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Results for “Umbrella Sampling”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Reaction Rate Theory in Coordination Number Space: An Application to Ion Solvation

Understanding reaction mechanisms in many chemical and biological processes require application of rare event theories. In these theories, an effective choice of a reaction coordinate to describe a reaction pathway is essential. To this end, we study ion solvation in water using molecular dynamics simulations and explore the utility of coordination number (n = number of water molecules in the first solvation shell) as the reaction coordinate. Here we compute the potential of mean force (W(n)) using umbrella sampling, predicting multiple metastable n-states for both cations and anions. We find with increasing ionic size, these states become more stable and structured for cations when compared to anions. We have extended transition state theory (TST) to calculate transition rates between n-states. TST overestimates the rate constant due to solvent-induced barrier recrossings that are not accounted for. We correct the TST rates by calculating transmission coefficients using the reactive flux method. This approach enables a new way of understanding rare events involving coordination complexes. We gratefully acknowledge Liem Dang and Panos Stinis for useful discussion. This research used resources of the National Energy Research Scientific Computing Center, a DOE Office of Science User Facility supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231. SR, CJM, and GKS were supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences. MDB was supported by MS3 (Materials Synthesis and Simulation Across Scales) Initiative, a Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory (PNNL). PNNL is a multiprogram national laboratory operated by Battelle for the U.S. Department of Energy.

Roy, Santanu↗
DOE OSTI2019

Effect of Interlayer Co 2+ on Structure and Charge Transfer in NiFe Layered Double Hydroxides

We present that the intercalation of Co in Ni/Fe layered double hydroxides (LDH) significantly improves the electrocatalytic performance of the LDH for the oxygen evolution reaction. The mechanism behind the improvement and the structure of the Co-intercalated LDHs, however, is not precisely known. We use classical molecular dynamics (CMD) to study the impact of intercalated Co on the structure of Ni/Fe LDH and the electron transfer process. CMD studies find that the Co ions form small clusters, pushing apart the surrounding hydroxide sheets to form small “pockets” around these clusters, disrupting the planar nature of the sheets in the absence of intercalated Co clusters. The structure of the “pockets” is a strong function of force field parameters and the accuracy of the LDH bulk modulus. Lastly, we use umbrella sampling to study electron transfer and show that the clusters of Co in the interlayer are important for electron transfer, such that solvent molecules have greater freedom to reorient with a change in charge state, thereby reducing the barrier to electron transfer.

36 MATERIALS SCIENCE↗
DOE OSTI2015

Self-Assembled Monolayers of an Azobenzene Derivative on Silica and Their Interactions with Lysozyme

The capability of the photoresponsive isomerization of azobenzene derivatives in self-assembled monolayer (SAM) surfaces to control protein adsorption behavior has very promising applications in antifouling materials and biotechnology. In this study, we performed an atomistic molecular dynamics (MD) simulation in combination with free-energy calculations to study the morphology of azobenzene-terminated SAMs (Azo-SAMs) grafted on a silica substrate and their interactions with lysozyme. Results show that the Azo-SAM surface morphology and the terminal benzene rings’ packing are highly correlated with the surface density and the isomer state. Higher surface coverage and the trans-isomer state lead to a more ordered polycrystalline backbone as well as more ordered local packing of benzene rings. On the Azo-SAM surface, water retains a high interfacial diffusivity, whereas the adsorbed lysozyme is found to have extremely low mobility but a relative stable secondary structure. The moderate desorption free energy (~60 kT) from the trans-Azo-SAM surface was estimated by using both the nonequilibrium-theorem-based Jarzynski’s equality and equilibrium umbrella sampling.

Chemistry↗
DOE OSTI2018

Molecular Simulations of the Hydration Behavior of a Zwitterion Brush Array and Its Antifouling Property in an Aqueous Environment

We carried out umbrella sampling and molecular dynamics (MD) simulations to investigate molecular interactions between sulfobetaine zwitterions or between sulfobetaine brushes in different media. Simulation results show that it is more energetically favorable for the two sulfobetaine zwitterions or brushes to be fully hydrated in aqueous solutions than in vacuum where strong ion pairs are formed. Structural properties of the hydrated sulfobetaine brush array and its antifouling behavior against a foulant gel are subsequently studied through steered MD simulations. We find that sulfobetaine brush arrays with different grafting densities have different structures and antifouling mechanisms. At a comparably higher grafting density, the sulfobetaine brush array exhibits a more organized structure which can hold a tightly bound hydration water layer at the interface. Compression of this hydration layer results in a strong repulsive force. However, at a comparably lower grafting density, the brush array exhibits a randomly oriented structure in which the antifouling of the brush array is through the deformation of the sulfobetaine branches.

