Effective Interaction Potential Research Articles

Effective mechanical potential of cell-cell interaction in tissues harboring cavity and in cell sheet toward morphogenesis.

Measuring mechanical forces of cell-cell interactions is important for studying morphogenesis in multicellular organisms. We previously reported an image-based statistical method for inferring effective mechanical potentials of pairwise cell-cell interactions by fitting cell tracking data with a theoretical model. However, whether this method is applicable to tissues with non-cellular components such as cavities remains elusive. Here we evaluated the applicability of the method to cavity-harboring tissues. Using synthetic data generated by simulations, we found that the effect of expanding cavities was added to the pregiven potentials used in the simulations, resulting in the inferred effective potentials having an additional repulsive component derived from the expanding cavities. Interestingly, simulations by using the effective potentials reproduced the cavity-harboring structures. Then, we applied our method to the mouse blastocysts, and found that the inferred effective potentials can reproduce the cavity-harboring structures. Pairwise potentials with additional repulsive components were also detected in two-dimensional cell sheets, by which curved sheets including tubes and cups were simulated. We conclude that our inference method is applicable to tissues harboring cavities and cell sheets, and the resultant effective potentials are useful to simulate the morphologies.

Electron–ion collision and polarization of X-ray fluorescence radiation under hot quantum plasma conditions

In the current article, the spectral properties and electron collision (total and magnetic) excitation cross sections of ions taking placed in quantum plasmas are investigated. These cross sections are further used to study the polarization and angular distribution characteristics of the de-excitation radiation X-ray spectra, which play an important role in basic theoretical research, the diagnosis of the plasma environment, and the design of optical devices. To do so, a distorted wave method within the relativistic Dirac–Coulomb atomic structure scheme is suggested. The effective interaction potential between electrons and particles in hot quantum plasmas in the method is determined using a quantum approach that incorporates the influence of effective plasma screening effects caused by collective plasma oscillations. This potential replaces the traditional Coulomb interaction potential and is used in solving the modified Dirac equation to obtain the bound and continuum electron wave functions. Higher-order relativistic effects, such as the Breit interaction and the dominant quantum electrodynamics corrections, are added to enhance the accuracy of the method. Detailed calculations for the relativistic atomic structure and collision excitation dynamics process are carried out, taking the highly stripped H-like O7+ ion of astrophysical importance as an illustrative example. Detailed investigations are also conducted on the variation of energies, collision cross sections, and fluorescence polarizations as functions of the plasma parameters. Our results suggest that the joint effects of shielding and plasma coupling lead the energies, cross sections and fluorescence polarizations decrease (compared with the isolated case). The angular distribution of the X-ray fluorescence emission shows large change, suggesting their sensitivity to these effects. This study not only offers a valuable approach to investigating the plasma shielding and plasmon coupling effects in quantum plasmas but also holds significant relevance for applications in controlled nuclear fusion, astrophysical plasmas and so on.

Transferable local density-dependent friction in tert-butanol/water mixtures.

Coarse-grained (CG) models informed from molecular dynamics simulations provide a way to represent the structure of an underlying all-atom (AA) model by deriving an effective interaction potential. However, this leads to a speed-up in dynamics due to the lost friction, which is especially pronounced in CG implicit solvent models. Applying a thermostat based on the Langevin equation (LE) provides a way to represent the long-time dynamics of CG particles by reintroducing friction to the system. To improve the representability CG models of heterogeneous molecular mixtures and their transferability over the mixture compositions, we parameterize an LE thermostat in which the friction coefficient depends on the local particle density (LD). The thermostat friction was iteratively optimized with a Markovian variant of the recently introduced Iterative Optimization of Memory Kernels (IOMK) method. We simulated tert-butanol/water mixtures over a range of compositions, which show a distinct clustering behavior. Our model with LD-dependent friction reproduces the AA diffusion coefficients well over the full range of mixtures and is, therefore, transferable with respect to dynamics.

Search of effective interaction in dipole bands of an odd–odd trans-lead Nucleus: the case of 204At

Role of effective interaction potential in shears band structure in [Formula: see text]At has been investigated in more detail than in previous studies. A semi-classical geometric model is used to obtain the interaction strengths between valence protons and neutron holes constituting the shears blades. The value produces overall good agreement with this region’s nuclei. Band crossing is observed in the spin-parity range [Formula: see text] – [Formula: see text]. Configurations of the Magnetic Rotational (MR) band are assigned in the light of the Shears mechanism with the Principal Axis Cranking (SPAC) model. Experimental rotational frequencies and the deduced ratio of [Formula: see text] are well reproduced by SPAC calculations, suggesting the dipole band in [Formula: see text]At can undoubtedly be interpreted as the MR band resulting from the effective interaction of repulsive potential.

