Molecular Dynamics Simulation and Binding Energy Calculation for Estimation of Oligonucleotide Duplex Thermostability in RNA-Based Therapeutics

2011 ◽  
Vol 51 (8) ◽  
pp. 1957-1965 ◽  
Author(s):  
Lingling Shen ◽  
Theresa L. Johnson ◽  
Susan Clugston ◽  
Hongwei Huang ◽  
Kenneth J. Butenhof ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Binding Energy ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Oligonucleotide Duplex ◽  
Binding Energy Calculation

Study the Interaction Mechanism and Mechanical Properties of PVA/HA by a Molecular Dynamics Simulation

2017 ◽  
Vol 737 ◽  
pp. 299-306
Author(s):  
Ming Ming Yang ◽  
Ya Nen Wang ◽  
Qing Hua Wei ◽  
Wei Hong Chai ◽  
Sheng Min Wei
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Binding Energy ◽  
Pair Correlation ◽  
Interaction Mechanism ◽  
Crystallographic Plane ◽  
Dynamics Simulation ◽  
Ionic Bonds ◽  
Crystallographic Planes

To investigate the interaction mechanism of PVA on the surface of HA, the molecular dynamics simulation was applied to simulate and calculate the binding energy between PVA of different monomers and HA crystallographic planes (001), (100) and (110), and then the mechanical properties and radial distribution function of the PVA/HA(110) system were calculated and analyzed. The results show that HA (110) has the higher binding energy with PVA than that of HA (001) and (100). The binding energy and the Young’s modulus of HA(110)/PVA system increase with the rising of PVA monomer number at the same crystallographic plane in a certain range, however, the descending trend takes place while monomers number reaching a certain value. This change trend is relating to the effective contact between two single components. By calculating the pair correlation function of HA(110)/PVA, there is a strong interaction between HA crystallographic plane (110) and PVA, it is mainly derived from the hydrogen bonds between O atoms of PVA and H atoms in HA crystal, besides, the ionic bonds interactions existing between OaandCa.

Accurate ab initio Calculations of Methane Dimer Interaction Energies and Molecular Dynamics Simulation of Fluid Methane

2009 ◽  
Vol 1177 ◽  
Author(s):  
Arvin Huang-Te Li ◽  
Sheng Der Chao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Binding Energy ◽  
Ab Initio ◽  
Bond Length ◽  
Dynamics Simulation ◽  
Basis Set ◽  
Basis Sets ◽  
Equilibrium Bond Length ◽  
Basis Size

AbstractIntermolecular interaction potentials of the methane dimers have been calculated for 12 symmetric conformations using the Hartree-Fock (HF) self-consistent theory, the second-order M�ller-Plesset (MP2) perturbation theory, and the coupled-cluster with single and double and perturbative triple excitations (CCSD(T)) theory. The HF calculations yield unbound potentials largely due to the exchange-repulsion interaction. In MP2 and CCSD(T) calculations, the basis set effects on the repulsion exponent, the equilibrium bond length, the binding energy, and the asymptotic behavior of the calculated intermolecular potentials have been thoroughly studied. We have employed basis sets from the Slater-type orbitals fitted with Gaussian functions, Pople�s medium size basis sets to Dunning�s correlation consistent basis sets. With increasing basis size, the repulsion exponent and the equilibrium bond length converge at the 6-31G** basis set and the 6-311++G(2d, 2p) basis set, respectively, while a large basis set (aug-cc-pVTZ) is required to converge the binding energy at a chemical accuracy (˜0.01 kcal/mol). We used the BSSE corrected results that systematically converge to the destined potential curve with increasing basis size. The binding energy calculated and the equilibrium bond length using the CCSD(T) method are close to the results at the basis set limit. For molecular dynamics simulation, a 4-site potential model with sites located at the hydrogen atoms was used to fit the ab initio potential data. This model stems from a hydrogen-hydrogen repulsion mechanism to explain the stability of the dimer structure. MD simulations using the ab initio PES show good agreement on both the atom-wise radial distribution functions and the self-diffusion coefficients over a wide range of experimental conditions.

An Investigation of PT/PT (111) Homoepitaxy with Molecular Dynamics Simulation and Static-Energy Calculation.

1993 ◽  
Vol 317 ◽  
Author(s):  
Ruoping wang ◽  
Bryan S. Kalp ◽  
Kristen A. Fichthorn
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Film Growth ◽  
Effective Medium Theory ◽  
Layer Growth ◽  
Dynamics Simulation ◽  
Energy Calculation ◽  
Layer By Layer ◽  
Static Energy ◽  
Step Edges

ABSTRACTWe present the results of a study of Pt/Pt (111) epitaxial thin-film growth with Molecular-dynamics simulation and static-energy calculation. Interatomic forces are modeled with Corrected-Effective-Medium theory. Atomic details of deposition, such as dissipation of the kinetic energy of an impinging gas atom, adatom motion on and approaching descending step edges, effects of the geometry of a step edge on the interlayer transport of adatoms, etc., have been intensively investigated. We have observed a novel mechanism for adatom incorporation into descending-step edges which involves a concerted motion of the adatom and edge atoms. Our study supports the “island size and shape” model which has been proposed to explain the reentrant layer-by-layer growth mode seen experimentally in Pt/Pt (111) homoepitaxy.

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