Motor proteins transporting cargos

Processive motor proteins such as kinesin and myosin-V are enzymes that use the energy of ATP hydrolysis to travel along polar cytoskeletal filaments. One of the functions of these proteins is the transport of vesicles and protein complexes that are linked to the light chains of the motors. Modeling the light chain by a linear elastic spring, and using the two-state model for one- and two-headed molecular motors, we study the influence of thermal fluctuations of the cargo on the motion of the motor-cargo complex. We solve numerically the Fokker-Planck equations of motor motion, and find that the mean velocity of the motor-cargo complex decreases monotonously as the spring becomes softer. This effect is due to the random force of thermal fluctuations of the cargo disrupting the operation of the motor. Increasing the size (thus, the friction coefficient) of the cargo also decreases the velocity. Surprisingly, we find that for a given size of the cargo, the velocity has a maximum for a certain friction of the motor. We explain this effect by the interplay between the characteristic length of thermal fluctuations of the cargo on a spring, the motor diffusion length, and the filament period. Our results may be relevant for the interpretation of single-molecule experiments with molecular motors (bead assays), where the motor motion is observed by tracking of a bead attached to the motor.     

The kinetic MC modelling of reversible pattern formation in initial stages of thin metallic film growth on crystalline substrates

The results of kinetic MC simulations of the reversible pattern formation during the adsorption of mobile metal atoms on crystalline substrates are discussed. Pattern formation, simulated for submonolayer metal coverage, is characterized in terms of the joint correlation functions for a spatial distribution of adsorbed atoms. A wide range of situations, from the almost irreversible to strongly reversible regimes, is simulated. We demonstrate that the patterns obtained are defined by a key dimensionless parameter: the ratio of the mutual attraction energy between atoms to the substrate temperature. Our ab initio calculations for the nearest Ag-Ag adsorbate atom interaction on an MgO substrate give an attraction energy as large as 1.6 eV, close to that in a free molecule. This is in contrast to the small Ag adhesion and migration energies (0.23 and 0.05 eV, respectively) on a defect-free MgO substrate.     

First-principles study of lattice dynamics of LiFePO4

Lattice dynamics of lithium iron orthophosphate (LiFePO₄) isostructural with olivine have been investigated using the first-principles calculations taking into account the on-site Coulomb interaction within the GGA + U scheme. Born effective charge tensors, phonon frequencies at the Brillouin zone center and phonon dispersion curves are calculated and analyzed. The Born effective charge tensors exhibit anisotropy, which gives a convincing evidence for the one-dimensional Li migration tunnel along the [010] direction in LiFePO₄, which has been proposed by other theoretical calculations and experimental observation. The calculated phonon frequencies at the Γ point of the Brillouin zone show good agreement with the available experimental observations.     

Vectorial representation of single- and multi-domain protein folds

We discuss a vectorial representation applicable to both single- and multi-domain protein folds. This generalized vectorial representation is essentially identical to the previously described vectorial representation for single-domain proteins folds when applied to these, but allows for the additional consistent representation of multi-domain structures. We show that the generalized vectorial representation enables the accurate analytical prediction of site-specific amino acid distributions for both single- and multi-domain protein folds, similarly as the previously described vectorial representation does for single-domain folds.     

Quantum chemical modelling of ‘green’ luminescence in self activated perovskite-type oxides

We discuss the origin of the intrinsic visible band emission of ABO₃ perovskite oxides (so-called ‘green luminescence’) which remains a topic of high interest during the last quarter of the century. We present a theoretical calculation modelling of this emission in the framework of a concept of charge transfer vibronic excitons [Phys. Solid State, 40 (1998) 834], i.e. as a result of radiative recombination of correlated (bound) self-trapped electron and hole polarons in the highly polarizable ABO₃-type matrix. The Intermediate Neglect of Differential Overlap method combined with the Large Unit Cell periodic defect model was used for quantum chemical calculations and theoretical simulation of the green emission for a series of model ABO₃ perovskites. The ‘green’ luminescence energies for PbTiO₃, SrTiO₃, BaTiO₃, KNbO₃ and KTaO₃ perovskite-type crystals agree well with those experimentally observed earlier.     

Unfolding designable structures

Among an infinite number of possible folds, nature has chosen only about 1000 distinct folds to form protein structures. Theoretical studies suggest that selected folds are intrinsically more designable than others; these selected folds are unusually stable, a property called the designability principle. In this paper we use the 2D hydrophobic-polar lattice model to classify structures according to their designability, and Langevin dynamics to account for their time evolution in the presence of shear flow. We demonstrate that, among all possible folds, the more designable ones are easier to unfold due to their large number of surface-core bonds.     

The importance of non-local shadowing for the topography evolution of a-C:H films grown by toluene based plasma enhanced chemical vapor deposition

The topography evolution of hydrogenated diamond-like carbon coatings deposited through toluene based capacitively coupled plasma enhanced chemical vapor deposition has been studied experimentally and with continuum growth models. The experimentally observed mound formation and surprisingly large growth exponents (β≈ 0.9±0.1) cannot be reproduced by familiar local stochastic differential equations that are successfully used for other thin film deposition techniques. Here we introduce a novel numerical approach to simulate a continuum growth model that takes into account non-local shadowing effects. We show that the major characteristics of the experimentally observed topography evolution can be accurately represented by this model.     

Smoothing of ultrathin silver films by transition metal seeding

The nucleation and coalescence of silver islands on coated glass was investigated by in situ measurements of the sheet resistance. Sub-monolayer amounts of niobium and other transition metals were deposited prior to the deposition of silver. It was found that in some cases, the transition metals lead to coalescence of silver at nominally thinner films with smoother topology. The smoothing or roughening effects by the presence of the transition metal can be explained by kinetically limited transition metal islands growth and oxidation, followed by defect-dominated nucleation of silver.     

Conduction transition of nano-scaled molecular wires driven by environment coupling

We propose a hybridization model to simulate a molecular wire coupling with the environmental molecules. Results reveal that the conduction transition from conducting to semiconducting depends on the coupling strength. In our simulations, the non-equilibrium Green's function method is employed to calculate the current-voltage relationship for the molecular wire through metallic contacts. Our calculations show that the band gap can be manipulated from the outside molecules coupling. Temperature dependence of the conductivity is represented in our results with strong dependence in high temperature range, which is qualitatively comparable with the experimental results of DNA. In our results, with small coupling, the current is enhanced by the exchange. On the contrary, too large a coupling results in localization of the transport carriers, leading to a semiconducting like property. We try to associate this study with the conducting property of DNA, which can be manipulated by environmental modulation.     

Effects of population mixing on the spread of SIR epidemics

We study dynamics of spread of epidemics of SIR type in a realistic spatially-explicit geographical region, Southern and Central Ontario, using census data obtained from Statistics Canada, and examine the role of population mixing in epidemic processes. Our model incorporates the random nature of disease transmission, the discreteness and heterogeneity of distribution of host population.We find that introduction of a long-range interaction destroys spatial correlations very easily if neighbourhood sizes are homogeneous. For inhomogeneous neighbourhoods, very strong long-range coupling is required to achieve a similar effect. Our work applies to the spread of influenza during a single season.