Molecular Dissection of Mycobacterium tuberculosis Integration Host Factor Reveals Novel Insights into the Mode of DNA Binding and Nucleoid Compaction

The annotated whole-genome sequence of Mycobacterium tuberculosis indicated that Rv1388 (Mtihf) likely encodes a putative 20 kDa integration host factor (mIHF). However, very little is known about the functional properties of mIHF or organization of mycobacterial nucleoid. Molecular modeling of the mIHF three-dimensional structure, based on the cocrystal structure of Streptomyces coelicolor IHF-duplex DNA, a bona fide relative of mIHF, revealed the presence of Arg170, Arg171, and Arg173, which might be involved in DNA binding, and a conserved proline (P150) in the tight turn. The phenotypic sensitivity of Escherichia coli Delta ihfA and Delta ihfB strains to UV and methylmethanesulfonate could be complemented with the wild-type Mtihf, but not its alleles bearing mutations in the DNA-binding residues. Protein DNA interaction assays revealed that wild-type mIHF, but not its DNA-binding variants, bind with high affinity to fragments containing attB and attP sites and curved DNA. Strikingly, the functionally important amino acid residues of mIHF and the mechanism(s) underlying its binding to DNA, DNA bending, and site-specific recombination are fundamentally different from that of E. coli IHF alpha beta. Furthermore, we reveal novel insights into IHF-mediated DNA compaction depending on the placement of its preferred binding sites; mIHF promotes compaction of DNA into nucleoid-like or higher-order filamentous structures. We hence propose that mIHF is a distinct member of a subfamily of proteins that serve as essential cofactors in site-specific recombination and nucleoid organization and that these findings represent a significant advance in our understanding of the role(s) of nucleoid-associated proteins.

Insights into the Functional Roles of N-Terminal and C-Terminal Domains of Helicobacter pylori DprA

DNA processing protein A (DprA) plays a crucial role in the process of natural transformation. This is accomplished through binding and subsequent protection of incoming foreign DNA during the process of internalization. DprA along with Single stranded DNA binding protein A (SsbA) acts as an accessory factor for RecA mediated DNA strand exchange. H. pylori DprA (HpDprA) is divided into an N-terminal domain and a C-terminal domain. In the present study, individual domains of HpDprA have been characterized for their ability to bind single stranded (ssDNA) and double stranded DNA (dsDNA). Oligomeric studies revealed that HpDprA possesses two sites for dimerization which enables HpDprA to form large and tightly packed complexes with ss and dsDNA. While the N-terminal domain was found to be sufficient for binding with ss or ds DNA, C-terminal domain has an important role in the assembly of poly-nucleoprotein complex. Using site directed mutagenesis approach, we show that a pocket comprising positively charged amino acids in the N-terminal domain has an important role in the binding of ss and dsDNA. Together, a functional cross talk between the two domains of HpDprA facilitating the binding and formation of higher order complex with DNA is discussed.

Physical Layer Data Fusion Via Distributed Co-Phasing With General Signal Constellations

This paper studies a pilot-assisted physical layer data fusion technique known as Distributed Co-Phasing (DCP). In this two-phase scheme, the sensors first estimate the channel to the fusion center (FC) using pilots sent by the latter; and then they simultaneously transmit their common data by pre-rotating them by the estimated channel phase, thereby achieving physical layer data fusion. First, by analyzing the symmetric mutual information of the system, it is shown that the use of higher order constellations (HOC) can improve the throughput of DCP compared to the binary signaling considered heretofore. Using an HOC in the DCP setting requires the estimation of the composite DCP channel at the FC for data decoding. To this end, two blind algorithms are proposed: 1) power method, and 2) modified K-means algorithm. The latter algorithm is shown to be computationally efficient and converges significantly faster than the conventional K-means algorithm. Analytical expressions for the probability of error are derived, and it is found that even at moderate to low SNRs, the modified K-means algorithm achieves a probability of error comparable to that achievable with a perfect channel estimate at the FC, while requiring no pilot symbols to be transmitted from the sensor nodes. Also, the problem of signal corruption due to imperfect DCP is investigated, and constellation shaping to minimize the probability of signal corruption is proposed and analyzed. The analysis is validated, and the promising performance of DCP for energy-efficient physical layer data fusion is illustrated, using Monte Carlo simulations.

