Browsing by Author "Phillips, George"

Now showing 1 - 6 of 6
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    A Fast Newton's Algorithm for Entropy Maximization in Phase Determination
    (1999-05) Wu, Zhijun; Phillips, George; Tapia, Richard; Zhang, Yin
    A long-standing problem in X-ray crystallography, known as the phase problem, is to determine the phases for a large set of complex variables, called the structure factors of the crystal, given their magnitudes obtained from X-ray diffraction experiments. We introduce a statistical phase estimation approach to the problem. This approach requires solving a special class of entropy maximization problems repeatedly to obtain the joint probability distribution of the structure factors. The entropy maximization problem is a semi-infinite convex program, which can be solved in a finite dual space by using a standard Newton's method. The Newton's method converges quadratically, but is costly in general, requiring O(n log n) floating point operations in every iteration, where n is the number of variables. We present a fast Newton's algorithm for solving the entropy maximization problem. The algorithm requires only O(n log n) floating point operations for each of its iterates, yet has the same convergence rate as the standard Newton. We describe the algorithm and discuss related computational issues. Numerical results on simple test cases will also be presented to demonstrate the behavior of the algorithm.
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    Conformational Dynamics of the Glutamate Receptors via single Molecule Förster Resonance Energy Transfer
    (2015-04-21) Cooper, David; Landes, Christy F; Clementi, Cecilia; Phillips, George
    Glutamate receptors perform a critical role in the nervous system, mediating synaptic transmission through cellular membranes. These proteins have developed a quick response to agonist presence and, when activated, undergo a conformational shift that allows calcium ion transport across the membrane. In a number of neurological diseases, genetic variants can cause mutations that disrupt the balance between fast binding response and desensitization resulting in over- or under- signaling in affected cells. Herein it describes the use of single molecule Förster resonance energy transfer to observe the bound form of the glutamate receptors and subsequent dynamics. For a complete understanding of the dynamics involved in the conformational landscape, the response of the receptor to a variety of known full and partial agonists is tested. Additionally multiple receptor types are investigated to determine if the conformational pathway is conserved between the different types of glutamate receptors. The results from this project allows for a more complete understanding of the relationship between conformation and functionality of glutamate receptors.
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    Novel enzymes and pathways facilitating biological utilization of one carbon compounds
    (2018-11-30) Chou, Alex; Gonzalez, Ramon; Segatori, Laura; Phillips, George
    Although biological systems hold great potential for the sustainable production of fuels and chemicals from one-carbon (C1) feedstocks (1), their C1 utilization reactions rely on specific acceptor molecules, complex metabolic pathways, and originate from difficult to engineer microorganisms, limiting applicability and implementation in the biotechnology industry (2–4). As a result, to date no non-native C1 utilizing organism has been engineered for growth or product synthesis from solely C1 substrates. In this thesis, we report that 2-hydroxyacyl-CoA lyase (HACL), an enzyme involved in the α-oxidation of long-chain fatty acids, catalyzes a novel C1 addition reaction resulting in the ligation of carbonyl-containing molecules with formyl-CoA to produce C1-elongated 2-hydroxyacyl-CoAs. We characterized the first prokaryotic variant of HACL and found that it can use a wide range of carbonyl substrates of different chain lengths, including both aldehydes and ketones, which when combined with enzymes comprising a de novo designed pathway, supported the conversion of C1 feedstocks to industrially relevant chemicals such as glycolate, ethylene glycol, ethanol, acetate, glycerate, and 2-hydroxyisobutyrate. Homology-guided mutagenesis allowed the identification of key residues influencing the in vivo activity of HACL and its ability to support C1 bioconversion. We implemented an HACL-based pathway in E. coli to utilize formaldehyde as the sole carbon substrate for glycolate production and demonstrated the potential of the pathway to support growth in a two-strain system, which was supported by genome scale modeling and flux balance analysis. The previously undescribed condensation reaction catalyzed by HACL is a direct and flexible means for C1 addition that can facilitate engineering of C1 bioconversion and synthetic methylotrophy/autotrophy in industrial organisms.
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    Selective Search for Global Optimization of Zero or Small Residual Least-Squares Problems: A Numerical Study
    (1999-09) Velazquez, Leticia; Phillips, George; Tapia, Richard; Zhang,Yin
    In this paper, we consider searching for global minima of zero or small residual, nonlinear least-squares problems. We propose a selective search approach based on the concept of selective minimization recently introduced in Zhang et al[14]. To test the viability of the proposed approach, we construct a simple implementation using a Levenberg-Marquardt type method combined with a multi-start scheme, and compare it with several existing global optimization techniques. Numerical experiments were performed on zero residual nonlinear least-squares problem chosen from structural biology applications as well as from the literature. On the problems of larger sizes, the performance of the new approach compared favorably with the other tested methods, indicating that the new approach is promising for the intended class of problems.
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    The Bayesian Statistical Approach to the Phase Problem in Protein X-ray Crystallography
    (1999-04) Wu, Zhijun; Phillips, George; Tapia, Richard; Zhang, Yin
    We review a Bayesian statistical approach to the phase problem in protein X-ray crystallography. We discuss the mathematical foundations and the computational issues. The introduction to the theory and the algorithms does not require strong background in X-ray crystallography and related physical disciplines.
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    Transcriptional delay in synthetic genetic cascades
    (2017-04-19) Cheng, Yu-Yu; Phillips, George; Bennett, Matthew
    Transcription factors (TFs) and their target promoters are central to synthetic biology. By arranging these components into complex regulatory networks, synthetic biologists have been able to create a wide variety of phenotypes, including bistable switches, oscillators, and logic gates. However, transcription factors do not instantaneously regulate downstream targets. After the gene encoding a TF is turned on, it must first be transcribed, the transcripts must be translated, and sufficient TF must accumulate in order to bind operator sites of the target promoter. The time to complete this process, here called the “transcriptional delay,” is a critical aspect in the design of dynamic regulatory networks, yet it remains poorly characterized. In this work, I measured the delay of two TFs in Escherichia coli, which are commonly used in synthetic biology: the activator AraC and the repressor LacI. I found that the delay can range from a few to tens of minutes, and are affected by the expression rate of the TF. The single-cell data also shows that the variability of the delay increases with its mean. To validate these time measurements, I constructed a two-step genetic cascade, and showed that the timing of the full cascade can be predicted from those of its constituent steps. These results demonstrate the timescale of transcriptional regulation in living cells, which is important for understanding the dynamics of synthetic transcriptional gene circuits.