Slowdown Of Dynamics Research Articles

Heterogeneous Slowdown of Dynamics in the Condensate of an Intrinsically Disordered Protein.

The high concentration of proteins and other biological macromolecules inside biomolecular condensates leads to dense and confined environments, which can affect the dynamic ensembles and the time scales of the conformational transitions. Here, we use atomistic molecular dynamics (MD) simulations of the intrinsically disordered low complexity domain (LCD) of the human fused in sarcoma (FUS) RNA-binding protein to study how self-crowding inside a condensate affects the dynamic motions of the protein. We found a heterogeneous retardation of the protein dynamics in the condensate with respect to the dilute phase, with large-amplitude motions being strongly slowed by up to 2 orders of magnitude, whereas small-scale motions, such as local backbone fluctuations and side-chain rotations, are less affected. The results support the notion of a liquid-like character of the condensates and show that different protein motions respond differently to the environment.

Universal Time-Entanglement Trade-Off in Open Quantum Systems

We demonstrate a surprising connection between pure steady-state entanglement and relaxation time scales in an extremely broad class of Markovian open systems, where two (possibly many-body) systems, A and B, interact locally with a common dissipative environment. This setup also encompasses a broad class of adaptive quantum dynamics based on continuous measurement and feedback. As steady-state entanglement increases, there is generically an emergent strong symmetry that leads to a dynamical slow-down. Using this, we can prove rigorous bounds on relaxation times set by steady-state entanglement. We also find that this time must necessarily diverge for maximal entanglement. To test our bound, we consider the dynamics of a random ensemble of local Lindbladians that support pure steady states, finding that the bound does an excellent job of predicting how the dissipative gap varies with the amount of entanglement. Our work provides general insights into how dynamics and entanglement are connected in open systems and has specific relevance to quantum reservoir engineering. Published by the American Physical Society 2024

How Single-Photon Switching Is Quenched with Multiple Λ-Level Atoms.

Single-photon nonlinearity, namely, the change in the response of the system as the result of the interaction with a single photon, is generally considered an inherent property of a single quantum emitter. Although the dependence on the number of emitters is well understood for the case of two-level systems, deterministic operations such as single-photon switching or photon-atom gates inherently require more complex level structures. Here, we theoretically consider single-photon switching in ensembles of emitters with a Λ-level scheme and show that the switching efficiency vanishes with the number of emitters. Interestingly, the mechanism behind this behavior is the quantum Zeno effect, manifested in a slowdown of the photon-controlled dynamics of the atomic ground states.

Slowdown of solvent structural dynamics in aqueous DMF solutions

This study presents a comprehensive investigation into the molecular dynamics of solvation environments through an integrated approach combining Fourier-transform infrared (FTIR) spectroscopy, molecular dynamics (MD) simulations, and two-dimensional infrared (2D IR) spectroscopy. We explore the solvation of an ionic solute (ammonium thiocyanate) in various solvent systems, including N,N-dimethylformamide (DMF), water, and a 0.5 mole fraction of DMF in water, aiming to unravel the intricate interplay between solute-solvent interactions and solvent dynamics across diverse solvation environments. By integrating FTIR spectral analysis with radial distribution functions and coordination numbers obtained from MD simulations, we decipher the solvent composition around the solute molecule. Analysis of 2D IR spectra and hydrogen bond, as well as dipolar autocorrelation function from MD simulations, further elucidates the nuances of solute-solvent interactions, highlighting the impact of solvent dynamics on solvation structures. Our results reveal a significant slowdown of the solvent structural dynamics in the equimolar binary solvent mixture compared to the neat solvents. This slowdown underscores the complex relationship between solute-solvent interactions and solvent dynamics. The integration of FTIR, MD simulations, and 2D IR spectroscopy provides a unified framework for obtaining a holistic understanding of solvation dynamics, offering valuable insights into the underlying molecular mechanisms governing solute-solvent interactions in complex systems. These results pave the way for future studies to delve deeper into the molecular intricacies of solvation phenomena.

