Polaron Crossover in Molecular Solids

An analytical variational method is applied to the molecular Holstein Hamiltonian in which the dispersive features of the dimension dependent phonon spectrum are taken into account by a force constant approach. The crossover between a large and a small size polaron is monitored, in one, two and three dimensions and for different values of the adiabatic parameter, through the behavior of the effective mass as a function of the electron-phonon coupling. By increasing the strength of the inter-molecular forces the crossover becomes smoother and occurs at higher {\it e-ph} couplings. These effects are more evident in three dimensions. We show that our Modified Lang-Firsov method starts to capture the occurence of a polaron self-trapping transition when the electron energies become of order of the phonon energies. The self-trapping event persists in the fully adiabatic regime. At the crossover we estimate polaron effective masses of order $\sim 5 - 40$ times the bare band mass according to dimensionality and value of the adiabatic parameter. Modified Lang-Firsov polaron masses are substantially reduced in two and three dimensions. There is no self-trapping in the antiadiabatic regime.Comment: To be published in J.Phys.:Condensed Matte

Mass enhancement in narrow band systems

A perturbative study of the Holstein Molecular Crystal Model which accounts for lattice structure and dimensionality effects is presented. Antiadiabatic conditions peculiar of narrow band materials and an intermediate to strong electron-phonon coupling are assumed. The polaron effective mass depends crucially in all dimensions on the intermolecular coupling strengths which also affect the size of the lattice deformation associated with the small polaron formation.Comment: Istituto Nazionale di Fisica della Materia - Dipartimento di Matematica e Fisica, Istituto Nazionale di Fisica della Materia Universita' di Camerino, 62032 Camerino, Ital

Path Integral Method for DNA Denaturation

The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the second law of thermodynamics. The number of paths contributing to the partition function strongly increases around and above a specific temperature $T^*_c$ whereas the fraction of unbound base pairs grows continuosly around and above $T^*_c$. The latter is identified with the denaturation temperature. Thus, the separation of the two complementary strands appears as a highly cooperative phenomenon displaying a smooth crossover versus $T$. The thermodynamical properties have been computed in a large temperature range by varying the size of the path ensemble at the lower bound of the range. No significant physical dependence on the system size has been envisaged. The entropy grows continuosly versus $T$ while the specific heat displays a remarkable peak at $T^*_c$. The location of the peak versus $T$ varies with the stiffness of the anharmonic stacking interaction along the strand. The presented results suggest that denaturation in homogeneous DNA has the features of a second order phase transition. The method accounts for the cooperative behavior of a very large number of degrees of freedom while the computation time is kept within a reasonable limit.Comment: Physical Review E 2009 in pres

Helix untwisting and bubble formation in circular DNA

The base pair fluctuations and helix untwisting are examined for a circular molecule. A realistic mesoscopic model including twisting degrees of freedom and bending of the molecular axis is proposed. The computational method, based on path integral techniques, simulates a distribution of topoisomers with various twist numbers and finds the energetically most favorable molecular conformation as a function of temperature. The method can predict helical repeat, openings loci and bubble sizes for specific sequences in a broad temperature range. Some results are presented for a short DNA circle recently identified in mammalian cells.Comment: The Journal of Chemical Physics, vol. 138 (2013), in pres

Polaron self-trapping in a honeycomb net

Small polaron behavior in a two dimensional honeycomb net is studied by applying the strong coupling perturbative method to the Holstein molecular crystal model. We find that small optical polarons can be mobile also if the electrons are strongly coupled to the lattice. Before the polarons localize and become very heavy, there is infact a window of {\it e-ph} couplings in which the polarons are small and have masses of order $\simeq 5 - 50$ times the bare band mass according to the value of the adiabaticity parameter. The 2D honeycomb net favors the mobility of small optical polarons in comparison with the square lattice.Comment: 6 pages, 3 figures, to appear in J.Phys.:Condensed Matter {PACS: 63.10.+a, 63.20.Dj, 71.38.+i

Parasitological prevalence of bovine trypanosomosis in the Faro and Deo division valley of the Adamaoua plateau, Cameroon