36 MATERIALS SCIENCE↗
DOE OSTI2019

A Quantitative Molecular Atlas for Interactions Between Lignin and Cellulose

Lignin and cellulose are two of the most abundant polymers on Earth, and are found in close proximity within plant cell walls. Despite their ubiquity, relatively little is known quantitatively about their interactions within plants, and by extension how their interaction may affect industrial biomass utilization. Given the inherent heterogeneity of the lignin polymer and the structural complexity of cellulose, quantitative relationships between given cellulose faces and specific lignin chemistries have been challenging to ascertain experimentally. In this study, we use molecular simulation to examine individual combinations of cellulose binding face and lignin chemistry to build a quantitative lignin-cellulose interaction atlas, including contributions from both specific hydrogen bonds observed in simulation and nonspecific interactions between lignin and cellulose driven by solvent considerations. Over all monomeric and dimeric lignin chemistries tested, the hydrophobic 100 face is the preferred cellulose interaction site. Among the hydrophilic crystalline faces, binding of these molecules is strongest to the 110 cellulose face. The chemical composition of lignin monomers and dimers is also found to modulate the binding affinity, with additional methoxy groups increasing the contact area to the cellulose surface, which we hypothesize may protect native cellulose from degradation. Additional methoxylation and monomer linkages that facilitate planar aromatic ring orientations increase the binding affinity between small lignin-related molecules and cellulose, with the planar linkages between guaiacyl-type monomers leading to higher binding affinities. These trends can be extended to larger lignin polymers, where we quantify the relationships between lignin polymer size and binding affinity through replica exchange umbrella sampling simulations. Rather than molecular weight, the binding surface area between the lignin polymer and the cellulose surface dictates the interaction strength. As a result, based on the findings here, we expect there to be abundant and durable interaction between cellulose and lignin, particularly on the hydrophobic face of cellulose where cellulase enzymes typically bind.

09 BIOMASS FUELS↗
DOE OSTI2012

Accurate rates of the complex mechanisms for growth and dissolu-tion of minerals using a combination of rare event theories

Mineral growth and dissolution are often treated as occurring via a single, reversible process that governs the rate of reaction. We show that multiple, distinct intermediate states can occur during both growth and dissolution. Specifically, we have used metadynamics, a method to efficiently explore the free energy landscape of a system, coupled to umbrella sampling and reactive flux calculations, to examine the mechanism and rates of attachment and detachment of a barium ion onto a stepped, barite (BaSO4) surface. The activation energies calculated for the rate limiting reactions, which are different for attachment and detachment, precisely match those measured experimentally during both growth and dissolution. These results can potentially explain anomalous, non-steady state mineral reaction rates observed experimentally, and will enable the design of more efficient growth inhibitors and facilitate an understanding of the effect of impurities.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2015

Computational Molecular Simulation of the Oxidative Adsorption of Ferrous Iron at the Hematite (001)-Water Interface

The interaction of Fe(II) with ferric oxide/oxyhydroxide phases is central to the biogeochemical redox chemistry of iron. Molecular simulation techniques were employed to determine the mechanisms and quantify the rates of Fe(II) oxidative adsorption at the hematite (001)-water interface. Molecular dynamics potential of mean force calculations of Fe(II) adsorbing on the hematite surface revealed the presence of three free energy minima corresponding to Fe(II) adsorbed in an outersphere complex, a monodentate innersphere complex, and a tridentate innersphere complex. The free energy barrier for adsorption from the outersphere position to the monodentate innersphere site was calculated to be similar to the activation enthalpy for water exchange around aqueous Fe(II). Adsorption at both innersphere sites was predicted to be unfavorable unless accompanied by release of protons. Molecular dynamics umbrella sampling simulations and ab initio cluster calculations were performed to determine the rates of electron transfer from Fe(II) adsorbed as an innersphere and outersphere complex. The electron transfer rates were calculated to range from 10^-4 to 10^2 s-1, depending on the adsorption site and the potential parameter set, and were generally slower than those obtained in the bulk hematite lattice. The most reliable estimate of the rate of electron transfer from Fe(II) adsorbed as an outersphere complex to lattice Fe(III) was commensurate with the rate of adsorption as an innersphere complex suggesting that adsorption does not necessarily need to precede oxidation.

