The three-dimensional (3D) organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state-accessibility and amount of gene expression-of the chromatin. Recent advances in chromosome conformation capture experiments provide partial information on the chromatin organization in a cell population, namely the contact count between any segment pairs, but not on the interaction strength that leads to these contact counts. However, given the contact matrix, determining the complete 3D organization of the whole chromatin polymer is an inverse problem. In this work, a novel inverse Brownian dynamics method based on a coarse-grained bead-spring chain model has been proposed to compute the optimal interaction strengths between different segments of chromatin such that the experimentally measured contact count probability constraints are satisfied. Applying this method to the a-globin gene locus in two different cell types, we predict the 3D organizations corresponding to active and repressed states of chromatin at the locus. We show that the average distance between any two segments of the region has a broad distribution and cannot be computed as a simple inverse relation based on the contact probability alone. The results presented for multiple normalization methods suggest that all measurable quantities may crucially depend on the nature of normalization. We argue that by experimentally measuring predicted quantities, one may infer the appropriate form of normalization.
The universality of the swelling of the radius of gyration of a homopolymer relative to its value in the θ state, independent of polymer-solvent chemistry, in the crossover regime between θ and athermal solvent conditions, is well known. Here we study, by Brownian dynamics, a polymer model where a subset of monomers is labelled as "stickers". The mutual interaction of the stickers is more attractive than those of the other ("backbone") monomers, and has the additional important characteristic of "functionality" ϕ, i.e., the maximum number of stickers that can locally bind to a given sticker. A saturated bond formed in this manner remains bound until it breaks due to thermal fluctuations, a requirement which can be viewed as an additional Boolean degree of freedom that describes the bonding. This, in turn, makes the question of the order of the collapse transition a non-trivial one. Nevertheless, for the parameters that we have studied (in particular, ϕ = 1), we find a standard second-order θ collapse, using a renormalised solvent quality parameter that takes into account the increased average attraction due to the presence of stickers. We examine the swelling of the radius of gyration of such a sticky polymer relative to its value in the altered θ state, using a novel potential to model the various excluded volume interactions that occur between the monomers on the chain. We find that the swelling of such sticky polymers is identical to the universal swelling of homopolymers in the thermal crossover regime. Additionally, for our model, the Kuhn segment length under θ conditions is found to be the same for chains with and without stickers. arXiv:1903.07356v2 [cond-mat.soft]
In this paper, we present an output feedback based design of event-triggered sliding mode control for delta operator systems. For discretetime systems, multi-rate output sampling based state estimation technique is very useful if the output information is available. But at high sampling rates, the discrete-time representation of the system using shift operator becomes numerically ill-conditioned and as a result, the observability matrix becomes singular as the sampling period tends to zero. Here, a new formulation of multi-rate state estimation (MRSE) for a small sampling period is presented. We first propose a new observability matrix and then discuss its relationship with the observability matrix defined in the conventional sense. For the delta operator system with matched uncertainty, we have presented the design of MRSE based sliding mode control (SMC). Additionally, to make the control efficient in terms of resource utilization, MRSE based event-triggered SMC is proposed. The absence of Zeno phenomenon is guaranteed as the control input is inherently discrete in nature. Finally, the effectiveness of the proposed method is illustrated through numerical simulations, considering a ball and beam system and a general linear system as a numerical example.
In(Ga)As/GaAs-based quantum dot infrared photodetectors (QDIPs) have emerged as one of the most suitable devices for infrared detection. However, quantum dot devices suffer from lower efficiencies due to a low fill-factor (∼20%–25%) of dots. Here, we report a post-growth technique for improving the QDIP performance using low energy light ion (H−) implantation. At high bias, there is evidence of suppression in the field-assisted tunneling component of the dark current. Enhancement in peak detectivity (D*), a measure of the signal-to-noise ratio, by more than one order, from ∼109 to 2.44 × 1010 cm Hz1/2/W was obtained from the implanted devices.
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