Entropy-extreme model for predicting the development of cyber epidemics at early stages

The approaches used in biomedicine to analyze epidemics take into account features such as exponential growth in the early stages, slowdown in dynamics upon saturation, time delays in spread, segmented spread, evolutionary adaptations of the pathogen, and preventive measures based on universal communication protocols. All these characteristics are also present in modern cyber epidemics. Therefore, adapting effective biomedical approaches to epidemic analysis for the investigation of the development of cyber epidemics is a promising scientific research task. The article is dedicated to researching the problem of predicting the development of cyber epidemics at early stages. In such conditions, the available data is scarce, incomplete, and distorted. This situation makes it impossible to use artificial intelligence models for prediction. Therefore, the authors propose an entropy-extreme model, defined within the machine learning paradigm, to address this problem. The model is based on estimating the probability distributions of its controllable parameters from input data, taking into account the variability characteristic of the last ones. The entropy-extreme instance, identified from a set of such distributions, indicates the most uncertain (most negative) trajectory of the investigated process. Numerical methods are used to analyze the generated set of investigated process development trajectories based on the assessments of probability distributions of the controllable parameters and the variability characteristic. The result of the analysis includes characteristic predictive trajectories such as the average and median trajectories from the set, as well as the trajectory corresponding to the standard deviation area of the parameters’ values. Experiments with real data on the infection of Windows-operated devices by various categories of malware showed that the proposed model outperforms the classical competitor (least squares method) in predicting the development of cyber epidemics near the extremum of the time series representing the deployment of such a process over time. Moreover, the proposed model can be applied without any prior hypotheses regarding the probabilistic properties of the available data.

Salt induced slowdown of kinetics and dynamics during thermal gelation of egg-yolk.

We investigated the effect of the NaCl concentration (0.3-2M) on the structure and dynamics of hen egg yolk at room temperature and during thermal gelation at temperatures in the range of 66-90 °C utilizing low-dose x-ray photon correlation spectroscopy in ultra-small angle x-ray scattering geometry. With an increase in the salt concentration, we observe progressive structural and dynamic changes at room temperature, indicating the disruption of yolk components such as yolk-granules and yolk-plasma proteins. Temperature- and salt-dependent structural and dynamic investigations suggest a delay in the gel formation and aggregation of yolk low-density lipoproteins with increasing ionic strength. However, the time-temperature superposition relationship observed in all samples suggests an identical mechanism underlying protein aggregation-gelation with a temperature-dependent reaction rate. The sol-gel transition time extracted from kinetic and dynamic information follows Arrhenius's behavior, and the activation energy (460kJ/mol) is found to be independent of the salt concentration.

Durable benefit and slowdown in tumor growth dynamics with erdafitinib in a FGFR3-TACC3 fusion-positive IDH-wild type glioblastoma.

FGFR3-TACC3 fusion-positive IDH-wild-type (IDH-WT) glioblastoma (GB) is a rare GB subtype occurring in approximately 3% of cases. It is clinical behavior and molecular profile is different from those of fusion-negative IDH-WT GBs. Evidence on the role of FGFR inhibitors in FGFR-altered gliomas is limited. We present the case of a patient with a FGFR3-TACC3 fusion-positive IDH-WT GB that at its second recurrence was treated with the FGFR inhibitor erdafitinib through a compassionate use program. Although no objective response was achieved, an overt deceleration in tumor growth was evidenced and the patient remained on treatment for 5.5 months.

Nonlinear composition dependence of hydrogen bond lifetime in water-DMSO binary mixtures: The role of hydrophobic interaction.

The lifetime of a hydrogen bond between water and dimethyl sulfoxide (DMSO) is found to be considerably longer than that between two water molecules in neat water. This is counter-intuitive because the charge on the oxygen in DMSO is considerably less than that in water. Additionally, the strength of the water-dimethyl sulfoxide (w-D) hydrogen bond is found to be strongly composition dependent; the lifetime of the hydrogen bond is ten times larger at 30% than at very low concentrations. Using computer simulations, we perform microscopic structural and dynamic analysis to find that these anomalies arise at least partly from an "action-at-a-distance" effect where the attraction between the hydrophobic methyl groups results in the self-aggregation of DMSO molecules that "cages" both the rotational and linear motions of the molecules involved. This is reflected in the observed strong correlation of the lifetime with the local coordination number of the associated methyl groups. The elongated w-D h-bond lifetime causes a slowdown of collective dynamics and affects the lifetime of the w-w h-bond. This nonlinear feedback mechanism explains the strong composition dependence of viscosity and is anticipated to play a dominant role in many self-assemblies. Furthermore, the w-D hydrogen bond breaking mechanism changes from low to high DMSO concentration, a phenomenon not anticipated a priori. We introduce a new order parameter-based free energy surface of the bond breaking pathway. A two-dimensional transition state rate theory calculation is performed for the lifetime of the w-D h-bond that is found to be semi-quantitatively accurate.

