Entropy driven key-lock assembly

The effective interaction between a sphere with an open cavity (lock) and a spherical macroparticle (key), both immersed in a hard sphere fluid, is studied by means of Monte Carlo simulations. As a result, a 2d map of the key-lock effective interaction potential is constructed, which leads to the proposal of a self-assembling mechanism: there exists trajectories through which the key-lock pair could assemble avoiding trespassing potential barriers. Hence, solely the entropic contribution can induce their self-assembling even in the absence of attractive forces. This study points out the solvent contribution within the underlying mechanisms of substrate-protein assembly/disassembly processes, which are important steps of the enzyme catalysis and protein mediated transport

Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics

Linearized catalytic reaction equations modeling e.g. the dynamics of genetic regulatory networks under the constraint that expression levels, i.e. molecular concentrations of nucleic material are positive, exhibit nontrivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems the inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems, their basic properties allow to understand fundamental dynamical properties of complex biological reaction networks. We analyze the Lyapunov spectrum, determine the probability to find stationary oscillating solutions, demonstrate the effect of the nonlinearity on the effective in- and out-degree of the active interaction network and study how the frequency distributions of oscillatory modes of such system depend on the average connectivity.Comment: 11 pages, 5 figure

Stub model for dephasing in a quantum dot

As an alternative to Buttiker's dephasing lead model, we examine a dephasing stub. Both models are phenomenological ways to introduce decoherence in chaotic scattering by a quantum dot. The difference is that the dephasing lead opens up the quantum dot by connecting it to an electron reservoir, while the dephasing stub is closed at one end. Voltage fluctuations in the stub take over the dephasing role from the reservoir. Because the quantum dot with dephasing lead is an open system, only expectation values of the current can be forced to vanish at low frequencies, while the outcome of an individual measurement is not so constrained. The quantum dot with dephasing stub, in contrast, remains a closed system with a vanishing low-frequency current at each and every measurement. This difference is a crucial one in the context of quantum algorithms, which are based on the outcome of individual measurements rather than on expectation values. We demonstrate that the dephasing stub model has a parameter range in which the voltage fluctuations are sufficiently strong to suppress quantum interference effects, while still being sufficiently weak that classical current fluctuations can be neglected relative to the nonequilibrium shot noise.Comment: 8 pages with 1 figure; contribution for the special issue of J.Phys.A on "Trends in Quantum Chaotic Scattering

Scale-Free topologies and Activatory-Inhibitory interactions

A simple model of activatory-inhibitory interactions controlling the activity of agents (substrates) through a "saturated response" dynamical rule in a scale-free network is thoroughly studied. After discussing the most remarkable dynamical features of the model, namely fragmentation and multistability, we present a characterization of the temporal (periodic and chaotic) fluctuations of the quasi-stasis asymptotic states of network activity. The double (both structural and dynamical) source of entangled complexity of the system temporal fluctuations, as an important partial aspect of the Correlation Structure-Function problem, is further discussed to the light of the numerical results, with a view on potential applications of these general results.Comment: Revtex style, 12 pages and 12 figures. Enlarged manuscript with major revision and new results incorporated. To appear in Chaos (2006

Geometric Universality of Currents

We discuss a non-equilibrium statistical system on a graph or network. Identical particles are injected, interact with each other, traverse, and leave the graph in a stochastic manner described in terms of Poisson rates, possibly dependent on time and instantaneous occupation numbers at the nodes of the graph. We show that under the assumption of constancy of the relative rates, the system demonstrates a profound statistical symmetry, resulting in geometric universality of the statistics of the particle currents. This phenomenon applies broadly to many man-made and natural open stochastic systems, such as queuing of packages over the internet, transport of electrons and quasi-particles in mesoscopic systems, and chains of reactions in bio-chemical networks. We illustrate the utility of our general approach using two enabling examples from the two latter disciplines.Comment: 15 pages, 5 figure

Michaelis-Menten dynamics in protein subnetworks

To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past, and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain a description of subnetwork dynamics, including memory functions, starting directly from any given network of unary, binary and Michaelis-Menten reactions. Numerical tests show that this closed form enzyme elimination gives a much more accurate description of the subnetwork dynamics than the simpler method that represents enzymes explicitly, and is also more efficient computationally

Patterns and localized structures in bistable semiconductor resonators

We report experiments on spatial switching dynamics and steady state structures of passive nonlinear semiconductor resonators of large Fresnel number. Extended patterns and switching front dynamics are observed and investigated. Evidence of localization of structures is given.Comment: 5 pages with 9 figure

Interactions at the silica-peptide interface: influence of the extent of functionalization on the conformational ensemble

In this contribution, the effect of silica particle size (28 and 210 nm) and surface chemistry (i.e. hydroxyl, methyl or amino groups) on peptide binding response is studied with a specific emphasis on the effect of extent of functionalization on binding. Exhaustive characterization of the silica surfaces was crucial for knowledge of the chemistry and topography of the solid surface under study; and thus, to understand their impact on adsorption and the conformational ensemble of the peptides. The extent of surface functionalization was shown to be particle-size dependent, a higher level of 3-aminopropyl functionality being obtained for smaller particles, while a higher degree of methyl group functionality was found on the larger particles. We demonstrated that peptide interactions at the aqueous interface were not only influenced by the surface chemistry but by the extent of functionalization where a 'switch' of peptide adsorption behavior was observed, while changes in the conformational ensemble revealed by circular dichroism were independent of the extent of functionalization. In addition to electrostatic interactions and hydrogen bonding driving interaction at the silica-peptide interface the data obtained suggested that stronger interactions such as hydrophobic and/or covalent interactions may moderate interaction. The insights gained from this peptide-mineral study give a more comprehensive view of mechanisms concerning mineral-peptide interactions which may allow for the design and synthesis of novel (nano)materials with properties tailored for specific applications

Coherent population trapping in a dressed two-level atom via a bichromatic field

We show theoretically that by applying a bichromatic electromagnetic field, the dressed states of a monochromatically driven two-level atom can be pumped into a coherent superposition termed as dressed-state coherent population trapping. Such effect can be viewed as a new doorknob to manipulate a two-level system via its control over dressed-state populations. Application of this effect in the precision measurement of Rabi frequency, the unexpected population inversion and lasing without inversion are discussed to demonstrate such controllability.Comment: 14 pages, 6 figure

Theory of electronic transport through a triple quantum dot in the presence of magnetic field

Theory of electronic transport through a triangular triple quantum dot subject to a perpendicular magnetic field is developed using a tight binding model. We show that magnetic field allows to engineer degeneracies in the triple quantum dot energy spectrum. The degeneracies lead to zero electronic transmission and sharp dips in the current whenever a pair of degenerate states lies between the chemical potential of the two leads. These dips can occur with a periodicity of one flux quantum if only two levels contribute to the current or with half flux quantum if the three levels of the triple dot contribute. The effect of strong bias voltage and different lead-to-dot connections on Aharonov-Bohm oscillations in the conductance is also discussed