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http://academiccommons.columbia.edu/catalog.rss?f%5Bdepartment_facet%5D%5B%5D=Chemical+Physics&q=&rows=500&sort=record_creation_date+desc
Academic Commons Search Resultsen-usMicroscopic theories of excitons and their dynamics
http://academiccommons.columbia.edu/catalog/ac:177103
Berkelbach, Timothy Charleshttp://dx.doi.org/10.7916/D8BP010FFri, 01 Aug 2014 00:00:00 +0000This thesis describes the development and application of microscopically-defined theories of excitons in a wide range of semiconducting materials. In Part I, I consider the topic of singlet exciton fission, an organic photophysical process which generates two spin-triplet excitons from one photoexcited spin-singlet exciton. I construct a theoretical framework that couples a realistic treatment of the static electronic structure with finite-temperature quantum relaxation techniques. This framework is applied separately, but consistently, to the problems of singlet fission in pentacene dimers, crystalline pentacene, and crystalline hexacene. Through this program, I am able to rationalize observed behaviors and make non-trivial predictions, some of which have been confirmed by experiment. In Part II, I present theoretical developments on the properties of neutral excitons and charged excitons (trions) in atomically thin transition metal dichalcogenides. This work includes an examination of material trends in exciton binding energies via an effective mass approach. I also present an experimental and theoretical collaboration, which links the unconventional disposition of excitons in the Rydberg series to the peculiar screening properties of atomically thin materials. The light-matter coupling in these materials is examined within low-energy models and is shown to give rise to bright and dark exciton states, which can be qualitatively labeled in analogy with the hydrogen series. In Part III, I explore theories of relaxation dynamics in condensed phase environments, with a focus on methodology development. This work is aimed towards biological processes, including resonant energy transfer in chromophore complexes and electron transfer in donor-bridge-acceptor systems. Specifically, I present a collaborative development of a numerically efficient but highly accurate hybrid approach to reduced dynamics, which exploits a partitioning of environmental degrees of freedom into those that evolve "fast" and "slow," as compared to the internal system dynamics. This method is tested and applied to the spin-boson model, a two-site Frenkel exciton model, and the seven-site Fenna-Matthews-Olson complex. I conclude with a collaborative analysis of a recently developed polaron-transformed quantum master equation, which is shown to accurately interpolate between the well-known Redfield and Forster theories, even in challenging donor-bridge-acceptor arrangements.Physical chemistry, Condensed matter physics, Chemistrytcb2112Chemistry, Chemical PhysicsDissertationsConnections between structure and dynamics in model supercooled liquids
http://academiccommons.columbia.edu/catalog/ac:188849
Hocky, Glen Maxhttp://dx.doi.org/10.7916/D80C4SZDWed, 30 Jul 2014 00:00:00 +0000In this thesis, we examine the relationship between structure and dynamics in supercooled liquids from five unique perspectives. We first study a static length scale in the liquid and compare its growth on decreasing temperature with the growth of the logarithm of relaxation times, and find them to be almost strongly correlated. We find that this length scale can distinguish between several specially chosen model liquids whose structure at the level of two-body correlations are identical but whose dynamics at a given temperature are quite different. We then study the number of normal modes necessary to capture the rearrangements in a two-dimensional supercooled liquid as it moves between inherent structures. We find that the number of modes is quite small and decreases as the system is further cooled. After that, we study the effect of a frozen amorphous boundary on the dynamics of supercooled liquids and find that the range of the effect plateaus near that system's mode coupling temperature. We also identify a dynamical crossover at a higher temperature from these data by contrasting the relaxation behavior in the directions perpendicular and parallel to the boundary. After this work, we compare particle mobility with the position of particles deemed to be in preferred local packing arrangements. We find that the correlation between slow dynamics and the location of these locally preferred structures is highly dependent on the model investigated. Finally, we study supercooled liquids that have a fraction of particles randomly fixed in equilibrium positions. We find from annealing and rapid heating experiments on these samples behavior reminiscent of experimentally produced ultrastable glasses.Chemistry, Physical chemistrygmh2123Chemistry, Chemical PhysicsDissertationsNovel Quantum Monte Carlo Approaches for Quantum Liquids
http://academiccommons.columbia.edu/catalog/ac:188891
