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DEVELOPMENT OF THEORETICAL AND COMPUTATIONAL METHODS FOR FEW-BODY PROCESSES IN ULTRACOLD QUANTUM GASES
Title
DEVELOPMENT OF THEORETICAL AND COMPUTATIONAL METHODS FOR FEW-BODY PROCESSES IN ULTRACOLD QUANTUM GASES.
Creator
Blandon, Juan, Kokoouline, Viatcheslav, University of Central Florida
Abstract / Description
We are developing theoretical and computational methods to study two related three-body processes in ultracold quantum gases: three-body resonances and three-body recombination. Three-body recombination causes the ultracold gas to heat up and atoms to leave the trap where they are confined. Therefore, it is an undesirable effect in the process of forming ultracold quantum gases. Metastable three-body states (resonances) are formed in the ultracold gas. When decaying they also give additional...
Show moreWe are developing theoretical and computational methods to study two related three-body processes in ultracold quantum gases: three-body resonances and three-body recombination. Three-body recombination causes the ultracold gas to heat up and atoms to leave the trap where they are confined. Therefore, it is an undesirable effect in the process of forming ultracold quantum gases. Metastable three-body states (resonances) are formed in the ultracold gas. When decaying they also give additional kinetic energy to the gas, that leads to the heating too. In addition, a reliable method to obtain three-body resonances would be useful in a number of problems in other fields of physics, for example, in models of metastable nuclei or to study dissociative recombination of H3 +. Our project consists of employing computer modeling to develop a method to obtain three-body resonances. The method uses a novel two-step diagonalization approach to solve the three-body Schrödinger equation. The approach employs the SVD method of Tolstikhin et al. coupled with a complex absorbing potential. We tested this method on a model system of three identical bosons with nucleon mass and compared it to the results of a previous study. This model can be employed to understand the 3He nucleus . We found one three-body bound state and four resonances. We are also studying Efimov resonances using a 4He-based model. In a system of identical spinless bosons, Efimov states are a series of loosely bound three-body states which begin to appear as the energy of the two-body bound state approaches zero . Although they were predicted 35 years ago, recent evidence of Efimov states found by Kraemer et al. in a gas of ultracold Cs atoms has sparked great interest by theorists and experimentalists. Efimov resonances are a kind of pre-dissociated Efimov trimer. To search for Efimov resonances we tune the diatom interaction potential, V(r): V(r) → λV(r) as Esry et al. did . We calculated the first two values of λ for which there is a "condensation" (infinite number) of Efimov states. They are λEfimov1 = 0.9765 and λEfimov2 = 6.834. We performed calculations for λ = 2.4, but found no evidence of Efimov resonances. For future work we plan to work with λ ≈ 4 and λ ≈ λEfimov2 where we might see d-wave and higher l-wave Efimov resonances. There is also a many-body project that forms part of this thesis and consists of a direct diagonalization of the Bogolyubov Hamiltonian, which describes elementary excitations of a gas of bosons interacting through a pairwise interaction. We would like to reproduce the corresponding energy spectrum. So far we have performed several convergence tests, but have not observed the desired energy spectrum. We show preliminary results.
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Date Issued
2006
Identifier
CFE0001320, ucf:47026
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0001320
NONLINEAR OPTICAL PROPERTIES OF ORGANIC CHROMOPHORES CALCULATED WITHIN TIME DEPENDENT DENSITY FUNCTIONAL THEORY
Title
NONLINEAR OPTICAL PROPERTIES OF ORGANIC CHROMOPHORES CALCULATED WITHIN TIME DEPENDENT DENSITY FUNCTIONAL THEORY.
Creator
Tafur, Sergio, Kokoouline, Viatcheslav, University of Central Florida
Abstract / Description
Time Dependent Density Functional Theory offers a good accuracy/computational cost ratio among different methods used to predict the electronic structure for molecules of practical interest. The Coupled Electronic Oscillator (CEO) formalism was recently shown to accurately predict Nonlinear Optical (NLO) properties of organic chromophores when combined with Time Dependent Density Functional Theory. Unfortunately, CEO does not lend itself easily to interpretation of the structure activity...
