"Cellular behavior is governed by gene regulatory processes that are intrinsically dynamic and nonlinear, and are subject to non-negligible amounts of random fluctuations. Such conditions are ubiquitous in physical systems, where they have been studied for decades using the tools of statistical and nonlinear physics. The goal of this review is to show how approaches traditionally used in physics can help in reaching a systems-level understanding of living cells. To that end, we present an overview of the dynamical phenomena exhibited by genetic circuits and their functional significance. We also describe the theoretical and experimental approaches that are being used to unravel the relationship between circuit structure and function in dynamical cellular processes under the influence of noise, both at the single-cell level and in cellular populations, where intercellular coupling plays an important role."

"Much of the complexity observed in gene regulation originates from cooperative protein-DNA binding. While studies of the target search of proteins for their specific binding sites on the DNA have revealed design principles for the quantitative characteristics of protein-DNA interactions, no such principles are known for the cooperative interactions between DNA-binding proteins. We consider a simple theoretical model for two interacting transcription factor (TF) species, searching for and binding to two adjacent target sites hidden in the genomic background. We study the kinetic competition of a dimer search pathway and a monomer search pathway, as well as the steady-state regulation function mediated by the two TFs over a broad range of TF-TF interaction strengths. Using a transcriptional AND-logic as exemplary functional context, we identify the functionally desirable regime for the interaction. We find that both weak and very strong TF-TF interactions are favorable, albeit with different characteristics. However, there is also an unfavorable regime of intermediate interactions where the genetic response is prohibitively slow."

"The response of complex networks to perturbations is of utmost importance in areas as diverse as ecosystem management, emergency response, and cell reprogramming. A fundamental property of networks is that the perturbation of one node can affect other nodes, in a process that may cause the entire or substantial part of the system to change behavior and possibly collapse. Recent research in metabolic and food-web networks has demonstrated the concept that network damage caused by external perturbations can often be mitigated or reversed by the application of compensatory perturbations. Compensatory perturbations are constrained to be physically admissible and amenable to implementation on the network. However, the systematic identification of compensatory perturbations that conform to these constraints remains an open problem. Here, we present a method to construct compensatory perturbations that can control the fate of general networks under such constraints. Our approach accounts for the full nonlinear behavior of real complex networks and can bring the system to a desirable target state even when this state is not directly accessible. Applications to genetic networks show that compensatory perturbations are effective even when limited to a small fraction of all nodes in the network and that they are far more effective when limited to the highest-degree nodes. The approach is conceptually simple and computationally efficient, making it suitable for the rescue, control, and reprogramming of large complex networks in various domains."

"The design of genetic networks with specific functions is one of the major goals of synthetic biology. However, constructing biological devices that work "as required" remains challenging, while the cost of uncovering flawed designs experimentally is large. To address this issue, we propose a fully automated framework that allows the correctness of synthetic gene networks to be formally verified in silico from rich, high level functional specifications.
Given a device, we automatically construct a mathematical model from experimental data characterizing the parts it is composed of. The specific model structure guarantees that all experimental observations are captured and allows us to construct finite abstractions through polyhedral operations. The correctness of the model with respect to temporal logic specifications can then be verified automatically using methods inspired by model checking.
Overall, our procedure is conservative but it can filter through a large number of potential device designs and select few that satisfy the specification to be implemented and tested further experimentally. Illustrative examples of the application of our methods to the design of simple synthetic gene networks are included."

"As we have shown, Cluster Reverberation is a mechanism available to neural systems for robust short-term memory without synaptic learning. To the best of our knowledge, this is the first mechanism proposed which has these charac- teristics – essential for, say, sensory memory or certain working-memory tasks. All that is needed is for the network topology to be highly clustered or modu- lar, and for small groups of neurons to store one bit of information, as opposed to the conventional view which assumes one bit per neuron. Considering the enormous number of neurons in the brain, and the fact that real individual neu- rons are probably too noisy to store information reliably, these hypotheses do not seem farfetched.…"

"This expository review is devoted to fish swimming and bird/insect flight.…"

"Genetic oscillators are a major theme of interest in the emerging field of synthetic biology. Until recently, most work has been carried out using intra-cellular oscillators, but this approach restricts the broader applicability of such systems. Motivated by a desire to develop large-scale, spatially-distributed cell-based computational systems, we present an initial design for a population-level oscillator which uses three different bacterial strains. Our system is based on the client-server model familiar to computer science, and uses quorum sensing for communication between nodes. We present the results of extensive in silico simulation tests, which confirm that our design is both feasible and robust."

"A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms. The fact that different viruses adopt similar structural forms is an indication of a common underlying design, motivating the use of simplified, low-resolution models in exploring the assembly process. Several versions of a molecular dynamics approach are described. Polyhedral shells of different sizes are involved, the assembly pathways are either irreversible or reversible, and an explicit solvent is optionally included. …Among the key observations are that efficient growth proceeds by means of a cascade of highly reversible stages, and that while there are a large variety of possible partial assemblies, only a relatively small number of strongly bonded configurations are actually encountered."

ME: what would 'well-designed' biochemical nets look like, if you evolved them in silico?

