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41.
The mechanism of a protein's diffusion along a DNA segment is a subject of much current interest because of the involvement of this diffusion in numerous biological processes, including the recognition of DNA sequences and chemical modifications of DNA. In this work we present a theoretical derivation of the diffusion coefficient of a nonspecifically bound protein, assuming that the protein follows a helical track along the DNA. It is shown that, for protein-sized molecules, the principal contribution to the total translational friction comes from the curvilinear motion along the helix, and this contribution is given by 6pietaRR(oc)(2) + 8pietaR(3), where R is the protein radius, ROC is the distance of separation between the center of mass of the protein and the helical axis of DNA, and eta is the viscosity of the medium. The translational diffusion of the protein along the helical track of DNA is thus predicted to have a nearly R(-3) size dependence, not the R(-1) dependence characterizing simple translational diffusion. It is shown that this expression gives rather good estimates of the translational diffusion coefficient measured in single molecule experiments. 相似文献
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The ultrafast vibrational phase relaxation of O–H stretch in bulk water is investigated in molecular dynamics simulations. The dephasing time (T2) of the O–H stretch in bulk water calculated from the frequency fluctuation time correlation function (Cω(t)) is in the range of 70–80 femtosecond (fs), which is comparable to the characteristic timescale obtained from the vibrational echo peak shift measurements using infrared photon echo [W.P. de Boeij, M.S. Pshenichnikov, D.A. Wiersma, Ann. Rev. Phys. Chem. 49 (1998) 99]. The ultrafast decay of Cω(t) is found to be responsible for the ultrashort T2 in bulk water. Careful analysis reveals the following two interesting reasons for the ultrafast decay of Cω(t). (A) The large amplitude angular jumps of water molecules (within 30–40 fs time duration) provide a large scale contribution to the mean square vibrational frequency fluctuation and gives rise to the rapid spectral diffusion on 100 fs time scale. (B) The projected force, due to all the atoms of the solvent molecules on the oxygen (FO(t)) and hydrogen (FH(t)) atom of the O–H bond exhibit a large negative cross-correlation (NCC). We further find that this NCC is partly responsible for a weak, non-Arrhenius temperature dependence of the dephasing rate. 相似文献
45.
Das PK Banerjee D Bagchi S 《Spectrochimica acta. Part A, Molecular and biomolecular spectroscopy》2007,67(1):225-229
Electronic absorption and steady state emission properties of a hemicyanine dye [4-[4-(dimethylamino)styryl]-1-docosylpyridinium bromide], have been studied in several pure solvents and two mixed binary solvents (water+ethanol and water+acetonitrile). In pure solvents the band-width of the absorption spectrum correlates well with the Stoke's shift. In mixed aqueous solvents two different molecular forms of the solute, viz. the monomer and the dimer of the solute exists in equilibrium. Thermodynamic parameters (e.g. the Delta G degrees and Delta H degrees ) characterizing the equilibrium have been determined. While the value of Delta G degrees changes very slightly with the composition of the binary mixture, the value of Delta H degrees has been observed to depend significantly with solvent composition. 相似文献
46.
Recent optical Kerr effect experiments have revealed a power law decay of the measured signal with a temperature independent exponent at short-to-intermediate times for a number of liquid crystals in the isotropic phase near the isotropic-nematic transition and supercooled molecular liquids above the mode coupling theory critical temperature. In this work, the authors investigate the temperature dependence of short-to-intermediate time orientational relaxation in a model thermotropic liquid crystal across the isotropic-nematic transition and in a binary mixture across the supercooled liquid regime in molecular dynamics simulations. The measure of the experimentally observable optical Kerr effect signal is found to follow a power law decay at short-to-intermediate times for both systems in agreement with recent experiments. In addition, the temperature dependence of the power law exponent is found to be rather weak. As the model liquid crystalline system settles into the nematic phase upon cooling, the decay of the single-particle second-rank orientational time correlation function exhibits a pattern that is similar to what has been observed for supercooled liquids. 相似文献
47.
Synthesis of metal–organic framework (MOF) based on tetra-pyridyl porphyrin and palladium (II) salt resulted in the formation of palladium oxide nano-crystals. The palladium oxide nano-crystals were characterized by PXRD, TEM, HRTEM, ED, UV–Vis spectroscopy, DLS, SEM and AFM. A plausible mechanism for the in situ generation of nano-crystals has been proposed. 相似文献
48.
