Fluctuations in protein synthesis from a single RNA template: Stochastic kinetics of ribosomes

Proteins are polymerized by cyclic machines called ribosomes, which use their messenger RNA (mRNA) track also as the corresponding template, and the process is called translation. We explore, in depth and detail, the stochastic nature of the translation. We compute various distributions associated with the translation process; one of them-namely, the dwell time distribution-has been measured in recent single-ribosome experiments. The form of the distribution, which fits best with our simulation data, is consistent with that extracted from the experimental data. For our computations, we use a model that captures both the mechanochemistry of each individual ribosome and their steric interactions. We also demonstrate the effects of the sequence inhomogeneities of real genes on the fluctuations and noise in translation. Finally, inspired by recent advances in the experimental techniques of manipulating single ribosomes, we make theoretical predictions on the force-velocity relation for individual ribosomes. In principle, all our predictions can be tested by carrying out in vitro experiments.

The rα structure, chemical shift anisotropy, and the abnormal orientation of methyldichlorophosphine from the NMR spectrum

NMR studies of methyldichlorophosphine have been undertaken in the nematic phase of mixed liquid crystals of opposite diamagnetic anisotropies. The rα structure is derived. The proton chemical-shift anisotropy has been determined from the studies without the use of a reference compound and without a change of experimental conditions. It is shown that the molecule orients in the liquid crystal with positive diamagnetic anisotropy in such a way that the C3 symmetry axis of the CH3P moiety is preferentially aligned perpendicular to the direction of the magnetic field, unlike other similar systems. This is interpreted in terms of the formation of a weak solvent-solute molecular complex. The heteronuclear indirect spin-spin coupling constants are determined. The sign of the two-bond JPH is found to be positive.

Constant conductance fluctuations in disordered metals

We discuss the effect of fluctuations of the random potential in directions transverse to the current flow in a modified Migdal-Kadanoff approach to probabilistic scaling of conductance with size L, in d-dimensional metallic systems. The conductance cumulants are finite and vary as Ld−1−n for n greater-or-equal, slanted 2 i.e. conductance fluctuations are constant for d = 3. The mean conductance has a non-classical correction with Image Full-size image (<1K) for d greater-or-equal, slanted 2. The form of the higher cumulants is strongly influenced by the transverse potential fluctuations and may be compared with the results of perturbative diagrammatic approaches.

Wall Shear Fluctuations in a Turbulent Boundary Layer

IN the last two decades, the instantaneous structure of a turbulent boundary layer has been examined by many in an effort to understand the dynamics of the flow. Distinct and well-defined flow patterns that seem to have great relevance to the turbulence production mechanism have been observed in the wall region.1'2 The flow near the wall is intermittent with periodic eruptions of the fluid, a phenomenon generally termed "bursting process." Earlier investigations in this field were limited to liquid flows at low speeds and the entire flowpattern was observed using flow visualization techniques.Study was later extended to boundary-layer flows in windtunnels at higher speeds and Reynolds numbers using hot-wiresignals for the analysis of the bursting phenomenon.

Coalescence of rigid droplets in a stirred dispersion-II. Band-limited force fluctuations

The coalescence of nearly rigid liquid droplets in a turbulent flow field is viewed as the drainage of a thin film of liquid under the action of a stochastic force representing the effect of turbulence. The force squeezing the drop pair is modelled as a correlated random function of time. The drops are assumed to coalesce once the film thickness becomes smaller than a critical thickness while they are regarded as separated if their distance of separation is larger than a prescribed distance. A semi-analytical solution is derived to determine the coalescence efficiency. The veracity of the solution procedure is established via a Monte-Carlo solution scheme. The model predicts a reversing trend of the dependence of the coalescence efficiency on the drop radii, the film liquid viscosity and the turbulence energy dissipation per unit mass, as the relative fluctuation increases. However, the dependence on physical parameters is weak (especially at high relative fluctuation) so that for the smallest droplets (which are nearly rigid) the coalescence efficiency may be treated as an empirical constant. The predictions of this model are compared with those of a white-noise force model. The results of this paper and those in Muralidhar and Ramkrishna (1986, Ind. Engng Chem. Fundam. 25, 554-56) suggest that dynamic drop deformation is the key factor that influences the coalescence efficiency.