"The reliability with which a network can transmit a particular frequency component of the input signal tra- jectory is determined by the gain-to-noise ratio of the net- work as a function of frequency. For systems that obey the spectral addition rule [32], that is those for which downstream reactions do not affect the input signal, the gain-to-noise ratio is an intrinsic property of the processing network. For networks that do not obey the spectral addition rule the gain-to-noise ratio will be dependent on the statistics of the input signal. The mutual information between input and output signals, which quantifies the information which can be transmitted about a particular input ensemble, also depends on the particular choice of the input signal.…"

"There seems to be a brief recognition period for Bdellovibrio to identify its prey after a collision with another cell (Shilo, 1969). Initially, the attachment to a cell surface is reversible. Bdellovibrio is still able to swim away a few seconds after recognizing that the cell is not a right target (gram- positive bacteria). When a gram-negative bacterium is encountered, Bdellovibrio cell becomes committed to invasion. The whole process usually takes around 5 – 10 minutes. Bdellovibrio drops its flagellum. It has been hypothesized that Bdellovibrio may adhere to the cell surface using pilus-like fibre structure expressed on its penetration pole."

"The paper is structured as follows. Methods of cultivating and experimenting with plasmodium of Physarum polycephalum are described in Sect. 2. In Sect. 3 we provide experimental evidence of ‘ballistic’ behavior of traveling plasmod- ium localizations. Experimental Physarum gates are discussed in Sect. 4. In Sect. 5 experimental results are supported by numerical simulation of propa- gating localizations. The gates are cascaded in one-bit half-adder in Sect. 6. Importance of non-nutrient substrate for gate implementation is highlighted in Sect. 7."

"The results from the computational approximation of Physarum support the findings of [15] that the organism can be used to construct simple logic gates, and also the computing schemes within this paper which explored the creation of more complex combined gates and half adder circuitry. The findings suggest that, although such circuits can indeed be built, the presence of both timing errors and junctional (search) errors would severely limit the effectiveness and practicality with even more complex circuits."

"Microbial ecosystems have been widely used in industrial production, but the inter-relationships of organisms within them haven't been completely clarified due to complex composition and structure of natural microbial ecosystems. So it is challenging for ecologists to get deep insights on how ecosystems function and interplay with surrounding environments. But the recent progresses in synthetic biology show that construction of artificial ecosystems where relationships of species are comparatively clear could help us further uncover the meadow of those tiny societies. By using two quorum-sensing signal transduction circuits, this research designed, simulated and constructed a synthetic ecosystem where various population dynamics formed by changing environmental factors."

"Staged self-assembly with RNA removal is a model of tile-based algorithmic self-assembly that was introduced by Abel, Benbernou, Damian, Demaine, Demaine, Flatland, Kominers and Schweller (Shape Replication through Self-Assembly and RNase Enzymes, SODA 2010) and is a model that allows for the periodic removal of all tiles in a given assembly that belong to a specially designated group of (RNA) tiles. In this paper, we study the self-assembly of arbitrary shapes in staged assembly systems with RNA removal. We analyze the performance of our assembly systems with respect to their tile complexity, stage complexity as well as the scale factor, connectivity and addressability of the uniquely produced final assembly."

"A Sensitivity Tuner: To avoid being limited to the sensitivity of the promoter and in order to be able to detect distinct concentrations of an inducer using just one promoter, we see the need for a set of sensitivity tuners. These devices allow you to "tune" your biosensor, such that it reports meaningful concentrations of the inducer appropriate to the biosensor's application. The sensitivity tuner also modifies the PoPS output from the promoter's native behavior to a sigmoidal "on" or "off" response pattern."

"This page reports the result of the iGEM competition for 2009. You can visit the team's wiki by clicking on the team's name. You can see what medal the team won and view the slides from their presentation, a video of their presentation, and their poster using the other icons."

[Watch the video] "The sensor meanwhile detects surrounding pH levels--the higher the pH concentration, the faster the electromagnetic pulses emitted by the micro-machine. The external computer uses these signals to direct a swarm of about 3,000 magnetically-sensitive bacteria, which push the micro-machine around as it pulses. The bacteria push the micro-machine closer to the higher pH concentration."

"VIB researchers, such as Siegbert Melzer in Tom Beeckman's group, have studied two such flower-inducing genes. They have deactivated them in thale cress (Arabidopsis thaliana), a typical annual. The VIB researchers found that mutant plants can no longer induce flowering, but they can continue to grow vegetatively or come into flower much later. Melzer had found that modified crops did not use up their store of non-specialised cells, enabling perennial growth. They can therefore continue to grow for a very long time.

As with real perennials these plants show secondary growth with wood formation creating shrub-like Arabidopsis plants."

"As explained by the Court, the test serves as a proxy for assessing the more fundamental concern – ensuring that the claim does not seek to impermissibly "preempt the use of a fundamental principle." This might make sense in the context of so-called business method patents, where the fundamental principle implicated is typically characterized as an abstract idea or mental process. But it is unclear to what extent this test will prove applicable to patent claims arising out of the life sciences, where patentable subject matter challenges more often allege preemption of a natural phenomena or law of nature, rather than an abstract idea or mental process."