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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 1,135 records · Page 63
All sourcesNASA NTRSDOE OSTI
NASA NTRS2022

Electromagnetic Time and Wavelength Domain Predictions for Accreting Binary Black Holes

Accreting massive binary black holes in gaseous environments are keymulti-messenger sources for the LISA mission. We will present some ofthe latest predictions of the observational signatures of accreting binary black holes across the electromagnetic spectrum from the fieldand provide some of our own. In particular, we will provide a briefsummary of the progress made in our group to understand these systemstheoretically using high-performance simulations of generalrelativistic magnetohydrodynamics (MHD) and dynamic spacetimes.Simulating these systems realistically is challenging asradiation-coupled MHD must be considered over large dynamic ranges inspace and time. Constraining our view to the circumbinary disk regionfirst, we will show how the evolution duration, accretion disk size,mass ratio, and thermodynamics model affect the structure andvariability of the accretion flow. We particularly emphasize how theseparameters influence the over-density feature, or "lump", which orbitsthe binary near the edge of the cavity, since it is responsible formost of the electromagnetic emission's variability---a key signatureof a system being a binary. Extending to smaller length scales, wewill report on simulations following accretion all the down to theevent horizons so that we may begin to investigate how black hole spinaffects mini-disk dynamics, accretion rate, and jet power. We willalso report on our radiative transfer predictions for how black holespin alters the spectral energy distribution of these systems.Wrapping up, we will itemize the remaining key theoreticaltechnologies and directions needed to be accomplished to betterunderstand these sources, and assess strategies for searching for themin the coming decade.

Scott C Noble↗
NASA NTRSDate not supplied

The Interplay of Humor and Team Cohesion Over Time

Team bonding and interpersonal relationships are increasingly important as we continue understanding the effects of the pandemic on team dynamics. Specifically, team cohesion, defined as having a sense of belonging and commitment towards the group, has been found to be important for key team outcomes such as performance, relationships, and productivity (Beal, Cohen, Burke, & McLendon, 2003; Bell & Marentette, 2011). Research has stressed the benefits of positive humor on cohesion, with humor creating positive emotions and decreasing social distance (e.g., Robert & Wilbanks, 2012; Robinson & Smith-Lovin, 2001; Romero & Pescosolido, 2008). However, research around the impact of negative humor on cohesion is scarce. This study aims to examine the impact of both positive and negative humor on cohesion for teams over time. The longitudinal design allows us to examine the interplay of humor and cohesion throughout a team’s lifecycle to guide relationship development and management (Romero & Pescosolido, 2008). Humor is defined as remarks recognized as amusing or funny (Martin, 2007). Positive humor can be categorized as good-natured aimed to create mutual agreement, while negative humor is defined as aggressive, hostile, and unreciprocated (Coan & Gottman, 2007). Research has concluded the many benefits of positive humor, showing it can increase open communication, social support, and create a pleasant environment (Martineau, 1972; Robinson & Smith-Lovin, 2001; Romero & Pescosolido, 2008). The Humor Wheel model suggests that positive humor is contagious due to the positive affect produced and mimicked (Lehmann-Willenbrock & Allen 2014). Research has suggested positive humor would increase over time based on the norm of reciprocity; those treated positively are likely to respond similarly (Gouldner, 1960). Multiple parties’ involvement in humor exchanges highlights the interpersonal nature of humor. Thus, long-term consequences on relationships should be considered, such as cohesion (Robert & Wilbanks, 2012). It would be instrumental to understand how humor interactions could weaken or strengthen group cohesion through relational and emotional bonds over time (Martineau, 1972; Romero & Pescosolido, 2008). Positive humor should fundamentally increase team cohesion (Mesmer-Magnus, Glew, & Viswesvaran, 2012; Walter & Baruch, 2008) by promoting group harmony, team member attractiveness, and ingroup identity (Holmes, 2006). Thus, it is expected there is a positive relationship between positive humor and team cohesion over time (hypothesis 1). Humor is not always beneficial, especially when it elicits negative emotions (Dikkers, Doosje, & de Lange, 2011). Negative humor can be used to humiliate, tease, or insult (Coan & Gottman, 2007; Collinson, 1988; Romero & Cruthirds, 2006). It tends to cause distress and damage relationships, and in turn, decrease organizational performance and production (Avolio, Howell, & Sosik, 1999; Janes & Olson, 2000; Yerkes, 2001). Research concludes negative humor may create subgroups and decrease cooperation (Romero & Arendt, 2011). Research has also indicated positive implications for negative humor under specific circumstances. Negative humor could help to solidify ingroup identity and strengthen bonds when directed outside the team (Terrion & Ashforth, 2002; Thomae & Pina, 2015). For example, sport teams may use negative humor towards their opponent before a game, which emphasizes their differences and lowers the status and power of their opponent, ultimately promoting solidarity and cohesion inside the group. For this study, it is anticipated that negative humor toward other teammates will decrease team cohesion over time due to the damage to relationships and negative affect produced (Duncan, Smeltzer, & Leap, 1990; Maples, Dupey, Torres‐Rivera, Phan, Vereen, & Garrett, 2001). We also predicted that negative humor focused on something or someone outside the team will increase cohesion by enhancing ingroup ties and creating a common identity (Thomae & Pina, 2015). Thus, the relationship between negative humor and cohesion will be moderated by the target of the humor. The relationship will be negative when the target is within the team and positive when the target is outside (hypothesis 2).

