Related papers: Emergence of information transmission in a prebiot…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
A binary fluid mixture in contact with lateral particle reservoirs is considered. By imposing different particle concentrations in these reservoirs, the system can be maintained under controlled non-equilibrium conditions. Previous…
A hallmark of living systems is the ability to employ a common set of versatile building blocks that can self-organize into a multitude of different structures, in a way that can be controlled with minimal cost. This capability can only be…
We investigate the properties of large random conservative chemical reaction networks composed of elementary reactions endowed with either mass-action or saturating kinetics, assigning kinetic parameters in a thermodynamically-consistent…
Information transmission in biological signaling circuits has often been described using the metaphor of a noise filter. Cellular systems need accurate, real-time data about their environmental conditions, but the biochemical reaction…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
Templated copying is the central operation by which biology produces complex molecules. Cells copy sequence information from DNA to RNA and on into proteins, which are the molecules responsible for the function and regulation of cellular…
We experimentally demonstrate that information replication by templated ligation of DNA strands inherits a kinetic proofreading mechanism and achieves significant error suppression through cascade replication. A simple simulation model…
We study evolutionary processes induced by spatio-temporal dynamics in prebiotic evolution. Using numerical simulations we demonstrate that hypercycles emerge from complex interaction structures in multispecies systems. In this work we also…
There are many problems in biochemistry that are difficult to study experimentally. Simulation methods are appealing due to direct availability of atomic coordinates as a function of time. However, direct molecular simulations are…
Transcription of the genetic message encoded chemically in the sequence of the DNA template is carried out by a molecular machine called RNA polymerase (RNAP). Backward or forward slippage of the nascent RNA with respect to the DNA template…
Biochemical networks can respond to temporal characteristics of time-varying signals. To understand how reliably biochemical networks can transmit information we must consider how an input signal as a function of time--the input…
Stochastic reaction network models are widely utilized in biology and chemistry to describe the probabilistic dynamics of biochemical systems in general, and gene interaction networks in particular. Most often, statistical analysis and…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
The emergence of membranous compartments (protocells) with encapsulated genetic material was a crucial step life's origin and evolution. The hot spring hypothesis for the origin of life suggests that protocells could have formed in hot…
Machine learning has recently emerged as a powerful tool for generating new molecular and material structures. The success of state-of-the-art models stems from their ability to incorporate physical symmetries, such as translation,…
Molecular communication (MC) allows nanomachines to communicate and cooperate with each other in a fluid environment. The diffusion-based MC is popular but is easily constrained by the transmit distance due to the severe attenuation of…
Developing accurate models for chemical reactors is often challenging due to the complexity of reaction kinetics and process dynamics. Traditional approaches require retraining models for each new system, limiting generalizability and…
Biochemistry, ecology, and neuroscience are examples of prominent fields aiming at describing interacting systems that exhibit non-trivial couplings to complex, ever-changing environments. We have recently shown that linear interactions and…
A mechanism of the replication of proto-RNAs in oligomer world is proposed. The replication is carried out by a minimum cycle which is sustained by a ligase and a helicase. We expect that such a cycle actually worked in the primordial soup…