Classical dynamics of triatomic systems: Energized harmonic molecules

The dynamical assumptions underlying the Slater and RRK classical-mechanical theories of unimolecular reaction rates are investigated. The predictions of these theories for several nonlinear, triatomic, harmonically bonded molecular models are compared with the results obtained from the integration of the classical equations of motion. The accuracy of the small-vibration and weak-coupling assumptions are found to break down at energies above about one-quarter of a bond dissociation energy. Nonetheless, the small-vibration approximation predicts reaction frequencies in good agreement with the exact results for the models. The effects of rotation on intramolecular energy exchange are examined and found to be significant

Hooke's law correlation in two-electron systems

We study the properties of the Hooke's law correlation energy (\Ec), defined as the correlation energy when two electrons interact {\em via} a harmonic potential in a $D$-dimensional space. More precisely, we investigate the $^1S$ ground state properties of two model systems: the Moshinsky atom (in which the electrons move in a quadratic potential) and the spherium model (in which they move on the surface of a sphere). A comparison with their Coulombic counterparts is made, which highlights the main differences of the \Ec in both the weakly and strongly correlated limits. Moreover, we show that the Schr\"odinger equation of the spherium model is exactly solvable for two values of the dimension ($D = 1 \text{and} 3$), and that the exact wave function is based on Mathieu functions.Comment: 7 pages, 5 figure

A unified electrostatic and cavitation model for first-principles molecular dynamics in solution

The electrostatic continuum solvent model developed by Fattebert and Gygi is combined with a first-principles formulation of the cavitation energy based on a natural quantum-mechanical definition for the surface of a solute. Despite its simplicity, the cavitation contribution calculated by this approach is found to be in remarkable agreement with that obtained by more complex algorithms relying on a large set of parameters. Our model allows for very efficient Car-Parrinello simulations of finite or extended systems in solution, and demonstrates a level of accuracy as good as that of established quantum-chemistry continuum solvent methods. We apply this approach to the study of tetracyanoethylene dimers in dichloromethane, providing valuable structural and dynamical insights on the dimerization phenomenon

A simple and surprisingly accurate approach to the chemical bond obtained from dimensional scaling

We present a new dimensional scaling transformation of the Schrodinger equation for the two electron bond. This yields, for the first time, a good description of the two electron bond via D-scaling. There also emerges, in the large-D limit, an intuitively appealing semiclassical picture, akin to a molecular model proposed by Niels Bohr in 1913. In this limit, the electrons are confined to specific orbits in the scaled space, yet the uncertainty principle is maintained because the scaling leaves invariant the position-momentum commutator. A first-order perturbation correction, proportional to 1/D, substantially improves the agreement with the exact ground state potential energy curve. The present treatment is very simple mathematically, yet provides a strikingly accurate description of the potential energy curves for the lowest singlet, triplet and excited states of H_2. We find the modified D-scaling method also gives good results for other molecules. It can be combined advantageously with Hartree-Fock and other conventional methods.Comment: 4 pages, 5 figures, to appear in Phys. Rev. Letter

The tensor hypercontracted parametric reduced density matrix algorithm: coupled-cluster accuracy with O(r^4) scaling

Tensor hypercontraction is a method that allows the representation of a high-rank tensor as a product of lower-rank tensors. In this paper, we show how tensor hypercontraction can be applied to both the electron repulsion integral (ERI) tensor and the two-particle excitation amplitudes used in the parametric reduced density matrix (pRDM) algorithm. Because only O(r) auxiliary functions are needed in both of these approximations, our overall algorithm can be shown to scale as O(r4), where r is the number of single-particle basis functions. We apply our algorithm to several small molecules, hydrogen chains, and alkanes to demonstrate its low formal scaling and practical utility. Provided we use enough auxiliary functions, we obtain accuracy similar to that of the traditional pRDM algorithm, somewhere between that of CCSD and CCSD(T).Comment: 11 pages, 1 figur

The Addition of Arachidin 1 or Arachidin 3 to Human Rotavirus-infected Cells Inhibits Viral Replication and Alters the Apoptotic Cell Death Pathway

