Properties of Soliton-Transported Bio-energy in α-Helix Protein Molecules with Three Channels

We study numerically the propagating properties of soliton-transported bio-energy excited in the α-helix protein molecules with three channels in the cases of the short-time and long-time motions and its features of collision at temperature T = 0 and biological temperature T = 300 K by the dynamic equations in the improved Davydov theory and fourth-order Runge-Kutta method, respectively. From these simulation experiments we see that the new solitons in the improved model can move without dispersion at a constant speed retaining its shape and energy in the cases of motion of both short-time or T = 0 and long time or T = 300 K and can go through each other without scattering in their collisions. In these cases its lifetime is, at least, 120 ps at 300 K, in which the soliton can travel over about 700 amino acid residues. This result is consistent with analytic result obtained by quantum perturbed theory in this model. In the meanwhile, the influences of structure disorder of α-helix protein molecules, including the inhomogeneous distribution of amino acids with different masses and fluctuations of spring constant, dipole-dipole interaction, exciton-phonon coupling constant and diagonal disorder, on the solitons are also studied by the fourth-order Runge-Kutta method. The results show that the soliton still is very robust against the structure disorders and thermal perturbation of proteins at biological temperature 300 K. Therefore we can conclude that the new soliton in the α-helix protein molecules with three channels is a possible carrier of bio-energy transport and the improved model is possibly a candidate for the mechanism of this transport.     

The Features of Infrared Absorption of the Protein Molecules in the Living System

We utilize a vibron-soliton model for amide-I vibrational quanta interacting with optical phonons to study the feature of infrared absorption of the protein molecules with finite temperatuse.The self-trapping of amide-Ik vibrational quantum results in red shift of the main peak and largely anomalous band to occur in the infrared absorption for the protein molecules.utilizing the concise model of vibron and improved theory of color centers we have given theoretically the value of red shifts of the main peak and the intensity of anomalous band in infrared absorption,respectively,the latter reduces with increasing temperature which is consistent with the experimental result.     

Vibrational Energy—Spectra and Infraned Absorption of α—Helical Protein Molecules

The quantum energy spectran,including high excited states,of vibrational amide-I or of intramolecular excitations in α-helical protein molecules,are calculated by the discrete nonlinear Schrodinger equation together with the parameters appropriate to the systems.The distribution of energy levels obtained is basically consistent with the experimental values obtained by infrared absorption and Raman scattering.Utilizing the energy spectra we explain the laser Raman spectrum from metabolically active escherichia coli and we present some further features of the infrared absorption of the protein molecules.     

Computer study of the spectral characteristics of the disperse water methane system

The interaction of water clusters that adsorbed methane molecules with infrared radiation is studied by molecular dynamics. The presence of methane molecules in the disperse water system leads to an increase in absorption and emission of infrared radiation and a strong depletion of the Raman spectrum. In this case, the reflection coefficient of a monochromatic plane electromagnetic wave increases and its frequency spectrum significantly changes. The comparison of experimental data for similar characteristics of water, methane, or their mixtures is presented.     

The theory and experiment of solute migration caused by excited state absorptions

Nonsymmetrical transition from reverse-saturable absorption (RSA) to saturable absorption (SA) caused by excited state absorption induced mass transport of the CuPcTs dissolved in dimethyl sulfoxide is observed in an open aperture Z-scan experiment with a 21-ps laser pulse. The nonsymmetrical transition from RSA to SA is ascribed neither to saturation of excited state absorption nor to thermal induced mass transport, the so-called Soret effect. In our consideration, strong nonlinear absorption causes the rapid accumulation of the non-uniform kinetic energy of the solute molecules. The non-uniform kinetic field in turn causes the migration of the solute molecules. Additionally, an energy-gradient-induced mass transport theory is presented to interpret the experimental results, and the theoretical calculations are also taken to fit our experimental results.     

Hydration effect on the electronic transport properties of oligomeric phenylene ethynylene molecular junctions

A first-principles computational method based on the hybrid density functional theory is developed to simulate the electronic transport properties of oligomeric phenylene ethynylene molecular junctions with H₂O molecules accumulated in the vicinity as recently reported by Na {\it et al.} [\wx{Nanotechnology}{18} 424001 (2007)]. The numerical results show that the hydrogen bonds between the oxygen atoms of the oligomeric phenylene ethynylene molecule and H₂O molecules result in the localisation of the molecular orbitals and lead to the lower transition peaks. The H₂O molecular chains accumulated in the vicinity of the molecular junction can not only change the electronic structure of the molecular junctions, but also open additional electronic transport pathways. The obvious influence of H₂O molecules on the electronic structure of the molecular junction and its electronic transport properties is thus demonstrated.     

