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At least 703 records · Page 39

Development of a coarse-grained molecular dynamics model for poly(dimethyl- co -diphenyl)siloxane

Polydimethylsiloxane is an important polymeric material with a wide range of applications. However, environmental effects like low temperature can induce crystallization in this material with resulting changes in its structural and dynamic properties. The incorporation of phenyl-siloxane components, e.g., as in a poly(dimethyl-co-diphenyl)siloxane random copolymer, is known to suppress such crystallization. Molecular dynamics (MD) simulations can be a powerful tool to understand such effects in atomistic detail. Unfortunately, all-atomistic molecular dynamics (AAMD) is limited in both spatial dimensions and simulation times it can probe. Here, to overcome such constraints and to extend to more useful length- and time-scales, we systematically develop a coarse-grained molecular dynamics (CGMD) model for the poly(dimethyl-co-diphenyl)siloxane system with bonded and non-bonded interactions determined from all-atomistic simulations by the iterative Boltzmann inversion (IBI) method. Additionally, we propose a lever rule that can be useful to generate non-bonded potentials for such systems without reference to the all-atomistic ground truth. Our model captures the structural and dynamic properties of the copolymer material with quantitative accuracy and is useful to study long-time dynamics of highly-entangled systems, sequence-dependent properties, phase behaviour, etc.

36 MATERIALS SCIENCE↗

The dynamical state of eROSITA clusters and its impact on the brightest cluster galaxy luminosity

The first Spectrum-Roentgen-Gamma (SRG) eROSITA public release contains 12 247 clusters and groups from its first 6 months of operation. We used the offset between the brightest cluster galaxy (BCG) and the X-ray peak ( D BCG − X ) to classify the cluster dynamical state of 3946 galaxy clusters and groups. We aim to investigate the evolution of the merger and relaxed cluster distributions with redshift and mass, and the distributions’ impact on the BCG. We used the X-ray peak from the eROSITA survey and the BCG position from the LS DR10 optical data, which includes the DECam eROSITA Survey optical data, to measure the D BCG − X offset. We modelled the distribution of D BCG − X , in units of R 500 , as the sum of two Rayleigh distributions representing the cluster’s relaxed and disturbed populations, and explored their evolution with redshift and mass. To explore the impact of the cluster’s dynamical state on the BCG luminosity, we separated the main sample according to the dynamical state. We defined clusters as relaxed if D BCG − X < 0.25R500, disturbed if D BCG − X > 0.5R500, and ‘diverse’ if 0.25R500 < D BCG − X < 0.5R500. We find no evolution of the merging fraction with redshift or mass. The width of the relaxed distribution increases with redshift, while the width of the two Rayleigh distributions decreases with mass. The analysis reveals that BCGs in relaxed clusters are brighter than BCGs in both the disturbed and diverse cluster populations. The most significant differences are found for high-mass clusters at higher redshifts. The results suggest that BCGs in low-mass clusters are less centrally bound than those in high-mass systems, irrespective of the dynamical state. Over time, BCGs in relaxed clusters progressively align with the potential centre. This alignment correlates with their luminosity growth relative to BCGs in dynamically disturbed clusters, underscoring the critical role of the cluster’s dynamical state in regulating BCG evolution.

galaxy clusters↗

Interference of electrical double layers: Confinement effects on structure, dynamics, and screening of ionic liquids

Ionic liquids are widely used as electrolytes in electronic devices in which they are subject to nanoconfinement within nanopores or nanofilms. Because the intrinsic width of an electrical double layer is on the order of several nanometers, nanoconfinement is expected to fundamentally alter the double layer properties. Furthermore, in confined systems, a large portion of the ions are interfacial, e.g., at the electrode interface, leading to significant deviations of electrostatic screening and ion dynamics as compared to bulk properties. In this article, we systematically investigate the interference between electrical double layers for nanoconfined ionic liquids and the resulting influence on the structure, dynamics, and screening behavior. We perform molecular dynamics simulations for the ionic liquids [BMIm + ][BF$^-_4$] and [BMIm + ][PF$^-_6$] confined between two flat electrodes at systematic separation distances between 1.5 nm and 4.5 nm for both conducting and insulating boundary conditions. We find that while ion dynamics is expectedly slower than in the bulk (by ~2 orders of magnitude), there is an unexpected non-linear trend with the confinement length that leads to a local maximum in dynamic rates at ~3.5–4.5 nm confinement. We show that this nonlinear trend is due to the ion correlation that arises from the interference between opposite double layers. We further evaluate confinement effects on the ion structure and capacitance and investigate the influence of electronic polarization of the ionic liquid on the resulting properties. This systematic evaluation of the connection between electrostatic screening and structure and dynamics of ionic liquids in confined systems is important for the fundamental understanding of electrochemical supercapacitors.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Physics-based compact modeling of electro-thermal memristors: Negative differential resistance, local activity, and non-local dynamical bifurcations