Rubenstein, Brenda M.http://dx.doi.org/10.7916/D8N58KRKTue, 20 Aug 2013 00:00:00 +0000Quantum Monte Carlo methods are a powerful suite of techniques for solving the quantum many-body problem. By using random numbers to stochastically sample quantum properties, QMC methods are capable of studying low-temperature quantum systems well beyond the reach of conventional deterministic techniques. QMC techniques have likewise been indispensible tools for augmenting our current knowledge of superfluidity and superconductivity. In this thesis, I present two new quantum Monte Carlo techniques, the Monte Carlo Power Method and Bose-Fermi Auxiliary-Field Quantum Monte Carlo, and apply previously developed Path Integral Monte Carlo methods to explore two new phases of quantum hard spheres and hydrogen. I lay the foundation for a subsequent description of my research by first reviewing the physics of quantum liquids in Chapter One and the mathematics behind Quantum Monte Carlo algorithms in Chapter Two. I then discuss the Monte Carlo Power Method, a stochastic way of computing the first several extremal eigenvalues of a matrix too memory-intensive to be stored and therefore diagonalized. As an illustration of the technique, I demonstrate how it can be used to determine the second eigenvalues of the transition matrices of several popular Monte Carlo algorithms. This information may be used to quantify how rapidly a Monte Carlo algorithm is converging to the equilibrium probability distribution it is sampling. I next present the Bose-Fermi Auxiliary-Field Quantum Monte Carlo algorithm. This algorithm generalizes the well-known Auxiliary-Field Quantum Monte Carlo algorithm for fermions to bosons and Bose-Fermi mixtures. Despite some shortcomings, the Bose-Fermi Auxiliary-Field Quantum Monte Carlo algorithm represents the first exact technique capable of studying Bose-Fermi mixtures of any size in any dimension. In Chapter Six, I describe a new Constant Stress Path Integral Monte Carlo algorithm for the study of quantum mechanical systems under high pressures. While the eventual hope is to apply this algorithm to the exploration of yet unidentified high-pressure, low-temperature phases of hydrogen, I employ this algorithm to determine whether or not quantum hard spheres can form a low-temperature bcc solid if exchange is not taken into account. In the final chapter of this thesis, I use Path Integral Monte Carlo once again to explore whether glassy para-hydrogen exhibits superfluidity. Physicists have long searched for ways to coax hydrogen into becoming a superfluid. I present evidence that, while glassy hydrogen does not crystallize at the temperatures at which hydrogen might become a superfluid, it nevertheless does not exhibit superfluidity. This is because the average binding energy per p-H2 molecule poses a severe barrier to exchange regardless of whether the system is crystalline. All in all, this work extends the reach of Quantum Monte Carlo methods to new systems and brings the power of existing methods to bear on new problems.Theoretical physicsbr2197Chemistry, Chemical PhysicsDissertationsInvestigation of Slow Dynamics in Proteins: NMR Pulse Sequence Development and Application in Triosephosphate Isomerase
http://academiccommons.columbia.edu/catalog/ac:178828
Li, Wenbohttp://hdl.handle.net/10022/AC:P:15173Fri, 02 Nov 2012 00:00:00 +0000The dynamics of proteins on the millisecond time scale are on the same time scale as typical catalytic turnover rates, and can sometimes be closely related to enzymes' functions. Solid state NMR, equipped with magic angle spinning, is a very good technique to detect such millisecond dynamics, because it is suitable for many protein systems such as membrane proteins, and the anisotropic interactions recoupled in the solid state NMR can supply valuable geometric information regarding the dynamics. In this thesis, I mainly focus on the developing new dynamics detection pulse sequences based on previous Centerband-Only Detection of Exchange (CODEX) experiment and applying CODEX experiments to an enzyme system, triosephosphate isomerase (TIM), for studying the function of the millisecond dynamics in catalysis. Two newly developed pulse sequences, Dipolar CODEX and R-CODEX use the 13C-15N (Dipolar CODEX) and 1H-13C or 1H-15N (R-CODEX) dipolar couplings to detect dynamics. Compared with the chemical shift anisotropy used in the CODEX experiment, the dipolar coupling has a more direct relationship with the molecular geometry and could be better for extracting geometric information regarding reorientations. A special characteristic of the R-CODEX sequence is that the use of an R-type dipolar recoupling sequence can suppress the effect of 1H-1H homonuclear couplings. This approach paves the way to detect both the correlation time and reorientational angle of the dynamics in fully protonated samples. These two pulse sequences are tested by detecting the π flip motion of urea and methylsulfone imidazole. The R-CODEX experiment is compared with two other millisecond dynamics detection methods: 2D-exchange experiments and line-shape analysis, using the example of in crystalline L-phenylalanine hydrochloride. The millisecond ring flip motion of the aromatic ring in L-phenylalanine hydrochloride is characterized in detail for the first time. The comparison between these three methods shows that the R-CODEX experiment does not require a chemical shift change in the process of the motion and that it can detect the dynamics even if there is the peak overlap in the spectra. Triosephosphate isomerase (TIM) is a well-known highly efficient enzyme. Its loop motion (loop 6) has been extensively studied and been proven to be correlated with product release and be a rate-limiting step for the catalysis. Another highly conserved loop near the active site, loop 7 also has large changes in dihedral angles during ligand binding. Its motion is suspected