Show moreTime Dependent Density Functional Theory offers a good accuracy/computational cost ratio among different methods used to predict the electronic structure for molecules of practical interest. The Coupled Electronic Oscillator (CEO) formalism was recently shown to accurately predict Nonlinear Optical (NLO) properties of organic chromophores when combined with Time Dependent Density Functional Theory. Unfortunately, CEO does not lend itself easily to interpretation of the structure activity relationships of chromophores. On the other hand, the Sum Over States formalism in combination with semiempirical wavefunction methods has been used in the past for the design of simplified essential states models. These models can be applied to optimization of NLO properties of interest for applications. Unfortunately, TD-DFT can not be combined directly with SOS because state-to-state transition dipoles are not defined in the linear response TD approach. In this work, a second order CEO approach to TD-DFT is simplified so that properties of double excited states and state-to-state transition dipoles may be expressed through the combination of linear response properties. This approach is termed the a posteriori Tamm-Dancoff approximation (ATDA), and validated against high-level wavefunction theory methods. Sum over States (SOS) and related Two-Photon Transition Matrix formalism are then used to predict Two-Photon Absorption (2PA) profiles and anisotropy, as well as Second Harmonic Generation (SHG) properties. Numerical results for several conjugated molecules are in excellent agreement with CEO and finite field calculations, and reproduce experimental measurements well.
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Date Issued
2007
Identifier
CFE0001853, ucf:47372
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0001853
SYMMETRY IN THE DISSOCIATIVE RECOMBINATION OF POLYATOMIC IONS AND IN ULTRA-COLD FEW BODY COLLISIONS
Title
SYMMETRY IN THE DISSOCIATIVE RECOMBINATION OF POLYATOMIC IONS AND IN ULTRA-COLD FEW BODY COLLISIONS.
Creator
Douguet, Nicolas, Kokoouline, Viatcheslav, University of Central Florida
Abstract / Description
We discuss the role of symmetries in the dissociative recombinations (DR) of three polyatomic ions, namely the linear HCO+ (formyl) ion and the two highly symmetric H3+ and H3O+ (hydronium) molecular ions. Regarding the HCO+ ion, we apply a quantum mechanical treatment using the Multi-channel Quantum Defect Theory (MQDT) formalism to describe the ion-electron scattering process. Our study takes into account the Renner-Teller effect in order to model the non Born-Oppenheimer vibronic coupling...
Show moreWe discuss the role of symmetries in the dissociative recombinations (DR) of three polyatomic ions, namely the linear HCO+ (formyl) ion and the two highly symmetric H3+ and H3O+ (hydronium) molecular ions. Regarding the HCO+ ion, we apply a quantum mechanical treatment using the Multi-channel Quantum Defect Theory (MQDT) formalism to describe the ion-electron scattering process. Our study takes into account the Renner-Teller effect in order to model the non Born-Oppenheimer vibronic coupling in linear polyatomic ions. The coupling has shown to represent the main mechanism responsible for electronic capturing in highly excited Rydberg states associated with excited vibrational levels of the ionic core. We consider all internal degrees of freedom of HCO+ and obtain the dissociative cross section as a function of the incident electron kinetic energy. We have also improved the theoretical approach by including the large permanent dipole moment of HCO+ using a generalization of the MQDT formalism. To our knowledge, this is the first time the permanent dipole moment of an ion is included in a DR study. The obtained results are in good agreement with experimental data. W also study the DR of H3+ and H3O+ symmetric ions using a simplified theoretical treatment, which focuses on the key ingredient of the DR process, the electron capture in the first excited degenerate vibrational normal mode of the ions through non Born-Oppenheimer Jahn-Teller coupling. For both ions the obtained cross sections are in very good agreement with the available experimental data. Moreover, in the case of H3+, the results reproduce previous calculations from two independent theoretical studies. Finally, we investigate the role of symmetries in few body ultra-cold collisions by considering both three and four identical atoms systems. We derive allowed rearrangements of different fragments of the system, satisfying the complete symmetry of the molecular Hamiltonian. For that purpose we establish a correspondence between constants of motion of the system in different large-distance configurations and irreducible representations of the total symmetry group. Selection rules (forbidden transitions) and allowed states, which depend on the fermionic or bosonic nature of the atoms, can be derived from these results.
