Related papers: Towards the Understanding of Stability Puzzles in …
We present a comprehensive computational study of some 900 possible "lambda-lac" mutants of the lysogeny maintenance switch in phage lambda, of which up to date 19 have been studied experimentally (Atsumi & Little, PNAS 103: 4558-4563,…
Robustness of biochemical systems has become one of the central questions in systems biology although it is notoriously difficult to formally capture its multifaceted nature. Maintenance of normal system function depends not only on the…
Simple nonlinear dynamical systems with multiple stable stationary states are often taken as models for switchlike biological systems. This paper considers the interaction of multiple such simple multistable systems when they are embedded…
A great part of the effort in the study of coarse grained models of transcription networks is directed to the analysis of their dynamical features. In this letter, we consider the \emph{equilibrium} properties of such systems, showing that…
Phenotype of biological systems needs to be robust against mutation in order to sustain themselves between generations. On the other hand, phenotype of an individual also needs to be robust against fluctuations of both internal and external…
Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence…
Determining mechanistic models of gene regulation, especially underlying phenotypic variation, is a central goal of both mathematical biology and modern evolutionary biology. However, several challenges, involving both common…
The existence of instabilities, for example in the form of adversarial examples, has given rise to a highly active area of research concerning itself with understanding and enhancing the stability of neural networks. We focus on a popular…
Gene regulatory networks can be successfully modeled as Boolean networks. A much discussed hypothesis says that such model networks reproduce empirical findings the best if they are tuned to operate at criticality, i.e. at the borderline…
It is well known that the kinetics of an intracellular biochemical network is stochastic. This is due to intrinsic noise arising from the random timing of biochemical reactions in the network as well as due to extrinsic noise stemming from…
Robustness to perturbation is a key topic in the study of complex systems occurring across a wide variety of applications from epidemiology to biochemistry. Here we analyze the eigenspectrum of the Jacobian matrices associated to a general…
Several controversial issues concerning the packing of linear DNA in bacteriophages and globules are discussed. Exact relations for the osmotic pressure, capsid pressure and loading force are derived in terms of the hole size inside phages…
The paper describes the robust algorithm for linear time-invariant plants under parametric uncertainties, external disturbances and high-frequency noises in measurements. The proposed algorithm allows one to reduce the noise impact on the…
We comment on some recent, yet unpublished results concerning instabilities in complex systems and their applications. In particular, we briefly describe main observations during extensive computer simulations of two lattice nonequilibrium…
The recent discovery of a lateral organization in cell membranes due to small structures called 'rafts' has motivated a lot of biological and physico-chemical studies. A new experiment on a model system has shown a spectacular budding…
We suggest to simulate evolution of complex organisms constrained by the sole requirement of robustness in their expression patterns. This scenario is illustrated by evolving discrete logical networks with epigenetic properties. Evidence…
The functioning of a living cell is largely determined by the structure of its regulatory network, comprising non-linear interactions between regulatory genes. An important factor for the stability and evolvability of such regulatory…
When a biological system robustly corrects component-level errors, the direct pressure on component performance declines. Components may become less reliable, maintain more genetic variability, or drift neutrally in design, creating the…
We analyse a collection of empirical networks in a wide spectrum of disciplines and show that strong non-normality is ubiquitous in network science. Dynamical processes evolving on non-normal networks exhibit a peculiar behaviour, as…
The study of fluctuations in gene regulatory networks is extended to the case of Gaussian colored noise. Firstly, the solution of the corresponding Langevin equation with colored noise is expressed in terms of an Ito integral. Then, two…