Emergence of bacterial glass.

Densely packed, motile bacteria can adopt collective states not seen in conventional, passive materials. These states remain in many ways mysterious, and their physical characterization can aid our understanding of natural bacterial colonies and biofilms as well as materials in general. Here, we overcome challenges associated with generating uniformly growing, large, quasi-two-dimensional bacterial assemblies by a membrane-based microfluidic device and report the emergence of glassy states in two-dimensional suspension of Escherichia coli. As the number density increases by cell growth, populations of motile bacteria transition to a glassy state, where cells are packed and unable to move. This takes place in two steps, the first one suppressing only the orientational modes and the second one vitrifying the motion completely. Characterizing each phase through statistical analyses and investigations of individual motion of bacteria, we find not only characteristic features of glass such as rapid slowdown, dynamic heterogeneity, and cage effects, but also a few properties distinguished from those of thermal glass. These distinctive properties include the spontaneous formation of micro-domains of aligned cells with collective motion, the appearance of an unusual signal in the dynamic susceptibility, and the dynamic slowdown with a density dependence generally forbidden for thermal systems. Our results are expected to capture general characteristics of such active rod glass, which may serve as a physical mechanism underlying dense bacterial aggregates.

Unraveling the dynamic slowdown in supercooled water: The role of dynamic disorder in jump motions.

When a liquid is rapidly cooled below its melting point without inducing crystallization, its dynamics slow down significantly without noticeable structural changes. Elucidating the origin of this slowdown has been a long-standing challenge. Here, we report a theoretical investigation into the mechanism of the dynamic slowdown in supercooled water, a ubiquitous yet extraordinary substance characterized by various anomalous properties arising from local density fluctuations. Using molecular dynamics simulations, we found that the jump dynamics, which are elementary structural change processes, deviate from Poisson statistics with decreasing temperature. This deviation is attributed to slow variables competing with the jump motions, i.e., dynamic disorder. The present analysis of the dynamic disorder showed that the primary slow variable is the displacement of the fourth nearest oxygen atom of a jumping molecule, which occurs in an environment created by the fluctuations of molecules outside the first hydration shell. As the temperature decreases, the jump dynamics become slow and intermittent. These intermittent dynamics are attributed to the prolonged trapping of jumping molecules within extended and stable low-density domains. As the temperature continues to decrease, the number of slow variables increases due to the increased cooperative motions. Consequently, the jump dynamics proceed in a higher-dimensional space consisting of multiple slow variables, becoming slower and more intermittent. It is then conceivable that with further decreasing temperature, the slowing and intermittency of the jump dynamics intensify, eventually culminating in a glass transition.

Financial instruments of crisis reversal in the Russian economy

Aim. To study the economic crises that occurred in the Russian Federation (RF) from 1991 to 2022 from the point of view of analyzing the causes of their occurrence and the factors of reversal, as well as identifying the chances of overcoming the stages of slowdown and decline in economic dynamics, including those associated with digitalization.Objectives. To reveal the causes of economic crises by identifying the risks realized during this or that crisis; to determine the financial instruments of economic crises reversal in the Russian economy since 1991; to identify the chances of the economic system to overcome the stages of slowdown and decline in economic dynamics and to turn the economic system to sustainable growth.Methods. General scientific methods, including comparative, retrospective and analogy methods, were used as methodological tools.Results. The article identifies the realized risks of economic crises in the Russian Federation, from the crisis of 1991 to the crisis of 2022. As chances of economic growth in the period of digital transformation of the economy and the financial sector, the risks of innovative financial technologies, risks of digitalization of the banking sector, risks of insurance and financial services were identified. Financial and non-financial tools to turn the economic crisis to the recovery period and subsequent sustainable growth were identified.Conclusions. Any crisis is based not only on factors that aggravate and destabilize its parameters, but also on factors that present new chances for further economic development. When assessing economic dynamics during crises, one should take into account the realized risks, possible chances and tools for economic turnaround, including financial and non-financial instruments. Financial instruments, which allow to implement extraordinary management decisions, serve as instruments of turnaround. Additional state budget expenditures from the reserve fund (until 2017) or from the national welfare fund represent corrective financing in periods of uncertainty and are associated with emergency management decisions during crises, including during a special military operation. The main task of the regulator is to limit the negative effects of realized internal and external risks.

