Related papers: Non-normality Can Facilitate Pulsing in Biomolecul…
It has been generally recognized that stochasticity can play an important role in the information processing accomplished by reaction networks in biological cells. Most treatments of that stochasticity employ Gaussian noise even though it…
Pulse-coupled systems such as spiking neural networks exhibit nontrivial invariant sets in the form of attracting yet unstable saddle periodic orbits where units are synchronized into groups. Heteroclinic connections between such orbits may…
The propagation of noise through parallel regulatory pathways is a characteristic feature of feed-forward loops in genetic networks. Although the contributions of the direct and indirect regulatory pathways of feed-forward loops to output…
Particle-in-Cell (PIC) simulation codes have wide applicability to first-principles modeling of multidimensional nonlinear plasma phenomena, including wake-field accelerators. This review addresses both finite difference and pseudo-spectral…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
The calcium transport in biological systems is modelled as a reaction-diffusion process. Nonlinear calcium waves are then simulated using a stochastic cellular automaton whose rules are derived from the corresponding coupled partial…
The dynamics of non-polar diatomic molecules interacting with a far-detuned narrow-band laser field, that only may drive rotational transitions, is studied. The rotation of the molecule is considered both classically and quantum…
Due to its ubiquitous presence, turbulence is often invoked to explain the origin of nonthermal particles in astrophysical sources of high-energy emission. With particle-in-cell simulations, we study decaying turbulence in…
Large and complex molecules are building blocks for life. We compute probabilities for their formation from an average non-equilibrium model. As the distance from thermodynamic equilibrium is increased in this model, so too are the chances…
Understanding quantum system dynamics driven by nonclassical light pulses is challenging, particularly for general light states with large photon numbers. Here we introduce an efficient framework that makes this task tractable. By…
The population of radio pulsars is observed to demonstrate certain polarization properties not explained by the conventional picture of pulsar polarization, namely frequency evolution of polarization, deviations of the linear polarization…
Molecular biology and biochemistry interpret microscopic processes in the living world in terms of molecular structures and their interactions, which are quantum mechanical by their very nature. Whereas the theoretical foundations of these…
Experiments performed on a wide range of glassy materials display many interesting phenomena, such as aging behavior. In recent years, a large body of experiments probed this nonequilibrium glassy dynamics through elaborate protocols, in…
This note analyzes incoherent feedforward loops in signal processing and control. It studies the response properties of IFFL's to exponentially growing inputs, both for a standard version of the IFFL and for a variation in which the output…
We consider the theory of the non-linear spectroscopy for a single molecule undergoing stochastic dynamics and interacting with a sequence of two laser pulses. General expressions for photon counting statistics are obtained, and an exact…
Most biological signals are non-Gaussian, reflecting their origins in highly nonlinear physiological systems. A versatile set of techniques for studying non-Gaussian signals relies on the spectral representations of higher moments, known as…
We review generalized Fluctuation-Dissipation Relations which are valid under general conditions even in ``non-standard systems'', e.g. out of equilibrium and/or without a Hamiltonian structure. The response functions can be expressed in…
Oscillations represent a ubiquitous phenomenon in biological systems. The conventional models of biological periodic oscillations are usually proposed as interconnecting transcriptional feedback loops. Some specific proteins function as…
We consider the failure of localized control in a nonlinear spatially extended system caused by extremely small amounts of noise. It is shown that this failure occurs as a result of a nonlinear instability. Nonlinear instabilities can occur…
It has been recognized for quite some time that for some matrices the spectra are not enough to tell the complete story of the dynamics of the system, even for linear ODEs. While it is true that the eigenvalues control the asymptotic…