Melissa M. Vazquez↗
NASA NTRSDate not supplied

James Webb Space Telescope Fuel Slosh Estimation

The mitigation of fuel slosh in microgravity environments is a pressing matter for the control of both manned and unmanned spacecraft. This paper investigates the attitude perturbations caused by fuel slosh aboard the James Webb Space Telescope (JWST). We develop a dynamical model to parse these perturbations from slew telemetry data. This model uses special Euclidean group SE(3) as well as a novel, N-body variational integrator. The enhanced ability to validate fuel slosh models offers the reduction of settling time after slew operations and, accordingly, the maximization of available science time.

GN&C↗
DOE OSTI2024

Dynamic Binary Complexes (DBC) as Super-Adjustable Viscosity Modifiers for Hydraulic Fracturing Fluids

In the preceding project year two, we refined three DBC formulations from a selection of over 50 different chemistries. The optimization study primarily encompassed testing for (i) reversibility extent, (ii) performance in the presence of chemical additives, (iii) adhesion and friction behavior during displacement in wellbores and pipelines, (iv) corrosion protection performance, and (v) injection performance with model fracture systems at the laboratory scale. Highly promising results obtained from all these tests signify the significant potential of DBCs in enhancing hydrocarbon recovery from unconventional reservoirs. The primary activities in the third project year included publishing experimental findings across multiple articles and conducting outreach initiatives. Throughout the year, we undertook tasks such as replicating experimental results, further optimizing various formulations and their associated experimental sets, and conducting additional tests to address missing components based on reviewer feedback and suggestions. We also explored the surfactant and friction-reduction aspects of selected formulations through drag reduction tests. In addition, we constructed an improved fracturing performance setup and performed flow injection tests. The specific DBC formulations focused on during this project period were A8/B1, A12/B5, and A10/B12. We also obtained results for additional DBC formulations and a select few commercial fracturing fluids for the purpose of comparison. Within the project's scope, we aim to enhance the experimental findings with the development of various models. The first two years focused on two key aspects: (i) the creation of a high-fidelity hydraulic fracturing model for non-Newtonian fluids to gain insights into the implementation of DBC fluids in fracking environments, and (ii) the development of a multiphase flow simulator for estimating total production, fluid saturation in the reservoir, and the creation of a fracture propagation model and kinetic Monte Carlo (kMC) models for diverse applications. In the third year, we delved into the fundamental nanostructural properties of DBCs, exploring aspects such as material chemistry, pH tunability, and control of DBC formation and stability. Subsequently, in the extension year, we conducted a systematic investigation of various building blocks containing primary, secondary, and tertiary amine functional groups to understand their impact on rheological and viscoelastic properties. Furthermore, we explored a Dissipative Particle Dynamics (DPD) model to simulate self-assembly processes with precision, creating a high-fidelity representation of relevant nanostructures. The tasks performed this year with the significant results obtained have been discussed in Section 2.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

Solution NMR Structures of Oxidized and Reduced Ehrlichia chaffeensis thioredoxin: NMR-Invisible Structure Owing to Backbone Dynamics

