T型双量子点分子Aharonov-Bohm干涉仪的电输运

利用非平衡格林函数方法, 理论研究T型双量子点分子Aharonov-Bohm (A-B)干涉仪的电荷及其自旋输运性质. 通过控制T型双量子点分子内量子点间有无耦合, 能够实现在同一电子能级位置处分别出现共振和反共振状态, 根据此性质, 能将体系设计成量子开关器件. 当将两个完全相同的T型双量子点分子分别嵌入A-B干涉仪两臂中时, 磁通取适当数值, 能够出现完全的量子相消干涉. 通过调节量子点能级、左右两电极间的偏压和Rashba自旋轨道相互作用强度, 可对体系自旋流进行调控. 关键词： 非平衡格林函数 T型双量子点分子 Aharonov-Bohm干涉仪 自旋输运     

Influence of Environmental Parameters on the Stability of the DNA Molecule

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation—dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases’ vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.     

Mapping the phase diagram of single DNA molecule force-induced melting in the presence of ethidium

When a single DNA molecule is stretched beyond its normal contour length, a force-induced melting transition is observed. Ethidium binding increases the DNA contour length, decreases the elongation upon melting, and increases the DNA melting force in a manner that is consistent with the ethidium-induced changes in duplex DNA stability known from thermal melting studies. The DNA stretching curves map out a phase diagram and critical point in the force-extension-ethidium concentration space. Intercalation occurs between alternate base pairs at low forces and between every base pair at high forces.     

Elastic rod model of a supercoiled DNA molecule

We study the elastic behaviour of a supercoiled DNA molecule. The simplest model is that of a rod-like chain, involving two elastic constants, the bending and the twist rigidities. Writing this model in terms of Euler angles, we show that the corresponding Hamiltonian is singular and needs a small distance cut-off, which is a natural length scale giving the limit of validity of the model, of the order of the double-helix pitch. The rod-like chain in the presence of the cut-off is able to reproduce quantitatively the experimentally observed effects of supercoiling on the elongation-force characteristics, in the small supercoiling regime. An exact solution of the model, using both transfer matrix techniques and its mapping to a quantum mechanics problem, allows to extract, from the experimental data, the value of the twist rigidity. We also analyse the variation of the torque and the writhe-to-twist ratio versus supercoiling, showing analytically the existence of a rather sharp crossover regime which can be related to the excitation of plectoneme-like structures. Finally we study the extension fluctuations of a stretched and supercoiled DNA molecule, both at fixed torque and at fixed supercoiling angle, and we compare the theoretical predictions to some preliminary experimental data. Received 1 April 1999 and Received in final form 4 January 2000     

Thermomechanics of DNA: theory of thermal stability under load

A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B-DNA, supercoiling, optimally stable torque, and the overstretching transition as force-induced DNA melting. Agreement with available single molecule manipulation experiments is excellent.     

DNA tertiary structure and changes in DNA supercoiling upon interaction with ethidium bromide and gyrase monitored by UV resonance Raman spectroscopy

The tertiary structure of DNA is important for many of its biological functions. In this work supercoiled and relaxed forms of purified plasmid DNA pBR322 in dilute aqueous solutions are investigated by means of UVRR spectroscopy to assess changes in B‐DNA conformation. Spectral variation in the CO and exocyclic NH₂ vibration above 1600 cm⁻¹ indicate changes in hydrogen bonding. A minor shift of the CN stretching mode of adenosine and guanosine at 1487 cm⁻¹ supports these findings. Changes in ribose conformation are visible in the spectral region 1320–1360 cm⁻¹ by vibrational coupling of the ribose pucker to the vibrations of the purine and pyrimidine bases. The intercalating phenanthridinium drug ethidium bromide is known to reduce the negative supercoiling of DNA. This change in DNA topology is reflected in variations of the UVRR marker bands of DNA identified above. Principal component analysis helped to extract the features of interest from the complex spectra of the intercalation complex. Within the bacterial cells the change in DNA topology is achieved by the action of topoisomerases. In this work, the DNA‐binding subunit GyrA of the enzyme gyrase was extracted from E. coli and applied to relaxed and supercoiled pBR322. The observed changes in the vibrational signature of the relaxed DNA in the presence of GyrA indicate a change of topology towards the supercoiled form. With already supercoiled DNA no further change in DNA topology is observed. Copyright © 2007 John Wiley & Sons, Ltd.     

Linking topology of large DNA molecules

Double helix DNA molecules, the carriers of genetic instructions in cells, are strongly affected by their topological properties. Two distinct and biologically important types of linking are associated with double helix DNAs: ‘internal’ linking of the two strands of individual double helices, and ‘external’ linking of separate double helix DNAs. The constraint of internal linking gives rise to internal torsional stress and supercoiling of circular DNAs. External linking is a likely outcome of DNA replication, and must be eliminated by the cell in order to separate duplicated DNAs. I outline some of the physics and biology connected with both internal and external linking.     

