1,720,960 research outputs found
Densities of states for disordered systems from free probability
No full textWe investigate how free probability allows us to approximate the density of states in tight-binding models of disordered electronic systems. Extending our previous studies of the Anderson model in one dimension with nearest-neighbor interactions [Chen et al., Phys. Rev. Lett. 109, 036403 (2012)], we find that free probability continues to provide accurate approximations for systems with constant interactions on two- and three-dimensional lattices or with next-nearest-neighbor interactions, with the results being visually indistinguishable from the numerically exact solution. For systems with disordered interactions, we observe a small but visible degradation of the approximation. To explain this behavior of the free approximation, we develop and apply an asymptotic error analysis scheme to show that the approximation is accurate to the eighth moment in the density of states for systems with constant interactions, but is only accurate to sixth order for systems with disordered interactions. The error analysis also allows us to calculate asymptotic corrections to the density of states, allowing for systematically improvable approximations as well as insight into the sources of error without requiring a direct comparison to an exact solution.National Science Foundation (U.S.) (SOLAR Grant 1035400)National Science Foundation (U.S.). Graduate Research Fellowshi
Performance of Bootstrap Embedding for long-range interactions and 2D systems
Get PDFFragment embedding approaches offer the possibility of accurate description of strongly correlated systems with low-scaling computational expense. In particular, wave function embedding approaches have demonstrated the ability to subdivide systems across highly entangled regions, promising wide applicability for a number of challenging systems. In this paper, we focus on the wave function embedding method Bootstrap Embedding, extending it to the Pariser–Parr–Pople and 2D Hubbard models in order to evaluate the behaviour of the method in systems that are less amenable to local fragment embedding. We find that Bootstrap Embedding remains accurate for these systems, and we investigate how fragment size, shape, and choice of matching conditions affect the results. We also evaluate the properties of Bootstrap Embedding that lead to the method's favourable convergence properties. Keywords: Embedding; correlation; Bootstrap; DMETNational Science Foundation (U.S.) (Grant CHE-1464804
Salt Effect Accelerates Site-Selective Cysteine Bioconjugation
No full textHighly efficient and selective chemical reactions are desired. For small molecule chemistry, the reaction rate can be varied by changing the concentration, temperature, and solvent used. In contrast for large biomolecules, the reaction rate is difficult to modify by adjusting these variables because stringent biocompatible reaction conditions are required. Here we show that adding salts can change the rate constant over 4 orders of magnitude for an arylation bioconjugation reaction between a cysteine residue within a four-residue sequence (π- clamp) and a perfluoroaryl electrophile. Biocompatible ammonium sulfate significantly enhances the reaction rate without influencing the site-specificity of π-clamp mediated arylation, enabling the fast synthesis of two site-specific antibody-drug conjugates that selectively kill HER2-positive breast cancer cells. Computational and structure-reactivity studies indicate that salts may tune the reaction rate through modulating the interactions between the π-clamp hydrophobic side chains and the electrophile. On the basis of this understanding, the salt effect is extended to other bioconjugation chemistry, and a new regioselective alkylation reaction at π-clamp cysteine is developed.MIT Faculty Start-up FundNational Institutes of Health (U.S.) (R01GM110535)Sontag Foundation (Distinguished Scientist Award)Bristol-Myers Squibb Company (Graduate Fellowship in Synthetic Organic Chemistry)David H. Koch Institute for Integrative Cancer Research at MIT (Koch Graduate Fellowship in Cancer Research)Massachusetts Institute of Technology. Department of Chemistry (George Büchi Research Fellowship)National Science Foundation (U.S.). Graduate Research Fellowship ProgramGreat Britain. Royal Commission for the Exhibition of 1851 (Research Fellowship)National Science Foundation (U.S.) (0070319)National Institutes of Health (U.S.) (S10 OD016326
-SCF: A Direct Energy-targeting Method To Mean-field Excited States
No full textThe mean-field solutions of electronic excited states are much less
accessible than ground state (e.g.\ Hartree-Fock) solutions. Energy-based
optimization methods for excited states, like -scf, tend to fall into
the lowest solution consistent with a given symmetry -- a problem known as
"variational collapse". In this work, we combine the ideas of direct
energy-targeting and variance-based optimization in order to describe excited
states at the mean-field level. The resulting method, -scf, has several
advantages. First, it allows one to target any desired excited state by
specifying a single parameter: a guess of the energy of that state. It can
therefore, in principle, find \emph{all} excited states. Second, it avoids
variational collapse by using a variance-based, unconstrained local
minimization. As a consequence, all states -- ground or excited -- are treated
on an equal footing. Third, it provides an alternate approach to locate
-scf solutions that are otherwise inaccessible by the usual non-aufbau