Thioredoxins (Trxs) are small ubiquitous proteins that participate in a diverse variety of redox reactions via the reversible oxidation of two cysteine thiol groups in a structurally conserved active site, CGPC. Here, we describe the NMR solution structures of a Trx from Ehrlichia chaffeensis (Ec-Trx, ECH_0218), the etiological agent responsible for human monocytic ehrlichiosis, in both the oxidized and reduced states. The overall topology of the calculated structures is similar in both redox states and similar to other Trx structures, a five-strand, mixed -sheet (1:3:2:4:5) surrounded by four -helices. Unlike other Trxs studied by NMR in both redox states, the 1H-15N HSQC spectra of reduced Ec-Trx was missing eight amide cross peaks relative to the spectra of oxidized Ec-Trx. These missing amides correspond to residues C32-E39 in the active site containing helix (2) and S72-I75 in a loop near the active site and suggest a substantial change in the backbone dynamics associated with the formation of an intramolecular C32-C35 disulfide bond.

Environmental Molecular Sciences Laboratory↗
NASA NTRS1974

The dynamic response of visual accommodation over a seven-day period

Four college students, ranging in age from 18 to 21 years, were tested on their dynamic, monocular accommodation responses to a square wave stimulus and sine waves of two frequencies. The tests were conducted over a period of seven days in a controlled environment, each subject being tested once every three hours. Latency, magnitude, velocity, gain and phase lag of the responses were measured, and means and standard deviations were computed. The latency of response was stable throughout and agreed fairly well with previous studies. The response magnitude was relatively stable. Three of the subjects had higher velocities on receding targets; one was faster on approaching targets. The group mean velocity increased over the seven days of the study. In keeping with the trend to faster dynamics over the seven days, both gain and phase lag improved.

Randle, R. J.↗
DOE OSTI2017

Na-Montmorillonite Edge Structure and Surface Complexes: An Atomistic Perspective

The edges of montmorillonite (MMT) react strongly with metals and organic matter, but the atomic structure of the edge and its surface complexes are not unambiguous since the experimental isolation of the edge is challenging. In this study, we introduce an atomistic model of a Na MMT edge that is suitable for classical molecular dynamics (MD) simulations, in particular for the B edge, a representative edge surface of 2:1 phyllosilicates. Our model possesses the surface groups identified through density functional theory (DFT) geometry optimizations performed with variation in the structural charge deficit and Mg substitution sites. The edge structure of the classical MD simulations agreed well with previous DFT-based MD simulation results. Our MD simulations revealed an extensive H-bond network stabilizing the Na-MMT edge surface, which required an extensive simulation trajectory. Some Na counter ions formed inner-sphere complexes at two edge sites. The stronger edge site coincided with the exposed vacancy in the dioctahedral sheet; a weaker site was associated with the cleaved hexagonal cavity of the tetrahedral sheet. The six-coordinate Na complexes were not directly associated with the Mg edge site. Our simulations have demonstrated the heterogeneous surface structures, the distribution of edge surface groups, and the reactivity of the MMT edge.

58 GEOSCIENCES↗
DOE OSTI2025

Tuning the Lifetimes of Photoinduced Deligation in a Metal–Organic Framework via Linker Functionalization

Recently photoinduced dynamic ligation in a metal–organic frameworks (MOFs) was reported, where a long-lived charge-transfer excited state (ca. 30 μs) featuring partial dissociation between the carboxylate linker and metal-based node was probed by time-resolved infrared (TRIR) spectroscopy. The study offers a new mechanistic perspective to evaluate the potential contribution from the excited state molecular configuration to the performance of MOF photocatalysts. In this work, by employing MIL-101(Fe) as the study platform, we have further explored the influence of intramolecular interactions on the stability of relevant excited states and demonstrated the effective tuning of their lifetimes through the incorporation of different functional groups into the system. The correlations between the varied excited state lifetimes and coordination configurations with specific functional groups (−NH 2 or −NO 2 ) was inferred from the analyses of infrared spectroscopic data and theoretical calculations, revealing the essential role of the intramolecular interactions (i.e., between the added functional groups and the carboxylate group) in the modulation of system energetics. Overall, the work presents a pathway to tune the excited state dynamics and expands the knowledge regarding the photoinduced dynamic ligation in carboxylate-based MOFs.

