Related papers: Spontaneous Reaction Silencing in Metabolic Optimi…
Motivation: Stochastic reaction networks are a widespread model to describe biological systems where the presence of noise is relevant, such as in cell regulatory processes. Unfortu-nately, in all but simplest models the resulting discrete…
In the context of epigenetic transformations in cancer metastasis, a puzzling effect was recently discovered, in which the elimination (knock-out) of an activating regulatory element leads to increased (rather than decreased) activity of…
Cells can show not only spontaneous movement but also tactic responses to environmental signals. Since the former can be regarded as the basis to realize the latter, playing essential roles in various cellular functions, it is important to…
Self-sustained activity in the brain is observed in the absence of external stimuli and contributes to signal propagation, neural coding, and dynamic stability. It also plays an important role in cognitive processes. In this work, by means…
We investigate the stability properties of two different classes of metabolic cycles using a combination of analytical and computational methods. Using principles from structural kinetic modeling (SKM), we show that the stability of…
Fueled by the hydrolysis of ATP, the motor protein kinesin literally walks on two legs along the biopolymer microtubule. The number of accidental backsteps that kinesin takes appears to be much larger than what one would expect given the…
Presented with sensory challenges, living cells employ extensive noisy, fluctuating signalling and communication among themselves to compute a physiologically proper response which often results in symmetry breaking. We propose, based on…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
Experiments have found that diffusion in metabolically active cells is much faster than in dormant cells, especially for large particles. However, the mechanism of this size-dependent diffusion enhancement in living cells is still unclear.…
Response time-delay is an ubiquitous phenomenon in biological systems. Here we use a simple stochastic population model with time-delayed switching-rate conversion to quantitatively study the biological influence of the response time-delay…
Optimization-based models have been used to predict cellular behavior for over 25 years. The constraints in these models are derived from genome annotations, measured macro-molecular composition of cells, and by measuring the cell's growth…
All cells derive nutrition by absorbing some chemical and energy resources from the environment; these resources are used by the cells to reproduce the chemicals within them, which in turn leads to an increase in their volume. In this…
We study a stochastic process describing the continuous time evolution of the membrane potentials of finite system of neurons in the absence of external stimuli. The values of the membrane potentials evolve under the effect of {\it chemical…
Slowing down of the relaxation of the fluctuations around equilibrium is investigated both by stochastic simulations and by analysis of Master equation of reversible reaction networks consisting of resources and the corresponding products…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
Large networks of spiking neurons show abrupt changes in their collective dynamics resembling phase transitions studied in statistical physics. An example of this phenomenon is the transition from irregular, noise-driven dynamics to…
A new method is introduced allowing to solve exactly the reactions A+A->inert and A+A->A on the 1D lattice with synchronous diffusional dynamics (simultaneous hopping of all particles). Exact connections are found relating densities and…
The large scale behaviour of a population of cells that grow and interact through the concentration field of the chemicals they secrete is studied using dynamical renormalization group methods. The combination of the effective long-range…
The spontaneous generation of electrical activity underpins a number of essential physiological processes, and is observed even in tissues where specialized pacemaker cells have not been identified. The emergence of periodic oscillations in…