Distribution of Vibrational Energy Levels of Protein Molecular Chains

The distributions of the quantum vibrational energy levels of the protein molecular chain are found by the discretely nonlinear Schoedinger equation appropriate to protein obtained from the Davydov theory.The results calculated by this method are basically consistent with the experimental values.Furthermore,the energy spectra at high excited states have also been obtained for the molecular chain which is helpful in researching the properties of infrared absoption and Raman Scattering of the protein molecules.     

Features of Motion of Soliton Transported Bio-energy in Aperiodic α-Helix Protein Molecules with Three Channels

The structure aperiodicities can influence seriously the features of motion of soliton excited in the α-helix protein molecules with three channels. We study the influence of structure aperiodicities on the features of the soliton in the improved model by numerical simulation and Runge-Kulta method. The results obtained show that the new soliton is very robust against the structure aperiodieities including large disorder in the sequence of mass of the amino acids and fluctuations of spring constant, coupling constant, dipole-dipole interactional constant, ground state energy and chain-chain interaction. However, very strong structure aperiodieities can also destroy the stability of the soliton in the α-helix protein molecules.     

Spectral-Luminescent and Lasing Properties of Aminocoumarin Derivatives in Thin Polymer Films

The absorption and fluorescence spectra and the lasing ability of aminocoumarin derivatives in thin polymer layers (0.5–0.8 μm) based on the copolymer methylmethacrylate with a methacrylic acid and the copolymer methylmethacrylate with glycidylmethacrylate formed by coating of optically transparent glass substrates have been studied. It is found that the intensity of absorption and luminescence as well as the lasing resource of coumarins are determined by the structure of the latter and by the nature of the polymer medium. Compositions based on the copolymer methylmethacrylate with glycidylmethacrylate and aminocoumarin derivatives with a fluorized methyl group at the 4th molecular position can be of interest in optical technologies (light transformers, amplifiers). __________ Translated from Zhurnal Prikladnoi Spektroskopii, Vol. 72, No. 4, pp. 464–467, July–August, 2005.     

Multi-Band Absorption Properties and Near-Field Enhancement in Mid-Infrared Based on the Interference Theory

We numerically study the multi-band absorption properties and near-field enhancement inside the microcavity based on the interference theory. The compact single unit cell consists of a gold square patch placed on the top of a metallic ground plane, separated by a dielectric layer. At the normal incidence of electromagnetic radiation, four bands of a maximum absorption of 98% are accomplished by appropriate sizes of the square patch. Furthermore, we demonstrate that the four bands, which are corresponding to the fundamental mode and higher modes of the standing wave, can be readily tuned in the mid-infrared region and associated with the near-field enhancement in the cuboid mierocavity. Since chemical and biological fingerprints of the common functional groups can be found in the mid-infrared region, we may readily tune the multi-bands of interest in the mid-infrared range and identify the molecular stretches of groups. Moreover, the proposed structure is insensitive to the polarization of the incident wave due to the complete rotational symmetry （C4 symmetry）. The unique properties of the optical metamaterial indicate that this approach is a promising strategy for surface-enhanced infrared absorption spectroscopy and for the tracking of characteristic molecular vibrational modes     

Modified Transition State Theory for Evaporation and Condensation

A modification of the transition state theory for evaporation and condensation is presented by analysing the kinetic characteristics of liquid-vapour interphase transport.In the modified transition state theory,the moving orientation of molecules is introduced into the calculation of the free volume of the activated complex.The condensation coefficients of argon at different temperatures are calculated with the modified transition state theory.The results agree well with those from molecular dynamics simulations.     