Infrared spectra and stability of CO and H2O sorption over Ag-exchanged ZSM-5 zeolite: DFT study

The infrared spectra and stability of CO and H₂O sorption over Ag-exchanged ZSM-5 zeolite were investigated by using density function theory (DFT). The changes of NBO charge show that the electron transfers from CO molecule to the Ag⁺ cation to form an σ-bond, and it accompanies by the back donation of d-electrons from Ag⁺ cation to the CO (π*) orbital as one and two CO molecules are adsorbed on Ag-ZSM-5. The free energy changes ΔG, −5.55 kcal/mol and 6.52 kcal/mol for one and two CO molecules, illustrate that the Ag⁺(CO)₂ complex is unstable at the room temperature. The vibration frequency of C-O stretching of one CO molecule bonded to Ag⁺ ion at 2211 cm⁻¹ is in good agreement with the experimental results. The calculated C-O symmetric and antisymmetric stretching frequencies in the Ag⁺(CO)₂ complex shift to 2231 cm⁻¹ and 2205 cm⁻¹ when the second CO molecule is adsorbed. The calculated C-O stretching frequency in CO-Ag-ZSM-5-H₂O complex shifts to 2199 cm⁻¹, the symmetric and antisymmetric O-H stretching frequencies are 3390 cm⁻¹ and 3869 cm⁻¹, respectively. The Gibbs free energy change (ΔGH₂O) is −6.58 kcal/mol as a H₂O molecule is adsorbed on CO-Ag-ZSM-5 complex at 298 K. The results show that CO-Ag-ZSM-5-H₂O complex is more stable at room temperature.     

Analytical description of extension, torque, and supercoiling radius of a stretched twisted DNA

We study the mixture of extended and supercoiled DNA that occurs in a twisted DNA molecule under tension. Closed-form asymptotic solutions for the supercoiling radius, extension, and torque of the molecule are obtained in the high-force limit where electrostatic and elastic effects dominate. We demonstrate that experimental data obey the extension and torque scaling laws apparent in our formulas, in the regime where thermal fluctuation effects are quenched by applied force.     

The adsorption of cyclic hydrocarbons on Ru(001): II. Cyclohexane

The adsorption of cyclohexane on Ru(001) at 90 K has been investigated by thermal desorption mass spectrometry, EELS, UV photoemission and LEED. Thermal desorption indicates the adsorption of the undissociated molecule first in a chemisorbed monolayer (T_d = 200 K) with subsequent formation of multilayers (T_d = 165 K) at higher exposures. The vibrational spectrum obtained by EELS is characterized by a frequency shift of the C-H stretching mode from 2920 cm^?1 (multilayer) to 2560 cm^?1 for the chemisorbed monolayer. Off-specular EELS data indicate two different electron scattering mechanisms for the C-H stretching mode. Whereas for the C-H stretching mode of the multilayer, large angle electron impact scattering is observed, the C-H soft-mode of the monolayer is largely due to small angle dipolar scattering. The He I photoelectron spectra of cyclohexane multilayers are characteristic of the undissociated molecule. A new assignment of C(2s) and the lowest C(2p) level, based on a comparison with benzene, shows that the chemisorbed monolayer is characterized by the absence of emission or broadening of the 2a_1u level. This is attributed to C_3v symmetry of the chemisorbed layer and to a possible interaction of the 2a_Iu orbital with the metal surface.     

Mechanically controlled DNA extrusion from a palindromic sequence by single molecule micromanipulation

A magnetic tweezers setup is used to control both the stretching force and the relative linking number DeltaLk of a palindromic DNA molecule. We show here, in absence of divalent ions, that twisting negatively the molecule while stretching it at approximately 1 pN induces the formation of a cruciform DNA structure. Furthermore, once the cruciform DNA structure is formed, the extrusion of several kilo-base pairs of palindromic DNA sequence is directly and reversibly controlled by varying DeltaLk. Indeed the branch point behaves as a nanomechanical gear that links rotation with translation, a feature related to the helicity of DNA. We obtain experimentally a very good linear relationship between the extension of the molecule and DeltaLk. We use then this experiment to obtain a precise measurement of the pitch of B-DNA in solution: 3.61 +/- 0.03 nm/turn.     

Biophysical characterization of DNA binding from single molecule force measurements

Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.     

Elastic response of single DNA molecules exhibits a reentrant collapsing transition

We measured the elastic response of single DNA molecules at various concentrations of the trivalent cation, spermidine. When added spermidine caused the DNA to collapse, the force-extension curves showed either plateaus or stick-release patterns depending on the concentration. The periodic stick-release response determines a characteristic length, which may reflect toroidal supercoiling. At high concentrations of spermidine, we observed the reelongation of single molecules of collapsed DNA. Thus condensation occurs between lower and upper critical concentrations, verifying that the transition is reentrant as theoretically predicted.     

