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At least 307 records · Page 17

A modular and extensible CHARMM-compatible model for all-atom simulation of polypeptoids

Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics. Extension of this force field to new peptoid side chains has historically required reparameterization of side chain bonded interactions against ab initio data. This fitting protocol improves the accuracy of the force field but is also burdensome and precludes modular extensibility of the model to arbitrary peptoid sequences. In this work, we develop and demonstrate a Modular Side Chain CGenFF-NTOID (MoSiC-CGenFF-NTOID) as an extension of CGenFF-NTOID employing a modular decomposition of the peptoid backbone and side chain parameterizations, wherein arbitrary side chains within the large family of substituted methyl groups (i.e., –CH 3 , –CH 2 R, –CHRR', and –CRR'R") are directly ported from CGenFF. We validate this approach against ab initio calculations and experimental data to develop a MoSiC-CGenFF-NTOID model for all 20 natural amino acid side chains along with 13 commonly used synthetic side chains and present an extensible paradigm to efficiently determine whether a novel side chain can be directly incorporated into the model or whether refitting of the CGenFF parameters is warranted. We make the model freely available to the community along with a tool to perform automated initial structure generation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Targeted energy transfer in laminar vortex-induced vibration of a sprung cylinder with a nonlinear dissipative rotator

We computationally investigate the dynamics of a linearly-sprung circular cylinder immersed in an incompressible flow and undergoing transverse vortex-induced vibration (VIV), to which is attached a rotational nonlinear energy sink (NES) consisting of a mass that freely rotates at constant radius about the cylinder axis, and whose motion is restrained by a rotational linear viscous damper. The inertial coupling between the rotational motion of the attached mass and the rectilinear motion of the cylinder is “essentially nonlinear”, which, in conjunction with dissipation, allows for one-way, nearly irreversible targeted energy transfer (TET) from the oscillating cylinder to the nonlinear dissipative attachment. At the intermediate Reynolds number , the NES-equipped sprung cylinder undergoes repetitive cycles of slowly decaying oscillations punctuated by intervals of chaotic instabilities. During the slowly decaying portion of each cycle, the dynamics of the cylinder is regular and, for large enough values of the ratio of the NES mass to the total mass (i.e., NES mass plus cylinder mass), can lead to significant vortex street elongation with partial stabilization of the wake. As approaches zero, no such vortex elongation is observed and the wake patterns appear similar to that for a sprung cylinder with no NES. Here we apply proper orthogonal decomposition (POD) to the velocity flow field during a slowly decaying portion of the solution and show that, in situations where vortex elongation occurs, the NES, though not in direct contact with the surrounding fluid, has a drastic effect on the underlying flow structures, imparting significant and continuous passive redistribution of energy among POD modes. We construct a POD-based reduced-order model for the lift coefficient to characterize energy transactions between the fluid and the cylinder throughout the slowly decaying cycle. We introduce a quantitative signed measure of the work done by the fluid on the cylinder over one quasi-period of the slowly decaying response and find that vortex elongation is associated with a sign change of that measure, indicating that a reversal of the direction of energy transfer, with the cylinder “leaking energy back” to the flow, is responsible for partial stabilization and elongation of the wake. We interpret these findings in terms of the spatial structure and energy distribution of the POD modes, and relate them to the mechanism of transient resonance capture into a slow invariant manifold of the fluid–structure interaction dynamics.

42 ENGINEERING↗

Microbial Models for Simulating Soil Carbon Dynamics: A Review

Abstract Soils store the largest amount of carbon (C) in the biosphere, and the C pool in soil is critical to the global C balance. Numerous microbial models have been developed over the last few decades to represent microbial processes that regulate the responses of soil organic carbon (SOC) to climate change. However, the representation of microbial processes varies, and how microbial processes are incorporated into SOC models has not been well explored. Here, we reviewed 71 microbial models to characterize the microbial processes incorporated into SOC models and analyzed variations in mechanistic complexity. We revealed that (a) four processes (microbial‐mediated decomposition, mineral interaction, microbial necromass recycling, and active and dormant microbial dynamics) are commonly incorporated in microbial models, (b) ∼48% of models simulate only one microbial process (i.e., microbial‐mediated decomposition) and 35% of models simulate two microbial processes: for example, microbial‐mediated decomposition and mineral interaction, (c) more than 80% microbial models use nonlinear equations, such as forward Michaelis‐Menten kinetics, to represent SOC decomposition, (d) the concept of persistence of SOC due to its intrinsic properties has been replaced by organo‐mineral interaction (∼39% of microbial models) that protects SOC from decomposition, and (e) various temperature and moisture modifiers and pH effects have been used to explain the environmental effect on microbial processes. In the future, to realistically incorporate microbial processes into Earth System Models, it is imperative to identify experimental evidence on rate limitation processes and firmly ground model structure on the field and laboratory data.