Photoacoustic spectroscopy of diamond powders and polycrystalline films

Photoacoustic spectroscopy is used to study optical absorption in diamond powders and polycrystalline films. The photoacoustic spectra of diamond powders with crystallite sizes in the range from ∼100 μm to 4 nm and diamond films grown by chemical vapor deposition (CVD) had a number of general characteristic features corresponding to the fundamental absorption edge for light with photon energies exceeding the width of the diamond band gap (∼5.4 eV) and to absorption in the visible and infrared by crystal-structure defects and the presence of non-diamond carbon. For samples of thin (∼10 μm) diamond films on silicon, the photoacoustic spectra revealed peculiarities associated with absorption in the silicon substrate of light transmitted by the diamond film. The shape of the spectral dependence of the amplitude of the photoacoustic signal in the ultraviolet indicates considerable scattering of light specularly reflected from the randomly distributed faces of the diamond crystallites both in the polycrystalline films and in the powders. The dependence of the shape of the photoacoustic spectra on the light modulation frequency allows one to estimate the thermal conductivity of the diamond films, which turns out to be significantly lower than the thermal conductivity of single-crystal diamond. Fiz. Tverd. Tela (St. Petersburg) 39, 1787–1791 (October 1997)     

Enhancement of water permeation across nanochannels by partial charges mimicked from biological channels

In biological water channel aquaporins （AQPs）, it is believed that the bipolar orientation of the single-file water molecules inside the channel blocks proton permeation but not water transport. In this paper, the water permeation and particularly the water-selective behaviour across a single-walled carbon nanotube （SWNT） with two partial charges adjacent to the wall of the SWNT are studied by molecular dynamics simulations, in which the distance between the two partial charges is varied from 0.14 nm to 0.5 nm and the charges each have a quantity of 0.5 e. The two partial charges are used to mimic the charge distribution of the conserved non-pseudoautosomal （NPA） （asparagine/proline/alanine） regions in AQPs. Compared with across the nanochannel in a system with one ＋1 ε charge, the water permeation across the nanochannel is greatly enhanced in a system with two ＋0.5 e charges when charges are close to the nanotube, i.e. the two partial charges permit more rapid water diffusion and maintain better bipolar order along the water file when the distance between the two charges and the wall of SWNT is smaller than about 0.05 nm. The bipolar orientation of the single-file water molecules is crucial for the exclusion of proton transfer. These findings may serve as guidelines for the future nanodevices by using charges to transport water and have biological implications because membrane water channels share a similar single-file water chain and positive charged region at centre and provide an insight into why two residues are necessitated in the central region of water channel protein.     

CO分子在肌红蛋白结合口袋的QM/MM动力学模拟

Myoglobin has important biological functions in storing and transporting small diatomic molecules in human body. Two possible orientations of carbon monoxide (CO) in the heme distal pocket (named as B₁ and B₂ states) of myoglobin have been experimentally indicated. In this study, ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation of CO in myoglobin was carried out to investigate the two possible B states. Our results demonstrate that the B₁ and B₂ states correspond to Fe…CO (with carbon atom closer to iron center of heme) and Fe…OC (with oxygen atom closer to Fe), by comparing with the experimental infrared spectrum. QM electrostatic polarization effect on CO brought from the protein and solvent environment is the main driving force, which anchors CO in two distinctive orientations and hinders its rotation. The calculated vibrational frequency shift between the state B₁ and B₂ is 13.1 cm^-1, which is in good agreement with experimental value of 11.5 cm^-1. This study also shows that the electric field produced by the solvent plays an important role in assisting protein functions by exerting directional electric field at the active site of the protein. From residue-based electric field decomposition, several residues were found to have most contributions to the total electric field at the CO center, including a few charged residues and three adjacent uncharged polar residues (namely, HIS64, ILE107, and PHE43). This study provides new physical insights on rational design of enzyme with higher electric field at the active site.     

Effects of Relative Orientation of Molecules on Electron Transport in Molecular Devices

Effects of relative orientation of the molecules on electron transport in molecular devices are studied by the non-equilibrium Green function method based on density functional theory. In particular, two molecular devices with planar Au7 and Ag3 clusters sandwiched between the Al（100） electrodes axe studied. In each device, two typical configurations with the clusters parallel and vertical to the electrodes are considered. It is found that the relative orientation affects the transport properties of these two devices completely differently. In the Al（100）- Au7-Al（100） device, the conductance and the current of the parallel configuration are much larger than those in the vertical configuration, while in the Al（100）-Ag3-Al（100） device, an opposite conclusion is obtained.     

