Simulations In Conjunction Research Articles

Network analysis of proton transfer in liquid water.

Proton transfer in macromolecular systems is a fascinating yet elusive process. In the last ten years, molecular simulations have shown to be a useful tool to unveil the atomistic mechanism. Notwithstanding, the large number of degrees of freedom involved make the accurate description of the process very hard even for the case of proton diffusion in bulk water. Here, multi-state empirical valence bond molecular dynamics simulations in conjunction with complex network analysis are applied to study proton transfer in liquid water. Making use of a transition network formalism, this approach takes into account the time evolution of several coordinates simultaneously. Our results provide evidence for a strong dependence of proton transfer on the length of the hydrogen bond solvating the Zundel complex, with proton transfer enhancement as shorter bonds are formed at the acceptor site. We identify six major states (nodes) on the network leading from the "special pair" to a more symmetric Zundel complex required for transferring the proton. Moreover, the second solvation shell specifically rearranges to promote the transfer, reiterating the idea that solvation beyond the first shell of the Zundel complex plays a crucial role in the process.

Quasi-static mode II fracture tests and simulations of Z-pinned woven composites

Experimental results from quasi-static mode II ENF (end notch flexure) fracture tests for Z-pinned woven composites are used to investigate the influence of Z-pin density and Z-pin diameter on Mode II fracture toughness. The experimental results show that the 2% Z-pin composite and the 3% Z-pin composite have larger fracture toughness than the 1% Z-pin composite and a composite without Z-pins. Crack propagation changes from unstable propagation to stable propagation (crack arrest) as the Z-pin density increases. The additional fracture toughness provided by Z-pins prevents the primary crack to further propagate, enabling secondary and tertiary cracks to consume additional energy. While the primary crack is held from propagating by the frictional forces provided by Z-pins, the matrix in the composite is driven into the plastic state and enables the composite to absorb more energy. For numerical simulations, a discrete cohesive zone model (DCZM) is used to perform simulations. The simulations in conjunction with experimental results provide critical fracture toughness values.

Transport in aluminized RDX under shock compression explored using molecular dynamics simulations

Shock response of energetic materials is controlled by a combination of mechanical response, thermal, transport, and chemical properties. How these properties interplay in condensed-phase energetic materials is of fundamental interest for improving predictive capabilities. Due to unknown nature of chemistry during the evolution and growth of high-temperature regions within the energetic material (so called hot spots), the connection between reactive and unreactive equations of state contain a high degree of empiricism. In particular, chemistry in materials with high degree of heterogeneity such as aluminized HE is of interest. In order to identify shock compression states and transport properties in high-pressure/temperature (HP-HT) conditions, we use molecular dynamics (MD) simulations in conjunction with the multi-scale shock technique (MSST). Mean square displacement calculations enabled us to track the diffusivity of stable gas products. Among decomposition products, H2O and CO2 are found to be the dominant diffusing species under compression conditions. Heat transport and diffusion rates in decomposed RDX are compared and the comparison shows that around 2000 K, transport can be a major contribution during propagation of the reaction front.

Free energetics of rigid body association of ubiquitin binding domains: A biochemical model for binding mediated by hydrophobic interaction

Weak intermolecular interactions, such as hydrophobic associations, underlie numerous biomolecular recognition processes. Ubiquitin is a small protein that represents a biochemical model for exploring thermodynamic signatures of hydrophobic association as it is widely held that a major component of ubiquitin's binding to numerous partners is mediated by hydrophobic regions on both partners. Here, we use atomistic molecular dynamics simulations in conjunction with the Adaptive Biasing Force sampling method to compute potentials of mean force (the reversible work, or free energy, associated with the binding process) to investigate the thermodynamic signature of complexation in this well-studied biochemical model of hydrophobic association. We observe that much like in the case of a purely hydrophobic solute (i.e., graphene, carbon nanotubes), association is favored by entropic contributions from release of water from the interprotein regions. Moreover, association is disfavored by loss of enthalpic interactions, but unlike in the case of purely hydrophobic solutes, in this case protein-water interactions are lost and not compensated for by additional water-water interactions generated upon release of interprotein and moreso, hydration, water. We further find that relative orientations of the proteins that mutually present hydrophobic regions of each protein to its partner are favored over those that do not. In fact, the free energy minimum as predicted by a force field based method recapitulates the experimental NMR solution structure of the complex.

