Three-body free-energy terms and effective potentials in polar fluids and ionic solutions

1974 ◽  
Vol 25 (4) ◽  
pp. 519-522 ◽  
Author(s):  
J.C. Rasaiah ◽  
G. Stell
Keyword(s):  
Free Energy ◽  
Ionic Solutions ◽  
Polar Fluids ◽  
Effective Potentials ◽  
Three Body

Physics-based predictions of RNA loop stability and structures

2012 ◽  
Author(s):  
◽  
Liang Liu
Keyword(s):  
Free Energy ◽  
Building Blocks ◽  
Conformational Ensemble ◽  
Scoring Functions ◽  
Rna Structures ◽  
Cellular Functions ◽  
Entropy Model ◽  
University Of Missouri ◽  
Knowledge Based ◽  
Three Body

[ACCESS RESTRICTED TO THE UNIVERSITY OF MISSOURI AT AUTHOR'S REQUEST.] RNA (ribonucleic acid) molecules play a variety of crucial roles in cellular functions at the level of transcription, translation and gene regulation. RNA functions are tied to structures. We aim to develop a novel free energy-based model for RNA structures, especially for RNA loops and junctions. In the first project, we develop a new conformational entropy model for RNA structures consisting of multiple helices connected by cross-linked loops. The basic strategy of our approach is to decompose the whole structure into a number of three-body building blocks, where each building block consists of a loop and two helices that are directly connected to the two ends of the loop. Assembly of the building blocks gives the entropy of the whole structure. The method provide a solid first step toward a systematic development of an entropy and free energy model for complex tertiary folds for RNA and other biopolymer. In the second project, based on the survey of all the known RNA structures, we derive a set of virtual bond-based scoring functions for the different types of dinucleotides. To circumvent the problem of reference state selection, we apply an iterative method to extract the effective potential, based on the complete conformational ensemble. With such a set of knowledge-based energy parameters, for a given sequence, we can successfully identify the native structure (the best-scored structure) from a set of structural decoys.

ROVIBRATIONAL BOUND STATES OF THE Ar2Ne COMPLEX

2013 ◽  
Vol 12 (01) ◽  
pp. 1250107 ◽  
Author(s):  
BENHUI YANG ◽  
BILL POIRIER
Keyword(s):  
Quantum Dynamics ◽  
Bound States ◽  
Energy Levels ◽  
Effective Potentials ◽  
Spectral Transform ◽  
Physical Insight ◽  
Rovibrational States ◽  
Three Body ◽  
Massive Parallelization ◽  
Variable Representation

We report exact quantum dynamics calculations of the eigenstate energy levels for the bound rovibrational states of the Ar2Ne complex, across the range of J values for which such states are observed (J = 0–35). All calculations have been carried out using the ScalIT suite of parallel codes. These codes employ a combination of highly efficient methods, including phase-space optimized discrete variable representation, optimal separable basis, and preconditioned inexact spectral transform (PIST) methods, together with an effective massive parallelization scheme. The Ar2Ne energy levels were computed using a pair-wise Aziz potential plus a three-body correction, in Jacobi co-ordinates. Effective potentials for the radial co-ordinates are constructed, which reveal important physical insight into the two distinct dissociation pathways, Ar2Ne → NeAr + Ar and Ar2Ne → Ar2 + Ne . A calculation of the bound vibrational (J = 0) levels, computed using the Tang–Toennies potential, is also performed for comparison with results from the previous literature.

scholarly journals Molar Interactions of Some Aromatic Hydrocarbons in n-Heptane by Viscometric Measurements at 298.15K

2018 ◽  
Vol 40 (1) ◽  
pp. 97-110
Author(s):  
Md Kamrul Hossain ◽  
M Abdur Rahaman ◽  
Shamim Akhtar
Keyword(s):  
Free Energy ◽  
Aromatic Hydrocarbons ◽  
Binary Systems ◽  
Composition Range ◽  
The Other ◽  
Excess Gibbs Free Energy ◽  
Geometric Fitting ◽  
Free Energy Of Activation ◽  
Three Body ◽  
Kister Equation

