Effective Interaction Potential Research Articles

Segmental Lennard-Jones interactions for semi-flexible polymer networks

ABSTRACT Simulating soft matter systems such as the cytoskeleton can enable deep understanding of experimentally observed phenomena. One challenge of modelling such systems is realistic description of the steric repulsion between nearby polymers. Previous models of the polymeric excluded volume interaction have the deficit of being non-analytic, being computationally expensive, or allowing polymers to erroneously cross each other. A recent solution to these issues, implemented in the MEDYAN simulation platform, uses analytical expressions obtained from integrating an interaction kernel along the lengths of two polymer segments to describe their repulsion. Here, we extend this model by re-deriving it for lower-dimensional geometrical configurations, deriving similar expressions using a steeper interaction kernel, comparing it to other commonly used potentials, and showing how to parameterise these models. We also generalise this new integrated style of potential by introducing a segmental Lennard-Jones potential, which enables modelling both attractive and repulsive interactions in semi-flexible polymer networks. These results can be further generalised to facilitate the development of effective interaction potentials for other finite elements in simulations of softmatter systems.

Bottom-Up Coarse-Grained Modeling of DNA.

Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, “melting,” and DNA condensation.

Bose-Einstein condensates in an atom-optomechanical system with effective global nonuniform interaction

We consider a hybrid atom-optomechanical system consisting of a mechanical membrane inside an optical cavity and an atomic Bose-Einstein condensate outside the cavity. The condensate is confined in an optical lattice potential formed by a traveling laser beam reflected off one cavity mirror. We derive the cavity-mediated effective atom-atom interaction potential, and find that it is non-uniform, site-dependent, and does not decay as the interatomic distance increases. We show that the presence of this effective interaction breaks the Z$_2$ symmetry of the system and gives rise to new quantum phases and phase transitions. When the long-range interaction dominates, the condensate breaks the translation symmetry and turns into a novel self-organized lattice-like state with increasing particle densities for sites farther away from the cavity. We present the phase diagram of the system, and investigate the stabilities of different phases by calculating their respective excitation spectra. The system can serve as a platform to explore various self-organized phenomena induced by the long-range interactions.

Investigating the energetic and entropic components of effective potentials across a glass transition

By eliminating unnecessary details, coarse-grained (CG) models provide the necessary efficiency for simulating scales that are inaccessible to higher resolution models. However, because they average over atomic details, the effective potentials governing CG degrees of freedom necessarily incorporate significant entropic contributions, which limit their transferability and complicate the treatment of thermodynamic properties. This work employs a dual-potential approach to consider the energetic and entropic contributions to effective interaction potentials for CG models. Specifically, we consider one- and three-site CG models for ortho-terphenyl (OTP) both above and below its glass transition. We employ the multiscale coarse-graining (MS-CG) variational principle to determine interaction potentials that accurately reproduce the structural properties of an all-atom (AA) model for OTP at each state point. We employ an energy-matching variational principle to determine an energy operator that accurately reproduces the intra- and inter-molecular energy of the AA model. While the MS-CG pair potentials are almost purely repulsive, the corresponding pair energy functions feature a pronounced minima that corresponds to contacting benzene rings. These energetic functions then determine an estimate for the entropic component of the MS-CG interaction potentials. These entropic functions accurately predict the MS-CG pair potentials across a wide range of liquid state points at constant density. Moreover, the entropic functions also predict pair potentials that quite accurately model the AA pair structure below the glass transition. Thus, the dual-potential approach appears a promising approach for modeling AA energetics, as well as for predicting the temperature-dependence of CG effective potentials.

