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At least 253 records · Page 14

Limits on the evolutionary rates of biological traits

Abstract This paper focuses on the maximum speed at which biological evolution can occur. I derive inequalities that limit the rate of evolutionary processes driven by natural selection, mutations, or genetic drift. These rate limits link the variability in a population to evolutionary rates. In particular, high variances in the fitness of a population and of a quantitative trait allow for fast changes in the trait’s average. In contrast, low variability makes a trait less susceptible to random changes due to genetic drift. The results in this article generalize Fisher’s fundamental theorem of natural selection to dynamics that allow for mutations and genetic drift, via trade-off relations that constrain the evolutionary rates of arbitrary traits. The rate limits can be used to probe questions in various evolutionary biology and ecology settings. They apply, for instance, to trait dynamics within or across species or to the evolution of bacteria strains. They apply to any quantitative trait, e.g., from species’ weights to the lengths of DNA strands.

59 BASIC BIOLOGICAL SCIENCES↗

Interfacial Cation Arrangement Controls Electrocatalytic Kinetics in CO 2 Reduction

The identity of electrolyte cations is known to strongly influence electrocatalytic activity, but the relationship between their interfacial arrangement and observed performance remains poorly understood. Organic cations, with their molecular tunability, provide a powerful platform for systematically probing these effects. Here, we leverage phosphonium-based geminal dications to control interfacial cation arrangement and identify the variables that most strongly influence catalytic rates. As a case study, we examine CO 2 reduction to CO over polycrystalline silver electrodes in dry aprotic acetonitrile. Through a combination of rotating disk electrode measurements, electrochemical impedance spectroscopy, and molecular dynamics simulations, we decouple the effects of cation–electrode distance and interfacial cation density on catalytic rates. We find that smaller, more densely packed cations induce stronger interfacial electric fields, which lower the activation barrier for CO 2 adsorption and increase reaction rates. Using geminal phosphonium dications [C n (P mmm ) 2 ][ClO 4 ] 2 , we demonstrate that both the vertical and lateral positioning of organic cations within the electrical double layer independently affect reactivity. These results demonstrate that electrolyte cation identity primarily influences catalytic kinetics by determining how efficiently charge can be arranged at electrochemical interfaces. Altogether, our findings support an electrostatic view of cation effects in catalysis and provide design principles for next-generation electrolytes.

Cations↗

Prediction of vacancy defect diffusion paths in high entropy alloys via machine learning on molecular dynamics data

Identifying the diffusion path of point defects is a critical step in understanding their evolution and the mechanisms of related phenomena. Defect diffusion occurs at small length and time scales, with impacts on material properties that may continue to evolve over ns to μs, ms, and the continuum scale (s, min, etc., and cm, m, etc.). The time scale accessible to molecular dynamics (MD) simulations is limited by small step sizes, typically in the fs range. Thus, surrogate models of MD simulations through machine learning (ML)-based algorithms are of great interest, especially for complex systems such as high entropy alloys (HEAs). In this work, dynamics governing vacancy migration in HEA were approximated with graph convolutional network (GCN) models as ansatzes for kinetic Monte Carlo (KMC) rate catalogs. Network design considered that diffusion in crystalline solids generally depends on interactions between defects and their immediate neighbor atoms. Graphs represented the vacancy surroundings, MD-generated trajectories provided training and comparison datasets, and unsupervised GCN models approximated interatomic dynamics governing vacancy migration in HEAs as ansatzes for KMC. A proof-of-concept model trained on MD data for the Fe, Ni, Cr, Co, and Cu HEA environment was used with two different neighbor interactions to assess the feasibility of training a GCN to predict vacancy defect transition rates in the HEA environment. The resulting setup rapidly generated MD-formatted synthetic trajectories based on dynamics learned from the MD training set, with a time acceleration of roughly two orders of magnitude and a similar diffusion coefficient to MD observations. Additionally, Nudged Elastic Band (NEB) calculations were performed on randomly generated FeNiCrCoCu HEA structures to determine vacancy migration barriers across nearest-neighbor sites. Transition probabilities for each jump, categorized by atomic type, were extracted from these calculations. NEB-based and GCN-based approaches led to similar outcomes.