Leon Chua's Local Activity theory quantitatively relates the compact model of an isolated nonlinear circuit element, such as a memristor, to its potential for desired dynamical behaviors when externally coupled to passive elements in a circuit. However, the theory's use has often been limited to potentially unphysical toy models and analyses of small-signal linear circuits containing pseudo-elements (resistors, capacitors, and inductors), which provide little insight into required physical, material, and device properties. Furthermore, the Local Activity concept relies on a local analysis and must be complemented by examining dynamical behavior far away from the steady-states of a circuit. In this work, we review and study a class of generic and extended one-dimensional electro-thermal memristors (i.e., temperature is the sole state variable), re-framing the analysis in terms of physically motivated definitions and visualizations to derive intuitive compact models and simulate their dynamical behavior in terms of experimentally measurable properties, such as electrical and thermal conductance and capacitance and their derivatives with respect to voltage and temperature. Within this unified framework, we connect steady-state phenomena, such as negative differential resistance, and dynamical behaviors, such as instability, oscillations, and bifurcations, through a set of dimensionless nonlinearity parameters. In particular, we reveal that the reactance associated with electro-thermal memristors is the result of a phase shift between oscillating current and voltage induced by the dynamical delay and coupling between the electrical and thermal variables. We thus, demonstrate both the utility and limitations of local analyses to understand non-local dynamical behavior. Critically for future experimentation, the analyses show that external coupling of a memristor to impedances within modern sourcing and measurement instruments can dominate the response of the total circuit, making it impossible to characterize the response of an uncoupled circuit element for which a compact model is desired. However, these effects can be minimized by proper understanding of the Local Activity theory to design and utilize purpose-built instruments.

Brown, Timothy D. (ORCID:0000000347068355)↗

Fluid dynamic mathematical aspects of supernova remnants

Supernovae—explosions of stars—are a central problem in astrophysics since they contain information on the entire process of stellar evolution and nucleosynthesis. Rayleigh–Taylor (RT) and Richtmyer–Meshkov (RM) instabilities, developing during the supernova blast, lead to intense interfacial RT/RM mixing of the star's materials and couple astrophysical to atomic scales. This work analyzes some fluid dynamic mathematical aspects of the titanic task of supernova's blast. We handle mathematical challenges of RT/RM dynamics in supernova relevant conditions by directly linking the conservation laws governing RT/RM dynamics to symmetry-based momentum model, by exactly deriving the model parameters in the scale-dependent and scale-invariant regimes, and by exploring the special self-similar class for RT/RM interfacial mixing with variable accelerations. Here we reveal that RT/RM dynamics is strongly influenced by deterministic (the initial and the flow) conditions in the scale-dependent linear and nonlinear regimes and in the self-similar mixing regime. The theory outcomes are consistent with the observations of supernova remnants, explain the results of the scaled laboratory experiments in high energy density plasmas, and yield the design of future experiments for the accurate quantification of RT/RM dynamics in supernova relevant conditions. We find that from fluid dynamic mathematical perspectives, supernovae can be regarded as an astrophysical initial value problem. Along with the guidance of what explodes at microscopic scales, supernova remnants encapsulate information on the explosion hydrodynamics and the associated deterministic conditions at macroscopic scales. We urge such effects be considered in interpretations of the observational data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Large-scale molecular dynamics simulations of bubble collapse in water: Effects of system size, water model, and nitrogen

