Stochastic kinetics of ribosomes: single motor properties and collective behavior

Synthesis of protein molecules in a cell are carried out by ribosomes. A ribosome can be regarded as a molecular motor which utilizes the input chemical energy to move on a messenger RNA (mRNA) track that also serves as a template for the polymerization of the corresponding protein. The forward movement, however, is characterized by an alternating sequence of translocation and pause. Using a quantitative model, which captures the mechanochemical cycle of an individual ribosome, we derive an {\it exact} analytical expression for the distribution of its dwell times at the successive positions on the mRNA track. Inverse of the average dwell time satisfies a ``Michaelis-Menten-like'' equation and is consistent with the general formula for the average velocity of a molecular motor with an unbranched mechano-chemical cycle. Extending this formula appropriately, we also derive the exact force-velocity relation for a ribosome. Often many ribosomes simultaneously move on the same mRNA track, while each synthesizes a copy of the same protein. We extend the model of a single ribosome by incorporating steric exclusion of different individuals on the same track. We draw the phase diagram of this model of ribosome traffic in 3-dimensional spaces spanned by experimentally controllable parameters. We suggest new experimental tests of our theoretical predictions.Comment: Final published versio

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

Instability of dilute granular flow on rough slope

We study numerically the stability of granular flow on a rough slope in collisional flow regime in the two-dimension. We examine the density dependence of the flowing behavior in low density region, and demonstrate that the particle collisions stabilize the flow above a certain density in the parameter region where a single particle shows an accelerated behavior. Within this parameter regime, however, the uniform flow is only metastable and is shown to be unstable against clustering when the particle density is not high enough.Comment: 4 pages, 6 figures, submitted to J. Phys. Soc. Jpn.; Fig. 2 replaced; references added; comments added; misprints correcte

Probing the superconducting ground state of the noncentrosymmetric superconductors CaTSi3 (T = Ir, Pt) using muon-spin relaxation and rotation

The superconducting properties of CaTSi3 (where T = Pt and Ir) have been investigated using muon spectroscopy. Our muon-spin relaxation results suggest that in both these superconductors time-reversal symmetry is preserved, while muon-spin rotation data show that the temperature dependence of the superfluid density is consistent with an isotropic s-wave gap. The magnetic penetration depths and upper critical fields determined from our transverse-field muon-spin rotation spectra are found to be 448(6) and 170(6) nm, and 3800(500) and 1700(300) G, for CaPtSi3 and CaIrSi3 respectively. The superconducting coherence lengths of the two materials have also been determined and are 29(2) nm for CaPtSi3 and 44(4) nm for CaIrSi3.Comment: 6 pages, 7 figure

Anomalous transport in disordered exclusion processes with coupled particles

We consider one-dimensional asymmetric exclusion processes with a simple attractive interaction, where the distance between consecutive particles is not allowed to exceed a certain limit and investigate the consequences of this coupling on the transport properties in the presence of random-force type disorder by means of a phenomenological random trap picture. In the phase-separated steady state of the model defined on a finite ring, the properties of the density profile are studied and the exponent governing the decay of the current with the system size in the biased phase is derived. In case all consecutive particles are coupled with each other and form a closed string, the current is found to be enhanced compared to the model without coupling, while if groups of consecutive particles form finite strings, the current is reduced. The motion of a semi-infinite string entering an initially empty lattice is also studied. Here, the diffusion of the head of the string is found to be anomalous, and two phases can be distinguished, which are characterised by different functional dependences of the diffusion exponent on the bias. The obtained results are checked by numerical simulation.Comment: 20 pages, 11 figure

Two-dimensional Burgers Cellular Automaton

A two-dimensional cellular automaton(CA) associated with a two-dimensional Burgers equation is presented. The 2D Burgers equation is an integrable generalization of the well-known Burgers equation, and is transformed into a 2D diffusion equation by the Cole-Hopf transformation. The CA is derived from the 2D Burgers equation by using the ultradiscrete method, which can transform dependent variables into discrete ones. Some exact solutions of the CA, such as shock wave solutions, are studied in detail.Comment: Latex2.09, 17 pages including 7 figure

Asymmetric exclusion process with next-nearest-neighbor interaction: some comments on traffic flow and a nonequilibrium reentrance transition

We study the steady-state behavior of a driven non-equilibrium lattice gas of hard-core particles with next-nearest-neighbor interaction. We calculate the exact stationary distribution of the periodic system and for a particular line in the phase diagram of the system with open boundaries where particles can enter and leave the system. For repulsive interactions the dynamics can be interpreted as a two-speed model for traffic flow. The exact stationary distribution of the periodic continuous-time system turns out to coincide with that of the asymmetric exclusion process (ASEP) with discrete-time parallel update. However, unlike in the (single-speed) ASEP, the exact flow diagram for the two-speed model resembles in some important features the flow diagram of real traffic. The stationary phase diagram of the open system obtained from Monte Carlo simulations can be understood in terms of a shock moving through the system and an overfeeding effect at the boundaries, thus confirming theoretical predictions of a recently developed general theory of boundary-induced phase transitions. In the case of attractive interaction we observe an unexpected reentrance transition due to boundary effects.Comment: 12 pages, Revtex, 7 figure

Weakly coupled, antiparallel, totally asymmetric simple exclusion processes

We study a system composed of two parallel totally asymmetric simple exclusion processes with open boundaries, where the particles move in the two lanes in opposite directions and are allowed to jump to the other lane with rates inversely proportional to the length of the system. Stationary density profiles are determined and the phase diagram of the model is constructed in the hydrodynamic limit, by solving the differential equations describing the steady state of the system, analytically for vanishing total current and numerically for nonzero total current. The system possesses phases with a localized shock in the density profile in one of the lanes, similarly to exclusion processes endowed with nonconserving kinetics in the bulk. Besides, the system undergoes a discontinuous phase transition, where coherently moving delocalized shocks emerge in both lanes and the fluctuation of the global density is described by an unbiased random walk. This phenomenon is analogous to the phase coexistence observed at the coexistence line of the totally asymmetric simple exclusion process, however, as a consequence of the interaction between lanes, the density profiles are deformed and in the case of asymmetric lane change, the motion of the shocks is confined to a limited domain.Comment: 14 pages, 15 figures, to appear in Phys. Rev.

Micellar Aggregates of Gemini Surfactants: Monte Carlo Simulation of a Microscopic Model

We propose a "microscopic" model of gemini surfactants in aqueous solution. Carrying out extensive Monte Carlo simulations, we study the variation of the critical micellar concentration (CMC) of these model gemini surfactants with the variation of the (a) length of the spacer connecting the two hydrophilic heads, (b) length of the hydrophobic tail and (c) the bending rigidity of the hydrocarbon chains forming the spacer and the tail; some of the trends of variation are counter-intuitive but are in excellent agreement with the available experimental results. Our simulations also elucidate the dependence of the shapes of the micellar aggregates and the magnitude of the CMC on the geometrical shape and size of the surfactant molecules and the electrical charge on the hydrophilic heads

Extinction of the N=20 neutron-shell closure for 32Mg examined by direct mass measurements

The 'island of inversion' around $^{32}$Mg is one of the most important paradigm for studying the disappearance of the stabilizing 'magic' of a shell closure. We present the first Penning-trap mass measurements of the exotic nuclides $^{29-31}$Na and $^{30-34}$Mg, which allow a precise determination of the empirical shell gap for $^{32}$Mg. The new value of 1.10(3) MeV is the lowest observed shell gap for any nuclide with a canonical magic number.Comment: 6 pages, 4 figures, submitted to Physical Review