Browse Articles

Defensive responses of titan triggerfish to tiger sharks at a provisioned reef

Phase behavior of a machine-learning potential trained on stress–strain curves: The case of superionic water ice

We analyze the transferability of a Deep Potential Machine Learning (DP-ML) model trained to reproduce stress–strain curves of high-temperature/high-pressure crystalline phases of water, determining the coexistence lines for the phase transitions between the insulating ice X and the superionic ice XVIII and that between ice XVIII and its melt. Using a set of various free-energy calculation techniques, we find the resulting coexistence lines to be in good agreement with previous data, indicating that the deformation-trained DP-ML model also transfers to thermodynamic properties. This suggests that the inclusion of deformed solid states in training sets may also be a beneficial general strategy in the development of ML interaction models for other condensed-matter systems. Furthermore, the DP-ML model should be useful to investigate other aspects of the considered phase transitions. One of these involves the possible characterization of the XVIII–liquid transition as weakly first-order, with its potentially associated continuous-like behavior. This is an interesting prospect since it might be the first example of such a transition in a three-dimensional structural solid–liquid transformation.

Lactiplantibacillus plantarum from Thai fermented pork with inulin ameliorates metabolic disturbances through proteomic mechanisms

Repetitive proteins that undergo large conformational changes evade structural prediction algorithms

Protein structure prediction algorithms, such as AlphaFold, have accelerated protein design and advanced the understanding of the relationship between amino acid sequence and protein structure. However, these algorithms are limited in their ability to predict the structures of conformationally dynamic, intrinsically disordered, and stimuli-responsive proteins. To evaluate sequence-to-structure predictions of such challenging proteins, we explored a class of conformationally dynamic, repeats-in-toxin (RTX) proteins. RTX proteins adopt intrinsically disordered conformations in the absence of calcium and undergo reversible folding into β-roll structures upon binding to calcium. RTX proteins are characterized by tandem repeats of the sequence GGXGXDXUX, in which X can be any amino acid and U is an aliphatic amino acid. We designed RTX sequence variants with global substitutions of nonconserved amino acids, tandem repeats of consensus sequences GGAGXDTLY, and tandem repeats of scrambled sequences GGAGXDTYL. AlphaFold2 and AlphaFold3 predicted that all of these RTX variants adopt β-roll structures, characteristic of wild-type RTX bound to calcium. However, modeling the predicted structures with molecular dynamics simulations and characterizing the protein variants with circular dichroism spectroscopy, small-angle x-ray scattering, and x-ray crystallography revealed that variants adopt diverse, sequence-dependent structures in the absence and presence of calcium. To better design proteins for applications in biotechnology and sustainability, it is critical to build predictive tools that consider intrinsically disordered protein states and validate these tools with multi-mode, multi-scale experimental data.

Investigating the influence of astringent compounds on oral lubrication and the protective role of proline-rich proteins

Abstract Astringency, characterized by dryness and roughness in the mouth, is a major challenge for the acceptance of plant-based protein-rich foods. The mechanisms behind this sensation, particularly the role of mucins and the oral epithelium, remain unclear. This study investigates the impact of tannins, specifically epigallocatechin gallate (EgCG), on oral lubrication and examines the role of MUC1 protein in the lubrification and potentially in the astringency perception. The protective effect of proline-rich proteins (PRPs) is also explored. In vitro tribological tests were performed on four oral epithelial models expressing different MUC1 isoforms, using a reconstructed mucosal pellicle. A homemade biotribometer measured friction and dissipated energy to assess tannin-mucin interactions. Results confirm that EgCG disrupts epithelial lubrication, increasing frictional forces. However, MUC1 expression, particularly its structure, reduces these effects by preventing tannin aggregation and preserving lubrication. PRPs also enhance lubrication by binding tannins, limiting their interaction with mucins. This study highlights the roles of MUC1 and PRPs in oral lubrication in the presence of tannins.

Quantum hierarchical Fokker–Planck equations with U(1) gauge fields [U(1)-QHFPE]: A computational framework for Aharonov–Bohm effects

We present a software package that solves the quantum Fokker–Planck equation with gauge fields, formulated within the hierarchical equations of motion framework [U(1)-QHFPE]. The framework rigorously preserves gauge invariance and rotational symmetry under non-Markovian and non-perturbative system–bath (S–B) interactions, enabling accurate simulations of transport phenomena such as the Aharonov–Bohm effect under thermal environments. In a strong S–B coupling regime, quantum S–B entanglement emerges naturally. The demonstration programs perform calculations of response functions in Aharonov–Bohm ring geometries with a mechanical potential that may induce quantum tunneling, thereby illustrating the software’s capability to resolve topological quantum interference in dissipative open systems. Written in C++, the code includes a central processing unit version with highly readable OpenMP directives and a graphics processing unit version tailored for high-performance computing.

