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Academic Commons Search Resultsen-usDelving Into Dissipative Quantum Dynamics: From Approximate to Numerically Exact Approaches
https://academiccommons.columbia.edu/catalog/ac:206281
Chen, Hsing-Ta10.7916/D8M32WBNThu, 15 Jun 2017 16:09:44 +0000In this thesis, I explore dissipative quantum dynamics of several prototypical model systems via various approaches, ranging from approximate to numerically exact schemes. In particular, in the realm of the approximate I explore the accuracy of Padé–resummed master equations and the fewest switches surface hopping (FSSH) algorithm for the spin–boson model, and non-crossing approximations (NCA) for the Anderson–Holstein model. Next, I develop new and exact Monte Carlo approaches and test them on the spin–boson model. I propose well–defined criteria for assessing the accuracy of Padé-resummed quantum master equations, which correctly demarcate the regions of parameter space where the Padé approximation is reliable. I continue the investigation of spin–boson dynamics by benchmark comparisons of the semiclassical FSSH algorithm to exact dynamics over a wide range of parameters. Despite small deviations from golden-rule scaling in the Marcus regime, standard surface hopping algorithm is found to be accurate over a large portion of parameter space. The inclusion of decoherence corrections via the augmented FSSH algorithm improves the accuracy of dynamical behavior compared to exact simulations, but the effects are generally not dramatic for the cases I consider. Next, I introduce new methods for numerically exact real-time simulation based on real-time diagrammatic Quantum Monte Carlo (dQMC) and the inchworm algorithm. These methods optimally recycle Monte Carlo information from earlier times to greatly suppress the dynamical sign problem. In the context of the spin–boson model, I formulate the inchworm expansion in two distinct ways: the first with respect to an expansion in the system–bath coupling and the second as an expansion in the diabatic coupling. In addition, a cumulant version of the inchworm Monte Carlo method is motivated by the latter expansion, which allows for further suppression of the growth of the sign error. I provide a comprehensive comparison of the performance of the inchworm Monte Carlo algorithms to other exact methodologies as well as a discussion of the relative advantages and disadvantages of each. Finally, I investigate the dynamical interplay between the electron–electron interaction and the electron–phonon coupling within the Anderson–Holstein model via two complementary NCAs: the first is constructed around the weak-coupling limit and the second around the polaron limit. The influence of phonons on spectral and transport properties is explored in equilibrium, for non-equilibrium steady state and for transient dynamics after a quench. I find the two NCAs disagree in nontrivial ways, indicating that more reliable approaches to the problem are needed. The complementary frameworks used here pave the way for numerically exact methods based on inchworm dQMC algorithms capable of treating open systems simultaneously coupled to multiple fermionic and bosonic baths.Quantum chemistry, Phonons, Electron-phonon interactions, Quantum theory, Condensed matterhc2602Chemical PhysicsThesesGeneralized quantum master equations: Getting more for less
https://academiccommons.columbia.edu/catalog/ac:208929
Montoya-Castillo, Andrés10.7916/D86973Q9Thu, 15 Jun 2017 15:05:36 +0000This thesis describes the development of practical and efficient computational approaches to the quantum dynamics of complex systems. Most of the work presented here relies on the generalized quantum master equation (GQME) formalism, which provides a simple equation of motion of reduced dimensionality for a set of dynamical quantities, e.g., nonequilibrium averages and equilibrium time correlation functions. The reduced dimensionality of the GQME comes at a cost: the introduction of the memory kernel, which accounts for the influence of all ``excluded'' degrees of freedom. Focusing first on the second-order perturbative treatment of the memory kernel known as Redfield theory, I present a collaborative effort to extend its applicability into highly non-Markovian regions via a mode freezing approach. In this method, a portion of bath modes characterized by low frequencies are treated as sources of static disorder and used to calculate modified Redfield dynamics. Application of the method to the spin-boson and FMO complex models indicates that the Redfield+frozen modes scheme consistently produces dynamics that are as good or better than bare Redfield dynamics. Next, we explore GQME approach coupled to the self-consistent solution of the memory kernel, which requires the calculation of auxiliary kernels. Previous implementations of