State Model Research Articles

Flow Matching for Optimal Reaction Coordinates of Biomolecular Systems.

We present flow matching for reaction coordinates (FMRC), a novel deep learning algorithm designed to identify optimal reaction coordinates (RC) in biomolecular reversible dynamics. FMRC is based on the mathematical principles of lumpability and decomposability, which we reformulate into a conditional probability framework for efficient data-driven optimization using deep generative models. While FMRC does not explicitly learn the well-established transfer operator or its eigenfunctions, it can effectively encode the dynamics of leading eigenfunctions of the system transfer operator into its low-dimensional RC space. We further quantitatively compare its performance with several state-of-the-art algorithms by evaluating the quality of Markov state models (MSM) constructed in their respective RC spaces, demonstrating the superiority of FMRC in three increasingly complex biomolecular systems. In addition, we successfully demonstrated the efficacy of FMRC for bias deposition in the enhanced sampling of a simple model system. Finally, we discuss its potential applications in downstream applications such as enhanced sampling methods and MSM construction.

New Constraints on the Melting Temperature and Phase Stability of Shocked Iron up to 270 GPa Probed by Ultrafast X-Ray Absorption Spectroscopy

Studying the properties and phase diagram of iron at high-pressure and high-temperature conditions has relevant implications for Earth’s inner structure and dynamics and the temperature of the inner core boundary (ICB) at 330 GPa. Also, a hexagonal-closed packed to body-centered cubic (bcc) phase transition has been predicted by many theoretical works but observed only in a few experiments. The recent coupling of high-power laser with advanced x-ray sources from synchrotrons allows for novel approaches to address these issues. Here, we present a study on shock compressed iron up to 270 GPa and 5800 K probed by single-pulse (100 ps FWHM) x-ray absorption spectroscopy (XAS). Based on the analysis of the XAS spectra, we provide structural identification and bulk temperature measurements along the Hugoniot up to the melting. These results rule out the predicted transition to a high-temperature bcc phase and allow one to discriminate among existing equations of state models and melting curves. In particular, we report the first bulk temperature measurement in shock compressed iron on the melting plateau at 240(20) GPa and 5345(600) K. The melting curve resulting from our work extrapolates to a temperature of 6202(514) K at 330 GPa and represents a refined upper bound for the ICB temperature. Published by the American Physical Society 2024

Fiat-Shamir for Proofs Lacks a Proof Even in the Presence of Shared Entanglement

We explore the cryptographic power of arbitrary shared physical resources. The most general such resource is access to a fresh entangled quantum state at the outset of each protocol execution. We call this the Common Reference Quantum State (CRQS) model, in analogy to the well-known Common Reference String (CRS). The CRQS model is a natural generalization of the CRS model but appears to be more powerful: in the two-party setting, a CRQS can sometimes exhibit properties associated with a Random Oracle queried once by measuring a maximally entangled state in one of many mutually unbiased bases. We formalize this notion as a Weak One-Time Random Oracle (WOTRO), where we only ask of the m-bit output to have some randomness when conditioned on the n-bit input.We show that when n−m∈ω(lg⁡n), any protocol for WOTRO in the CRQS model can be attacked by an (inefficient) adversary. Moreover, our adversary is efficiently simulatable, which rules out the possibility of proving the computational security of a scheme by a fully black-box reduction to a cryptographic game assumption. On the other hand, we introduce a non-game quantum assumption for hash functions that implies WOTRO in the CRQS model (where the CRQS consists only of EPR pairs). We first build a statistically secure WOTRO protocol where m=n, then hash the output.The impossibility of WOTRO has the following consequences. First, we show the fully-black-box impossibility of a quantum Fiat-Shamir transform, extending the impossibility result of Bitansky et al. (TCC 2013) to the CRQS model. Second, we show a fully-black-box impossibility result for a strenghtened version of quantum lightning (Zhandry, Eurocrypt 2019) where quantum bolts have an additional parameter that cannot be changed without generating new bolts. Our results also apply to 2-message protocols in the plain model.

