The surface science of enzymes

One of the largest challenges to science in the coming years is to find the relation between enzyme structure and function. Can we predict which reactions an enzyme catalyzes from knowledge of its structure—or from its amino acid sequence? Can we use that knowledge to modify enzyme function? To solve these problems we must understand in some detail how enzymes interact with reactants from its surroundings. These interactions take place at the surface of the enzyme and the question of enzyme function can be viewed as the surface science of enzymes. In this article we discuss how to describe catalysis by enzymes, and in particular the analogies between enzyme catalyzed reactions and surface catalyzed reactions. We do this by discussing two concrete examples of reactions catalyzed both in nature (by enzymes) and in industrial reactors (by inorganic materials), and show that although analogies exist and the two kinds of catalyst can be described by similar tools, nature and human effort have come up with different solutions. This on the other hand implies that new and improved catalysts may be made by learning from nature.     

Implications of glutathione-S transferase P1 in MAPK signaling as a CRAF chaperone: In memory of Dr. Irving Listowsky

Glutathione-S transferase P1 (GSTP1) is one of the glutathione-S transferase isozymes that belong to a family of phase II metabolic isozymes. The unique feature of GSTP1 compared with other GST isozymes is its relatively high expression in malignant tissues. Thus, clinically, GSTP1 serves as a tumor marker and as a refractory factor against certain types of anticancer drugs through its primary function as a detoxifying enzyme. Additionally, recent studies have identified a chaperone activity of GSTP1 involved in the regulation the function of various intracellular proteins, including factors of the growth signaling pathway. In this review, we will first describe the function of GSTP1 and then extend the details onto its role in the mitogen-activated protein kinase signal pathway, referring to the results of our recent study that proposed a novel autocrine signal loop formed by the CRAF/GSTP1 complex in mutated KRAS and BRAF cancers. Finally, the possibilities of new therapeutic approaches for these cancers by targeting this complex will be discussed.     

Wall-Crossing,Free Fermions and Crystal Melting

We describe wall-crossing for local, toric Calabi-Yau manifolds without compact four-cycles, in terms of free fermions, vertex operators, and crystal melting. Firstly, to each such manifold we associate two states in the free fermion Hilbert space. The overlap of these states reproduces the BPS partition function corresponding to the non-commutative Donaldson-Thomas invariants, given by the modulus square of the topological string partition function. Secondly, we introduce the wall-crossing operators which represent crossing the walls of marginal stability associated to changes of the B-field through each two-cycle in the manifold. BPS partition functions in non-trivial chambers are given by the expectation values of these operators. Thirdly, we discuss crystal interpretation of such correlators for this whole class of manifolds. We describe evolution of these crystals upon a change of the moduli, and find crystal interpretation of the flop transition and the DT/PT transition. The crystals which we find generalize and unify various other Calabi-Yau crystal models which appeared in literature in recent years.     

On the incorporation of cubic and hexagonal interfacial energy anisotropy in phase field models using higher order tensor terms

In this paper, we show how to incorporate cubic and hexagonal anisotropies in interfacial energies in phase field models; this incorporation is achieved by including up to sixth rank tensor terms in the free energy expansion, assuming that the free energy is only a function of coarse-grained composition, its gradient, curvature and aberration. We derive the number of non-zero and independent components of these tensors. Further, by demanding that the resultant interfacial energy is positive definite for inclusion of each of the tensor terms individually, we identify the constraints imposed on the independent components of these tensors. The existing results in the invariant group theory literature can be used to simplify the process of construction of some (but not all) of the higher order tensors. Finally, we derive the relevant phase field evolution equations and describe some preliminary results from our 1D simulations.     

力和扩散机理下外延形貌的演化分析

本文提出了一个新的基于扩散界面的相场模型来描述外延生长中岛的形核、生长及熟化过程. 该模型同时考虑了弹性场、表面能、沉积、扩散、解吸和能量势垒等热力学及动力学过程对表面纳米形貌的影响. 采用经典的BCF模型来描述生长中的扩散形核过程, 而采用一个新的包含弹性应变能的自由能函数, 通过变分得到一个描述多层岛生长的相场方程, 该方法可以有效地描述外延生长中复杂的外延形貌. 采用有限差分格式对非线性耦合方程组进行求解. 数值结果显示, 该模型可以真实地再现外延生长中多层岛结构(即山丘状形貌)的演化过程, 模拟结果与已有实验结果一致. 同时模拟了生长过程中随外延形貌演化而形成的复杂生长应力, 研究表明, 在生长过程中, 岛中存在着复杂的应力分布, 且在岛边界处应力达到局部最大, 这与实验结果定性一致. 此外, 本文的重要发现是, 外延生长中的应力演化明显地影响原子的扩散过程, 当应力存在时, 外延结构变化较无弹性场时变快. 该项研究对理解外延生长中各物理机理的协同作用有重要的指导意义.     

