# Browsing by Subject "Physics, Theory"

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Item Open Access Extraction of Hot QCD Matter Transport Coefficients utilizing Microscopic Transport Theory(2010) Demir, Nasser SolimanUltrarelativistic heavy-ion collisions at the Relativistic Heavy-Ion Collider (RHIC) are thought to have produced a state of matter called the Quark-Gluon-Plasma (QGP). The QGP forms when nuclear matter governed by Quantum Chromodynamics (QCD) reaches a temperature and baryochemical potential necessary to achieve the transition of hadrons (bound states of quarks and gluons) to {it deconfined} quarks and gluons. Such conditions have been achieved at RHIC, and the resulting QGP created exhibits properties of a near perfect fluid. In particular, strong evidence shows that the QGP exhibits a very small shear viscosity to entropy density ratio &eta/s, near the lower bound predicted for that quantity by Anti-deSitter space/Conformal Field Theory (AdS/CFT) methods of &eta/s = $hbar$/ 4 &pi $k_B$ where $hbar$ is Planck's constant and $k_B$ is Boltzmann's constant. As the produced matter expands and cools, it evolves through a phase described by a hadron gas with rapidly increasing $eta/s$.

This thesis presents robust calculations of $eta/s$ for hadronic and partonic media as a function of temperature using the Green-Kubo formalism. An analysis is performed for the behavior of $eta/s$ to mimic situations of the hadronic media at RHIC evolving out of chemical equilibrium, and systematic uncertainties are assessed for our method. In addition, preliminary results are presented for the bulk viscosity to entropy density ratio $zeta/s$, whose behavior is not well-known in a relativistic heavy ion collisions. The diffusion coefficient for baryon number is investigated, and an algorithm is presented to improve upon the previous work of investigation of heavy quark diffusion in a thermal QGP.

By combining the results of my investigations for $eta/s$ from our microscopic transport models with what is currently known from the experimental results on elliptic flow from RHIC, I find that the trajectory of $eta/s$ in a heavy ion collision has a rich structure, especially near the deconfinement transition temperature $T_c$. I have helped quantify the viscous hadronic effects to enable investigators to constrain the value of $eta/s$ for the QGP created at RHIC.

Item Open Access Network Dynamics and Systems Biology(2009) Norrell, Johannes AdrieThe physics of complex systems has grown considerably as a field in recent decades, largely due to improved computational technology and increased availability of systems level data. One area in which physics is of growing relevance is molecular biology. A new field, systems biology, investigates features of biological systems as a whole, a strategy of particular importance for understanding emergent properties that result from a complex network of interactions. Due to the complicated nature of the systems under study, the physics of complex systems has a significant role to play in elucidating the collective behavior.

In this dissertation, we explore three problems in the physics of complex systems, motivated in part by systems biology. The first of these concerns the applicability of Boolean models as an approximation of continuous systems. Studies of gene regulatory networks have employed both continuous and Boolean models to analyze the system dynamics, and the two have been found produce similar results in the cases analyzed. We ask whether or not Boolean models can generically reproduce the qualitative attractor dynamics of networks of continuously valued elements. Using a combination of analytical techniques and numerical simulations, we find that continuous networks exhibit two effects -- an asymmetry between on and off states, and a decaying memory of events in each element's inputs -- that are absent from synchronously updated Boolean models. We show that in simple loops these effects produce exactly the attractors that one would predict with an analysis of the stability of Boolean attractors, but in slightly more complicated topologies, they can destabilize solutions that are stable in the Boolean approximation, and can stabilize new attractors.

Second, we investigate ensembles of large, random networks. Of particular interest is the transition between ordered and disordered dynamics, which is well characterized in Boolean systems. Networks at the transition point, called critical, exhibit many of the features of regulatory networks, and recent studies suggest that some specific regulatory networks are indeed near-critical. We ask whether certain statistical measures of the ensemble behavior of large continuous networks are reproduced by Boolean models. We find that, in spite of the lack of correspondence between attractors observed in smaller systems, the statistical characterization given by the continuous and Boolean models show close agreement, and the transition between order and disorder known in Boolean systems can occur in continuous systems as well. One effect that is not present in Boolean systems, the failure of information to propagate down chains of elements of arbitrary length, is present in a class of continuous networks. In these systems, a modified Boolean theory that takes into account the collective effect of propagation failure on chains throughout the network gives a good description of the observed behavior. We find that propagation failure pushes the system toward greater order, resulting in a partial or complete suppression of the disordered phase.

Finally, we explore a dynamical process of direct biological relevance: asymmetric cell division in A. thaliana. The long term goal is to develop a model for the process that accurately accounts for both wild type and mutant behavior. To contribute to this endeavor, we use confocal microscopy to image roots in a SHORTROOT inducible mutant. We compute correlation functions between the locations of asymmetrically divided cells, and we construct stochastic models based on a few simple assumptions that accurately predict the non-zero correlations. Our result shows that intracellular processes alone cannot be responsible for the observed divisions, and that an intercell signaling mechanism could account for the measured correlations.

Item Open Access The Response of Hot QCD Matter to Hard Partons(2009) Neufeld, Richard BryonThe quark gluon plasma (QGP) forms when matter governed by quantum chromodynamics (QCD) undergoes a transition at high temperature or high density from hadronic bound states to deconfined quarks and gluons. The QGP at high temperature is believed to be experimentally accessible in relativistic heavy-ion collisions, such as those done at the Relativistic Heavy-Ion Collider (RHIC) at Brookhaven National Lab and in the near future at the Large Hadron Collider (LHC) at CERN. The results obtained so far reveal the production of energetic (hard) partons in the early stages of a heavy-ion collision which propagate through the plasma. Results also show that the QGP produced at RHIC is a nearly ideal fluid and that hard partons may generate conical, Mach-like, disturbances in the QGP.

This thesis uses theoretical methods to address how the QGP responds to a hard parton that propagates through the plasma and contains the first rigorous derivation of how a hard parton deposits energy and momentum in a QGP which lead to the formation of a Mach cone. A comparison of experimental results with the theory introduced in this thesis could shed light on important properties of the QGP such as its equation of state and transport coefficients like viscosity. I investigate this problem by evaluating the source of energy and momentum generated by the hard parton in the QGP. Formalisms are developed and applied for evaluating the source of energy and momentum in perturbation theory with three different methods: classical kinetic theory, finite temperature field theory, and by including the energy lost by the hard parton to radiation. Having obtained the source of energy and momentum generated by the hard parton, I evaluate the medium response using linearized hydrodynamics. My results show Mach cone formation in the medium. I compare the medium response for different viscosities and speeds of sound, from which I find the Mach cone weakens and broadens as viscosity is increased. By studying the time evolution of the medium response once the source of energy and momentum is turned off, which occurs in a heavy-ion collision during the hadronic phase, I find that the conical disturbance is enhanced relative to diffusive contributions over a time period of several fm/c.