Matching Items (4)

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An integrative method to decode regulatory logics in gene transcription

Description

Modeling of transcriptional regulatory networks (TRNs) has been increasingly used to dissect the nature of gene regulation. Inference of regulatory relationships among transcription factors (TFs) and genes, especially among multiple

Modeling of transcriptional regulatory networks (TRNs) has been increasingly used to dissect the nature of gene regulation. Inference of regulatory relationships among transcription factors (TFs) and genes, especially among multiple TFs, is still challenging. In this study, we introduced an integrative method, LogicTRN, to decode TF–TF interactions that form TF logics in regulating target genes. By combining cis-regulatory logics and transcriptional kinetics into one single model framework, LogicTRN can naturally integrate dynamic gene expression data and TF-DNA-binding signals in order to identify the TF logics and to reconstruct the underlying TRNs. We evaluated the newly developed methodology using simulation, comparison and application studies, and the results not only show their consistence with existing knowledge, but also demonstrate its ability to accurately reconstruct TRNs in biological complex systems.

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Date Created
  • 2017-10-19

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Passive Radar Signal Generation and Scenario Simulation

Description

Passive radar can be used to reduce the demand for radio frequency spectrum bandwidth. This paper will explain how a MATLAB simulation tool was developed to analyze the feasibility of

Passive radar can be used to reduce the demand for radio frequency spectrum bandwidth. This paper will explain how a MATLAB simulation tool was developed to analyze the feasibility of using passive radar with digitally modulated communication signals. The first stage of the simulation creates a binary phase-shift keying (BPSK) signal, quadrature phase-shift keying (QPSK) signal, or digital terrestrial television (DTTV) signal. A scenario is then created using user defined parameters that simulates reception of the original signal on two different channels, a reference channel and a surveillance channel. The signal on the surveillance channel is delayed and Doppler shifted according to a point target scattering profile. An ambiguity function detector is implemented to identify the time delays and Doppler shifts associated with reflections off of the targets created. The results of an example are included in this report to demonstrate the simulation capabilities.

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Created

Date Created
  • 2014-05

Hydrodynamics of Diamond-Shaped Gradient Nanopillar Arrays for Effective DNA Trans location into Nano channels

Description

Effective DNA translocation into nanochannels is critical for advancing genome mapping and future single-molecule DNA sequencing technologies. We present the design and hydrodynamic study of a diamond-shaped gradient pillar array

Effective DNA translocation into nanochannels is critical for advancing genome mapping and future single-molecule DNA sequencing technologies. We present the design and hydrodynamic study of a diamond-shaped gradient pillar array connected to nanochannels for enhancing the success of DNA translocation events. Single-molecule fluorescence imaging is utilized to interrogate the hydrodynamic interactions of the DNA with this unique structure, evaluate key DNA translocation parameters, including speed, extension, and translocation time, and provide a detailed mapping of the translocation events in nanopillar arrays coupled with 10 and 50 μm long channels. Our analysis reveals the important roles of diamond-shaped nanopillars in guiding DNA into as small as 30 nm channels with minimized clogging, stretching DNA to nearly 100% of their dyed contour length, inducing location-specific straddling of DNA at nanopillar interfaces, and modulating DNA speeds by pillar geometries. Importantly, all critical features down to 30 nm wide nanochannels are defined using standard photolithography and fabrication processes, a feat aligned with the requirement of high-volume, low-cost production.

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Created

Date Created
  • 2015-02-01

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Sensor management algorithms for measurement of diffusion processes

Description

Modern systems that measure dynamical phenomena often have limitations as to how many sensors can operate at any given time step. This thesis considers a sensor scheduling problem in

Modern systems that measure dynamical phenomena often have limitations as to how many sensors can operate at any given time step. This thesis considers a sensor scheduling problem in which the source of a diffusive phenomenon is to be localized using single point measurements of its concentration. With a linear diffusion model, and in the absence of noise, classical observability theory describes whether or not the system's initial state can be deduced from a given set of linear measurements. However, it does not describe to what degree the system is observable. Different metrics of observability have been proposed in literature to address this issue. Many of these methods are based on choosing optimal or sub-optimal sensor schedules from a predetermined collection of possibilities. This thesis proposes two greedy algorithms for a one-dimensional and two-dimensional discrete diffusion processes. The first algorithm considers a deterministic linear dynamical system and deterministic linear measurements. The second algorithm considers noise on the measurements and is compared to a Kalman filter scheduling method described in published work.

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Created

Date Created
  • 2016