FireCastNet: earth-as-a-graph for seasonal fire prediction

Calculating excitonic interactions using transition currents with application to PTCDA

We consider assemblies of molecules where the electronic wavefunctions of different molecules do not overlap. Typically, the interaction Hamiltonian between two molecules is then described by their Coulomb interaction, and matrix-elements between products of single-molecule energy eigenstates are calculated using the corresponding (transition) charge densities. In the present work, we compare this approach with one based on (transition) current densities. As an example, we perform calculations for 3,4,9,10-perylenetetracarboxylicacid-dianhydride (PTCDA) molecules in different arrangements. We find that for exact molecular wavefunctions, both methods agree, but there are marked differences for the wavefunctions that we obtained from electronic-structure theory. The main difference can be attributed to the error in the molecular transition energy and results in an arrangement-independent ratio between the interactions calculated with the two approaches. At small separations between the molecules, additional deviations occur, which we trace back to the quality of the molecular electronic wavefunctions. Within both approaches, we calculate interactions for the arrangement of PTCDA on KCl and NaCl surfaces and compare to the ones obtained using the point–dipole approximation. Finally, we provide a simple algorithm that allows fast and accurate calculations of the involved integrals.

Constructing a prognostic signature of tumor-associated B lymphocytes in hepatocellular carcinoma via machine learning integration

Revisiting the access conductance of a nanopore in a charged membrane

Electric-field-driven electrolyte transport through nanoporous membranes is important for applications including osmotic power generation, sensing, and iontronics. We derive an analytical equation in the Debye–Hückel regime and a semi-analytical equation for arbitrary surface potentials for the electric-field-driven electric current through a pore in an ultrathin membrane, which predict scaling with fractional powers of the pore size and Debye length. We show that our theory for arbitrary electric potentials accurately quantifies the ionic conductance through an ultrathin membrane in finite-element method numerical simulations for a wide range of parameters and generalizes a widely used theory for the access electrical conductance of a membrane nanopore to a broader range of conditions. Our theory predicts that fractional power-law scaling of the ionic conductance with electrolyte concentration at low concentrations is an intrinsic property of charged ultrathin membranes and also occurs for thicker membranes for which the access contribution to the conductance dominates, which could help to explain experimental observations of this widely debated phenomenon.

Anatomical and anthropometric predictors of femoral and saphenous nerve location for ultrasound guided procedures

pH-dependent orientation of pyruvic acid and interfacial water at the air–water interface: Insights from sum-frequency generation spectroscopy and molecular dynamics

The molecular orientation and interfacial behavior of pyruvic acid at the air–water interface were investigated as a function of pH using phase-sensitive sum-frequency generation (SFG) spectroscopy combined with density functional theory molecular dynamics simulations. By performing polarization-resolved SFG measurements on both the protonated and deprotonated forms of pyruvic acid, we characterized the vibrational signatures of the carbonyl, carboxyl, and carboxylate groups, gaining insights into their relative orientations in each state. Our results reveal a pH-dependent shift in the deprotonation equilibrium at the interface, accompanied by distinct reorientations of pyruvic acid functional groups: the deprotonated COO− and C=O groups preferentially tilt toward the bulk aqueous phase. Furthermore, the orientation and hydrogen-bonding network of interfacial water molecules respond sensitively to pyruvic acid deprotonation, as evidenced by a reversal in the sign of the O–D stretching mode, indicating a reorientation of water dipoles. These findings offer detailed molecular-level insights into the structural dynamics of pyruvic acid at aqueous interfaces, with significant implications for understanding interfacial acid–base chemistry and solvation processes, which may serve as a foundational step toward unraveling pyruvic acid photochemistry.

