Browsing by Author "AspuruGuzik, Alan"
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Absence of Quantum Oscillations and Dependence on Site Energies in Electronic Excitation Transfer in the Fenna–Matthews–Olson Trimer
Ritschel, Gerhard; Roden, Jan; Strunz, Walter T.; AspuruGuzik, Alán; Eisfeld, Alexander Jurgen (American Chemical Society, 2011)Energy transfer in the photosynthetic Fenna–Matthews–Olson (FMO) complex of green sulfur bacteria is studied numerically taking all three subunits (monomers) of the FMO trimer and the recently found eighth bacteriochlorophyll ... 
Accelerated Computational Discovery of HighPerformance Materials for Organic Photovoltaics by Means of Cheminformatics
OlivaresAmaya, Roberto; AmadorBedolla, Carlos; Hachmann, Johannes; AtahanEvrenk, Sule; SánchezCarrera, Roel S.; Vogt, Leslie; AspuruGuzik, Alán (Royal Society of Chemistry, 2011)In this perspective we explore the use of strategies from drug discovery, pattern recognition, and machine learning in the context of computational materials science. We focus our discussion on the development of donor ... 
Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units
Watson, Mark A.; OlivaresAmaya, Roberto; Edgar, Richard G.; Arias, Tomás; AspuruGuzik, Alán (Institute of Electrical and Electronics Engineers, 2010)Graphical processing units are now being used with dramatic effect to accelerate quantum chemistry calculations. However, early work exposed challenges involving memory bottlenecks and insufficient numerical precision. ... 
Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library
OlivaresAmaya, Roberto; Watson, Mark A.; Edgar, Richard G; Vogt, Leslie Ann; Shao, Yihan; AspuruGuzik, Alan (American Chemical Society, 2010)Two new tools for the acceleration of computational chemistry codes using graphical processing units (GPUs) are presented. First, we propose a general blackbox approach for the efficient GPU acceleration of matrix−matrix ... 
Accelerating ResolutionoftheIdentity Second Order MøllerPlesset Quantum Chemistry Calculations with Graphical Processing Units
Vogt, Leslie Ann; OlivaresAmaya, Roberto; Kermes, Sean; Shao, Yihan; AmadorBedolla, Carlos; AspuruGuzik, Alan (American Chemical Society, 2008)The modification of a general purpose code for quantum mechanical calculations of molecular properties (QChem) to use a graphical processing unit (GPU) is reported. A 4.3x speedup of the resolutionoftheidentity ... 
Adiabatic quantum optimization in the presence of discrete noise: Reducing the problem dimensionality
Mandra, Salvatore; Guerreschi, Gian Giacomo; AspuruGuzik, Alan (American Physical Society (APS), 2015)Adiabatic quantum optimization is a procedure to solve a vast class of optimization problems by slowly changing the Hamiltonian of a quantum system. The evolution time necessary for the algorithm to be successful scales ... 
Adiabatic Quantum Simulation of Quantum Chemistry
Babbush, Ryan Joseph; Love, Peter; AspuruGuzik, Alan (Nature Publishing Group, 2014)We show how to apply the quantum adiabatic algorithm directly to the quantum computation of molecular properties. We describe a procedure to map electronic structure Hamiltonians to 2body qubit Hamiltonians with a small ... 
Adiabatic Quantum Simulators
Biamonte, J. D; Bergholm, V.; Whitfield, James D.; Fitzsimons, J.; AspuruGuzik, Alan (2011)In his famous 1981 talk, Feynman proposed that unlike classical computers, which would presumably experience an exponential slowdown when simulating quantum phenomena, a universal quantum simulator would not. An ideal ... 
Advances in Ab Initio Modeling of the ManyBody Effects of Dispersion Interactions in Functional Organic Materials
Forsythe, Martin Blood Zwirner (20151204)Accurate treatment of the longrange electron correlation energy, including dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate ... 
Algorithms Bridging Quantum Computation and Chemistry
McClean, Jarrod Ryan (20150513)The design of new materials and chemicals derived entirely from computation has long been a goal of computational chemistry, and the governing equation whose solution would permit this dream is known. Unfortunately, the ... 
Analytical nuclear gradients for the rangeseparated manybody dispersion model of noncovalent interactions
BloodForsythe, Martin; Markovich, Thomas Lee; DiStasio, Robert A.; Car, Roberto; AspuruGuzik, Alan (Royal Society of Chemistry (RSC), 2016)An accurate treatment of the longrange electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. ... 
