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Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
The majority of dynamical studies in power systems focus on the high voltage transmission grids where models consider large generators interacting with crude aggregations of individual small loads. However, new phenomena have been observed…
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…
A model is proposed that describes the evolution of a mixed state of a quantum system for which gain and loss of energy or amplitude are present. Properties of the model are worked out in detail. In particular, invariant subspaces of the…
Spontaneous symmetry-breaking in phase transitions occurs when the system Hamiltonian is symmetric under a certain transformation, but the equilibrium states observed in nature are not. Here, we prove that when a discrete symmetry is…
The transfer of population between two intersecting quantum states is the most fundamental dynamical event that governs a broad variety of processes in physics, chemistry, biology and material science. Whereas any two-state description…
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
Microphase separation of membrane components is thought to play an important role in many physiological processes, from cell signaling to endocytosis and cellular trafficking. Here, we study how variations in the membrane composition can be…
The phase transition kinetics in three phase systems was investigated using the numerically efficient cell dynamics method. A phasefield model with a simple analytical free energy and single order parameter was used to study the kinetics…
Understanding the interplay among processes that occur over different timescales is a challenging issue in the physics of systems regulation. In gene regulation, the timescales for changes in chromatin states can differ from those for…
An important task in quantitative biology is to understand the role of stochasticity in biochemical regulation. Here, as an extension of our recent work [Phys. Rev. Lett. 107, 148101 (2011)], we study how input fluctuations affect the…
Many intracellular processes continue to oscillate during the cell cycle. Although it is not well-understood how they are affected by discontinuities in the cellular environment, the general assumption is that oscillations remain robust…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
To study the dynamics of chemical processes, we often adopt rate equations to observe the change in chemical concentrations. However, when the number of the molecules is small, the fluctuations cannot be neglected. We often study the…
Reaction diffusion systems with Turing instability and mass conservation are studied. In such systems, abrupt decays of stripes follow quasi-stationary states in sequence. At steady state, the distance between stripes is much longer than…
Gene expression is a noisy process that leads to regime shift between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been…
We analyse the effect of intrinsic fluctuations on the properties of bistable stochastic systems with time scale separation operating under1 quasi-steady state conditions. We first formulate a stochastic generalisation of the quasi-steady…
Small (but still containing many atoms) quantum systems (traditionally termed nano-systems) are dramatically different from their macroscopic or genuine microscopic (atomic) cousins. Microscopic molecular systems (with a few atoms) obey a…
We introduce novel characterizations for many-body phase transitions between delocalized and localized phases based on the system's sensitivity to boundary conditions. In particular, we change boundary conditions from periodic to…