Variability of entropy force and its coupling with electrostatic and steric hindrance interactions

We investigated the effective interaction potential (EIP) between charged surfaces in solvent comprised of dipole dimer molecules added with a certain amount of ionic liquid. Using classical density functional theory, the EIP is calculated and decoupled into entropic and energy terms. Unlike the traditional Asakura–Oosawa (AO) depletion model, the present entropic term can be positive or negative, depending on the entropy change associated with solvent molecule migration from bulk into slit pore. This is determined by pore congestion and disruption of the bulk dipole network. The energy term is determined by the free energy associated with hard-core repulsion and electrostatic interactions between surface charges, ion charges, and polarized charges carried by the dipole dimer molecules. The calculations in this article clearly demonstrate the variability of the entropy term, which contrasts sharply with the traditional AO depletion model, and the corrective effects of electrostatic and spatial hindrance interactions on the total EIP; we revealed several non-monotonic behaviors of the EIP and its entropic and energy terms concerning solvent bulk concentration and solvent molecule dipole moment; additionally, we demonstrated the promoting effect of dipolar solvent on the emergence of like-charge attraction, even in 1:1 electrolyte solutions. The microscopic origin of the aforementioned phenomena was analyzed to be due to the non-monotonic change of dipolar solvent adsorption with dipole moment under conditions of low solution dielectric constant. The present findings offer novel approaches and molecular-level guidance for regulating the EIP. This insight has implications for understanding fundamental processes in various fields, including biomolecule-ligand binding, activation energy barriers, ion tunneling transport, as well as the formation of hierarchical structures, such as mesophases, micro-, and nanostructures, and beyond.

Electron–ion temperature relaxation in nonideal plasmas: High accuracy classical molecular dynamics simulations

AbstractIn this work, we prepare a simulation framework for a high‐accuracy numerical study of electron–ion temperature relaxation in nonideal (strongly coupled) plasmas. The existing relaxation rate theories require either parameter selection or some pre‐knowledge of the electron–ion correlation functions and effective interaction potentials. This makes non‐equilibrium classical and quantum molecular dynamics simulations a crucial stage in the study of energy transfer rates. We begin by revisiting the classical molecular dynamics simulations of a system of equally charged particles with different masses on a neutralizing background. We accurately simulate this simple ab‐initio (parameterless) system with controlled precision in terms of number of particles, mass ratio, and energy convergence. The predictions for the equally charged system are compared to the previous simulations and theories, which are reproduced with higher accuracy. We also perform a series of classical molecular dynamics simulations of the system of oppositely charged particles with the corrected Kelbg potential based on the quantum statistical approach. We analyze the differences and similarities between the same‐charge and opposite‐charge systems. Some remarks about the forthcoming application of quantum simulations with the help of WPMD or WPMD‐DFT methods are given.

Formation of catalyst particles for the CNT growth from thin films: Experiment and simulation

The formation of Ni nanoparticles for the growth of carbon nanotubes on a TiNbarrier layer obtained by atomic layer deposition was studied. The interaction of the catalyst with the barrier layer is revealed. It consists of diffusion of Ni into TiN with activation energy of 0.75 eV.Assuming the melting of a nanosized Ni film, we simulated the formation of catalyst particles in terms of wetting transition theory. Comparison of simulation results and experimental data on catalyst particle formation allowed us to estimate effective interaction potential of Ni film and barrier layer. A change of the interaction potential due to variation of the film or barrier layer properties (e.g., material, structure, etc.) is responsible for change of the dynamics of catalyst particle formation including dynamics of their average size, number density and the shape of the size distribution function.