Reimer, C↗

Dynamic Electric Field Assisted CO 2 Methanation

Energy-efficient advanced chemical reactions are essential for accelerating the growth of hydrocarbon economy. Sabatier reaction stands out for its potential to effectively transform carbon dioxide into valuable hydrocarbons and is an asset for long-duration Mars missions. This study explores a novel catalytic approach that harnesses electric field-assisted catalysis to substantially enhance the efficiency of the Sabatier reaction. Application of a dynamically perturbed electric field at 1000 Hz resulted in remarkable enhancements, increasing methane formation rates by over 100% at 350 °C and by 74% at 400 °C. Post-reaction catalyst characterization further revealed reduced blockage of active catalytic surface area under the applied electric field, emphasizing improved catalytic longevity and sustained activity. These results underscore the potential of tailored electric field waveforms to dynamically modulate elementary reaction kinetics and surface processes, positioning electric field-assisted catalysis as a transformative strategy for energy-efficient, cost-effective chemical manufacturing and energy conversion technologies.

42 - ENGINEERING↗

Molten pool dynamics and humping suppression in high-speed laser welding via tailored beam configurations

High-speed laser welding is essential for increasing the production rate of fuel cell fabrication. However, when the welding speed exceeds a critical limit, humping occurs and reduces the weld quality. In this study, two tailored beam configurations, including an adjustable ring mode and a dual-beam configuration, were employed to suppress humping. Computational fluid dynamics simulations were performed to elucidate the underlying suppression mechanisms. Here, the results show that, in the adjustable ring mode, humping mitigation arises from a reduced backward cross-sectional melt flow rate and a more stable molten pool. In the dual-beam configuration, humping suppression is attributed to the deceleration of melt flow, the conduction-mode behavior of the trailing beam, and the widening of the molten pool induced by the trailing laser. Furthermore, because the dual-beam configuration directly modifies the trailing molten pool dynamics, it achieves more effective humping suppression, extending the welding speed limit to 1.50 m/s, compared with 1.00 m/s for the adjustable ring mode.

08 HYDROGEN↗

Thermodynamic and Kinetic Mechanisms Governing the Synthesis of Nickel-Poor Cathodes

A deeper understanding of the thermodynamics and kinetics governing the lithiation and layering mechanisms of NMC cathode materials (LiNixMnyCozO 2 , where x + y + z = 1) offers valuable insights for enhancing synthesis methods and improving cathode performance. By employing atomistic and mesoscale approaches informed by in situ powder X-ray diffraction (PXRD) experiments, critical parameters for comprehending lithiation and layering processes and reaction rates were identified. The mesoscale approach captured the evolution of the phases and crystallite size observed in the in situ PXRD, revealing the differences in reaction rates with the use of different lithium salts and starting precursors. Ab initio molecular dynamics (AIMD) underscored the importance of vacancies and structural defects in promoting ion mobility and facilitating the nucleation of a layered domain. This nucleation disrupts the symmetry of disordered phases, ultimately creating a strained phase that serves as a buffer between layered and disordered regions. The lithiation and layering processes reflect a dynamic balance between the thermodynamic drive for a low-energy layered structure and the kinetic of diffusion, which is influenced by temperature and lithium vacancy concentration. Overall, reaction mechanisms are driven by the inherent defects of the intermediate phase that differ for NMC cathode materials. The lithium salts impact the rates of lithiation and layering, with a much slower process for Li 2 CO 3 .

25 ENERGY STORAGE↗

The importance of accounting for the Tolman correction to surface tension for nucleation and growth modeling of Fe clusters

Gibbs free energies of clusters are required for predictive modeling of cluster growth during condensation of a cooling vapor. Here, we present a straightforward method of calculating free energies of cluster formation using the data from molecular dynamics (MD) simulations. We apply this method to iron clusters having from 2 to 100 atoms. The energies obtained are verified by comparing to an MD-simulated equilibrium cluster size distribution in a sub-saturated vapor. We show that these free energies differ significantly from those obtained with a commonly used spherical cluster approximation, which relies on a surface tension coefficient of a flat surface, as it is used in the classical nucleation theory (CNT). We show that the spherical cluster approximation in CNT can be improved by using a cluster-size-dependent Tolman correction for the surface tension. The Tolman length and effective surface tension values were derived for iron clusters, and they significantly differ from the commonly used experimentally measured values. This improved approximation does not account for geometric magic number effects responsible for spikes and troughs in densities of neighbor cluster sizes. Nonetheless, it allows to more accurately model cluster formation from a cooling vapor. It better reproduces the condensation timeline, overall shape of the cluster size distribution, average cluster size, and the distribution width. In contrast, using a constant surface tension coefficient (as done in CNT) resulted in incorrect condensation dynamics and cluster size distributions. The analytical expression for cluster nucleation rate from CNT was updated to account for the size-dependence of cluster surface tension.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Generalized gluon distribution for quarkonium dynamics in strongly coupled N = 4 Yang-Mills theory

