Globally coupled stochastic two-state oscillators: Fluctuations due to finite numbers

Infinite arrays of coupled two-state stochastic oscillators exhibit well-defined steady states. We study the fluctuations that occur when the number N of oscillators in the array is finite. We choose a particular form of global coupling that in the infinite array leads to a pitchfork bifurcation from a monostable to a bistable steady state, the latter with two equally probable stationary states. The control parameter for this bifurcation is the coupling strength. In finite arrays these states become metastable: The fluctuations lead to distributions around the most probable states, with one maximum in the monostable regime and two maxima in the bistable regime. In the latter regime, the fluctuations lead to transitions between the two peak regions of the distribution. Also, we find that the fluctuations break the symmetry in the bimodal regime, that is, one metastable state becomes more probable than the other, increasingly so with increasing array size. To arrive at these results, we start from microscopic dynamical evolution equations from which we derive a Langevin equation that exhibits an interesting multiplicative noise structure. We also present a master equation description of the dynamics. Both of these equations lead to the same Fokker-Planck equation, the master equation via a 1/N expansion and the Langevin equation via standard methods of Ito calculus for multiplicative noise. From the Fokker-Planck equation we obtain an effective potential that reflects the transition from the monomodal to the bimodal distribution as a function of a control parameter. We present a variety of numerical and analytic results that illustrate the strong effects of the fluctuations. We also show that the limits N -> infinity and t -> infinity(t is the time) do not commute. In fact, the two orders of implementation lead to drastically different results.

Frequency-domain stimulated and spontaneous light emission signals at molecular junctions

Using a diagrammatic superoperator formalism we calculate optical signals at molecular junctions where a single molecule is coupled to two metal leads which are held at different chemical potentials. The molecule starts in a nonequilibrium steady state whereby it continuously exchanges electrons with the leads with a constant electron flux. Expressions for frequency domain optical signals measured in response to continuous laser fields are derived by expanding the molecular correlation functions in terms of its many-body states. The nonunitary evolution of molecular states is described by the quantum master equation. (C) 2014 AIP Publishing LLC.

Statistics of an adiabatic charge pump

We investigate the effect of time-dependent cyclic-adiabatic driving on the charge transport in a quantum junction. We propose a nonequilibrium Green's function formalism to study the statistics of the charge pumped (at zero bias) through the junction. The formulation is used to demonstrate charge pumping in a single electronic level coupled to two (electronic) reservoirs with time-dependent couplings. An analytical expression for the average pumped current for a general cyclic driving is derived. It is found that for zero bias, for a certain class of driving, the Berry phase contributes only to the odd cumulants. In contrast, a quantum master equation formulation does not show a Berry-phase effect at all.

Gain bandwidth characterization of surface-emitting quantum well laser gain structures for femtosecond operation

We present a method to experimentally characterize the gain filter and calculate a corresponding parabolic gain bandwidth of lasers that are described by "class A" dynamics by solving the master equation of spectral condensation for Gaussian spectra. We experimentally determine the gain filter, with an equivalent parabolic gain bandwidth of up to 51 nm, for broad-band InGaAs/GaAs quantum well gain surface-emitting semiconductor laser structures capable of producing pulses down to 60 fs width when mode-locked with an optical Stark saturable absorber mirror. © 2010 Optical Society of America.

Noise and stability in giant-chirp oscillators mode-locked with a nanotube-based saturable absorber

We compare experimental results showing stable dissipative-soliton solutions exist in mode-locked lasers with ultra-large normal dispersion (as large as 21.5 ps2), with both the analytic framework provided by Haus' master-equation and full numerical simulations. © 2010 Optical Society of America.

在激波波面中氧分子的非平衡离解

对强激波作用下双原子分子振动与离解耦合的非平衡离解过程进行了理论计算.本工作的特点是将计算起点建立在分子基本参数上,采用主方程理论处理振动与离解的耦合,振动跃迁几率用SSH理论计算,在离解限附近考虑多量子数跃迁并计及原子复合的影响.对O2-Ar体系,计算给出了在正激波后O2分子振动能级分布、振动弛豫时间、离解孕育时间、离解产物浓度、离解速率系数等物理量随时间的演化.计算结果分别与Camac和Wray的实验相符.计算显示,在激波作用的后期,有准稳态的振动能级布居分布.计算结果显示,Park模型低估了非平衡离解速率系数,Hansen模型则高估了非平衡离解速率系数.