Dawn‐dusk asymmetry in solar wind ion entry and dayside precipitation: Results from large‐scale simulations

AbstractWe present the results of numerical studies of the interaction of solar wind ions with the dayside magnetospheric boundary for a southward interplanetary magnetic field and two solar wind speeds (250 and 500 km/s) using the results of global magnetohydrodynamics simulations in conjunction with large‐scale kinetic calculations. Results of these studies show that a dawn‐dusk asymmetry is found in the precipitation of low‐ to middle‐energy ions over the high‐latitude dayside magnetosphere. This asymmetry is consistent with statistical studies of DMSP data showing that ion precipitation from the mantle is predominantly seen over the morning and prenoon sector. Analysis of energy‐latitude spectra and study of individual particle trajectories from the simulations revealed that low‐energy ions can enter the magnetopause at high latitudes in regions where the parallel electric field associated with the magnetopause current is positive and strong enough for the ions to gain energies of the order of the parallel potential drop across the magnetopause. Because the parallel electric field in the Northern Hemisphere is positive in the prenoon sector and negative in the afternoon‐evening sector, solar wind ions reaching the magnetopause in these regions are accelerated toward the ionosphere on the dawnside and outward on the duskside, creating the asymmetry in precipitation. The same dawn‐dusk asymmetry is found in the Southern Hemisphere because both parallel electric field and magnetic field are reversed in direction.

Ionic Liquids Can Selectively Change the Conformational Free-Energy Landscape of Sugar Rings.

We investigated the conformational free energy landscape of glucose solvated in water and in the ionic liquids (ILs) 1-butyl-3-methylimidazolium chloride ([Bmim][Cl]) and 1-butyl-3-methylimidazoulim boron tetrafluoride ([Bmim][BF4]). To quantify equilibrium thermodynamic solvent effects, molecular dynamics simulations in conjunction with enhanced sampling based on the metadynamics framework were used. The results show that the solvent choice induces significant differences in the equilibrium ring structures, which may help further resolve the molecular mechanism governing IL-mediated cellulose dissolution.

Fine-Grained Spatial and Temporal Resolution of Water and Protein Contributions to Ultra-Fast and Slower Fluorescence Shifts from MD + QM Simulations

Vibrant discussion persists as to the origin of the time dependent fluorescence spectral (Stokes) shift (TDFSS) in the range 100 fs to 100 ps for a number of tryptophan (Trp)-containing proteins. TDFSS reports on the dynamic reorganization of the local environment around the large dipole of Trp following excitation to the 1La state. Much of the discussion centers on the ubiquitous “slow” (10 ps-5 ns) TDFSS component found only in proteins. Details of what determines the fast (< 2ps) component in proteins are also of interest. Two questions of interest are: (1) the relative contributions of protein and water; and (2) what length scales characterize these contributions. To help answer these ongoing questions we have performed molecular dynamics simulations in conjunction with semiempirical quantum mechanics (MD + QM) for the proteins STNase, GB1, and monellin, each of which has been the subject of ultrafast experiments. We have examined the spatial contributions to shifts at 1pm intervals of distance, which has revealed that only 5-10 waters less than 0.8nm from Trp contribute to the TDFSS, while ∼100 waters out to 1.5 nm often contribute blue shifts that are the same in the ground and excited state. These simulations raise a further question as to the mechanism of fast anti-correlated fluctuations of protein and water contributions to the fluorescence shift.

Non-equilibrium effects evidenced by vibrational spectra during the coil-to-globule transition in poly(N-isopropylacrylamide) subjected to an ultrafast heating–cooling cycle

