The influence of simulation conditions in molecular dynamics investigations of model β-sheet peptides

The influence of simulation methods, cutoff based and particle mesh Ewald (PME) on the accuracy by which experimentally derived nuclear Overhauser effect (NOE) data are reproduced, has been investigated using 500-ns-long molecular dynamics simulations on a model -sheet peptide in explicit solvent. The structural and conformational features under the different conditions were evaluated in terms of flexibility, secondary structure content, hydrogen-bonding pattern and percent of native contacts as a function of time. It was found that the different simulation methods strongly influence the dynamics of the peptide, confirming previous observations based on ideal peptide models simulated for much shorter times. Moreover, the results of our simulations prove once more that it is necessary to reach extremely long time scales to obtain enough statistics to accurately reproduce experimental NOE restraints even in the case of the PME method, despite its tendency to the stabilization of conformations which are structurally closely related to the ones derived through experiment. Possible implications regarding the stabilization and folding mechanisms, together with their relationship to the experimental study of peptide models, are discussed.     

Charge generation and electrostatic equilibrium for single granules during sliding

Electrostatic phenomena are commonly observed in the processing of solids. However, the working mechanism of electrostatic charge generation for single granules and particularly, their electrostatic equilibria have not been properly understood. In this work, repeated-sliding charging experiments with single granules were investigated for their electrostatic generation particularly from the perspective of triboelectrification equilibrium. Factors including granule length-ratio, sliding face shape, sliding times, sliding area, sliding velocity, front-facing edge, and sliding-plate inclined-angle were found to have an obvious effect on granule charge generation. Length-ratio and sliding area have significant effects as the granules evolved toward an equilibrium state. Equilibrium charge is suggested as a variable expressing the charging propensity of the material. In addition, under the same working conditions, a semi-cylindrical granule generates greater charge than a rectangular granule.     

A velocity program using the Kanade–Lucas–Tomasi feature-tracking algorithm with demonstration for pressure and electroosmosis conditions

Investigating microfluidic flow profiles is of interest in the microfluidics field for the determination of various characteristics of a lab-on-a-chip system. Microparticle tracking velocimetry uses computational methods upon recording video footage of microfluidic flow to ultimately visualize motion within a microfluidic system across all frames of a video. Current methods are computationally expensive or require extensive instrumentation. A computational method suited to microparticle tracking applications is the robust Kanade–Lucas–Tomasi (KLT) feature-tracking algorithm. This work explores a microparticle tracking velocimetry program using the KLT feature-tracking algorithm. The developed program is demonstrated using pressure-driven and EOF and compared with the respective mathematical fluid flow models. An electrostatics analysis of EOF conditions is performed in the development of the mathematical using a Poisson's Equation solver. This analysis is used to quantify the zeta potential of the electroosmotic system. Overall, the KLT feature-tracking algorithm presented in this work proved to be highly reliable and computationally efficient for investigations of pressure-driven and EOF in a microfluidic system.     

Aerial electrostatic spray deposition and canopy penetration in cotton

Daylight visible fluorescent dye (10% v/v) mixed with water was aerially applied on mature field cotton with electrostatic and rotary atomizer nozzles. The spray rates for the electrostatic and rotary atomizer nozzles were 9.4 and 28 L/ha, respectively. Images of spray droplets on cotton leaves were digitally analyzed with ImageJ software. Charged spray cloud increased deposition nearly two to three times on adaxial and abaxial surfaces, respectively, of top canopy leaves compared to uncharged spray. Canopy penetration of the spray into the lower layers of the plant foliage was unaffected by spray application method.     

Correspondences between the classical electrostatic Thomson problem and atomic electronic structure

Correspondences between the Thomson problem and atomic electron shell-filling patterns are observed as systematic non-uniformities in the distribution of potential energy necessary to change configurations of N ≤ 100 electrons into discrete geometries of neighboring N ? 1 systems. These non-uniformities yield electron energy pairs, intra-subshell pattern similarities with empirical ionization energy, and a salient pattern that coincides with size-normalized empirical ionization energies. Spatial symmetry limitations on discrete charges constrained to a spherical volume are conjectured as underlying physical mechanisms responsible for shell-filling patterns in atomic electronic structure and the Periodic Law.     