The Paradoxical State: The Political Economy of Multidimensional Gender Inequality in Korea

ABSTRACT Why do Korean women, who live in one of the most technologically and economically dynamic countries in the world, lag so far behind men in most important aspects of social life? Conventional answers to this question believe that more government intervention is needed, but Korea has followed state feminist policies since democratisation with limited success. This article draws on insights from the field of feminist political economy and the theory of performativity to propose a revised model of state–society interaction that better explains this puzzle. Historically, the South Korean state has oscillated between creating gender inequality for its economic and political nation-building projects, and then seeking to reduce it for the purposes of social reproduction. However, this reverse movement is ‘sticky’ because many non-state actors’ performances of gender inequality are resistant to state feminism, and others are closely associated with national identity. We conduct a plausibility probe of our model by applying it to three key performances of gender in Korea: traditional culture, conscription, and sex work. Our findings suggest the need for more bottom-up activism and campaigns against actors within and beyond the state who continue to resist gender equality.

Ideologies that South Africa can borrow from selected high-growth nations in efforts to re-establish its developmental state model

This article examines the philosophies that South Africa can adopt from specific high-growth nations to reinstate its "developmental state" paradigm. In the post-Apartheid period, following South Africa's liberation from the governing National Party, numerous initiatives were suggested to rejuvenate the nation and enhance its presence on both national and global stages. The newly established ANC government, under the leadership of Nelson Mandela, formulated and implemented several people-centric policies and strategic initiatives. The administration embraced "developmental state" ideals, believing that state economic engagement may improve its ability to address the legacy of apartheid, especially the challenges of poverty, unemployment, and widespread inequalities. Nevertheless, despite three decades of democracy, the purported "developmental state" continues to exhibit numerous governance and socioeconomic issues, including elevated poverty rates, social inequality, disparate land access, unemployment, and disparities in public service availability. The discourse on South Africa's status as a "developmental state" persists, along with enquiries into how the nation may realign itself to achieve its goal of being a "developmental state." This document seeks to compile methods that South Africa could use based on examples from selected high-growth nations. This paper will examine how South Africa might reverse its economic decline, the necessary institutional and structural reforms, and the social and political contexts required to establish itself as a more credible "developmental state". This research utilises a qualitative secondary analysis of existing textual data regarding the relationship between South Africa, the "developmental state," and the chosen high-growth countries.

Numerical Study of Biomass Combustion Using a Transient State Approach

The behavior of the temperature and velocity, as well as the mass fraction of water (H2O) and wood inside a combustion chamber under specific operating conditions, were numerically investigated using a transient state model. For the computational fluid dynamics (CFD) simulation, the software Ansys Fluent 2024 R2 was used to analyze a turbulent flow in two dimensions. The species transport with volumetric responses and eddy dissipation were included in the combustion simulation. The study was conducted for the first 150 s. The findings show that in the lower and upper zones of the combustion chamber close to the walls, the temperature rises over time. The velocity between the outlets rises over time. Due to the fact that the wood goes through a process that reduces the amount of wood and produces H2O, it exhibits the opposite behavior for the mass fractions of wood and H2O.

Kalman filter time scale algorithm based on noise characteristics of optically pumped cesium clock

Abstract The time scale algorithm plays an important role in time keeping. Currently, the time scale algorithm primarily adopts the predictability weighting algorithm for microwave clocks. Due to the different working principles and performance of optically pumped small cesium clocks compared with microwave clocks, a new time scale algorithm must be developed to adapt to optically pumped clocks. Based on the noise characteristics of the optically pumped clocks, the state model is established and the time scale is calculated using the Kalman filtering algorithm. The state model of the optically pumped clocks simultaneously considers the effects of white frequency modulation, flicker frequency modulation, and random walk frequency modulation. The proposed algorithm models the flicker frequency modulation for filtering estimation, which effectively improves the stability of the time scale. Here, the flicker frequency modulation is modeled through the linear combination of Markov processes, and the impact of different numbers of Markov processes on the time scale stability is analyzed. Compared with the predictability weighted algorithm, the results obtained by the proposed algorithm demonstrate that the frequency stability of the Kalman filtering time scale based on the noise characteristics was better than that of the predictability algorithm. Taking rapid Coordinated Universal Time (UTCr) as a reference, the frequency stabilities of the time scale based on three optically pumped clocks obtained by the proposed algorithm were 1.14 × 10−14 for 15 days and 5.50 × 10−15 for 30 days.

