Related papers: A computational systems biology study of the lambd…
Phage lambda is one of the most studied biological models in modern molecular biology. Over the past 50 years quantitative experimental knowledge on this biological model has been accumulated at all levels: physics, chemistry, genomics,…
Gene regulatory network of lambda phage is one the best studied model systems in molecular biology. More 50 years of experimental study has provided a tremendous amount of data at all levels: physics, chemistry, DNA, protein, and function.…
Our previously presented method for high throughput computational screening of mutant activity (Hediger et al., arXiv:1203.2950) is benchmarked against experimentally measured amidase activity for 22 mutants of Candida antarctica lipase B…
The bistable gene regulatory switch controlling the transition from lysogeny to lysis in bacteriophage lambda presents a unique challenge to quantitative modeling. Despite extensive characterization of this regulatory network, the origin of…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…
Multistable gene regulatory systems sustain different levels of gene expression under identical external conditions. Such multistability is used to encode phenotypic states in processes including nutrient uptake and persistence in bacteria,…
We discuss two aspects, the in vivo and in vitro difference and the modeling of noise, of integrative modeling of network dynamics in biology, using phage lambda as an example. We believe those two aspects have not been seriously…
The lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding CI and CRO proteins. Here we address the Physics of this transition in terms of an energy function that…
Plasticity-led evolution is a form of evolution where a change in the environment induces novel traits via phenotypic plasticity, after which the novel traits are genetically accommodated over generations under the novel environment. This…
We present results from an experiment similar to one performed by Packard (1988), in which a genetic algorithm is used to evolve cellular automata (CA) to perform a particular computational task. Packard examined the frequency of evolved CA…
When software evolves, opportunities for introducing faults appear. Therefore, it is important to test the evolved program behaviors during each evolution cycle. We conduct an exploratory study to investigate the properties of…
Substantial efforts have been applied to engineer CA with desired emergent properties, such as supporting gliders. Recent work in continuous CA has generated a wide variety of compelling bioreminiscent patterns, and the expansion of CA…
In this paper we apply mutation testing in an in-time fashion, i.e., across multiple project releases. Thus, we investigate how the mutants of the current version behave in the future versions of the programs. We study the characteristics…
Locked intrinsic localized modes (ILMs) and large amplitude lattice spatial modes (LSMs) have been experimentally measured for a driven 1-D nonlinear cyclic electric transmission line, where the nonlinear element is a saturable capacitor.…
Interacting many-body quantum systems and their dynamics, while fundamental to modern science and technology, are formidable to simulate and understand. However, by discovering their symmetries, conservation laws, and integrability one can…
Prior behavioural work suggests that some LLMs alter choices when options are framed as causing pain or pleasure, and that such deviations can scale with stated intensity. To bridge behavioural evidence (what the model does) with…
We study discrete time linear constrained switching systems with additive disturbances, in which the switching may be on the system matrices, the disturbance sets, the state constraint sets or a combination of the above. In our general…
This paper investigates manipulability of interactive Lagrangian systems with parametric uncertainty and communication/sensing constraints. Two standard examples are teleoperation with a master-slave system and teaching operation of robots.…
This paper presents an algorithm for approximating certain types of dynamical systems given by a system of ordinary delay differential equations by a Boolean network model. Often Boolean models are much simpler to understand than complex…
The enterobacteria lambda phage is a paradigm temperate bacteriophage. Its lysogenic and lytic life cycles echo competition between the DNA binding $\lambda$-repressor (CI) and CRO proteins. Here we scrutinize the structure, stability and…