Colloidal gelation induced by ring polymers

We provide unambiguous experimental evidence that ring polymers are stronger depleting agents in colloidal suspensions than their linear counterparts. We use an intermediate volume fraction (ϕc=0.44) colloidal gel based on the classic poly(methyl methacrylate) (PMMA) hard spheres, in which the polystyrene depletant is either linear or ring of the same molar mass or the same size. We systematically increase the depletant concentration from zero (no attraction) to well above the gelation point and find that in the presence of rings, gels are formed at smaller concentrations and possess a larger storage modulus in comparison to those induced by the linear chains. Consequently, the yield stress is enhanced; however, the yield strain (gel deformability) remains concomitantly unaffected. Our experimental findings are in agreement with theoretical calculations based on effective interaction potentials. Hence, polymer architecture is a powerful entropic tool to tailor the strength of colloidal gels. Published by the American Physical Society 2024

Baryons and tetraquarks using instanton-induced interactions

We analyze some aspects of the perturbative and nonperturbative interactions in the composition of heavy quarkonia, heavy and light baryons (ccc and uuu ones), as well as all charm tetraquarks (ccc¯c¯). Using the hyperspherical approximation and effective radial potentials (in six and nine dimensions, respectively) we derive their spectra and wave functions. In all of the cases, we focus on the splittings between the S-shell levels, which are remarkably insensitive to the quark masses, but proportional to the effective interaction potentials. We use the traditional Cornell-like potentials, and the nonperturbative instanton-induced static potentials, from correlators of two, three, and four Wilson lines, and find rather satisfactory description of spectra in all cases. Published by the American Physical Society 2024

Coarse-Grained Many-Body Potentials of Ligand-Stabilized Nanoparticles from Machine-Learned Mean Forces.

Colloidal nanoparticles self-assemble into a variety of superstructures with distinctive optical, structural, and electronic properties. These nanoparticles are usually stabilized by a capping layer of organic ligands to prevent aggregation in the solvent. When the ligands are sufficiently long compared to the dimensions of the nanocrystal cores, the effective coarse-grained forces between pairs of nanoparticles are largely affected by the presence of neighboring particles. In order to efficiently investigate the self-assembly behavior of these complex colloidal systems, we propose a machine-learning approach to construct effective coarse-grained many-body interaction potentials. The multiscale methodology presented in this work constitutes a general bottom-up coarse-graining strategy where the coarse-grained forces acting on coarse-grained sites are extracted from measuring the vectorial mean forces on these sites in reference fine-grained simulations. These effective coarse-grained forces, i.e., gradients of the potential of mean force or of the free-energy surface, are represented by a simple linear model in terms of gradients of structural descriptors, which are scalar functions that are rotationally invariant. In this way, we also directly obtain the free-energy surface of the coarse-grained model as a function of all coarse-grained coordinates. We expect that this simple yet accurate coarse-graining framework for the many-body potential of mean force will enable the characterization, understanding, and prediction of the structure and phase behavior of relevant soft-matter systems by direct simulations. The key advantage of this method is its generality, which allows it to be applicable to a broad range of systems. To demonstrate the generality of our method, we also apply it to a colloid-polymer model system, where coarse-grained many-body interactions are pronounced.

Mixing Linear Polymers with Rings and Catenanes: Bulk and Interfacial Behavior.

We derive and parameterize effective interaction potentials between a multitude of different types of ring polymers and linear chains, varying the bending rigidity and solvent quality for the former species. We further develop and apply a density functional treatment for mixtures of both disconnected (chain-ring) and connected (chain-polycatenane) mixtures of the same, drawing coexistence binodals and exploring the ensuing response functions as well as the interface and wetting behavior of the mixtures. We show that worsening of the solvent quality for the rings brings about a stronger propensity for macroscopic phase separation in the linear-polycatenane mixtures, which is predominantly of the demixing type between phases of similar overall particle density. We formulate a simple criterion based on the effective interactions, allowing us to determine whether any specific linear-ring mixture will undergo a demixing phase separation.

On charged particle dynamics near flat solid surface

The motion of a non-relativistic charged particle near flat solid surface at small sliding angles is examined within the formalism of the effective potential composed by interaction of a particle with surface atoms and excited plasmons. As known, the presence of curvature in a solid surface can result in forming a set of discrete quantum states for a particle in the potential well of interaction with the surface.In this work we demonstrate that, at the glancing to flat-surface motion of fast charged particles, small channeling oscillations can be also observed for some special conditions. It is shown that the effective interaction potential represents a shallow well capable to hold a particle in a bound state. We succeeded to analytically determine the energy levels of a particle in such a potential well, as well as the critical angle for a particle to be trapped, in terms of known critical angle of channeling in crystals and a newly proposed function for simplification.

Pair interaction of localized topological structures in confined chiral media.

