Comparison of the mass preconditioned HMC and the DD-HMC algorithm for two-flavour QCD

Mass preconditioned HMC and DD-HMC are among the most popular algorithms to simulate Wilson fermions. We present a comparison of the performance of the two algorithms for realistic quark masses and lattice sizes. In particular, we use the locally deflated solver of the DD-HMC environment also for the mass preconditioned simulations.Comment: 7 pages, 2 figures. Presented at the XXVIII International Symposium on Lattice Field Theory (Lattice 2010), June 14-19 2010, Villasimius, Ital

Full QCD Algorithms towards the Chiral Limit

I discuss the behaviour of algorithms for dynamical fermions as the sea-quark mass decreases. I focus on the Hybrid-Monte-Carlo (HMC) algorithm applied to two degenerate flavours of Wilson fermions. First, I briefly review the performance obtained in large scale HMC simulations. Then I discuss a modified pseudo-fermion action for the HMC simulation that has been introduced three years ago. I summarize recent results obtained with this pseudo-fermion action by the QCDSF and the ALPHA collaborations. I comment on alternatives to the HMC, like the Multiboson algorithm and variants of it.Comment: 7 pages, Lattice 2003 plenary talk, typos corrected, references updated, discussion of the MB algorithm corrected/extende

5-hydroxymethylcytosine is a key epigenetic regulator of keratinocyte stem cells during psoriasis pathogenesis

Epigenetic regulation is now known to play an important role in determining stem cell fate during normal tissue development and disease pathogenesis. In this study, we report loss of 5-hydroxymethylcytosine (5-hmC) mediated by ten-eleven translocation (TET) methylcytosine dioxygenases in keratinocyte stem cells (KSCs) and in their progenitor transit-amplifying (TA) cells of psoriatic lesions. We establish the DNA hydroxymethylation profile in both human psoriasis as well as in the imiquimod (IMQ)-induced mouse psoriasis model. Genome-wide mapping of 5-hmC in IMQ-treated mice epithelium revealed a loci-specific reduction of 5-hmC in genes associated with maintaining stem cell homeostasis including those involved in the RAR and Wnt/β-catenin signaling pathways. Restoration of TET expression in human KSC cultures via vitamin C treatment increased 5-hmC levels and induced more normal KSC differentiation. We found that by modulating 5-hmC levels in vitro, we could alter downstream expression of genes important in regulating stem cell homeostasis like nestin as well as IL-17R known to promote the psoriatic phenotype. Our findings demonstrate that loss of 5-hmC is a critical epigenomic phenomenon in KSCs and TA cells during psoriasis pathogenesis.2019-12-17T00:00:00

Bayesian estimation of GARCH model by hybrid Monte Carlo

The hybrid Monte Carlo (HMC) algorithm is used for Bayesian analysis of the generalized autoregressive conditional heteroscedasticity (GARCH) model. The HMC algorithm is one of Markov chain Monte Carlo (MCMC) algorithms and it updates all parameters at once. We demonstrate that how the HMC reproduces the GARCH parameters correctly. The algorithm is rather general and it can be applied to other models like stochastic volatility models.Comment: The 9th Joint Conference on Information Sciences (JCIS), October 8-11, 200