We study the generalized gluon distribution that governs the dynamics of quarkonium inside a non-Abelian thermal plasma characterizing its dissociation and recombination rates. This gluon distribution can be written in terms of a correlation function of two chromoelectric fields connected by an adjoint Wilson line. We formulate and calculate this object in N = 4 supersymmetric Yang-Mills theory at strong coupling using the AdS/CFT correspondence, allowing for a nonzero center-of-mass velocity v of the heavy quark pair relative to the medium. The effect of a moving medium on the dynamics of the heavy quark pair is described by the simple substitution T → γ T in agreement with previous calculations of other observables at strong coupling, where T is the temperature of the plasma in its rest frame, and γ = ( 1 − v 2 ) − 1 / 2 is the Lorentz boost factor. Such a velocity dependence can be important when the quarkonium momentum is larger than its mass. Contrary to general expectations for open quantum systems weakly coupled with large thermal environments, the contributions to the transition rates that are usually thought of as the leading ones in Markovian descriptions vanish in this strongly coupled plasma. This calls for new theoretical developments to assess the effects of strongly coupled non-Abelian plasmas on in-medium quarkonium dynamics. Finally, we compare our results with those from weakly coupled QCD, and find that the QCD result moves toward the N = 4 strongly coupled result as the coupling constant is increased within the regime of applicability of perturbation theory. This behavior makes it even more pressing to develop a non-Markovian description of quarkonium in-medium dynamics. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Regional Inertia Estimation Using Actual Event Measurements: Florida Case

As inverter-based resources’ integration in power grids increases, their uneven distribution across the electrical network leads to the formation of local regions that are weakly coupled to the larger interconnection. This signifies the necessity of regional frequency dynamics investigation and analyzing various inertia metrics. This paper presents a practical methodology for estimating regional rate-of-change of frequency (RoCoF) using actual event recordings, which is then used to evaluate regional inertia. Florida (FL) is selected as the region of interest due to its distinct regional frequency dynamics and the rising levels of solar generation. We identify and analyze confirmed events from 2017 to 2024 that occurred in FL. The results indicate that FL contributes about 14% to the total inertia of the US Eastern Interconnection, which approximately matches its share of generation capacity. Results also highlight seasonal fluctuations in energy generation, which play a significant role in influencing inertia and thus the RoCoF levels. This emphasizes the importance of estimating regional inertia to enhance grid operations for a future that focuses on distributed generation.

Dulal, Saurav [University of Tennessee, Knoxville ↗

Charged- and Multi-Exciton Dynamics in Colloidal Quantum Dot Molecules

Multicarrier states in quantum dots are confined to small volumes, resulting in increased nonradiative Auger recombination rates with implications for different optoelectronic applications. Recently, the fusion of two core-shell quantum dots into a dimer has provided a new physical landscape for multiexciton states, since the excitons may share a core (intradot, localized) or occupy different cores (interdot, segregated). Here, in this study, we employ transient absorption spectroscopy to investigate the multiexciton dynamics in coupled quantum dot dimers. We observe that multiexciton populations in the dimers live significantly longer in comparison to the parent monomers, in contrast to the single exciton regime. A kinetic model that accounts for the statistical differences between monomers and dimers reveals that, while intradot multiexcitons show Auger rates similar to the monomers, interdot states have reduced Auger rates. These results pave the way for the rational design of new quantum dot molecules with tailored multiexciton properties.

Auger recombination↗

Generating forces in confinement via polymerization

Understanding how to produce forces using biomolecular building blocks is essential for the development of adaptive synthetic cells and living materials. Here we ask whether a dynamic polymer system can generate deformation forces in soft shells by pure self-assembly, motivated by the fact that biological polymer networks like the cytoskeleton can exert forces, move objects, and deform membranes by simply growing, even in the absence of molecular motors. We address this question by investigating polymer force generation by varying the release rate, the structure, and the interactions of self-assembling monomers. First, we develop a toy computational model of polymerization in a soft elastic shell that reveals the emergence of spontaneous bundling which enhances shell deformation. We then extend our model to account more explicitly for monomer binding dynamics. We find that the rate at which monomers are released into the interior of the shell is a crucial parameter for achieving deformation through polymer growth. Lastly, we demonstrate that the introduction of multivalent particles that can join polymers can either improve or impede polymer performance, depending on the amount and on the structure of the multivalent particles. Our results provide guidance for the experimental realization of polymer systems that can perform work at the nanoscale, for example through rationally designed self-assembling proteins or nucleic acids.

