Atomistic Monte Carlo Simulations Research Articles

Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins

There is growing interest in the topic of intrinsically disordered proteins (IDPs). Atomistic Metropolis Monte Carlo (MMC) simulations based on novel implicit solvation models have yielded useful insights regarding sequence-ensemble relationships for IDPs modeled as autonomous units. However, a majority of naturally occurring IDPs are tethered to ordered domains. Tethering introduces additional energy scales and this creates the challenge of broken ergodicity for standard MMC sampling or molecular dynamics that cannot be readily alleviated by using generalized tempering methods. We have designed, deployed, and tested our adaptation of the Nested Markov Chain Monte Carlo sampling algorithm. We refer to our adaptation as Hamiltonian Switch Metropolis Monte Carlo (HS-MMC) sampling. In this method, transitions out of energetic traps are enabled by the introduction of an auxiliary Markov chain that draws conformations for the disordered region from a Boltzmann distribution that is governed by an alternative potential function that only includes short-range steric repulsions and conformational restraints on the ordered domain. We show using multiple, independent runs that the HS-MMC method yields conformational distributions that have similar and reproducible statistical properties, which is in direct contrast to standard MMC for equivalent amounts of sampling. The method is efficient and can be deployed for simulations of a range of biologically relevant disordered regions that are tethered to ordered domains.

Density Functional Theory Study of Oxygen Reduction Reaction Mechanism on Pt Alloy Catalysts

Power generation is one of the key challenges in the current century due to decreasing natural energy resources, population growth and the goal to reduction of carbon emissions. Proton exchange membrane fuel cells (PEMFCs) have attracted significant attention for potential power generation technology especially for mobile application. However, PEMFC currently faces several challenges: high cost of Platinum group metals catalysts, the slow kinetics of oxygen reduction reaction (ORR) at the cathode and the durability of cathode catalysts in harsh acidic environment.Alloying Pt modifies the surface electronic structures and at the same time reduces the use of expensive Pt from the catalyst design. Recently, 3d-transition metals (TMs) alloyed Pt catalysts have been reported to show superior ORR activity as compared to pure Pt catalyst.1-5 For example, the ORR activity enhancement for bimetallic Pt3Ni(111) extended single crystal surface is reported to be 10 times (10´) higher than pure Pt(111) surface and 90´ higher than the commercial Pt/C nanoparticle catalysts.1 With these encouraging studies, catalysts design by controlling composition, sizes and shapes of Pt-based alloy nanoparticle are now under extensive investigations.Within this contribution, we employed an atomistic Monte Carlo (MC) simulation method to predict the equilibrium surface structures of Pt alloy surfaces. Based on the calculated surface composition profile, we built Pt surface-segregated surface slab models for Pt and Pt alloy catalysts. The possible ORR mechanism on the (111) and (100) surfaces of Pt and Pt alloys are explained by first-principles density functional theory (DFT) calculations. Our DFT computations predict that alloying Pt with transition metal alters the adsorption energetics of the ORR intermediates and changes the mechanism of ORR compared to pure Pt catalyst. The ORR on Pt and Pt alloy catalysts can proceed via one of the following ORR mechanisms: O2 dissociation, OOH dissociation or H2O2 dissociation ORR mechanism.Our calculations show that the ORR occurs via an OOH dissociation mechanism on the pure Pt(111) surface. In contrast, we predict that the ORR on Pt(100) surface proceeds via an O2 dissociation ORR mechanism. Our calculated activation energy for the rate determining step (RDS) on the Pt(111) surface (0.79 e V)3 is very similar to that (0.80 eV)4 on the Pt(100) surface. This suggests that the (111) and (100) facets of Pt nanocrystals show similar catalytic activity for ORR.We further studied the mechanism of ORR on Pt surface segregated modified Pt/TM(111) (TM =Fe, Co, Ni) and Pt3TM(111) (TM=Ti, V, Fe, Ni) surfaces. We found that the activation energy of the RDS on modified Pt/TM(111) and Pt3TM(111) surfaces is always smaller than that on the pure Pt(111) surface. Thus modified Pt/TM(111) and Pt3TM(111) surfaces have superior catalytic activity for ORR compared to the ORR activity of pure Pt(111) surface. The DFT calculations further predict that the most favorable ORR mechanism on the modified Pt(111) surfaces is H2O2 dissociation ORR mechanism. We found that Ni modified Pt/TM(111) and Pt3TM(111) surfaces show highest catalytic activity for ORR. Contrarily, our DFT calculations demonstrates that the catalytic activity of modified Pt/Ni(100) surface is very similar to that of pure Pt(100) surface. All these predictions are in excellent agreement with previous experimental measurements. Acknowledgements This work was funded by Chemical Sciences Research Programs, Office of Basic Energy Sciences, U.S. Department of Energy (Grant no. DE-FG02-09ER16093). We also acknowledge the research grant from the EERE program of the U.S. Department of Energy (Grant no. DE-AC02-06CH11357). References (1) Stamenkovic, V. R.; Fowler, B.; Mun, B. S.; Wang, G. F.; Ross, P. N.; Lucas, C. A.; Markovic, N. M. Science 2007, 315, 493-497.(2) Stamenkovic, V. R.; Mun, B. S.; Arenz, M.; Mayrhofer, K. J. J.; Lucas, C. A.; Wang, G. F.; Ross, P. N.; Markovic, N. M. Nat. Mater. 2007, 6, 241-247.(3) Duan, Z. Y.; Wang, G. F. Phys. Chem. Chem. Phys. 2011, 13, 20178-20187.(4) Duan, Z. Y.; Wang, G. F. J. Phys. Chem. C 2013, 117, 6284−6292.(5) Kattel, S.; Duan, Z. Y.; Wang, G. F. J. Phys. Chem. C 2013, 117, 7107−7113.

