Related papers: The heterodimer auto-repression loop: a robust and…
Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated…
A practical approach is proposed for efficiently generating ultrashort attosecond pulses (APs) from realistic solid-state materials, aiming to optimize pulse width effectively. By adjusting the photon energy while maintaining a constant…
The formation of DNA loops by proteins and protein complexes that bind at distal DNA sites plays a central role in many cellular processes, such as transcription, recombination, and replication. Here we review the basic thermodynamic…
An improved system for creating a pulsed, low-temperature molecular beam of OH radicals has been developed. We use a pulsed discharge to create OH from H$_2$O seeded in Xe during a supersonic expansion, where the high-voltage pulse duration…
Many organisms possess both a cell cycle to control DNA replication and a circadian clock to anticipate changes between day and night. In some cases, these two rhythmic systems are known to be coupled by specific, cross-regulatory…
The paper proposes a modular-based approach to constraint handling in process optimization and control. This is partly motivated by the recent interest in learning-based methods, e.g., within bioproduction, for which constraint handling…
We report supercontinuum generation and pulse compression in two stacked multipass cells based on dielectric mirrors. The 230 fs pulses at 1 MHz containing 12 $\mu$J were compressed by factor 33 down to 7 fs, corresponding to 1.0 GW peak…
Based on previously published experimental observations and mathematical models for Hes1, p53 and NF-kB gene expression, we improve these models through a distributed delay formulation of the time lag between transcription factor binding…
The mechanics of complex soft matter often cannot be understood in the classical physical frame of flexible polymers or rigid rods. The underlying constituents are semiflexible polymers, whose finite bending stiffness ($\kappa$) leads to…
Characterization of self-consistent laser-plasma evolutions serves as a fundamental issue in the field of relativistic laser-plasma interactions. In this paper, we present an analysis framework for description of these evolutions during…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
Two synthetic gene circuits -- the genetic toggle switch and the repressilator -- are analyzed quantitatively and discussed in the context of an educational module on gene circuits and feedback that constitutes the final topic of a…
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…
Few-cycle pulses present an essential tool to track ultrafast dynamics in matter and drive strong field effects. To address photon-hungry applications, high average power lasers are used which, however, cannot directly provide sub-100 fs…
At laser wavelengths longer than the prominent 1 {\mu}m range of high-power ytterbium-doped lasers, nonlinear phase shifts produced in nonlinear media for spectral broadening and subsequent pulse compression decrease drastically.…
We use plasmon rulers to follow the conformational dynamics of a single protein for up to 24 h at a video rate. The plasmon ruler consists of two gold nanospheres connected by a single protein linker. In our experiment, we follow the…
Many viruses have the cunning ability to enter a hibernative or off state, termed latency or lysogeny. When in a latent state, the virus is unable to replicate, and its gene expression program is largely shut down. This facility for lying…
We report on the polarization dynamics of regenerative light pulses in a micropillar laser with integrated saturable absorber coupled to an external feedback mirror. The delayed self-coupled microlaser is operated in the excitable regime,…
A single gene, regulating its own expression via a positive feedback loop, constitutes a common motif in gene regulatory networks and signalling cascades. Recent experiments on the development of competence in the bacterial population…
The lytic-lysogenic switch of the temperate lactococcal phage TP901-1 is fundamentally different from that of phage lambda. In phage TP901-1, the lytic promoter PL is repressed by CI whereas repression of the lysogenic promoter PR requires…