Modeling of negative autoregulated genetic networks in single cells

We discuss recent developments in the modeling of negative autoregulated genetic networks. In particular, we consider the temporal evolution of the population of mRNA and proteins in simple networks using rate equations. In the limit of low copy numbers, fluctuation effects become significant and more adequate modeling is then achieved using the master equation formalism. The analogy between regulatory gene networks and chemical reaction networks on dust grains in the interstellar medium is discussed. The analysis and simulation of complex reaction networks are also considered.Comment: 15 pages, 4 figures. Published in Gen

Current-voltage Characteristics of Molecular Conductors: Two versus Three Terminal

This paper addresses the question of whether a ``rigid molecule'' (one which does not deform in an external field) used as the conducting channel in a standard three-terminal MOSFET configuration can offer any performance advantage relative to a standard silicon MOSFET. A self-consistent solution of coupled quantum transport and Poisson's equations shows that even for extremely small channel lengths (about 1 nm), a ``well-tempered'' molecular FET demands much the same electrostatic considerations as a ``well-tempered'' conventional MOSFET. In other words, we show that just as in a conventional MOSFET, the gate oxide thickness needs to be much smaller than the channel length (length of the molecule) for the gate control to be effective. Furthermore, we show that a rigid molecule with metallic source and drain contacts has a temperature independent subthreshold slope much larger than 60 mV/decade, because the metal-induced gap states in the channel prevent it from turning off abruptly. However, this disadvantage can be overcome by using semiconductor contacts because of their band-limited nature.Comment: 9 pages, 9 figures. Major changes in text. One new result added (Fig 8). Accepted for publication in IEEE Trans. on Nanotechnolog

STM contrast of a CO dimer on a Cu(1 1 1) surface: a wave-function analysis

We present a method used to intuitively interpret the STM contrast by investigating individual wave functions originating from the substrate and tip side. We use localized basis orbital density functional theory, and propagate the wave functions into the vacuum region at a real-space grid, including averaging over the lateral reciprocal space. Optimization by means of the method of Lagrange multipliers is implemented to perform a unitary transformation of the wave functions in the middle of the vacuum region. The method enables (i) reduction of the number of contributing tip-substrate wave function combinations used in the corresponding transmission matrix, and (ii) to bundle up wave functions with similar symmetry in the lateral plane, so that (iii) an intuitive understanding of the STM contrast can be achieved. The theory is applied to a CO dimer adsorbed on a Cu(1 1 1) surface scanned by a single-atom Cu tip, whose STM image is discussed in detail by the outlined method.Comment: 9 pages, 5 figure

Unified description of inelastic propensity rules for electron transport through nanoscale junctions

We present a method to analyze the results of first-principles based calculations of electronic currents including inelastic electron-phonon effects. This method allows us to determine the electronic and vibrational symmeties in play, and hence to obtain the so-called propensity rules for the studied systems. We show that only a few scattering states -- namely those belonging to the most transmitting eigenchannels -- need to be considered for a complete description of the electron transport. We apply the method on first-principles calculations of four different systems and obtain the propensity rules in each case.Comment: 4 pages, 4 figures, 1 table http://link.aps.org/abstract/PRL/v100/e22660

Modeling inelastic phonon scattering in atomic- and molecular-wire junctions

Computationally inexpensive approximations describing electron-phonon scattering in molecular-scale conductors are derived from the non-equilibrium Green's function method. The accuracy is demonstrated with a first principles calculation on an atomic gold wire. Quantitative agreement between the full non-equilibrium Green's function calculation and the newly derived expressions is obtained while simplifying the computational burden by several orders of magnitude. In addition, analytical models provide intuitive understanding of the conductance including non-equilibrium heating and provide a convenient way of parameterizing the physics. This is exemplified by fitting the expressions to the experimentally observed conductances through both an atomic gold wire and a hydrogen molecule.Comment: 5 pages, 3 figure