Atomistic Monte Carlo simulation of lipid membranes.

Biological membranes are complex assemblies of many different molecules of which analysis demands a variety of experimental and computational approaches. In this article, we explain challenges and advantages of atomistic Monte Carlo (MC) simulation of lipid membranes. We provide an introduction into the various move sets that are implemented in current MC methods for efficient conformational sampling of lipids and other molecules. In the second part, we demonstrate for a concrete example, how an atomistic local-move set can be implemented for MC simulations of phospholipid monomers and bilayer patches. We use our recently devised chain breakage/closure (CBC) local move set in the bond-/torsion angle space with the constant-bond-length approximation (CBLA) for the phospholipid dipalmitoylphosphatidylcholine (DPPC). We demonstrate rapid conformational equilibration for a single DPPC molecule, as assessed by calculation of molecular energies and entropies. We also show transition from a crystalline-like to a fluid DPPC bilayer by the CBC local-move MC method, as indicated by the electron density profile, head group orientation, area per lipid, and whole-lipid displacements. We discuss the potential of local-move MC methods in combination with molecular dynamics simulations, for example, for studying multi-component lipid membranes containing cholesterol.

ChemInform Abstract: In situ Transmission Electron Microscopy of Catalyst Sintering

AbstractReview: 78 refs.

Role of Intrinsic Helicity Within N-Terminal Flanking Sequences on Huntingtin Aggregation Mechanisms

Huntington's disease (HD) is associated with CAG repeats within exon 1 that lead to polyglutamine (polyQ) expansions in the protein huntingtin (htt). Aberrant splicing of htt transcripts generates N-terminal fragments in a polyQ length dependent manner that span exon 1 of htt. These N-terminal fragments can be trafficked into the nucleus and form neuronal nuclear inclusions. Within exon 1 of htt the polyQ region is flanked by a N-terminal 17-residue amphipathic stretch (N17) and a C-terminal proline-rich stretch. Modulation of these flanking sequences has profound effects on HD progression. Specifically, post-translational modifications and single / double point mutations within N17 can modulate the intrinsic helicity of N17, as well as aggregation in vitro and HD phenotypes in animal models. However, the role of helicity within N17 on the modulation of polyQ aggregation remains unresolved. Here, we focus on understanding the synergy between the intrinsic helicity within N17 and polyQ length on htt aggregation mechanisms. Through the use of atomistic Monte Carlo simulations utilizing the ABSINTH implicit solvation model, we examine the monomeric properties of N17 permutants with varying degrees of intrinsic helicity as a function of polyQ length. Results suggest that the degree of coupling between N17 constructs and polyQ is dependent on the intrinsic helicity within N17 constructs. A comparative analysis of N17 constructs in cis with a range of polyQ lengths will be combined with biophysical experiments to understand how monomeric properties of N17 modulate the solubility and mechanism of polyQ aggregation.

Confined phase separation in SiOX nanometric thin layers

Phase separation in silicon-rich silica/silica multilayers was investigated using Atom Probe Tomography and Atomistic Kinetic Monte Carlo simulation. It is shown that the thickness of silicon-rich silicon oxide sublayers plays an important role during phase transformation. It determines the morphology of Si-rich phase formed after subsequent annealing, which is of prime interest for microelectronic and optoelectronic applications. Monte Carlo simulation reveals that the formation of isolated Si clusters can be achieved even in the case of spinodal decomposition and is directly related to the ratio between the spinodal wavelength and the sublayer thickness.