Activity-induced stiffness, entanglement network and dynamic slowdown in unentangled semidilute polymer solutions.

Active polymers possess numerous unique properties that are quite different from those observed in the system of small active molecules due to the intricate interplay between their activity and topological constraints. This study focuses on the conformational changes induced by activity, impacting effective stiffness and crucially influencing entanglement and dynamics. When the two terminals of a linear chain undergo active modification through coupling to a high-temperature thermal bath, there is a substantial increase in chain size, indicating a notable enhancement in effective stiffness. Unlike in passive semiflexible chains where stiffness predominantly affects local bond angles, activity-induced stiffness manifests at the scale of tens of monomers. While activity raises the ambient temperature, it significantly decreases diffusion by over an order of magnitude. The slowdown of the dynamics observed can be attributed to increased entanglement due to chain elongation.

Constrained Series PI, PID and PIDA Controller Design Inspired by Ziegler–Nichols

Abstract The present paper complements the results of several recent papers on higher-order (HO) controllers with automatic-reset. A modification of the two-step tuning of the constrained second-order derivative controllers based on integrator-plus-dead-time (IPDT) models is proposed. In the first step, the linear controller is designed using the multiple real dominant poles (MRDPs) method to avoid the slowdown of the closed-loop dynamics due to the presence of slow poles. In the second step, the smallest time constant of the numerator of the MRDP-optimal controller transfer function is selected as the automatic-reset time constant. The derived control method was tested on a thermal system for the filament disc dryer to demonstrate the deployment, tuning, use and impact of controllers with increasing derivative degree in practical applications. It is shown that the use of HO controllers is similar to the traditional hyper-reset controllers (i.e. series proportional-integral-derivative [PID] controllers) from the user’s point of view. However, the advantages are faster transient responses while maintaining sufficiently smooth input and output shapes of the process with a minimum number of monotonic intervals. The overall design can be seen as a generalisation and discretisation of the Ziegler and Nichols graphical tuning method. One of the main new features is the consideration of a constrained control signal, as is typical for a pulse width modulated (PWM) actuator. Such actuators are often used in speed-controlled electric drives and in power electronics, among other applications.

Новые тенденции в развитии мировой экономики и их влияние на Россию

Fragmentation processes are developing in the world economy since the 2010s. They are characterized by the active use of protectionist measures in foreign trade. Manifestations of fragmentation include a slowdown in global trade dynamics, a reduction in international capital flows relative to global GDP, and increased volatility in global commodity and financial markets. However, we can not find statistical confirmation for the full-scale development of the process of fragmentation in the world economy. It should also be noted that there are also the global debt problem, currently manifested in increasing debt servicing costs, and the problem of currency competition from both private digital currencies and competition for the US dollar from the Chinese yuan as a currency of an alternative center of the global economy. The Russian economy has experienced the full-fledged impact from the fragmentation trend through the unprecedented sanctions regime imposed on it in 2022, and has also faced the impact of increased global inflationary pressures. At the same time, the consequences of sanctions against Russia have also affected the dynamics of global commodities markets due to the “big country trap” effect. The economic policy pursued in Russia contributed to overcoming the negative short-term consequences of the sanctions shock. Currently, economic policy is faced with the task of solving medium- and long-term problems, first of all, contributing the structural changes in the Russian economy.

Ion effects on minimally hydrated polymers: hydrogen bond populations and dynamics.

