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Artemis is an endonuclease responsible for breaking hairpin DNA strands during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance, its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, and the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulations, both classically and at the hybrid quantum mechanics/molecular mechanics level, we evidenced the stable interaction modes of Artemis with a model DNA strand. We also analyzed the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.

In this work we study the effect of different synthetic conditions on thermal transport properties of poly(3,4-ethylenedioxythiophene) (PEDOT) by focusing in particular on the role of proton scavengers. To this aim, different PEDOT samples were generated in silico using a novel computational algorithm based on a combination of first-principles density functional theory and classical molecular dynamics simulations. The corresponding thermal conductivities were then estimated using the approach to equilibrium molecular dynamics methodology. The results show that the initial synthetic conditions strongly affect the corresponding thermal conductivities, which display variations up to a factor of $\ensuremath{\sim}2$ depending on the proton scavenger. By decomposing the thermal conductivity tensor along the direction of maximum chain alignment and the corresponding perpendicular directions, we attribute the thermal conductivity differences to the variations in the average polymer chain length ${\ensuremath{\lambda}}_{\mathrm{ave}}$. A dependence of the thermal conductivity with the polydispersity index was finally observed, suggesting a possible role of intercrystallite chains in enhancing thermal transport properties. By means of the Green-Kubo modal analysis, we eventually characterize the vibrational modes involved in PEDOT thermal transport and investigate how they are related to the thermal conductivity values of the samples.

One of the ultimate goals of computational modeling in condensed matter is to be able to accurately compute materials properties with minimal empirical information. First-principles approaches such as density functional theory (DFT) provide the best possible accuracy on electronic properties but they are limited to systems up to a few hundreds, or at most thousands of atoms. On the other hand, classical molecular dynamics (CMD) simulations and the finite element method (FEM) are extensively employed to study larger and more realistic systems, but conversely depend on empirical information. Here, we show that machine-learning interatomic potentials (MLIPs) trained over short ab initio molecular dynamics trajectories enable first-principles multiscale modeling, in which DFT simulations can be hierarchically bridged to efficiently simulate macroscopic structures. As a case study, we analyze the lattice thermal conductivity of coplanar graphene/borophene heterostructures, recently synthesized experimentally (Sci. Adv., 2019, 5, eaax6444), for which no viable classical modeling alternative is presently available. Our MLIP-based approach can efficiently predict the lattice thermal conductivity of graphene and borophene pristine phases, the thermal conductance of complex graphene/borophene interfaces and subsequently enable the study of effective thermal transport along the heterostructures at continuum level. This work highlights that MLIPs can be effectively and conveniently employed to enable first-principles multiscale modeling via hierarchical employment of DFT/CMD/FEM simulations, thus expanding the capability for computational design of novel nanostructures., B. M. and X. Z. appreciate the funding by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy within the Cluster of Excellence PhoenixD (EXC 2122, Project ID 390833453). E. V. P and A. V. S. were supported by the Russian Science Foundation (Grant No. 18-13-00479). ICN2 is supported by the Severo Ochoa program from Spanish MINECO (Grant No. SEV-2017-0706) and funded by the CERCA Programme/Generalitat de Catalunya.

The widespread biomedical applications of silver and gold nanoparticles (AgNPs and AuNPs, respectively) prompt the need for mechanistic evaluation of their interaction with biomolecules. In biological media, metallic NPs are known to transform by various pathways, especially in the presence of thiols. The interplay between metallic NPs and thiols may lead to unpredictable consequences for the health status of an organism. This study explored the potential events occurring during biotransformation, dissolution, and reformation of NPs in the thiol-rich biological media. The study employed a model system evaluating the interaction of cysteine with small- sized AgNPs and AuNPs. The interplay of cysteine on transformation and reformation pathways of these NPs was experimentally investigated by nuclear magnetic resonance (NMR) spectroscopy and supported by light scattering techniques and transmission electron microscopy (TEM). As the main outcome, Ag- or Au-catalyzed oxidation of cysteine to cystine was found to occur through generation of reactive oxygen species (ROS). Computational simulations confirmed this mechanism and the role of ROS in the oxidative dimerization of biothiol during NPs reformation. The obtained results represent valuable mechanistic data about the complex events during the transport of metallic NPs in thiol-rich biological systems that should be considered for the future biomedical applications of metal-based nanomaterials.

International audience; Following our previous work where the existence of a special 2-Dimensional H-Bond (2D-HB)-Network was revealed at the air-water interface [S. Pezzotti et al., J. Phys. Chem. Lett. 8, 3133 (2017)], we provide here a full structural and dynamical characterization of this specific arrangement by means of both Density Functional Theory based and Force Field based molecular dynamics simulations. We show in particular that water at the interface with air reconstructs to maximize H-Bonds formed between interfacial molecules, which leads to the formation of an extended and non-interrupted 2-Dimensional H-Bond structure involving on average ∼90% of water molecules at the interface. We also show that the existence of such an extended structure, composed of H-Bonds all oriented parallel to the surface, constrains the reorientional dynamics of water that is hence slower at the interface than in the bulk. The structure and dynamics of the 2D-HB-Network provide new elements to possibly rationalize several specific properties of the air-water interface, such as water surface tension, anisotropic reorientation of interfacial water under an external field, and proton hopping.