Physical 2D Morphware and Power Reduction Methods for Everyone

Dynamic and partial reconfiguration discovers more and more the focus in academic and industrial research. Modern systems in e.g. avionic and automotive applications exploit the parallelism of hardware in order to reduce power consumption and to increase performance. State of the art reconfigurable FPGA devices allows reconfiguring parts of their architecture while the other configured architecture stays undisturbed in operation. This dynamic and partial reconfiguration allows therefore adapting the architecture to the requirements of the application while run-time. The difference to the traditional term of software and its related sequential architecture is the possibility to change the paradigm of brining the data to the respective processing elements. Dynamic and partial reconfiguration enables to bring the processing elements to the data and is therefore a new paradigm. The shift from the traditional microprocessor approaches with sequential processing of data to parallel processing reconfigurable architectures forces to introduce new paradigms with the focus on computing in time and space

Rotation of a single acetylene molecule on Cu(001) by tunneling electrons in STM

We study the elementary processes behind one of the pioneering works on STM controlled reactions of single molecules [Stipe et al., Phys. Rev. Lett. 81, 1263 (1998)]. Using the Keldysh-Green function approach for the vibrational generation rate in combination with DFT calculations to obtain realistic parameters we reproduce the experimental rotation rate of an acetylene molecule on a Cu(100) surface as a function of bias voltage and tunneling current. This combined approach allows us to identify the reaction coordinate mode of the acetylene rotation and its anharmonic coupling with the C-H stretch mode. We show that three different elementary processes, the excitation of C-H stretch, the overtone ladder climbing of the hindered rotational mode, and the combination band excitation together explain the rotation of the acetylene molecule on Cu(100).Comment: 5+5 pages, 4+2 figure

From tunneling to contact: Inelastic signals in an atomic gold junction

The evolution of electron conductance in the presence of inelastic effects is studied as an atomic gold contact is formed evolving from a low-conductance regime (tunneling) to a high-conductance regime (contact). In order to characterize each regime, we perform density functional theory (DFT) calculations to study the geometric and electronic structures, together with the strength of the atomic bonds and the associated vibrational frequencies. The conductance is calculated by first evaluating the transmission of electrons through the system, and secondly by calculating the conductance change due to the excitation of vibrations. As found in previous studies [Paulsson et al., Phys. Rev. B. 72, 201101(R) (2005)] the change in conductance due to inelastic effects permits to characterize the crossover from tunneling to contact. The most notorious effect being the crossover from an increase in conductance in the tunneling regime to a decrease in conductance in the contact regime when the bias voltage matches a vibrational threshold. Our DFT-based calculations actually show that the effect of vibrational modes in electron conductance is rather complex, in particular when modes localized in the contact region are permitted to extend into the electrodes. As an example, we find that certain modes can give rise to decreases in conductance when in the tunneling regime, opposite to the above mentioned result. Whereas details in the inelastic spectrum depend on the size of the vibrational region, we show that the overall change in conductance is quantitatively well approximated by the simplest calculation where only the apex atoms are allowed to vibrate. Our study is completed by the application of a simplified model where the relevant parameters are obtained from the above DFT-based calculations.Comment: 8 pages, 5 figure

Influence of vibrations on electron transport through nanoscale contacts

In this article we present a novel semi-analytical approach to calculate first-order electron-vibration coupling constants within the framework of density functional theory. It combines analytical expressions for the first-order derivative of the Kohn-Sham operator with respect to nuclear displacements with coupled-perturbed Kohn-Sham theory to determine the derivative of the electronic density matrix. This allows us to efficiently compute accurate electron-vibration coupling constants. We apply our approach to describe inelastic electron tunneling spectra of metallic and molecular junctions. A gold junction bridged by an atomic chain is used to validate the developed method, reproducing established experimental and theoretical results. For octane-dithiol and octane-diamine single-molecule junctions we discuss the influence of the anchoring group and mechanical stretching on the inelastic electron tunneling spectra.Comment: 13 pages, 5 figure