Sequence-function relationships in E. coli transcriptional regulation

Understanding how transcriptional regulatory sequence maps to regulatory function remains a difficult problem in regulatory biology. Given a particular DNA sequence for a bacterial promoter region, we would like to be able to say which transcription factors bind there, how strongly they bind, and whether they interact with each other and/or RNA polymerase, with the ultimate objective of integrating knowledge of these parameters into a prediction of gene expression levels. The theoretical framework of statistical thermodynamics provides a useful framework for doing so, enabling us to predict how gene expression levels depend on transcription factor binding energies and concentrations. We used thermodynamic models, coupled with models of the sequence-dependent binding energies of transcription factors and RNAP, to construct a genotype to phenotype map for the level of repression exhibited by the lac promoter, and tested it experimentally using a set of promoter variants from E. coli strains isolated from different natural environments. For this work, we sought to ``reverse engineer'' naturally occurring promoter sequences to understand how variations in promoter sequence affects gene expression. The natural inverse of this approach is to ``forward engineer'' promoter sequences to obtain targeted levels of gene expression. We used a high precision model of RNAP-DNA sequence dependent binding energy, coupled with a thermodynamic model relating binding energy to gene expression, to predictively design and verify a suite of synthetic E. coli promoters whose expression varied over nearly three orders of magnitude.

However, although thermodynamic models enable predictions of mean levels of gene expression, it has become evident that cell-to-cell variability or ``noise'' in gene expression can also play a biologically important role. In order to address this aspect of gene regulation, we developed models based on the chemical master equation framework and used them to explore the noise properties of a number of common E. coli regulatory motifs; these properties included the dependence of the noise on parameters such as transcription factor binding strength and copy number. We then performed experiments in which these parameters were systematically varied and measured the level of variability using mRNA FISH. The results showed a clear dependence of the noise on these parameters, in accord with model predictions.

Finally, one shortcoming of the preceding modeling frameworks is that their applicability is largely limited to systems that are already well-characterized, such as the lac promoter. Motivated by this fact, we used a high throughput promoter mutagenesis assay called Sort-Seq to explore the completely uncharacterized transcriptional regulatory DNA of the E. coli mechanosensitive channel of large conductance (MscL). We identified several candidate transcription factor binding sites, and work is continuing to identify the associated proteins.

Nonclassical excitation and quantum interference in a three level atom

Non-classical properties and quantum interference (QI) in two-photon excitation of a three level atom (|1〉), |2〉, |3〉) in a ladder configuration, illuminated by multiple fields in non-classical (squeezed) and/or classical (coherent) states, is studied. Fundamentally new effects associated with quantum correlations in the squeezed fields and QI due to multiple excitation pathways have been observed. Theoretical studies and extrapolations of these findings have revealed possible applications which are far beyond any current capabilities, including ultrafast nonlinear mixing, ultrafast homodyne detection and frequency metrology. The atom used throughout the experiments was Cesium, which was magneto-optically trapped in a vapor cell to produce a Doppler-free sample. For the first part of the work the |1〉 → |2〉 → |3〉 transition (corresponding to the 6S_1/2F = 4 → 6P_3/2F' = 5 → 6D_5/2F" = 6 transition) was excited by using the quantum-correlated signal (Ɛ_s) and idler (Ɛ_i) output fields of a subthreshold non-degenerate optical parametric oscillator, which was tuned so that the signal and idler fields were resonant with the |1〉 → |2〉 and |2〉 → |3〉 transitions, respectively. In contrast to excitation with classical fields for which the excitation rate as a function of intensity has always an exponent greater than or equal to two, excitation with squeezed-fields has been theoretically predicted to have an exponent that approaches unity for small enough intensities. This was verified experimentally by probing the exponent down to a slope of 1.3, demonstrating for the first time a purely non-classical effect associated with the interaction of squeezed fields and atoms. In the second part excitation of the two-photon transition by three phase coherent fields Ɛ₁ , Ɛ₂ and Ɛ₀, resonant with the dipole |1〉 → |2〉 and |2〉 → |3〉 and quadrupole |1〉 → |3〉 transitions, respectively, is studied. QI in the excited state population is observed due to two alternative excitation pathways. This is equivalent to nonlinear mixing of the three excitation fields by the atom. Realizing that in the experiment the three fields are spaced in frequency over a range of 25 THz, and extending this scheme to other energy triplets and atoms, leads to the discovery that ranges up to 100's of THz can be bridged in a single mixing step. Motivated by these results, a master equation model has been developed for the system and its properties have been extensively studied.

