Large deviations for Markov jump processes with uniformly diminishing rates

We prove a large-deviation principle (LDP) for the sample paths of jump Markov processes in the small noise limit when, possibly, all the jump rates vanish uniformly, but slowly enough, in a region of the state space. We further discuss the optimality of our assumptions on the decay of the jump rates. As a direct application of this work we relax the assumptions needed for the application of LDPs to, e.g., Chemical Reaction Network dynamics, where vanishing reaction rates arise naturally particularly the context of mass action kinetics

A Predictive Model for the Pd-Catalyzed Site-Selective Oxidation of Diols

A predictive model, shaped as a set of rules, is presented that predicts site-selectivity in the mono-oxidation of diols by palladium-neocuproine catalysis. For this, the factors that govern this site-selectivity within diols and between different diols have been studied both experimentally and with computation. It is shown that an electronegative substituent antiperiplanar to the C-H bond retards hydride abstraction, resulting in a lower reactivity. This explains the selective oxidation of axial hydroxy groups in vicinal cis-diols. Furthermore, DFT calculations and competition experiments show how the reaction rate of different diols is determined by their configuration and conformational freedom. The model has been validated by the oxidation of several complex natural products, including two steroids. From a synthesis perspective, the model predicts whether a natural product comprising multiple hydroxy groups is a suitable substrate for site-selective palladium-catalyzed oxidation.</p

HP1 proteins compact DNA into mechanically and positionally stable phase separated domains

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Keenen, M. M., Brown, D., Brennan, L. D., Renger, R., Khoo, H., Carlson, C. R., Huang, B., Grill, S. W., Narlikar, G. J., & Redding, S. HP1 proteins compact DNA into mechanically and positionally stable phase separated domains. Elife, 10, (2021): e64563, https://doi.org/10.7554/eLife.64563.In mammals, HP1-mediated heterochromatin forms positionally and mechanically stable genomic domains even though the component HP1 paralogs, HP1α, HP1β, and HP1γ, display rapid on-off dynamics. Here, we investigate whether phase-separation by HP1 proteins can explain these biological observations. Using bulk and single-molecule methods, we show that, within phase-separated HP1α-DNA condensates, HP1α acts as a dynamic liquid, while compacted DNA molecules are constrained in local territories. These condensates are resistant to large forces yet can be readily dissolved by HP1β. Finally, we find that differences in each HP1 paralog’s DNA compaction and phase-separation properties arise from their respective disordered regions. Our findings suggest a generalizable model for genome organization in which a pool of weakly bound proteins collectively capitalize on the polymer properties of DNA to produce self-organizing domains that are simultaneously resistant to large forces at the mesoscale and susceptible to competition at the molecular scale.MMK was supported by the Discovery Fellows Program at UCSF and NCI grants F31CA243360 and F99CA245719. RR was support from the NOMIS foundation, Rostock, Germany. BH acknowledges support though NIH R21 GM129652, R01 CA231300 and R01 GM131641. BH is also a Chan Zuckerberg Biohub Investigator. SWG was supported by the DFG (SPP 1782, GSC 97, GR 3271/2, GR 3271/3, GR 3271/4) and the European Research Council (grant 742712). GJN acknowledges support from NIH grant R35 GM127020 and NSF grant 1921794. Support to SR through the UCSF Program for Breakthrough Biomedical Research (PBBR), Sandler Foundation, and Whitman Foundation at the Marine Biological Laboratories

Electronic Coherence Dephasing in Excitonic Molecular Complexes: Role of Markov and Secular Approximations

We compare four different types of equations of motion for reduced density matrix of a system of molecular excitons interacting with thermodynamic bath. All four equations are of second order in the linear system-bath interaction Hamiltonian, with different approximations applied in their derivation. In particular we compare time-nonlocal equations obtained from so-called Nakajima-Zwanzig identity and the time-local equations resulting from the partial ordering prescription of the cummulant expansion. In each of these equations we alternatively apply secular approximation to decouple population and coherence dynamics from each other. We focus on the dynamics of intraband electronic coherences of the excitonic system which can be traced by coherent two-dimensional spectroscopy. We discuss the applicability of the four relaxation theories to simulations of population and coherence dynamics, and identify features of the two-dimensional coherent spectrum that allow us to distinguish time-nonlocal effects.Comment: 14 pages, 8 figure

Challenges facing an understanding of the nature of low-energy excited states in photosynthesis

© 2016 Elsevier B.V. While the majority of the photochemical states and pathways related to the biological capture of solar energy are now well understood and provide paradigms for artificial device design, additional low-energy states have been discovered in many systems with obscure origins and significance. However, as low-energy states are naively expected to be critical to function, these observations pose important challenges. A review of known properties of low energy states covering eight photochemical systems, and options for their interpretation, are presented. A concerted experimental and theoretical research strategy is suggested and outlined, this being aimed at providing a fully comprehensive understanding

Revisiting the optical properties of the FMO protein

We review the optical properties of the FMO complex as found by spectroscopic studies of the Qy band over the last two decades. This article emphasizes the different methods used, both experimental and theoretical, to elucidate the excitonic structure and dynamics of this pigment–protein complex

Search For Exotic Tau-decays

The Crystal Ball detector at the Doris II storage ring at DESY was used to search for the exotic decay processes tau -&gt; e gamma, tau -&gt; e pi0, tau -&gt; e eta. No signal was observed. We obtained the following 90% CL upper limits on the branching fractions:B(tau -&gt; e gamma)&lt; 2.0x10^(-4),B(tau -&gt; e pi0) &lt; 1.4x10^(-4),B(tau -&gt; e eta) &lt; 2.4x10^(-4)