Osmanović, Dino [University of California at Los A↗

Machine learning modeling and model predictive control of a closed-circuit reverse osmosis system

Closed-circuit reverse osmosis (CCRO) offers a flexible and energy-efficient alternative to conventional reverse osmosis by operating in a semi-batch mode that recycles brine, enabling higher recovery rates and reduced specific energy consumption (SEC). However, developing accurate, system-level dynamic models for CCRO remains challenging due to its nonlinear, multi-phase operation and sensitivity to variable feed water conditions. Traditional modeling approaches, such as NARMAX (nonlinear autoregressive moving average with exogenous inputs), often struggle to generalize across varying inlet feed concentrations, necessitating frequent parameter re-estimation and limiting their utility for real-time control applications. To address these limitations, we developed a long short-term memory (LSTM) neural network model trained on an extensive experimental data set from a CCRO pilot plant. The model accepts three inputs, feed flow rate, recirculation flow rate, and initial feed conductivity, and predicts three key outputs: reject conductivity, feed pump power draw, and recirculation pump power draw. We validated the LSTM model against experimental data, demonstrating its ability to distinguish between different feed conductivities and adapt to variable flow rates. Subsequently, we incorporated the LSTM model within a nonlinear model predictive control (MPC) scheme and conducted closed-loop simulations to optimize the integrated SEC (iSEC). In conclusion, the results project up to a 6% reduction in iSEC by using MPC to optimize performance over the entire experiment duration, without requiring any random excitation for data collection or parameter re-estimation.

Desalination↗

Quantifying electron transport in aggregated colloidal suspensions in the strong flow regime

Electron transport in complex fluids, biology, and soft matter is a valuable characteristic in processes ranging from redox reactions to electrochemical energy storage. These processes often employ conductor–insulator composites in which electron transport properties are fundamentally linked to the microstructure and dynamics of the conductive phase. While microstructure and dynamics are well recognized as key determinants of the electrical properties, a unified description of their effect has yet to be determined, especially under flowing conditions. In this work, the conductivity and shear viscosity are measured for conductive colloidal suspensions to build a unified description by exploiting both recent quantification of the effect of flow-induced dynamics on electron transport and well-established relationships between electrical properties, microstructure, and flow. These model suspensions consist of conductive carbon black (CB) particles dispersed in fluids of varying viscosities and dielectric constants. In a stable, well-characterized shear rate regime where all suspensions undergo self-similar agglomerate breakup, competing relationships between conductivity and shear rate were observed. To account for the role of variable agglomerate size, equivalent microstructural states were identified using a dimensionless fluid Mason number, Mn f , which allowed for isolation of the role of dynamics on the flow-induced electron transport rate. At equivalent microstructural states, shear-enhanced particle–particle collisions are found to dominate the electron transport rate. This work rationalizes seemingly contradictory experimental observations in literature concerning the shear-dependent electrical properties of CB suspensions and can be extended to other flowing composite systems.

Science & Technology - Other Topics↗

Dynamic modelling and control strategy of a temperature-driven metal hydride cooling system for buildings

A temperature-driven coupled metal hydride (MH) based thermal energy storage (TES) system can allow to shave and shift the peak energy demand in buildings. The high energy density and long-term (seasonal) energy storage capability are its major advantages over other energy storage methods. The dynamic nature of the MH operation, however, requires controlled hydrogen transfer between the coupled MHs at a rate needed to meet the building's transient load. While temperature-driven MH systems are studied in the literature, their application in buildings and control are scarcely reported. Here, this paper presents a control-based dynamic modeling of the temperature-driven coupled MH-TES system for building cooling applications. The dynamic model is developed in MATLAB(R) Simulink environment, considering the thermodynamic and kinetic behaviors of the MH systems. Based on a preliminary analysis of a property database of over 337 hydrides, we select around 1600 MH pairs suitable for building cooling applications. Each of these MH pairs is studied for their performance using the dynamic model, and among all, Zr 0.76 Ti 0.24 Ni 1.16 Mn 0.63 V 0.14 Fe 0.18 -Ti 0.85 Zr 0.15 Cr 1.2 Mn 0.8 MH pair showed fast dynamics along with high coefficient of performance (COP) of 0.71. A parametric investigation is performed on this MH pair to understand the effect of operating temperatures. Finally, three proportional-integral (PI) feedback controllers are investigated to regulate the temperature, pressure and mass exchange between the coupled MH pairs. The developed PI controller is sufficiently capable of rejecting the signal noise from the hydrogen flow and internal heat exchange processes with root mean square error of 5.78 W between reference and actual cooling load.