Barrier impermeability is associated with migratory ungulate survival rates

Analytical analysis of the conformational and rheological properties of flexible active polar linear polymers under shear flow

The conformational and rheological properties of active polar linear polymers under linear shear flow are studied analytically. We describe a discrete active polar linear polymer as an inextensible flexible Gaussian bead–spring chain supplemented by active forces along the bonds. The linear, non-Hermitian equations of motion are solved by an eigenfunction expansion in terms of a biorthogonal basis set. The model reveals an intimate coupling between activity and shear flow, which implies activity-enhanced polymer conformational and rheological properties. Compared to a passive polymer, we find a significantly enhanced shrinkage transverse to the flow direction with increasing shear rate, with a power-law exponent of −4/3, compared to the passive value of −2/3. This conformational change is tightly linked with a strongly amplified shear-thinning behavior, where the shear viscosity exhibits the same power law. The characteristic shear rate for the onset of these effects is determined by the activity. In the asymptotic limit of large activities, the shear-induced features become independent of activity and equal to those of passive polymers.

Effects of rear-foot instability devices on lower-limb muscle activation during the Bulgarian split squat in male football players

Abstract Unilateral resistance exercises such as the Bulgarian Split Squat (BSS) are commonly used to develop lower-limb strength, postural control, and neuromuscular coordination, depending on training variables (e.g., load and intensity). Although instability training increases muscle activation, few studies have examined the effect of rearfoot instability on neuromuscular responses during BSS. This randomized crossover study investigated the acute effects of three rear-foot instability devices on muscle activation during the ascent and descent phases of the BSS in 23 trained male football players. Participants performed body-weight BSS under four conditions: stable platform, BOSU ball, Swiss ball (Swiss), and TRX suspension. Surface electromyography (sEMG) recorded activation of the rectus femoris (RF), vastus lateralis (VL), vastus medialis (VM), biceps femoris (BF), semitendinosus (ST), and gluteus maximus (GM). Two‑way repeated‑measures ANOVA showed significantly greater activation during ascent for BF ( p  < 0.001), ST ( p  = 0.006), VL ( p  < 0.001), VM ( p  < 0.001), and GM ( p  < 0.001). Quadriceps activation during descent was highest on the Swiss: RF (Swiss vs. stable: p  = 0.002; Swiss vs. BOSU: p  < 0.001; Swiss vs. TRX: p  = 0.006), VL (Swiss vs. stable: p  = 0.017; Swiss vs. BOSU: p  = 0.001), and VM (Swiss vs. stable: p  = 0.024; Swiss vs. BOSU: p  = 0.046). TRX increased ST activation during the ascent compared to the Swiss ( p  = 0.034), and the BOSU showed higher ST activation than the Swiss during the descent ( p  = 0.004). Surface significantly affected activation (ST: p  = 0.018; RF: p  < 0.001; VL: p  < 0.001; VM: p  = 0.013; GM: p  = 0.042), and there was a significant surface × phase interaction for GM ( p  = 0.041). The findings highlight rearfoot instability as an effective programming variable to selectively enhance muscle activation without external loading, supporting its application in strength and rehabilitation programs.

An anomalous high-pressure phase and decompression-induced amorphization in dinitrotoluene

We investigate the high-pressure behavior of 2,4-dinitrotoluene (2,4-DNT), an energetic molecular solid, using in situ Raman spectroscopy (up to ∼19 GPa) and synchrotron x-ray diffraction (up to ∼12.3 GPa). Raman spectra reveal conformational rearrangements of the ortho-NO2 group near 1.5 GPa and a structural phase transition between 4 and 8 GPa. X-ray diffraction measurements corroborate this transition, showing the onset at ∼4.5 GPa and sluggish completion by ∼8.4 GPa. The ambient phase shows pronounced anisotropic compression, consistent with its layered crystal structure, while both phases display negative linear compressibility. In the high-pressure phase, only one-dimensional long-range order is preserved, accompanied by the formation of new hydrogen bonds. A larger phonon gap in 2,4-DNT (∼104 cm−1) indicates reduced impact sensitivity compared to trinitrotoluene [trinitrotoluene (TNT), ∼80 cm−1]. Upon decompression, two distinct recovery pathways are observed: samples released from P ≤ 10 GPa revert to the ambient phase with hysteresis, while those released from P ≥ 12.3 GPa undergo decompression-induced amorphization due to the changes in the hydrogen bonding network. The contrasting compression and recovery behavior of 2,4-DNT and TNT are also discussed, highlighting the critical role of functional-group interactions and pressure history in governing phase stability and amorphization in energetic molecular crystals.