Environmental Molecular Sciences Laboratory↗
DOE OSTI2022

Molecular dynamics simulations of the secondary-binding site in disaccharide-modified glycopeptide antibiotics

Oritavancin is a semisynthetic glycopeptide antibiotic used to treat severe infections by multidrug-resistant Gram-positive pathogens. Oritavancin is known to be a thousand times more potent than vancomycin against Gram-positive bacteria due to the additional interactions with bacterial peptidoglycan (PG) facilitated by a secondary-binding site. The presence of this secondary-binding site is evident in desleucyl-oritavancin, an Edman degradation product of oritavancin, still retaining its potency against Gram-positive bacteria, whereas desleucyl-vancomycin is devoid of any antimicrobial activities. Herein, using explicit solvent molecular dynamics (MD) simulations, steered MD simulations, and umbrella sampling, we show evidence of a secondary-binding site mediated by the disaccharide-modified hydrophobic sidechain of oritavancin interactions with the pentaglycyl-bridge segment of the PG. The interactions were characterized through comparison to the interaction of PG with chloroeremomycin, vancomycin, and the desleucyl analogs of the glycopeptides. Our results show that the enhanced binding of oritavancin to PG over the binding of the other complexes studied is due to an increase in the hydrophobic effect, electrostatic and van der Waals interactions, and not the average number of hydrogen bonds. Our ranking of the binding interactions of the biomolecular complexes directly correlates with the order based on their experimental minimum inhibitory concentrations. The results of our simulations provide insight into the modification of glycopeptides to increase their antimicrobial activities or the design of novel antibiotics against pathogenic Gram-positive bacteria.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Calculation of critical nucleation rates by the persistent embryo method: application to quasi hard sphere models

Here, we study the crystal nucleation of the Weeks–Chandler–Andersen (WCA) model, using the recently introduced persistent embryo method (PEM). The method provides detailed characterization of pre-critical, critical and post-critical nuclei, as well as nucleation rates that compare favorably with those obtained using other methods (umbrella sampling, forward flux sampling or seeding). We further map our results to a hard sphere model allowing comparison with other existing predictions. Implications for experiments are also discussed.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication

Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with viral genome replication. Here in this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can initially bind in a comparatively stabilized state to the viral RdRp active site, as it primarily forms base stacking with the template uracil nucleotide (nt +1), which under freely fluctuations supports a low free energy barrier of the RDV-TP insertion (~1.5 kcal mol -1 ). In comparison, the corresponding natural substrate ATP binds initially to the RdRp active site in Watson–Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~2.6 kcal mol -1 ), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be specifically stabilized by motif C-S759, S682 (near motif B) with the base, and motif G-K500 with the template backbone. Although the RDV-TP insertion can be hindered by motif F-R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif A-D623, respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Solvent effects on extractant conformational energetics in liquid–liquid extraction: a simulation study of molecular solvents and ionic liquids

Extractant design in liquid–liquid extraction (LLE) is a research frontier of metal ion separations that typically focuses on the direct extractant–metal interactions. However, a more detailed understanding of energetic drivers of separations beyond primary metal coordination is often lacking, including the role of solvent in the extractant phase. In this work, we propose a new mechanism for enhancing metal-complexant energetics with nanostructured solvents. Using molecular dynamics simulations with umbrella sampling, we find that the organic solvent can reshape the energetics of the extractant's intramolecular conformational landscape. Here, we calculate free energy profiles of different conformations of a representative bidentate extractant, n-octyl(phenyl)-N,N-diisobutyl carbamoyl methyl phosphinoxide (CMPO), in four different solvents: dodecane, tributyl phosphate (TBP), and dry and wet ionic liquid (IL) 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([EMIM][Tf 2 N]). By promoting reorganization of the extractant molecule into its binding conformation, our findings reveal how particular solvents can ameliorate this unfavorable step of the metal separation process. In particular, the charge alternating nanodomains formed in ILs substantially reduce the free energy penalty associated with extractant reorganization. Importantly, using alchemical free energy calculations, we find that this stabilization persists even when we explicitly include the extracted cation. These findings provide insight into the energetic drivers of metal ion separations and potentially suggest a new approach to designing effective separations using a molecular-level understanding of solvent effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

Free energy calculations using dual-level Born-Oppenheimer molecular dynamics

We describe an efficient and accurate method to compute free energy changes in complex chemical systems that cannot be described through classical molecular dynamics simulations, examples of which are chemical and photochemical reactions in solution, enzymes, interfaces, etc. It is based on the use of dual-level Born-Oppenheimer molecular dynamics simulations. A low-level quantum mechanical method is employed to calculate the potential of mean force through the umbrella sampling technique. Then, a high-level quantum mechanical method is used to estimate a free energy correction on selected points of the reaction coordinate using perturbation theory. The precision of the results is comparable to that of ab initio molecular dynamics methods such as the Car-Parrinello approach but the computational cost is much lower, roughly by two to three orders of magnitude. The method is illustrated by discussing the association free energy of simple organometallic compounds, although the field of application is very broad.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

