156 research outputs found
Fluctuation Theorems for Entropy Production and Heat Dissipation in Periodically Driven Markov Chains
Asymptotic fluctuation theorems are statements of a Gallavotti-Cohen symmetry
in the rate function of either the time-averaged entropy production or heat
dissipation of a process. Such theorems have been proved for various general
classes of continuous-time deterministic and stochastic processes, but always
under the assumption that the forces driving the system are time independent,
and often relying on the existence of a limiting ergodic distribution. In this
paper we extend the asymptotic fluctuation theorem for the first time to
inhomogeneous continuous-time processes without a stationary distribution,
considering specifically a finite state Markov chain driven by periodic
transition rates. We find that for both entropy production and heat
dissipation, the usual Gallavotti-Cohen symmetry of the rate function is
generalized to an analogous relation between the rate functions of the original
process and its corresponding backward process, in which the trajectory and the
driving protocol have been time-reversed. The effect is that spontaneous
positive fluctuations in the long time average of each quantity in the forward
process are exponentially more likely than spontaneous negative fluctuations in
the backward process, and vice-versa, revealing that the distributions of
fluctuations in universes in which time moves forward and backward are related.
As an additional result, the asymptotic time-averaged entropy production is
obtained as the integral of a periodic entropy production rate that generalizes
the constant rate pertaining to homogeneous dynamics
A Taxonomy of Causality-Based Biological Properties
We formally characterize a set of causality-based properties of metabolic
networks. This set of properties aims at making precise several notions on the
production of metabolites, which are familiar in the biologists' terminology.
From a theoretical point of view, biochemical reactions are abstractly
represented as causal implications and the produced metabolites as causal
consequences of the implication representing the corresponding reaction. The
fact that a reactant is produced is represented by means of the chain of
reactions that have made it exist. Such representation abstracts away from
quantities, stoichiometric and thermodynamic parameters and constitutes the
basis for the characterization of our properties. Moreover, we propose an
effective method for verifying our properties based on an abstract model of
system dynamics. This consists of a new abstract semantics for the system seen
as a concurrent network and expressed using the Chemical Ground Form calculus.
We illustrate an application of this framework to a portion of a real
metabolic pathway
Mathematical modeling of postmenopausal osteoporosis and its treatment by the anti-catabolic drug denosumab
Denosumab, a fully human monoclonal antibody, has been approved for the treatment of postmenopausal osteoporosis. The therapeutic effect of denosumab rests on its ability to inhibit osteoclast differentiation. Here, we present a computational approach on the basis of coupling a pharmacokinetics model of denosumab with a pharmacodynamics model for quantifying the effect of denosumab on bone remodeling. The pharmacodynamics model comprises an integrated systems biology-continuum micromechanics approach, including a bone cell population model, considering the governing biochemical factors of bone remodeling (including the action of denosumab), and a multiscale micromechanics-based bone mechanics model, for implementing the mechanobiology of bone remodeling in our model. Numerical studies of postmenopausal osteoporosis show that denosumab suppresses osteoclast differentiation, thus strongly curtailing bone resorption. Simulation results also suggest that denosumab may trigger a short-term bone volume gain, which is, however, followed by constant or decreasing bone volume. This evolution is accompanied by a dramatic decrease of the bone turnover rate by more than one order of magnitude. The latter proposes dominant occurrence of secondary mineralization (which is not anymore impeded through cellular activity), leading to higher mineral concentration per bone volume. This explains the overall higher bone mineral density observed in denosumab-related clinical studies
Application of the Convection–Dispersion Equation to Modelling Oral Drug Absorption
Models of systemic drug absorption after oral administration are frequently based on a direct or a delayed first-order rate process. In practice, the use of the first-order approach to predict drug concentrations in blood plasma frequently yields a considerable mismatch between predicted and measured concentration profiles. This is particularly true for the upswing of the plasma concentration after oral administration. The current investigation explores an alternative model to describe the absorption rate based on the convection–dispersion equation describing the transport of chemicals through the GI tract. This equation is governed by two parameters, transport velocity and dispersion coefficient. One solution of this equation for a specific set of initial and boundary conditions was used to model absorption of paracetamol in a 22-year-old man after oral administration. The GI-tract passage rate in this subject was influenced by co-administration of drugs that stimulate or delay gastric emptying. The transport-limited absorption function is more accurate in describing the plasma concentration versus time curve after oral administration than the first-order model. Additionally, it provides a mechanistic explanation for the observed curve through the differences in GI-tract passage rate
Dissolution profile evaluation of solid pharmaceutical forms containing chloramphenicol marketed in Brazil
Non-clinical studies in the process of new drug development - Part II: Good laboratory practice, metabolism, pharmacokinetics, safety and dose translation to clinical studies
A micromethod for quantitation of debrisoquine and 4-hydroxydebrisoquine in urine by liquid chromatography
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