Related papers: A global convergence result for processive multisi…
Motivation: Many biochemical pathways are known, but the numerous parameters required to correctly explore the dynamics of the pathways are not known. For this reason, algorithms that can make inferences by looking at the topology of a…
Both polydispersity and the presence of a gravitational field are inherent to essentially any colloidal experiment. While several theoretical works have focused on the effect of polydispersity on the bulk phase behavior of a colloidal…
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell-types. This developmental differentiation process typically involves intracellular regulatory and stochastic…
Molecular systems containing donor-bridge-acceptor sites or molecular antennas constitute promising candidates for organic photovoltaic device implementation. Photo-induced electron transfer in multi-chromophore molecular systems is defined…
The practical description of disordered chemical reactions, where reactions involve multiple species at multiple sites, is presently challenge using correlated electronic structure methods. Here we describe the gradient theory of…
Under the assumption of mass-action kinetics, a dynamical system may be induced by several different reaction networks and/or parameters. It is therefore possible for a mass-action system to exhibit complex-balancing dynamics without being…
In this article, we study the mixing properties of metastable diffusion processes which possess a Gibbs invariant distribution. For systems with multiple stable equilibria, so-called metastable transitions between these equilibria are…
Discrete models have a long tradition in engineering, including finite state machines, Boolean networks, Petri nets, and agent-based models. Of particular importance is the question of how the model structure constrains its dynamics. This…
The study of networks plays a crucial role in investigating the structure, dynamics, and function of a wide variety of complex systems in myriad disciplines. Despite the success of traditional network analysis, standard networks provide a…
A class of distributed systems with a cyclic interconnection structure is considered. These systems arise in several biochemical applications and they can undergo diffusion driven instability which leads to a formation of spatially…
We study a class of mass transport models where mass is transported in a preferred direction around a one-dimensional periodic lattice and is globally conserved. The model encompasses both discrete and continuous masses and parallel and…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
We initiate the combinatorial study of factorization systems on finite lattices, paying special attention to the role that reflective and coreflective factorization systems play in partitioning the poset of factorization systems on a fixed…
Living cells exhibit a complex organization comprising numerous compartments, among which are RNA- and protein-rich membraneless, liquid-like organelles known as biomolecular condensates. Energy-consuming processes regulate their formation…
The MAP kinase cascade is a network of enzymatic reactions arranged in layers. In each layer occurs a multiple futile cycle of phosphorylations. The fully phosphorylated substrate then serves as an enzyme for the layer below. This papers…
Biological adhesion is a critical mechanical function of complex organisms operating at multiple scales. At the cellular scale, cell-cell adhesion is remarkably tunable to enable both cohesion and malleability during development,…
In complex systems, the interplay between nonlinear and stochastic dynamics, e.g., J. Monod's necessity and chance, gives rise to an evolutionary process in Darwinian sense, in terms of discrete jumps among attractors, with punctuated…
This short review covers a wide selection of topics from a multidisciplinary area of dynamics of nonequilibrium systems in physics, chemistry, biology. Theoretical models of colloid particle and protein deposition and adhesion at surfaces,…
Experimental studies of cell motility in culture have shown that under adequate conditions these living organisms possess the ability to organize themselves into complex structures. Such structures may exhibit a synergy that greatly…
A model for the study of the effective quasistatic conductivity and permittivity of dispersed systems with particle-host interphase, within which many-particle polarization and correlation contributions are effectively incorporated, is…