+publisher:"Rutgers University" +contributor:("Sontag, Eduardo")

Rutgers University

1. Škatarić, Maja, 1986-. Scale invariance in biological systems.

Degree: PhD, Electrical and Computer Engineering, 2014, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/45463/

► In this dissertation we will discuss various techniques related to modeling and identification problems arising in complex biological networks, and demonstrate how control theory approaches… (more)

▼ In this dissertation we will discuss various techniques related to modeling and identification problems arising in complex biological networks, and demonstrate how control theory approaches can be used to validate mathematical models coming from exhaustive computational experiments or noisy experimental data. The methodology based on systematic exploration of the basic dynamic processes, feedback control loops, and signal processing mechanisms in complex networks or their parts provides powerful tools for guiding the reverse-engineering of networks, and allows one to design artificial systems that are capable of achieving various objectives. Adaptation is an essential property of many cellular systems and it means that the measured variables return to their basal levels after a transient response to a step increase in stimulus. By definition, neither the concepts of perfect nor approximate adaptation address the characteristics of the transient signaling which occurs prior to a return to steady state, which are physiologically relevant. It has been recently observed that some adapting systems, ranging from bacterial chemotaxis pathways to signal transduction mechanisms in eukaryotes exhibit an additional feature: scale invariance, meaning that transient behavior remains approximately the same when the background signal level is scaled. Recent interest in scale-invariance was triggered by a pair of papers published in 2009, in which scale-invariant behavior was experimentally observed in several highly conserved eukaryotic signaling pathways that play roles in embryonic patterning, stem cell homeostasis, cell division, and other central processes, and their misregulation results in diseases including several types of cancer. In this thesis we will review the biological phenomena of adaptation and scale invariance, and present the relevant mathematical results for several classes of systems that exhibit these properties. We will use a model from the literature which describes the class of enzyme networks, to prove the impossibility of perfect scale invariance, and develop the mechanism which gives rise to an approximate scale invariance. We will demonstrate results on a biological example of soil-living amoeba Dictyostelium discoideum. Additionally, it has been often remarked in the literature that certain systems whose output variables respond at a faster time scale than internal components, give rise to an approximate scale-invariant behavior. We will state a fundamental limitation of such a mechanism, showing that there is a minimal error that cannot be overcome, no matter how large the separation of time scales is. We will highlight the extensions and challenges in analyzing adaptation and scale-invariance in a stochastic setting. Finally, we will discuss the development of tools for the identification of time-varying parameters in nonhomogeneous Poisson processes, in applications where discrete measurements such as "spikes" or "tumbles" are observed from the behavior of free swimming… Advisors/Committee Members: Sontag, Eduardo (chair), Gajic, Zoran (internal member), Daut, David (internal member), Orfanidis, Sophocles (internal member), Baykal-Gursoy, Melike (outside member).

Subjects/Keywords: Scaling laws (Statistical physics); Control theory; Biological models

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APA (6^th Edition):

Škatarić, Maja, 1. (2014). Scale invariance in biological systems. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/45463/

Chicago Manual of Style (16^th Edition):

Škatarić, Maja, 1986-. “Scale invariance in biological systems.” 2014. Doctoral Dissertation, Rutgers University. Accessed January 20, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/45463/.

MLA Handbook (7^th Edition):

Škatarić, Maja, 1986-. “Scale invariance in biological systems.” 2014. Web. 20 Jan 2021.

Vancouver:

Škatarić, Maja 1. Scale invariance in biological systems. [Internet] [Doctoral dissertation]. Rutgers University; 2014. [cited 2021 Jan 20]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45463/.

Council of Science Editors:

Škatarić, Maja 1. Scale invariance in biological systems. [Doctoral Dissertation]. Rutgers University; 2014. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45463/

Rutgers University

2. Kennedy, Benjamin B. Differential delay equations with several fixed delays.

Degree: PhD, Mathematics, 2007, Rutgers University

URL: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.16409

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We study nonlinear autonomous real-valued differential delay equations with several fixed delays x'(t) = sum_i=1 D F_i(x(t-d_i)), where the F_i are continuous, have nonzero limits… (more)

Subjects/Keywords: Delay differential equations; Functional differential equations

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APA (6^th Edition):

Kennedy, B. B. (2007). Differential delay equations with several fixed delays. (Doctoral Dissertation). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.16409

Chicago Manual of Style (16^th Edition):

Kennedy, Benjamin B. “Differential delay equations with several fixed delays.” 2007. Doctoral Dissertation, Rutgers University. Accessed January 20, 2021. http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.16409.

