Phenomenological Interaction Potential Research Articles

Bayesian analysis on interactions of exotic nuclear systems

Even though the Bayesian method has been proved to be powerful in the field of nuclear physics, it has not yet been implemented to study the properties of the reaction systems with exotic nuclei, for instance, the gross feature of the phenomenological interaction potential. So far, the optical model potential was typically evaluated by the traditional frequentist approach. However, contradictive conclusions were drawn, especially on the near-threshold behavior of the imaginary potential: threshold anomaly and abnormal threshold anomaly were derived for 6Li+209Bi and 6He+208Pb even with the same elastic scattering data. In this study, we first applied the Bayesian framework to analyze the elastic scattering data of 6Li+209Bi. It was found that the results of Bayesian statistics strongly depend on the imposed prior distributions. Therefore, the Bayesian method has to be used with extreme caution, since the improper prior knowledge could lead to completely wrong conclusions. Since the elastic scattering data is not informative enough to constrain the prior and posterior distributions, our analysis further indicates that the results from the non-constraint frequentist approach or the flat prior distribution with a reasonable physical-boundary can be employed as convincing prior knowledge of the Bayesian framework. Based on this result, we further applied the Bayesian approach to the transfer reaction 208Pb(7Li,6He)209Bi, to investigate the optical potentials of the neutron halo system 6He+209Bi in the outgoing channel. With the proper prior distributions, the Bayesian analysis on both the 6Li+209Bi and 6He+208Pb confirm the presence of the abnormal threshold anomaly. Therefore the applicability of the dispersion relation remains in doubt.

A New Approach for Obtaining the Non-Strange Baryons Spectrum in a Phenomenological Interaction Potential

In our work, we present the nonrelativistic quark model and a new mass formula for study the non-strange baryons octet and decuplet masses. Our model contains a dominant SU(6)-invariant part accounting for the average multiplet energies, and a perturbative SU(6)-violating interaction for the splitting within the multiplets, a structure which is inspired by early Lattice QCD calculations. For our purpose we introduced a spin independent description for SU(6) invariant part of the spectrum, we presented the analytical solution of three particle Schrodinger equation under the suitable phenomenological interaction potential by using the anzast method, through which the average energy values of the nonstrange resonances are reproduced. To describe the hyperfine structure of the baryon and splittings within the SU(6)-multiplets, we used the generalized Gursey Radicati mass formula. A comparison between our calculations and the experimental data shows that the spectrum of the Roper resonances, the ground states and the excited multiplets up to three GeV are in general well reproduced and comparable with the experimental spectrum. Also one can conclude that; the interaction between the quark constituents of baryon resonances could be described adequately by using the combination of Killingbeck and isotonic oscillator potentials form.

Distinction in binding of peptides (P2E) and its mutations (P2G, P2Q) to a graphene sheet via a hierarchical coarse-grained Monte Carlo simulation

A hierarchical coarse-grained approach is used to study the binding of peptides (P2E: (1)E(2)P(3)L(4)Q(5)L(6)K(7)M) and variants (P2G: (1)G(2)P(3)L(4)Q(5)L(6)K(7)M and P2Q: (1)Q(2)L(3)P(4)M(5)E(6)K(7)L) with a graphene sheet. Simulation-based residue-substrate and hydropathy index-based residue-residue interaction is used as input to a phenomenological interaction potential for peptide chains to execute the stochastic motion with a graphene sheet at the center of a box. Large-scale Monte Carlo simulations are performed at a range (low to high) of temperatures to identify peptides binding with the graphene sheet with a constant peptide concentration (Cp = 0.01). A number of local (energy, mobility, and substrate contact profiles) and global (density profiles, mean square displacement of the center of mass of a peptide and its radius of gyration) physical quantities are examined to monitor the patterns. We find that each peptide can bind to a graphene sheet at low temperatures but the residues that can anchor their binding vary among these three peptides. For example, P2E is anchored by (1)E, (4)Q, and (6)K, P2Q by (1)Q, (5)E, and (6)K, and P2G by nearly all its residues with about the same strength except (1)G and (2)P. The site-specific binding is reflected in the thermal response of the radius of gyration of the peptides. Despite the lack of a large difference in binding patterns, a systematic variation in radius of gyration and surface binding profile with the temperature reveals the distinction in their binding: the probability of P2E binding is the highest and that of P2G is the lowest.

Multiscale Modeling of Functionalized Nanocarriers in Targeted Drug Delivery.