A cross sectional survey to determine the distribution and prevalence of trypanosomosis was conducted in the Faro and Deo division valley, on the Adamaoua Plateau in Cameroon. A total of 334 adult cattle from 5 sedentary herds were examined in 5 villages. Dark field buffy coat method, as well as stained thin blood film examination and packed cell volume (PCV) evaluation were the diagnostic techniques used. The overall prevalence of bovine trypanosomosis in the area was 23%. Among the positive animals, 44 (57.1%), 26 (33.8%), 5 (6.5%) and 2 (2.6%) were due to Trypanosoma congolense, Trypanosoma brucei, Trypanosoma vivax and mixed infection (T. congolense and T. brucei) respectively. The mean PCV of the positive and negative animals ranged between 21.1-27% and 28.2-30.1% respectively. The mean PCV of negative animals (29.1±0.7%) was significantly higher than the mean PCV of positive animals (24.2±2.5%) (P< 0.005). In view of the high risk of trypanosomosis, in the area, an integrated intervention approach to which combines the strategic application of appropriate tsetse fly control methods to reduce host fly contact and chemotherapy and chemoprophylaxis against trypanosomosis is recommended.© 2009 International Formulae Group. All rights reserved.Key words: Adamaoua, Cameroon, Cattle, Prevalence, Trypanosomosis, Tsetse

J-factors of short DNA molecules

The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair fluctuations with respect to the helix diameter are treated as path trajectories in the imaginary time path integral formalism. The partition function for the sub-ensemble of closed molecules is computed by imposing chain ends boundary conditions both on the radial fluctuations and on the angular degrees of freedom. The cyclization probability, the J-factor, proves to be highly sensitive to the stacking potential, mostly to its nonlinear parameters. We find that the J-factor generally decreases by reducing the sequence length ( N ) and, more significantly, below N = 100 base pairs. However, even for very small molecules, the J-factors remain sizeable in line with recent experimental indications. Large bending angles between adjacent base pairs and anharmonic stacking appear as the causes of the helix flexibility at short length scales.Comment: The Journal of Chemical Physics - May 2016 ; 9 page

Thermodynamic properties of Holstein polarons and the effects of disorder

The ground state and finite temperature properties of polarons are studied considering a two-site and a four-site Holstein model by exact diagonalization of the Hamiltonian. The kinetic energy, Drude weight, correlation functions involving charge and lattice deformations, and the specific heat have been evaluated as a function of electron-phonon (e-ph) coupling strength and temperature. The effects of site diagonal disorder on the above properties have been investigated. The disorder is found to suppress the kinetic energy and the Drude weight, reduces the spatial extension of the polaron, and makes the large-to-small polaron crossover smoother. Increasing temperature also plays similar role. For strong coupling the kinetic energy arises mainly from the incoherent hopping processes owing to the motion of electrons within the polaron and is almost independent of the disorder strength. From the coherent and incoherent contributions to the kinetic energy, the temperature above which the incoherent part dominates is determined as a function of e-ph coupling strength.Comment: 17 pages. 17 figure

Commentary

COMMENT ON: Journal of Neurosciences in Rural Practice 2019, v.10(1):113-118. Burr-Hole Evacuation of Chronic Subdural Hematoma: Biophysically and Evidence-Based Technique Improvement / Martin M\ue1jovsk\ufd, David Netuka, Vladim\uedr Bene\u161, Pavel Ku\u10der

Influence of Y2O3 addition on the mechanical and oxidation behaviour of carbon fibre reinforced ZrB2/SiC composites

The influence of Y2O3 addition on the microstructure, thermo-mechanical properties and oxidation resistance of carbon fibre reinforced ZrB2/SiC composites was investigated. Y2O3 reacted with oxide impurities present on the surface of ZrB2 and SiC grains and formed a liquid phase, effectively lowering the sintering temperature and allowing to reach full density at 1900 °C. The presence of a carbon source (fibres) led to additional reactions which resulted in the formation of new secondary phases such as yttrium boro-carbides. Mechanical properties were significantly enhanced compared to the un-doped composite. Further tests at high temperatures resulted in strength increase up to 700 MPa at 1500 °C which was attributed to stress relaxation. Oxidation tests carried out at 1500 °C and 1650 °C in air showed that the presence of the Y-based secondary phases enhanced the growth of ZrO2 grains, but offered limited protection to oxygen due to the lower availability of surficial SiO2 formed from SiC