Asymptotic Behavior for Rayleigh Problem Based on Kinetic Theory

We investigate the dynamics of the gas bounded by an infinite flat plate which is initially in equilibrium and set at some instant impulsively into uniform motion in its own plane. We use the Boltzmann equation to describe intermolecular collisions and assume the diffuse reflection to describe the interaction of the gas with the boundary. The Mach number of the plate is assumed to be small so that we can linearize the Boltzmann equation as well as the boundary condition. We show that the asymptotic behavior of the gas represents a perturbation to the free molecular gas when the time is much less than the mean free time. On the other hand, if the time is much greater than the mean free time, we show that the gas dynamics is governed by the linearized Navier–Stokes equation with a slip flow on the boundary and establish a boundary layer correction with thickness of the order of the mean free path. We also establish the singularity of velocity distribution function along the particle trajectory near the boundary.     

Tracking enzymatic steps of DNA topoisomerases using single-molecule micromanipulation

In this article, we describe single-molecule assays using magnetic traps and we applied these assays to topoisomerase enzymes which unwind and disentangle DNA molecules. First, the elasticity of single DNA molecule is characterized using the magnetic trap. We show that a twisting constraint may be easily applied and that its effect upon DNA may be measured accurately. Then we describe how the topoisomerase activity may be observed at the single-molecule level giving direct access to the important biological parameters of the enzyme such as velocity and processivity. Furthermore, individual cycles of unwinding can be observed in real time. This permits an accurate characterization of the enzyme's biochemical cycle. The data treatment required to identify and analyze individual topoisomerization cycles will be presented in detail. This analysis is applicable to a wide variety of molecular motors. To cite this article: T.R. Strick et al., C. R. Physique 3 (2002) 595–618.     

周期受击陀螺系统波函数的分形

研究了周期受击陀螺系统波函数的分形. 发现在打击强度系数较弱时 (即≤ 1时), 相空间是规则的, 分形维接近于1; 随着打击强度系数的增大, 相空间开始变得混沌, 分形维也随之增大; 当打击强度系数达到6时, 相空间完全混沌, 分形维将达到最大值, 此时若继续增大打击强度系数, 分形维保持基本不变. 关键词： 陀螺 波函数 分形维 相空间     

金属表面在反射方向产生光学二次谐波的研究(Ⅰ)

用Rudnick和Stern引入的唯象参数“a”和“b”来描述表面电流,本文推导了金属表面在反射方向产生的光学二次谐波的表达式.由此证明了:从谐波信号随入射光偏振态的变化可以直接得到关于参数“a”的信息.和过去的实验相比,这种方法能更加精确、可靠地测定“a”的数值.     

Mode oscillation and harmonic distortions associated with sinusoidal modulation of semiconductor lasers

Techniques to deal with Feshbach resonances are applied to describe resonant light scattering off one dimensional photonic crystal slabs. Accurate expressions for scattering amplitudes, free of any fitting parameter, are obtained for isolated as well as overlapping resonances. They relate the resonance properties to the properties of the optical structure and of the incident light. For the most common case of a piecewise constant dielectric function, the calculations can be carried out essentially analytically. After establishing the accuracy of this approach we demonstrate its potential in the analysis of the reflection coefficients for the diverse shapes of overlapping, interacting resonances.     

Landscape of finite-temperature equilibrium behaviour of curvature-inducing proteins on a bilayer membrane explored using a linearized elastic free energy model

Using a recently developed multiscale simulation methodology, we describe the equilibrium behaviour of bilayer membranes under the influence of curvature-inducing proteins using a linearized elastic free energy model. In particular, we describe how the cooperativity associated with a multitude of protein-membrane interactions and protein diffusion on a membrane-mediated energy landscape elicits emergent behaviour in the membrane phase. Based on our model simulations, we predict that, depending on the density of membrane-bound proteins and the degree to which a single protein molecule can induce intrinsic mean curvature in the membrane, a range of membrane phase behaviour can be observed including two different modes of vesicle-bud nucleation and repressed membrane undulations. A state diagram as a function of experimentally tunable parameters to classify the underlying states is proposed.     

Landscape of finite-temperature equilibrium behaviour of curvature-inducing proteins on a bilayer membrane explored using a linearized elastic free energy model

Using a recently developed multiscale simulation methodology, we describe the equilibrium behaviour of bilayer membranes under the influence of curvature-inducing proteins using a linearized elastic free energy model. In particular, we describe how the cooperativity associated with a multitude of protein–membrane interactions and protein diffusion on a membrane-mediated energy landscape elicits emergent behaviour in the membrane phase. Based on our model simulations, we predict that, depending on the density of membrane-bound proteins and the degree to which a single protein molecule can induce intrinsic mean curvature in the membrane, a range of membrane phase behaviour can be observed including two different modes of vesicle-bud nucleation and repressed membrane undulations. A state diagram as a function of experimentally tunable parameters to classify the underlying states is proposed.     