Anion Stabilization in Electrostatic Environments
OlivaresAmaya, Roberto; Stopa, Michael P; Andrade, Xavier; Watson, Mark A.; AspuruGuzik, Alan (American Chemical Society, 2011)Excess charge stabilization of molecules in metallic environments is of particular importance for fields such as molecular electronics and surface chemistry. We study the energetics of benzene and its anion between two ... 
Anomalously Rapid Tunneling: Charge Transport across SelfAssembled Monolayers of Oligo(ethylene glycol)
Baghbanzadeh, Mostafa; Bowers, Carleen M.; Rappoport, Dmitrij; ?aba, Tomasz; Yuan, Li; Kang, Kyungtae; Liao, KungChing; Gonidec, Mathieu; Rothemund, Philipp Josef Michael; Cyganik, Piotr; AspuruGuzik, Alan; Whitesides, George McClelland (American Chemical Society (ACS), 2017)This paper describes charge transport by tunneling across selfassembled monolayers (SAMs) of thiolterminated derivatives of oligo(ethylene glycol) (HS(CH2CH2O)nCH3; HS(EG)nCH3); these SAMs are positioned between gold ... 
Application of Compressed Sensing to the Simulation of Atomic Systems
Andrade, Xavier; Sanders, Jacob Nathan; AspuruGuzik, Alan (Proceedings of the National Academy of Sciences, 2012)Compressed sensing is a method that allows a significant reduction in the number of samples required for accurate measurements in many applications in experimental sciences and engineering. In this work, we show that ... 
Atomistic Study of Energy Funneling in the LightHarvesting Complex of Green Sulfur Bacteria
Huh, Joonsuk; Saikin, Semion K.; Brookes, Jennifer Clare; Valleau, Stephanie; Fujita, Takatoshi; AspuruGuzik, Alan (American Chemical Society (ACS), 2014)Phototrophic organisms such as plants, photosynthetic bacteria, and algae use microscopic complexes of pigment molecules to absorb sunlight. Within the lightharvesting complexes, which frequently have several functional ... 
Atomistic Study of the LongLived Quantum Coherences in the FennaMatthewsOlson Complex
Shim, Sangwoo; Rebentrost, Patrick; Valleau, Stephanie; AspuruGuzik, Alan (Biophysical Society, 2011)A remarkable amount of theoretical research has been carried out to elucidate the physical origins of the recently observed longlived quantum coherence in the electronic energy transfer process in biological photosynthetic ... 
Automatic Chemical Design Using a DataDriven Continuous Representation of Molecules
GómezBombarelli, Rafael; Wei, Jennifer Nansean; Duvenaud, David; HernándezLobato, José Miguel; SánchezLengeling, Benjamín; Sheberla, Dennis; AguileraIparraguirre, Jorge; Hirzel, Timothy D.; Adams, Ryan Prescott; AspuruGuzik, Alan (American Chemical Society (ACS), 2018)We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through ... 
A Bayesian approach to calibrating highthroughput virtual screening results and application to organic photovoltaic materials
PyzerKnapp, Edward O.; Simm, Gregor N.; AspuruGuzik, Alan (Royal Society of Chemistry (RSC), 2016)A novel approach for calibrating quantumchemical properties determined as part of a highthroughput virtual screen to experimental analogs is presented. Information on the molecular graph is extracted through the use of ... 
Bayesian network structure learning using quantum annealing
O’Gorman, B.; Babbush, Ryan Joseph; PerdomoOrtiz, A.; AspuruGuzik, Alan; Smelyanskiy, V. (Springer Science + Business Media, 2015)We introduce a method for the problem of learning the structure of a Bayesian network using the quantum adiabatic algorithm. We do so by introducing an efficient reformulation of a standard posteriorprobability scoring ... 
A Benchmark Quantum Monte Carlo Study of Molecular Crystal Polymorphism: A Challenging Case for DensityFunctional Theory
Watson, Mark A.; Hongo, Kenta; Iitaka, Toshiaki; AspuruGuzik, Alan (American Chemical Society, 2012)We have applied the diffusion Monte Carlo (DMC) method, for the first time, to an organic molecular crystal (paradiiodobenzene) in order to determine the relative stability of its two well known polymorphs. The DMC result ...