A controller design method for 3 phase 4 wire grid connected VSI with LCL filter

Closed loop control of a grid connected VSI requires line current control and dc bus voltage control. The closed loop system comprising PR current controller and grid connected VSI with LCL filter is a higher order system. Closed loop control gain expressions are therefore difficult to obtain directly for such systems. In this work a simplified approach has been adopted to find current and voltage controller gain expressions for a 3 phase 4 wire grid connected VSI with LCL filter. The closed loop system considered here utilises PR current controller in natural reference frame and PI controller for dc bus voltage control. Asymptotic frequency response plot and gain bandwidth requirements of the system have been used for current control and voltage controller design. A simplified lower order model, derived for closed loop current control, is used for the dc bus voltage controller design. The adopted design method has been verified through experiments by comparison of the time domain response.

Uncertainty Quantification in Ultrasonic Wave Based Detection of Delamination in Composite Structures

In this paper we consider the problem of guided wave scattering from delamination in laminated composite and further the problem of estimating delamination size and layer-wise location from the guided wave measurement. Damage location and region/size can be estimated from time of flight and wave packet spread, whereas depth information can be obtained from wavenumber modulation in the carrier packet. The key challenge is that these information are highly sensitive to various uncertainties. Variation in reflected and transmitted wave amplitude in a bar due to boundary/interface uncertainty is studied to illustrate such effect. Effect of uncertainty in material parameters on the time of flight are estimated for longitudinal wave propagation. To evaluate the effect of uncertainty in delamination detection, we employ a time domain spectral finite element (tSFEM) scheme where wave propagation is modeled using higher-order interpolation with shape function have spectral convergence properties. A laminated composite beam with layer-wise placement of delamination is considered in the simulation. Scattering due to the presence of delamination is analyzed. For a single delamination, two identical waveforms are created at the two fronts of the delamination, whereas waves in the two sub-laminates create two independent waveforms with different wavelengths. Scattering due to multiple delaminations in composite beam is studied.

Time-Instant Sampling Based Encoding of Time-Varying Acoustic Spectrum

The inner ear has been shown to characterize an acoustic stimuli by transducing fluid motion in the inner ear to mechanical bending of stereocilia on the inner hair cells (IHCs). The excitation motion/energy transferred to an IHC is dependent on the frequency spectrum of the acoustic stimuli, and the spatial location of the IHC along the length of the basilar membrane (BM). Subsequently, the afferent auditory nerve fiber (ANF) bundle samples the encoded waveform in the IHCs by synapsing with them. In this work we focus on sampling of information by afferent ANFs from the IHCs, and show computationally that sampling at specific time instants is sufficient for decoding of time-varying acoustic spectrum embedded in the acoustic stimuli. The approach is based on sampling the signal at its zero-crossings and higher-order derivative zero-crossings. We show results of the approach on time-varying acoustic spectrum estimation from cricket call signal recording. The framework gives a time-domain and non-spatial processing perspective to auditory signal processing. The approach works on the full band signal, and is devoid of modeling any bandpass filtering mimicking the BM action. Instead, we motivate the approach from the perspective of event-triggered sampling by afferent ANFs on the stimuli encoded in the IHCs. Though the approach gives acoustic spectrum estimation but it is shallow on its complete understanding for plausible bio-mechanical replication with current mammalian auditory mechanics insights.

Simple lattice Boltzmann model for traffic flows

A lattice Boltzmann model with 5-bit lattice for traffic flows is proposed. Using the Chapman-Enskog expansion and multi-scale technique, we obtain the higher-order moments of equilibrium distribution function. A simple traffic light problem is simulated by using the present lattice Boltzmann model, and the result agrees well with analytical solution.

A new hardening law for strain gradient plasticity

A new hardening law of the strain gradient theory is proposed in this paper, which retains the essential structure of the incremental version of conventional J(2) deformation theory and obeys thermodynamic restrictions. The key feature of the new proposal is that the term of strain gradient plasticity is represented as an internal variable to increase the tangent modulus. This feature which is in contrast to several proposed theories, allows the problem of incremental equilibrium equations to be stated without higher-order stress, higher-order strain rates or extra boundary conditions. The general idea is presented and compared with the theory given by Fleck and Hutchinson (Adv. in Appl. Mech. (1997) 295). The new hardening law is demonstrated by two experimental tests i.e. thin wire torsion and ultra-thin beam bending tests. The present theoretical results agree well with the experiment results.