Environmental Sciences & Ecology↗

Bulge growth and quenching since z = 2.5 in CANDELS/3D-HST

Exploiting the deep high-resolution imaging of all five CANDELS fields, and accurate redshift information provided by 3D-HST, we investigate the relation between structure and stellar populations for a mass-selected sample of 6764 galaxies above 10{sup 10} M {sub ☉}, spanning the redshift range 0.5 < z < 2.5. For the first time, we fit two-dimensional models comprising a single Sérsic fit and two-component (i.e., bulge + disk) decompositions not only to the H-band light distributions, but also to the stellar mass maps reconstructed from resolved stellar population modeling. We confirm that the increased bulge prominence among quiescent galaxies, as reported previously based on rest-optical observations, remains in place when considering the distributions of stellar mass. Moreover, we observe an increase of the typical Sérsic index and bulge-to-total ratio (with median B/T reaching 40%-50%) among star-forming galaxies above 10{sup 11} M {sub ☉}. Given that quenching for these most massive systems is likely to be imminent, our findings suggest that significant bulge growth precedes a departure from the star-forming main sequence. We demonstrate that the bulge mass (and ideally knowledge of the bulge and total mass) is a more reliable predictor of the star-forming versus quiescent state of a galaxy than the total stellar mass. The same trends are predicted by the state-of-the-art, semi-analytic model by Somerville et al. In this model, bulges and black holes grow hand in hand through merging and/or disk instabilities, and feedback from active galactic nuclei shuts off star formation. Further observations will be required to pin down star formation quenching mechanisms, but our results imply that they must be internal to the galaxies and closely associated with bulge growth.

79 ASTRONOMY AND ASTROPHYSICS↗

Ab initio calculation of the electronic absorption spectrum of liquid water

The electronic absorption spectrum of liquid water was investigated by coupling a one-body energy decomposition scheme to configurations generated by classical and Born-Oppenheimer Molecular Dynamics (BOMD). A Frenkel exciton Hamiltonian formalism was adopted and the excitation energies in the liquid phase were calculated with the equation of motion coupled cluster with single and double excitations method. Molecular dynamics configurations were generated by different approaches. Classical MD were carried out with the TIP4P-Ew and AMOEBA force fields. The BLYP and BLYP-D3 exchange-correlation functionals were used in BOMD. Theoretical and experimental results for the electronic absorption spectrum of liquid water are in good agreement. Emphasis is placed on the relationship between the structure of liquid water predicted by the different models and the electronic absorption spectrum. The theoretical gas to liquid phase blue-shift of the peak positions of the electronic absorption spectrum is in good agreement with experiment. The overall shift is determined by a competition between the O–H stretching of the water monomer in liquid water that leads to a red-shift and polarization effects that induce a blue-shift. The results illustrate the importance of coupling many-body energy decomposition schemes to molecular dynamics configurations to carry out ab initio calculations of the electronic properties in liquid phase.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NSR&D FY14 Final Report: Friction/Impact Modeling

The LANL-developed CartaBlanca code uses advanced techniques, including the Dual Domain Material Point (DDMP) method, to calculate fluid, solid motions and fluid-structure interactions. In the last year we have implemented the ViscoSCRAM material model in CartaBlanca based on Clements’ Abaqus-Explicit Finite Element implementation. In this fiscal year, we study numerical properties of this implementation. To consider coupled mechanical, thermal and chemical effects, we have implemented Henson’s HE decomposition model to couple with the thermal and mechanical packages in CartaBlanca. We have also developed porous media flow modules to consider heat convection effects of the reaction product gas inside pores of HE. The next immediate step is to perform numerical simulations to study interactions among these different mechanisms. We have started such calculation and obtained interesting initial results at the end of this fiscal year.

