Entropy production of a mechanically driven single oligomeric enzyme: a consequence of fluctuation theorem

In this work we have shown how an applied mechanical force affects an oligomeric enzyme kinetics in a chemiostatic condition where the statistical characteristics of random walk of the substrate molecules over a finite number of active sites of the enzyme plays important contributing factors in governing the overall rate and nonequilibrium thermodynamic properties. The analytical results are supported by the simulation of single trajectory based approach of entropy production using Gillespie’s stochastic algorithm. This microscopic numerical approach not only gives the macroscopic entropy production from the mean of the distribution of entropy production which depends on the force but also a broadening of the distribution by the applied mechanical force, a kind of power broadening. In the nonequilibrium steady state (NESS), both the mean and the variance of the distribution increases and then saturates with the rise in applied force corresponding to the situation when the net rate of product formation reaches a limiting value with an activationless transition. The effect of the system-size and force on the entropy production distribution is shown to be constrained by the detailed fluctuation theorem.     

Mono- and multi-layer adsorption of an ionic liquid on Au(110)

Ultraviolet photoelectron spectroscopy (UPS), work function measurements, low energy electron diffraction (LEED) and scanning tunnelling microscopy (STM) have been used to study the adsorption and desorption of 1-ethyl-3-methylimidazolium bis[(trifluoromethyl)sulfonyl]imide, [C(2)C(1)Im][Tf(2)N], on the (1×2) clean surface reconstruction of Au(110) in the temperature range 100-674 K. The ionic liquid adsorbed without decomposition, and desorbed without leaving any residue on the surface. For adsorption at room temperature a monolayer of strongly bound ionic liquid was formed with four interface states visible in UP spectra. STM at 100 K showed that the monolayer consisted of well-ordered rows of adsorbed ionic liquid aligned parallel to the close packed rows of surface gold atoms (the [110] direction) with a separation of ×2 (the same as the clean surface reconstruction) between the rows in the orthogonal [001] direction. Multilayer adsorption at room temperature occurred by droplet formation followed by smoothing of the droplets to a layered morphology with time. Heating caused multilayer desorption at temperatures in the 363-383 K range, followed by partial monolayer desorption at 548 K to produce a Au(110)-(1×3) reconstructed surface with sub-monolayer domains of ionic liquid. Desorption of the remaining ionic liquid at 600 K caused the gold surface to reconstruct back to the clean (1×2) reconstruction.     

Entropic estimate of cooperative binding of substrate on a single oligomeric enzyme: an index of cooperativity

Here we have systematically studied the cooperative binding of substrate molecules on the active sites of a single oligomeric enzyme in a chemiostatic condition. The average number of bound substrate and the net velocity of the enzyme catalyzed reaction are studied by the formulation of stochastic master equation for the cooperative binding classified here as spatial and temporal. We have estimated the entropy production for the cooperative binding schemes based on single trajectory analysis using a kinetic Monte Carlo technique. It is found that the total as well as the medium entropy production shows the same generic diagnostic signature for detecting the cooperativity, usually characterized in terms of the net velocity of the reaction. This feature is also found to be valid for the total entropy production rate at the non-equilibrium steady state. We have introduced an index of cooperativity, C, defined in terms of the ratio of the surprisals or equivalently, the stochastic system entropy associated with the fully bound state of the cooperative and non-cooperative cases. The criteria of cooperativity in terms of C is compared with that of the Hill coefficient of some relevant experimental result and gives a microscopic insight on the mechanism of cooperative binding of substrate on a single oligomeric enzyme which is usually estimated from the macroscopic reaction rate.     

Theoretical studies of electron transfer through dendrimeric architecture

We have analyzed the steady-state electron transfer rate through a bridge of dendrimeric architecture. The difference between the linear chain and the dendrimeric architecture has also been demonstrated with steady-state rate as a main observable in the coherent and incoherent regimes of interactions. It is shown that generally the rate of electron transfer in dendrimeric architecture is faster than the rate associated with their linear chain counterpart with similar kind of bonding connectivities. The rate depends upon the size of the molecule, core branching, and the nature of the coupling among the different nodes on the dendrimer molecule. Depending upon the nature of the donor and acceptor, phenomenological dephasing coefficient due to environment and the geometry of the dendrimeric architecture, the modification of electron transfer rate has been studied. In the regime of fully coherent interactions where all quantum effects are considered the rate shows a multiple inversion due to the dendrimer architecture which is neither available in the regime of incoherent interaction nor in the linear chain case in similar condition. We have discussed about the applicability of our model in metal-molecule-metal junction, photoinduced electron transfer process, and molecular conductor.     