Rotavirus (RV) infections are a leading cause of severe gastroenteritis in infants and children under the age of five. There are two vaccines available in the United States and one in India that can be administered early in childhood, however they only protect against specific strains1. From our previous work, both arachidin-1 (A1) and arachidin-3 (A3) from peanut (Arachis hypogaea) hairy root cultures significantly inhibit simian RV replication2,3,4. The purpose of this study was to determine if a human intestinal cell line, HT29.f8, infected with a human RV, Wa, was affected by A1 and A3. Cell viability assays were utilized to determine if A1 and A3 affect the HT29.f8 cells with/without RV infections. At eighteen hours post infection (hpi), supernatants from the RV-infected HT29.f8 cells with/without the arachidins were used in plaque forming assays to quantify and compare the amount of infectious RV particles that are produced during an infection. Transmission electron microscopy (TEM) was used to visualize cell ultrastructure and individual RV particles. Additionally, tunable resistive pulse sensing technology (TRPS) using the qNano system by IZON was employed to quantify and measure virus particle sizes, and display the size distribution of RV particles. Likewise, quantitative real time polymerase chain reactions (qRT-PCR) were performed to determine if A1 and A3 regulated cell death pathways in the HT29.f8 cell line. This data will guide our future studies to determine the antiviral mechanism(s) of action of A1 and A3

Strain Modulated Electronic Properties of Ge Nanowires - A First Principles Study

We used density-functional theory based first principles simulations to study the effects of uniaxial strain and quantum confinement on the electronic properties of germanium nanowires along the [110] direction, such as the energy gap and the effective masses of the electron and hole. The diameters of the nanowires being studied are up to 50 {\AA}. As shown in our calculations, the Ge [110] nanowires possess a direct band gap, in contrast to the nature of an indirect band gap in bulk. We discovered that the band gap and the effective masses of charge carries can be modulated by applying uniaxial strain to the nanowires. These strain modulations are size-dependent. For a smaller wire (~ 12 {\AA}), the band gap is almost a linear function of strain; compressive strain increases the gap while tensile strain reduces the gap. For a larger wire (20 {\AA} - 50 {\AA}), the variation of the band gap with respect to strain shows nearly parabolic behavior: compressive strain beyond -1% also reduces the gap. In addition, our studies showed that strain affects effective masses of the electron and hole very differently. The effective mass of the hole increases with a tensile strain while the effective mass of the electron increases with a compressive strain. Our results suggested both strain and size can be used to tune the band structures of nanowires, which may help in design of future nano-electronic devices. We also discussed our results by applying the tight-binding model.Comment: 1 table, 8 figure

Equivalence of particle-particle random phase approximation correlation energy and ladder-coupled-cluster doubles

We present an analytical proof and numerical demonstrations of the equivalence of the correlation energy from particle-particle random phase approximation (pp-RPA) and ladder-couple-cluster-doubles (ladder-CCD). These two theories reduce to the identical algebraic matrix equation and correlation energy expressions, under the assumption that the pp-RPA equation is stable. The numerical examples illustrate that the correlation energy missed by pp-RPA in comparison with couple-cluster single and double is largely canceled out when considering reaction energies. This theoretical connection will be beneficial to future pp-RPA studies based on the well established couple cluster theory

Paradoxical lesions, plasticity and active inference

Paradoxical lesions are secondary brain lesions that ameliorate functional deficits caused by the initial insult. This effect has been explained in several ways; particularly by the reduction of functional inhibition, or by increases in the excitatory-to-inhibitory synaptic balance within perilesional tissue. In this article, we simulate how and when a modification of the excitatory–inhibitory balance triggers the reversal of a functional deficit caused by a primary lesion. For this, we introduce in-silico lesions to an active inference model of auditory word repetition. The first in-silico lesion simulated damage to the extrinsic (between regions) connectivity causing a functional deficit that did not fully resolve over 100 trials of a word repetition task. The second lesion was implemented in the intrinsic (within region) connectivity, compromising the model’s ability to rebalance excitatory–inhibitory connections during learning. We found that when the second lesion was mild, there was an increase in experience-dependent plasticity that enhanced performance relative to a single lesion. This paradoxical lesion effect disappeared when the second lesion was more severe because plasticity-related changes were disproportionately amplified in the intrinsic connectivity, relative to lesioned extrinsic connections. Finally, this framework was used to predict the physiological correlates of paradoxical lesions. This formal approach provides new insights into the computational and neurophysiological mechanisms that allow some patients to recover after large or multiple lesions