We study the stability of twin boundaries and slip in crystalline orthorhombic polyethylene by means of density functional theory (DFT), using a nonempirical, truly nonlocal density function, and by means of classical molecular dynamics (MD). The results show that, in accordance with experimental observations, there is a clear preference to chain slip over transverse slip for all considered slip planes. The activation energy for pure chain slip lies in the range 10–20 mJ/m2 while that for transverse slip corresponds to 40–280 mJ/m2. For the (11¯0)-slip plane the energy landscape is non-convex with multiple potential energy minima, indicating the presence of stable stacking faults. This suggests that dissociation of perfect dislocations into partials may occur. For the two low-energy twin boundaries considered in this work, {110} and {310}, we find that the former is more stable than the latter, with ground state energies corresponding to 8.9 and 28 mJ/m2, respectively. We have also evaluated how well the empirical MD simulations with the all-atom optimized potential for liquid MD simulations (OPLS-AA) and the coarse-grained united atom (UA) potential concur with the DFT results. It is found that an all-atom potential is necessary to partially capture the γ-surface energy landscapes obtained from the DFT calculations. The OPLS-AA predicts chain slip activation energies comparable with DFT data, while the transverse slip energy thresholds are low in comparison, which is attributed to weak close ranged monomer repulsion. Finally, we find that the H-H interaction dominates the slip activation. While not explicitly represented in the UA potential, its key role is revealed by correlating the DFT energy landscape with changes in the electron distributions and by MD simulations in which components of the OPLS-AA intermolecular potential are selectively silenced. © 2017 Elsevier Ltd

The origin of the dissolution of methylammonium lead trihalide (MAPI) crystals in liquid water is clarified by finite-temperature molecular dynamics by developing a MYP-based force field (MYP1) for water–MAPI systems. A thermally activated process is found with an energy barrier of 0.36 eV consisting of a layer-by-layer degradation with generation of inorganic PbI2 films and solvation of MA and I ions. We rationalize the effect of water on MAPI by identifying a transition from a reversible absorption and diffusion in the presence of vapor to the irreversible destruction of the crystal lattice in liquid due to a cooperative action of water molecules. A strong water–MAPI interaction is found with a binding energy of 0.41 eV/H2O and wetting energy of 0.23 N/m. The water vapor absorption is energetically favored (0.29 eV/H2O), and the infiltrated molecules can migrate within the crystal with a diffusion coefficient D = 1.7 × 10–8 cm2/s and activation energy of 0.28 eV.

This paper pertains to elastic properties of InAs and GaAs semiconducting crystals containing various amounts of vacancies--the relevant issue in the case of nanostructured electronic materials. The linear relationship between elastic constants and point defects concentration deduced from our classical molecular dynamic and ab initio calculations, confirms that an increasing vacancy content results in a decrease of pertinent elastic parameters, namely the crystal elastic stiffness-tensor components, the effect called herein "the softening of material" for simplicity. The pseudo-potential-based approach provides us results compatible with the available experimental data, while the alternatively used empirical potentials failed to account for different kind of vacancies on the elastic properties of semiconductors. Our results provide an expanded insight into the problems of modeling of the properties of the defected InAs and GaAs crystal structures. This issue is of interest to nanoelectronics and production of nanomaterials currently.

Description of the local microscopic structure in ionic liquids (ILs) is a prerequisite to obtain a comprehensive understanding of the influence of the nature of ions on the properties of ILs. The local structure is mainly determined by the spatial arrangement of the nearest neighboring ions. Therefore, the main interaction patterns in ILs, such as cation-anion H-bond-like motifs, cation-cation alkyl tail aggregation, and ring stacking, were considered within the framework of the nearest-neighbor approach with respect to each particular interaction site. We employed classical molecular dynamics (MD) simulations to study in detail the spatial, radial, and orientational relative distribution of ions in a set of imidazolium-based ILs, in which the 1-butyl-3-methylimidazolium (C4mim+) cation is coupled with the acetate (OAc-), chloride (Cl-), tetrafluoroborate (BF4-), hexafluorophosphate (PF6-), trifluoromethanesulfonate (TfO-), or bis(trifluoromethanesulfonyl)amide (TFSA-) anion. It was established that several structural properties are strongly anion-specific, while some can be treated as universally applicable to ILs, regardless of the nature of the anion. Namely, strongly basic anions, such as OAc- and Cl-, prefer to be located in the imidazolium ring plane next to the C-H2/4-5 sites. By contrast, the other four bulky and weakly coordinating anions tend to occupy positions above/below the plane. Similarly, the H-bond-like interactions involving the H2 site are found to be particularly enhanced in comparison with the ones at H4-5 in the case of asymmetric and/or more basic anions (C4mimOAc, C4mimCl, C4mimTfO, and C4mimTFSA), in accordance with recent spectroscopic and theoretical findings. Other IL-specific details related to the multiple H-bond-like binding and cation stacking issues are also discussed in this paper. The secondary H-bonding of anions with the alkyl hydrogen atoms of cations as well as the cation-cation alkyl chain aggregation turned out to be poorly sensitive to the nature of the anion.

