Stochastic mechano-chemical kinetics of molecular motors: A multidisciplinary enterprise from a physicist’s perspective

A molecular motor is made of either a single macromolecule or a macromolecular complex. Just like their macroscopic counterparts, molecular motors “transduce” input energy into mechanical work. All the nano-motors considered here operate under isothermal conditions far from equilibrium. Moreover, one of the possible mechanisms of energy transduction, called Brownian ratchet, does not even have any macroscopic counterpart. But, molecular motor is not synonymous with Brownian ratchet; a large number of molecular motors execute a noisy power stroke, rather than operating as Brownian ratchet. We review not only the structural design and stochastic kinetics of individual single motors, but also their coordination, cooperation and competition as well as the assembly of multi-module motors in various intracellular kinetic processes. Although all the motors considered here execute mechanical movements, efficiency and power output are not necessarily good measures of performance of some motors. Among the intracellular nano-motors, we consider the porters, sliders and rowers, pistons and hooks, exporters, importers, packers and movers as well as those that also synthesize, manipulate and degrade “macromolecules of life”. We review mostly the quantitative models for the kinetics of these motors. We also describe several of those motor-driven intracellular stochastic processes for which quantitative models are yet to be developed. In part I, we discuss mainly the methodology and the generic models of various important classes of molecular motors. In part II, we review many specific examples emphasizing the unity of the basic mechanisms as well as diversity of operations arising from the differences in their detailed structure and kinetics. Multi-disciplinary research is presented here from the perspective of physicists.     

Inertial spin Hall effect in non-commutative space

In the present Letter the study of inertial spin current (that appears in an accelerated frame of reference) is extended to Non-Commutative (NC) space. In the Hamiltonian framework, the Dirac Hamiltonian in an accelerating frame is computed in the low energy regime by exploiting the Foldy–Wouthuysen scheme. The NC θ-effect appears from the replacement of normal products and commutators by Moyal ?-products and ?-commutators. In particular, the commutator between the external magnetic vector potential and the potential induced by acceleration becomes non-trivial. Expressions for θ-corrected inertial spin current and conductivity are derived explicitly. We have provided yet another way of experimentally measuring θ. The θ bound is obtained from the out of plane spin polarization, which is experimentally observable.     

Iron(III) amine-bis(phenolate) complexes as catalysts for the coupling of alkyl halides with aryl Grignard reagents

Catalytic cross-coupling of aryl Grignard reagents with primary and secondary alkyl halides bearing beta-hydrogens is achieved using Fe(III) amine-bis(phenolate) halide complexes.     

Micellar effect on quinquivalent vanadium ion oxidation of D‐glucose in aqueous acid media: A kinetic study

Vanadium(V) oxidation of D ‐glucose shows first‐order dependence on D ‐glucose, vanadium(V), H⁺, and HSO. These observations remain unaltered in the presence of externally added surfactants. The effect of the cationic surfactant (i.e., N‐cetylpyridinium chloride [CPC]), anionic surfactant (i.e., sodium dodecyl sulfate [SDS]), and neutral surfactant (i.e., Trion X‐100 [TX‐100]) has been studied. CPC inhibits the reactions, whereas SDS and TX‐100 accelerate the reaction to different extents. Observed effects have been explained by considering the hydrophobic and electrostatic interaction between the surfactants and reactants. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 282–286, 2008     

First-principles characterisation of the pressure-dependent elastic anisotropy of SnO2 polymorphs