Gelation of amphiphilic janus particles in an apolar medium

HypothesisThe anisotropic nature of colloidal particles results in orientation-dependent interactions that organize the particles into peculiar structures different from those formed by isotropic colloids. Particles with a hydrophilic hemisphere are expected to assemble in hydrophobic solvents due to the contribution of hydrophobic interactions as observed for molecular amphiphiles. ExperimentsAsymmetrically decorated silica-based Janus particles are dispersed in an apolar solvent, chloroform, and their structure and dynamics are studied by light scattering and compared with computer simulations. FindingsGelation of amphiphilic Janus particles with asymmetric surface decoration is observed in a hydrophobic medium. The influence of particle asymmetry on gel structure and dynamics is discussed. Unlike particles with long-range repulsive interactions in water, these systems rapidly form rather compact structures that are nevertheless more ramified than those made of isotropic hydrophobic particles. Comparison with computer simulations allows visualization of the gel and reveals a contribution of asymmetric short-range attractions and cross-term repulsions to the net effective interaction potential.

Static and dynamic properties of block copolymer based grafted nanoparticles across the non-ergodicity transition

We present a systematic investigation of static and dynamic properties of block copolymer micelles with cross-linked cores, representing model polymer-grafted nanoparticles, over a wide concentration range from a dilute regime to an arrested (crystalline) state, by means of light and neutron scattering, complemented by linear viscoelasticity. We have followed the evolution of their scattering intensity and diffusion dynamics throughout the non-ergodicity transition, and the observed results have been contrasted against those of appropriately coarse-grained Langevin dynamics simulations. These stable model soft particles of the core–shell type are situated between ultrasoft stars and hard spheres, and the well-known star pair interaction potential is not appropriate to describe them. Instead, we have found that an effective brush interaction potential provides very satisfactory agreement between experiments and simulations, offering insights into the interplay of softness and dynamics in spherical colloidal suspensions.

Metastable soliton necklaces supported by fractional diffraction and competing nonlinearities.

We demonstrate that the fractional cubic-quintic nonlinear Schrödinger equation, characterized by its Lévy index, maintains ring-shaped soliton clusters ("necklaces") carrying orbital angular momentum. They can be built, in the respective optical setting, as circular chains of fundamental solitons linked by a vortical phase field. We predict semi-analytically that the metastable necklace-shaped clusters persist, corresponding to a local minimum of an effective potential of interaction between adjacent solitons in the cluster. Systematic simulations corroborate that the clusters stay robust over extremely large propagation distances, even in the presence of strong random perturbations.

On temperature effects on the structural phase transitions of GaP

In this presentation by employing a combination of calculations based on Density Functional Theory (DFT) and Molecular Dynamics simulations (MD), we show that temperature has an unquestionable role in the behavior of Gallium Phosphide under pressure, shedding a new light in the controversial interpretation of experimental results. For example, we justify the absence of some structures predicted by early theoretical works, which remained up to now misunderstood. Moreover, we predict transitions to new structures at high temperature that may encourage new experiments. The differences in the observed transition sequences at low and high temperatures indicate that the vibrational corrections we included in the DFT calculations are fundamental to the description of the stability of higher pressure structures, and may be employed on other materials. Additionally, the good agreement between DFT and MD shows the suitability of the classical effective many-body interaction potential used to describe the different high-pressure phases of GaP in the Molecular Dynamics simulations. Finally, we discuss the behavior of GaP under extreme conditions for temperatures up to 1400 K and pressures up to 50 GPa, predicting new phases.

Consistent description of ion-specificity in bulk and at interfaces by solvent implicit simulations and mean-field theory.

Solvent-implicit Monte Carlo (MC) simulations and mean-field theory are used to predict activity coefficients and excess interfacial tensions for NaF, NaCl, NaI, KF, KCl, and KI solutions in good agreement with experimental data over the entire experimentally available concentration range. The effective ionic diameters of the solvent-implicit simulation model are obtained by fits to experimental activity coefficient data. The experimental activity coefficients at high salt concentrations are only reproduced if the ion-specific concentration-dependent decrement of the dielectric constant is included. The dielectric-constant dependent contribution of the single-ion solvation free energy to the activity coefficient is significant and is included. To account for the ion-specific excess interfacial tension of salt solutions, in addition to non-ideal solution effects and the salt-concentration-dependent dielectric decrement, an ion-specific ion-interface interaction must be included. This ion-interface interaction, which acts in addition to the dielectric image-charge repulsion, is modeled as a box potential, is considerably more long-ranged than the ion radius, and is repulsive for all ions considered except iodide, in agreement with previous findings and arguments. By comparing different models that include or exclude bulk non-ideal solution behavior, dielectric decrement effects, and ion-interface interaction potentials, we demonstrate how bulk and interfacial ion-specific effects couple and partially compensate each other. Our MC simulations, which correctly include ionic correlations and interfacial dielectric image-charge repulsion, are used to determine effective ion-surface interaction potentials that can be used in a modified Poisson-Boltzmann theory.