97 MATHEMATICS AND COMPUTING↗

Advanced Microscopy and Spectroscopy for Probing and Optimizing Electrode-Electrolyte Interphases in High Energy Lithium Batteries (Final Scientific/Technical Report)

The earliest developed LiCoO 2 layered oxide cathode material sparked the development of other layered cathode materials, dominating the positive electrode materials for lithium ion batteries. Within the practical operating conditions of today, the current generation layered oxide materials do not meet the future energy storage demands of 350 Wh kg -1 at cell level. Li-rich layered oxide (LRLO) materials have the potential to meet the high energy demands. Unlike the classical layered oxides, LRLO materials exhibit capacities that go beyond conventional topotactic mechanistic theoretical values. Despite its high capacities, this material has several challenges (voltage fading, structural instability, sluggish kinetics, cathode electrolyte interphase instability, etc.) that must be overcome in order to reach commercialization. In the past five years, our research group has made great progress on developing advanced characterization techniques coupled with atomic scale modeling to properly characterize the dynamic phenomena that govern the performance limitations of LRLO materials. Furthermore, our efforts have guided the material synthesis and surface modification to improve capacity retention. By carefully controlling the oxygen activities through the creation of uniform oxygen vacancies, we were able to avoid structural decomposition in LRLO. Our materials deliver a discharge capacity as high as 306 mAh g -1 with an initial coulombic efficiency of 90.6%. Furthermore, they do not exhibit obvious capacity decay with a reversible capacity over 300 mAh g -1 after 100 cycles at 0.1 C-rate. Our approach demonstrates the critical needs for advanced diagnosis and characterization. It is through the in-depth understanding of these high voltage cathode materials at atomistic and molecular level and their dynamic changes during the operation of batteries; we can successfully formulate strategies to further optimize this class of cathode materials, especially for the voltage instabilities. The diagnostic tools developed here can also be leveraged to study anode materials such as Li metal anode. The challenge of probing Li metal is the low dose tolerance (high beam sensitivity) of Li metal. We will have to apply cryogenic method (low-temperature) and low-dose electron microscopy and specialized camera to enable the characterization of the lithium metal.

25 ENERGY STORAGE↗

Analysis of limit cycles in control systems for joint dominated structures

An approach to the modeling of limit cycles due to joint nonlinearities in large joint dominated space structures is presented which makes it possible to predict limit cycles and determine their stability. An actively controlled truss structure with nonlinear joints is modeled as a linear system with nonlinear feedback by separating the joint load-displacement characteristics into a linear part, which prevails at large displacements, and a nonlinear part. By replacing the joints by their linear parts, it is possible to perform a standard model decomposition which yields a reduced order linear model. Linear control laws can be easily included into the linear part of the system; nonlinear control laws can be implemented but they must be fed back to the linear model. The modeling approach described here allows straightforward limit cycle analysis.

Mercadal, M.↗

Decomposition of methane diluted with inert gas in an RF discharge cell

Decomposition of methane using non-thermal plasmas is an attractive route for producing hydrogen-rich gases and valuable carbon nanomaterials. Understanding how plasma discharge modes influence methane decomposition in optimizing plasma-assisted chemical conversion remains unexplored. This study explores the coupling between the discharge structure and product selectivity in RF capacitively coupled discharges operating in methane/inert gas mixtures in the pressure range of 2–3 torr. Under our experimental conditions the discharge exhibits mode transitions from uniform to striated in Ar and Kr and from diffuse to contracted in Ar and Kr with <5% CH 4 . The discharges in He and Ne remained uniform under our operating conditions, and their mixtures with CH 4 remained diffuse. A 0-d model for Ar/CH 4 discharge established a threshold for contraction while also asserting the importance of Ar$^{*}_{\textrm{m}}$ in the dissociation and ionization processes. The highest degree of methane decomposition, >99.7% with the main products of acetylene and graphitized solid carbon was achieved in the contracted discharge mode for both Kr or Ar with ⩽5% CH 4 . We demonstrate that contraction can play a crucial role in the effective decomposition of methane with value-added products and that both the electronic and thermal properties of plasma gas are responsible for this effect.