Targeted drug delivery using functionalized nanocarriers (NCs) is a strategy in therapeutic and diagnostic applications. In this paper we review the recent development of models at multiple length and time scales and their applications to targeting of antibody functionalized nanocarriers to antigens (receptors) on the endothelial cell (EC) surface. Our mesoscale (100 nm-1 μm) model is based on phenomenological interaction potentials for receptor-ligand interactions, receptor-flexure and resistance offered by glycocalyx. All free parameters are either directly determined from independent biophysical and cell biology experiments or estimated using molecular dynamics simulations. We employ a Metropolis Monte Carlo (MC) strategy in conjunction with the weighted histogram analysis method (WHAM) to compute the free energy landscape (potential of mean force or PMF) associated with the multivalent antigen-antibody interactions mediating the NC binding to EC. The binding affinities (association constants) are then derived from the PMF by computing absolute binding free energy of binding of NC to EC, taking into account the relevant translational and rotational entropy losses of NC and the receptors. We validate our model predictions by comparing the computed binding affinities and PMF to a wide range of experimental measurements, including in vitro cell culture, in vivo endothelial targeting, atomic force microscopy (AFM), and flow chamber experiments. The model predictions agree closely and quantitatively with all types experimental measurements. On this basis, we conclude that our computational protocol represents a quantitative and predictive approach for model driven design and optimization of functionalized NCs in targeted vascular drug delivery.

AN OVERVIEW OF THE STRETCHED INTERMEDIATE MODEL OF B–Z DNA TRANSITION

Recently, the stretched intermediate model was proposed for the B–Z deoxyribonucleic acid (DNA) transition based on simulation results carried out using the Stochastic Difference Equation (SDE) that showed unwinding and elongation of the oligomer during the transition. This model has proven to be successful in resolving the steric dilemma in short oligomers. However, extending the simulation method to larger DNA strands may prove to be computationally challenging. Such difficulty has led us to adopt a mean field approach using phenomenological interaction potentials to simulate the transition. Like the atomistic approach, the SDE simulations based on the mean field approach, also suggest the presence of a stretched intermediate during the transition.

Improved mass of the bottom quark

A recent determination of the mass of the b quark, based exclusively on quantum chromodynamics (by avoiding strictly to introduce any phenomenological interaction potential of nonperturbative origin), may be improved by allowing for a merely numerical solution of the corresponding eigenvalue problem.

Hydrogen Adsorption in Nanotubes

Model calculations are presented of the adsorption of hydrogen in carbon nanotubes. Using a phenomenological interaction potential, we compute the low coverage thermodynamic properties, showing explicitly the quantum effects in the Feynman (semiclassical) effective potential approximation. The effects of interactions are evaluated with a quasi-one dimensional classical Lennard-Jones approximation.

Observation of rotationally mediated focused inelastic resonances inD2scattering from Cu(001)

Rotationally mediated focused inelastic resonances (RMFIR's) in the angular distributions of ${\mathrm{D}}_{2}$ scattered from Cu(001) are observed. The FIR effect involves a phonon-assisted focusing of an incident beam of arbitrary energy and direction into a final channel of one single well-defined energy and direction. Surprisingly for an incident energy ${E}_{i}=27\mathrm{meV}$ the RMFIR conditions for the scattered beam coincide with the kinematic conditions required for a further elastic selective adsorption mechanism called the rotationally mediated critical kinematic (RMCK) effect. By taking advantage of the RMFIR and elastic RMCK effects, three effective bound states of energy ${\ensuremath{\epsilon}}_{n,J}=\ensuremath{-}21.5\mathrm{meV},$ $\ensuremath{-}12.4\mathrm{meV},$ and $\ensuremath{-}10.3\mathrm{meV}$ are determined. They are attributed to the lowest bound states ${\ensuremath{\epsilon}}_{0}=\ensuremath{-}28.9\mathrm{meV}$ and ${\ensuremath{\epsilon}}_{1}=\ensuremath{-}19.8\mathrm{meV}$ combined with the rotational excitation energy for $J=1$ to be ${B}_{\mathrm{rot}}J(J+1)=7.41\mathrm{meV},$ respectively, and ${\ensuremath{\epsilon}}_{3}=\ensuremath{-}10.3\mathrm{meV}$ combined with the rotational ground state $(J=0).$ While the ${\ensuremath{\epsilon}}_{1}$ and ${\ensuremath{\epsilon}}_{3}$ states appear as maxima in the angular distribution at RMFIR conditions, the ${\ensuremath{\epsilon}}_{0}$ yields a striking minimum which represents the first evidence of what we call an anti-FIR feature. Theoretical arguments to explain the different FIR signatures observed are provided. A fit of a phenomenological interaction potential to the experimental bound-state values yields a value for the well depth $D=32.5\mathrm{meV}$ which is somewhat deeper than that found previously.

PION PRODUCTION DIFFERENTIAL CROSS SECTION OF HEAVY ION COLLISIONS AT SUBTHRESHOLD ENERGIES

The Lorentz-invariant differential cross section (LIDCS) for π production in heavy ion collisions was studied through the two-step process, NN→NΔ→NNπ. A phenomenological interaction potential containing central and tensor terms was used. The effect of inclusion of the tensor term on the LIDCS was little. The target nucleus 12C was excited to one of its giant resonance states, Jπ=1+, T=1, while the projectile nucleus 16O was excited to an isobar Δ (M=1232 MeV , ΓΔ=115.11 MeV ) which decayed (NΔ→NNπ), giving a nucleon and a pion mπ=138 MeV . In comparison with available experimental data, the shape was reproduced, but the theoretical results were higher.