Orientation of discotic and ferroelectric liquid crystals in a macroporous silicon matrix

Macroporous silicon with deep regular channels 3–4.5 μm in diameter was infiltrated with discotic and ferroelectric liquid crystals (LCs) at the temperature of the isotropic phase, and then, the system was slowly cooled to room temperature, with the liquid crystalline mesophase formed. The orientation of the LC molecules in the porous matrix was studied by FTIR spectroscopy. The alignment of LCs was ascertained by comparing the behavior of various vibrational bands of a liquid crystal introduced into the porous matrix with that for LC inside the bulk cells of planar and homeotropic alignment. The molecules of the discotic LC show a planar orientation of their column’s axis with respect to the surface of the macroporous silicon wafer; i.e., they are perpendicular to the channel axis. The long molecular axis of the ferroelectric LC is aligned with the pore walls, having homeotropic orientation with respect to the wafer surface. In a macroporous silicon matrix, both kinds of LCs show unexpected enhancement of the low-frequency vibrational bands. From Fizika Tverdogo Tela, Vol. 44, No. 6, 2002, pp. 1145–1150. Original English Text Copyright ? 2002 by Perova, Astrova, Tsvetkov, Tkachenko, Vij, Kumar. This article was submitted by the authors in English.     

Chaos game representation of functional protein sequences, and simulation and multifractal analysis of induced measures

Investigating the biological function of proteins is a key aspect of protein studies. Bioinformatic methods become important for studying the biological function of proteins. In this paper, we first give the chaos game representation (CGR) of randomly-linked functional protein sequences, then propose the use of the recurrent iterated function systems (RIFS) in fractal theory to simulate the measure based on their chaos game representations. This method helps to extract some features of functional protein sequences, and furthermore the biological functions of these proteins. Then multifractal analysis of the measures based on the CGRs of randomly-linked functional protein sequences are performed. We find that the CGRs have clear fractal patterns. The numerical results show that the RIFS can simulate the measure based on the CGR very well. The relative standard error and the estimated probability matrix in the RIFS do not depend on the order to link the functional protein sequences. The estimated probability matrices in the RIFS with different biological functions are evidently different. Hence the estimated probability matrices in the RIFS can be used to characterise the difference among linked functional protein sequences with different biological functions. From the values of the D_q curves, one sees that these functional protein sequences are not completely random. The D_q of all linked functional proteins studied are multifractal-like and sufficiently smooth for the C_q (analogous to specific heat) curves to be meaningful. Furthermore, the D_q curves of the measure \mu based on their CGRs for different orders to link the functional protein sequences are almost identical if q\geq 0. Finally, the C_q curves of all linked functional proteins resemble a classical phase transition at a critical point.     

Evolution of the structural and phase states of a Ti-6Al-4V alloy in forming submicrocrystalline structure with the use of temporary hydrogenation

The special features of the evolution of the structural and phase states of a Ti-6Al-4V alloy in forming submicrocrystalline structure with the use of temporary hydrogen treatment are studied by electron microscopy and x-ray diffraction analysis. Plastic deformation in the α + β two-phase region at 1023 K is found to initiate a complete β → α transformation in a Ti-6Al-4V-H alloy to form an α phase with lattice parameters different from those of the equilibrium α phase. Isothermal annealing at a dehydrogenation temperature of 873 K gives rise to α + β two-phase submicrocrystalline structure with a grain size of ∼ 0.3 μm. The use of nonequilibrium hydrogen release in the deformed Ti-6Al-4V-H alloy exposed to electron beams is shown to result in one-phase submicrocrystalline structure and grain refining. Possible reasons underlying the phase transformations in the alloy under study are discussed. __________ Translated from Izvestiya Vysshikh Uchebnykh Zavedenii, Fizika, No. 4, pp. 86–91, April, 2006.     

Two Possible Configurations for Silver-C60-Silver Molecular Devices and Their Conductance Characteristics

Coherent electronic transport properties of silver-C60-silver molecular junctions in different configurations are studied using hybrid density function theory. The experimentally measured current flows of （760 molecules adsorbed on the silver surface are well reproduced by theoretical calculations. It is found that the current-voltage characteristics of the molecular junctions depend strongly on the configurations of the junctions. Transmission spectra combined with density of states can help us to understand in depth the transport properties. Different kinds of electrode construction are also discussed. With the help of the calculation, two possible configurations of silver-C60-silver molecular junctions are suggested.     

Investigation of transient two-photon excited fluorescence in biological tissue

The fluorescence power from biological tissue excited by a femtosecond laser pulse compared with excitation power does not appear to obey a simple quadratic relationship given by the steady non-linear theory.A more reliable analysis is developed based on transient two-photon absorption because the response time of two-photon absorption is longer than the width of a femtosecond pulse.Good agreement is obtained between the theoretical analysis and the experimental results of fluorescence power versus excitation power.This letter offers potential value to non-linear optics in biological tissues.