the method had shown impressive boosts in efficiency and, when approximate methods were used to calculate the auxiliary kernels, accuracy over direct calculation of nonequilibrium averages. We show that this method, when formulated from the Mori perspective, is equally applicable to nonequilibrium averages and equilibrium correlation functions. In addition, we examine the dependence of the improvements afforded by the GQME framework on the choice projection operator and kernel closure. In particular, we demonstrate that improvements in efficiency, which rely on short memory lifetimes, are sensitively dependent on the choice of projection operator, and that the choice of kernel closure directly dictates the improvements in accuracy. In addition, we present evidence that indicates that the success of the GQME formalism when the auxiliary kernels are calculated via semi- and quasi-classical methods is largely due to the exact sampling of bath operators at t=0 required by the calculation of specific kernel closures. Next, we provide analytical arguments that delineate when the GQME framework coupled to the self-consistent solution of the memory kernel is likely to provide improvements in efficiency and accuracy. Finally, we present a path integral framework that can efficiently render the partially Wigner-transformed canonical density operator for systems coupled linearly to harmonic baths. This approach permits the direct calculation of any thermodynamic quantity and can be integrated into dynamical schemes like the Ehrenfest, surface hopping, or linearized semi-classical initial value representation methods to calculate equilibrium correlation functions.Quantum theory, Chemistry, Physical and theoretical, Condensed matter, Chemistryam3720Chemical PhysicsThesesOptical Spectroscopy of Excitons at the Interfaces of Nanostructures
https://academiccommons.columbia.edu/catalog/ac:208539
Raja, Archana10.7916/D82R3RMJThu, 15 Jun 2017 15:00:37 +0000Atomically thin quasi-two-dimensional materials like graphene and transition metal dichalcogenide (TMDC) layers exhibit extraordinary optical and electrical properties. They have not only been used as testing grounds for fundamental research but also show promise for their viability in optoelectronics, photovoltaics and photocatalysis, to name a few technological applications. In practice, seldom are these materials used in isolation. One often finds them as part of a multicomponent structure, or heterostructure. In a similar spirit as the influence of solvents on the properties of molecular complexes, nanomaterials are also affected by their dielectric environment. Engineering the effect of the surroundings on the excitations in these materials is both a challenge and an opportunity. Moreover, understanding the transport of energy and charge through these heterostructures is crucial for device design. In this dissertation I will explore the properties of excitations in zero-dimensional and two-dimensional nanostructures and their dependence on the details of the environment using optical spectroscopy. Here, I discuss three of the projects that I undertook during my graduate studies.
The first project concerns the efficient near-field, non-radiative energy transfer (NRET) of photo-excited carriers from semiconductor nanocrystals to graphene and a TMDC, molybdenum disulfide. Photoluminescence quenching of single quantum dots and time-resolved photoluminescence were used to quantify the rate of energy transfer. The NRET rate exhibited surprisingly opposite trends with increasing number of layers of the acceptor 2D sheet. The rate increased with increasing thickness of adjacent graphene layers but decreased with increasing thickness of MoS₂. A model based on classical electromagnetism could successfully explain the countervailing trends in terms of the competition between the dissipative channels and reduction of the electric field within the 2D material.
In the next project, the exciton binding energy and band gap in another TMDC, monolayer WS₂, were tuned via dielectric screening from the environment. Monolayers of WS₂ were capped with graphene layers of varying thickness (1 – 4 layers). The excitonic states of WS₂ in the resulting heterostructures were detected using reflectance contrast spectroscopy and theoretically studied by a semi-classical model. The binding energy of the exciton was halved to 150 meV by placement of a single layer of graphene adjacent to the WS₂. Furthermore, this dramatic decrease in the binding energy is accompanied by a reduction of the band gap by the same amount. Additionally, the average spacing between the graphene and WS₂ was also identified to be a critical parameter with respect to dielectric screening of the electron - hole interaction. This offers a flexible alternative for the external manipulation of the Coulomb interaction.
