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Herein we provide a closed form perturbative solution to a general M-node network susceptible-infected-susceptible (SIS) model using the transport rates between nodes as a perturbation parameter. We separate the dynamics into a short-time regime and a medium-to-long-time regime. We solve the short-time dynamics of the system and provide a limit before which our explicit, analytical result of the f
Coarse-grained, self-contained polymer models are powerful tools in the study of protein folding. They are also essential to assess predictions from less rigorous theoretical approaches that lack an explicit-chain representation. Here we review advances in coarse-grained modeling of cooperative protein folding, noting in particular that the Levinthal paradox was raised in response to the experimen
This study was undertaken to characterize the water-soluble polysaccharides isolated from an herbal tea, the leaves of L. lucidus Turcz. HPLC analysis showed that L. lucidus polysaccharides (LLPs) were mainly composed of galactose (50.1 mol %), followed by galacturonic acid (14.2 mol %), accounting for 64.3 mol % of all quantitative nine monosaccharides. Furthermore, we evaluated the systemic immu
In order to establish a reference for analysis of the function of auxin and the auxin biosynthesis regulators SHORT INTERNODE/STYLISH (SHI/STY) during Physcomitrella patens reproductive development, we have described male (antheridial) and female (archegonial) development in detail, including temporal and positional information of organ initiation. This has allowed us to define discrete stages of
The circadian clock measures time across a 24h period, increasing fitness by phasing biological processes to the most appropriate time of day. The interlocking feedback loop mechanism of the clock is conserved across species; however, the number of loops varies. Mathematical and computational analyses have suggested that loop complexity affects the overall flexibility of the oscillator, including
We present measurements of J/psi yields in d + Au collisions at root S-NN = 200 GeV recorded by the PHENIX experiment and compare them with yields in p + p collisions at the same energy per nucleon-nucleon collision. The measurements cover a large kinematic range in J/psi rapidity (-2.2 < y < 2.4) with high statistical precision and are compared with two theoretical models: one with nuclear shadow
Recent protein design experiments have demonstrated that proteins can migrate between folds through the accumulation of substitution mutations without visiting disordered or nonfunctional points in sequence space. To explore the biophysical mechanism underlying such transitions we use a three-letter continuous protein model with seven atoms per amino acid to provide realistic sequence-structure an
The standard setup for single-file diffusion is diffusing particles in one dimension which cannot overtake each other, where the dynamics of a tracer (tagged) particle is of main interest. In this article, we generalize this system and investigate first-passage properties of a tracer particle when flanked by identical crowder particles which may, besides diffuse, unbind (rebind) from (to) the one-
We consider the dynamics of a one-dimensional system consisting of dissimilar hardcore interacting (bouncy) random walkers. The walkers' (diffusing particles') friction constants ξ(n), where n labels different bouncy walkers, are drawn from a distribution ϱ(ξ(n)). We provide an approximate analytic solution to this recent single-file problem by combining harmonization and effective medium techniqu
Bio-inspired crossover:Natural genomes are affected by various kinds of mutations, manifesting as variations in the genome. This includes modifications to individual base pairs (single nucleotide polymorphism, SNP), but also short insertions and deletions (indels), and variations in the position (translocations) or multiplicity (copy number variations) of genetic sequences. While SNPs are historic
The direct reprogramming of adult skin fibroblasts to neurons is thought to be controlled by a small set of interacting gene regulators. Here, we investigate how the interaction dynamics between these regulating factors coordinate cellular decision making in direct neuronal reprogramming. We put forward a quantitative model of the governing gene regulatory system, supported by measurements of mRNA
This report summarizes the presentations and discussions during the Rapid Reaction Task Force “Dynamics of critical fluctuations: Theory – phenomenology – heavy-ion collisions”, which was organized by the ExtreMe Matter Institute EMMI and held at GSI, Darmstadt, Germany in April 2019. We address the current understanding of the dynamics of critical fluctuations in QCD and their measurement in heav
We deal with some halos generated by the divergent light from a nearby source. After discussing how the divergent light transforms some halo features, we give an outline of a method of handling the simulation of a divergent-light halo. The simulation method is then successfully tested on some well-documented halo observations. We also present a "simulation atlas" that shows halos produced by cryst
We investigate the mechanical unfolding of the tenth type III domain from fibronectin (FnIII(10)) both at constant force and at constant pulling velocity, by all-atom Monte Carlo simulations. We observe both apparent two-state unfolding and several unfolding pathways involving one of three major, mutually exclusive intermediate states. All three major intermediates lack two of seven native beta-st
Divergent-light halos are halos produced by light from nearby light sources, like street lamps being scattered by small crystals of ice floating in the air. The use of "brute-force" Monte Carlo methods to simulate such halos is extremely inefficient, as most scattered rays will not hit the eye of the observer. I present a new procedure for Monte Carlo simulations of divergent-light halos. This pro
Experimental and theoretical studies of lifetimes and transition probabilities for doubly ionized mercury, Hg III, are reported. Such data are currently of great astrophysical interest because observations with the Goddard high resolution spectrograph on board the Hubble space telescope have shown some 5d(9)6s-5d(9)6p transitions of Hg III in the spectrum of the chemically peculiar star chi Lupi.
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded states of this protein is found to be weak, even at the folding temperature. Nevertheless, we find that melting curves to a good approximation can be described
Recent studies show that plant organ positioning may be mediated by localized concentrations of the plant hormone auxin. Auxin patterning in the shoot apical meristem is in turn brought about by the subcellular polar distribution of the putative auxin efflux mediator, PIN1. However, the question of what signals determine PIN1 polarization and how this gives rise to regular patterns of auxin concen
An automated peak picking strategy is presented where several peak sets with different signal-to-noise levels are combined to form a more reliable statement on the protein identity. The strategy is compared against both manual peak picking and industry standard automated peak picking on a set of mass spectra obtained after tryptic in gel digestion of 2D-gel samples from human fetal fibroblasts. Th