In situ Transmission Electron Microscopy of catalyst sintering

Recent advancements in the field of electron microscopy, such as aberration correctors, have now been integrated into Environmental Transmission Electron Microscopes (TEMs), making it possible to study the behavior of supported metal catalysts under operating conditions at atomic resolution. Here, we focus on in situ electron microscopy studies of catalysts that shed light on the mechanistic aspects of catalyst sintering. Catalyst sintering is an important mechanism for activity loss, especially for catalysts that operate at elevated temperatures. Literature from the past decade is reviewed along with our recent in situ TEM studies on the sintering of Ni/MgAl2O4 catalysts. These results suggest that the rapid loss of catalyst activity in the earliest stages of catalyst sintering could result from Ostwald ripening rather than through particle migration and coalescence. The smallest particles are found to disappear in a few seconds as soon as the catalyst reaches the operating temperature. While particle migration and coalescence is evident in some of these in situ studies, it does not follow the classical model where the smallest particles are most mobile. Deterministic models of Ostwald ripening as well as atomistic Monte Carlo simulations are both in good agreement with these experimental observations, predicting a steep loss in catalyst activity at short times on stream. The in situ studies show the importance of direct observations to deduce mechanisms and show the important role played by the support and the gas atmosphere (especially the presence of H2O) on the rates of catalyst sintering.

On the mobility of vacancy clusters in reduced activation steels: an atomistic study in the Fe–Cr–W model alloy

Reduced activation steels are considered as structural materials for future fusion reactors. Besides iron and the main alloying element chromium, these steels contain other minor alloying elements, typically tungsten, vanadium and tantalum. In this work we study the impact of chromium and tungsten, being major alloying elements of ferritic Fe–Cr–W-based steels, on the stability and mobility of vacancy defects, typically formed under irradiation in collision cascades. For this purpose, we perform ab initio calculations, develop a many-body interatomic potential (EAM formalism) for large-scale calculations, validate the potential and apply it using an atomistic kinetic Monte Carlo method to characterize the lifetime and diffusivity of vacancy clusters. To distinguish the role of Cr and W we perform atomistic kinetic Monte Carlo simulations in Fe–Cr, Fe–W and Fe–Cr–W alloys. Within the limitation of transferability of the potentials it is found that both Cr and W enhance the diffusivity of vacancy clusters, while only W strongly reduces their lifetime. The cluster lifetime reduction increases with W concentration and saturates at about 1–2 at.%. The obtained results imply that W acts as an efficient ‘breaker’ of small migrating vacancy clusters and therefore the short-term annealing process of cascade debris is modified by the presence of W, even in small concentrations.

Calculation of the surface tension of liquid copper from atomistic Monte Carlo simulations

Monte Carlo simulations of heterogeneous systems of copper at liquid-vapor equilibrium have been performed at several temperatures from 1400 to 2000 K, using the EAM potential of Zhou et al. [Phys. Rev. B 69, 144113 (2004)]. Surface tension of the corresponding planar interfaces has been evaluated using thermodynamic and mechanical approaches. We have investigated the impact of the potential and the temperature on the surface tension of liquid copper. For the first time, calculation results are in very good agreement with experiments with a maximum deviation of 2% from experiments. Additionally, the Monte Carlo simulations provide a temperature coefficient (the derivative of surface tension in regard with temperature) in excellent agreement with the experimental coefficient. This was one of the main challenges of the present simulations.

Microscopic structure of water in a water/oil emulsion

We have determined the microscopic structure of water within a water/oil emulsion, by combining neutron diffraction data, exploiting the isotopic H/D substitution, and a fully atomistic Monte Carlo simulation of a portion of a water droplet, containing the water/oil interface. The dependence of the data on the simulation box size and the reliability of the water-water radial distribution functions are discussed. Although water in the emulsion forms shorter and stronger hydrogen bonds compared to pure bulk water, its overall microscopic structure looks more disordered.