In the final part, I study how excitons in WS₂ couple and scatter with the excitations of the lattice or phonons. The importance of this study stems from the contribution of the scattering rates to the spectral width of the excitonic feature, the dephasing dynamics and thermal transport. The transition from direct to indirect band gap semiconductor from mono- to bilayer is expected to add an additional scattering channel via phonon emission. Through temperature dependent reflectance contrast and photoluminescence spectroscopy, the scattering rate for the phonon emission and absorption processes have been quantified. Comparing the results to data reported in the literature, it is understood that the striking change for the scattering rates is expected only at the mono- to bilayer transition for WS₂. The results suggest material thickness as a handle for engineering exciton - phonon interactions at the nanoscale.Nanostructures, Graphene, Heterostructures, Nanostructured materials, Chemistry, Physical and theoretical, Physics, Materials sciencear3125Chemical PhysicsThesesWinning the cellular lottery: how proteins reach and recognize targets in DNA
https://academiccommons.columbia.edu/catalog/ac:202311
Redding, Sy Eugene10.7916/D8FF3RMVWed, 14 Jun 2017 19:49:16 +0000Many aspects of biology depend on the ability of DNA-binding proteins to locate specific binding sites within the genome. This search process is required at the beginning of all site-specific protein-DNA interactions, and has the potential to act as the first stage of biological regulation. Given the difficulty of pinpointing a small region of DNA, within even simple genomes, it is expected that proteins are adapted to use specialized mechanisms, collectively referred to as facilitated diffusion [Berg et al., 1981], to effectively reduce the dimensionality of their searches, and rapidly find their targets. Here, we use a combination of nanofabricated microfluidic devices and single-molecule microscopy to determine whether facilitated diffusion contributes to all DNA target searches. We investigate promoter binding by E. coli RNA polymerase, foreign DNA recognition by CRISPR-Cas complexes, and Rad51’s homology search during recombination. In each example, we observe that the target searches proceed without extensive use of facilitated diffusion; rather, consideration of these non-facilitated target searches reveals an alternative search strategy. We show that instead of reducing the dimensionality of their searches, these proteins, reduce search complexity by minimizing unproductive interactions with DNA, thereby increase the probability of locating a specific DNA target.Promoters (Genetics), DNA-protein interactions, DNA-binding proteins, Biophysics, Biochemistry, Biologyser2153Chemical PhysicsThesesUltrafast Exciton Dynamics at Molecular Surfaces
https://academiccommons.columbia.edu/catalog/ac:194127
Monahan, Nicholas R.10.7916/D84T6J7KWed, 14 Jun 2017 19:48:34 +0000Further improvements to device performance are necessary to make solar energy conversion a compelling alternative to fossil fuels. Singlet exciton fission and charge separation are two processes that can heavily influence the power conversion efficiency of a solar cell. During exciton fission one singlet excitation converts into two triplet excitons, potentially doubling the photocurrent generated by higher energy photons. There is significant discord over the singlet fission mechanism and of particular interest is whether the process involves a multiexciton intermediate state. I used time-resolved two-photon photoemission to investigate singlet fission in hexacene thin films, a model system with strong electronic coupling. My results indicate that a multiexciton state forms within 40 fs of photoexcitation and loses singlet character on a 280 fs timescale, creating two triplet excitons. This is concordant with the transient absorption spectra of hexacene single crystals and definitively proves that exciton fission in hexacene proceeds through a multiexciton state. This state is likely common to all strongly-coupled systems and my results suggest that a reassessment of the generally-accepted singlet fission mechanism is required. Charge separation is the process of splitting neutral excitons into carriers that occurs at donor-acceptor heterojunctions in organic solar cells. Although this process is essential for device functionality, there are few compelling explanations for why it is highly efficient in certain organic photovoltaic systems. To investigate the charge separation process, I used the model system of charge transfer excitons at hexacene surfaces and time-resolved two-photon photoemission. Charge transfer excitons with sufficient energy spontaneously delocalize, growing from about 14 nm to over 50 nm within 200 fs. Entropy drives this delocalization, as the density of states within the Coulomb potential increases significantly with energy. This charge separation mechanism should occur at all donor-acceptor interfaces. My results show that entropy facilitates charge separation and indicate that the density of acceptor states should be a design consideration when constructing organic solar cells.Excited state chemistry, Solar cells--Technological innovations, Solar cells--Design and construction, Picosecond pulses, Exciton theory, Chemistry, Physical and theoretical, Condensed matternrm2136Chemical PhysicsThesesAntibody loop modeling methods and applications