excited states↗
DOE OSTI2014

Revisiting the relaxation dynamics of isolated pyrrole

Herein, the interpretation of the femtosecond-scale temporal evolution of the pyrrole ion signal, after excitation in the 267–217 nm interval, recently published by our group [R. Montero, A. Peralta Conde, V. Ovejas, M. Fernández-Fernández, F. Castaño, J. R. Vázquez de Aldana, and A. Longarte, J. Chem. Phys.137, 064317 (2012)] is re-visited. The observation of a shift in the pyrrole{sup +} transient respect to zero delay reference, initially attributed to ultrafast dynamics on the πσ{sup *} type state (3s a{sub 1} ← π 1a{sub 2}), is demonstrated to be caused by the existence of pump + probe populated states, along the ionization process. The influence of these resonances in pump-prone ionization experiments, when multi-photon probes are used, and the significance of a proper zero-time reference, is discussed. The possibility of preparing the πσ{sup *} state by direct excitation is investigated by collecting 1 + 1 photoelectron spectra, at excitation wavelengths ranging from 255 to 219 nm. No conclusive evidences of ionization through this state are found.

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

Adapting SAFT-γ perturbation theory to site-based molecular dynamics simulation. II. Confined fluids and vapor-liquid interfaces

In this work, a new classical density functional theory is developed for group-contribution equations of state (EOS). Details of implementation are demonstrated for the recently-developed SAFT-γ WCA EOS and selective applications are studied for confined fluids and vapor-liquid interfaces. The acronym WCA (Weeks-Chandler-Andersen) refers to the characterization of the reference part of the third-order thermodynamic perturbation theory applied in formulating the EOS. SAFT-γ refers to the particular form of “statistical associating fluid theory” that is applied to the fused-sphere, heteronuclear, united-atom molecular models of interest. For the monomer term, the modified fundamental measure theory is extended to WCA-spheres. A new chain functional is also introduced for fused and soft heteronuclear chains. The attractive interactions are taken into account by considering the structure of the fluid, thus elevating the theory beyond the mean field approximation. The fluctuations of energy are also included via a non-local third-order perturbation theory. The theory includes resolution of the density profiles of individual groups such as CH{sub 2} and CH{sub 3} and satisfies stoichiometric constraints for the density profiles. New molecular simulations are conducted to demonstrate the accuracy of each Helmholtz free energy contribution in reproducing the microstructure of inhomogeneous systems at the united-atom level of coarse graining. At each stage, comparisons are made to assess where the present theory stands relative to the current state of the art for studying inhomogeneous fluids. Overall, it is shown that the characteristic features of real molecular fluids are captured both qualitatively and quantitatively. For example, the average pore density deviates ∼2% from simulation data for attractive pentadecane in a 2-nm slit pore. Another example is the surface tension of ethane/heptane mixture, which deviates ∼1% from simulation data while the theory reproduces the excess accumulation of ethane at the interface.

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

Why genetic modification of lignin leads to low-recalcitrance biomass

Genetic modification of plants via down-regulation of cinnamyl alcohol dehydrogenase leads to incorporation of aldehyde groups in the lignin polymer. Moreover, the resulting lignocellulosic biomass has increased bioethanol yield. However, a molecular-scale explanation of this finding is currently lacking. We perform molecular dynamics simulation of the copolymer with hemicellulose of wild type and the genetically modified lignin, in aqueous solution. We find that the non-covalent association with hemicellulose of lignin containing aldehyde groups is reduced compared to the wild-type. This phase separation may increase the cell wall porosity in the mutant plants, thus explaining their easier deconstruction to biofuels. The thermodynamic origin of the reduced lignin-hemicellulose association is found to be a more favorable self-interaction energy and less favorable interaction with hemicellulose for the mutant lignin. Furthermore, reduced hydration water density fluctuations are found for the mutant lignin, implying a more hydrophobic lignin surface. Our results provide a detailed description of how aldehyde incorporation makes lignin more hydrophobic and reduces its association with hemicellulose, thus suggesting that increased lignin hydrophobicity may be an optimal characteristic required for improved biofuel production.