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Date Issued
2010
Identifier
CFE0003552, ucf:48896
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0003552
DEVELOPMENT OF THEORETICAL AND COMPUTATIONAL METHODS FOR THREE-BODY PROCESSES
Title
DEVELOPMENT OF THEORETICAL AND COMPUTATIONAL METHODS FOR THREE-BODY PROCESSES.
Creator
Blandon Zapata, Juan, Kokoouline, Viatcheslav, University of Central Florida
Abstract / Description
This thesis discusses the development and application of theoretical and computational methods to study three-body processes. The main focus is on the calculation of three-body resonances and bound states. This broadly includes the study of Efimov states and resonances, three-body shape resonances, three-body Feshbach resonances, three-body pre-dissociated states in systems with a conical intersection, and the calculation of three-body recombination rate coefficients. The method was applied...
Show moreThis thesis discusses the development and application of theoretical and computational methods to study three-body processes. The main focus is on the calculation of three-body resonances and bound states. This broadly includes the study of Efimov states and resonances, three-body shape resonances, three-body Feshbach resonances, three-body pre-dissociated states in systems with a conical intersection, and the calculation of three-body recombination rate coefficients. The method was applied to a number of systems. A chapter of the thesis is dedicated to the related study of deriving correlation diagrams for three-body states before and after a three-body collision. More specifically, the thesis discusses the calculation of the H+H+H three-body recombination rate coefficient using the developed method. Additionally, we discuss a conceptually simple and effective diabatization procedure for the calculation of pre-dissociated vibrational states for a system with a conical intersection. We apply the method to H_3, where the quantum molecular dynamics are notoriously difficult and where non-adiabatic couplings are important, and a correct description of the geometric phase associated with the diabatic representation is crucial for an accurate representation of these couplings. With our approach, we were also able to calculate Efimov-type resonances. The calculations of bound states and resonances were performed by formulating the problem in hyperspherical coordinates, and obtaining three-body eigenstates and eigen-energies by applying the hyperspherical adiabatic separation and the slow variable discretization. We employed the complex absorbing potential to calculate resonance energies and lifetimes, and introduce an uniquely defined diabatization procedure to treat X_3 molecules with a conical intersection. The proposed approach is general enough to be applied to problems in nuclear, atomic, molecular and astrophysics.
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Date Issued
2009
Identifier
CFE0002669, ucf:48225
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0002669
THEORETICAL AND COMPUTATIONAL STUDIES OF DISSOCIATIVE RECOMBINATION OF H3+ WITH LOW KINETIC ENERGY ELECTRONS: TIME-INDEPENDENT AND TIME-DEPENDENT APPROACH
Title
THEORETICAL AND COMPUTATIONAL STUDIES OF DISSOCIATIVE RECOMBINATION OF H3+ WITH LOW KINETIC ENERGY ELECTRONS: TIME-INDEPENDENT AND TIME-DEPENDENT APPROACH.
Creator
Santos, Samantha, Kokoouline, Viatcheslav, University of Central Florida
Abstract / Description
Dissociative recombination of molecular ions by collisions with electrons is a reactive collision, in which the electronic kinetic energy is transferred to the excitation of the molecule that, then, dissociates. The goals of this dissertation was (1) to improve existing approaches in theory of DR of triatomic ions in the time-independent framework developed in recent years by Kokoouline and Greene, and (2) to develop a time-dependent theoretical framework for DR treatment based on quantum...