https://academiccommons.columbia.edu/catalog/ac:200598
Murrett, Colleen10.7916/D8HQ3XZSMon, 12 Jun 2017 17:37:22 +0000This thesis describes improvements to our protein loop structure prediction algorithm and use of this algorithm to inform a computational investigation of anti-HIV antibodies. First, in Section I, we outline improvements to the Protein Local Optimization Program ("Plop") that allow us to reliably restore long loops containing secondary structure elements, and predict nativelike conformations for loops whose surroundings deviate from the native crystal structure context. Shifting to focus exclusively on antibody hypervariable loop prediction, we also benchmark our results in the community-wide Second Antibody Modeling Assessment. Plop can now be reliably deployed as a tool for understanding important biological systems. In Section II, we start from a system of interest - broadly neutralizing antibodies against HIV-1 - with the long-term goal of computationally identifying more potent VRC01-class anti-HIV antibodies. We show proof of concept results for predicting relative binding affinity upon mutation using free energy perturbation (FEP) simulations for the VRC01 antibody binding to glycoprotein gp120. Using the protocols developed in Section I, we provide case studies for using Plop to understand key FEP results and guide future experiments.HIV antibodies, Homology (Biology), Proteins--Structure--Mathematical models, Algorithms, Chemistry, Biophysicscsm2161Chemical PhysicsThesesAdvancing Loop Prediction to Ultra-High Resolution Sampling
https://academiccommons.columbia.edu/catalog/ac:201952
Miller, Edward Blake10.7916/D8R78CJ1Thu, 08 Jun 2017 20:17:42 +0000Homology modeling is integral to structure-based drug discovery. Robust homology modeling to atomic-level accuracy requires in the general case successful prediction of protein loops containing small segments of secondary structure. For loops identified to possess α-helical segments, an alternative dihedral library is employed composed of (phi,psi) angles commonly found in helices. Even with imperfect knowledge coming from sequence-based secondary structure, helix or hairpin embedded loops, up to 17 residues in length, are successfully predicted to median sub-angstrom RMSD. Having demonstrated success with these cases, performance costs for these and other similar long loop predictions will be discussed. Dramatic improvements in both speed and accuracy are possible through the development of a Cβ-based scoring function, applicable to hydrophobic residues, that can be applied as early as half-loop buildup. With this scoring function, up to a 30-fold reduction in the cost to produce competitive sub-2 A loops are observed. Through the use of this scoring function, an efficient method will be presented to achieve ultra-high resolution buildup that restrains combinatorial explosion and offers an alternative to the current approach to full-loop buildup. This novel method is designed to be inherently suitable for homology model refinement.Sequence alignment (Bioinformatics), Proteins--Mathematical models, Chemistry, Physical and theoretical, Chemistryebm2134Chemical PhysicsThesesConnections between structure and dynamics in model supercooled liquids
https://academiccommons.columbia.edu/catalog/ac:188849
Hocky, Glen Max10.7916/D80C4SZDThu, 08 Jun 2017 20:14:25 +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, Chemistry, Physical and theoreticalgmh2123Chemical PhysicsThesesMicroscopic theories of excitons and their dynamics
https://academiccommons.columbia.edu/catalog/ac:177103
Berkelbach, Timothy Charles10.7916/D8BP010FThu, 08 Jun 2017 20:09:29 +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.Chemistry, Physical and theoretical, Condensed matter, Chemistrytcb2112Chemical PhysicsThesesNovel Quantum Monte Carlo Approaches for Quantum Liquids
https://academiccommons.columbia.edu/catalog/ac:188891
Rubenstein, Brenda M.10.7916/D8N58KRKThu, 08 Jun 2017 16:06:47 +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.Physicsbr2197Chemical PhysicsThesesSpectroscopic Studies of Abiotic and Biological Nanomaterials: Silver Nanoparticles, Rhodamine 6G Adsorbed on Graphene, and c-Type Cytochromes and Type IV Pili in Geobacter sulfurreducens
https://academiccommons.columbia.edu/catalog/ac:152155
Thrall, Elizabeth Simmons10.7916/D8CF9X66Wed, 07 Jun 2017 17:01:50 +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.Chemistry, Physical and theoretical, Nanoscience, Biophysicsest2104Chemical PhysicsThesesSelf-organization in systems of anisotropic particles
https://academiccommons.columbia.edu/catalog/ac:147671
Miller, William Leneal10.7916/D8PC38GRWed, 07 Jun 2017 16:59:56 +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.Chemistry, Physical and theoreticalwlm2105Chemical PhysicsThesesInvestigation of Slow Dynamics in Proteins: NMR Pulse Sequence Development and Application in Triosephosphate Isomerase
https://academiccommons.columbia.edu/catalog/ac:178828
Li, Wenbo10.7916/D8QJ7QDSWed, 07 Jun 2017 16:59:17 +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.Biophysicswl2215Chemical PhysicsThesesInteractions between 0-Dimensional and 2-Dimensional Materials
https://academiccommons.columbia.edu/catalog/ac:137554
Chen, Zheyuan10.7916/D8WQ09SCWed, 07 Jun 2017 02:48:17 +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 Ï€ 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.Chemistry, Physical and theoreticalzc2145Chemical PhysicsTheses