First principle-based AKMC modelling of the formation and medium-term evolution of point defect and solute-rich clusters in a neutron irradiated complex Fe–CuMnNiSiP alloy representative of reactor pressure vessel steels

The formation and medium-term evolution of point defect and solute-rich clusters under neutron irradiation have been modelled in a complex Fe–CuMnNiSiP alloy representative of RPV steels, by means of first principle-based atomistic kinetic Monte Carlo simulations. The results obtained reproduce most features observed in available experimental studies, highlighting the very good agreement between both series. According to simulation, solute-rich clusters form and develop via an induced segregation mechanism on either the vacancy or interstitial clusters, and these point defect clusters are efficiently generated only in cascade debris and not Frenkel pair flux. The results have revealed the existence of two distinct populations of clusters with different characteristic features. Solute-rich clusters in the first group are bound essentially to interstitial clusters and they are enriched in Mn mostly, but also Ni to a lesser extent. Over the low dose regime, their density increases in the alloy as a result of the accumulation of highly stable interstitial clusters. In the second group, the solute-rich clusters are merged with vacancy clusters, and they contain mostly Cu and Si, but also substantial amount of Mn and Ni. The formation of a sub-population of pure solute clusters has been observed, which results from annihilation of the low stable vacancy clusters on sinks. The results indicate finally that the Mn content in clusters is up to 50%, Cu, Si, and Ni sharing the other half in more or less equivalent amounts. This composition has not demonstrated any noticeable modification with increasing dose over irradiation.

Mechanism of adsorption of p-cresol uremic toxin into faujasite zeolites in presence of water and sodium cations – A Monte Carlo study

Atomistic Monte Carlo simulations on the adsorption of p-cresol and water in faujasite zeolites have been performed. Two types of zeolites were used, namely a hypothetical, pure silica faujasite and the NaY one. The comparison of the results obtained for both zeolites on the adsorption of p-cresol shows that the molecules are mainly adsorbed at the supercage and few of them are located at the cage windows. The presence of the sodium cations in the framework of NaY does not modify substantially the qualitative observations made for pure-silica faujasite. By contrast, the presence of the cations modifies notably the shape of the adsorption isotherm of water (either in presence or absence of p-cresol molecules in the zeolite pores) which can be correlated with the energetics of interaction between the species in the system.

Decomposition kinetics of Fe-Cr solid solutions during thermal aging

The decomposition of Fe-Cr solid solutions during thermal aging is modeled by atomistic kinetic Monte Carlo simulations, using a rigid lattice approximation with pair interactions that depend on the local composition and temperature. The pair interactions are fitted on ab initio calculations of mixing energies and vacancy migration barriers at 0 K. The entropic contributions to the mixing of Fe-Cr alloys and to the vacancy formation and migration free energies are taken into account. The model reproduces the change in sign of the mixing energy with the alloy composition and gives realistic thermodynamic and kinetic properties, including an asymmetrical miscibility gap at low temperature and diffusion coefficients in good agreement with available experimental data. Simulations of short-range ordering and $\ensuremath{\alpha}\ensuremath{-}\ensuremath{\alpha}$${}^{\ensuremath{'}}$ decomposition are performed at 773 and 813 K for Cr concentrations between 10$%$ and 50$%$. They are compared with experimental kinetics based on three-dimensional atom probe and neutron scattering measurements. The possible effect of magnetic properties on diffusion in the $\ensuremath{\alpha}$ and ${\ensuremath{\alpha}}^{\ensuremath{'}}$ phases, and therefore on the decomposition kinetics, is emphasized.

Manipulation of surface energy anisotropy in iron using surface segregation of phosphorus: An atomistic simulation

The possibility of developing a {1 0 0}〈0 0 1〉 cube texture in steel sheets by altering the surface energy by phosphorus segregation has been investigated using atomistic Monte Carlo simulations. It is found that the change in order in the amount of surface energy, from (1 1 0)

Patterning of martensitic nanotwins

We perform the atomistic Monte Carlo simulations of formation of nanostructured martensites in nickel–titanium thin films . The results reveal the atomistically resolved patterning of martensitic nanotwins, including coarsening, branching and twinning within twins, as mediated by temperature and substrate constraints. A scaling law is derived to elucidate the physical effects governing the characteristic nanostructure length scale of the twin width. Our modeling approach opens up possibilities for the atomistically based design of martensitic nanostructures to produce advanced alloys with optimized properties.

Towards control of carbon nanotube synthesis process using prediction-based fast Monte Carlo simulations

Precise control of the lengths of carbon nanotube (CNT) and other nanostructures is important for various industrial applications. However, time-resolution (∼1min) of current in situ measurements does not allow control of lengths to within 20nm. We present an approach to combine intermittent in situ measurements with length estimates from a fast atomistic Monte Carlo (MC) simulation of CNT synthesis. The MC simulation time was reduced by >70% through prediction of the nonlinear and nonstationary growth increments, and initialization of relaxation process (the most computationally intensive step in MC simulations) with the near-optimum predicted positions, leading to one of the longest (∼194nm) CNTs from atomistic simulations. A utility function of growth predictions was defined so that its maximization specified the end-point of the synthesis process. Extensive simulation studies indicate that the approach can be used to control CNT lengths to within 1nm of specifications.