TiO2-x-MoS2 heterostructure: A study of kinetic, thermodynamic, and scavenging agents’ effects in photodegradation

Numerous applications for photocatalysis exist in the energy and environmental sectors. In this study, a heterojunction system comprising oxygen vacancies-mediated TiO2 nanorods (TiO2-x) modified with MoS2 nanosheets (TiO2-x-MoS2) was prepared using the hydrothermal method. The photocatalytic activity of TiO2-x-MoS2 heterostructure is about 3 times higher than that of pure TiO2. The heterostructure significantly improved the photoinduced charge carrier separation efficiency, resulting in an increase in active species including ˙OH, O2˙−, and h+. Additionally, the Langmuir-Hinshelwood (L-H) model was employed to model kinetic and equilibrium data. The results of scavenging studies indicated that the photocatalytic process heavily relies on superoxide radicals. Additionally, the sensitivity of photocatalytic rates to temperature through kinetic studies based on Arrhenius and transition state models was investigated, which yielded an activation energy of 23.01 kJ/mol for the process. A positive activation entropy (ΔS = +0.017 kJ/mol) was obtained, along with positive ΔH and ΔG values, for the Rhodamine B photodegradation. This work underscores the critical role of oxygen vacancies and heterostructures in advancing wastewater treatment approaches.

YUGOSLAVIA AND EUROCOMMUNIST PARTIES DURING THE ‘LONG YEAR’ OF EUROPEAN DEMOCRATIC SOCIALISM (1974–1976)

In the late 1960s and early 1970s, Mediterranean communist parties’ political practices and party ideologies, the League of Communists of Yugoslavia’s (LCY) policies, and the socialist model of the Yugoslav state, underwent gradual changes according to similar principles. This allowed existing cooperation between the LCY and future Eurocommunist parties to expand. At this time, the countries of Western Europe were experiencing a period of unprecedented economic growth and a reduction in social inequalities. This period eventually ended in political turmoil and crisis caused by ideological and cultural changes significantly driven by the same long-term consequences of developing welfare state models in the Western Bloc’s largest economies. A new social reality in Western Europe, the Mediterranean region, and Yugoslavia, the Mediterranean’s closest socialist country, would influence the events leading to the zenith of the LCY’s influence on the European far left and also to the eventual downfall of the international leftist initiatives launched by the LCY and the Eurocommunist parties. This article will present findings from archival research regarding certain aspects that may have influenced these changes in the international positions of and relations between the LCY and the Eurocommunist parties. It will compare it to those of previous studies within the humanities and social sciences.

Measuring and modeling the solubility of sulfasalazine in supercritical carbon dioxide to select methods for producing nanoparticles

In the present study, the solubility of sulfasalazine in carbon dioxide was investigated at temperatures ranging from 313 K to 343 K and pressures ranging from 12 to 30 MPa. The experimentally determined molar solubilities of sulfasalazine in ScCO2 were found to be in the range of 4.08 × 10− 5 to 8.61 × 10− 5 at 313 K, 3.54 × 10− 5 to 11.41 × 10− 5 at 323 K, 3.04 × 10− 5 to 13.64 × 10− 5 at 333 K, and 2.66 × 10− 5 to 16.35 × 10− 5 at 343 K. The solubility values were correlated via a number of different types of equations, such as semi-empirical correlations, the Peng-Robinson, the PC-SAFT equation, and the regular solution. Furthermore, the findings demonstrate that semi-empirical, equation of state models, and the regular solution model possess the capability of precisely determining the solubility. Moreover, the solubility magnitude suggests that the gas anti-solvent method may be a viable approach for nanoparticle production.

A thermodynamic critical state model for sands

A thermodynamic critical state model for sands

3D geological fine modeling and dynamic updating method of fault slope in open-pit coal mine

Combining the requirements for refined modeling and dynamic update of fault slope geological models in open-pit coal mines, we systematically elaborated on the elements and rules of slope 3D geological modeling and proposed a fine modeling and dynamic updating method based on digital elevation model (DEM) and half-edge boundary representation (B-Rep) data structures. Initially, the stratigraphic division of the study area is conducted based on borehole and section data, combined with the geological evolution history and the level set theory. Applying inverse distance weighting (IDW) for estimation, the geological interface triangular irregular network (TIN) is constructed using the TIN algorithm. Secondly, fine reconstruction of fault surfaces through Morphing transformation improves the accuracy and smoothness of fault surface shape reconstruction under sparse data conditions. Then, the intersection-cutting processing method of fault-fault and fault-stratum for slope geological ground state model modeling under complex fault segmentation is investigated. Finally, constructing 3D geological models of fault slopes and the integrated correction of surface and subsurface are realized through dynamic updating methods for 3D surfaces and strata. Taking the 3D geological modeling of a fault slope of an open-pit coal mine in China as an example, the feasibility of the technical method is verified.