Measurement of the spatial backscattering impulse-response at short length scales with polarized enhanced backscattering

In this Letter, we describe an easy to implement technique to measure the spatial backscattering impulse-response at length scales shorter than a transport mean free path with resolution of better than 10 μm using the enhanced backscattering phenomenon. This technique enables spectroscopic measurements throughout the visible range and sensitivity to all polarization channels. Through a combination of Monte Carlo simulations and experimental measurements of latex microspheres, we explore the various sensitivities of our technique to both intrinsic sample properties and extrinsic instrumental properties. We conclude by demonstrating the extraordinary sensitivity of our technique to the shape of the scattering phase function, including higher order shape parameters than the anisotropy factor (or first moment).     

淀粉自由基弛豫发光

为了研究淀粉自由基的变化规律,以生物光子辐射理论为基础.根据化学发光的动力学模型,建立了淀粉自由基的发光动力学方程,并根据自由基发光强度与自由基浓度的关系,通过分析得到了淀粉自由基的湮没方程,得到了光强随时间的变化函数.通过拟合发现,函数在不同温度下随时间的变化曲线与实验曲线的相关系数都在0.98以上,能很精确地刻画自由基的弛豫发光规律.     

Analog model for quantum gravity effects: phonons in random fluids

We describe an analog model for quantum gravity effects in condensed matter physics. The situation discussed is that of phonons propagating in a fluid with a random velocity wave equation. We consider that there are random fluctuations in the reciprocal of the bulk modulus of the system and study free phonons in the presence of Gaussian colored noise with zero mean. We show that, in this model, after performing the random averages over the noise function a free conventional scalar quantum field theory describing free phonons becomes a self-interacting model.     

影响X光热激波数值模拟结果的若干因素

 是否考虑康普顿散射光子的输运，用何种材料模型描述熔化、汽化和应变率效应，选用怎样的迎光自由面差分格式以及空间步长大小等因素，对X光热激波数值模拟结果都会产生重要的影响。依据热激波一维数值模拟结果，对上述各种因素的影响进行了定量分析。计算表明：在X光能谱比较软和辐照量较大时，物态方程、迎光自由面差分格式和空间步长大小对热激波的计算结果都会造成重要影响；在X光能增变硬时，康普顿散射的影响增大；在低压时，本构关系和屈服强度基本上控制了热激波的衰减规律。     

Molecular torsion: Comparison of harmonic oscillator and free rotor bases

In this work we describe a method of solving the eigenvalue problem of torsional motion in polyatomic molecules by expanding the eigenfunctions in a harmonic oscillator basis. By comparing the eigenvalues obtained with a harmonic oscillator basis and those calculated with a free rotor basis, it is found that a basis with only 5–7 oscillator functions will reproduce the low-lying energy levels for large torsional barriers with the same accuracy as a basis with about 10 free rotor functions. The method has been applied to a calculation of the barriers to internal rotation for methyl ammonium chloride. The barriers were obtained from a least squares fit of the torsional frequencies of methyl ammonium chloride and seven of its deuterated derivatives, treating the molecule as a double rotor. The method is recommended for the calculation of large rotational barriers from spectroscopic data on systems in any state of aggregation, and may therefore be useful in the testing of theoretical models.     

The inverse problem for the vocal tract: numerical methods, acoustical experiments, and speech synthesis

In this article we will describe our recent experiments on the estimation of vocal tract area functions from transient acoustical measurements at the lips. Since the theoretical basis for such measurements has been discussed in several earlier publications we will concentrate on the measurement technique and the numerical procedures used to estimate the area functions from the measurements. The two main accomplishments we will report on are (1) We are now able to make measurements and compute and display the area function about 18 times per second. Such a display, which has not been possible before, allow one to visualize the shape of one's vocal tract as one changes the position of one's articulators. This display could form the basis of a visual aid for the improvement of the speech of profoundly deaf persons. (2) We have synthesized intelligible though not yet high quality speech from several sentence-length sequences of measured area functions. To the best of our knowledge, this is the first instance of continuous speech synthesized from direct measurements of area functions.     

Exact Solutions of the Equilibrium Shape Equations in a General WLC Model for DNA Forms

In this letter,we are going to use a geometrical approach to describe the free energy of DNA structures.The exact solutions of the equilibrium shape equations in a general WLC model for DNA forms by using the Feoli's formalism [A.Feoli,et al.,Nucl.Phys.B 705(2005) 577] are studied.Then,the free energy of transition between Band Z-DNA is calculated in this formalism.