Potential energy landscape and robustness of a gene regulatory network: Toggle switch

Finding a multidimensional potential landscape is the key for addressing important global issues, such as the robustness of cellular networks. We have uncovered the underlying potential energy landscape of a simple gene regulatory network: a toggle switch. This was realized by explicitly constructing the steady state probability of the gene switch in the protein concentration space in the presence of the intrinsic statistical fluctuations due to the small number of proteins in the cell. We explored the global phase space for the system. We found that the protein synthesis rate and the unbinding rate of proteins to the gene were small relative to the protein degradation rate; the gene switch is monostable with only one stable basin of attraction. When both the protein synthesis rate and the unbinding rate of proteins to the gene are large compared with the protein degradation rate, two global basins of attraction emerge for a toggle switch. These basins correspond to the biologically stable functional states. The potential energy barrier between the two basins determines the time scale of conversion from one to the other. We found as the protein synthesis rate and protein unbinding rate to the gene relative to the protein degradation rate became larger, the potential energy barrier became larger. This also corresponded to systems with less noise or the fluctuations on the protein numbers.

投资时间序列的混沌分维研究

以某市固定资产投资同比增长数据为根据 ,利用混沌动力学中的相空间重构技术、幅值谱分析、庞加莱截面等方法进行分析 ,并计算其关联分维 ,得出其饱和嵌入维数为 5、关联分维约为 1 7,初步确定某市固定资产投资增长过程具有混沌特性 ,有 5个因素影响着某市固定资产投资的同比增长幅度 ,其中 2个因素起决定作用·该法可用于复杂的经济系统的分析研究·

地震波场模拟及叠前深度偏移的李群方法

The processes of seismic wave propagation in phase space and one way wave extrapolation in frequency-space domain, if without dissipation, are essentially transformation under the action of one parameter Lie groups. Consequently, the numerical calculation methods of the propagation ought to be Lie group transformation too, which is known as Lie group method. After a fruitful study on the fast methods in matrix inversion, some of the Lie group methods in seismic numerical modeling and depth migration are presented here. Firstly the Lie group description and method of seismic wave propagation in phase space is proposed, which is, in other words, symplectic group description and method for seismic wave propagation, since symplectic group is a Lie subgroup and symplectic method is a special Lie group method. Under the frame of Hamiltonian, the propagation of seismic wave is a symplectic group transformation with one parameter and consequently, the numerical calculation methods of the propagation ought to be symplectic method. After discrete the wave field in time and phase space, many explicit, implicit and leap-frog symplectic schemes are deduced for numerical modeling. Compared to symplectic schemes, Finite difference (FD) method is an approximate of symplectic method. Consequently, explicit, implicit and leap-frog symplectic schemes and FD method are applied in the same conditions to get a wave field in constant velocity model, a synthetic model and Marmousi model. The result illustrates the potential power of the symplectic methods. As an application, symplectic method is employed to give synthetic seismic record of Qinghai foothills model. Another application is the development of Ray+symplectic reverse-time migration method. To make a reasonable balance between the computational efficiency and accuracy, we combine the multi-valued wave field & Green function algorithm with symplectic reverse time migration and thus develop a new ray+wave equation prestack depth migration method. Marmousi model data and Qinghai foothills model data are processed here. The result shows that our method is a better alternative to ray migration for complex structure imaging. Similarly, the extrapolation of one way wave in frequency-space domain is a Lie group transformation with one parameter Z and consequently, the numerical calculation methods of the extrapolation ought to be Lie group methods. After discrete the wave field in depth and space, the Lie group transformation has the form of matrix exponential and each approximation of it gives a Lie group algorithm. Though Pade symmetrical series approximation of matrix exponential gives a extrapolation method which is traditionally regarded as implicit FD migration, it benefits the theoretic and applying study of seismic imaging for it represent the depth extrapolation and migration method in a entirely different way. While, the technique of coordinates of second kind for the approximation of the matrix exponential begins a new way to develop migration operator. The inversion of matrix plays a vital role in the numerical migration method given by Pade symmetrical series approximation. The matrix has a Toepelitz structure with a helical boundary condition and is easy to inverse with LU decomposition. A efficient LU decomposition method is spectral factorization. That is, after the minimum phase correlative function of each array of matrix had be given by a spectral factorization method, all of the functions are arranged in a position according to its former location to get a lower triangular matrix. The major merit of LU decomposition with spectral factorization (SF Decomposition) is its efficiency in dealing with a large number of matrixes. After the setup of a table of the spectral factorization results of each array of matrix, the SF decomposition can give the lower triangular matrix by reading the table. However, the relationship among arrays is ignored in this method, which brings errors in decomposition method. Especially for numerical calculation in complex model, the errors is fatal. Direct elimination method can give the exact LU decomposition But even it is simplified in our case, the large number of decomposition cost unendurable computer time. A hybrid method is proposed here, which combines spectral factorization with direct elimination. Its decomposition errors is 10 times little than that of spectral factorization, and its decomposition speed is quite faster than that of direct elimination, especially in dealing with a large number of matrix. With the hybrid method, the 3D implicit migration can be expected to apply on real seismic data. Finally, the impulse response of 3D implicit migration operator is presented.