Collapse of Four-Arm Stars Polyelectrolyte Brushes Under An Electric Field in the Presence of Trivalent Salt Coions

Langevin dynamics simulations were conducted to study the collapse of grafted partially charged 4-arm star chains onto the oppositely charged grafting electrode in the presence of trivalent salt coions. Simulation results reveal that the average charge fraction of the grafted star chains and the salt concentration play critical roles in the competitive adsorption of charged monomers and trivalent salt coions onto the oppositely charged electrode. For grafted star chains with relatively high charge fraction, charged monomers are the dominant species collapsing on the oppositely charged electrode with the emergence of charge reversal on the grafting electrode. At a low charge fraction such that the total amount of charges on a grafted star molecule is comparable to that of a trivalent salt coion, trivalent salt coions absorb more strongly onto the electrode than grafted stars even at very low salt concentration. It is found that at relatively low charge fraction of star chains, the addition of trivalent salt coions does not lead to charge overcompensation of the surface charges on the grafting electrode. The stretching of star brushes under an electric field in the presence of trivalent salt coions was also briefly investigated.     

MLIMC: Machine Learning-Based Implicit-Solvent Monte Carlo

Monte Carlo (MC) methods are important computational tools for molecular structure optimizations and predictions. When solvent effects are explicitly considered, MC methods become very expensive due to the large degree of freedom associated with the water molecules and mobile ions. Alternatively implicit-solvent MC can largely reduce the computational cost by applying a mean field approximation to solvent effects and meanwhile maintains the atomic detail of the target molecule. The two most popular implicit-solvent models are the Poisson-Boltzmann (PB) model and the Generalized Born (GB) model in a way such that the GB model is an approximation to the PB model but is much faster in simulation time. In this work, we develop a machine learning-based implicit-solvent Monte Carlo (MLIMC) method by combining the advantages of both implicit solvent models in accuracy and efficiency. Specifically, the MLIMC method uses a fast and accurate PB-based machine learning (PBML) scheme to compute the electrostatic solvation free energy at each step. We validate our MLIMC method by using a benzene-water system and a protein-water system. We show that the proposed MLIMC method has great advantages in speed and accuracy for molecular structure optimization and prediction.     

Column size effects of DER fluids

The static yield stress of dielectric electrorheological (DER) fluids of infinite column state and chain state are calculated from the first principle method. The results indicate that the column surface contributions to ER effects is very small and both states will give correct results to the real DER fluids. Received 29 January 2001 and Received in final form 30 April 2001     

Universal behavior in non-stationary Mean Field Games

Mean Field Games provide a powerful framework to analyze the dynamics of a large number of controlled objects in interaction. Though these models are much simpler than the underlying differential games they describe in some limit, their behavior is still far from being fully understood. When the system is confined, a notion of “ergodic state” has been introduced that characterizes most of the dynamics for long optimization times. Here we consider a class of models without such an ergodic state, and show the existence of a scaling solution that plays a similar role. Its universality and scaling behavior can be inferred from a mapping to an electrostatic problem.     

Electrostatic interactions in peptides. Polarisation effects due to an α-helix

A quantum mechanical/molecular mechanical study of a dodecapeptide made of 11 alanine and one asparagine residues in a helical conformation is carried out by means of the local self-consistent field/molecular mechanical and integrated molecular orbital and molecular mechanics computational schemes. The electronic properties of the asparagine side chain are analysed to extract the influence of electrostatic and induction interaction. One finds that induction may play an important role in the energetic and structural features of the systems modelled with mixed methods. The importance of performing quantum computations which explicitly take account of the electrostatic interactions is pointed out.Contribution to the Jacopo Tomasi Honorary Issue