configuration initial guess. We present results for this new method for small
atoms (He, Be) and molecules (H2, HF).Comment: This paper has been withdrawn by the author due to a crucial sign
error in equation 1
π-Clamp-mediated cysteine conjugation
No full textSite-selective functionalization of complex molecules is one of the most significant challenges in chemistry. Typically, protecting groups or catalysts must be used to enable the selective modification of one site among many that are similarly reactive, and general strategies that selectively tune the local chemical environment around a target site are rare. Here, we show a four-amino-acid sequence (Phe-Cys-Pro-Phe), which we call the ‘π-clamp’, that tunes the reactivity of its cysteine thiol for site-selective conjugation with perfluoroaromatic reagents. We use the π-clamp to selectively modify one cysteine site in proteins containing multiple endogenous cysteine residues. These examples include antibodies and cysteine-based enzymes that would be difficult to modify selectively using standard cysteine-based methods. Antibodies modified using the π-clamp retained binding affinity to their targets, enabling the synthesis of site-specific antibody–drug conjugates for selective killing of HER2-positive breast cancer cells. The π-clamp is an unexpected approach to mediate site-selective chemistry and provides new avenues to modify biomolecules for research and therapeutics.Massachusetts Institute of Technology (Start-up Funds)National Institutes of Health (U.S.) (NIH R01GM110535)Sontag Foundation (Distinguished Scientist Award)Massachusetts Institute of Technology. Department of Chemistry (George Buchi Research Fellowship)David H. Koch Institute for Integrative Cancer Research at MIT (Graduate Fellowship)Bristol-Myers Squibb Company (Graduate Fellowship in Synthetic Organic Chemistry)National Science Foundation (U.S.) (Graduate Research Fellow
Studies of and methods for electronic properties of large chemical systems
No full textThesis: Ph. D. in Physical Chemistry, Massachusetts Institute of Technology, Department of Chemistry, 2016.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Cataloged from student-submitted PDF version of thesis.Includes bibliographical references (pages 169-196).In this thesis, we explore various approaches to modeling electronic properties of large chemical systems, a challenge for theoretical and computational chemistry. We first model experimental systems with conventional electronic structure by excerpting a region of interest: a few amino acids near the reactive site of a protein, an exciplex dimer in a thin-film LED, and a few donor/acceptor molecules at an organic/organic interface. We find that these models work well for explaining experiments provided we can identify a local region that captures the property of interest. Second, we consider a situation in which the property of interest is not local. We investigate the Anderson model of localization in disordered materials, using the tools of random matrix theory. We use free probability to approximately compute the density of states of a Hamiltonian matrix ensemble without exact diagonalization. We develop an error analysis for this method, and show that it is accurate to the eighth moment of the density of states. Finally, we apply the method to various extensions of the Anderson model, to good result. Third, we develop a wavefunction-in-wavefunction embedding theory for strongly correlated systems. We base our work on Density Matrix Embedding Theory (DMET). We extend the original DMET equations to account for correlation in the bath via an antisymmetrized geminal power (AGP) wave function. The resulting formalism has a number of advantages. First, it allows one to properly treat the weak correlation limit of independent pairs, which DMET is unable to do with a mean-field bath. Second, it associates a size extensive correlation energy with a given density matrix (for the models tested), which AGP by itself is incapable of providing. Third, it provides a reasonable description of charge redistribution in strongly correlated but non-periodic systems. We then describe a new electronic embedding method based on DMET, dubbed "Bootstrap Embedding," a self-consistent wavefunction-in-wavefunction embedding theory that uses overlapping fragments to improve the description of fragment edges. We find Bootstrap Embedding converges rapidly with embedded fragment size, overcoming the surface-area-to-volume-ratio error typical of many embedding methods. Fourth, we employ semiempirical neglect of diatomic differential overlap (NDDO) methods as force fields for liquid water. Using force matching, we design a reparameterized NDDO model and find that it qualitatively reproduces the experimental radial distribution function of water, as well as various monomer, dimer, and bulk properties that standard NDDO method do not. This suggests that the apparent limitations of NDDO models are primarily due to poor parameterization and not to the NDDO approximations themselves. We identify the physical parameters that most influence the condensed phase properties. These results help to elucidate the chemistry that a semiempirical molecular orbital picture of water must capture. We conclude that properly parameterized NDDO models could be useful for simulations that require electronically detailed explicit solvent, including the calculation of redox potentials and simulation of charge transfer and photochemistry.by Matthew Gregory Welborn.Ph. D. in Physical Chemistr
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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