双聚焦偏移速度估计与可分表示叠前弹性反演

In exploration seismology, the geologic target of oil and gas reservoir in complex medium request the high accuracy image of the structure and lithology of the medium. So the study of the prestack image and the elastic inversion of seismic wave in the complex medium come to the leading edge. The seismic response measured at the surface carries two fundamental pieces of information: the propagation effects of the medium and the reflections from the different layer boundaries in the medium. The propagation represent the low-wavenumber component of the medium, it is so-called the trend or macro layering, whereas the reflections represent the high-wavenumber component of the medium, it is called the detailed or fine layering. The result of migration velocity analysis is the resolution of the low-wavenumber component of the medium, but the prestack elastic inversion provided the resolution of the high-wavvenumber component the medium. In the dissertation, the two aspects about the migration velocity estimation and the elastic inversion have been studied.Firstly, any migration velocity analysis methods must include two basic elements: the criterion that tell us how to know whether the model parameters are correct and the updating that tell us how to update the model parameters when they are incorrect, which are effected on the properties and efficiency of the velocity estimation method. In the dissertation, a migration velocity analysis method based on the CFP technology has been presented in which the strategy of the top-down layer stripping approach are adapted to avoid the difficult of the selecting reduce .The proposed method has a advantage that the travel time errors obtained from the DTS panel are defined directly in time which is the difference with the method based on common image gather in which the residual curvature measured in depth should be converted to travel time errors.In the proposed migration velocity analysis method, the four aspects have been improved as follow:? The new parameterization of velocity model is provided in which the boundaries of layers are interpolated with the cubic spline of the control location and the velocity with a layer may change along with lateral position but the value is calculated as a segmented linear function of the velocity of the lateral control points. The proposed parameterization is suitable to updating procedure.? The analytical formulas to represent the travel time errors and the model parameters updates in the t-p domain are derived under local lateral homogeneous. The velocity estimations are iteratively computed as parametric inversion. The zero differential time shift in the DTS panel for each layer show the convergence of the velocity estimation.? The method of building initial model using the priori information is provided to improve the efficiency of velocity analysis. In the proposed method, Picking interesting events in the stacked section to define the boundaries of the layers and the results of conventional velocity analysis are used to define the velocity value of the layers? An interactive integrate software environment with the migration velocity analysis and prestack migration is built.The proposed method is firstly used to the synthetic data. The results of velocity estimation show both properties and efficiency of the velocity estimation are very good.The proposed method is also used to the field data which is the marine data set. In this example, the prestack and poststack depth migration of the data are completed using the different velocity models built with different method. The comparison between them shows that the model from the proposed method is better and improves obviously the quality of migration.In terms of the theoretical method of expressing a multi-variable function by products of single-variable functions which is suggested by Song Jian (2001), the separable expression of one-way wave operator has been studied. A optimization approximation with separable expression of the one-way wave operator is presented which easily deal with the lateral change of velocity in space and wave number domain respectively and has good approach accuracy. A new prestack depth migration algorithm based on the optimization approximation separable expression is developed and used to testing the results of velocity estimation.Secondly, according to the theory of the seismic wave reflection and transmission, the change of the amplitude via the incident angle is related to the elasticity of medium in the subsurface two-side. In the conventional inversion with poststack datum, only the information of the reflection operator at the zero incident angles can be used. If the more robust resolutions are requested, the amplitudes of all incident angles should be used.A natural separable expression of the reflection/transmission operator is represented, which is the sum of the products of two group functions. One group function vary with phase space whereas other group function is related to elastic parameters of the medium and geological structure.By employing the natural separable expression of the reflection/transmission operator, the method of seismic wave modeling with the one-way wave equation is developed to model the primary reflected waves, it is adapt to a certain extent heterogeneous media and confirms the accuracy of AVA of the reflections when the incident angle is less than 45'. The computational efficiency of the scheme is greatly high.The natural separable expression of the reflection/transmission operator is also used to construct prestack elastic inversion algorithm. Being different from the AVO analysis and inversion in which the angle gathers formed during the prstack migration are used, the proposed algorithm construct a linear equations during the prestack migration by the separable expression of the reflection/transmission operator. The unknowns of the linear equations are related to the elasticity of the medium, so the resolutions of them provided the elastic information of the medium.The proposed method of inversion is the same as AVO inversion in , the difference between them is only the method processing the amplitude via the incident angle and computational domain.

