tower and the roughness of its surface. As the bacteria run out of food, we observe an exponentially rapid saturation to a carrying capacity distribution, similar in many respects to that found in a recently proposed phenomenological hierarchical population model, which uses heuristic parameters and macroscopic rules. Complementary to that phenomenological model, the simulation aims at giving more microscopic insight into the possible mechanisms for one of the recently much studied bacterial morphotypes, known as "towering biofilm", observed experimentally using confocal laser microscopy. A simulation suggesting a mechanism for biofilm resistance to antibiotics is also shown.

q-bio.PE↗