Compared to bulk water, the effect of ions in confined environments or heterogeneous aqueous solutions is less understood. In this study, we characterize the influence of ions on hydrogen bond populations and dynamics within minimally hydrated polyethylene glycol diacrylate (PEGDA) solutions using Fourier-transform infrared (FTIR) and two-dimensional infrared (2D IR) spectroscopies. We demonstrate that hydrogen bond populations and lifetimes are directly related to ion size and hydration levels within the polymer matrix. Specifically, larger monovalent cation sizes (Li+, Na+, K+) as well as anion sizes (F-, Cl-, Br-) increase hydrogen bond populations and accelerate hydrogen bond dynamics, with anions having more pronounced effects compared to cations. These effects can be attributed to the complex interplay between ion hydration shells and the polymer matrix, where larger ions with diffuse charge distributions are less efficiently solvated, leading to a more pronounced disruption of the local hydrogen bonding network. Additionally, increased overall water content results in a significant slowdown of dynamics. Increased water content enhances the hydrogen bonding network, yet simultaneously provides greater ionic mobility, resulting in a delicate balance between stabilization and dynamic restructuring of hydrogen bonds. These results contribute to the understanding of ion-specific effects in complex partially-hydrated polymer systems, highlighting the complex interplay between ion concentration, water structuring, and polymer hydration state. The study provides a framework for designing polymer membrane compositions with ion-specific properties.

Protein stability in a natural deep eutectic solvent: Preferential hydration or solvent slaving?

Deep eutectic solvents (DESs) emerged as potential alternative solvent media in multiple areas, including biomolecular (cryo)preservation. Herein, we studied the stability of a small protein (ubiquitin) in water and a betaine-glycerol-water (B:G:W) (1:2:ζ; ζ = 0, 1, 2, 5, 10) DES, through molecular dynamics. An AMBER-based model that accurately describes the density and shear viscosity of the DES is proposed. We find that water molecules are largely trapped in the solvent, precluding the formation of a full hydration layer, seemingly opposite to osmolytes’ preferential exclusion/preferential hydration mechanism. Although the protein is stable in the DES, structural fluctuations are largely suppressed and only recovered upon sufficient hydration. This is explained by a solvent-slaving mechanism where β-fluctuations are key, with the non-monotonic hydration of some amino acids with the water content providing an explanation to the non-monotonic folding of some proteins in aqueous DESs. A major thermal stability enhancement in the DES is also observed, caused by a similar slowdown of the backbone torsional dynamics. Our results support a kinetic stabilization of the protein in the DES, whereas a possible thermodynamic stabilization does not follow a preferential hydration or water entrapment mechanism.

Ultrafast Spectroscopy Reveals Slow Water Dynamics in Biocondensates.

Cells achieve high spatiotemporal control over biochemical processes through compartmentalization to membrane-bound as well as membraneless organelles that assemble by liquid-liquid phase separation. Characterizing the balance of forces within these environments is essential to understanding their stability and function, and water is an integral part of the condensate, playing an important role in mediating electrostatic and hydrogen-bonding interactions. Here, we investigate the ultrafast, picosecond hydrogen-bond dynamics of a model biocondensate consisting of a peptide poly-l-arginine (Poly-R) and the nucleic acid adenosine monophosphate (AMP) using coherent two-dimensional infrared (2D IR) spectroscopy. We investigated three vibrational modes: the arginine side-chain C═N stretches, an AMP ring mode, and the amide backbone carbonyl stretching modes. Dynamics slow considerably between the dilute phase and the condensate phase for each vibrational probe. For example, the arginine side-chain C═N modes slow from 0.38 to 2.26 ps due to strong electrostatic interactions. All-atom molecular dynamics simulations provide an atomistic interpretation of the H-bond network disruption resulting from electrostatic contributions as well as collapse within the condensate. Simulations predict that a fraction of water molecules are highly constrained within the condensate, explaining the observed slowdown in the H-bond dynamics.

