Isospin effect in the nuclear reaction induced by neutron-halo nuclei

We study the average property of the isospin effect of reaction induced by halo-neutron nuclei He-8 and He-10 in the intermediate energy heavy ion collisions using the isospin-dependent quantum molecular dynamics model (IQMD). This study is based on the extended neutron density distribution for the halo-neutron nuclei, which includes the average property of the isospin effect-of reaction mechanism and loose inner structure. The extended neutron density distribution brings an important isospin. effect into the average property of reaction mechanism because the interaction potential and nucleon-nucleon(N-N) cross section in IQMD model depend sensitively on the density distribution of colliding system. In order to see clearly the average properties of reaction mechanism induced by halo-neutron nuclei we also compare the results for the neutron-halo colliding systems with those for the corresponding stable colliding systems under the same incident channel condition. We found that the extended density distribution for the neutron-halo projectile brings an important isospin effect to the reaction mechanism, which leads to the decrease of nuclear stopping R, yet induces obvious increase of the neutron-proton ratio of nucleon emissions and isospin fractionation ratio for all beam energies studied in this work, compared to the corresponding stable colliding system. In this case, nuclear stopping, the neutron-proton ratio of nucleon emissions and isospin fractionation ratio induced by halo-neutron nuclei can be used as possible probes for studying the average property of the isospin effect of reaction mechanism and extracting the information of symmetry potential and in-medium N-N cross section by the neutron-halo nuclei in heavy ion collisions.

Probing the symmetrical potential in nuclear reaction iinduced by neutron-halo nuclei

In terms of the isospin-dependent quantum molecular dynamics model (IQMD), important isospin effect in the halo-neutron nucleus induced reaction mechanism is. investigated, and consequently, the symmetrical potential form is extracted in the intermediate energy heavy ion collision. Because the interactive potential and in-medium nucleon-nucleon (N-N) cross section in the IQMD model sensitively depend on the density distribution of the colliding system, this type of study is much more based on the extended density distribution with a looser inner nuclear structure of the halo-neutron nucleus. Such a density distribution includes averaged characteristics of the isospin effect of the reaction mechanism and the looser inner nuclear structure. In order to understand clearly the isospin effect of the halo-neutron nucleus induced reaction mechanism, the effects caused by the neutron-halo nucleus and by the stable nucleus with the same mass are compared under the same condition of the incident channel. It is found that in the concerned beam energy region, the ratio of the emitted neutrons and protons and the ratio of the isospin fractionations in the neutron-halo nucleus case are considerably larger than those in the stable nucleus case. Therefore, the information of the symmetry potential in the heavy ion collision can be extracted through such a procedure.

Average property of isospin effects induced by neutron-halo nuclei

We study the average property of the isospin effects of reaction mechanism induced by neutron-halo nuclei within the isospin-dependent quantum molecular dynamics model. We find that the extended neutron density distribution for the neutron-halo projectile brings an important isospin effect into the reaction mechanism, which induces the decrease of nuclear stopping R; however, it induces the obvious increases of the neutron-proton ratio of nucleon emissions (n/p)(nucl) for all of the beam energies in this work, compared to the same mass stable colliding system.

Study on dynamic fusion barrier in heavy-ion fusion reactions

By means of the improved quantum molecular dynamics model, the incident energy dependent dynamical fusion potential barriers for heavy nucleus reaction systems are investigated. It is found that with decrease of incident energy the lowest dynamic barrier is obtained which approaches to the adiabatic static barrier and with increase of the incident energy the dynamic barrier goes up to the diabatic static barrier. Based on the dynamical study a microscopic understanding of the extra-push in fusion reactions of heavy systems and a new explanation of tunneling process for the fusion at the incident energy below the static and above the lowest dynamic barrier are presented. In order to understand the energy dependence of the dynamical barrier we also pay a great attention to study the neck formation and shape deformation during the dynamic lowering of the barrier.

Entrance channel effects on the role of isospin-dependent momentum interaction in isospin fractionation in heavy ion collisions

An isospin degree of freedom is inserted into the momentum dependent interaction in the quantum molecular dynamics model to obtain an isospin dependent momentum interaction given in a form practically usable in isospin dependent quantum molecular dynamics model. We investigate the entrance channel effects for the role of isospin momentum dependent interaction on the isospin fractionation ratio and its dynamical mechanism in the intermediate energy heavy ion collisions. It is found that the isospin dependent momentum interaction induces a significant reduction of isospin fractionation ratio under all entrance channel conditions. However the strong dependence of isospin fractionation ratio on the symmetry potential is preserved after considering the isospin degree of freedom in the momentum dependent interaction.