Molecular dynamics simulations in conjunction with finite element calculations are used to explore the conformational dynamics of a thermo-sensitive oligomer, namely poly(N-isopropylacrylamide) (PNIPAM), subjected to an ultra-fast heating-cooling cycle. Finite element (FE) calculations were used to predict the temperature profile resulting from laser-induced heating of the polymer-aqueous system. The heating rate (∼0.6 K ps(-1)) deduced from FE calculations was used to heat an aqueous solution of PNIPAM consisting of 30 monomeric units (30-mer) from 285 K to 315 K. Non-equilibrium effects arising from the ultra-fast heating-cooling cycle results in a hysteresis during the coil-to-globule transition. The corresponding atomic scale conformations were characterized by monitoring the changes in the vibrational spectra, which provided a reliable metric to study the coil-to-globule transition in PNIPAM and vice-versa across the LCST. The vibrational spectra of bonds involving atoms from the oligomer backbone and the various side-groups (amide I, amide II, and the isopropyl group of PNIPAM) of the oligomers were analyzed to study the conformational changes in the oligomer corresponding to the observed hysteresis. The differences in the vibrational spectra calculated at various temperatures during heating and cooling cycles were used to understand the coil-to-globule and globule-to-coil transitions in the PNIPAM oligomer and identify the changes in the relative interactions between various atoms in the backbone and in the side groups of the oligomer with water. The shifts in the computed vibrational spectral peaks and the changes in the intensity of peaks for the different regions of PNIPAM, seen across the LCST during the heating cycle, are in good agreement with previous experimental studies. The changes in the radius of gyration (Rg) and vibrational spectra for amide I and amide II regions of PNIPAM suggest a clear coil-to-globule transition at ∼301 K during the heating cycle from 285 K to 315 K. During the heating cycle, a comparison of the vibrational spectra of isopropyl groups in PNIPAM at 285 K and 315 K suggests dehydration of the isopropyl moieties at 315 K. This implies that the oligomer-water interactions are dominant below the LCST whereas oligomer-oligomer interactions pre-dominate above the LCST. On the other hand, during the cooling cycle minor changes in the Rg and vibrational spectra of the PNIPAM oligomer in going from 315 K to 285 K indicate that the interactions between oligomer-oligomer and between the oligomer and water are less perturbed during the cooling cycle. Our simulations suggest that the observed hysteresis is a consequence of ultrafast heating-cooling kinetics, which allows insufficient relaxation times for the solvated oligomer.

SPECIFIC BINDING OF A SHORT miRNA SEQUENCE BY ZINC KNUCKLES OF Lin28: A MOLECULAR DYNAMICS SIMULATION STUDY

Protein Lin28 recognizes pre-let-7 microRNAs (miRNAs) through direct interactions between its zinc-knuckle type zinc-finger (ZnF) domains and the terminal loop of pre-let-7, resulting in the inhibition of the synthesis of mature let-7 miRNAs. Despite the physiological importance, the involved conformational changes and energetic factors contributing to the binding affinity and specificity remain unclear. We conducted molecular dynamics (MD) simulations in conjunction with molecular mechanics/generalized born surface area (MM/GBSA) and energy decomposition calculations to investigate the RNA binding-induced conformational changes of the ZnFs and the residual level energetic factors that influence the binding affinity and specificity. We showed that the binding of the RNA results in the inter-domain conformational changes of the two ZnF domains, including changes of the spatial relationships of several nucleobase-binding amino acids. We also observed mutation-induced weakening of the affinity of the Lin28–pre-let-7 binding, which reveals the importance of the stacking interactions between the side-chains of Tyr140, His148, His162 and the bases of nucleic acid G2 and G5 in the specific recognition of pre-let-7 by the ZnFs of Lin28.

Towards more accurate microcavity sensors: maximum likelihood estimation applied to a combination of quality factor and wavelength shifts

Optical microcavities are widely used for biological and chemical sensing applications. In these devices, a sensing event is estimated by measuring the shift in the resonant wavelength, or in the quality factor of the microcavity. However, all published works to date only use one of these measures to estimate the sensing event. Here, we show that the estimation accuracy of a sensing event can be improved by employing a combination of both the quality factor and the resonant wavelength measurements in a microcavity sensor. We further demonstrate an experimental application of this model by introducing a refractive index change for a microtoroidal cavity sensor immersed in a liquid. By further using the finite element method simulations in conjunction with the estimator model, we show the existence of three distinct measurement regimes as a function of the quality factor of the microcavity. Finally, the estimator model is extended to develop a sensing metric to compare performance of optical or non-optical sensors.

Use of a small peptide fragment as an inhibitor of insulin fibrillation process: a study by high and low resolution spectroscopy.

A non-toxic, nine residue peptide, NIVNVSLVK is shown to interfere with insulin fibrillation by various biophysical methods. Insulin undergoes conformational changes under certain stress conditions leading to amyloid fibrils. Fibrillation of insulin poses a problem in its long-term storage, reducing its efficacy in treating type II diabetes. The dissociation of insulin oligomer to monomer is the key step for the onset of fibrillation. The time course of insulin fibrillation at 62°C using Thioflavin T fluorescence shows an increase in the lag time from 120 min without peptide to 236 min with peptide. Transmission electron micrographs show branched insulin fibrils in its absence and less inter-fibril association in its presence. Upon incubation at 62°C and pH 2.6, insulin lost some α-helical structure as seen by Fourier transformed infra-red spectroscopy (FT-IR), but if the peptide is added, secondary structure is almost fully maintained for 3 h, though lost partially at 4 h. FT-IR spectroscopy also shows that insulin forms the cross beta structure indicative of fibrils beyond 2 h, but in the presence of the peptide, α-helix retention is seen till 4 h. Both size exclusion chromatography and dynamic light scattering show that insulin primarily exists as trimer, whose conversion to a monomer is resisted by the peptide. Saturation transfer difference nuclear magnetic resonance confirms that the hydrophobic residues in the peptide are in close contact with an insulin hydrophobic groove. Molecular dynamics simulations in conjunction with principal component analyses reveal how the peptide interrupts insulin fibrillation. In vitro hemolytic activity of the peptide showed insignificant cytotoxicity against HT1080 cells. The insulin aggregation is probed due to the inter play of two key residues, PheB24 and TyrB26 monitored from molecular dynamics simulations studies. Further new peptide based leads may be developed from this nine residue peptide.