陆相砂泥岩层序的高精度检测方法研究及应用

Ordos Basin is a typical cratonic petroliferous basin with 40 oil-gas bearing bed sets. It is featured as stable multicycle sedimentation, gentle formation, and less structures. The reservoir beds in Upper Paleozoic and Mesozoicare are mainly low density, low permeability, strong lateral change, and strong vertical heterogeneous. The well-known Loess Plateau in the southern area and Maowusu Desert, Kubuqi Desert and Ordos Grasslands in the northern area cover the basin, so seismic data acquisition in this area is very difficult and the data often takes on inadequate precision, strong interference, low signal-noise ratio, and low resolution. Because of the complicated condition of the surface and the underground, it is very difficult to distinguish the thin beds and study the land facies high-resolution lithologic sequence stratigraphy according to routine seismic profile. Therefore, a method, which have clearly physical significance, based on advanced mathematical physics theory and algorithmic and can improve the precision of the detection on the thin sand-peat interbed configurations of land facies, is in demand to put forward.Generalized S Transform (GST) processing method provides a new method of phase space analysis for seismic data. Compared with wavelet transform, both of them have very good localization characteristics; however, directly related to the Fourier spectra, GST has clearer physical significance, moreover, GST adopts a technology to best approach seismic wavelets and transforms the seismic data into time-scale domain, and breaks through the limit of the fixed wavelet in S transform, so GST has extensive adaptability. Based on tracing the development of the ideas and theories from wavelet transform, S transform to GST, we studied how to improve the precision of the detection on the thin stratum by GST.Noise has strong influence on sequence detecting in GST, especially in the low signal-noise ratio data. We studied the distribution rule of colored noise in GST domain, and proposed a technology to distinguish the signal and noise in GST domain. We discussed two types of noises: white noise and red noise, in which noise satisfy statistical autoregression model. For these two model, the noise-signal detection technology based on GST all get good result. It proved that the GST domain noise-signal detection technology could be used to real seismic data, and could effectively avoid noise influence on seismic sequence detecting.On the seismic profile after GST processing, high amplitude energy intensive zone, schollen, strip and lentoid dead zone and disarray zone maybe represent specifically geologic meanings according to given geologic background. Using seismic sequence detection profile and combining other seismic interpretation technologies, we can elaborate depict the shape of palaeo-geomorphology, effectively estimate sand stretch, distinguish sedimentary facies, determine target area, and directly guide oil-gas exploration.In the lateral reservoir prediction in XF oilfield of Ordos Basin, it played very important role in the estimation of sand stretch that the study of palaeo-geomorphology of Triassic System and the partition of inner sequence of the stratum group. According to the high-resolution seismic profile after GST processing, we pointed out that the C8 Member of Yanchang Formation in DZ area and C8 Member in