Crack Tip Field and J-Integral with Strain Gradient Effect

The mode I plane strain crack tip field with strain gradient effects is presented in this paper based on a simplified strain gradient theory within the framework proposed by Acharya and Bassani. The theory retains the essential structure of the incremental version of the conventional J_2 deformation theory No higher-order stress is introduced and no extra boundary value conditions beyond the conventional ones are required. The strain gradient effects are considered in the constitutive relation only through the instantaneous tangent modulus. The strain gradient measures are included into the tangent modulus as internal parameters. Therefore the boundary value problem is the same as that in the conventional theory Two typical crack Problems are studied: (a) the crack tip field under the small scale yielding condition induced by a linear elastic mode-I K-field and (b) the complete field for a compact tension specimen. The calculated results clearly show that the stress level near the crack tip with strain gradient effects is considerable higher than that in the classical theory The singularity of the strain field near the crack tip is nearly equal to the square-root singularity and the singularity of the stress field is slightly greater than it. Consequently, the J-integral is no longer path independent and increases monotonically as the radius of the calculated circular contour decreases.

A closure theory of intermittency of turbulence

The variational approach to the closure problem of turbulence theory, proposed in an earlier article [Phys. Fluids 26, 2098 (1983); 27, 2229 (1984)], is extended to evaluate the flatness factor, which indicates the degree of intermittency of turbulence. Since the flatness factor is related to the fourth moment of a turbulent velocity field, the corresponding higher-order terms in the perturbation solution of the Liouville equation have to be considered. Most closure methods discard these higher-order terms and fail to explain the intermittency phenomenon. The computed flatness factor of the idealized model of infinite isotropic turbulence ranges from 9 to 15 and has the same order of magnitude as the experimental data of real turbulent flows. The intermittency phenomenon does not necessarily negate the Kolmogorov k−5/3 inertial range spectrum. The Kolmogorov k−5/3 law and the high degree of intermittency can coexist as two consistent consequences of the closure theory of turbulence. The Kolmogorov 1941 theory [J. Fluid Mech. 62, 305 (1974)] cannot be disqualified merely because the energy dissipation rate fluctuates.

摄动有限体积法重构近似高精度的意义

研讨有限体积(FV)方法重构近似高精度的作用问题．FV方法中积分近似采用中点规则为二阶精度时，重构近似高精度(精度高于二阶)的意义和作用是一个有争议的问题．利用数值摄动技术"。0构造了标量输运方程的积分近似为二阶精度、重构近似为任意阶精度的迎风型和中心型摄动有限体积(PFV)格式．迎风 PFV格式无条件满足对流有界准则(CBC)，中心型PFV格式为正型格式，两者均不会产生数值振荡解．利用 PFV格式求解模型方程的数值结果表明：与一阶迎风和二阶中心格式相比，PFV格式精度高、对解的问断分辨率高、稳定性好、雷诺数的适用范围大，数值地"证实"重构近似高精度和PFV格式的实际意义和好处．

Numerical-Value Perturbation Method with Application of Solving Convective-Diffusion Integral Equation

The convective--diffusion equation is of primary importance in such fields as fluid dynamics and heat transfer hi the numerical methods solving the convective-diffusion equation, the finite volume method can use conveniently diversified grids (structured and unstructured grids) and is suitable for very complex geometry The disadvantage of FV methods compared to the finite difference method is that FV-methods of order higher than second are more difficult to develop in three-dimensional cases. The second-order central scheme (2cs) offers a good compromise among accuracy, simplicity and efficiency, however, it will produce oscillatory solutions when the grid Reynolds numbers are large and then very fine grids are required to obtain accurate solution. The simplest first-order upwind (IUW) scheme satisfies the convective boundedness criteria, however. Its numerical diffusion is large. The power-law scheme, QMCK and second-order upwind (2UW) schemes are also often used in some commercial codes. Their numerical accurate are roughly consistent with that of ZCS. Therefore, it is meaningful to offer higher-accurate three point FV scheme. In this paper, the numerical-value perturbational method suggested by Zhi Gao is used to develop an upwind and mixed FV scheme using any higher-order interpolation and second-order integration approximations, which is called perturbational finite volume (PFV) scheme. The PFV scheme uses the least nodes similar to the standard three-point schemes, namely, the number of the nodes needed equals to unity plus the face-number of the control volume. For instanc6, in the two-dimensional (2-D) case, only four nodes for the triangle grids and five nodes for the Cartesian grids are utilized, respectively. The PFV scheme is applied on a number of 1-D problems, 2~Dand 3-D flow model equations. Comparing with other standard three-point schemes, The PFV scheme has much smaller numerical diffusion than the first-order upwind (IUW) scheme, its numerical accuracy are also higher than the second-order central scheme (2CS), the power-law scheme (PLS), the QUICK scheme and the second-order upwind(ZUW) scheme.

