Ab initio calculations of optical properties of silver clusters: Cross-over from molecular to nanoscale behavior

Electronic and optical properties of silver clusters were calculated using two different \textit{ab initio} approaches: 1) based on all-electron full-potential linearized-augmented plane-wave method and 2) local basis function pseudopotential approach. Agreement is found between the two methods for small and intermediate sized clusters for which the former method is limited due to its all-electron formulation. The latter, due to non-periodic boundary conditions, is the more natural approach to simulate small clusters. The effect of cluster size is then explored using the local basis function approach. We find that as the cluster size increases, the electronic structure undergoes a transition from molecular behavior to nanoparticle behavior at a cluster size of 140 atoms (diameter $\sim 1.7$\,nm). Above this cluster size the step-like electronic structure, evident as several features in the imaginary part of the polarizability of all clusters smaller than Ag$_\mathrm{147}$, gives way to a dominant plasmon peak localized at wavelengths 350\,nm$\le\lambda\le$ 600\,nm. It is, thus, at this length-scale that the conduction electrons' collective oscillations that are responsible for plasmonic resonances begin to dominate the opto-electronic properties of silver nanoclusters

The good, the bad and the user in soft matter simulations

\u3cp\u3eMolecular dynamics (MD) simulations have become popular in materials science, biochemistry, biophysics and several other fields. Improvements in computational resources, in quality of force field parameters and algorithms have yielded significant improvements in performance and reliability. On the other hand, no method of research is error free. In this review, we discuss a few examples of errors and artifacts due to various sources and discuss how to avoid them. Besides bringing attention to artifacts and proper practices in simulations, we also aim to provide the reader with a starting point to explore these issues further. In particular, we hope that the discussion encourages researchers to check software, parameters, protocols and, most importantly, their own practices in order to minimize the possibility of errors. The focus here is on practical issues. This article is part of a Special Issue entitled: Biosimulations edited by Ilpo Vattulainen and Tomasz Róg. .\u3c/p\u3

Ionic surfactant aggregates in saline solutions: Sodium dodecyl sulfate (SDS) in the presence of excess sodium chloride (NaCl) or calcium chloride (CaCl2)

The properties of sodium dodecyl sulfate (SDS) aggregates in saline solutions of excess sodium chloride (NaCl) or calcium chloride (CaCl2) ions were studied through extensive molecular dynamics simulations with explicit solvent. We find that the ionic strength of the solution affects not only the aggregate size of the resulting anionic micelles but also their structure. Specifically, the presence of CaCl2 induces more compact and densely packed micelles with a significant reduction in gauche defects in the SDS hydrocarbon chains in comparison with NaCl. Furthermore, we observe significantly more stable salt bridges between the charged SDS head groups mediated by Ca2+ than Na+. The presence of these salt bridges helps stabilize the more densely packed micelles

Fracture in mesoscopic disordered systems

A simple mechanical model of planar fibrous materials with mesoscopic disorder is introduced and analyzed. In this scalar model a shear modulus controls the stress transfer in the transverse direction. The system is studied using the effective medium approximation and computer simulations; the comparison between them is quite favorable. In the disorder-controlled regime the stress-strain relation, the number of broken cells at the onset of crack propagation, and the length of the final crack scale with the system size as L2, L1.7, and L, respectively. The mechanical properties are controlled by the interplay between disorder and shear modulus, which is studied in detail

Reptational dynamics in dissipative particle dynamics simulations of polymer melts

Understanding the fundamental properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for topological constraints, i.e., uncrossability of chains, in polymeric liquids using the dissipative particle dynamics (DPD) method. No new length scales or forces are added. To demonstrate that this approach really prevents chain crossings, we study a melt of linear homopolymers. We show that for short chains the model correctly reproduces Rouse-like dynamics whereas for longer chains the dynamics becomes reptational as the chain length is increased—something that is not attainable using standard DPD or other coarse-grained soft potential methods