BM area are the same deposit. It provided the foundation for getting 430 million tons predicting reserves and unite building 3 million tons off-take potential.In tackling key problem study for SLG gas-field, according to the high-resolution seismic sequence profile, we determined that the deposit direction of H8 member is approximately N-S or NNE-SS W. Using the seismic sequence profile, combining with layer-level profile, we can interpret the shape of entrenched stream. The sunken lenticle indicates the high-energy stream channel, which has stronger hydropower. By this way we drew out three high-energy stream channels' outline, and determined the target areas for exploitation. Finding high-energy braided river by high-resolution sequence processing is the key technology in SLG area.In ZZ area, we studied the distribution of the main reservoir bed-S23, which is shallow delta thin sand bed, by GST processing. From the seismic sequence profile, we discovered that the schollen thick sand beds are only local distributed, and most of them are distributary channel sand and distributary bar deposit. Then we determined that the S23 sand deposit direction is NW-SE in west, N-S in central and NE-SW in east. The high detecting seismic sequence interpretation profiles have been tested by 14 wells, 2 wells mismatch and the coincidence rate is 85.7%. Based on the profiles we suggested 3 predicted wells, one well (Yu54) completed and the other two is still drilling. The completed on Is coincident with the forecastThe paper testified that GST is a effective technology to get high- resolution seismic sequence profile, compartmentalize deposit microfacies, confirm strike direction of sandstone and make sure of the distribution range of oil-gas bearing sandstone, and is the gordian technique for the exploration of lithologic gas-oil pool in complicated areas.

Spatial and energetic mode dynamics of cold atomic systems

In this thesis we relate the formal description of various cold atomic systems in the energy eigenbasis, to the observable spatial mode dynamics. Herein the `spatial mode dynamics' refers to the direction of photon emission following the spontaneous emission of an excited fermion in the presence of a same species and spin ideal anisotropic Fermi sea in its internal ground state. Due to the Pauli principle, the presence of the ground state Fermi sea renders the phase space, anisotropic and only partially accessible, thereby a ecting the direction of photon emission following spontaneous emission. The spatial and energetic mode dynamics also refers to the quantum `tunneling' interaction between localised spatial modes, synonymous with double well type potentials. Here we relate the dynamics of the wavefunction in both the energetic and spatial representations. Using this approach we approximate the relationship between the spatial and energetic representations of a wavefunction spanning three spatial and energetic modes. This is extended to a process known as Spatial Adiabatic Passage, which is a technique to transport matter waves between localised spatial modes. This approach allows us to interpret the transport of matter waves as a signature of a geometric phase acquired by the one of the internal energy eigenstates of the system during the cyclical evolution. We further show that this geometric phase may be used to create spatial mode qubit and qutrit states.

