Final nanoparticle size distribution under unusual parameter regimes.

We explore the large-scale behavior of a stochastic model for nanoparticle growth in an unusual parameter regime. This model encompasses two types of reactions: nucleation, where n monomers aggregate to form a nanoparticle, and growth, where a nanoparticle increases its size by consuming a monomer. Reverse reactions are disregarded. We delve into a previously unexplored parameter regime. Specifically, we consider a scenario where the growth rate of the first newly formed particle is of the same order of magnitude as the nucleation rate, in contrast to the classical scenario where, in the initial stage, nucleation dominates over growth. In this regime, we investigate the final size distribution as the initial number of monomers tends to infinity through extensive simulation studies utilizing state-of-the-art stochastic simulation methods with an efficient implementation and supported by high-performance computing infrastructure. We observe the emergence of a deterministic limit for the particle's final size density. To scale up the initial number of monomers to approximate the magnitudes encountered in real experiments, we introduce a novel approximation process aimed at faster simulation. Remarkably, this approximating process yields a final size distribution that becomes very close to that of the original process when the available monomers approach infinity. Simulations of the approximating process further support the conjecture of the emergence of a deterministic limit.

Transition graph decomposition for complex balanced reaction networks with non-mass-action kinetics.

Reaction networks are widely used models to describe biochemical processes. Stochastic fluctuations in the counts of biological macromolecules have amplified consequences due to their small population sizes. This makes it necessary to favor stochastic, discrete population, continuous time models. The stationary distributions provide snapshots of the model behavior at the stationary regime, and as such finding their expression in terms of the model parameters is of great interest. The aim of the present paper is to describe when the stationary distributions of the original model, whose state space is potentially infinite, coincide exactly with the stationary distributions of the process truncated to finite subsets of states, up to a normalizing constant. The finite subsets of states we identify are called copies and are inspired by the modular topology of reaction network models. With such a choice we prove a novel graphical characterization of the concept of complex balancing for stochastic models of reaction networks. The results of the paper hold for the commonly used mass-action kinetics but are not restricted to it, and are in fact stated for more general setting.

A hidden integral structure endows absolute concentration robust systems with resilience to dynamical concentration disturbances.

Biochemical systems that express certain chemical species of interest at the same level at any positive steady state are called 'absolute concentration robust' (ACR). These species behave in a stable, predictable way, in the sense that their expression is robust with respect to sudden changes in the species concentration, provided that the system reaches a (potentially new) positive steady state. Such a property has been proven to be of importance in certain gene regulatory networks and signaling systems. In the present paper, we mathematically prove that a well-known class of ACR systems studied by Shinar and Feinberg in 2010 hides an internal integral structure. This structure confers these systems with a higher degree of robustness than was previously known. In particular, disturbances much more general than sudden changes in the species concentrations can be rejected, and robust perfect adaptation is achieved. Significantly, we show that these properties are maintained when the system is interconnected with other chemical reaction networks. This key feature enables the design of insulator devices that are able to buffer the loading effect from downstream systems-a crucial requirement for modular circuit design in synthetic biology. We further note that while the best performance of the insulators are achieved when these act at a faster timescale than the upstream module (as typically required), it is not necessary for them to act on a faster timescale than the downstream module in our construction.

Addition of flow reactions preserving multistationarity and bistability.

We consider the question whether a chemical reaction network preserves the number and stability of its positive steady states upon inclusion of inflow and outflow reactions. Often a model of a reaction network is presented without inflows and outflows, while in fact some of the species might be degraded or leaked to the environment, or be synthesized or transported into the system. We provide a sufficient and easy-to-check criterion based on the stoichiometry of the reaction network alone and discuss examples from systems biology.

Discrepancies between extinction events and boundary equilibria in reaction networks.

Reaction networks are mathematical models of interacting chemical species that are primarily used in biochemistry. There are two modeling regimes that are typically used, one of which is deterministic and one that is stochastic. In particular, the deterministic model consists of an autonomous system of differential equations, whereas the stochastic system is a continuous-time Markov chain. Connections between the two modeling regimes have been studied since the seminal paper by Kurtz (J Chem Phys 57(7):2976-2978, 1972), where the deterministic model is shown to be a limit of a properly rescaled stochastic model over compact time intervals. Further, more recent studies have connected the long-term behaviors of the two models when the reaction network satisfies certain graphical properties, such as weak reversibility and a deficiency of zero. These connections have led some to conjecture a link between the long-term behavior of the two models exists, in some sense. In particular, one is tempted to believe that positive recurrence of all states for the stochastic model implies the existence of positive equilibria in the deterministic setting, and that boundary equilibria of the deterministic model imply the occurrence of an extinction event in the stochastic setting. We prove in this paper that these implications do not hold in general, even if restricting the analysis to networks that are bimolecular and that conserve the total mass. In particular, we disprove the implications in the special case of models that have absolute concentration robustness, thus answering in the negative a conjecture stated in the literature in 2014.

Non-explosivity of Stochastically Modeled Reaction Networks that are Complex Balanced.

We consider stochastically modeled reaction networks and prove that if a constant solution to the Kolmogorov forward equation decays fast enough relatively to the transition rates, then the model is non-explosive. In particular, complex-balanced reaction networks are non-explosive.

Node balanced steady states: Unifying and generalizing complex and detailed balanced steady states.

We introduce a unifying and generalizing framework for complex and detailed balanced steady states in chemical reaction network theory. To this end, we generalize the graph commonly used to represent a reaction network. Specifically, we introduce a graph, called a reaction graph, that has one edge for each reaction but potentially multiple nodes for each complex. A special class of steady states, called node balanced steady states, is naturally associated with such a reaction graph. We show that complex and detailed balanced steady states are special cases of node balanced steady states by choosing appropriate reaction graphs. Further, we show that node balanced steady states have properties analogous to complex balanced steady states, such as uniqueness and asymptotic stability in each stoichiometric compatibility class. Moreover, we associate an integer, called the deficiency, to a reaction graph that gives the number of independent relations in the reaction rate constants that need to be satisfied for a positive node balanced steady state to exist. The set of reaction graphs (modulo isomorphism) is equipped with a partial order that has the complex balanced reaction graph as minimal element. We relate this order to the deficiency and to the set of reaction rate constants for which a positive node balanced steady state exists.

Comparison of embolic load in femoropopliteal interventions: percutaneous transluminal angioplasty versus stenting.

PURPOSE: To compare the incidence of distal emboli occurring during percutaneous transluminal angioplasty (PTA) and primary stent on the superficial femoral artery (SFA) METHODS: A total of 50 consecutive patients were entered in a prospective, randomized trial. Inclusion criteria were the presence of symptomatic limb ischemia due to stenosis or occlusion of the SFA. An embolic protection device was placed in the popliteal artery. The patients were then randomly assigned to undergo primary stent implantation or PTA. The filters were retrieved and sent for histologic examination. RESULTS: Stenting in the SFA produced more emboli (1.44 mm(3)) than PTA (0.772 mm(3)), P = .031. Reanalyzing the patients according to actual treatment performed, volume of debris in the stent group was 1.271 mm(3) and in the PTA group was 0.191 mm(3), P = .00087. CONCLUSION: Volume of embolized material during endovascular interventions in the SFA-above-knee popliteal artery is higher when a stent is used.