Related papers: Autocatalytic sets in a partitioned biochemical ne…
We develop a theory of enzyme catalysis within biological cells where the substrate concentration [S](t) is time dependent, in contrast to the Michaelis-Menten theory that assumes a steady state. We find that the time varying concentration…
Recently the first chemical systems which show the amplification of enantiometric excess (ee) was found. Inspired by these experiments, we propose a few chemical reaction models in a closed system. The reactions consist of autocatalytic…
Even when concepts similar to emergence have been used since antiquity, we lack an agreed definition. However, emergence has been identified as one of the main features of complex systems. Most would agree on the statement ``life is…
Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to…
A poorly understood step in the transition from a chemical to a biological world is the emergence of self-replicating molecular systems. We study how a precursor for such a replicator might arise in a hydrothermal RNA reactor, which…
The apparent difficulty of designing simple autocatalysts that grow exponentially in the absence of enzymes, external drives or ingenious internal mechanisms severely constrains scenarios for the emergence of evolution by natural selection…
In this work we developed a RAFT polymerization model taking into account the main reactions of the experimental RAFT process and implemented that model in dissipative particle dynamics (DPD). With a help of a kinetic model based on the…
As cells grow and divide under a given environment, they become crowded and resources are limited, as seen in bacterial biofilms and multicellular aggregates. These cells often show strong interactions through exchanging chemicals, as in…
Many models for the origin of life have focused on understanding how evolution can drive the refinement of a preexisting enzyme, such as the evolution of efficient replicase activity. Here we present a model for what was, arguably, an even…
In most natural sciences there is currently the insight that it is necessary to bridge gaps between different processes which can be observed on different scales. This is especially true in the field of chemical reactions where the…
We propose a model to show the self-assembling of network-like structures between a set of nodes without using preexisting positional information or long-range attraction of the nodes. The model is based on Brownian agents that are capable…
External flows of energy, entropy, and matter can cause sudden transitions in the stability of biological and industrial systems, fundamentally altering their dynamical function. How might we control and design these transitions in chemical…
Cellular actin structures are continuously turned over while keeping similar sizes. Since they all compete for a shared pool of actin monomers, the question arises how they can coexist in these dynamic steady states. Recently, the…
Biological networks are a very convenient modelling and visualisation tool to discover knowledge from modern high-throughput genomics and postgenomics data sets. Indeed, biological entities are not isolated, but are components of complex…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
The persistence conjecture is a long-standing open problem in chemical reaction network theory. It concerns the behavior of solutions to coupled ODE systems that arise from applying mass-action kinetics to a network of chemical reactions.…
Isologous diversification theory for cell differentiation is proposed, based on simulations of interacting cells with biochemical networks and cell division process following consumption of some chemicals. According to the simulations of…
Chemical reaction networks are often used to model and understand biological processes such as cell signaling. Under the framework of chemical reaction network theory, a process is modeled with a directed graph and a choice of kinetics,…
The observed single-handedness of biological amino acids and sugars has long been attributed to autocatalysis. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross inhibition of the two chiral…
It is commonly accepted that a collection of pumped atoms without a resonator, which provides feedback, cannot lase. We show that intermodal coupling via active atoms pulls the frequencies of the free-space modes towards the transition…