Molecular dynamics simulations in the microcanonical ensemble are performed to study the collapse of a bubble in liquid water using the single-site mW and the four-site TIP4P/2005 water models. To study system size effects, simulations for pure water systems are performed using periodically replicated simulation boxes with linear dimensions, L, ranging from 32 to 512 nm with the largest systems containing 8.7 × 10 6 and 4.5 × 10 9 molecules for the TIP4P/2005 and mW water models, respectively. The computationally more efficient mW water model allows us to reach converging behavior when the bubble dynamics results are plotted in reduced units, and the limiting behavior can be obtained through linear extrapolation in L –1 . Qualitative differences are observed between simulations with the mW and TIP4P/2005 water models, but they can be explained by the models’ differences in predicted viscosity and surface tension. Although bubble collapse occurs on time scales of only hundreds of picoseconds, the system sizes used here are sufficiently large to obtain bubble dynamics consistent with the Rayleigh–Plesset equation when using the models’ thermophysical properties as input. For the conditions explored here, extreme heating of the interfacial water molecules near the time of collapse is observed for the larger mW water systems (but the model underpredicts the viscosity), whereas heating is less pronounced for the TIP4P/2005 water systems because its larger viscosity contribution slows the collapse dynamics. The presence of nitrogen within the bubble only starts to affect bubble dynamics near the very end of the initial collapse, leading to an incomplete collapse and strong rebound for the mW water model. Although nitrogen is non-condensable at 300 K, it becomes highly compressed and reaches a liquid-like density near the collapse point. We find that the dissolution of nitrogen is much slower than the movement of the collapsing water front, and the re-expansion of the dense nitrogen droplet gives rise to bubble rebound. The incompatibility of the collapse and dissolution time scales should be considered for continuum-scale modeling of bubble dynamics. Finally, we also confirm that the diffusion coefficient for dissolved nitrogen is insensitive to pressure as the liquid transitions from a compressed to a stretched state.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Quantum simulation of Lindbladian dynamics via repeated interactions

The Lindblad equation generalizes the Schrödinger equation to quantum systems that undergo dissipative dynamics. The quantum simulation of Lindbladian dynamics is therefore non-unitary, preventing a naive application of state-of-the-art quantum algorithms. Here, we make use of an approximate correspondence between Lindbladian dynamics and evolution based on repeated interaction (RI) CPTP maps to write down a Hamiltonian formulation of the Lindblad dynamics and derive a rigorous error bound on the master equation. Specifically, we show that the number of interactions needed to simulate the Liouvillian within error e scales in most physical scenarios as . This is significant because the error in the Lindbladian approximation to the dynamics is not explicitly bounded in existing quantum algorithms for open system simulations. We then provide quantum algorithms to simulate RI maps using an iterative qubitization approach and Trotter–Suzuki formulas, and specifically show that for iterative qubitization the number of operations needed to simulate the dynamics (for a fixed value of ?) scales as in the limit where a0 (the coefficient 1-norm for the system and bath Hamiltonians) asymptotically dominates over the corresponding factor for the interaction Hamiltonian, which is often the case in weak coupling. This scaling would appear to be optimal if the complexity of ? is not considered, which underscores the importance of considering the error in the Liouvillian that we reveal in this work.

Quantum Computing↗

Predicting images for the dynamics of stellar clusters ( π-DOC ): a deep learning framework to predict mass, distance, and age of globular clusters

ABSTRACT Dynamical mass estimates of simple systems such as globular clusters (GCs) still suffer from up to a factor of 2 uncertainty. This is primarily due to the oversimplifications of standard dynamical models that often neglect the effects of the long-term evolution of GCs. Here, we introduce a new approach to measure the dynamical properties of GCs, based on the combination of a deep-learning framework and the large amount of data from direct N-body simulations. Our algorithm, π-DOC (Predicting Images for the Dynamics Of stellar Clusters) is composed of two convolutional networks, trained to learn the non-trivial transformation between an observed GC luminosity map and its associated mass distribution, age, and distance. The training set is made of V-band luminosity and mass maps constructed as mock observations from N-body simulations. The tests on π-DOC demonstrate that we can predict the mass distribution with a mean error per pixel of 27 per cent, and the age and distance with an accuracy of 1.5 Gyr and 6 kpc, respectively. In turn, we recover the shape of the mass-to-light profile and its global value with a mean error of 12 per cent, which implies that we efficiently trace mass segregation. A preliminary comparison with observations indicates that our algorithm is able to predict the dynamical properties of GCs within the limits of the training set. These encouraging results demonstrate that our deep-learning framework and its forward modelling approach can offer a rapid and adaptable tool competitive with standard dynamical models.