09 BIOMASS FUELS↗
DOE OSTI2020

Atomic scale understanding of organic anion separations using ion-exchange resins

A combination of ab initio and classical molecular dynamic simulations was used to explore the adsorption/desorption and diffusion characteristics of ion-exchange resins for extraction of organic anions in electrically-driven separation processes. We considered two classes of carboxylate mixtures that are commonly encountered in bioprocessing separations: a short chain fatty acid mixture (acetate/butyrate) and an aromatic mixture (ferulate/coumarate). The suitability of several resin materials including PFC100E, IRC86, PFA444 and IRA67 was interrogated. The decomposition of the interaction energies by the symmetry-adapted perturbation theory and the classical molecular dynamic simulations of organic diffusion together reveal that the geometries of the organic anions and the functional groups of the resins, as well as their Columbic interactions, are the controlling factors in the diffusion process of the organic compounds in these resins. Additionally, classical simulations also show that modifying the functionality of resin beads, the magnitude of electric fields, and the ratio of organic mixtures may provide an effective way to control the diffusion rate and obtain selective separation of these organic mixtures. Finally, a general suggestion for favorable separation conditions is summarized.

36 MATERIALS SCIENCE↗
DOE OSTI2017

On properties of low-lying spin-1 hadron resonances

Properties of low-lying spin-1 hadron resonances are described in the review. It is shown how the Nambu-Jona-Lasinio model can be extended in the chiral invariant way by new tensor interactions. New mass formulas are obtained, which are not based on unitary symmetry groups but involve particles from different multiplets even with opposite parity. They all are in good agreement with experimental data. Dynamic properties of spin-1 mesons confirmed by the calculations performed using the QCD sum rule technique and the lattice calculations are understood and explained.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

Chromium Isotopic Evidence for Mixing of NC and CC Reservoirs in Polymict Ureilites: Implications for Dynamical Models of the Early Solar System

Nucleosynthetic isotope anomalies show that the first few million years of solar system history were characterized by two distinct cosmochemical reservoirs, CC (carbonaceous chondrites and related differentiated meteorites) and NC (the terrestrial planets and all other groups of chondrites and differentiated meteorites), widely interpreted to correspond to the outer and inner solar system, respectively. At some point, however, bulk CC and NC materials became mixed, and several dynamical models offer explanations for how and when this occurred. We use xenoliths of CC materials in polymict ureilite (NC) breccias to test the applicability of such models. Polymict ureilites represent regolith on ureilitic asteroids but contain carbonaceous chondrite-like xenoliths. We present the first 54 Cr isotope data for such clasts, which, combined with oxygen and hydrogen isotopes, show that they are unique CC materials that became mixed with NC materials in these breccias. It has been suggested that such xenoliths were implanted into ureilites by outer solar system bodies migrating into the inner solar system during the gaseous disk phase ~3–5 Myr after CAI, as in the "Grand Tack" model. However, combined textural, petrologic, and spectroscopic observations suggest that they were added to ureilitic regolith at ~50–60 Myr after CAI, along with ordinary, enstatite, and Rumuruti-type chondrites, as a result of the breakup of multiple parent bodies in the asteroid belt at this time. This is consistent with models for an early instability of the giant planets. The C-type asteroids from which the xenoliths were derived were already present in inner solar system orbits.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The Arecibo Galaxy Environment Survey. XII. Optically Dark H i Clouds in the Leo I Group

Using data from the Arecibo Galaxy Environment Survey, we report the discovery of five H i clouds in the Leo I group without detected optical counterparts. Three of the clouds are found midway between M96 and M95, one is only from the southeast side of the well-known Leo Ring, and the fifth is relatively isolated. H i masses range from 2.6 × 10 6 M ⊙ to 9.0 × 10 6 M ⊙ , and velocity widths (W50) range from 16 to 42 km s -1 . Although a tidal origin is the most obvious explanation, this formation mechanism faces several challenges. For the most isolated cloud, the difficulties are its distance from neighboring galaxies and the lack of any signs of disturbance in the H i disks of those systems. Some of the clouds also appear to follow the baryonic Tully–Fisher relation between mass and velocity width for normal, stable galaxies, which is not expected if they are tidal in origin. Three clouds are found between M96 and M95 that have no optical counterparts but have otherwise similar properties and locations to the optically detected galaxy LeG 13. While overall we favor a tidal debris scenario to explain the clouds, we cannot rule out a primordial origin. If the clouds were produced in the same event that gave rise to the Leo Ring, they may provide important constraints on any model attempting to explain that structure.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Non-adiabatic dynamics of isolated green fluorescent protein chromophore anion

