New space warping method for the simulation of large-scale macromolecular conformational changes

A space warping method, facilitating the modeling of large-scale conformational changes in mesoscopic systems, is presented. The method uses a set of "global (or collective) coordinates" that capture overall behavior, in conjunction with the set of atomic coordinates. Application of the space warping method to energy minimization is discussed. Several simulations where the method is used to determine the energy minimizing structures of simple central force systems are analyzed. Comparing the results and behavior of the space warping method to simulations involving atomic coordinates only, it is found that the space warping method scales better with system size and also finds lower minima when the potential energy surface has multiple minima. It is shown that the transformation of [Ala16]+ in vacuo from linear to globular is captured efficiently using the space warping method.     

Spherical tensor theory of long-range intermolecular forces

General expressions are given for the electrostatic, induction and dispersion energies of a pair of interacting, molecules in terms of spherical tensor components of the molecular multipole moments and polarizabilities. The orientation dependence is given in terms of the scalar expansion functions S_l1l2l^k1k2.     

The Hellmann-Feynman theorem applied to long-range forces

The relations between the Hellmann-Feynman forces in laboratory fixed (L-) and relative (R-) coordinate systems are clarified. In the usualL-coordinate system, the force is interpreted as force on nucleus, while in theR-coordinate system, it means force on whole particles consisting of the electrons and nuclei of each interacting subsystem. From a perturbation theoretical viewpoint, the concept of the force on whole particles correctly corresponds to the perturbation energy and is superior to the force on the nucleus.     

Excluded volume effects in macromolecular forces and ion-interface interactions

A charged Yukawa liquid confined in a slit nanopore is studied in order to understand excluded volume effects in the interaction force between the pore walls. A previously developed self-consistent scheme [S. Buyukdagli, C. V. Achim, and T. Ala-Nissila, J. Stat. Mech. 2011, P05033] and a new simpler variational procedure that self-consistently couple image forces, surface charge induced electric field, and pore modified core interactions are used to this aim. For neutral pores, it is shown that with increasing pore size, the theory predicts a transition of the interplate pressure from an attractive to a strongly repulsive regime associated with an ionic packing state, an effect observed in previous Monte Carlo simulations for hard core charges. We also establish the mean-field theory of the model and show that for dielectrically homogeneous pores, the mean-field regime of the interaction between the walls corresponds to large pores of size d > 4 ?. The role of the range of core interactions in the ionic rejection and interplate pressure is thoroughly analyzed. We show that the physics of the system can be split into two screening regimes. The ionic packing effect takes place in the regime of moderately screened core interactions characterized with the bare screening parameter of the Yukawa potential b ? 3/l(B), where l(B) is the Bjerrum length. In the second regime of strongly screened core interactions b ? 3/l(B), solvation forces associated with these interactions positively contribute to the ionic rejection driven by electrostatic forces and enhance the magnitude of the attractive pressure. For weakly charged pores without a dielectric discontinuity, core interactions make a net repulsive contribution to the interplate force and also result in oscillatory pressure curves, whereas for intermediate surface charges, these interactions exclusively strengthen the external pressure, thereby reducing the magnitude of the net repulsive interplate force. The pronounced dependence of the interplate pressure and ionic partition coefficients on the magnitude and the range of core interactions indicates excluded volume effects as an important ion specificity and a non-negligible ingredient for the stability of macromolecules in electrolyte solutions.     

Certain results obtained in research on long-range surface forces

Conclusions Research over the last 45 years has revealed the existence of long-range surface forces of three types: molecular, ionic-electrostatic, and structural. These forces lie at the foundation of the theory of stability of disperse systems and colloids, and are the basis of many processes: swelling, frost-heaving of soils, wetting phenomena, and thermoosmotic phenomena. The structural features of boundary layers of polar liquids and water lead to their anisotropy and to changes in their heat capacity and density.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 8, pp. 1721–1725, August, 1982.     

Computer simulation of macromolecular materials

Computer simulation of model systems with Monte Carlo methods enables the detailed study of structure and thermodynamic properties of these systems and thus constitutes a link between analytic theory and experiment. Typical applications that are discussed include polymer blends, dynamics of local motions in polymer melts, and the adsorption of polymers on walls.Invited talk at the Tagung der Deutschen Physikalischen Gesellschaft (DPG), Fachausschuß Polymerphysik, Hamburg, March 14–16, 1988.     

On long-range forces of repulsion between biological cells

We have established experimentally that when biological cells, for example, blood, are suspended in concentrated solutions of inorganic electrolytes (for instance, in a 15% solution of sodium chloride) then around some cells (leucocytes, especially tumour cells) there form haloes, i.e., circular spaces free from background cells (erythrocytes, yeast cells, colloidal particles of Indian ink). In the medium made up of erythrocytes the haloes form during 5–10 min as a result of the background cells drawing apart from the central halo-forming cell (HFC) at a distance of 10–100 μm and more.