力学2000

本书收录关于力学领域的论文301篇。内容包括：回顾20世纪力学在中国的发展，描绘了2000年中国和世界在力学各主要领域的发展现状；展望力学在21世纪的发展方向，探论新世纪中可能面临的新的重大力学等问题。

Nonlinear oscillations in discrete and continuous systems

The first thesis topic is a perturbation method for resonantly coupled nonlinear oscillators. By successive near-identity transformations of the original equations, one obtains new equations with simple structure that describe the long time evolution of the motion. This technique is related to two-timing in that secular terms are suppressed in the transformation equations. The method has some important advantages. Appropriate time scalings are generated naturally by the method, and don't need to be guessed as in two-timing. Furthermore, by continuing the procedure to higher order, one extends (formally) the time scale of valid approximation. Examples illustrate these claims. Using this method, we investigate resonance in conservative, non-conservative and time dependent problems. Each example is chosen to highlight a certain aspect of the method.

The second thesis topic concerns the coupling of nonlinear chemical oscillators. The first problem is the propagation of chemical waves of an oscillating reaction in a diffusive medium. Using two-timing, we derive a nonlinear equation that determines how spatial variations in the phase of the oscillations evolves in time. This result is the key to understanding the propagation of chemical waves. In particular, we use it to account for certain experimental observations on the Belusov-Zhabotinskii reaction.

Next, we analyse the interaction between a pair of coupled chemical oscillators. This time, we derive an equation for the phase shift, which measures how much the oscillators are out of phase. This result is the key to understanding M. Marek's and I. Stuchl's results on coupled reactor systems. In particular, our model accounts for synchronization and its bifurcation into rhythm splitting.

Finally, we analyse large systems of coupled chemical oscillators. Using a continuum approximation, we demonstrate mechanisms that cause auto-synchronization in such systems.

I. Exact solution of some nonlinear evolution equations. II. The similarity solution for the Korteweg-De Vries equation and the related Painleve Transcendent

In Part I, a method for finding solutions of certain diffusive dispersive nonlinear evolution equations is introduced. The method consists of a straightforward iteration procedure, applied to the equation as it stands (in most cases), which can be carried out to all terms, followed by a summation of the resulting infinite series, sometimes directly and other times in terms of traces of inverses of operators in an appropriate space.

We first illustrate our method with Burgers' and Thomas' equations, and show how it quickly leads to the Cole-Hopft transformation, which is known to linearize these equations.

We also apply this method to the Korteweg and de Vries, nonlinear (cubic) Schrödinger, Sine-Gordon, modified KdV and Boussinesq equations. In all these cases the multisoliton solutions are easily obtained and new expressions for some of them follow. More generally we show that the Marcenko integral equations, together with the inverse problem that originates them, follow naturally from our expressions.

Only solutions that are small in some sense (i.e., they tend to zero as the independent variable goes to ∞) are covered by our methods. However, by the study of the effect of writing the initial iterate u_1 = u_(1)(x,t) as a sum u_1 = ^∼/u_1 + ^≈/u_1 when we know the solution which results if u_1 = ^∼/u_1, we are led to expressions that describe the interaction of two arbitrary solutions, only one of which is small. This should not be confused with Backlund transformations and is more in the direction of performing the inverse scattering over an arbitrary “base” solution. Thus we are able to write expressions for the interaction of a cnoidal wave with a multisoliton in the case of the KdV equation; these expressions are somewhat different from the ones obtained by Wahlquist (1976). Similarly, we find multi-dark-pulse solutions and solutions describing the interaction of envelope-solitons with a uniform wave train in the case of the Schrodinger equation.

Other equations tractable by our method are presented. These include the following equations: Self-induced transparency, reduced Maxwell-Bloch, and a two-dimensional nonlinear Schrodinger. Higher order and matrix-valued equations with nonscalar dispersion functions are also presented.

In Part II, the second Painleve transcendent is treated in conjunction with the similarity solutions of the Korteweg-de Vries equat ion and the modified Korteweg-de Vries equation.