On-the-fly ab initio molecular dynamics calculations have been performed to investigate the relaxation mechanism of green fluorescent protein chromophore anion under vacuum. The CASSCF surface hopping simulation method based on Zhu-Nakamura theory is applied to present the real-time conformational changes of the target molecule. The static calculations and dynamics simulation results suggest that not only the twisting motion around bridging bonds between imidazolinone and phenoxy groups but the strength mode of C=O and pyramidalization character of bridging atom are major factors on the ultrafast fluorescence quenching process of the isolated chromophore anion. The abovementioned factors bring the molecule to the vicinity of conical intersections on its potential energy surface and to finish the internal conversion process. A Hula-like twisting pattern is displayed during the relaxation process and the entire decay process disfavors a photoswitching pattern which corresponds to cis-trans photoisomerization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2013

Surface Charge Densities and Acidities of Biogeochemically Important Organic Adlayers at Mineral/Water Interfaces Studied by Nonlinear Optics

At a given bulk solution pH, mineral/water interfaces contain a corresponding number of charged and neutral species consisting of either SiOH, SiO - and SiOH 2 + groups in the case of fused quartz or of Si-R-COOH and Si-R-COO - groups in the case of the carboxylic acid-functionalized fused quartz/water interfaces. In the "$\chi^{(3)}$ method", as it has been termed by Eisenthal and co-workers who pioneered it and which is related to electric field induced SHG (EFISH), the SHG E-field depends on the interfacial potential that is produced by the interfacial charges. In the $\chi^{(3)}$ method, the SHG E-field is modeled with the familiar second-order response11 to which one adds a third-order term according to E SHG =$\chi^{(2)}$ E ω E ω + $\chi^{(3)}$ E ω E ω Φ o . The third order response is given by the product of the third order nonlinear susceptibility, $\chi^{(3)}$, the two applied electromagnetic probe fields oscillating at frequency ω, E ω , and the interfacial potential, Φ o , which is produced by the interfacial charges, the corresponding spatial distribution of the counter charges, and dipolar arrays of aligned water molecules, whose structure and dynamics have been studied using sum frequency generation. Note that the localization of the protonatable and deprotonatable groups at the interface and the high sensitivity of the $\chi^{(3)}$ method to the Φ o make the experiment interface-specific. In addition, the signal detection formalism can be viewed as a self-heterodyned detection scheme in which the second order response would be the local oscillator and the third order response would be the signal. As part of work focusing on metal ion adsorption to oxide/water interfaces, we published $\chi^{(3)}$ charge screening experiments carried out on fused quartz/water and single crystal α-alumina/water interfaces that agree very well with data by Eisenthal and coworkers as well as Higgins et al.

58 GEOSCIENCES↗
DOE OSTI2012

A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation

Lipopolysaccharides (LPS) comprise the outermost layer of the Gram-negative bacteria cell envelope. Packed onto a lipid layer, the outer membrane displays remarkable physical-chemical differences compared to cell membranes. The carbohydrate-rich region confers a membrane asymmetry that underlies many biological processes such as endotoxicity, antibiotic resistance, and cell adhesion. Furthermore, unlike membrane proteins from other sources, integral outer-membrane proteins do not consist of transmembrane α helices; instead they consist of antiparallel β-barrels, which highlights the importance of the LPS membrane as a medium. In this work, we present an extension of the GLYCAM06 force field that has been specifically developed for LPS membranes using our Wolf2Pack program. This new set of parameters for lipopolysaccharide molecules expands the GLYCAM06 repertoire of monosaccharides to include phosphorylated N- and O-acetylglucosamine, 3-deoxy-D-manno-oct-2- ulosonic acid, L-glycero-D-manno-heptose and its O-carbamoylated variant, and N-alanine-D-galactosamine. A total of 1 µs of molecular dynamics simulations of the rough LPS membrane of Pseudomonas aeruginosa PA01 is used to showcase the added parameter set. The equilibration of the LPS membrane is shown to be signi!cantly slower compared to phospholipid membranes, on the order of 500 ns. It is further shown that water molecules penetrate the hydrocarbon region up to the terminal methyl groups, much deeper than commonly observed for phospholipid bilayers, and in agreement with neutron diffraction measurements. A comparison of simulated structural, dynamical, and electrostatic properties against corresponding experimentally available data shows that the present parameter set reproduces well the overall structure and the permeability of LPS membranes in the liquid-crystalline phase.

59 BASIC BIOLOGICAL SCIENCES↗