In the medium made of the Indian ink particles, the haloes form during 2–4 s and attain a thickness of about 10–20 μm. The erythrocytes and the haloes forming in their medium can be preserved for about three to five days at room temperature.

It has been established that, when tumour HFCs are present at sufficient concentrations, they form hexagonal periodic structures having a mean spacing between cells of up to 60 μm.

The authors put forward as one probable suggestion that the formation of haloes is largely determined by long-range repulsive forces arising from the phenomenon of diffusiophoresis generated by the diffusion currents that emerge from the surface of halo-forming cells.     

Application of Ewald summations to long-range dispersion forces

Results illustrating the effects of using explicit summation terms for the r(-6) dispersion term on the interfacial properties of a Lennard-Jones fluid and SPC/E water are presented. For the Lennard-Jones fluid, we find that the use of long-range summations, even with a short "crossover radius," yields results that are consistent with simulations using large cutoff radii. Simulations of SPC/E water demonstrate that the long-range dispersion forces are of secondary importance to the Coulombic forces. In both cases, we find that the ratio of the box size L( parallel) to the crossover radius r(c) (k) plays an important role in determining the magnitude of the long-range dispersion correction, although its effect is secondary when Coulombic interactions are also present.     

Capillary bridging and long-range attractive forces in a mean-field approach

When a mixture is confined, one of the phases can condense out. This condensate, which is otherwise metastable in the bulk, is stabilized by the presence of surfaces. In a sphere-plane geometry, routinely used in atomic force microscope and surface force apparatus, it can form a bridge connecting the surfaces. The pressure drop in the bridge gives rise to additional long-range attractive forces between them. By minimizing the free energy of a binary mixture we obtain the force-distance curves as well as the structural phase diagram of the configuration with the bridge. Numerical results predict a discontinuous transition between the states with and without the bridge and linear force-distance curves with hysteresis. We also show that similar phenomenon can be observed in a number of different systems, e.g., liquid crystals and polymer mixtures.     

A note on the theory of interatomic long-range forces

A comment is made on the multipolar expansion formula of the long-range force between hydrogen atoms previously obtained. The second-order perturbation energy neglecting exchange in the framework of the Unsöld approximation is evaluated exactly. An extension is made to helium atoms, and to other s-electron interactions. An approximate method is suggested to estimate the interatomic force between two atoms in general.     

Modern state of the investigation of long-range surface forces

Development of the concept of surface long-range forces and, in particular, the equilibrium disjoining pressure of liquid and gaseous interlayers has been set forth. Considered are the molecular, adsorption, electrical, structural, and electronic components of disjoining pressure. The contribution of the disjoining pressure to the hydrodynamics of thin layers is considered. The first theory of the frost heaving of soils has been formulated. Stated are the investigations of surface forces, in particular, in the processes of the formation of new interfaces and arising phenomena of the emission of electrons, ions, photons, and neutrons.     

Direct measurements of long-range surface forces in gas and liquid media

A modified set-up was applied to carry out direct measurements of the forces of molecular attraction of gold spheres and crossed quartz filaments in air within the region of distances from 10 to 100 nm. Some quantitative deviations from Lifshitz's theory for gold may be attributed to an insufficient reliability of the spectral data used in the calculations. The DLVO theory adequately describes the interaction of glass threads in KCl (10^?3 ÷ 10^?5 N) solutions within the region of 5 to 100 nm. At a distance smaller than 5 nm, the deviations from DLVO theory are attributable to the influence of structural forces.When the contact between crossed hydrophobized quartz threads in water is broken, the attraction forces (which exceed the molecular forces by several orders of magnitude) at a distance of up to 300 nm are detected.     

Mapped grid methods for long-range molecules and cold collisions

The paper discusses ways of improving the accuracy of numerical calculations for vibrational levels of diatomic molecules close to the dissociation limit or for ultracold collisions, in the framework of a grid representation. In order to avoid the implementation of very large grids, Kokoouline et al. [J. Chem. Phys. 110, 9865 (1999)] have proposed a mapping procedure through introduction of an adaptive coordinate x subjected to the variation of the local de Broglie wavelength as a function of the internuclear distance R. Some unphysical levels ("ghosts") then appear in the vibrational series computed via a mapped Fourier grid representation. In the present work the choice of the basis set is reexamined, and two alternative expansions are discussed: Sine functions and Hardy functions. It is shown that use of a basis set with fixed nodes at both grid ends is efficient to eliminate "ghost" solutions. It is further shown that the Hamiltonian matrix in the sine basis can be calculated very accurately by using an auxiliary basis of cosine functions, overcoming the problems arising from numerical calculation of the Jacobian J(x) of the R-->x coordinate transformation.     

The current state of the theory of long-range surface forces

Interactions between surfaces and particles are considered on the basis of isotherms of disjoining pressure ∏(h), which include molecular, electrostatical, structural and steric forces. A review of the present day theory of long-range surface forces is given with special attention to the structural forces of hydrophilic repulsion and hydrophobic attraction. Effects of electrolyte concentration, degree of hydrophilization and temperature on the structural forces are discussed.     

