Related papers: Protein sequestration versus Hill-type repression …
The paper proposes a modular-based approach to constraint handling in process optimization and control. This is partly motivated by the recent interest in learning-based methods, e.g., within bioproduction, for which constraint handling…
Gene regulatory networks, i.e. DNA segments in a cell which interact with each other indirectly through their RNA and protein products, lie at the heart of many important intracellular signal transduction processes. In this paper we analyse…
Living things benefit from exquisite molecular sensitivity in many of their key processes, including DNA replication, transcription and translation, chemical sensing, and morphogenesis. At thermodynamic equilibrium, the basic biophysical…
The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We study the confinement of the reaction to lipid vesicles, which permit the exchange with an…
Macroscopic oscillations of different brain regions show multiple phase relationships that are persistent across time and have been implicated routing information. Various cellular level mechanisms influence the network dynamics and…
Weakly coupled oscillators adjust their dynamics to work in unison: they synchronize. This ubiquitous phenomenon is observed for oscillating pendulum, electronic devices, as well as clapping crowds or flashing fireflies. In effect,…
Newly-translated glycoproteins in the endoplasmic reticulum (ER) often undergo cycles of chaperone binding and release in order to assist in folding. Quality control is required to distinguish between proteins that have completed native…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
We introduce a new logic called Signal Convolution Logic (SCL) that combines temporal logic with convolutional filters from digital signal processing. SCL enables to reason about the percentage of time a formula is satisfied in a bounded…
The trapezoidal rule, which is a special case of the Newmark family of algorithms, is one of the most widely used methods for transient hyperbolic problems. In this work, we show that this rule conserves linear and angular momenta and…
Causal ordering of key events in the cell cycle is essential for proper functioning of an organism. Yet, it remains a mystery how a specific temporal program of events is maintained despite ineluctable stochasticity in the biochemical…
Systems with the coexistence of different stable attractors are widely exploited in systems biology in order to suitably model the differentiating processes arising in living cells. In order to describe genetic regulatory networks several…
Cellular appendages conferring motility, such as flagella or cilia, are known to synchronise their periodic beats. The origin of synchronisation is a combination of long-range hydrodynamic interactions with physical mechanisms allowing the…
Discrete control systems, as considered here, refer to the control theory of discrete-time Lagrangian or Hamiltonian systems. These discrete-time models are based on a discrete variational principle, and are part of the broader field of…
Cyclic predator-prey systems have been shown to give rise to rich, and novel, space-time patterns, as for example coarsening domains with non-trivial in-domain dynamics. In this work we study numerically the responses of a cyclic…
How biological networks achieve robust control despite relying on imperfect, local information remains an important open question. Here, we identify thermodynamic constraints that can curtail non-equilibrium steady-state responses so…
A possible mechanism of time is formulated by developing an idea of time replaced by quantum correlations, with the aid of modern quantum information theory. We invent a microscopic model, where correlations of a closed system are steadily…
Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The…
Spin chains with open boundaries, such as the transverse field Ising model, can display coherence times for edge spins that diverge with the system size as a consequence of almost conserved operators, the so-called strong zero modes. Here,…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…