Information theory and resistance fluctuations in one-dimensional disordered conductors

A novel method is proposed to treat the problem of the random resistance of a strictly one-dimensional conductor with static disorder. For the probability distribution of the transfer matrix R of the conductor we propose a distribution of maximum information entropy, constrained by the following physical requirements: (1) flux conservation, (2) time-reversal invariance, and (3) scaling with the length of the conductor of the two lowest cumulants of ω, where R=exp(iω→⋅Jbhat). The preliminary results discussed in the text are in qualitative agreement with those obtained by sophisticated microscopic theories.

A chitotetrose specific lectin from Luffa acutangula :Physico-chemical properties and the assignment of orientation of sugars in the lectin binding site

A chitooligosaccharide specific lectin (Luffa acutangula agglutinin) has been purified from the exudate of ridge gourd fruits by affinity chromatography on soybean agglutininglycopeptides coupled to Sepharose-6B. The affinity purified lectin was found homogeneous by polyacrylamide gel electrophoresis, in sodium dodecyl sulphate-polyacrylamide gels, by gel filtration on Sephadex G-100 and by sedimentation velocity experiments. The relative molecular weight of this lectin is determined to be 48,000 ± 1,000 by gel chromatography and sedimentation equilibrium experiments. The sedimentation coefficient (S20, w) was obtained to be 4·06 S. The Stokes’ radius of the protein was found to be 2·9 nm by gel filtration. In sodium dodecyl sulphate-polyacrylamide gel electrophoresis the lectin gave a molecular weight of 24,000 in the presence as well as absence of 2-mercaptoethanol. The subunits in this dimeric lectin are therefore held by non-covalent interactions alone. The lectin is not a glycoprotein and circular dichroism spectral studies indicate that this lectin has 31% α-helix and no ß-sheet. The lectin is found to bind specifically to chitooligosaccharides and the affinity of the lectin increases with increasing oligosaccharide chain length as monitored by near ultra-violetcircular dichroism and intrinsic fluorescence titration. The values of ΔG, ΔΗ and ΔS for the binding process showed a pronounced dependence on the size of the oligosaccharide. The values for both ΔΗ and ΔS show a significant increase with increase in the oligosaccharide chain length showing that the binding of higher oligomers is progressively more favoured thermodynamically than chitobiose itself. The thermodynamic data is consistent with an extended binding site in the lectin which accommodates a tetrasaccharide. Based on the thermodynamic data, blue shifts and fluorescence enhancement, spatial orientation of chitooligosaccharides in the combining site of the lectin is assigned.

On the orientation of grain boundaries in cadmium recrystallized during hot deformatio

The authors are grateful to Professor K. P. Abraham for the provision of facilities and encouragement. One of us (PRR) acknowledges the award of a National Associateship by the UGC which facilitated a short-time visit to the Indian Institute of Science.

Average Orientation of Molecules Dissolved in Nematic Liquid Crystals of Opposite Diamagnetic Anisotropies

ZLI-1167 is a ternary mixture of nematic liquid crystals with negative diamagnetic anisotropy. It has, therefore, been used as a solvent where the spinning of the samples around the vertical axis in the conventional electromagnets without destroying the orientation of the dissolved molecules is possible in NMR experiments. This results in sharp lines with widths up to 1 Hz in the spectra.1,2 In an NMR system using a superconducting magnet (where the magnetic field direction is along the axis of spinning of the sample), it is possible to use even the nematic liquid crystals with positive diamagnetic anisotropy such as N-(p'-methoxybenzylidene)-p-n-butylaniline (MBBA) or N-(p'-ethoxybenzylidene)-p-n-butylaniline (EBBA) to obtain the spectra with sample spinning with equally sharp lines.3 The orientational behaviour of the dissolved molecules as a function of relative concentrations of the two solvents is investigated and the results are reported in the present communication.

Large Low-Frequency Fluctuations in the Velocity of a Driven Vortex Lattice in a Single Crystal of 2H-NbSe2 Superconductor

The driven state of a well-ordered flux line lattice in a single crystal of 2H-NbSe2 in the time domain has revealed the presence of substantial fluctuations in velocity, with large and distinct time periods (similar to seconds). A superposition of a periodic drive in the driven vortex lattice causes distinct changes in these fluctuations. We propose that prior to the onset of the peak effect there exists a heretofore unexplored regime of coherent dynamics, with unexpected behavior in velocity fluctuations.