MLA Handbook (7^th Edition):

Kennedy, Benjamin B. “Differential delay equations with several fixed delays.” 2007. Web. 20 Jan 2021.

Vancouver:

Kennedy BB. Differential delay equations with several fixed delays. [Internet] [Doctoral dissertation]. Rutgers University; 2007. [cited 2021 Jan 20]. Available from: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.16409.

Council of Science Editors:

Kennedy BB. Differential delay equations with several fixed delays. [Doctoral Dissertation]. Rutgers University; 2007. Available from: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.16409

Rutgers University

3. Riley, Todd Robert. Modeling p53 transcriptional regulation.

Degree: PhD, Computational Biology and Molecular Biophysics, 2008, Rutgers University

URL: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.17551

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The p53 protein has been called the "gatekeeper" of the cell. After DNA damage, p53 transcriptionally activates downstream pathways to prevent cancer from occurring. Target… (more)

Subjects/Keywords: p53 antioncogene; Genetic transcription; Transcription factors

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APA (6^th Edition):

Riley, T. R. (2008). Modeling p53 transcriptional regulation. (Doctoral Dissertation). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.17551

Chicago Manual of Style (16^th Edition):

Riley, Todd Robert. “Modeling p53 transcriptional regulation.” 2008. Doctoral Dissertation, Rutgers University. Accessed January 20, 2021. http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.17551.

MLA Handbook (7^th Edition):

Riley, Todd Robert. “Modeling p53 transcriptional regulation.” 2008. Web. 20 Jan 2021.

Vancouver:

Riley TR. Modeling p53 transcriptional regulation. [Internet] [Doctoral dissertation]. Rutgers University; 2008. [cited 2021 Jan 20]. Available from: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.17551.

Council of Science Editors:

Riley TR. Modeling p53 transcriptional regulation. [Doctoral Dissertation]. Rutgers University; 2008. Available from: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.17551

Rutgers University

4. Wang, Liming, 1978-. Dynamics and asymptotic behaviors of biochemical networks.

Degree: PhD, Mathematics, 2008, Rutgers University

URL: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469

►

The purpose of this dissertation is to study the dynamics and asymptotic behaviors of biochemical networks using a "modular'' approach. New mathematics is motivated and… (more)

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The purpose of this dissertation is to study the dynamics and asymptotic behaviors of biochemical networks using a "modular'' approach. New mathematics is motivated and developed to analyze modules in terms of the number of steady states and the stability of the steady states. One of the main contributions of the thesis is to extend Hirsch's generic convergence result from monotone systems to systems "close'' to monotone using geometric singular perturbation theory. A monotone system is a dynamical system for which the comparison principle holds, that is, "bigger'' initial states lead to "bigger'' future states. In monotone systems, every net feedback loop is positive. On the other hand, negative feedback loops are important features of many systems, since they are required for adaptation and precision. We show that, provided that these negative loops act at a comparatively fast time scale, the generic convergence property still holds. This is an appealing result, which suggests that monotonicity has broader implications than previously thought. One particular application of great interest is that of double phosphorylation dephosphorylation cycles. Other recurring modules in biochemical networks are also analyzed in detail. For systems without time scale separation, we study the global stability of one special class of systems, called monotone tridiagonal systems with negative feedback. The key technique is to rule out periodic orbits using the theory of second compound matrices. We also investigate the effect of diffusion on the stability of a constant steady state for systems with more general structures represented by graphs. This work extends the passivity-based stability criterion developed by Arcak and Sontag to reaction diffusion equations. Upon assembling different modules, the dynamics of individual modules might be affected. One particular effect is called "retroactivity'' in the systems biology literature. We propose designs and conditions under which the retroactivity can be attenuated.

Advisors/Committee Members: Wang, Liming, 1978- (author), Sontag, Eduardo (chair), Mischaikow, Konstantin (internal member), Li, YanYan (internal member), Gajic, Zoran (outside member).

Subjects/Keywords: Biological systems – Mathematical models; Computational biology; Stochastic analysis

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APA (6^th Edition):

Wang, Liming, 1. (2008). Dynamics and asymptotic behaviors of biochemical networks. (Doctoral Dissertation). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469

Chicago Manual of Style (16^th Edition):

Wang, Liming, 1978-. “Dynamics and asymptotic behaviors of biochemical networks.” 2008. Doctoral Dissertation, Rutgers University. Accessed January 20, 2021. http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469.

