Speed of adaptation in structured populations

Adaptation of populations takes place with the occurrence and subsequent fixation of mutations that confer some selective advantage to the individuals which acquire it. For this reason, the study of the process of fixation of advantageous mutations has a long history in the population genetics literature. Particularly, the previous investigations aimed to find out the main evolutionary forces affecting the strength of natural selection in the populations. In the current work, we investigate the dynamics of fixation of beneficial mutations in a subdivided population. The subpopulations (demes) can exchange migrants among their neighbors, in a migration network which is assumed to have either a random graph or a scale-free topology. We have observed that the migration rate drastically affects the dynamics of mutation fixation, despite of the fact that the probability of fixation is invariant on the migration rate, accordingly to Maruyama's conjecture. In addition, we have noticed a topological dependence of the adaptive evolution of the population when clonal interference becomes effective.     

Effect of Incident Intensity on Films Growth in Pulsed Laser Deposition

Incident intensity, defined by the amount of particles deposited per pulse, is an important parameter in the film growth process of pulsed laser deposition （PLD）. Different from previous models, we investigate the irreversible and reversible growth processes by using a kinetic Monte Carlo method and find that island density and film morphology strongly depend on pulse intensity. At higher pulse intensities, lots of adatoms instantaneously diffuse on the substrate surface, and then nucleation easily occurs between the moving adatoms resulting in more smaller-size islands. In contrast, at the lower pulse intensities, nucleation event occurs preferentially between the single adatom and existing islands rather than forming new islands, and therefore the average island size becomes larger in this case. Additionally, our results show that substrate temperature plays an important role in film growth. In particular, it can determine the films shape and weaken the effect of pulse intensity on film growth at the lower temperatures by controlling the mobility rate of atoms. Our results can match the related theoretical and experimental results.     

Roles of quarks and gluons in the spin structure of nucleons

The spin structure of protons will be discussed by using MIT-bag model and considering constituent quarks to be combined from current quarks and gluons. It will be shown that the gluonic degrees of freedom play an important role in prediction of the recent EMC results.     

Modeling DNA beacons at the mesoscopic scale

We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free-energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.     

Statistical theory of force-induced unzipping of DNA

The unzipping transition under the influence of external force of a dsDNA molecule has been studied using the Peyrard-Bishop Hamiltonian. The critical force F_c(T) for unzipping calculated in the constant force ensemble is found to depend on the potential parameter k which measures the stiffness associated with a single strand of DNA and on D, the well depth of the on-site potential representing the strength of hydrogen bonds in a base pair. The dependence on temperature of F_c(T) is found to be (T_D - T)^1/2 (T_D being the thermal denaturation temperature) with F_c(T_D) = 0 and F_c(0) = . We used the constant extension ensemble to calculate the average force F(y) required to stretch a base pair a y distance apart. The value of F(y) needed to stretch a base pair located far away from the ends of a dsDNA molecule is found twice the value of the force needed to stretch a base pair located at one of the ends to the same distance for y 1.0 . The force F(y) in both cases is found to have a very large value for y 0.2 compared to the critical force found from the constant force ensemble to which F(y) approaches for large values of y. It is shown that the value of F(y) at the peak depends on the value of k which measures the energy barrier associated with the reduction in DNA strand rigidity as one passes from dsDNA to ssDNA and on the value of the depth of the on-site potential. The effect of defects on the position and height of the peak in the F(y) curve is investigated by replacing some of the base pairs including the one being stretched by defect base pairs. The formation and behaviour of a loop of Y shape when one of the ends base pair is stretched and a bubble of ssDNA with the shape of an eye when a base pair far from ends is stretched are investigated.     