Electron Momentum Spectroscopy of 1-Butene: A Theoretical Analysis Using Molecular Dynamics and Molecular Quantum Similarity

The results of experimental studies of the valence electronic structure of 1-butene by means of electron momentum spectroscopy (EMS) have been reinterpreted on the basis of molecular dynamical simulations in conjunction with the classical MM3 force field. The computed atomic trajectories demonstrate the importance of thermally induced nuclear dynamics in the electronic neutral ground state, in the form of significant deviations from stationary points on the potential energy surface and considerable variations of the C-C-C-C dihedral angle. These motions are found to have a considerable influence on the computed spectral bands and outer-valence electron momentum distributions. Euclidean distances between spherically averaged electron momentum densities confirm that thermally induced nuclear motions need to be fully taken into account for a consistent interpretation of the results of EMS experiments on conformationally flexible molecules.

Interactions and Stabilities of the UV RESISTANCE LOCUS8 (UVR8) Protein Dimer and Its Key Mutants

The dimeric UVR8 protein is an ultraviolet-B radiation (280-315 nm) photoreceptor responsible for the first step in UV-B regulation of gene expression in plants. Its action comprises the actual absorption of the UV quanta by a tryptophan array at the protein-protein interface, followed by monomerization and subsequent aggregation with downstream signaling components. A crystal structure of the Arabidopsis thaliana tryptophan-rich wild type UVR8 protein dimer was recently published, showing the presence of several salt bridges involving arginines R146, R286, R338, and R354. In this work, molecular dynamics simulations in conjunction with umbrella sampling were used to calculate the binding free energy for the wild type UVR8 dimer and three of its mutants (R286A, R338A, and R286A/R338A), in order to verify whether the key mutants are able to disrupt the dimeric structure as indicated experimentally.

Direct Evidence for Hydrogen Bonding in Glycans: A Combined NMR and Molecular Dynamics Study

We introduce the abundant hydroxyl groups of glycans as NMR handles and structural probes to expand the repertoire of tools for structure-function studies on glycans in solution. To this end, we present the facile detection and assignment of hydroxyl groups in a wide range of sample concentrations (0.5-1700 mM) and temperatures, ranging from -5 to 25 °C. We then exploit this information to directly detect hydrogen bonds, well-known for their importance in molecular structural determination through NMR. Via HSQC-TOCSY, we were able to determine the directionality of these hydrogen bonds in sucrose. Furthermore, by means of molecular dynamics simulations in conjunction with NMR, we establish that one out of the three detected hydrogen bonds arises from intermolecular interactions. This finding may shed light on glycan-glycan interactions and glycan recognition by proteins.

Nitridation ofAl2O3Surfaces: Chemical and Structural Change Triggered by Oxygen Desorption

We present theoretical investigations that clarify elemental nitridation processes of corundum Al2O3(0001) and (1102) surfaces. The calculations within the density functional theory framework reveal that the structures with substitutional N atoms beneath the surface are stabilized under nitridation conditions. We also find that the desorption of O atoms at the topmost layer induces outward diffusion of O atoms as well as inward diffusion of N atoms, leading to the transformation into AlN films. The kinetic Monte Carlo simulations in conjunction with density functional theory results indeed observe a dependence of these chemical and structural changes on temperature and pressure.