Two closely coupled lasers, dynamics & applications

The dynamics of two mutually coupled identical single-mode semi-conductor lasers are theoretically investigated. For small separation and large coupling between the lasers, symmetry-broken one-colour states are shown to be stable. In this case the light output of the lasers have significantly different intensities whilst at the same time the lasers are locked to a single common frequency. For intermediate coupling we observe stable two-colour states, where both single-mode lasers lase simultaneously at two optical frequencies which are separated by up to 150 GHz. For low coupling but possibly large separation, the frequency of the relaxation oscillations of the freerunning lasers defines the dynamics. Chaotic and quasi-periodic states are identified and shown to be stable. For weak coupling undamped relaxation oscillations dominate where each laser is locked to three or more odd number of colours spaced by the relaxation oscillation frequency. It is shown that the instabilities that lead to these states are directly connected to the two colour mechanism where the change in the number of optical colours due to a change in the plane of oscillation. At initial coupling, in-phase and anti-phase one colour states are shown to emerge from “on” uncoupled lasers using a perturbation method. Similarly symmetry-broken one-colour states come from considering one free-running laser initially “on” and the other laser initially “off”. The mechanism that leads to a bi-stability between in-phase and anti-phase one-colour states is understood. Due to an equivariant phase space symmetry of being able to exchange the identical lasers, a symmetric and symmetry-broken variant of all states mentioned above exists and is shown to be stable. Using a five dimensional model we identify the bifurcation structure which is responsible for the appearance of symmetric and symmetry-broken one-colour, symmetric and symmetry-broken two-colour, symmetric and symmetry-broken undamped relaxation oscillations, symmetric and symmetry-broken quasi-periodic, and symmetric and symmetry-broken chaotic states. As symmetry-broken states always exist in pairs, they naturally give rise to bi-stability. Several of these states show multistabilities between symmetric and symmetry-broken variants and among states. Three memory elements on the basis of bi-stabilities in one and two colour states for two coupled single-mode lasers are proposed. The switching performance of selected designs of optical memory elements is studied numerically.

Quantum teleportation via mixed two-mode squeezed states in the coherent-state representation

Quantum teleportation for continuous variables is generally described in phase space by using the Wigner functions. We study quantum teleportation via a mixed two-mode squeezed state in Hilbert-Schmidt space by using the coherent-state representation and operators. This shows directly how the teleported state is related to the original state.

Characterization of the entanglement of two squeezed states

We study a continuous-variable entangled state composed of two states which are squeezed in two opposite quadratures in phase space. Various entanglement conditions are tested for the entangled squeezed state and we study decoherence models for noise, producing a mixed entangled squeezed state. We briefly describe a probabilistic protocol for entanglement swapping based on the use of this class of entangled states and the main features of a general generation scheme.

Path-integral study of a two-dimensional Lennard-Jones glass

The glass transition in a quantum Lennard-Jones mixture is investigated by constant-volume path-integral simulations. Particles are assumed to be distinguishable, and the strength of quantum effects is varied by changing h from zero (the classical case) to one (corresponding to a highly quantum-mechanical regime). Quantum delocalization and zero point energy drastically reduce the sensitivity of structural and thermodynamic properties to the glass transition. Nevertheless, the glass transition temperature T-g can be determined by analyzing the phase space mobility of path-integral centroids. At constant volume, the T-g of the simulated model increases monotonically with increasing h. Low temperature tunneling centers are identified, and the quantum versus thermal character of each center is analyzed. The relation between these centers and soft quasilocalized harmonic vibrations is investigated. Periodic minimizations of the potential energy with respect to the positions of the particles are performed to determine the inherent structure of classical and quantum glassy samples. The geometries corresponding to these energy minima are found to be qualitatively similar in all cases. Systematic comparisons for ordered and disordered structures, harmonic and anharmonic dynamics, classical and quantum systems show that disorder, anharmonicity, and quantum effects are closely interlinked.

Solvation effects on equilibria: Triazoles and N-methyl piperidinol

We have performed calculations of the solvation effects on a number of equilibrium constants in water using a recently proposed hybrid quantum classical scheme in which the liquid environment is modelled using classical solvent molecules and the solute electronic structure is computed using modern quantum chemical methods. The liquid phase space is sampled from a fully classical simulation. We find that solvation effects on both triazole tautomeric equilibrium constants and piperidinol conformational equilibrium constants can be interpreted in terms of subtle differences in the local environment which can be seen in probability densities and radial distribution functions. Lower level calculations were performed for comparison and we conclude that the solvation thermodynamics can be predicted from a good classical model of solvent and solute molecules, but the implicit models that we tried are less successful.