CALCULATIONS OF STRETCHING VIBRATIONAL ENERGY LEVELS OF THE CH3I MOLECULE BY A NONLINEAR MODEL

A nonlinear model, i.e. the quantized discrete self-trapping equation, is applied to calculate the highly excited CH stretching vibrational energy levels of the CH₃I molecule in the liquid phase at the electronic ground state up to n=8. The obtained results agree well with the experimental data and with those obtained from local mode model calculations. We note that the dominant feature of the methyl CH stretching vibrational energy levels of the CH₃I molecule is a pattern of local mode pairs. When n≥7, all the vibrational energy of the CH₃ group can nearly be localized on a single CH bond.     

The infrared spectrum of methylenimine

Eleven isotopic species of methylenimine have been prepared by the mercury-arc photolysis of methyl azide isolated in argon, nitrogen, and carbon dioxide matrices at 4 and at 14 K. Sufficient concentrations of methylenimine were obtained for identification of all of the vibrational fundamentals except the NH stretching mode. Using a recent ab initio structural calculation for this molecule, it has been possible to derive a set of valence-force potential constants which provide a satisfactory fit to all of the infrared spectroscopic data. The magnitude of the carbon-nitrogen stretching force constant is appropriate for a double bond. The temperature dependence of the thermodynamic properties of methylenimine has also been calculated.     

REMPI and IR-UV double resonance spectroscopy of 3-aminophenol·(NH3)1 cluster in the gas phase

The electronic and geometric structures of the cluster consisting of 3-aminophenol (3AP) and one ammonia molecule were investigated using resonance-enhanced multiphoton ionization and IR-UV double resonance spectroscopy in the gas phase. Between the cis and trans isomers found for the bare 3AP molecule, only trans isomer was found for 3AP·(NH₃)₁. It was found that complete quenching of the excited state of cis isomer, e.g. by conformer-specific excited state hydrogen transfer reaction, does not seem to occur, but that efficient conformational cooling drives the ground state population into the most stable trans isomer. The 0-0 band of the trans-3AP·(NH₃)₁ at 34 409 cm⁻¹ is red-shifted by 68 cm⁻¹ from that of the trans-3AP at 34 477 cm⁻¹. The IR depletion spectrum shows that the OH stretching vibration (3296 cm⁻¹) is red-shifted by 362 cm⁻¹ from that of the bare molecule. The large red-shift in OH frequency, combined with MP2 calculation, reveals that the structure of the cluster is the one with the nitrogen atom of ammonia bound to the hydroxyl hydrogen of aminophenol.     

On the study of the vibrational energy levels of Arsine molecule

We compare two formalisms applied to the vibrational modes of the molecule of AsH₃ of C_3v molecular symmetry group. Indeed, the close stretching modes of this molecule may be considered as those of a three-dimensional oscillator whereas the bending modes may be considered either as a one-dimensional oscillator of symmetry A₁ and a two-dimensional oscillator of symmetry E or as an approximate three-dimensional oscillator. So, we have applied the U(p + 1) formalism to the both stretching and bending modes and introduced coupling terms acting on an appropriate coupled vibrational basis through a local mode formalism. We have then compared the result of our fitting with those obtained with the coupling of a local mode formalism adapted to the stretching vibrations with a normal mode formalism for the bending ones. Finally we compare our results with other methods recently proposed in the literature.     

The vibration-rotation problem in triatomic molecules allowing for two large-amplitude stretching vibrations

An expression for the Hamiltonian of a vibration-rotating triatomic molecule is derived, using two curvilinear stretching coordinates ?₁ and ?₃ and one rectilinear bending coordinate S₂, in such a way that the Hamiltonian obtained is applicable to any bent triatomic molecule and allows for large displacements along the stretching coordinates. From this, a zeroth-order Hamiltonian H_s⁰ (?₁, ?₃) is obtained, describing the energy levels associated with the two stretching vibrations ν₁ and ν₃. The vibrational energy levels (v₁, v₃^even) of an XY₂ molecule having unequal bond lengths at equilibrium are then calculated. The kinetic energy T₀ (?₁, ?₃) of the Hamiltonian effectively takes into account the two large-amplitude motions in ν₁ and ν₃ together with their interaction. A model calculation is described for a bent XY₂ molecule (SO₂ in its ¹A′ (¹B₂) excited state) in which the ν₃ oscillation occurs in a double-minimum potential. Coupling by kinetic energy terms in the Hamiltonian turns out to be very small in this example.     

Ashkin-Teller Formalism for Elastic Response of DNA Molecule to External Force and Torque

We propose an Ashkin-Teller-like model for elastic response of DNA molecule to external force and torque. The base-stacking interaction is described in a simple and uniform way. We obtain the phase diagram of dsDNA, and in particular, the transition from 13 form to the S state induced by stretching and twisting. The elastic response of the ssDNA is presented also in a unified formalism. The close relation of dsDNA molecule structure with elastic response is shown clearly. The calculated folding angle of the dsDNA molecule is 59.2°.