A practical perspective on the implementation of hyperdynamics for accelerated simulation

Consideration is given to several practical issues arising during the implementation of hyperdynamics, a methodology that extends the time scale of the conventional molecular dynamics simulation potentially by orders of magnitude. First, the methodology is reformulated in terms of the transition rate based on the buffer region approach (buffer rate), which can describe transitions in more general contexts than the transition state theory (TST). It will be shown that hyperdynamics can exactly preserve the buffer rate as well as the TST rate, which broadens the scope of the method. Next, the originally proposed scheme to compute the boost factor on-the-fly is reviewed and some alternative methods, one of which uses the umbrella sampling method, are presented. Finally, the methodology is validated in the context of a 1-dimensional example potential and a 3-dimensional simulation of the motion of an atomic force microscope tip moving along a surface.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Interactions of aqueous amino acids and proteins with the (110) surface of ZnS in molecular dynamics simulations

The growing usage of nanoparticles of zinc sulfide as quantum dots and biosensors calls for a theoretical assessment of interactions of ZnS with biomolecules. We employ the molecular-dynamics-based umbrella sampling method to determine potentials of mean force for 20 single amino acids near the ZnS (110) surface in aqueous solutions. We find that five amino acids do not bind at all and the binding energy of the remaining amino acids does not exceed 4.3 kJ/mol. Such energies are comparable to those found for ZnO (and to hydrogen bonds in proteins) but the nature of the specificity is different. Cysteine can bind with ZnS in a covalent way, e.g., by forming the disulfide bond with S in the solid. If this effect is included within a model incorporating the Morse potential, then the potential well becomes much deeper—the binding energy is close to 98 kJ/mol. We then consider tryptophan cage, a protein of 20 residues, and characterize its events of adsorption to ZnS. We demonstrate the relevance of interactions between the amino acids in the selection of optimal adsorbed conformations and recognize the key role of cysteine in generation of lasting adsorption. We show that ZnS is more hydrophobic than ZnO and that the density profile of water is quite different than that forming near ZnO—it has only a minor articulation into layers. Furthermore, the first layer of water is disordered and mobile.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Phase behavior of the 38-atom Lennard-Jones cluster

We have developed a coarse-grained description of the phase behavior of the isolated 38-atom Lennard-Jones cluster (LJ{sub 38}). The model captures both the solid-solid polymorphic transitions at low temperatures and the complex cluster breakup and melting transitions at higher temperatures. For this coarse model development, we employ the manifold learning technique of diffusion mapping. The outcome of the diffusion mapping analysis over a broad temperature range indicates that two order parameters are sufficient to describe the cluster's phase behavior; we have chosen two such appropriate order parameters that are metrics of condensation and overall crystallinity. In this well-justified coarse-variable space, we calculate the cluster's free energy landscape (FEL) as a function of temperature, employing Monte Carlo umbrella sampling. These FELs are used to quantify the phase behavior and onsets of phase transitions of the LJ{sub 38} cluster.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2014

Simulation study of the effects of surface chemistry and temperature on the conformations of ssDNA oligomers near hydrophilic and hydrophobic surfaces

We study the effects of the presence of a hydrophilic and a hydrophobic surface on the conformations and interactions of a single-stranded DNA (ssDNA) oligomer using atomistic molecular dynamics, umbrella sampling, and temperature-replica exchange. Our simulations capture the expected interactions between the ssDNA and the two surfaces (e.g., hydrogen bonds, hydrophobic interactions), but we find that the surface chemistry does not strongly affect the exposure of the relatively hydrophobic nucleobases or the hydrophilic phosphate backbone in a 16-base ssDNA. Likewise, the surfaces do not strongly affect the preferred size of the ssDNA compared to bulk solution, although the hydrophilic surface does favor slightly more compact ssDNA conformations than the hydrophobic surface. In more compact conformations, the negative charge of the ssDNA is more concentrated, and the energetic interactions of the DNA and DNA-bound counterions with the hydrophilic surface are more favorable, which consequently favors smaller ssDNA sizes. Increasing temperature, regardless of the presence or chemistry of a surface, makes it less unfavorable for the ssDNA to assume both compact and extended conformations. With increasing temperature the free energy cost of assuming a compact conformation is reduced to a greater extent than the cost of assuming an extended conformation. The reason for this difference is the entropically favorable release of DNA-bound water molecules upon assuming a compact conformation. Increasing temperature decreases water-DNA interactions while surprisingly increasing counterion-DNA interactions, changes which are attributed to the relative balance of entropic and energetic contributions for water molecules and counterions bound to the ssDNA.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