Simultaneous histories, path sums, and measurements for noncommuting variables

We analyze von Neumann-like quantum measurements in terms of simultaneous virtual paths constructed for two noncommuting variables. The approach is applied to measurements of operator functions of conjugate variables and to the joint measurements of such variables. The limits of applicability of the restricted phase space path integral are studied. We demonstrate that, for a simple joint measurement, using entangled meter states allows one to manipulate the order in which the measurements are conducted. The effects of '' weakening '' a measurement by choosing unsharp meter states are also discussed.

A frequency measure robust to linear filtering

It is noted that the determination of an oscillation frequency by used of the power spectrum of measured time series is susceptible to filtering of the signal. Similarly, frequency measurements made by period counting can yield different, results depending on how the signal is filtered for noise reduction. In an attempt to eliminate these ambiguities, a new measure of frequency, based on an approximate reconstruction of the phase-space trajectory of the oscillator from the signal, is introduced. This measure is shown to be invariant under linear filtering. For this reason, it is also inaccessible by spectral methods. The effect of filtering on frequency for weakly nonlinear, noisy oscillators, to which this definition applies only imperfectly, is quantified. This work provides the theoretical basis for frequency measurements employing MIRVA filtering.

Progress in proton radiography for diagnosis of ICF-relevant plasmas

Proton radiography using laser-driven sources has been developed as a diagnostic since the beginning of the decade, and applied successfully to a range of experimental situations. Multi-MeV protons driven from thin foils via the Target Normal Sheath Acceleration mechanism, offer, under optimal conditions, the possibility of probing laser-plasma interactions, and detecting electric and magnetic fields as well as plasma density gradients with similar to ps temporal resolution and similar to 5-10 mu m spatial resolution. In view of these advantages, the use of proton radiography as a diagnostic in experiments of relevance to Inertial Confinement Fusion is currently considered in the main fusion laboratories. This paper will discuss recent advances in the application of laser-driven radiography to experiments of relevance to Inertial Confinement Fusion. In particular we will discuss radiography of hohlraum and gasbag targets following the interaction of intense ns pulses. These experiments were carried out at the HELEN laser facility at AWE (UK), and proved the suitability of this diagnostic for studying, with unprecedented detail, laser-plasma interaction mechanisms of high relevance to Inertial Confinement Fusion. Non-linear solitary structures of relevance to space physics, namely phase space electron holes, have also been highlighted by the measurements. These measurements are discussed and compared to existing models.

Simulation of a collisionless planar electrostatic shock in a proton-electron plasma with a strong initial thermal pressure change

The localized deposition of the energy of a laser pulse, as it ablates a solid target, introduces high thermal pressure gradients in the plasma. The thermal expansion of this laser-heated plasma into the ambient medium (ionized residual gas) triggers the formation of non-linear structures in the collisionless plasma. Here an electron-proton plasma is modelled with a particle-in-cell simulation to reproduce aspects of this plasma expansion. A jump is introduced in the thermal pressure of the plasma, across which the otherwise spatially uniform temperature and density change by a factor of 100. The electrons from the hot plasma expand into the cold one and the charge imbalance drags a beam of cold electrons into the hot plasma. This double layer reduces the electron temperature gradient. The presence of the low-pressure plasma modifies the proton dynamics compared with the plasma expansion into a vacuum. The jump in the thermal pressure develops into a primary shock. The fast protons, which move from the hot into the cold plasma in the form of a beam, give rise to the formation of phase space holes in the electron and proton distributions. The proton phase space holes develop into a secondary shock that thermalizes the beam.