Chardin, Jonathan↗

CRAGE-mediated insertion of fluorescent chromosomal markers for accurate and scalable measurement of co-culture dynamics in Escherichia coli

Monitoring population dynamics in co-culture is necessary in engineering microbial consortia involved in distributed metabolic processes or biosensing applications. However, it remains difficult to measure strain-specific growth dynamics in high-throughput formats. This is especially vexing in plate-based functional screens leveraging whole-cell biosensors to detect specific metabolic signals. Here, we develop an experimental high-throughput co-culture system to measure and model the relationship between fluorescence and cell abundance, combining chassis-independent recombinase-assisted genome engineering (CRAGE) and whole-cell biosensing with a PemrR-green fluorescent protein (GFP) monoaromatic reporter used in plate-based functional screening. CRAGE was used to construct Escherichia coli EPI300 strains constitutively expressing red fluorescent protein (RFP) and the relationship between RFP expression and optical density (OD600) was determined throughout the EPI300 growth cycle. A linear equation describing the increase of normalized RFP fluorescence during deceleration phase was derived and used to predict biosensor strain dynamics in co-culture. Measured and predicted values were compared using flow cytometric detection methods. Induction of the biosensor lead to increased GFP fluorescence normalized to biosensor cell abundance, as expected, but a significant decrease in relative abundance of the biosensor strain in co-culture and a decrease in bulk GFP fluorescence. Taken together, these results highlight sensitivity of population dynamics to variations in metabolic activity in co-culture and the potential effect of these dynamics on the performance of functional screens in plate-based formats. The engineered strains and model used to evaluate these dynamics provide a framework for optimizing growth of synthetic co-cultures used in screening, testing and pathway engineering applications.

59 BASIC BIOLOGICAL SCIENCES↗

Dynamics of non-Gaussian fluctuations in model A

Motivated by the experimental search for the QCD critical point, we perform simulations of a stochastic field theory with purely relaxational dynamics (model A). We verify the expected dynamic scaling of correlation functions. Using a finite size scaling analysis, we obtain the dynamic critical exponent z = 2.026(56). We investigate time dependent correlation functions of higher moments M n (t) of the order parameter M(t) for n = 1, 2, 3, 4. We obtain dynamic scaling with the same critical exponent z for all n, but the relaxation constant depends on n. We also study the relaxation of M n (t) after a quench, where the simulation is initialized in the high temperature phase, and the dynamics is studied at the critical temperature T c . Finally, we find that the evolution does not follow simple scaling with the dynamic exponent z, and that it involves an early time rise followed by late stage relaxation.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

From ionic clusters dynamics to network constraints in ionic polymer solutions

Physical networks formed by ionizable polymers with ionic clusters as crosslinks are controlled by coupled dynamics that transcend from ionic clusters through chain motion to macroscopic response. Here, the coupled dynamics, across length scales, from the ionic clusters to the networks in toluene swollen polystyrene sulfonate networks, were directly correlated, as the electrostatic environment of the physical crosslinks was altered. The multiscale insight is attained by coupling neutron spin echo measurements with molecular dynamics simulations, carried out to times typical of relaxation of polymers in solutions. The experimental dynamic structure factor is in outstanding agreement with the one calculated from computer simulations, as the networks are perturbed by elevating the temperature and changing the electrostatic environment. In toluene, the long-lived clusters remain stable over hundreds of ns across a broad temperature range, while the polymer network remains dynamic. In conclusion, though the size of the clusters changes as the dielectric constant of the solvent is modified through the addition of ethanol, they remain stable but morph, enhancing the polymer chain dynamics.