to be correlated with loop 6 based on mutant experiments and solution NMR studies. However, the core sequence of loop 7, YGGS, is missing in the solution NMR spectrum. We assigned the GG pair in loop 7 (G209-G210) using 1-13C, 15N glycine labeling and solid state NMR experiments, and detected the loop 7's motion using 1-13C glycine labeling and CODEX experiments. We found that loop 7's motional rate (300+/-100 s-1) at -10oC agrees well with previously detected motional rates of loop 6 extrapolated from higher temperatures using an Arrhenius plot. This suggeststhat the motion of loop 6 probably correlates with loop 7. At the same time, the line-shape analysis for another GG pair (G232-G233), which forms hydrogen bonds with the ligand, indicates a ligand release rate (400+/-100 s-1) similar to loop 7's rate, supporting the hypothesis that the ligand release is also probably correlated with the motion of loop 7 and loop 6.Biophysicswl2215Chemistry, Chemical Engineering, Biological Sciences, Chemical PhysicsDissertationsSpectroscopic Studies of Abiotic and Biological Nanomaterials: Silver Nanoparticles, Rhodamine 6G Adsorbed on Graphene, and c-Type Cytochromes and Type IV Pili in Geobacter sulfurreducens
http://academiccommons.columbia.edu/catalog/ac:152155
Thrall, Elizabeth Simmonshttp://hdl.handle.net/10022/AC:P:14562Wed, 29 Aug 2012 00:00:00 +0000This thesis describes spectroscopic studies of three different systems: silver nanoparticles, the dye molecule rhodamine 6G adsorbed on graphene, and the type IV pili and c-type cytochromes produced by the dissimilatory metal-reducing bacterium Geobacter sulfurreducens. Although these systems are quite different in some ways, they can all be considered examples of nanomaterials. A nanomaterial is generally defined as having at least one dimension below 100 nm in size. Silver nanoparticles, with sub-100 nm size in all dimensions, are examples of zero-dimensional nanomaterials. Graphene, a single atomic layer of carbon atoms, is the paradigmatic two-dimensional nanomaterial. And although bacterial cells are on the order of 1 µm in size, the type IV pili and multiheme c-type cytochromes produced by G. sulfurreducens can be considered to be one- and zero-dimensional nanomaterials respectively. A further connection between these systems is their strong interaction with visible light, allowing us to study them using similar spectroscopic tools. The first chapter of this thesis describes research on the plasmon-mediated photochemistry of silver nanoparticles. Silver nanoparticles support coherent electron oscillations, known as localized surface plasmons, at resonance frequencies that depend on the particle size and shape and the local dielectric environment. Nanoparticle absorption and scattering cross-sections are maximized at surface plasmon resonance frequencies, and the electromagnetic field is amplified near the particle surface. Plasmonic effects can enhance the photochemistry of silver particles alone or in conjunction with semiconductors according to several mechanisms. We study the photooxidation of citrate by silver nanoparticles in a photoelectrochemical cell, focusing on the wavelength-dependence of the reaction rate and the role of the semiconductor substrate. We find that the citrate photooxidation rate does not track the plasmon resonance of the silver nanoparticles but instead rises monotonically with photon energy. These results are discussed in terms of plasmonic enhancement mechanisms and a theoretical model describing hot carrier photochemistry. The second chapter explores the electronic absorption and resonance Raman scattering of the dye molecule rhodamine 6G (R6G) adsorbed on graphene. Graphene has been shown to quench the fluorescence of adsorbed molecules and quantum dots, and some previous studies have reported that the Raman scattering from molecules adsorbed on graphene is enhanced. We show that reflective contrast spectroscopy can be used to obtain the electronic absorption spectrum of R6G adsorbed on graphene, allowing us to estimate the surface concentration of the dye molecule. From these results we are able to calculate the absolute Raman scattering cross-section for R6G adsorbed on bilayer graphene. We find that there is no evidence of enhancement but instead that the cross-section is reduced by more than three-fold from its value in solution. We further show that a model incorporating electromagnetic interference effects can reproduce the observed dependence of the R6G Raman intensity on the number of graphene layers. The third and final chapter describes the preliminary results from studies of the dissimilatory metal-reducing bacterium Geobacter sulfurreducens. This anaerobic bacterium couples the oxidation of organic carbon sources to the reduction of iron oxides and other extracellular electron acceptors, a type of anaerobic respiration that necessitates an electron transport chain that can move electrons from the interior of the cell to the extracellular environment. The electron transport chain in G. sulfurreducens has not been completely characterized and two competing mechanisms for the charge transport have been proposed. The first holds that G. sulfurreducens produces type IV pili, protein filaments several nanometers in width, with intrinsic metallic-like conductivity. According to this mechanism, the conductive pili mediate electron transport to extracellular acceptors. The second proposed mechanism is that charge transport proceeds by electron hopping between the heme groups in the many c-type cytochromes produced by G. sulfurreducens. In this picture, the observed conductivity of the pili is due to hopping through associated cytochrome proteins. Our aim is to explore these alternative mechanisms for electron transport in G. sulfurreducens through electrical and optical studies. We report the work we have done thus far to culture and characterize G. sulfurreducens, and we show that preliminary micro-Raman studies of G. sulfurreducens cells confirm that we can detect the spectroscopic signature of c-type cytochrome proteins. Future directions for this ongoing work are briefly discussed.Physical chemistry, Nanoscience, Biophysicsest2104Chemistry, Chemical Engineering, Chemical PhysicsDissertationsSelf-organization in systems of anisotropic particles
