Computational modeling to elucidate molecular mechanisms of epigenetic memory

How do mammalian cells that share the same genome exist in notably distinct phenotypes, exhibiting differences in morphology, gene expression patterns, and epigenetic chromatin statuses? Furthermore how do cells of different phenotypes differentiate reproducibly from a single fertilized egg? These are fundamental problems in developmental biology. Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. The complexity comes partly from the number of molecular species and the broad time scales involved. In recent years mathematical modeling has made significant contributions on elucidating the molecular mechanisms of DNA methylation and histone covalent modification inheritance. We will pedagogically introduce the typical procedure and some technical details of performing a mathematical modeling study, and discuss future developments.Comment: 36 pages, 4 figures, 2 tables, book chapte

The preparation, identification and properties of chlorophyll derivatives

In the investigation of 10-hydroxy chlorophylls a and b novel techniques included modification of chromatography and the use of fully-deuterated compounds isolated from fully-deuterated autotropic algae to determine the molecular structure of the chlorophylls

Coherent coupling of molecular resonators with a micro-cavity mode

The optical hybridization of the electronic states in strongly coupled molecule-cavity systems have revealed unique properties such as lasing, room temperature polariton condensation, and the modification of excited electronic landscapes involved in molecular isomerization. Here we show that molecular vibrational modes of the electronic ground state can also be coherently coupled with a micro-cavity mode at room temperature, given the low vibrational thermal occupation factors associated with molecular vibrations, and the collective coupling of a large ensemble of molecules immersed within the cavity mode volume. This enables the enhancement of the collective Rabi-exchange rate with respect to the single oscillator coupling strength. The possibility of inducing large shifts in the vibrational frequency of selected molecular bonds should have immediate consequences for chemistry.Comment: 22 pages, 6 figures (including Supplementary Information file

Beneficial influence of nanocarbon on the aryliminopyridylnickel chloride catalyzed ethylene polymerization

A series of 1-aryliminoethylpyridine ligands (L1―L3) was synthesized by condensation of 2-acetylpyridine with 1-aminonaphthalene, 2-aminoanthracene or 1-aminopyrene, respectively. Reaction with nickel dichloride afforded the corresponding nickel (II) chloride complexes (Ni1–Ni3). All compounds were fully characterized and the molecular structures of Ni1 and Ni3 are reported. Upon activation with methylaluminoxane (MAO), all nickel complexes exhibit high activities for ethylene polymerization, producing waxes of low molecular weight and narrow polydispersity. The presence of multi-walled carbon nanotubes (MWCNTs) or few layer graphene (FLG) in the catalytic medium can lead to an increase of productivity associated to a modification of the polymer structure

Molecular alignment and filamentation: comparison between weak and strong field models

The impact of nonadiabatic laser-induced molecular alignment on filamentation is numerically studied. Weak and strong field model of impulsive molecular alignment are compared in the context of nonlinear pulse propagation. It is shown that the widely used weak field model describing the refractive index modification induced by impulsive molecular alignment accurately reproduces the propagation dynamics providing that only a single pulse is involved during the experiment. On the contrary, it fails at reproducing the nonlinear propagation experienced by an intense laser pulse traveling in the wake of a second strong laser pulse. The discrepancy depends on the relative delay between the two pulses and is maximal for delays corresponding to half the rotational period of the molecule

Fine- and hyperfine-structure effects in molecular photoionization: II. Resonance-enhanced multiphoton ionization and hyperfine-selective generation of molecular cations

Resonance-enhanced multiphoton ionization (REMPI) is a widely used technique for studying molecular photoionization and producing molecular cations for spectroscopy and dynamics studies. Here, we present a model for describing hyperfine-structure effects in the REMPI process and for predicting hyperfine populations in molecular ions produced by this method. This model is a generalization of our model for fine- and hyperfine- structure effects in one-photon ionization of molecules presented in the preceding companion article. This generalization is achieved by covering two main aspects: (1) treatment of the neutral bound-bound transition including hyperfine structure that makes up the first step of the REMPI process and (2) modification of our ionization model to account for anisotropic populations resulting from this first excitation step. Our findings may be used for analyzing results from experiments with molecular ions produced by REMPI and may serve as a theoretical background for hyperfine-selective ionization experiments

The Tunneling Hybrid Monte-Carlo algorithm

The hermitian Wilson kernel used in the construction of the domain-wall and overlap Dirac operators has exceptionally small eigenvalues that make it expensive to reach high-quality chiral symmetry for domain-wall fermions, or high precision in the case of the overlap operator. An efficient way of suppressing such eigenmodes consists of including a positive power of the determinant of the Wilson kernel in the Boltzmann weight, but doing this also suppresses tunneling between topological sectors. Here we propose a modification of the Hybrid Monte-Carlo algorithm which aims to restore tunneling between topological sectors by excluding the lowest eigenmodes of the Wilson kernel from the molecular-dynamics evolution, and correcting for this at the accept/reject step. We discuss the implications of this modification for the acceptance rate.Comment: improved discussion in appendix B, RevTeX, 19 page

Measuring the quantum efficiency of single radiating dipoles using a scanning mirror

Using scanning probe techniques, we show the controlled manipulation of the radiation from single dipoles. In one experiment we study the modification of the fluorescence lifetime of a single molecular dipole in front of a movable silver mirror. A second experiment demonstrates the changing plasmon spectrum of a gold nanoparticle in front of a dielectric mirror. Comparison of our data with theoretical models allows determination of the quantum efficiency of each radiating dipole.Comment: 4 pages, 4 figure