Determination of Forming Limit Curves of Steel Pipes for Hydroformability Evaluation

The aims of this research are to establish the forming limit curve (FLC) of tubular material low carbon steels commonly used in Thai industry, verify these FLCs with real part forming experiments and compare these experimentally obtained FLCs against analytical ones available in FEA software database. A self-designed bulge forming apparatus of fixed bulge length and a hydraulic test machine with axial feeding are used to carry out the bulge tests. Loading paths resulting to linear strain paths at the apex of the bulging tube are determined by FE simulations in conjunction with a self-compiled subroutine. These loading paths are used to control the internal pressure and axial feeding punch of the test machine. In this work a common low carbon steel tubing grade STKM 11A, with 28.6 mm outer diameter and 1.2 mm thick is studied. Circular grids are electro chemically etched onto the surface of tube samples. Subsequently, the tube samples are bulge-formed. The forming process is stopped when a burst is observed on the forming sample. After conducting the bulge tests, major and minor strains of the grids located beside the bursting line on the tube surface are measured to construct the forming limit curve (FLC) of the tubes. The forming limit curves determined for these tubular materials are put to test in formability evaluations of test parts forming in real experiment. It was found that the tool geometry can keep the strain ratio constant is not dependent on the thickness but only on OD of the tube, as in equations L=OD and rd=(15xOD)/25.4. The experimen-tal FLDs have predicted failures in forming process consistently with the real experiments. The ex-perimentally obtained forming limit curves (determined following STKM 11A) differ from empiri-cal one (from FEA software) and analytical one by about 0.02339 and 0.15736 true strain respec-tively at FLD0, the corresponding plane strain values.

Growth of side facets in InP nanowires: First-principles-based approach

The initial growth processes on InP 11¯00 and InP 112¯0 surfaces are theoretically investigated to clarify temperature and pressure dependence of InP nanowire shape fabricated by selective area growth. Our Monte Carlo simulations in conjunction with density functional calculations for the growth processes with a realistic environment such as temperature and pressure reveal that there are several growth modes depending on the growth conditions. Due to lower growth rate on InP 112¯0 surface compared with InP 11¯00 surface, the nanowires grow along both vertical [0001] and lateral <112¯0> directions for low temperatures with high V/III ratio conditions. On the other hand, at high temperatures with low V/III ratio conditions, the nanowires grow along only vertical [0001] direction and form 11¯00 side facets due to lower surface energy on InP 11¯00 surface. The adsorption of P atoms on the surfaces are found to be crucial for the growth along the lateral direction of nanowires. The obtained results offer a possibility to predict and control nanowire shape by tuning growth conditions such as temperature and pressure.

Evolution of pore characteristics in the 3D numerical direct shear test

The quantitative analysis of the pore characteristics of granular materials has been often challenging due to arbitrarily shaped geometry of pores despite its significant implications. In this study, we investigate the size distribution and orientation of pores in dilative and contractive assemblies in the direct shear test by performing 3D discrete element simulations in conjunction with image processing of pore geometry. We quantitatively define unit pores by the Delaunay Tessellation followed by pore mergence and fitting them with ellipsoids. It is observed that the evolution of pore size distribution depends on the dilatancy of assemblies. Results also show that the direction of principal stresses governs the orientations of pores during shearing, with respect to the size of pores. This study highlights that the dominant factors of the pore characteristics upon shearing are stress anisotropy and particle mobilization to make the internal structure stable.

Plastic deformation of NiTi shape memory alloys

Dislocation slip in B2 NiTi is studied with atomistic simulations in conjunction with transmission electron microscopy (TEM). The atomistic simulations examine the generalized stacking fault energy (GSFE) curves for the {011}, {2¯11} and {001} planes. The slip directions considered are 〈100〉, 〈111〉 and 〈011〉. The results show the smallest energy barriers for the (011)[100] case, which is consistent with the experimental observations of dislocation slip reported in this study. To our knowledge, slip on the (011)[11¯1] system is illustrated for the first time in our TEM findings, and atomistic simulations confirm that this system has the second lowest energy barrier. Specimens that underwent thermal cycling and pseudoelasticity show dislocation slip primarily in the austenite domains while the bulk of martensite domains does not display dislocations. The results are discussed via calculation of the ideal slip nucleation stress levels for the five potential slip systems in austenite.

Energy harvesting from human motion: an evaluation of current nonlinear energy harvesting solutions

The concept of harvesting electrical energy from ambient vibration sources has been a popular topic of research in recent years. Recently, the realisation that the majority of ambient vibration sources are often stochastic in nature has led to a large body of work which has focused on the response of energy harvesters to random excitations – most of which approximate environmental excitations as being Gaussian white noise. Of particular interest here are recent findings which demonstrate the advantages that Duffing-type nonlinearities can introduce into energy harvesters. The aim of this paper is to identify how well these results can be applied to that of a real energy harvesting scenario. More specifically, the response of an energy harvester to excitation via human motion is studied using digital simulations in conjunction with acceleration data obtained from a human participant. As well as assessing whether Duffing-type nonlinearities can have a beneficial impact on device performance this paper aims to investigate whether Gaussian white noise can indeed be used as a good approximation for this particular ambient vibration source.