RF plasma↗

Canonical Structure and Orthogonality of Forces and Currents in Irreversible Markov Chains

We discuss a canonical structure that provides a unifying description of dynamical large deviations for irreversible finite state Markov chains (continuous time), Onsager theory, and Macroscopic Fluctuation Theory (MFT). For Markov chains, this theory involves a non-linear relation between probability currents and their conjugate forces. Within this framework, we show how the forces can be split into two components, which are orthogonal to each other, in a generalised sense. This splitting allows a decomposition of the pathwise rate function into three terms, which have physical interpretations in terms of dissipation and convergence to equilibrium. Similar decompositions hold for rate functions at level 2 and level 2.5. These results clarify how bounds on entropy production and fluctuation theorems emerge from the underlying dynamical rules. We discuss how these results for Markov chains are related to similar structures within MFT, which describes hydrodynamic limits of such microscopic models.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

MGS Radio Science Electron Density Profiles: Interannual Variability and Implications for the Martian Neutral Atmosphere

Martian electron density profiles provided by the Mars Global Surveyor (MGS) Radio Science (RS) experiment over the 95-200 km altitude range indicate what the height of the electron peak and the longitudinal structure of the peak height are sensitive indicators of the physical state of the Mars lower and upper atmospheres. The present analysis is carried out on five sets of occultation profiles, all at high solar zenith angles (SZA). Variations spanning 2 Martian years are investigated near aphelion conditions at high northern latitudes (64.7 - 77.6 N) making use of four of these data sets. A mean ionospheric peak height of 133.5 - 135 km is obtained near SZA = 78 - 82 deg.; a corresponding mean peak density of 7.3 - 8.5 x l0(exp 4)/ qu cm is also measured during solar moderate conditions at Mars. Strong wave number 2 - 3 oscillations in peak heights are consistently observed as a function of longitude over the 2 Martian years. These observed ionospheric features are remarkably similar during aphelion conditions 1 Martian year apart. This year-to-year repeatability in the thermosphere-ionosphere structure is consistent with that observed in multiyear aphelion temperature data of the Mars lower atmosphere. Coupled Mars general circulation model (MGCM) and Mars thermospheric general circulation model (MTGCM) codes are run for Mars aphelion conditions, yielding mean and longitude variable ionospheric peak heights that reasonably match RS observations. A tidal decomposition of MTGCM thermospheric densities shows that observed ionospheric wave number 3 features are linked to a non-migrating tidal mode with semidiurnal period (sigma = 2) and zonal wave number 1 (s = -1) characteristics. The height of this photochemically determined ionospheric peak should be monitored regularly.

Bougher, S. W.↗

Multifidelity Neural Network Formulations for Prediction of Reactive Molecular Potential Energy Surfaces

Here, this paper focuses on the development of multifidelity modeling approaches using neural network surrogates, where training data arising from multiple model forms and resolutions are integrated to predict high-fidelity response quantities of interest at lower cost. We focus on the context of quantum chemistry and the integration of information from multiple levels of theory. Important foundations include the use of symmetry function-based atomic energy vector constructions as feature vectors for representing structures across families of molecules and single-fidelity neural network training capabilities that learn the relationships needed to map feature vectors to potential energy predictions. These foundations are embedded within several multifidelity topologies that decompose the high-fidelity mapping into model-based components, including sequential formulations that admit a general nonlinear mapping across fidelities and discrepancy-based formulations that presume an additive decomposition. Methodologies are first explored and demonstrated on a pair of simple analytical test problems and then deployed for potential energy prediction for C 5 H 5 using B2PLYP-D3/6-311++G(d,p) for high-fidelity simulation data and Hartree–Fock 6-31G for low-fidelity data. For the common case of limited access to high-fidelity data, our computational results demonstrate that multifidelity neural network potential energy surface constructions achieve roughly an order of magnitude improvement, either in terms of test error reduction for equivalent total simulation cost or reduction in total cost for equivalent error.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fast high-resolution prediction of multi-phase flow in fractured formations

The success of a thermal water flood for enhanced oil recovery (EOR) depends on a detailed representation of the geometrical and hydraulic properties of the fracture network, which induces discrete, channelized flow behavior. The resulting high-resolution model is typically computationally very demanding. Here, we use the Proper Orthogonal Decomposition Mapping Method to reconstruct high-resolution solutions based on efficient low-resolution solutions. The method requires training a reduced order model (ROM) using high- and low-resolution solutions determined for a relatively short simulation time. For a cyclic EOR operation, the oil production rate and the heterogeneous structure of the oil saturation are accurately reproduced even after 105 cycles, reducing the computational cost by at least 85%. Finally, the method described is general and can be potentially utilized with any multiphase flow model.

