125 research outputs found
Controlled spontaneous emission
The problem of spontaneous emission is studied by a direct computer
simulation of the dynamics of a combined system: atom + radiation field. The
parameters of the discrete finite model, including up to 20k field oscillators,
have been optimized by a comparison with the exact solution for the case when
the oscillators have equidistant frequencies and equal coupling constants.
Simulation of the effect of multi-pulse sequence of phase kicks and emission by
a pair of atoms shows that both the frequency and the linewidth of the emitted
spectrum could be controlled.Comment: 25 pages including 11 figure
Excited-State Electronic Structure with Configuration Interaction Singles and TammâDancoff Time-Dependent Density Functional Theory on Graphical Processing Units
Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response TammâDancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results)
Using metadynamics to explore complex free-energy landscapes
Metadynamics is an atomistic simulation technique that allows, within the same framework, acceleration of rare events and estimation of the free energy of complex molecular systems. It is based on iteratively \u2018filling\u2019 the potential energy of the system by a sum of Gaussians centred along the trajectory followed by a suitably chosen set of collective variables (CVs), thereby forcing the system to migrate from one minimum to the next. The power of metadynamics is demonstrated by the large number of extensions and variants that have been developed. The first scope of this Technical Review is to present a critical comparison of these variants, discussing their advantages and disadvantages. The effectiveness of metadynamics, and that of the numerous alternative methods, is strongly influenced by the choice of the CVs. If an important variable is neglected, the resulting estimate of the free energy is unreliable, and predicted transition mechanisms may be qualitatively wrong. The second scope of this Technical Review is to discuss how the CVs should be selected, how to verify whether the chosen CVs are sufficient or redundant, and how to iteratively improve the CVs using machine learning approaches
Optoelectronic and Excitonic Properties of Oligoacenes: Substantial Improvements from Range-Separated Time-Dependent Density Functional Theory
The optoelectronic and excitonic properties in a series of linear acenes
(naphthalene up to heptacene) are investigated using range-separated methods
within time-dependent density functional theory (TDDFT). In these rather simple
systems, it is well-known that TDDFT methods using conventional hybrid
functionals surprisingly fail in describing the low-lying La and Lb valence
states, resulting in large, growing errors for the La state and an incorrect
energetic ordering as a function of molecular size. In this work, we
demonstrate that the range-separated formalism largely eliminates both of these
errors and also provides a consistent description of excitonic properties in
these systems. We further demonstrate that re-optimizing the percentage of
Hartree-Fock exchange in conventional hybrids to match wavefunction-based
benchmark calculations still yields serious errors, and a full 100%
Hartree-Fock range separation is essential for simultaneously describing both
of the La and Lb transitions. Based on an analysis of electron-hole transition
density matrices, we finally show that conventional hybrid functionals
overdelocalize excitons and underestimate quasiparticle energy gaps in the
acene systems. The results of our present study emphasize the importance of
both a range-separated and asymptotically-correct contribution of exchange in
TDDFT for investigating optoelectronic and excitonic properties, even for these
simple valence excitations.Comment: Accepted by the Journal of Chemical Theory and Computatio
Ab Initio Screening Approach for the Discovery of Lignin Polymer Breaking Pathways
The directed depolymerization of lignin biopolymers is of utmost relevance for the valorization or commercialization of biomass fuels. We present a computational and theoretical screening approach to identify potential cleavage pathways and resulting fragments that are formed during depolymerization of lignin oligomers containing two to six monomers. We have developed a chemical discovery technique to identify the chemically relevant putative fragments in eight known polymeric linkage types of lignin. Obtaining these structures is a crucial precursor to the development of any further kinetic modeling. We have developed this approach by adapting steered molecular dynamics calculations under constant force and varying the points of applied force in the molecule to diversify the screening approach. Key observations include relationships between abundance and breaking frequency, the relative diversity of potential pathways for a given linkage, and the observation that readily cleaved bonds can destabilize adjacent bonds, causing subsequent automatic cleavage.Massachusetts Institute of Technology (Research Support Corporation, Reed Grant)United States. Dept. of Energy. Computational Science Graduate Fellowship Program (DOE-CSGF)Burroughs Wellcome Fund (Career Award at the Scientific Interface
Computational Investigation of Acene-Modified Zinc-Porphyrin Based Sensitizers for Dye-Sensitized Solar Cells
Increased Expression of Catalase in Human Hepatoma Cells by the Soy Isoflavone, Daidzein
Silymarin alleviates hepatic oxidative stress and protects against metabolic disorders in high-fat diet-fed mice
Demonstrating the Transferability and the Descriptive Power of Sketch-Map
Increasingly, it is recognized that new automated forms of analysis are required to understand the high-dimensional output obtained from atomistic simulations. Recently, we introduced a new dimensionality reduction algorithm, sketch-map, that was designed specifically to work with data from molecular dynamics trajectories. In what follows, we provide more details on how this algorithm works and on how to set its parameters. We also test it on two well-studied Lennard-Jones clusters and show that the coordinates we extract using this algorithm are extremely robust. In particular, we demonstrate that the coordinates constructed for one particular Lennard-Jones cluster can be used to describe the configurations adopted by a second, different cluster and even to tell apart different phases of bulk Lennard-Jonesium. © 2013 American Chemical Society
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