MLA Handbook (7^th Edition):

Wang, Liming, 1978-. “Dynamics and asymptotic behaviors of biochemical networks.” 2008. Web. 20 Jan 2021.

Vancouver:

Wang, Liming 1. Dynamics and asymptotic behaviors of biochemical networks. [Internet] [Doctoral dissertation]. Rutgers University; 2008. [cited 2021 Jan 20]. Available from: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469.

Council of Science Editors:

Wang, Liming 1. Dynamics and asymptotic behaviors of biochemical networks. [Doctoral Dissertation]. Rutgers University; 2008. Available from: http://hdl.rutgers.edu/1782.2/rucore10001600001.ETD.000050469

Rutgers University

5. Tsitron, Julia, 1976-. Computational analysis of olfaction and artificial nose technologies.

Degree: Computational Biology and Molecular Biophysics, 2013, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/41937/

Subjects/Keywords: Olfactory sensors; Bayesian statistical decision theory

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APA (6^th Edition):

Tsitron, Julia, 1. (2013). Computational analysis of olfaction and artificial nose technologies. (Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/41937/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

Tsitron, Julia, 1976-. “Computational analysis of olfaction and artificial nose technologies.” 2013. Thesis, Rutgers University. Accessed January 20, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/41937/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

Tsitron, Julia, 1976-. “Computational analysis of olfaction and artificial nose technologies.” 2013. Web. 20 Jan 2021.

Vancouver:

Tsitron, Julia 1. Computational analysis of olfaction and artificial nose technologies. [Internet] [Thesis]. Rutgers University; 2013. [cited 2021 Jan 20]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/41937/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Tsitron, Julia 1. Computational analysis of olfaction and artificial nose technologies. [Thesis]. Rutgers University; 2013. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/41937/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rutgers University

6. White, Amelia, 1977-. Automated and quantitative phenotyping of C. elegans genetic screens from high-throughput image data.

Degree: Computational Biology and Molecular Biophysics, 2013, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/41948/

Subjects/Keywords: Computational biology; Diagnostic imaging; Caenorhabditis elegans – Research

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APA (6^th Edition):

White, Amelia, 1. (2013). Automated and quantitative phenotyping of C. elegans genetic screens from high-throughput image data. (Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/41948/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16^th Edition):

White, Amelia, 1977-. “Automated and quantitative phenotyping of C. elegans genetic screens from high-throughput image data.” 2013. Thesis, Rutgers University. Accessed January 20, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/41948/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7^th Edition):

White, Amelia, 1977-. “Automated and quantitative phenotyping of C. elegans genetic screens from high-throughput image data.” 2013. Web. 20 Jan 2021.

Vancouver:

White, Amelia 1. Automated and quantitative phenotyping of C. elegans genetic screens from high-throughput image data. [Internet] [Thesis]. Rutgers University; 2013. [cited 2021 Jan 20]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/41948/.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

White, Amelia 1. Automated and quantitative phenotyping of C. elegans genetic screens from high-throughput image data. [Thesis]. Rutgers University; 2013. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/41948/

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Rutgers University

7. Škatarić, Maja, 1986-. Fold change detection in 3-node enzymatic networks.

Degree: MS, Electrical and Computer Engineering, 2011, Rutgers University

URL: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061515

► Complex networks are studied across many fields of science. To discover design principles that underlie these networks, network motifs are introduced, as sub-graphs of interconnections… (more)

Subjects/Keywords: Multienzyme complexes

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APA (6^th Edition):

Škatarić, Maja, 1. (2011). Fold change detection in 3-node enzymatic networks. (Masters Thesis). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061515

Chicago Manual of Style (16^th Edition):

Škatarić, Maja, 1986-. “Fold change detection in 3-node enzymatic networks.” 2011. Masters Thesis, Rutgers University. Accessed January 20, 2021. http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061515.

MLA Handbook (7^th Edition):

Škatarić, Maja, 1986-. “Fold change detection in 3-node enzymatic networks.” 2011. Web. 20 Jan 2021.

Vancouver:

Škatarić, Maja 1. Fold change detection in 3-node enzymatic networks. [Internet] [Masters thesis]. Rutgers University; 2011. [cited 2021 Jan 20]. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061515.