Epitaxial Growth Without Slope Selection: Energetics,Coarsening, and Dynamic Scaling

We study a continuum model for epitaxial growth of thin films in which the slope of mound structure of film surface increases. This model is a diffusion equation for the surface height profile h which is assumed to satisfy the periodic boundary condition. The equation happens to possess a Liapunov or free-energy functional. This functional consists of the term | h|², which represents the surface diffusion, and - log (1 + | h|²), which describes the effect of kinetic asymmetry in the adatom attachment-detachment. We first prove for large time t that the interface width---the standard deviation of the height profile---is bounded above by O(t^1/2), the averaged gradient is bounded above by O(t^1/4), and the averaged energy is bounded below by O(- log t). We then consider a small coefficient ² of | h|² with = 1/L and L the linear size of the underlying system, and study the energy asymptotics in the large system limit 0. We show that global minimizers of the free-energy functional exist for each > 0, the L²-norm of the gradient of any global minimizer scales as O(1/), and the global minimum energy scales as O( log ). The existence of global energy minimizers and a scaling argument are used to construct a sequence of equilibrium solutions with different wavelengths. Finally, we apply our minimum energy estimates to derive bounds in terms of the linear system size L for the saturation interface width and the corresponding saturation time.     

Ion-beam synthesis and growth mechanism of diamond-like materials

Opposite to most other deposition methods, the dominating nucleation and growth mechanism during ion-beam deposition of energetic ions in the range between 10 eV and 10 keV occurs in a region of a few nanometers below the surface of the growing film. This process is called ‘subplantation’ – emphasizing the implantation of ions into a subsurface region. Ordering and phase formation is a result of the interaction of the deposited ions with the solid state that takes place within the short time scale of femto- and picoseconds. This extreme non-equilibrium process can result in metastable amorphous or crystalline structures. This review will present several examples of the influence of the deposition parameters on the properties of diamond-like materials synthesized using mass-selected ion-beam deposition. Furthermore, several existing models of the deposition process will be presented and critically discussed. Received: 11 November 2002 / Accepted: 12 November 2002 / Published online: 4 April 2003 RID="*" ID="*"Corresponding author. Fax: +49-551/39-4493, E-mail: carsten.ronning@phys.uni-goettingen.de     

Growth of thin Si oxide in a cyclic oxygen plasma environment below 200 °C

The growth of Si oxide by means of a cyclic radio-frequency (rf) plasma oxidation process has been explored in a low temperature range of 100-200 °C. The growth mechanism exhibits Cabrera-Mott (CM) oxidation, that is, the transport of mobile ionic species is assisted by an electric field. The low activation energy of 0.3 eV is attributed to the small size of O⁻ and the assistance of the electric field. The oxide becomes off-stoichiometric as one approaches to the exterior surface of the oxide layer.     

Surface-diffusion induced growth of ZnO nanowires

The growth rate of ZnO nanowires grown epitaxially on GaN/sapphire substrates is studied. An inverse proportional relation between diameter and length of the nanowires is observed, i.e., nanowires with smaller diameters grow faster than larger ones. This unexpected result is attributed to surface diffusion of ZnO admolecules along the sidewalls of the nanowires. In addition, the unique c-axis growth of ZnO nanowires, which does not require a catalytic particle at the tip of the growing nanowires is discussed by taking into account polarity, surface free energy, and ionicity. Activation energies of the nanowire growth are determined as well.     

Synthesis and characterization of nanostructured bimetallic films on α-Al2O3 substrates using electroless deposition

The Pt-Pd and Pd-Ag nanostructured bimetallic films on porous α-Al₂O₃ substrates are successfully synthesized by chemical deposition using lyotropic liquid crystalline templating strategy. The co-reduction of two metallic species in the presence of liquid crystalline phase by hydrazine hydrate produces hexagonal nanostructured Pt-Pd and lamellar nanostructured Pd-Ag films. Low-angle X-ray diffraction (XRD) and transmission electron microscopy (TEM) studies show the ordered nanostructure of both Pt-Pd and Pd-Ag films. The energy dispersive X-ray (EDX) and wide-angle XRD analyses of the bimetallic films have verified the coexistence and uniform distribution of constituent metallic species. By taking into account of catalytic activities, well-defined nanochannels and higher surface areas, the nanostructured bimetallic films might have application potential in microreactors.