We study pairwise interactions between localized topological structures in chiral magnetic and cholesteric liquid crystal (CLC) systems confined in the planar geometry. Our calculations for magnetics are based on the lattice model that takes into account the bulk and surface anisotropies along with the exchange and the Dzyaloshinskii-Moriya interactions. In CLC cells, these anisotropies describe the energy of interaction with an external magnetic or electric field and the anchoring energy assuming that the magnetic or electric anisotropy is negative and the boundary conditions are homeotropic. We have selected the region of the phase diagram, where various localized solitonlike structures, including skyrmion tubes, torons, and leeches, embedded in the ground state of the z-cone (conical phase) coexist, and carried out numerical analysis of the distance dependencies of the effective intersoliton interaction potentials. For skyrmions and torons, the potentials are found to be attractive in the large separation region. It turned out that for these potentials, the effects of axial asymmetry are negligible. By contrast, it turned out that for the intermediate structures between the skyrmions and torons known as the leeches, the leech-leech potentials generally depend on the orientation of the intersoliton separation vector and their large distance parts may become repulsive at certain directions of the vector. All the potentials have the short distance repulsive parts and the local minima located at the equilibrium separations. It is found that the skyrmion-skyrmion potential has an additional metastable configuration shifted towards the short-distance region.

Effective mechanical potential of cell-Cell interaction explains three-dimensional morphologies during early embryogenesis.

Mechanical forces are critical for the emergence of diverse three-dimensional morphologies of multicellular systems. However, it remains unclear what kind of mechanical parameters at cellular level substantially contribute to tissue morphologies. This is largely due to technical limitations of live measurements of cellular forces. Here we developed a framework for inferring and modeling mechanical forces of cell-cell interactions. First, by analogy to coarse-grained models in molecular and colloidal sciences, we approximated cells as particles, where mean forces (i.e. effective forces) of pairwise cell-cell interactions are considered. Then, the forces were statistically inferred by fitting the mathematical model to cell tracking data. This method was validated by using synthetic cell tracking data resembling various in vivo situations. Application of our method to the cells in the early embryos of mice and the nematode Caenorhabditis elegans revealed that cell-cell interaction forces can be written as a pairwise potential energy in a manner dependent on cell-cell distances. Importantly, the profiles of the pairwise potentials were quantitatively different among species and embryonic stages, and the quantitative differences correctly described the differences of their morphological features such as spherical vs. distorted cell aggregates, and tightly vs. non-tightly assembled aggregates. We conclude that the effective pairwise potential of cell-cell interactions is a live measurable parameter whose quantitative differences can be a parameter describing three-dimensional tissue morphologies.

Multibody Terms in Protein Coarse-Grained Models: A Top-Down Perspective.

Coarse-grained models allow computational investigation of biomolecular processes occurring on long time and length scales, intractable with atomistic simulation. Traditionally, many coarse-grained models rely mostly on pairwise interaction potentials. However, the decimation of degrees of freedom should, in principle, lead to a complex many-body effective interaction potential. In this work, we use experimental data on mutant stability to parametrize coarse-grained models for two proteins with and without many-body terms. We demonstrate that many-body terms are necessary to reproduce quantitatively the effects of point mutations on protein stability, particularly to implicitly take into account the effect of the solvent.

Effective Interactions between Double-Stranded DNA Molecules in Aqueous Electrolyte Solutions: Effects of Molecular Architecture and Counterion Valency.

A computational investigation of the effects of molecular topology, namely, linear and circular, as well as counterion valency, on the ensuing pairwise effective interactions between DNA molecules in an unlinked state is presented. Umbrella sampling simulations have been performed through the introduction of bias potential along a reaction coordinate defined as the distance between the centers-of-mass of pairs of DNA molecules, and effective pair interaction potentials have been computed by employing the weighted histogram analysis method. An interesting comparison can be drawn between the different DNA topologies studied here, especially with regard to the contrasting effects of divalent counterions on the effective pair potentials: while DNA-DNA repulsion in short center-of-mass distances decreases significantly in the presence of divalent counterion-ions (as compared to monovalent ions) for linear DNA, the opposite effect occurs for the DNA minicircles. This can be attributed to the fact that linear DNA fragments can easily adopt relative orientations that minimize electrostatic and steric repulsions by rotating relative to one another and by exhibiting more pronounced bending due to the presence of free ends.

