Related papers: Lambda-prophage induction modeled as a cooperative…
The lysogeny maintenance switch in phage lambda is one of the simplest examples on the molecular level of computation, command and control in a living system. If, following infection of the bacterium E. coli, the virus enters the lysogenic…
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…
Recent experimental results suggest that the E. coli chromosome feels a self-attracting interaction of osmotic origin, and is condensed in foci by bridging interactions. Motivated by these findings, we explore a generic modeling framework…
The induction of the lac operon follows cooperative kinetics.The first mechanistic model of these kinetics is the de facto standard in the modeling literature (Yagil & Yagil, Biophys J, 11, 11-27, 1971). Yet, subsequent studies have shown…
The discharge structure of inductively coupled plasma is studied via fluid simulation and analytic theory collaboration. At low pressure, the discharge is stratified by the double layer, which is modelled as dipole moment. The parabolic…
The cage model for polymer reptation is extended to simulate DC electrophoresis. The drift velocity v of a polymer with length L in an electric field with strength E shows three different regions: if the strength of field is small, the…
The electrophoretic motion of a conducting particle, driven by an induced charge mechanism, is analyzed. The dependence of the motion upon particle shape is embodied in four tensorial coefficients that relate the particle velocities to the…
The analysis of stress response systems in microorganisms can reveal molecular strategies for regulatory control and adaptation. Here, we focus on the Cad module, a subsystem of E. coli's response to acidic stress, which is conditionally…
It is the goal of systems biology to understand the behavior of the whole in terms of the knowledge of the parts. This is hard to achieve in many cases due to the difficulty of characterizing the many constituents and their complex web of…
A model for the study of the effective quasistatic conductivity and permittivity of dispersed systems with particle-host interphase, within which many-particle polarization and correlation contributions are effectively incorporated, is…
For the coherently driven \Lambda-type three-level systems the general ready-to-calculate expression for the susceptibility tensor at the frequency of the weak probe field is obtained for the arbitrary polarization of the strong coupling…
We propose a compartmental lateral inhibition system that generates contrasting patterns of gene expression between neighboring compartments. The system consists of a set of compartments interconnected by channels. Each compartment contains…
We have developed a mathematical model of regulation of expression of the Escherichia coli lac operon, and have investigated bistability in its steady-state induction behavior in the absence of external glucose. Numerical analysis of…
Electrochemical capacitors are a class of energy devices in which complex mechanisms of accumulation and dissipation of electric energy take place when connected to a charging or discharging power system. Reliably modeling their…
Unconventional strongly correlated phases of the repulsive Fermi-Hubbard model, which could be emulated by ultracold vapors loaded in optical lattices, are investigated by means of energy minimizations with quantum number projection before…
Escherichia coli swims using flagella activated by rotary motors. The direction of rotation of the motors is indirectly regulated by the binding of a single messenger protein. The conformational spread model has been shown to accurately…
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…
Disorder-induced heating (DIH) prevents ultracold neutral plasma into electron strong coupling regime. Here we propose a scheme to suppress electronic DIH via optical lattice. We simulate the evolution dynamics of ultracold neutral plasma…
Electric susceptibility of a laser-dressed atomic medium is calculated for a model Lambda - like system including two lower states and a continuum structured by a presence of an autoionizing state or a continuum with a laser-induced…
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,…