Theoretical investigation of the influence of reaction and diffusion kinetics upon thin-film reactive diffusion

Atomistic kinetic Monte Carlo simulations, considering the thermodynamic model of the nonregular solid solution on a rigid fcc lattice and using the first-neighbor atomic pair interaction Ising model, were performed to investigate the influence of reaction and diffusion kinetics on thin-film reactive diffusion with a semi-infinite substrate. The simulations show that compound bulk energies have no effect on the phase sequence of appearance during sequential phase formation. However, a diffusion asymmetry between the elements composing the solid solution has a strong effect on sequential phase formation. Diffusion asymmetry increases the critical thickness of the simultaneous-to-sequential phase formation transition, modifies the phase formation sequence, and controls which phase is the first to form. Asymmetrical diffusion can promote transient phase formation and can prevent some phases of the bulk phase diagram from forming. In addition, it influences the thicknesses of phases and their lifetimes during thin-film reactive diffusion. Consequently, the control of atom diffusion during reactive diffusion, for example, thanks to the controlled introduction of impurities, should allow the phase formation sequence of a given binary system to be modified.

Diffusion and Cluster Growth of Binary Alloys on Surfaces

Abstract Metastable nanoclusters grown on surfaces by vapour deposition or molecular beam epitaxy techniques have become an active topic in surface science because of their potential to display new physical properties useful for applications. Atomistic modelling and Kinetic Monte Carlo (KMC) simulations of these processes are reviewed with emphasis on two-component adatom systems. The situation we consider is that two types of atoms are co-deposited to the substrate. In this field of binary growth, systematic theoretical investigation is only at its beginning. Surface diffusion and nucleation leads to the formation of two-dimensional islands, before two-dimensional cluster growth sets in. In distinction to well-known growth scenarios for one species of adatoms, a wealth of new aspects arises in binary systems. Already in the regime of submonolayer growth, differences in adatom diffusion coefficients and binding energies make it necessary to generalise traditional scaling relations for island densities. Surface segregation and compositional fluctuations in growing 3-D clusters are issues requiring renewed examination under the point of view that the atomic short-range order, which is frozen in the bulk, was generated through the surface kinetics during previous stages of growth. We discuss the current theoretical understanding and experimental implications of these problems, including a description of perpendicular magnetic anisotropy (PMA) in metastable CoPt3 nanoalloys, as detected recently.

Ordering Mechanisms in Epitaxial SiGe Nanoislands

We investigate and elucidate the surprising observation of atomically ordered domains in dome-shaped SiGe nanoislands. We show, through atomistic Monte Carlo simulations, that this ordering is a surface-related phenomenon, and that is driven by surface equilibrium rather than by surface kinetics. The ordering depends on facet orientation. The main source of ordering is the {15 3 23} facet, while the {105} and {113} facets contribute less. Subsurface ordered configurations self-organize under this facet and are frozen-in and buried during island growth, giving rise to the ordered domains. Ordering mechanisms based on constrained surface kinetics, requiring step-mediated segregation at the island facets, are shown to be much less likely.

“Order–Order” Kinetics In Ni50.5Al49.5 single crystal by quasi-residual resistometry

Kinetics of “order–order” reactions in B2-ordered Ni50.5Al49.5 intermetallic was examined by means of quasi-residual resistometry. Isothermal relaxations of quasi-residual electrical resistance of the sample, measured in liquid nitrogen bath, were associated with corresponding relaxations of the concentration of antisite defects, proportional to the long-range order parameter.Similarly as in the case of previous “in situ” experiments, the observed relaxations were very sluggish with relatively low activation energies: EA(ord) = (2.37 ± 0.10) eV for ordering and EA(dis) = (1.93 ± 0.19) eV for disordering process. These energies are lower than the activation energy for Ni self-diffusion in NiAl (3.0 eV), but somewhat higher than the one previously determined by means of “in situ” resistometry for “order–order” processes in Ni50.5Al49.5. The origin of low relaxation rates observed in the experiment has recently been elucidated by atomistic Kinetic Monte Carlo (KMC) simulations in terms of low disordering efficiency of atomic jumps in triple-defect B2-ordering binary systems.