S-wave resonance states below the Ps(n=2) threshold in positron-potassium system: Effects of weakly coupled classical plasma and dense quantum plasma

In this paper, the effects of plasmas on the S-wave resonance states in the positron-potassium system are investigated. Two different plasma conditions are considered, namely weakly coupled classical plasma (WCCP) and dense quantum plasma (DQP). The effective interaction potential in WCCP and DQP has been described by the Debye–Hückel model (static screened Coulomb potential) and a modified version of Debye–Hückel model (exponential cosine screened potential). Resonance parameters are determined by calculating the energy-density within the framework of the stabilization method. For the plasma-free case, three states, lying below the Ps[Formula: see text] threshold, are identified. The energy and the width agree well with the existing results in the literature. A detailed study is carried out to explore the changes emerging in the resonance parameters due to screening effects of WCCP and DQP. It is found that the energies of the three states are gradually pushed toward the Ps[Formula: see text] threshold due to the increasing plasma screening strength, whereas widths of the states vary differently.

Simulation study of cone-in-shell target for indirect-drive ion fast ignition concept under the theory of an effective interaction potential

The stopping power of charged particles released by the deuterium–tritium nuclear reactions has been extensively studied in the weakly to moderately coupled plasma regimes. We have modified the conventional effective potential theory (EPT) stopping framework to have a practical connection to investigate the ions energy loss characteristics in fusion plasma. Our modified EPT model differs from the original EPT framework by a coefficient of order 1 + {2 mathord{left/ {vphantom {2 {(5}}} right. kern-0pt} {(5}}ln overline{Xi }),(ln overline{Xi } is a velocity-dependent generalization of the Coulomb logarithm). Molecular dynamics simulations agree well with our modified stopping framework. To study the role of related stopping formalisms in ion fast ignition, we simulate the cone-in-shell configuration under laser-accelerated aluminum beam incidence. In ignition/burn phase, the performance of our modified model is in agreement with its original form and the conventional Li-Petrasso (LP) and Brown-Preston-Singleton (BPS) theories. The LP theory indicates the fastest rate in providing ignition/burn condition. Our modified EPT model with a discrepancy of sim 9%, has the most agreement with LP theory, while that of the original EPT (with a discrepancy of sim 47% to LP) and BPS (with a discrepancy of sim 48% to LP) methods maintain the third and fourth contributions in accelerating the ignition time, respectively.

A systematic analysis for one proton radioactivity of ground state nuclei

We systematically studied proton radioactivity half-lives in the atomic number range 53≤Z≤83 using macroscopic models such as Coulomb and Proximity potential model, effective liquid drop model (ELDM), Generalized liquid drop model (GLDM), Universal decay law for proton emission (UDLP), Gammow-like model (GLM) and Unified fission model (UFM). The proton decay half-lives produced by the macroscopic models are compared with those of semi-microscopic approach such as DDM3Y and using effective interaction potentials such as JLM, M3Y+EX, R3Y+EX, SLy4, SRG, SKC and SKD. After detail analysis, it is found that among macroscopic models ELDM and semi-empirical formula UDLP produce proton decay half-lives close to experiments. Furthermore, among semi-microscopic approach, DDM3Y produces proton decay half-lives close to the experiments. Thus, Both ELDM and DDM3Y model can be effectively used in the prediction of half-lives of unexplored proton emitters.

Entropic Origin of Ionic Interactions in Polar Solvents.

Implicit solvent models that reduce solvent degrees of freedom into effective interaction potentials are widely used in the study of soft materials and biophysical systems. For electrolyte and polyelectrolyte solutions, coarse-graining the solvent degrees of freedom into an effective dielectric constant embeds entropic contributions into the temperature dependence of the dielectric constant. Properly accounting for this electrostatic entropy is essential to discern whether a free energy change is enthalpically or entropically driven. We address the entropic origin of electrostatic interactions in a dipolar solvent and provide a clarified physical picture of the solvent dielectric response. We calculate the potential of mean force (PMF) between two oppositely charged ions in a dipolar solvent using molecular dynamics and dipolar self-consistent field theory. We find with both techniques that the PMF is dominated by the entropy gain from the dipole release, owing to the diminished orientational polarization of the solvent. We also find that the relative contribution of the entropy to the free energy change is nonmonotonic with temperature. We expect that our conclusions are applicable to a broad range of problems involving ionic interactions in polar solvents.