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Molecular dynamics simulations of proteins: can the explicit water model be varied?

In molecular mechanics simulations of biological systems, the solvation water is typically represented by a default water model which is an integral part of the force field. Indeed, protein nonbonding parameters are chosen in order to obtain a balance between water-water and protein-water interactions and hence a reliable description of protein solvation. However, less attention has been paid to the question of whether the water model provides a reliable description of the water properties under the chosen simulation conditions, for which more accurate water models often exist. Here we consider the case of the CHARMM protein force field, which was parametrized for use with a modified TIP3P model. Using quantum mechanical and molecular mechanical calculations, we investigate whether the CHARMM force field can be used with other water models: TIP4P and TIP5P. Solvation properties of N-methylacetamide (NMA), other small solute molecules, and a small protein are examined. The results indicate differences in binding energies and minimum energy geometries, especially for TIP5P, but the overall description of solvation is found to be similar for all models tested. The results provide an indication that molecular mechanics simulations with the CHARMM force field can be performed with water models other than TIP3P, thus enabling an improved description of the solvent water properties.

Electronic properties of liquid hydrogen fluoride: A sequential quantum mechanical/Born-Oppenheimer molecular dynamics approach

The electronic properties of liquid hydrogen fluoride (HF) were investigated by carrying out sequential quantum mechanics/Born-Oppenheimer molecular dynamics. The structure of the liquid is in good agreement with recent experimental information. Emphasis was placed on the analysis of polarisation effects, dynamic polarisability and electronic excitations in liquid HF. Our results indicate an increase in liquid phase of the dipole moment (similar to 0.5 D) and isotropic polarisability (5%) relative to their gas-phase values. Our best estimate for the first vertical excitation energy in liquid HF indicates a blue-shift of 0.4 +/- 0.2 eV relative to that of the gas-phase monomer (10.4 eV). (C) 2010 Elsevier B.V. All rights reserved.

Molecular Dynamics Investigation of Structure and Transport in the K2O-2SiO2 System Using a Partial Charge Based Model Potential

Potassium disilicate glass and melt have been investigated by using a new partial charge based potential model in which nonbridging oxygens are differentiated from bridging oxygens by their charges. The model reproduces the structural data pertaining to the coordination polyhedra around potassium and the various bond angle distributions excellently. The dynamics of the glass has been studied by using space and time correlation functions. It is found that K ions migrate by a diffusive mechanism in the melt and by hops below the glass transition temperature. They are also found to migrate largely through nonbridging oxygenrich sites in the silicate matrix, thus providing support to the predictions of the modified random network model.

Molecular dynamics Investigation of structure and transport in the K2O-2SiO2 system using a partial charge based model potential

Potassium disilicate glass and melt have been investigated by using anew partial charge based potential model in which nonbridging oxygens are differentiated from bridging oxygens by their charges. The model reproduces the structural data pertaining to the coordination polyhedra around potassium and the various bond angle distributions excellently. The dynamics of the glass has been studied by using space and time correlation functions. It is found that K ions migrate by a diffusive mechanism in the melt and by hops below the glass transition temperature. They are also found to migrate largely through nonbridging oxygen-rich sites in the silicate matrix, thus providing support to the predictions of the modified random network model.

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG(3)) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

Subquadratic quantum number dependence and other anomalies of vibrational dephasing in liquid nitrogen: Molecular dynamics simulation study from the triple point to the critical point and beyond

Vibrational phase relaxation near gas-liquid and liquid-solid phase coexistence has been studied by molecular dynamics simulations of N-N stretch in N-2. Experimentally observed pronounced insensitivity of phase relaxation from the triple point to beyond the boiling point is found to originate from a competition between density relaxation and resonant-energy transfer terms. The sharp rise in relaxation rate near the critical point (CP) can be attributed at least partly to the sharp, rise in vibration-rotation coupling contribution. Substantial subquadratic quantum number dependence of overtone dephasing rate is found near the CP and in supercritical fluids. [S0031-9007 (99)09318-7].

Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the beta-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable ``tense'' state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin. (C) 2015 Elsevier Inc. All rights reserved.

Correlative reference model and molecular dynamics simulation of dislocation emission process

A correlative reference model for computer molecular dynamics simulations is proposed. Based on this model, a flexible displacement boundary scheme is introduced and the dislocations emitted from a crack tip can continuously pass through the border of the inner discrete atomic region and pile up at the outer continuum region. The effect of the emitted dislocations within the plastic zone on the inner atomistic region can be clearly demonstrated. The simulations for a molybdinum crystal show that a full dislocation in a bcc crystal is dissociated into three partial dislocations and interaction between the crack and the emitted dislocations results in gradual decrease of the local stress intensity factor.