A Bayesian phylogenetic hidden Markov model for B cell receptor sequence analysis.

The human body generates a diverse set of high affinity antibodies, the soluble form of B cell receptors (BCRs), that bind to and neutralize invading pathogens. The natural development of BCRs must be understood in order to design vaccines for highly mutable pathogens such as influenza and HIV. BCR diversity is induced by naturally occurring combinatorial "V(D)J" rearrangement, mutation, and selection processes. Most current methods for BCR sequence analysis focus on separately modeling the above processes. Statistical phylogenetic methods are often used to model the mutational dynamics of BCR sequence data, but these techniques do not consider all the complexities associated with B cell diversification such as the V(D)J rearrangement process. In particular, standard phylogenetic approaches assume the DNA bases of the progenitor (or "naive") sequence arise independently and according to the same distribution, ignoring the complexities of V(D)J rearrangement. In this paper, we introduce a novel approach to Bayesian phylogenetic inference for BCR sequences that is based on a phylogenetic hidden Markov model (phylo-HMM). This technique not only integrates a naive rearrangement model with a phylogenetic model for BCR sequence evolution but also naturally accounts for uncertainty in all unobserved variables, including the phylogenetic tree, via posterior distribution sampling

An Investigation on Structural and Electrical Properties of RF-Sputtered Molybdenum Thin Film Deposited on Different Substrates

AbstractMolybdenum (Mo) is the prominent choice as the back contact for various thin film solar cells such as CIGS, CZTS and CdTe. Physical vapour deposition (PVD) technique especially sputtering process has been chosen as the foremost method to deposit Mo thin film on top of desired substrate due to ease of parametric control of growth conditions. In this paper, we reported the effect of various RF power, operating pressure as well as temperature on Mo films on top of Mo sheet and soda lime glass (SLG) deposited using RF magnetron sputtering. Uniform surface morphology was obtained as RF power, operating pressure and deposition temperature were optimised. However, at higher deposition temperature less uniform surface was observed. XRD pattern of Mo films showed two different peak of <200> and <211> in case of Mo sheet and single peak <110> in case of SLG. While peak intensity varies as deposition condition varies in case of Mo films deposited on Mo sheet. Electrical properties of Mo films on both Mo sheet and SLG were improved as RF power and deposition temperature are optimised. On the other hand, electrical properties are affected as operating pressure increased. Lower resistivity of 1.2x10-9Ω.m and 6.65x10-6Ω.m were found in case of Mo films deposited on Mo sheet and SLG. Surface roughness of 0.017 nm-19.32nm were found in case of Mo films deposited on Mo sheet and 0.002 nm-5.04nm were found in case of SLG. Roughness increased as RF power and deposition temperature increased. However, roughness decreased as operating pressure increased

Steady state, relaxation and first-passage properties of a run-and-tumble particle in one-dimension

We investigate the motion of a run-and-tumble particle (RTP) in one dimension. We find the exact probability distribution of the particle with and without diffusion on the infinite line, as well as in a finite interval. In the infinite domain, this probability distribution approaches a Gaussian form in the long-time limit, as in the case of a regular Brownian particle. At intermediate times, this distribution exhibits unexpected multi-modal forms. In a finite domain, the probability distribution reaches a steady state form with peaks at the boundaries, in contrast to a Brownian particle. We also study the relaxation to the steady state analytically. Finally we compute the survival probability of the RTP in a semi-infinite domain. In the finite interval, we compute the exit probability and the associated exit times. We provide numerical verifications of our analytical results

Dynamic Response of Ising System to a Pulsed Field

The dynamical response to a pulsed magnetic field has been studied here both using Monte Carlo simulation and by solving numerically the meanfield dynamical equation of motion for the Ising model. The ratio R_p of the response magnetisation half-width to the width of the external field pulse has been observed to diverge and pulse susceptibility \chi_p (ratio of the response magnetisation peak height and the pulse height) gives a peak near the order-disorder transition temperature T_c (for the unperturbed system). The Monte Carlo results for Ising system on square lattice show that R_p diverges at T_c, with the exponent $\nu z \cong 2.0$, while \chi_p shows a peak at $T_c^e$, which is a function of the field pulse width $\delta t$. A finite size (in time) scaling analysis shows that $T_c^e = T_c + C (\delta t)^{-1/x}$, with $x = \nu z \cong 2.0$. The meanfield results show that both the divergence of R and the peak in \chi_p occur at the meanfield transition temperature, while the peak height in $\chi_p \sim (\delta t)^y$, $y \cong 1$ for small values of $\delta t$. These results also compare well with an approximate analytical solution of the meanfield equation of motion.Comment: Revtex, Eight encapsulated postscript figures, submitted to Phys. Rev.

Turbulence and Multiscaling in the Randomly Forced Navier Stokes Equation

We present an extensive pseudospectral study of the randomly forced Navier-Stokes equation (RFNSE) stirred by a stochastic force with zero mean and a variance $\sim k^{4-d-y}$, where $k$ is the wavevector and the dimension $d = 3$. We present the first evidence for multiscaling of velocity structure functions in this model for $y \geq 4$. We extract the multiscaling exponent ratios $\zeta_p/\zeta_2$ by using extended self similarity (ESS), examine their dependence on $y$, and show that, if $y = 4$, they are in agreement with those obtained for the deterministically forced Navier-Stokes equation ($3d$NSE). We also show that well-defined vortex filaments, which appear clearly in studies of the $3d$NSE, are absent in the RFNSE.Comment: 4 pages (revtex), 6 figures (postscript

Logarithmic corrections of the avalanche distributions of sandpile models at the upper critical dimension

We study numerically the dynamical properties of the BTW model on a square lattice for various dimensions. The aim of this investigation is to determine the value of the upper critical dimension where the avalanche distributions are characterized by the mean-field exponents. Our results are consistent with the assumption that the scaling behavior of the four-dimensional BTW model is characterized by the mean-field exponents with additional logarithmic corrections. We benefit in our analysis from the exact solution of the directed BTW model at the upper critical dimension which allows to derive how logarithmic corrections affect the scaling behavior at the upper critical dimension. Similar logarithmic corrections forms fit the numerical data for the four-dimensional BTW model, strongly suggesting that the value of the upper critical dimension is four.Comment: 8 pages, including 9 figures, accepted for publication in Phys. Rev.

Efficiency of the Incomplete Enumeration algorithm for Monte-Carlo simulation of linear and branched polymers

We study the efficiency of the incomplete enumeration algorithm for linear and branched polymers. There is a qualitative difference in the efficiency in these two cases. The average time to generate an independent sample of $n$ sites for large $n$ varies as $n^2$ for linear polymers, but as $exp(c n^{\alpha})$ for branched (undirected and directed) polymers, where $0<\alpha<1$. On the binary tree, our numerical studies for $n$ of order $10^4$ gives $\alpha = 0.333 \pm 0.005$. We argue that $\alpha=1/3$ exactly in this case.Comment: replaced with published versio