Imaging and manipulation of the Si(100) surface by small-amplitude NC-AFM at zero and very low applied bias

We use a noncontact atomic force microscope in the qPlus configuration to investigate the structure and influence of defects on the Si(100) surface. By applying millivolt biases, simultaneous tunnel current data is acquired, providing information about the electronic properties of the surface at biases often inaccessible during conventional STM imaging, and highlighting the difference between the contrast observed in NC-AFM and tunnel current images. We also show how NC-AFM (in the absence of tunnel current) can be used to manipulate both the clean c(4 × 2) surface and dopant-related defects.     

Generalized hybrid derivative coupling model for finite nuclei

The generalized hybrid derivative coupling model has been applied to explore various ground state properties of different nuclei. In this work we have confined our calculation only to the model characterized by the hybridization parameter α = 1/4 which gives better results than the other models of the same class, as we have seen earlier, for nuclear matter calculations. The binding energy, single-particle energy spectra, density and charge radii of different doubly closed nuclei like ¹⁶O, ⁴⁰Ca, ⁴⁸Ca, ⁹⁰Zr, ¹³²Sn, ²⁰⁸Pb have been studied. The success of this model, in describing the doubly closed nuclei, motivates us to extend this calculation further in the case of open shell nuclei after incorporating the pairing interaction and using a BCS transformation. We have calculated the binding energy for such nuclei. We have also studied the isotopic shift for different Pb isotopes with respect to ²⁰⁸Pb. We have compared our results with the other standard theoretical results as well as with the experimental values. Received: 18 August 2000 / Accepted: 13 April 2001     

Novel Platinum(II) Complexes with Dipyridyl Containing Chelating Ligands and their Products with the Model Nucleobases 1‐Methylthymine and 1‐Methyluracil

The reactions of [Pt(dpma)(H₂O)₂]²⁺ (dpma = 2,2′‐dipyridylmethylamine) and [Pt(dpk)(H₂O)₂]²⁺ (dpk = 2,2′‐dipyridylketone) with the model nucleobases 1‐methylthymine (1‐MeT) and 1‐methyluracil (1‐MeU) were studied. Reaction products were characterized by ¹⁹⁵Pt NMR spectroscopy and by X‐ray structure analysis. The symmetric dpma and dpk diaqua complexes form dinuclear complexes with 1‐methylthymine, acting as secondary bridging ligand via its N3 and O4 donor atoms. [Pt₂(dpma)₂(1‐MeT)₂](ClO₄)₂ · H₂O ( 5 ) and [Pt₂(dpk)(dpk · H₂O)(1‐MeT)₂](PF₆)₂ · 4 H₂O ( 6 ) both show a head‐to‐head arrangement. Biological tests show a significant in vitro antitumor activity of [Pt(dpk)Cl₂] against the human glioma cell line U 87.     

Glycolytic Wave Patterns in a Simple Reaction-diffusion System with Inhomogeneous Influx: Dynamic Transitions

An inhomogeneous profile of chemostatted species generates a rich variety of patterns in glycolytic waves depicted in a Selkov reaction-diffusion framework here. A key role played by diffusion amplitude and symmetry in the chemostatted species profile in dictating the fate of local spatial dynamics involving periodic, quasiperiodic, and chaotic patterns and transitions among them are investigated systematically. More importantly, various dynamic transitions, including wave propagation direction changes, are illustrated in interesting situations. Besides numerical results, our analytical formulation of the amplitude equation connecting complex Ginzburg-Landau and Lambda-omega representation shed light on the phase dynamics of the system. This systematic study of the glycolytic reaction-diffusion wave is in line with previous experimental results in open spatial reactor and will provide a knowledge about the dynamics that shape and control biological information processing and related phenomena.