http://academiccommons.columbia.edu/catalog/ac:147671
Miller, William Lenealhttp://hdl.handle.net/10022/AC:P:13433Thu, 07 Jun 2012 00:00:00 +0000This dissertation presents studies on self-organization in soft matter systems. A wide variety of systems is studied, with the goal of understanding both the nonequilibrium and the equilibrium properties of this important process. In Chapter 2, we study the self-assembly of asymmetric Janus colloidal particles. We identify and systematically describe the effect of the ratio of hydrophobic to hydrophilic surface area on the nonequilibrium processes and structure formation. In Chapter 3, we examine systems of hard, aspherical particles. We demonstrate that the thermodynamics of self-organization of a system of these aspherical particle (either a system of identical particles or a polydisperse system of different-shaped particles) is well-predicted by a simple relationship between the crystallization pressure and two measures of particle asphericity borrowed from other fields. In Chapter 4, we shift focus to systems of soft particles in two dimensions and on the surface of a sphere. Soft particles are particles with a nite interaction potential at zero distance; such particles exhibit a surprisingly large variety of ordered structures at equilibrium. A similar phenomenon is seen when the study is extended to soft particles on the surface of a sphere.In Chapter 5, we study the free energy of two-component polymer brush systems in which polymers of different length are patterned in alternating stripes of specified widths on the surface of a cylinder. We present the dependence of the free energy on the polymer lengths and stripe width and a qualitative explanation of its functional form. Finally, in Chapter 6, we approach the reverse self-assembly problem. That is, we describe an algorithm for answering the reverse (and much more dicult) question, "Given a specic desired target self-assembled structure, what interparticle interactions will yield a system which will self-assemble into that structure?" We also describe a new model of interparticle interaction which should be able to generate interparticle interaction geometries with a high degree of flexibility.Physical chemistrywlm2105Chemistry, Chemical PhysicsDissertationsInteractions between 0-Dimensional and 2-Dimensional Materials
http://academiccommons.columbia.edu/catalog/ac:137554
Chen, Zheyuanhttp://hdl.handle.net/10022/AC:P:10964Mon, 22 Aug 2011 00:00:00 +0000This thesis describes two types of interactions between zero-dimensional and two-dimensional materials: energy transfer and surface diffusion. The first chapter introduces zero-dimensional and two-dimensional materials and their unique properties. Based on emerging properties different from bulk materials', several attempts have been shown to study the interaction between these two classes of materials. The second chapter presents the study on the energy transfer between zero-dimensional and two-dimensional materials, specifically semiconductor nanocrystals (or "quantum dots") and graphene. The fluorescence quenching was observed for quantum dots on graphene compared those in the absence of graphene. The strong energy transfer is through Coulomb interaction in the way similar to Forster resonant energy transfer. Based on simple assumptions, energy transfer between quantum dots and single-layer graphene was extended to quantum dots and few-layer graphene and quantitative agreement was achieved between experimental results and calculation from theory. The third chapter investigates the surface diffusion of zero-dimensional materials on a two-dimensional material. Metal adatoms diffuse on graphene and form different nanostructures depending on the supporting substrate for graphene. As a atomically thin material, graphene is susceptible to change in underlying supporting substrates. This susceptibility will introduce surface corrugation, chemical reactivity and electron-hole puddles to graphene, and finally will lead to different morphology of metal nanoparticles on graphene. Using classical nucleation theory, different diffusion constants of Au adatoms were reported on graphene supported by different substrate. Two major factors are identified to explain the difference: surface corrugation and π electronic stabilization. In the final chapter, the characterization of zero-dimensional and two-dimensional materials is discussed. It is mainly done using Raman spectroscopy, which is a non-destructive tool. Without knowing the pristine properties of materials, their interactions with other materials are beyond reach.Physical chemistryzc2145Chemistry, Chemical Engineering, Chemical PhysicsDissertations