GIS-integrated flood risk assessment for metro systems based on bayesian cosine maximization method: a case study in Beijing

Rotational relaxation of SH+ by collisions with He

The first two-dimensional potential energy surface for the interaction between He and SH+(3Σ−) has been calculated using CCSD(T)/aug-cc-pVXZ(X = T,Q,5) supplemented by a three-term extrapolation scheme. This surface is subsequently employed in close coupling calculations to investigate the collision dynamics of SH+ with He atoms. The collisional cross sections for fine structure energy levels are computed. The de-excitation rate coefficients for the lower fine structure levels of SH+ molecules due to collisions with He are determined over a temperature range of 10–500 K.

Novel structures of chaos-based parallel multiple image encryption and FPGA implementation

Abstract Image data has been generated massively by devices in medical imaging modalities, cameras, and even by artificial intelligence. Encryption is the powerful method to keep the image content confidential, in which an encryption algorithm must include the confusion and diffusion properties. For massive images, a efficient method of encryption must be chosen to meet the demands of encryption speed and confidentiality. So far, chaos-based image encryption has been an active topic of research because it is considered an effective method to remove the correlation in image data as well as to keep confidential by the involvement of chaotic system in the encryption process. Besides, multiple image encryption algorithms encrypt multiple images in parallel, and it provides highly efficient performance in term of speed if it is implemented on a parallel computing platform such as multiple core processing as well as digital hardware design. Chaos-based multiple image encryption is constructed by integrating a chaotic system into multiple image encryption. Recently, many algorithms of chaos-based multiple image encryption have been proposed, and they are proved to have high efficient in terms of both speed and confidentiality. However, all the existing algorithms of chaos-based multiple image encryption require images of the same size and of the same number of bits representing pixels. Further, they encrypt a cohort of plain images at the same time, and all ciphertext images of a cohort must also be decrypted at the same time. It means that if it does not allow to decrypt one or some selected ciphertext images from a cohort separately; and as a result, it wastes time and energy to decrypt unwanted images. In this paper, three novel structures of chaos-based multiple image encryption are proposed which overcome the drawbacks of existing algorithms. That is, the proposed cryptosystems accept cohort images of different sizes; pixels of images can be represented by different numbers of bits; and any selected ciphertext images from a cohort can be decrypted separately. The security is improved by using the session keys of image-content dependency. The proposed structures of multiple image encryption consist of permutation, substitution, and diffusion processes. The difference between three structures is the order of such processes. A perturbed chaotic map and a linear-feedback shift register are employed to generate pseudo-random bit sequences for session keys. The simulation results for the exemplar designs using the proposed structures show the effectiveness by means of the statistical analysis for the session keys using the NIST randomness test, information entropy, histogram, and correlation coefficients of adjacent pixels in ciphertext images, and security analysis by means of space and sensitivity of the secret key. The hardware implementation on the FPGA platform demonstrates the feasibility of the proposed structures by means of throughput and hardware efficiency.

Semiclassical analytic theory of multi-channel electronic energy transfer in nonadiabatic atomic collisions

The semiclassical theory of nonadiabatic energy transfer [Adamovich and Rich, J. Chem. Phys. 160, 194101 (2024)] is extended to include multi-channel electronic excitation and quenching in three-dimensional atomic collisions. The transition probabilities, cross sections, and rate coefficients predicted by the theory are compared with high-fidelity quantum scattering predictions for N + N, using state-of-the-art ab initio interaction potentials and nonadiabatic couplings, and with a few available experiments. The theory predictions are in good agreement with quantum scattering, both for conditions where the energy transfer is dominated by a single pair of adiabatic potentials and in cases where the energy transfer is affected by additional intermediate states. These cases include multiple curve crossings encountered during a single collision and pathways with the formation of closed channels, resulting in multiple resonances. The latter case is of particular interest, since it cannot be reduced to the interaction of individual potential pairs. Analytic expressions for the cross sections and rate coefficients are obtained using the same approach as in our previous work. The results quantify the effect of multi-channel interactions on the dynamics of energy transfer in atomic collisions. This approach can also be used to predict rate coefficients for electronic energy transfer in N + O and O + O collisions, as well as other atomic species collisions, such as involving Ar or He, over a wide range of temperatures. The fidelity of the theory predictions depends on the availability of accurate potentials for the interacting excited electronic states and their coupling (both spin–orbit and derivative). The results provide rate coefficients for the predictive simulation of low-temperature plasmas and plasmas generated behind hypersonic shock waves.