Council of Science Editors:

Škatarić, Maja 1. Fold change detection in 3-node enzymatic networks. [Masters Thesis]. Rutgers University; 2011. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000061515

Rutgers University

8. Marcondes de Freitas, Michael. A class of input/output random systems: monotonicity and a small-gain theorem.

Degree: PhD, Mathematics, 2014, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/45341/

►

We expand upon the theory of random dynamical systems (RDS) of L. Arnold, developing a theory of random dynamical systems with inputs and outputs (RDSIO)—an… (more)

Subjects/Keywords: Random dynamical systems; Monotonic functions

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APA (6^th Edition):

Marcondes de Freitas, M. (2014). A class of input/output random systems: monotonicity and a small-gain theorem. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/45341/

Chicago Manual of Style (16^th Edition):

Marcondes de Freitas, Michael. “A class of input/output random systems: monotonicity and a small-gain theorem.” 2014. Doctoral Dissertation, Rutgers University. Accessed January 20, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/45341/.

MLA Handbook (7^th Edition):

Marcondes de Freitas, Michael. “A class of input/output random systems: monotonicity and a small-gain theorem.” 2014. Web. 20 Jan 2021.

Vancouver:

Marcondes de Freitas M. A class of input/output random systems: monotonicity and a small-gain theorem. [Internet] [Doctoral dissertation]. Rutgers University; 2014. [cited 2021 Jan 20]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45341/.

Council of Science Editors:

Marcondes de Freitas M. A class of input/output random systems: monotonicity and a small-gain theorem. [Doctoral Dissertation]. Rutgers University; 2014. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/45341/

Rutgers University

9. Aminzare, Zahra, 1983-. On synchronous behavior in complex nonlinear dynamical systems.

Degree: PhD, Mathematics, 2015, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/47249/

►

The purpose of this dissertation is to study synchronous behavior of certain nonlinear dynamical systems by the method of contraction theory. Contraction theory provides an… (more)

Subjects/Keywords: Synchronization – Mathematics

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APA (6^th Edition):

Aminzare, Zahra, 1. (2015). On synchronous behavior in complex nonlinear dynamical systems. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/47249/

Chicago Manual of Style (16^th Edition):

Aminzare, Zahra, 1983-. “On synchronous behavior in complex nonlinear dynamical systems.” 2015. Doctoral Dissertation, Rutgers University. Accessed January 20, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/47249/.

MLA Handbook (7^th Edition):

Aminzare, Zahra, 1983-. “On synchronous behavior in complex nonlinear dynamical systems.” 2015. Web. 20 Jan 2021.

Vancouver:

Aminzare, Zahra 1. On synchronous behavior in complex nonlinear dynamical systems. [Internet] [Doctoral dissertation]. Rutgers University; 2015. [cited 2021 Jan 20]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/47249/.

Council of Science Editors:

Aminzare, Zahra 1. On synchronous behavior in complex nonlinear dynamical systems. [Doctoral Dissertation]. Rutgers University; 2015. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/47249/

10. Gould, David William, 1986-. A research summary 1) RNA binding proteins, 2) Selective constraint on copy number variation in human PIWI-interacting RNA loci.

Degree: MS, Computational Biology and Molecular Biophysics, 2013, Rutgers University

URL: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000068863

► The overall aim of my research dealt with the understanding of regulatory elements in various systems (most important, in humans) through two research projects 1)… (more)

Subjects/Keywords: RNA-protein interactions; Genetic regulation

8 more images…

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APA (6^th Edition):

Gould, David William, 1. (2013). A research summary 1) RNA binding proteins, 2) Selective constraint on copy number variation in human PIWI-interacting RNA loci. (Masters Thesis). Rutgers University. Retrieved from http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000068863

Chicago Manual of Style (16^th Edition):

Gould, David William, 1986-. “A research summary 1) RNA binding proteins, 2) Selective constraint on copy number variation in human PIWI-interacting RNA loci.” 2013. Masters Thesis, Rutgers University. Accessed January 20, 2021. http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000068863.

MLA Handbook (7^th Edition):

Gould, David William, 1986-. “A research summary 1) RNA binding proteins, 2) Selective constraint on copy number variation in human PIWI-interacting RNA loci.” 2013. Web. 20 Jan 2021.

Vancouver:

Gould, David William 1. A research summary 1) RNA binding proteins, 2) Selective constraint on copy number variation in human PIWI-interacting RNA loci. [Internet] [Masters thesis]. Rutgers University; 2013. [cited 2021 Jan 20]. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000068863.

Council of Science Editors:

Gould, David William 1. A research summary 1) RNA binding proteins, 2) Selective constraint on copy number variation in human PIWI-interacting RNA loci. [Masters Thesis]. Rutgers University; 2013. Available from: http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000068863

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