Show moreDissociative recombination of molecular ions by collisions with electrons is a reactive collision, in which the electronic kinetic energy is transferred to the excitation of the molecule that, then, dissociates. The goals of this dissertation was (1) to improve existing approaches in theory of DR of triatomic ions in the time-independent framework developed in recent years by Kokoouline and Greene, and (2) to develop a time-dependent theoretical framework for DR treatment based on quantum defect theory. The theoretical method developed by Kokoouline and Greene is based on multichannel quantum defect theory and accounts for the major non-Born-Oppenheimer Jahn-Teller interaction between electronic and vibrational motions of the molecule. The study of this dissertation is partially based on this method but improved, extended, and systematically applied in the framework of my thesis. This dissertation presents the calculated DR rate coefficient for H3+ within the time-independent framework and the description of the method used to obtain the (qualitative) flux with time-dependent method. The time-independent results show good agreement with experimental data from storage ring experiments. The DR rate coefficients for ortho- and para-H3+ were calculated separately and show a significant difference at very low electronic energies; a result that agrees with recent storage ring experiments. Also, it is discussed results for other isotopologues of H3+ (H2D+, D2H+, and D3+) and the results for vibrationally-excited initial states of H3+. It was found that the DR rate coefficients for vibrationally-excited initial states are larger than the rates for the ion initially in the ground vibrational state. At the end, this dissertation discuss the time-dependent calculations done with a diatomic model system.
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Date Issued
2009
Identifier
CFE0002668, ucf:48209
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0002668
The Relativistic Harmonic Oscillator and the Generalization of Lewis' Invariant
Title
The Relativistic Harmonic Oscillator and the Generalization of Lewis' Invariant.
Creator
Reinhart, Daniel, Shivamoggi, Bhimsen, Kokoouline, Viatcheslav, Dove, Adrienne, University of Central Florida
Abstract / Description
In this thesis, we determine an asymptotic solution for the one dimensional relativistic harmonicoscillator using multiple scale analysis and relate the resulting invariant to Lewis' invariant. Wethen generalize the equations leading to Lewis' invariant so they are relativistically correct. Nextwe attempt to find an asymptotic solution for the general equations by making simplifying assumptionson the parameter characterizing the adiabatic nature of the system. The first term inthe series for...
Show moreIn this thesis, we determine an asymptotic solution for the one dimensional relativistic harmonicoscillator using multiple scale analysis and relate the resulting invariant to Lewis' invariant. Wethen generalize the equations leading to Lewis' invariant so they are relativistically correct. Nextwe attempt to find an asymptotic solution for the general equations by making simplifying assumptionson the parameter characterizing the adiabatic nature of the system. The first term inthe series for Lewis' invariant corresponds to the adiabatic invariant for systems whose frequencyvaries slowly. For the relativistic case we find a new conserved quantity and seek to explore itsinterpretation.iii
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Date Issued
2019
Identifier
CFE0007712, ucf:52434
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0007712
Analysis of Nucleus Properties of the Enigmatic Comet 29P/Schwassmann-Wachmann 1
Title
Analysis of Nucleus Properties of the Enigmatic Comet 29P/Schwassmann-Wachmann 1.
Creator
Schambeau, Charles, Fernandez, Yan, Britt, Daniel, Kokoouline, Viatcheslav, Samarasinha, Nalin, University of Central Florida
Abstract / Description
We present results from a continuing effort to understand activity drivers for the enigmatic Comet 29P/Schwassmann-Wachmann 1 (SW1). SW1 has been of interest since its discovery almost 100 years ago because of its nearly continuous, quiescent activity beyond the water-sublimation line and its highly variable, outburst activity while receiving a nearly constant insolation due to its low eccentricity orbit. These characteristics make SW1 a useful target for investigating both distant cometary...