36 MATERIALS SCIENCE↗

Defect Spirograph: Dynamical Behavior of Defects in Spatially Patterned Active Nematics

We report that topological defects in active liquid crystals can be confined by introducing gradients of activity. Here, we examine the dynamical behavior of two defects confined by a sharp gradient of activity that separates an active circular region and a surrounding passive nematic material. Continuum simulations are used to explain how the interplay among energy injection into the system, hydrodynamic interactions, and frictional forces governs the dynamics of topologically required self-propelling + 1/2 defects. Our findings are rationalized in terms of a phase diagram for the dynamical response of defects in terms of activity and frictional damping strength. Different regions of the underlying phase diagram correspond to distinct dynamical modes, namely immobile defects, steady rotation of defects, bouncing defects, bouncing-cruising defects, dancing defects, and multiple defects with irregular dynamics. These dynamic states raise the prospect of generating synchronized defect arrays for microfluidic applications.

36 MATERIALS SCIENCE↗

Real-Time Operator Evolution in Two and Three Dimensions via Sparse Pauli Dynamics

We study real-time operator evolution using sparse Pauli dynamics, a recently developed method for simulating expectation values of quantum circuits. On the examples of energy and charge diffusion in one-dimensional (1D) spin chains and sudden quench dynamics in the 2D transverse-field Ising model, it is shown that this approach can compete with state-of-the-art tensor network methods. We further demonstrate the flexibility of the approach by studying quench dynamics in the 3D transverse-field Ising model that is highly challenging for tensor network methods. For the simulation of expectation value dynamics starting in a computational basis state, we introduce an extension of sparse Pauli dynamics that truncates the growing sum of Pauli operators by discarding terms with a large number of X and Y matrices. This is validated by our 2D and 3D simulations. Finally, we argue that sparse Pauli dynamics is not only capable of converging challenging observables to high accuracy, but can also serve as a reliable approximate approach even when given only limited computational resources. Published by the American Physical Society 2025

Begušić, Tomislav (ORCID:0000000279424134)↗

Effect of Mechanical Deformation on the Dielectric Electric Field in Dynamic Umbilical Cables

Wave energy converter (WEC) systems have unique umbilical cable design requirements compared to conventional marine designs. Due to their dynamic nature, WEC umbilical cables are required to handle increased loads and larger motions over longer deployment scenarios. However, the life expectancy of dynamic umbilical cables is predominantly analyzed for mechanical fatigue, with little consideration given to the effect of mechanical stress on the response of the dielectric as it has been previously assumed that the non-polymeric components will fail prior to the polymeric components. In this work, we explore the effects of mechanical bending on the concentration of the electric field in the insulation of a conceptual three-core dynamic umbilical cable to determine the limiting requirements for life expectancy. A conceptual industrial schematic of a medium voltage dynamic umbilical cable was used as the basis for the WEC system under study. Simulations on the dynamic umbilical cable were performed using COMSOL Multiphysics®. Mechanical loads up to the calculated limit (2.64 m minimum bend radius or 388 kN transverse load) were applied to the dynamic umbilical in a step-wise fashion with one end of the umbilical cable fixed. One-way coupling in three-dimensions was conducted by first determining the engineering strains, then using the engineering strains as the initial condition for determination of the Green-Lagrange strains, and lastly calculating the electric field in the deformed dielectric. Based upon the input load, deformation of the dielectric at the minimum bend radius produced an increase in the electric field of more than 12% when compared to the undeformed umbilical cable, which may lead to dielectric breakdown of the insulation prior to mechanical failure of the umbilical cable.

Spencer, Mychal P.↗

Conserved conformational dynamics determine enzyme activity

Homologous enzymes often exhibit different catalytic rates despite a fully conserved active site. The canonical view is that an enzyme sequence defines its structure and function and, more recently, that intrinsic protein dynamics at different time scales enable and/or promote catalytic activity. Here, we show that, using the protein tyrosine phosphatase PTP1B, residues surrounding the PTP1B active site promote dynamically coordinated chemistry necessary for PTP1B function. However, residues distant to the active site also undergo distinct intermediate time scale dynamics and these dynamics are correlated with its catalytic activity and thus allow for different catalytic rates in this enzyme family. We identify these previously undetected motions using coevolutionary coupling analysis and nuclear magnetic resonance spectroscopy. Our findings strongly indicate that conserved dynamics drives the enzymatic activity of the PTP family. Characterization of these conserved dynamics allows for the identification of novel regulatory elements (therapeutic binding pockets) that can be leveraged for the control of enzymes.