08 HYDROGEN↗

Scale Invariance of Hot Spot Formation in TATB High Explosives

Shock-induced detonation of insensitive high explosives based on 1,3,5-triamino-2,4,6-trinitrobenzene starts with formation of hot spots at microstructural defects but has eluded atomistic modeling treatment at micron length scales. To this end, we performed multimicron scale all-atom molecular dynamics (MD) simulations of hot spots that form during the collapse of cylindrical pores with diameters between 10 and 300 nm. Our MD simulations show that hot spots formed at pores larger than 20 nm exhibit temperature fields with scale-invariant features for sizes up to at least 300 nm. Through a continuum-based grain-scale modeling framework, we span and extend beyond the size scales currently accessible to MD and find that hot spot scale invariance is a general feature that arises when the mechanical strength is insensitive to strain rate. Finally, our results demonstrate the applicability of all-atom MD to simulate the complicated dynamical evolution of micron-sized systems and bolster confidence in insights from MD simulations of materials that exhibit strength with negligible rate dependence over the relevant intervals.

36 MATERIALS SCIENCE↗

Designing open quantum systems with known steady states: Davies generators and beyond

We provide a systematic framework for constructing generic models of nonequilibrium quantum dynamics with a target stationary (mixed) state. Our framework identifies (almost) all combinations of Hamiltonian and dissipative dynamics that relax to a steady state of interest, generalizing the Davies’ generator for dissipative relaxation at finite temperature to nonequilibrium dynamics targeting arbitrary stationary states. We focus on Gibbs states of stabilizer Hamiltonians, identifying local Lindbladians compatible therewith by constraining the rates of dissipative and unitary processes. Moreover, given terms in the Lindbladian not compatible with the target state, our formalism identifies the operations – including syndrome measurements and local feedback – one must apply to correct these errors. Our methods also reveal new models of quantum dynamics: for example, we provide a “measurement-induced phase transition” in which measurable two-point functions exhibit critical (power-law) scaling with distance at a critical ratio of the transverse field and rate of measurement and feedback. Time-reversal symmetry – defined naturally within our formalism – can be broken both in effectively classical and intrinsically quantum ways. Our framework provides a systematic starting point for exploring the landscape of dynamical universality classes in open quantum systems, as well as identifying new protocols for quantum error correction.

Guo, Jinkang [Department of Physics and Center for↗

Evolution of carbapenemase activity in the class C β-lactamase ADC-1

Antibiotic resistance in bacteria poses a significant threat to public health. Among dozens of available antimicrobial agents, carbapenems are used as drugs of choice for the treatment of serious infections caused by pathogens resistant to other antibiotics. However, their usefulness has been severely compromised due to the emergence and wide spread of carbapenem-resistant clinical isolates worldwide. High-level resistance to carbapenems in bacteria is mediated by the production of β-lactamases from three molecular classes, A, B, and D, but not by class C enzymes. In this study, we selected a triple mutant of the intrinsic class C Acinetobacter-derived cephalosporinase ADC-1 (ADC-1 TM ) that confers high-level resistance to the carbapenems meropenem, ertapenem, and doripenem. Kinetic experiments demonstrated that the apparent binding affinity, along with the acylation and deacylation rates, were all improved for the mutant enzyme. X-ray crystallography, molecular docking, and molecular dynamics simulations revealed that the amino acid substitutions in ADC-1 TM produce significant changes in the enzyme active site architecture and binding mode of the carbapenem ertapenem. These changes allow for better positioning of a deacylating water for nucleophilic attack, thus explaining the significantly improved rate of ertapenem deacylation by ADC-1 TM . In this study, we showed for the first time that a class C β-lactamase can produce high-level resistance to carbapenem antibiotics, which underlines the potential for enzymes of this class to evolve such resistance and could further exacerbate the problem of antibiotic resistance in bacteria.

59 BASIC BIOLOGICAL SCIENCES↗

Role of Exciton Diffusion in the Efficiency of Mn Dopant Emission in Two-Dimensional Perovskites

Two-dimensional (2D) metal-halide perovskites have promising characteristics for optoelectronic applications. By incorporating Mn 2+ ions into the perovskite structure, improved photoluminescence quantum yield can be achieved. This has been attributed to the formation of defect states that act as efficient recombination centers. Here, we make use of transient photoluminescence microscopy to characterize important material parameters of Mn 2+ -doped 2D perovskites with different doping levels. From these measurements, we visualize the importance of exciton transport as an intermediate step in the excitation of Mn 2+ . We model the spatiotemporal dynamics of the excited states to extract the diffusion constant and the transfer rate of the excitations to the Mn dopant sites. Interestingly, from these models, we find that the average distance an exciton needs to travel before transferring to a Mn site is significantly larger than expected from the Mn concentration obtained from elemental analysis. These insights are critical from a device design perspective.

2D perovskites↗