Show moreWe present results from a continuing effort to understand activity drivers for the enigmatic Comet 29P/Schwassmann-Wachmann 1 (SW1). SW1 has been of interest since its discovery almost 100 years ago because of its nearly continuous, quiescent activity beyond the water-sublimation line and its highly variable, outburst activity while receiving a nearly constant insolation due to its low eccentricity orbit. These characteristics make SW1 a useful target for investigating both distant cometary activity drivers and also cometary outburst behavior. We approach answering these ques- tions through a detailed analysis of SW1; first by measuring nucleus properties required for a more accurate nucleus thermophysical modeling and second, by applying thermal modeling to replicate its activity. Our project began with an analysis of Spitzer Space Telescope infrared observations of SW1 from 2003. Coma removal techniques when applied to the images provided nucleus photometry measurements. Application of the Near Earth Asteroid Thermal Model (NEATM) to these measured photometry values resulted in an effective nucleus radius of 32.3 (&)#177; 3.1 km and a thermal beaming parameter of 1.14 (&)#177;0.22. These results indicated that SW1 is one of the largest Jupiter Family Comets and also has a relatively smooth overall surface and/or a low thermal inertia. We next placed constraints on the nucleus' spin state through analysis of evolution seen in the coma's morphological structure through two sets of outburst coma observations. The first set analyzed are from the Kitt Peak 2.1-m telescope taken ~2 days after a major outburst in 2008. 3-D Monte Carlo coma modeling showed that the nucleus' spin period is on the order of days and/or the spin pole orientation was along the Earth's directions during observations. The second set are Hubble Space Telescope observations from 1996 taken ~15 hours after a major outburst. Modeling similarly showed a rotation period on the order of days. Due to the observing geometry differing between the 2008 and 1996 observations, we conclude the rotation period lower limit must be on the order of days even if the spin-pole direction was directed along the sub-Earth direction during one set of observations. The nucleus properties measured or constrained by our project were incorporated into a thermophysical model to replicate the quiescent activity via the sublimation of the supervolatile species CO or CO2. A progenitor nucleus was thermally evolved in SW1's current orbit using different plausible nucleus interior compositional and layering schemes. We discuss results of this analysis and additionally possibilities for future thermal modeling efforts.
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Date Issued
2018
Identifier
CFE0007585, ucf:52548
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0007585
Theoretical Study of Negative Molecular Ions Relevant to the Interstellar and Laboratory Plasma
Title
Theoretical Study of Negative Molecular Ions Relevant to the Interstellar and Laboratory Plasma.
Creator
Khamesian, Marjan, Kokoouline, Viatcheslav, Argenti, Luca, Saha, Haripada, Masunov, Artem, University of Central Florida
Abstract / Description
Recently, several negative molecular ions, CnN? (n = 1, 3, 5) and CnH? (n = 4, 6, 8), were observed in the interstellar medium (ISM). It was suggested that the anions are formed in the ISM by the process of radiative electron attachment (REA). A simple statistical model was developed in 1980's to estimate rate coefficients of the REA reactions. Some of the rate coefficients obtained in the model are consistent with the observations, the others are not. More importantly, some of the...
Show moreRecently, several negative molecular ions, CnN? (n = 1, 3, 5) and CnH? (n = 4, 6, 8), were observed in the interstellar medium (ISM). It was suggested that the anions are formed in the ISM by the process of radiative electron attachment (REA). A simple statistical model was developed in 1980's to estimate rate coefficients of the REA reactions. Some of the rate coefficients obtained in the model are consistent with the observations, the others are not. More importantly, some of the approximations employed in the model are not physically justified.The aim of this thesis is a development of a quantum-mechanical approach to study the process of radiative electron attachment to linear molecules of astrophysical interest. The approach is based on accurate ab initio calculations of electronic bound and continuum states of the negative ion. Cross sections and rate coefficients for formation of the following molecular negative ions by REA were determined: CN?, C2H?, C3N?, C4H?, C5N?, C6H?, and C8H?. All the calculations presented in the thesis were carried out using the MOLPRO and UK R-matrix (Quantemol)suites of programs. Uncertainty quantification of the results, obtained for each studied system, was performed. A second process, closely related to the radiative electron attachment, photodetachment (PD), was also studied in the thesis. Photodetachment cross sections for the CnN? (n = 1, 3, 5), CnH? (n = 4, 6, 8) and C2? molecules were determined using an approach similar to the one employed for REA from the same transition dipole moment matrix elements. The obtained REA cross sections and rate coefficients were validated by comparing the present theoretical results with the experimental data from recent photodetachment experiments.The present results suggest that the observed abundance of these ions in the ISM can hardly be explained by the REA process. In other words, these anions are formed in the interstellar medium by a process different than radiative electron attachment.Dissociative electron attachment (DEA) is another process of anion formation, which could possibly explain formation of certain molecular anions in the ISM. The ClF attachment was studied using a first principle approach.A good agreement with experimental data was demonstrated.A theoretical approach to evaluate cross sections for rotational excitation of linear neutral molecules by an electron impact was developed and applied to acetylene, HCCH. The differential cross sections for e-HCCH scattering were calculated between energies 0.1 eV and 10 eV. The momentum transfer cross section and eigenphases for e-HCCH scattering were also calculated.
