Electronically Excited Complex Formation in Magnesium Cluster-Halogen Atom Reactions.

A near ultraviolet transition of Mg2F has been observed in emission from the reaction between magnesium clusters, most likely Mg3, and fluorine atoms. Because there is little evidence for upper-state internal excitation, the spectrum is assigned assuming that the upper state is quenched to its lowest vibrational levels. Two of possibly three ground-state vibrational frequencies, υ1 = 516 ± 10 cm-1 and υ2 = 104 ± 10 cm-1, have been established. Dispersed laser-induced fluorescence studies extrapolating on the observed chemiluminescence indicate an excited-state symmetric stretch frequency of order 370 ± 30 cm-1. Electronic structure calculations at the CCSD(T)/CBS level predict that the ground state of Mg2F has C2v symmetry and can be described as an Mg2+F- ion pair with two Mg-F bonds. Like the MgF A-X transition that is largely a transition between Mg orbitals, the observed transition in Mg2F is largely between orbitals on the magnesium dimer ion. The asymmetric C∞v Mg2+F- complex is also a minimum and is predicted to be 6.7 kcal/mol higher in energy. Calculated structures for the Mg2Cl isomers are also presented and used to further interpret the experimental results for the reaction of Mg clusters with Cl atoms. In contrast to Mg2F, the ground state of Mg2Cl is a linear C∞v MgMgCl structure with the C2v and D∞h isomers of the MgClMg structure slightly higher in energy.

A Comparison of Weighted Stochastic Simulation Methods for the Analysis of Genetic Circuits.

Rare events are of particular interest in synthetic biology because rare biochemical events may be catastrophic to a biological system by, for example, triggering irreversible events such as off-target drug delivery. To estimate the probability of rare events efficiently, several weighted stochastic simulation methods have been developed. Under optimal parameters and model conditions, these methods can greatly improve simulation efficiency in comparison to traditional stochastic simulation. Unfortunately, the optimal parameters and conditions cannot be deduced a priori. This paper presents a critical survey of weighted stochastic simulation methods. It shows that the methods considered here cannot consistently, efficiently, and exactly accomplish the task of rare event simulation without resorting to a computationally expensive calibration procedure, which undermines their overall efficiency. The results suggest that further development is needed before these methods can be deployed for general use in biological simulations.

Design and analysis of a robust genetic Muller C-element.

This paper presents results on the design and analysis of a robust genetic Muller C-element. The Muller C-element is a standard logic gate commonly used to synchronize independent processes in most asynchronous electronic circuits. Synthetic biological logic gates have been previously demonstrated, but there remain many open issues in the design of sequential (state-holding) logic operations. Three designs are considered for the genetic Muller C-element: a majority gate, a toggle switch, and a speed-independent implementation. While the three designs are logically equivalent, each design requires different assumptions to operate correctly. The majority gate design requires the most timing assumptions, the speed-independent design requires the least, and the toggle switch design is a compromise between the two. This paper examines the robustness of these designs as well as the effects of parameter variation using stochastic simulation. The results show that robustness to timing assumptions does not necessarily increase reliability, suggesting that modifications to existing logic design tools are going to be necessary for synthetic biology. Parameter variation simulations yield further insights into the design principles necessary for building robust genetic gates. The results suggest that high gene count, cooperativity of at least two, tight repression, and balanced decay rates are necessary for robust gates. Finally, this paper presents a potential application of the genetic Muller C-element as a quorum-mediated trigger.

Efficient analysis methods in synthetic biology.

This chapter describes new analysis and verification techniques for synthetic genetic circuits. In particular, it applies stochastic model checking techniques to models of genetic circuits in order to ensure that they behave correctly and are as robust as possible for a variety of different inputs and parameter settings. In addition to stochastic model checking, this chapter proposes new variants to the incremental stochastic simulation algorithm (iSSA) that are capable of presenting a researcher with a simulation trace of the typical behavior of the system. Before the development of this algorithm, discerning this information was extremely error-prone as it involved performing many simulations and attempting to wade through the massive amounts of data. This algorithm greatly aids researchers in designing genetic circuits as it efficiently shows the researcher the most likely behavior of the circuit. Both the iSSA and stochastic model checking can be used in concert to give a researcher the likelihood that the system exhibits its most typical behavior, as well as, non-typical behaviors. This methodology is applied to several genetic circuits leading to new understanding of the effects of various parameters on the behavior of these circuits.

Performance of a high-speed transcutaneous link with error correction coding.

Several low-power communication strategies have been studied for interfacing with cortical implants via mutual inductance links. In this paper, we consider performance optimization strategies for a mutual-inductance link based on the Pulse Harmonic Modulation method. We consider two enhancements that may allow for increased throughput in the PHM system. First, a low-power error-correcting code is used to improve the system's robustness against noise, timing jitter and other non-ideal factors. Second, the system is adapted for multi-level modulation as a means of increasing the data rate. Our results characterize each systems' bit error rate as a function of pulse jitter, power interference and comparator offset.

125Mbps ultra-wideband system evaluation for cortical implant devices.

This paper evaluates the performance of a 125Mbps Impulse Ratio Ultra-Wideband (IR-UWB) system for cortical implant devices by using low-Q inductive coil link operating in the near-field domain. We examine design tradeoffs between transmitted signal amplitude, reliability, noise and clock jitter. The IR-UWB system is modeled using measured parameters from a reported UWB transceiver implemented in 90nm-CMOS technology. Non-optimized inductive coupling coils with low-Q value for near-field data transmission are modeled in order to build a full channel from the transmitter (Tx) to the receiver (Rx). On-off keying (OOK) modulation is used together with a low-complexity convolutional error correcting code. The simulation results show that even though the low-Q coils decrease the amplitude of the received pulses, the UWB system can still achieve acceptable performance when error correction is used. These results predict that UWB is a good candidate for delivering high data rates in cortical implant devices.