Formation and structures of tyrocidine B oligomers in solution in the presence of water

Small-angle x-ray scattering and quasi-elastic light scattering measurements were conducted to analyze correlations between the structure and short-time dynamics of tyrocidine B·hydrochloride (TrcB) in ethanol, acetonitrile, and (R,S)-2-methylbutanol dispersions in the presence of 20.0% (v/v) water at 278 K and 298 K. The three TrcB dispersions exhibited peak position shifts that varied with the volume fraction. The experimental data were fitted to a model that considered the effective interaction potential, short-range attraction, and long-range repulsion. This model of repulsively interacting single TrcB particles is incompatible with the presence of equilibrium aggregate phases. The self-diffusion coefficient at the short-time limit (Dsh) decreased more as the TrcB concentration increased than one would expect for a corresponding hard-sphere or charged particle at the same volume fraction. At low volume fractions, the system consisted of monomers, dimers, and trimers. At high TrcB volume fractions, the main particles were larger aggregates. The collective diffusion coefficient, Dc, was constant when Q > Qc, where Qc is the position of the interference peak, which implies that there were no inter-monomer TrcB oligomer dynamics. This is because Dsh/D0 decayed much more quickly than the TrcB monomer as a function of the volume fraction. In vitro experiments revealed that antimicrobial activities were preserved at all volume fractions notwithstanding the presence of various oligomers.

Classical simulation of spin-tagged collisional ionization at near-threshold energies

In this paper, we develop a spin dependent classical trajectory Monte Carlo approach to investigate the spin-tagged collisional ionization process. With the help of anti-symmetrized Gaussian wave packets, an effective interaction potential between the two spin-tagged electrons is derived to mimic the spin associated quantum effect of Pauli exclusion principle. Our model is applied to investigate the spin dependent collisional ionization of e–H system. The results are in good agreement with experimental data, ab initio quantum-mechanical calculations as well as a variety of characteristics of the Wannier theory for near-threshold ionization. In contrast, the popular Fermionic molecular dynamics model overestimates the total ionization cross section as high as ten times and predicts a totally inversed ionization spin asymmetry contrary to experimental results. Further applications of our model to laser-assisted collisional ionization are demonstrated and some interesting results are presented.

Vibrational Properties of Hard and Soft Spheres Are Unified at Jamming.

The unconventional thermal properties of jammed amorphous solids are directly related to their density of vibrational states. While the vibrational spectrum of jammed soft sphere solids has been fully described, the vibrational spectrum of hard spheres, a model glass former often related to physical colloidal glasses, is still unknown due to the difficulty of treating the nonanalytic interaction potential. We bypass this difficulty using the recently described effective interaction potential for the free energy of thermal hard spheres. By minimizing this effective free energy, we mimic the rapid compression of hard spheres and produce typical configurations of the thermal system. We measure the resulting vibrational spectrum and characterize its evolution toward the jamming point where configurations of hard and soft spheres are trivially unified. For densities approaching jamming from below, we observe low-frequency modes which agree with those found in numerical simulations of jammed soft spheres. Our measurements of the vibrational structure demonstrate that the jamming universality extends away from jamming: hard sphere thermal systems below jamming exhibit the same vibrational spectra as thermal and athermal soft sphere systems above the transition.