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Date Issued
2017
Identifier
CFE0006612, ucf:51295
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0006612
Translocation of a semiflexible polymer through a nanopore.
Title
Translocation of a semiflexible polymer through a nanopore.
Creator
Adhikari, Ramesh, Bhattacharya, Aniket, Chen, Bo, Kokoouline, Viatcheslav, Hernandez, Florencio, University of Central Florida
Abstract / Description
The transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology....
Show moreThe transport of a biomolecule through a nanopore occurs in many biological functions such as, DNA or RNA transport across nuclear pores and the translocation of proteins across the eukaryotic endoplasmic reticulum. In addition to the biological processes, it has potential applications in technology such as, drug delivery, gene therapy, and single molecule sensing. The DNA translocation through a synthetic nanopore device is considered as the basis for cheap and fast sequencing technology. Motivated by the experimental advances, many theoretical models have been developed. In this thesis, we explore the dynamics of driven translocation of a semiflexible polymer through a nanopore in two dimensions (2D) using Langevin dynamics (LD) simulation. By carrying out extensive simulation as a function of different parameters such as, driving force, length and rigidity of the chain, viscosity of the solvent, and diameter of the nanopore, we provide a detailed description of the translocation process. Our studies are relevant for fundamental understanding of the translocation process which is essential for making accurate nano-pore based devices.
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Date Issued
2015
Identifier
CFE0005915, ucf:50830
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0005915
Conformations and Dynamics of Semi-Flexible Polymers
Title
Conformations and Dynamics of Semi-Flexible Polymers.
Creator
Huang, Aiqun, Bhattacharya, Aniket, Kokoouline, Viatcheslav, Tatulian, Suren, Campiglia, Andres, University of Central Florida
Abstract / Description
In this dissertation, we investigate the conformations, transverse fluctuations and dynamics of two-dimensional (2D) semi-flexible polymers both in the bulk and under channel confinement. We present unified scaling relations in regard to various quantities of interest for a broad range of combinations of chain length and chain stiffness using Langevin dynamics simulation. We also present a three-dimensional (3D) heterogeneous semi-flexible chain model for a double stranded DNA (dsDNA). Our...
Show moreIn this dissertation, we investigate the conformations, transverse fluctuations and dynamics of two-dimensional (2D) semi-flexible polymers both in the bulk and under channel confinement. We present unified scaling relations in regard to various quantities of interest for a broad range of combinations of chain length and chain stiffness using Langevin dynamics simulation. We also present a three-dimensional (3D) heterogeneous semi-flexible chain model for a double stranded DNA (dsDNA). Our model not only confirms the established findings for homogeneous dsDNA, but also predicts new physical phenomenon for heterogeneous dsDNA. The problems studied in this dissertation are relevant to analysis of the conformations and dynamics of biopolymers (such as DNA) in living organisms, and also offer insights for developing devices which operate on the single-molecule level.In particular, we present a unified description for the dynamics of building-blocks (monomers) of a semi-flexible chain. We consider the full range of flexibility from the case where the chain is fully flexible (no stiffness at all) to the case where the chain behaves like a rod (infinite stiffness). Our theory predicts qualitatively different sub-diffusive regimes for the monomer dynamics originating from the chain stiffness by studying the mean square displacement (MSD) of the monomers before the chain dynamics become purely diffusive.For the conformations in the bulk, we present results confirmed and agreed by two completely different models of semi-flexible polymers, with one of which is the bead-spring model (studied by Langevin dynamics) in the continuum space, the other (studied by Monte Carlo) is a self-avoiding walk chain on the square lattice, where only discrete bond angles are possible. We point out the universal features of chain conformations and fluctuations which are independent of the models.For the conformations under channel confinement, we discover qualitatively different conformations and dynamics