The viscosities, η , of pure n-heptane, toluene, o-xylene, mesitylene, and some of their binary mixtures covering the whole composition range have been measured at 298.15K. Deviations in viscosity, ∆η , was calculated using experimental results. The concentration dependencies of η were correlated to polynomial expressions, whereas, ∆η were fitted to the Redlich–Kister equation. Moreover, the values of the excess Gibbs free energy of activation, ∆G#E, of these mixtures were determined. Viscosity measurements of the binary systems were correlated with Grunberg and Nissan the three-body and four-body McAllister expressions. In all systems, ∆η were found to be negative in the whole range of composition with a single lobe having minimum at 0.6 mple fraction of aromatic hydrocarbon. While dispersive forces are suggested to dominate in n-heptane + toluene, for the other two systems  ‘favourable geometric fitting’ overpowers them due to the increasing number of  – CH3 groups in the relevant aromatic hydrocarbons. The Chittagong Univ. J. Sci. 40 : 97-110, 2018

Nonvariational and nonadiabatic calculations on the hydrogen molecular ion and its µ – isotopes

2002 ◽  
Vol 80 (11) ◽  
pp. 1423-1432 ◽  
Author(s):  
V Yakhontov ◽  
M Jungen
Keyword(s):  
Molecular Ions ◽  
Nuclear Motion ◽  
Mass Ratio ◽  
Internuclear Separation ◽  
Nonadiabatic Coupling ◽  
Effective Potentials ◽  
Continuum States ◽  
Variational Techniques ◽  
Rovibrational States ◽  
Three Body

A nonadiabatic, nonvariational, and computationally inexpensive scheme to describe bound and continuum states of three-body molecular ions, including µ –-mesonic ions, is proposed. The method relies on treating perturbatively the nonadiabatic coupling between the Born–Oppenheimer (BO) particle states and nuclear motion terms, such that the appropriate expansion parameter is the mass ratio of the lightest particle in the system to that of the heaviest one. In practice, the method requires solving, numerically, a system of coupled inhomogeneous Schrödinger equations with effective potentials that depend on the "internuclear" separation, R, and allow for the mixing of BO states because of nonadiabatic terms in the Hamiltonian. The utility of our approach is clearly evidenced by the results of the numerical calculations carried out for rovibrational states of several lowest J in the H+2 and (ppµ–) molecules. These demonstrate that nonadiabatic eigenenergies and eigenstates, both of the bound and scattering type, for ordinary as well as µ-mesonic molecules can be directly and quite accurately calculated from the same principles in the entire range of R, without making use of the variational techniques that more sophisticated studies of this kind are usually based on. PACS Nos.: 31.15Ar, 31.15Pf

POLARIZATION EFFECTS IN THE 3He(d,p)4He FUSION REACTION

2003 ◽  
Vol 18 (02n06) ◽  
pp. 302-305
Author(s):  
S. GOJUKI ◽  
S. ORYU
Keyword(s):  
Cross Section ◽  
Fusion Reaction ◽  
Resonance State ◽  
Resonance Region ◽  
Group Method ◽  
Polarization Effects ◽  
Effective Potentials ◽  
Low Energies ◽  
Coulomb Effects ◽  
Three Body

We calculate the cross section of the reaction 3 He(d,p) 4 He at very low energies using the three-body Faddeev formalism in which the target nucleus 3 He is considered as a cluster with spin 1/2 and the projectile deuteron as a proton and a neutron. For the n-p interaction we adopted the AV14 potential while for the p -3 He and n -3 He channel we constructed effective potentials based on the well known Resonating Group Method (RGM). Since the n-3He and p -3 He effective potentials are essentially different, the three-body system is treated as a three-channel problem. A resonance state is found using the 1 S 0 and 3 S 1-3 D 1 input states for the n-p and the 1 S 0 and 3 S 1 input states for both nucleon-cluster interactions. Coulomb effects were taken into account for the initial and the final states only. The polarization effects on the total cross section around the resonance region are discussed.

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