EPR Evidence for Premonitory Charge-Ordering Fluctuations in Hydrothermally Grown Pr0.57Ca0.41Ba0.02MnO3 Nanowires

Electron paramagnetic resonance (EPR) and magnetic properties of nanowires of Pr0.57Ca0.41Ba0.02MnO3 (PCBMO) are studied and compared with those of the bulk material. PCBMO nanowires with diameter of 80-90 nm and length of similar to 3.5 mu m were synthesized by a low reaction temperature hydrothermal method and the bulk sample was prepared following a solid-state reaction route. The samples were characterized by X-ray diffraction, scanning electron microscopy and transmission electron microscopy. The bulk PCBMO manganite exhibits charge order at 230 K along with a ferromagnetic transition at 110 K. However, superconducting quantum interference device measurements on the PCBMO nanowires show a complete `melting' of charge ordering and a ferromagnetic transition at 115 K. This result is confirmed by the EPR intensity behavior as well. However, the EPR line width, which is reflective of the spin dynamics, shows a shallow minimum for nanowires at the temperature corresponding to the charge-ordering transition, i.e., 230 K. We interpret this result as an indication of the presence of charge-ordering fluctuations in the nanowires even though the static charge order is absent, thus heralding the occurrence of charge order in the bulk sample.

Long-lived giant number fluctuations in a swarming granular nematic

Coherently moving flocks of birds, beasts, or bacteria are examples of living matter with spontaneous orientational order. How do these systems differ from thermal equilibrium systems with such liquid crystalline order? Working with a fluidized monolayer of macroscopic rods in the nematic liquid crystalline phase, we find giant number fluctuations consistent with a standard deviation growing linearly with the mean, in contrast to any situation where the central limit theorem applies. These fluctuations are long-lived, decaying only as a logarithmic function of time. This shows that flocking, coherent motion, and large-scale inhomogeneity can appear in a system in which particles do not communicate except by contact.

Generalized survival in step fluctuations

The properties of the generalized survival probability, that is, the probability of not crossing an arbitrary location R during relaxation, have been investigated experimentally (via scanning tunneling microscope observations) and numerically. The results confirm that the generalized survival probability decays exponentially with a time constant tau(s)(R). The distance dependence of the time constant is shown to be tau(s)(R)=tau(s0)exp[-R/w(T)], where w(2)(T) is the material-dependent mean-squared width of the step fluctuations. The result reveals the dependence on the physical parameters of the system inherent in the prior prediction of the time constant scaling with R/L-alpha, with L the system size and alpha the roughness exponent. The survival behavior is also analyzed using a contrasting concept, the generalized inside survival S-in(t,R), which involves fluctuations to an arbitrary location R further from the average. Numerical simulations of the inside survival probability also show an exponential time dependence, and the extracted time constant empirically shows (R/w)(lambda) behavior, with lambda varying over 0.6 to 0.8 as the sampling conditions are changed. The experimental data show similar behavior, and can be well fit with lambda=1.0 for T=300 K, and 0.5

Low-frequency resistance fluctuations in metal films under current stressing at low temperature (T<0.3Tmelting)

In this paper, we report a systematic study of low frequency 1∕fα resistance fluctuation in thin metal films (Ag on Si) at different stages of damage process when the film is subjected to high current stressing. The resistance fluctuation (noise) measurement was carried out in situ using a small ac bias that has been mixed with the dc stressing current. The experiment has been carried out as a function of temperature in the range of 150–350 K. The experiment establishes that the current stressed film, as it undergoes damage due to various migration forces, develops an additional low-frequency noise spectral power that does not have the usual 1∕f spectral shape. The magnitude of extra term has an activated temperature dependence (activation energy of ≈0.1 eV) and has a 1∕f1.5 spectral dependence. The activation energy is the same as seen from the temperature dependence of the lifetime of the film. The extra 1∕f1.5 spectral power changes the spectral shape of the noise power as the damage process progress. The extra term likely arising from diffusion starts in the early stage of the migration process during current stressing and is noticeable much before any change can be detected in simultaneous resistance measurements. The experiment carried out over a large temperature range establish a strong correlation between the evolution of the migration process in a current stressed film and the low-frequency noise component that is not a 1∕f noise.

Study of thermal fluctuations during thermal denaturation of DNA

In this paper we address the fundamental issue of temperature fluctuation during the thermal denaturation (or the unzipping of the two strands on heating) of double stranded (ds) DNA. From our experiments we observe the presence of extremely high thermal fluctuations during DNA denaturation. This thermal fluctuation is several orders higher than the thermal fluctuation at temperatures away from the denaturation temperature range. This fluctuation is absent in single stranded (ss) DNA. The magnitude of fluctuation is much higher in heteropolymeric DNA and is almost absent in short homopolymeric DNA fragments. The temperature range over which the denaturation occurs (i.e., over which the thermal fluctuation is large) depends on the length of the DNA and is largest for the longest DNA.