of the chain as a function of the channel width and chain stiffness, and show how globule like shapes ((")de Gennes blobs(")) for more flexible chains continuously go over to shapes in the form of deflections from the wall ((")Odijk limit(")) for more stiff chains. We provide theoretical arguments how these regimes occur and interpolate among each other as one varies different parameters of the model. We also demonstrate the effect of physical dimensions (either 2D or 3D) on these regimes and argue that since in 2D the excluded volume (EV) effect is more severe compared to 3D, certain regimes do not exist in 2D.Finally, we study a model of a dsDNA , where both base-pairing and base-stacking interactions are accounted for albeit at a low computational cost compared to the other existing models. Our model correctly recovers the stiffness for dsDNA and ssDNA at different temperatures. Under most conditions of interest, a dsDNA can locally denature and form bubbles due to thermal fluctuations. At a critical temperature, a dsDNA undergoes a phase transition, in which the two strands of dsDNA completely melt to two single strands (two ssDNA). By considering EV interactions and calculating the bubble size distribution, recent studies have shown that this denaturation process is a first order transition. We show that for a homogeneous dsDNA made of only AT or GC pairs, our simulation results agree with the previous conclusion of first order transition, however, for sequences of periodic AT and GC regions, when the periodic size is relatively large compared to the sequence length, we show that the bubble size distribution exhibits peaks expressing the sequence pattern, and more importantly, the denaturation is no longer a first order transition.All these studies reported in the dissertation are relevant to the physics of living systems.
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Date Issued
2016
Identifier
CFE0006464, ucf:51429
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0006464
Studying Short-Period Comets and Long-Period Comets Detected by WISE/NEOWISE
Title
Studying Short-Period Comets and Long-Period Comets Detected by WISE/NEOWISE.
Creator
Kramer, Emily, Fernandez, Yan, Colwell, Joshua, Kokoouline, Viatcheslav, Klemm, Richard, Lisse, Carey, University of Central Florida
Abstract / Description
The Wide-field Infrared Survey Explorer (WISE) mission surveyed the sky in four infrared wavelength bands (3.4, 4.6, 12 and 22 ?m) between January 2010 and February 2011. During the mission, WISE serendipitously observed 160 comets, including 21 newly discovered objects. About 89 of the comets observed by WISE displayed a significant dust tail in the 12 and 22 ?m (thermal emission) bands, showing a wide range of activity levels and dust morphology. Since the observed objects are a mix of both...
Show moreThe Wide-field Infrared Survey Explorer (WISE) mission surveyed the sky in four infrared wavelength bands (3.4, 4.6, 12 and 22 ?m) between January 2010 and February 2011. During the mission, WISE serendipitously observed 160 comets, including 21 newly discovered objects. About 89 of the comets observed by WISE displayed a significant dust tail in the 12 and 22 ?m (thermal emission) bands, showing a wide range of activity levels and dust morphology. Since the observed objects are a mix of both long-period comets (LPCs) and short-period comets (SPCs), differences in their activity can be used to better understand the thermal evolution that each of these populations has undergone. For the comets that displayed a significant dust tail, we have estimated the sizes and ages of the particles using dynamical models based on the Finson-Probstein method [Finson and Probstein, 1968]. For a selection of 40 comets, we have then compared these models to the data using a novel tail-fitting method that allows the best-fit model to be chosen analytically rather than subjectively. For comets that were observed multiple times by WISE, the particle properties were estimated separately, and then compared. We find that the dust tails of both LPCs and SPCs are primarily comprised of ?mm-cm sized particles, which were the result of emission that occurred several months to several years prior to the observations. The LPCs nearly all have strong emission close to the comet's perihelion distance, and the SPCs mostly have strong emission close to perihelion, but some have strong emission well before perihelion.
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Date Issued
2014
Identifier
CFE0005823, ucf:50938
Format
Document (PDF)
PURL
http://purl.flvc.org/ucf/fd/CFE0005823