A computational study of the behavior of colloidal gel networks at low volume fraction

Colloidal gel networks appear in different scientific and industrial applications because of their unique properties. Molecular dynamics simulations could reveal the relation between molecular level and macroscopic properties of these systems. Nevertheless, the predictions of numerical simulations might depend on the specific form and parameters of interaction potentials. In this paper, a new effective interaction potential is used for characterizing the mechanical behavior of low volume fraction colloidal gels under large shear deformation. The findings are compared with those obtained from other available forms of interaction potentials in order to determine gel characteristics that are interaction potential independent. Furthermore, the macroscopic stress–strain behavior is discussed in terms of the behavior of different terms of the proposed interaction potential. The correlation between the stretch of interparticle bonds and their alignment in the direction of the maximum principal stress is also computed in order to provide microscopic explanations for the initial strain softening behavior. It is concluded that, in addition to topology, local mechanical interactions between colloidal particles are important in defining the mechanical response of soft gels.

Shielding effects in fusion reactions with a proton-halo nucleus * * Supported by National Natural Science Foundation of China (11965004, U1867212, 11711540016, 11847317, 11947413), Natural Science Foundation of Guangxi province (2016GXNSFFA380001, 2017GXNSFGA198001), Foundation of Guangxi innovative team and distinguished scholar in institutions of higher education, and Innovation project of Guangxi Graduate Education (XYCSZ2018051)

To explain the experimental observation that the fusion cross-section of a proton-halo nucleus with a heavy target nucleus is not enhanced as expected, the shielding hypothesis was proposed, where the proton-halo nucleus is polarized and the valence proton shielded by the core. In the frame of the improved quantum molecular dynamics model, the fusion reaction 17F on 208Pb around the Coulomb barrier is simulated. The existence of the shielding effect is verified by the microscopic dynamics simulations. Its influence on the effective interaction potential is also investigated.

Kinetics of nickel particle formation on silicon substrate with a buffer layer of niobium nitride

The size, form and distribution function of catalyst particles define the quality of synthesized arrays of carbon nanotubes. In this work, we study the kinetics of catalyst particle formation from the thin nickel film (9 nm) deposited on the silicon substrate (SiO2/Si) with a buffer layer of niobium nitride at the temperature of 880 °C. In the experiment, we have obtained the time dependences of the average radius, average height and concentration of nickel particles. The experimental data are satisfactorily described by simulations based on the wetting transition theory. Comparison of the simulation results and experimental data allows us to estimate the effective interaction potential between the nickel film and buffer layer of niobium nitride. Besides, we have estimated the viscosity of the nickel confirming an undercooled liquid state of the nanosized nickel film at the temperature of 880 °C.

Equilibrium clustering of colloidal particles at an oil/water interface due to competing long-range interactions

HypothesisColloids at fluid interfaces organize according to inter-particle interactions. The main contributions to an effective interaction potential are expected to be electrostatic dipole-dipole repulsion and capillary attraction due to fluid interface deformation. When these interactions are weak, a secondary minimum in the particle pair interaction potential is expected. ExperimentsClean bare silica particles were deposited at an oil/water interface and their organization as well as dynamics were observed under a light microscope and analyzed in terms of radial distribution function and mean squared displacement. FindingsWeak long-range competing interactions between colloids at an oil/water interface result in cluster formation. The clusters have a liquid-like structure and grow with increasing particle packing fraction. System ‘ergodicity’ suggests near-equilibrium assembly, which is confirmed by free particle dynamics outside the clusters. The interplay between dipole-dipole repulsion and capillary attraction responsible for the cluster formation is reflected in a secondary minimum of the effective interaction potential predicted theoretically but inaccessible experimentally from collective particle properties prior to this work.