Flow backward alleviated the river algal blooms

Mechanistic understanding and prediction of river algal blooms remain challenging. It is generally believed that these blooms are formed by the slowdown of water dynamics in tributaries due to the support of the main stream. However, few studies have investigated the impact of flow backward caused by the difference in water dynamics between the main stream and tributaries. Here, we focus on the eutrophication issue in the middle-lower reaches of the Han River, which is affected by the Middle Route of the South-to-North Water Diversion Project (SNWDP), the largest inter-basin water transfer project in Asia. We discover that the reversal of the Yangtze River water level could effectively alleviate the occurrence of Han River water blooms. The Yangtze River frequently back flows into the lower reaches of the Han River, with the probability of such events increasing as it nears the confluence (20km from the Yangtze: 9.5%, 10 km: 19.0%, 8 km: 28.6%). This flow backward carries nutrients that reduce the nitrogen to phosphorus ration (N:P), leading to a shift in the nutrient structure of the Han River. This change is concomitant with a significant decline in algae biomass (Chlorophyll-a=11.19 µg·L-1 and algae density=0.41×107 cells·L-1 under natural flow, Chlorophyll-a=5.19 µg·L-1 and algae density=0.18×107 cells·L-1 under flow backward), as well as a weakening of the correlation (R) between diatom density and chlorophyll-a concentration, i.e., R=0.38 (p>0.05) under flow backward conditions versus R=0.72 (p<0.01) under natural flow conditions. As phosphorus limitation typically suppresses algae growth, the correlation between diatom density and chlorophyll-a concentration can help to reveal the dominance of diatoms, with stronger correlations indicating greater diatom dominance. Consequently, our study provides evidence that the flow backward can alleviate river algal blooms by weakening the growth advantage of diatoms. This study could prove valuable in investigating the eutrophication mechanism within the complex hydrodynamic conditions of rivers. SYNOPSIS: Flow backward caused by the water level difference between the main streams and tributary alleviated the occurrence of river algal blooms in the confluence area.

Banking crises and exporter dynamics

ABSTRACT This article examines the effects of systemic banking crises on exporter dynamics using exporter data at the country-industry level from the Exporter Dynamics Database (EDD). By considering industries with varying levels of external finance dependence, we are able to capture the heterogeneous impacts of banking crises. Our results demonstrate that banking crises lead to a decrease in the number of successful market entries, a reduction in export market concentration, and a slowdown in both product dynamics and destination dynamics. These findings are robust when accounting for other financial crises, industry characteristics, and potential endogeneity concerns. Overall, our empirical evidence confirms the detrimental impact of banking crises on the extensive margin of exports.

Polymer architecture effect on rheology and segmental dynamics in poly (methyl methacrylate)-silica nanocomposite melts.

Architecturally different polymer chains lead to fundamentally different rheological responses and internal dynamics, which can be utilized to rationalize advanced thermoplastic nanocomposites with tunable mechanical behavior. In this work, three model poly (methyl methacrylate) (PMMA) polymers with linear, bottlebrush, and star architectures with the same total molar mass were investigated in their neat form, and nanocomposites with well-dispersed silica nanoparticles using rheology and broadband dielectric spectroscopy (BDS). The master curves of the dynamic moduli obtained by time-temperature superposition (TTS) over the entire range from the Rouse regime to the terminal flow and a sequence of significantly different relaxation modes were observed for the samples with linear and branch chains. While linear chains form an entangled polymer network, the branched bottlebrush, and star chains show a viscoelastic response with no sign of rubbery entanglement plateau and a weak arm relaxation regime between Rouse and terminal flow, akin to other branched polymers. Moreover, branched chains showed a higher fragility index (m = 3.46 for the bottlebrush and 5.36 for the star) compared to linear chains (m = 3.29) due to dynamical heterogeneities induced by arm relaxation. The addition of nanoparticles affects only the terminal relaxation regime, where the whole chain motion is hindered by the attractive nanoparticles. The dynamics of the polymer segment were investigated by performing broadband dielectric spectroscopy (BDS) at a frequency range from 10-2 Hz to 107 Hz. The results revealed more than 10 times slower segmental relaxation for the star homopolymers and a slowdown in the α-relaxation process for all three architectures in their composite form. The dynamical slowdown in the composites is temperature dependent and more pronounced at low temperatures (leading to approximately equal to 80 times slower dynamics for nanocomposite with bottlebrush PMMA at 150 °C) due to prolonged relaxation of the interfacial polymer compared to the matrix chains. The results from this study have practical applications in fields such as gas separation and polymeric electrolyte membranes, where simultaneous improvement of segmental mobility and mechanical moduli is highly desired.