Thermodynamically consistent equilibrium properties of normal-liquid Helium-3

The high-precision data for the specific heat C_{V}(T,V) of normal-liquid Helium-3 obtained by Greywall, taken together with the molar volume V(T_0,P) at one temperature T_0, are shown to contain the complete thermodynamic information about this phase in zero magnetic field. This enables us to calculate the T and P dependence of all equilibrium properties of normal-liquid Helium-3 in a thermodynamically consistent way for a wide range of parameters. The results for the entropy S(T,P), specific heat at constant pressure C_P(T,P), molar volume V(T,P), compressibility kappa(T,P), and thermal expansion coefficient alpha(T,P) are collected in the form of figures and tables. This provides the first complete set of thermodynamically consistent values of the equilibrium quantities of normal-liquid Helium-3. We find, for example, that alpha(T,P) has a surprisingly intricate pressure dependence at low temperatures, and that the curves alpha(T,P) vs T do not cross at one single temperature for all pressures, in contrast to the curves presented in the comprehensive survey of helium by Wilks. Corrected in cond-mat/9906222v3: The sign of the coefficient d_0 was misprinted in Table I of cond-mat/9906222v1 and v2. It now correctly reads d_0=-7.1613436. All results in the paper were obtained with the correct value of d_0. (We would like to thank for E. Collin, H. Godfrin, and Y. Bunkov for finding this misprint.)Comment: 19 pages, 19 figures, 9 tables; published version; note added in proof; v3: misprint correcte

Two-Component Genetic Switch as a Synthetic Module with Tunable Stability

Despite stochastic fluctuations, some genetic switches are able to retain their expression states through multiple cell divisions, providing epigenetic memory. We propose a novel rationale for tuning the functional stability of a simple synthetic gene switch through protein dimerization. Introducing an approximation scheme to access long-time stochastic dynamics of multiple-component gene circuits, we find that the spontaneous switching rate may exhibit greater than 8orders of magnitude variation. The manipulation of the circuit's biochemical properties offers a practical strategy for designing robust epigenetic memory with synthetic circuits.open101

Automatic Compilation from High-Level Biologically-Oriented Programming Language to Genetic Regulatory Networks

Background The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. Methodology/Principal Findings To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes () and latency of the optimized engineered gene networks. Conclusions/Significance Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.National Institutes of Health (U.S.) (Grant # 7R01GM74712-5)United States. Defense Advanced Research Projects Agency (contract HR0011-10-C-0168)National Science Foundation (U.S.) (NSF CAREER award 0968682)BBN Technologie

Synthetic biology: Understanding biological design from synthetic circuits

An important aim of synthetic biology is to uncover the design principles of natural biological systems through the rational design of gene and protein circuits. Here, we highlight how the process of engineering biological systems — from synthetic promoters to the control of cell–cell interactions — has contributed to our understanding of how endogenous systems are put together and function. Synthetic biological devices allow us to grasp intuitively the ranges of behaviour generated by simple biological circuits, such as linear cascades and interlocking feedback loops, as well as to exert control over natural processes, such as gene expression and population dynamics