54 ENVIRONMENTAL SCIENCES↗

Socioeconomic Effects of Pension Spending: Evidence from Spain

The purpose of this study is to provide broader understanding of the significant role that the pension system has in the Spanish economy by estimating the sectoral production, employment and income sustained by pensioners' consumption. Based on input-output tables by the World Input-Output Database and consumption data from the Household Budget Survey by the Spanish Statistical Office, a demoeconomic model is applied to quantify the direct impacts, indirect impacts from interindustry links and induced impacts from income-consumption connections over a nine-year period (2006–2014). Then, the factors driving the evolution of total output, employment and value added during such period have been examined by using structural decomposition analysis. The growing participation of consumption by pensioner households in final demand had proven crucial during the 2008 crisis to alleviate the negative trend in production and employment derived from the collapse in consumption suffered by the rest of households. Determining the underlying factors driving changes in both employment and income during the 2008 crisis can be of interest in political decision-making on the sustainability of the Spanish pension system. The results of estimating both the employment and income supported by pensioners' consumption reveal the significant stabilizing effect of the public spending on pensions, particularly during the 2008 crisis. The current Spanish approach of attaining the pension system sustainability by merely reducing social protection costs ignores the adverse consequences of a lower pensioners' demand. This paper addresses an alternative view in which pension spending is not considered a burden on economic growth but rather a means of improving the level of production and employment.

employment↗

Noise transmission into enclosures

This paper describes analytical and experimental studies of noise transmission into rectangular and cylindrical enclosures. The solutions of the governing acoustic-structural equations are developed by modal decomposition of structural vibrations and the interior acoustic field. Particular attention is directed toward the low frequencies, that is, frequencies up through the first few structural and cavity resonant modes. The structural vibrations are driven by the external acoustic and/or mechanical point loads which are taken to be Gaussian stationary random processes. The structural models include rectangular panels and cylindrical shells.

Vaicaitis, R.↗

A prototype computer-aided modelling tool for life-support system models

Based on the canonical decomposition of physical-chemical-biological systems, a prototype kernel has been developed to efficiently model alternative life-support systems. It supports (1) the work in an interdisciplinary group through an easy-to-use mostly graphical interface, (2) modularized object-oriented model representation, (3) reuse of models, (4) inheritance of structures from model object to model object, and (5) model data base. The kernel is implemented in Modula-II and presently operates on an IBM PC.

Preisig, H. A.↗

Dynamic Analysis and Control of Lightweight Manipulators with Flexible Parallel Link Mechanisms

The objective is the theoretical analysis and the experimental verification of dynamics and control of a two link flexible manipulator with a flexible parallel link mechanism. Nonlinear equations of motion of the lightweight manipulator are derived by the Lagrangian method in symbolic form to better understand the structure of the dynamic model. The resulting equation of motion have a structure which is useful to reduce the number of terms calculated, to check correctness, or to extend the model to higher order. A manipulator with a flexible parallel link mechanism is a constrained dynamic system whose equations are sensitive to numerical integration error. This constrained system is solved using singular value decomposition of the constraint Jacobian matrix. Elastic motion is expressed by the assumed mode method. Mode shape functions of each link are chosen using the load interfaced component mode synthesis. The discrepancies between the analytical model and the experiment are explained using a simplified and a detailed finite element model.

Lee, Jeh Won↗

Integrated controls-structures optimization of a large space structure

General-purpose control and structural codes are applied to a large detailed structural model including objective and constraint functions derived from actual design specifications. The approach is to divide the problem into a controls optimization step, a structural optimization step, and a system level coordination step. The objective is to minimize mass and power consumption with constraints on vibration characteristics, strength, and damping. This decomposition and optimization approach significantly enhances the design of a structure based on the COFS-I Mast Flight System, which is selected as a demonstration problem.

Pasula, S. L.↗