Tabassum S Al-Asbahy WM Afzal M Arjmand F Bagchi V 《Dalton transactions (Cambridge, England : 2003)》2012,41(16):4955-4964
To evaluate the biological preference of metallopeptide drugs in cancer cells, a new dinuclear copper(II) complex [Cu(2)(glygly)(2)(ppz)(H(2)O)(4)]·2H(2)O (1) (glygly = glycyl glycine anion and ppz = piperazine), was designed and synthesized as topoisomerase I inhibitor. The structural elucidation of the complex was done by elemental analysis, spectroscopic methods and single crystal X-ray diffraction. The in vitro DNA binding studies of complex 1 with CT DNA were carried out by employing different optical methods viz. UV-vis, fluorescence and circular dichroism. The molecular docking technique was also utilized to ascertain the mechanism and mode of action towards the molecular target DNA and enzymes. Complex 1 cleaves pBR322 DNA via an oxidative mechanism and strongly binds to the DNA minor groove. Furthermore, complex 1 exhibits significant inhibitory effects on the catalytic activity of topoisomerase I at a very low concentration, ~12.5 μM, in addition to its excellent SOD mimics (IC(50)~0.086 μM). 相似文献
49.
We present an analysis of membrane motion of deformable capsules and red blood cells suspended in a linear shear flow and undergoing swinging and tumbling motions using three-dimensional numerical simulations. This study is motivated by the theory of the shape-preserving cells which predicts that the direction of the membrane rotation depends on the cell orientation and reverses at every 45° inclination angle of the cell major axis with respect to the external flow direction. By considering large deformation of capsules and red blood cells, here we investigate how the shape oscillation affects the time dependence and the direction reversal of the membrane rotation. We find that the membrane tank-tread is highly time-dependent in nature and synchronized with the time-dependent deformation. The maximum and minimum of the tank-tread velocity occur at and near the minimum and maximum deformation, respectively. For the swinging capsules and red blood cells, the direction of the membrane rotation is always along the direction of the external fluid rotation; however, a direction reversal occurs during the tumbling motion in which case the membrane rotates in the direction of the external fluid rotation when the major axis is mostly in the extensional quadrant of the shear flow, and in the opposite direction when it is mostly in the compressional quadrant. Unlike the theory which predicts the direction reversal at every 45° inclination angle irrespective of the control parameters, namely, the capillary number, viscosity ratio, and asphericity, we find that the angle at which the direction reversal occurs depends on these parameters. In particular, if the tumbling motion occurs by decreasing the capillary number, the membrane rotation is in the direction of the external flow rotation in the entire extensional quadrant, but in the opposite direction in the compressional quadrant, irrespective of the specific values of the capillary number. If the tumbling motion occurs by increasing the viscosity ratio and asphericity, the angle at which the direction reversal occurs depends on the specific values of these two parameters. The spatial variation of the tank-tread velocity also is analyzed and attributed to the straining motion of the external flow. 相似文献
50.
Theoretical and computational investigations of nucleation have been plagued by the sensitivity of the phase diagram to the range of the interaction potential. As the surface tension depends strongly on the range of interaction potential and as the classical nucleation theory (CNT) predicts the free energy barrier to be directly proportional to the cube of the surface tension, one expects a strong sensitivity of nucleation barrier to the range of the potential; however, CNT leaves many aspects unexplored. We find for gas-liquid nucleation in Lennard-Jones system that on increasing the range of interaction the kinetic spinodal (KS) (where the mechanism of nucleation changes from activated to barrierless) shifts deeper into the metastable region. Therefore the system remains metastable for larger value of supersaturation and this allows one to explore the high metastable region without encountering the KS. On increasing the range of interaction, both the critical cluster size and pre-critical minima in the free energy surface of kth largest cluster, at respective kinetic spinodals, shift towards smaller cluster size. In order to separate surface tension contribution to the increase in the barrier from other non-trivial factors, we introduce a new scaling form for surface tension and use it to capture both the temperature and the interaction range dependence of surface tension. Surprisingly, we find only a weak non-trivial contribution from other factors to the free energy barrier of nucleation. 相似文献