Dust ring and gap formation by gas flow induced by low-mass planets embedded in protoplanetary disks

The observed dust rings and gaps in protoplanetary disks could be imprints of forming planets. Even low-mass planets in the 1-10 Earth-mass regime, which have not yet carved deep gas gaps, can generate such dust rings and gaps by driving a radially-outward gas flow, as shown in previous work. However, understanding the creation and evolution of these dust structures is challenging due to dust drift and diffusion, requiring an approach beyond previous steady state models. Here we investigate the time evolution of the dust surface density influenced by the planet-induced gas flow, based on post-processing three-dimensional hydrodynamical simulations. We find that planets larger than a dimensionless thermal mass of m = 0.05, corresponding to 0.3 Earth mass at 1 au or 1.7 Earth masses at 10 au, generate dust rings and gaps, provided that solids have small Stokes numbers (St ≲ 10−2) and that the disk midplane is weakly turbulent (αdiff ≲10−4). As dust particles pile up outside the orbit of the planet, the interior gap expands with time when the advective flux dominates over diffusion. Dust gap depths range from a factor of a few to several orders of magnitude, depending on planet mass and the level of midplane particle diffusion. We constructed a semi-analytic model describing the width of the dust ring and gap, and then compared it with the observational data. We find that up to 65% of the observed wide-orbit gaps could be explained as resulting from the presence of a low-mass planet, assuming αdiff = 10−5 and St = 10−3. However, it is more challenging to explain the observed wide rings, which in our model would require the presence of a population of small particles (St = 10−4). Further work is needed to explore the role of pebble fragmentation, planet migration, and the effect of multiple planets.

Internal states emerge early during learning of a perceptual decision-making task.

Recent work has shown that during perceptual decision-making tasks, animals frequently alternate between different internal states or strategies. However, the question of how or when these emerge during learning remains an important open problem. Does an animal alternate between multiple strategies from the very start of training, or only after extensive exposure to a task? Here we address this question by developing a dynamic latent state model, which we applied to training data from mice learning to perform a visual decision-making task. Remarkably, we found that mice exhibited distinct "engaged" and "biased" states even during early training, with multiple states apparent from the second training session onward. Moreover, our model revealed that the gradual improvement in task performance over the course of training arose from a combination of two factors: (1) increased sensitivity to stimuli across all states; and (2) increased proportion of time spent in a higher-accuracy "engaged" state relative to biased or disengaged states. These findings highlight the power of our approach for characterizing the temporal evolution of multiple strategies across learning.

The Real-Time Observation of Electric Vehicle Operating Points Using an Extended Kalman Filter

Electric Vehicles (EVs) are set to play a crucial role in the energy transition. Although EVs offer significant environmental benefits, their technology still faces major challenges related to performance optimization, energy efficiency improvement, and cost reduction. A key point to address these challenges is the accurate identification of the speed/torque operating points of the drive systems. However, this identification is generally achieved using mechanical sensors, which are fragile, bulky, and expensive. This paper aims to develop, implement, and validate a speed/torque observer in real time based on the Extended Kalman Filter (EKF) approach for an EV equipped with an Open-End Winding Induction Motor with Dual Inverter (OEWIM-DI). The implementation of the EKF is based on the state modeling of the OEWIM-DI, enabling the observation of the torque and speed using voltage and current measurements. The validation of this approach is conducted experimentally on the FPGA and DS1104 boards. The results show that this approach offers excellent performance in terms of accuracy, stability, and real-time response speed. These results suggest that the proposed method could significantly contribute to the advancement of EV technology by providing a more robust and cost-effective alternative to traditional mechanical sensors while improving the overall efficiency and performance of EV drive systems.

The G protein inhibitor YM-254890 is an allosteric glue.

Given the prominence of G protein coupled receptors (GPCRs) as drug targets, targeting their immediate downstream effectors, G proteins, could be of immense therapeutic value. The discovery that the natural product YM-254890 (YM) can arrest uveal melanoma by specifically inhibiting constitutively active Gq/11without impacting other G protein families demonstrates the potential of this approach. However, efforts to find other G protein family-specific inhibitors have had limited success. Better understanding the mechanism of YM could facilitate efforts to develop other highly specific G protein inhibitors. We hypothesized that differences between the conformational distributions of various G proteins play an important role in determining he specificity of inhibitors like YM. To explore this hypothesis, we built Markov state models (MSMs) from molecular dynamics simulations of the Gα subunits of three different G proteins, as YM predominantly contacts Gα. We also modeled the heterotrimeric versions of these proteins where Gα is bound to the Gβγ heterodimer. We find that YM-sensitive Gα proteins have a higher probability of adopting YM-bound-like conformations than insensitive variants. There is also strong allosteric coupling between the YM- and Gβγ-binding interfaces of Gα. This allostery gives rise to positive cooperativity, wherein the presence of Gβγ enhances preorganization for YM binding. We predict that YM acts as an "allosteric" glue that allosterically stabilizes the complex between Gα and Gβγ despite the minimal contacts between YM and Gβγ.

Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling.

As a model system, the binding pocket of the L99A mutant of T4 lysozyme has been the subject of numerous computational free energy studies. However, previous studies have failed to fully sample and account for the observed changes in the binding pocket of T4 L99A upon binding of a congeneric ligand series, limiting the accuracy of results. In this work, we resolve the closed, intermediate, and open states for T4 L99A previously reported in experiment in MD and establish definitions for these states based on the dynamics of the system. From this analysis, we arrive at two primary conclusions. First, assignment of simulation trajectories into discrete states should not be done simply based on RMSD to crystal structures as this can result in misassignment of states. Second, the different metastable conformations studied here need to be carefully treated, as we estimate the time scales for conformational interconversion to be on the order of 102 to 103 ns─far longer than time scales for typical binding calculations. We conclude with a discussion on the need to develop enhanced sampling methods to generally account for significant changes in protein conformation due to relatively small ligand perturbations.

When can flexible weak polyelectrolytes be treated as effective rigid objects?

Conformational and ionization equilibria of flexible weak polyelectrolytes (PEs) are, in general, strongly coupled. In this article, we analyze the effect of averaging over (or "contracting") the conformational degrees of freedom so that the original flexible molecule is replaced by an effective rigid object with the same ionization properties. As a result, one obtains the so-called Site Binding (SB) model, much easier to treat both theoretically and computationally, and extensively used to characterize the ionization properties of PE. The conformational averages can be performed in a systematic way by means of the Conformational Contraction Equations (CCEs), which relate the SB parameters to the underlying conformational equilibrium. The conditions for the convergence of the CCE are evaluated in the presence of both Short Range (SR) and Long Range (LR) electrostatic interactions. Two analytically solvable models based on the Freely Jointed Chain (FJC), involving only SR interactions, are analyzed at first. Despite the large chain flexibility, the resulting SB model reproduces the ionization properties with high accuracy. In the case of independent bonds, a very flexible chain can be exactly replaced by an effective rigid object with neighboring pairwise interactions. In general, however, triplet and higher order interactions emerge at the SB level. When LR electrostatic interactions are introduced and combined with the FJC large chain flexibility, the convergence of the CCE for long chains becomes problematic since the SB free energy must be truncated. Similar conclusions are reached for the freely rotating chain and rotational isomeric state models.

An Integrated Model for Dam Break Flood Including Reservoir Area, Breach Evolution, and Downstream Flood Propagation

The reasonable and efficient prediction of dam failure events is of great significance to the emergency rescue operations and the reduction in dam failure losses. This work presents a model that is based on the physical mechanism. It is coupled with a multi-architecture (multi-CPU and GPU) open-source two-dimensional flood model, which is based on high-precision terrain and land use data. The aim is to enhance the accuracy of dam break flood process simulations. The model uses DEM data as a computational grid and updates it at each time step to reflect breach evolution. Simultaneously, the breach evolution model incorporates an analysis of stress on sediment particles, establishing the initial erosion state and lateral expansion model while accounting for seepage. The determination of the overflow of the breach is resolved through the application of a two-dimensional hydrodynamic model. This approach achieves a robust connection between the upstream reservoir, the dam structure, and the downstream inundation area. The coupled model is utilized to calculate the failure of earth-rock dams and landslide dams, and a sensitivity analysis is conducted. Taum Sauk Dam and Tangjiashan landslide dam were selected to represent earth dam break and barrier lake break, respectively, which are the main types of dam breaks. The obtained results demonstrate strong concurrence with the measured data, the relative errors of the four important parameters of the application case, the peak discharge of the breach, the top width of the final breach, the depth of the breach and the arrival time of the maximum peak discharge are all within ±10%. Although the relative error of the completion time of the final breach is greater than 10%, it is about 30% less than the relative error of the physical model.

CASM-U: a unified critical state model for unsaturated clays and sands

CASM-U: a unified critical state model for unsaturated clays and sands