Role of long-range intermolecular forces in the formation of inorganic nanoparticle clusters

An understanding of the role played by intermolecular forces in terms of the electron density distribution is fundamental to the understanding of the self-assembly of molecules in the formation of a molecular crystal. Using ab initio methods capable of describing both short-range intramolecular interactions and long-range London dispersion interactions arising from electron correlation, analyses of inorganic dimers of As(4)S(4) and As(4)O(6) molecules cut from the structures of realgar and arsenolite, respectively, reveal that the molecules adopt a configuration that closely matches that observed for the crystal. Decomposition of the interaction energies using symmetry-adapted perturbation theory reveals that both model dimers feature significant stabilization from electrostatic forces as anticipated by a Lewis acid/Lewis base picture of the interaction. London dispersion forces also contribute significantly to the interaction, although they play a greater role in the realgar structure near equilibrium than in arsenolite.     

Recent advances in macromolecular engineering via ionic methods

Selected recent developments in the field of macromolecular engineering via ionic methods are presented: ω-functional polymers and macromonomers, ampholytic block copolymers and novel thermoplastic block copolymers, star shaped macromolecules of several kinds. Attention is called upon the absolute necessity of adequately characterizing the samples obtained, in order to check wether their structure meets with expectation.     

Effect of long-range hydrodynamic and direct intermacromolecular forces on translational diffusion

Within the framework of recently formulated microscopic theories of macromolecular diffusion it is shown that hydrodynamic forces act always to diminish the influence of direct forces, but never to reverse the sign of the correction term due to direct forces alone. Although the correction term D(k) to the intrinsic diffusion coefficient may vary with scattering vector |k|, it is shown that a reversal in sigh of the correction term with increasing |k|, if it occurs, must be associated with an amplitude of less than 10% of the correction term at |k| = 0. At |k| = 0 direct repulsive forces are predicted to always increase the apparent diffusion constant, even after accounting for hydrodynamic interactions. Although experiments on polylysine (1 mg/ml) at salt concentrations above 0.01 M are in qualitative accord with the theory, below 10^?3 M salt the apparent diffusion coefficient is reduced by a factor of about 20, concomitant with a much reduced intensity of scattered light. The strong contradiction of the theory implied by this observation is attributed to a dramatic rise in Stokes friction arising from long-range interionic forces in the low-salt solutions.     

A new parallel method for molecular dynamics simulation of macromolecular systems

Short-range molecular dynamics simulations of molecular systems are commonly parallelized by replicated-data methods, in which each processor stores a copy of all atom positions. This enables computation of bonded 2-, 3-, and 4-body forces within the molecular topology to be partitioned among processors straightforwardly. A drawback to such methods is that the interprocessor communication scales as N (the number of atoms) independent of P (the number of processors). Thus, their parallel efficiency falls off rapidly when large numbers of processors are used. In this article a new parallel method for simulating macromolecular or small-molecule systems is presented, called force-decomposition. Its memory and communication costs scale as N/√P, allowing larger problems to be run faster on greater numbers of processors. Like replicated-data techniques, and in contrast to spatial-decomposition approaches, the new method can be simply load balanced and performs well even for irregular simulation geometries. The implementation of the algorithm in a prototypical macromolecular simulation code ParBond is also discussed. On a 1024-processor Intel Paragon, ParBond runs a standard benchmark simulation of solvated myoglobin with a parallel efficiency of 61% and at 40 times the speed of a vectorized version of CHARMM running on a single Cray Y-MP processor. © 1996 by John Wiley & Sons, Inc.     

Monte carlo simulation of macromolecular ionization by nanoelectrospray

Electrospray ionization (ESI) is commonly used in macromolecular mass spectrometry, yet the dynamics of macromolecules in ESI droplets are not well understood. In this study, a Monte Carlo based model was developed, which can predict the efficiency of electrospray ionization for macromolecules, i.e., the number of macromolecular ions produced per macromolecules electrosprayed. The model takes into account ESI droplet evaporation, macromolecular diffusion within the droplet, droplet fissions, and the statistical nature of the ESI process. Two idealized representations of macromolecular analytes were developed, describing cluster prone, droplet surface inactive macromolecules and droplet surface active macromolecules, respectively. It was found that surface active macromolecules are preferentially ionized over surface inactive cluster prone macromolecules when the initial droplet size is large and the analyte concentration in solution is high. Simulations showed that ESI efficiency decreases with increasing initial droplet size and analyte molecular weight, and is influenced by analyte surface activity, the properties of the solvent, and the variance of the droplet size distribution. Model predictions are qualitatively supported by experimental measurements of macromolecular electrospray ionization made previously. Overall, this study demonstrates the potential capabilities of Monte Carlo based ESI models. Future developments in such models will allow for more accurate predictions of macromolecular ESI intensity.