Dense plasmas with partially degenerate semiclassical ions: screening and structural properties

The screened interaction potential between ions taking into account the wave nature of ions is presented. The parameters considered in this paper correspond to those of dense plasmas with ideal or weakly coupled quantum electrons and semiclassical non-ideal ions. The wave nature of ions is described using the concept of quantum potentials. The obtained effective interaction potential between ions takes into account screening by electrons and ionic quantum nonlocality. It is shown that the polarization of electrons around an ion leads to a decrease in the ion’s effective thermal wavelength and, conversely, screening of the ion field by electrons becomes weaker due to the wave nature of the ion. Furthermore, on the basis of the derived ion–ion interaction potential, we investigate the structural properties of semiclassical non-ideal ions. For hydrogen plasmas, the ionic quantum nonlocality effect is significant at rS < 0.3. The obtained results are relevant to high energy density physics.

Investigating the nature of discontinuous shear thickening: Beyond a mean-field description

Dense suspensions can undergo a dramatic increase in viscosity at a critical value of the shear stress. This phenomenon, termed discontinuous shear thickening (DST), has been attributed to an increase in the fraction of particle interactions becoming frictional with increasing shear stress, and a successful mean-field theory has been developed to explain various accompanying rheological properties. On a microscopic scale, however, conventional structural analysis measures such as the grain-position pair correlation function show no significant changes with the onset of DST, though recent work has shown that similar analysis in the dual space of contact forces does lead to marked changes at this transition. Furthermore, experimental results have suggested the existence of higher-order microscopic correlations and the importance of incorporating fluctuations away from a mean-field description. To this end, we use a higher-order cluster analysis tool to study the force networks obtained from simulations of dense suspensions to construct an effective interaction potential in force space. We show that there are significant changes occurring in this potential as a function of density and stress close to DST. We discuss the implications of these observations on an emergent field theory of the DST transition.

Static and dynamic properties of decane/water microemulsions stabilized by cetylpyridinium chloride cationic surfactant and octanol cosurfactant.

Molecular dynamics simulation (MD) is used to study the static and dynamic properties of positively charged decane/water microemulsions, for various volume fractions Φ (2.8%, 6.98%, 14%, and 26.5%). An effective hybrid potential combining three potentials, namely the hard-sphere repulsive potential, the van der Waals attractive potential, and the Yukawa repulsive potential, is used to describe the microemulsion interactions. The microemulsion shape is determined using the renormalized spectra in Porod representation. The appropriate potential parameters are tested using the Ornstein–Zernike integral equation approach with the Hypernetted Chain (HNC) closure relation by a comparison between the structure factor calculated from HNC and that obtained from Small Angle Neutron Scattering experiments (SANS). Thus, the micro arrangements of microemulsions have been analyzed using the pair correlation function g(r) and the structure factor S(q) obtained from HNC, SANS, and MD simulation using these parameters. The microemulsion dynamic properties were discussed using the mean-square displacement (MSD) and the diffusion coefficient Dc calculated from MD simulations.

Development of effective potentials for complex plasmas

In this article the review of interaction potentials for compound particles (i.e. atoms, clusters etc.) ofcomplex plasmas that have been derived and developed by academician Fazylkhan Baimbetov and hisstudents over the past 25 years is given. Complex plasmas such us dense non-ideal plasmas, partiallyionized plasmas, dusty plasmas are considered. We consider effective interaction potentials for classicalnon-ideal plasmas, semiclassical weakly coupled plasmas, and quantum plasmas. The effective potentialsinclude relevant effects of non-idelaity and quantum degeneracy. These effective potentials are forequilibrium and stationary out-of equilibrium state of plasmas. In the latter case, the effect of dynamicalscreening resulting in oscillatory pattern of the potential due to formation of the wakefield considered inboth classical and quantum plasmas is taken into account. There appears anomalous behavior of thewakefield in quantum plasmas. Atoms and dust particles are considered to be compound particles withallowance for polarization, i.e acquiring a dipole moment. The screening of the field of such dipoles areconsidered making use the multipole expansion of the screened Coulomb potential. Additionally, thediscussion of these results comparing to works of researchers from elsewhere is presented. The furtherdevelopment of the effective potential theory should determine what effect the plasma streaming willhave on transport properties such as viscosity and diffusion of non-ideal plasmas.