59 BASIC BIOLOGICAL SCIENCES↗

Simulating the Impact of Dynamic Rerouting on Metropolitan-scale Traffic Systems

The rapid introduction of mobile navigation aides that use real-time road network information to suggest alternate routes to drivers is making it more difficult for researchers and government transportation agencies to understand and predict the dynamics of congested transportation systems. Computer simulation is a key capability for these organizations to analyze hypothetical scenarios; however, the complexity of transportation systems makes it challenging for them to simulate very large geographical regions, such as multi-city metropolitan areas. In this article, we describe enhancements to the Mobiliti parallel traffic simulator to model dynamic rerouting behavior with the addition of vehicle controller actors and vehicle-to-controller reroute requests. The simulator is designed to support distributed-memory parallel execution using discrete event simulation and be scalable on high-performance computing platforms. We demonstrate the potential of the simulator by analyzing the impact of varying the population penetration rate of dynamic rerouting on the San Francisco Bay Area road network. Using high-performance parallel computing, we can simulate a day in the San Francisco Bay Area with 19 million vehicle trips with 50 percent dynamic rerouting penetration over a road network with 0.5 million nodes and 1 million links in less than three minutes. We present a sensitivity study on the dynamic rerouting parameters, discuss the simulator’s parallel scalability, and analyze system-level impacts of changing the dynamic rerouting penetration. Furthermore, we examine the varying effects on different functional classes and geographical regions and present a validation of the simulation results compared to real-world data.

97 MATHEMATICS AND COMPUTING↗

Cation Dynamics in Hybrid Halide Perovskites

Hybrid halide perovskite semiconductors exhibit complex, dynamical disorder while also harboring properties ideal for optoelectronic applications that include photovoltaics. However, these materials are structurally and compositionally distinct from traditional compound semiconductors composed of tetrahedrally coordinated elements with an average valence electron count of silicon. The additional dynamic degrees of freedom of hybrid halide perovskites underlie many of their potentially transformative physical properties. Neutron scattering and spectroscopy studies of the atomic dynamics of these materials have yielded significant insights into their functional properties. Specifically, inelastic neutron scattering has been used to elucidate the phonon band structure, and quasi-elastic neutron scattering has revealed the nature of the uncorrelated dynamics pertaining to molecular reorientations. Understanding the dynamics of these complex semiconductors has elucidated the temperature-dependent phase stability and origins of defect-tolerant electronic transport from the highly polarizable dielectric response. Furthermore, the dynamic degrees of freedom of the hybrid perovskites provide additional opportunities for application engineering and innovation.

Materials Science↗

Dynamic Subgrid Turbulence Modeling for Shallow Cumulus Convection Simulations beyond LES Resolutions

A scale-dependent dynamic Smagorinsky model is implemented in the Met Office/NERC Cloud (MONC) model using two averaging flavors, along Lagrangian pathlines and local moving averages. The dynamic approaches were compared against the conventional Smagorinsky–Lilly scheme in simulating the diurnal cycle of shallow cumulus convection. The simulations spanned from the LES to the near-gray-zone and gray-zone resolutions and revealed the adaptability of the dynamic model across the scales and different stability regimes. The dynamic model can produce a scale- and stability-dependent profile of the subfilter turbulence length scale across the chosen resolution range. At gray-zone resolutions the adaptive length scales can better represent the early precloud boundary layer leading to temperature and moisture profiles closer to the LES compared to the standard Smagorinsky. As a result, the initialization and general representation of the cloud field in the dynamic model is in good agreement with the LES. In contrast, the standard Smagorinsky produces a less well-mixed boundary layer, which fails to ventilate moisture from the boundary layer, resulting in the delayed spinup of the cloud layer. Moreover, strong downgradient diffusion controls the turbulent transport of scalars in the cloud layer. However, the dynamic approaches rely on the resolved field to account for nonlocal transports, leading to overenergetic structures when the boundary layer is fully developed and the Lagrangian model is used. Introducing the local averaging version of the model or adopting a new Lagrangian time scale provides stronger dissipation without significantly affecting model behavior.

54 ENVIRONMENTAL SCIENCES↗