International audience; Polycrystalline structure plays an important role in the macroscopic properties of a solid material. In this paper we propose a new code to generate a polycrystalline material at the atomic scale. Our polycrystalline systems are based on the random generation from initial germs. From a mechanical point of view, it brings new features as for example ductility of 3D polycrystalline aluminum. By using molecular dynamics simulations, we also show the eect of temperature on a geological material, olivine, one of the most abundant silicate mineral of the Earth upper mantle. The importance of porous media is also considered (e.g. metals).

Fluidity of lipid membranes is known to play an important role in the functioning of living organisms. The fluorescent probe Laurdan embedded in a lipid membrane is typically used to assess the fluidity state of lipid bilayers by utilizing the sensitivity of Laurdan emission to the properties of its lipid environment. In particular, Laurdan fluorescence is sensitive to gel vs liquid–crystalline phases of lipids, which is demonstrated in different emission of the dye in these two phases. Still, the exact mechanism of the environment effects on Laurdan emission is not understood. Herein, we utilize dipalmitoylphosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC) lipid bilayers, which at room temperature represent gel and liquid–crystalline phases, respectively. We simulate absorption and emission spectra of Laurdan in both DOPC and DPPC bilayers with quantum chemical and classical molecular dynamics methods. We demonstrate that Laurdan is incorporated in heterogeneous fashion in both DOPC and DPPC bilayers, and that its fluorescence depends on the details of this embedding.

International audience; This work is an improved continuation of a previous attempt to use classical molecular dynamics (MD) as a tool for the investigation of hot and dense "real" plasmas. "Real" in this context refers to ions and electrons interacting through Coulomb forces and undergoing ionization/recombination. The objective of designing such a non standard approach to plasma equilibrium is to explore a new way to discuss warm and dense matter with a method able to deal with the whole complexity of a N-body system of ions and electrons. Plasma relaxation times can be investigated up to a picosecond. The resulting equilibrium ion populations, built self consistently, are comparable to those found in literature and, potentially validate access to all the statistical data usually derived from MD simulations.

ACS AuthorChoice - This is an open access article published under an ACS AuthorChoice License, which permits copying and redistribution of the article or any adaptations for non-commercial purposes., A detailed understanding of the connections of fabrication and processing to structural and thermal properties of low-dimensional nanostructures is essential to design materials and devices for phononics, nanoscale thermal management, and thermoelectric applications. Silicon provides an ideal platform to study the relations between structure and heat transport since its thermal conductivity can be tuned over 2 orders of magnitude by nanostructuring. Combining realistic atomistic modeling and experiments, we unravel the origin of the thermal conductivity reduction in ultrathin suspended silicon membranes, down to a thickness of 4 nm. Heat transport is mostly controlled by surface scattering: rough layers of native oxide at surfaces limit the mean free path of thermal phonons below 100 nm. Removing the oxide layers by chemical processing allows us to tune the thermal conductivity over 1 order of magnitude. Our results guide materials design for future phononic applications, setting the length scale at which nanostructuring affects thermal phonons most effectively., This work is partly funded by the European Commission FP7-ENERGY-FET project MERGING, NMP QUANTIHEAT and ICT NANOTHERM, with Grant Agreement Nrs: 309150, 604668 and 318117, respectively. S.N. and D.D. acknowledge financial support from MPG under the MPRG program. J.S.R., M.R.W., and C.M.S.T. acknowledge support form the Spanish MINECO projects TAPHOR (MAT-2012-31392) and nanoTHERM (CONSOLIDER CSD2010-00044). M.R.W. acknowledges support of the Marie Curie Postdoctoral Fellowship HeatProNano (Grant No. 628197). M.P. and A.S. acknowledge funding from the Academy of Finland (Grant No. 252598).

International audience; The dynamic properties of ion-electron two-component plasmas (TCP) are studied by using classical molecular dynamics (MD) simulations. There is a variety of time dependent and structural results that MD is able to provide in complement to other methods, e.g., useful micro-field sequences can be generated. The method deals with some specific difficulties: the mass ratio between ions and electrons enforces very small time-steps appropriate to follow electrons motion while, ions must move significantly in order to build, self consistently, their spatial structure. This results in expensive simulations. Electron trajectories are trapped and de-trapped with multiple electron collisions around ions resulting in the occurrence of quasi metastable bound electron states. An analysis of micro-fields at neutral in a hydrogen plasma reveals the need to consider a complete hierarchy of time scales extended typically over 7 order of magnitude, i.e., from a time-step: 10^-19s, to a time required to obtain statistical averages, 10^-11s. In order to extend the MD capabilities in representing real coupled plasmas a classical ionization/recombination process has been implemented allowing to follow the evolution of plasmas involving several ion stages and model the ionization balance. Here again TCP simulations deal with extended time-scale providing information about relaxation of non equilibrium plasma states