Using DFT calculations, this study investigates the pressure-dependent variations of elastic anisotropy in the following SnO₂ phases: rutile-type (tetragonal; P4₂/mnm), CaCl₂-type (orthorhombic; Pnnm)-, α-PbO₂-type (orthorhombic; Pbcn)- and fluorite-type (cubic; Fm-3m). Experimentally, these polymorphs undergo sequential structural transitions from rutile-type → CaCl₂-type → α-PbO₂-type → fluorite-type with increasing pressure at 11.35, 14.69 and 58.22 GPa, respectively. We estimate the shear anisotropy (A₁ and A₃) on {1?0?0} and {0?0?1} crystallographic planes of the tetragonal phase and (A₁, A₂ and A₃) on {1?0?0}, {0?1?0} and {0?0?1} crystallographic planes of the orthorhombic phases. The rutile-type phase shows strongest shear anisotropy on the {0?0?1} planes (A₂ > 4.8), and the degree of anisotropy increases nonlinearly with pressure. In contrast, the anisotropy is almost absent on the {1?0?0} planes (ie A₁ ~ 1) irrespective of the pressure. The CaCl₂-type phase exhibits similar shear anisotropy behaviour preferentially on {0?0?1} (A₃ > 5), while A₁ and A₂ remain close to 1. The α-PbO₂-type phase shows strikingly different elastic anisotropy characterised by a reversal in anisotropy (A₃ > 1 to < 1) with increasing pressure at a threshold value of 38 GPa. We provide electronic density of states and atomic configuration to account for this pressure-dependent reversal in shear anisotropy. Our study also analyses the directional Young’s moduli for the tetragonal and orthorhombic phases as a function of pressure. Finally, we estimate the band gaps of these four SnO₂ phases as a function of pressure which are in agreement with the previous results.     

Response normalized liquid chromatography nanospray ionization mass spectrometry

The widely different LC-MS response observed for many structurally different compounds limits the use of LC-MS in full scan detection mode for quantitative determination of drugs and metabolites without using reference standard. The recently introduced nanospray ionization (NSI) technique shows comparable MS response for some compounds under non-LC-MS conditions. However, in the presence of numerous endogenous compounds commonly associated with biological samples such as urine, plasma, and bile, LC-MS is required to separate, detect, identify, and measure individual analytes. An LC-NSI-MS system was devised and the MS response obtained in this system for a variety of pharmaceutical drugs and their metabolites. The set-up involves two high-performance liquid chromatography (HPLC) systems, a chip-based NSI source and a quadrupole-time-of-flight (Q-TOF) mass spectrometer. Herein this is referred to as the response normalized-liquid chromatography NSI-MS (RNLC-NSI-MS) system. One HPLC unit performs the analytical separation, while the other unit adds solvent post-column with an exact reverse of the mobile phase composition such that the final composition entering the NSI source is isocratic throughout the entire HPLC run. The data obtained from four different structural classes of compounds [vicriviroc (VCV), desloratadine (DL), tolbutamide, and cocaine] and their metabolites indicate that by maintaining the solvent composition unchanged across the HPLC run, the influence of the solvent environment on the ionization efficiency is minimized. In comparison to responses obtained from radiochromatograms, responses from conventional LC-ESI-MS overestimated the VCV and DL responses, respectively, by 6- and 20-fold. Although VCV and DL responses obtained using LC-NSI-MS are within 2- to 6-fold from the respective radiochromatographic responses, the response normalization modification results in nearly uniform LC-NSI-MS response for all compounds evaluated.     

Thermally Stimulated Processes in a Liquid Crystal Polymer

Measurement of voltage-induced thermal depolarization current and calculation of the rate of depolarization as well as the parameters of drift mobility and conductivity of charge carriers for melt-extruded neat unreinforced grade A950 VECTRA® resin - a wholly aromatic copolyester - strongly suggest that an irreversible minor transition centered around 65°C is the primary thermal process related to molecular realignment. Changes in capacitance values with temperature also show this to be the most active temperature region. A major depolarization peak at 100°C having the characteristics of a T_g cannot be justified as due to glass transition but likely to result from molecular motions involving long range intermolecular order. The interpretation for both transitions can be supported by the mechanical response of this polymer. An important outcome of this work is the assertion that contrary to current thinking, it is the number of charge carriers and not viscosity alone that will have to be considered in future development of fast response liquid crystal displays along with the development of newer liquid crystal polymer structures.