Improved general-purpose five-point model for water: TIP5P/2018

A new five point potential for liquid water, TIP5P/2018, is presented along with the techniques used to derive its charges from ab initio per-molecule electrostatic potentials in the liquid phase using the split charge equilibration of Nistor et al. [J. Chem. Phys. 125, 094108 (2006)]. By taking the density and diffusion dependence on temperature as target properties, significant improvements to the behavior of isothermal compressibility were achieved along with improvements to other thermodynamic and rotational properties. While exhibiting a dipole moment close to ab initio values, TIP5P/2018 suffers from a too small quadrupole moment due to the charge assignment procedure and results in an overestimation of the dielectric constant

Effects of molecular crowding on the dynamics of intrinsically disordered proteins

Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in vitro. It has been shown that the stability and the folding rate of a globular protein can be altered by the excluded volume effect produced by a high density of macromolecules. However, macromolecular crowding effects on intrinsically disordered proteins (IDPs) are less explored. These proteins can be extremely dynamic and potentially sample a wide ensemble of conformations under non-denaturing conditions. The dynamic properties of IDPs are intimately related to the timescale of conformational exchange within the ensemble, which govern target recognition and how these proteins function. In this work, we investigated the macromolecular crowding effects on the dynamics of several IDPs by measuring the NMR spin relaxation parameters of three disordered proteins (ProTa, TC1, and a-synuclein) with different extents of residual structures. To aid the interpretation of experimental results, we also performed an MD simulation of ProTa. Based on the MD analysis, a simple model to correlate the observed changes in relaxation rates to the alteration in protein motions under crowding conditions was proposed. Our results show that 1) IDPs remain at least partially disordered despite the presence of high concentration of other macromolecules, 2) the crowded environment has differential effects on the conformational propensity of distinct regions of an IDP, which may lead to selective stabilization of certain target-binding motifs, and 3) the segmental motions of IDPs on the nanosecond timescale are retained under crowded conditions. These findings strongly suggest that IDPs function as dynamic structural ensembles in cellular environments

Pulling of double-stranded DNA by atomic force microscopy : a simulation in atomistic details

During pulling experiments or structural tasks in living and artificial environments, double-stranded DNA could be subjected to external tensile loadings that are not parallel with the helix axis of DNA. The aim of this work is to simulate the shear stretching of duplex DNA oligonucleotides via atomic force microscopy (AFM) at the atomistic scale. We focus on the response of the molecule to the process of angled pulling and conduct a series of modified steered molecular dynamics simulations with a generalized Born/surface area approach. The force–extension curves obtained from the implicit and explicit solvent simulations show very good agreement, providing an additional support for the use of the proposed implicit solvent model for DNA pulling simulations. The results reveal that pulling dsDNA at different angles may produce a variety of unexpected mechanical responses and unusual conformations. The values of the ultimate force used and ensuing displacements may depend significantly on the initial angle of stretching. However, the error introduced for the prediction of the DNA ultimate force is not significant if the DNA stretching initiates at angles smaller than 30°

Molecular dynamics simulation of thermal accommodation coefficients for laser-induced incandescence sizing of nickel particles

Extending time-resolved laser-induced incandescence (TiRe-LII), a diagnostic traditionally used to characterize soot and other carbonaceous particles, into a tool for measuring metal nanoparticles requires knowledge of the thermal accommodation coefficient for those systems. This parameter can be calculated using molecular dynamics (MD) simulations provided the interatomic potential is known between the gas molecule and surface atoms, but this is not often the case for many gas/surface combinations. In this instance, researchers often resort to the Lorentz–Berthelot combination rules to estimate the gas/surface potential using parameters derived for homogeneous systems. This paper compares this methodology with a more accurate approach based on ab initio derived potentials to estimate the thermal accommodation coefficient for laser-energized nickel nanoparticles in argon. Results show that the Lorentz–Berthelot combining rules overestimate the true potential well depth by an order of magnitude, resulting in perfect thermal accommodation, whereas the more accurate ab initio derived potential predicts an accommodation coefficient in excellent agreement with experimentally-determined values for other metal nanoparticle aerosols. This result highlights the importance of accurately characterizing the gas/surface potential when using MD to estimate thermal accommodation coefficients for TiRe-LII