Positive Correlations in Tunneling through coupled Quantum Dots

Due to the Fermi-Dirac statistics of electrons the temporal correlations of tunneling events in a double barrier setup are typically negative. Here, we investigate the shot noise behavior of a system of two capacitively coupled quantum dot states by means of a Master equation model. In an asymmetric setup positive correlations in the tunneling current can arise due to the bunching of tunneling events. The underlying mechanism will be discussed in detail in terms of the current-current correlation function and the frequency-dependent Fano factor.

Coulomb effects in tunneling through a quantum dot stack

Tunneling through two vertically coupled quantum dots is studied by means of a Pauli master equation model. The observation of double peaks in the current-voltage characteristic in a recent experiment is analyzed in terms of the tunnel coupling between the quantum dots and the coupling to the contacts. Different regimes for the emitter chemical potential indicating different peak scenarios in the tunneling current are discussed in detail. We show by comparison with a density matrix approach that the interplay of coherent and incoherent effects in the stationary current can be fully described by this approach.

Theory of high-power mode-locked lasers with a slow absorber

We develop an analytical theory of high-power passively mode-locked lasers with a slow absorber; the theory is valid at pulse energies well exceeding the saturation energy. We analyze the Haus modelocking master equation in the pulse-energy-domain representation, approximating the intensity profile function by a series in the vicinity of its peak value. We consider the high-power operation regime of subpicosecond blue-violet GaN mode-locked diode lasers, using the approach developed. © 2010 Springer Science+Business Media, Inc.

Noise and stability in giant-chirp oscillators mode-locked with a nanotube-based saturable absorber

We compare experimental results showing stable dissipative-soliton solutions exist in mode-locked lasers with ultra-large normal dispersion (as large as 21.5 ps2), with both the analytic framework provided by Haus' master-equation and full numerical simulations. © 2010 Optical Society of America.

Spin-dependent current noises in transport through coupled quantum dots

Current fluctuations can provide additional insight into quantum transport in mesoscopic systems. The present work is carried out for the fluctuation properties of transport through a pair of coupled quantum dots which are connected with ferromagnetic electrodes. Based on an efficient particle-number-resolved master equation approach, we are concerned with not only fluctuations of the total charge and spin currents, but also of each individual spin-dependent component. As a result of competition among the spin polarization, Coulomb interaction, and dot-dot tunnel coupling, rich behaviors are found for the self- and mutual-correlation functions of the spin-dependent currents.

Spontaneous relaxation of a charge qubit under electrical measurement

In this work we first derive a generalized conditional master equation for quantum measurement by a mesoscopic detector, then study the readout characteristics of qubit measurement where a number of remarkable new features are found. The work would, in particular, highlight the qubit spontaneous relaxation effect induced by the measurement itself rather than an external thermal bath.

Quantum transport from the perspective of quantum open systems

By viewing the non-equilibrium transport setup as a quantum open system, we propose a reduced-density-matrix based quantum transport formalism. At the level of self-consistent Born approximation, it can precisely account for the correlation between tunneling and the system internal many-body interaction, leading to certain novel behavior such as the non-equilibrium Kondo effect. It also opens a new way to construct time-dependent density functional theory for transport through large-scale complex systems. (c) 2006 Elsevier B.V. All rights reserved.