Differentiating cardiogenic pulmonary oedema (CPE) from non-cardiogenic and structurally normal lungs in lung ultrasound (LUS) videos remains challenging due to the high visual variability of non-cardiogenic inflammatory patterns (NCIP/ARDS-like), interstitial lung disease, and healthy lungs. This heterogeneity complicates automated classification as overlapping B-lines and pleural artefacts are common. We introduce ZACH-ViT (Zero-token Adaptive Compact Hierarchical Vision Transformer), a 0.25 M-parameter Vision Transformer variant that removes both positional embeddings and the [CLS] token, making it fully permutation-invariant and suitable for unordered medical image data. To enhance generalization, we propose ShuffleStrides Data Augmentation (SSDA), which permutes probe-view sequences and frame orders while preserving anatomical validity. ZACH-ViT was evaluated on 380 LUS videos from 95 critically ill patients against nine state-of-the-art baselines. Despite the heterogeneity of the non-cardiogenic group, ZACH-ViT achieved the highest validation and test ROC-AUC (0.80 and 0.79) with balanced sensitivity (0.60) and specificity (0.91), while all competing models collapsed to trivial classification. It trains 1.35x faster than Minimal ViT (0.62M parameters) with 2.5x fewer parameters, supporting real-time clinical deployment. These results show that aligning architectural design with data structure can outperform scale in small-data medical imaging.

This paper demonstrates the efficacy of a modified U-Net structure for the extraction of vascular tree masks for human fundus photographs. On limited compute resources and training data, the proposed model only slightly underperforms when compared to state of the art methods.

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or their complexes, are strongly influenced by protonation changes of their typically many titratable groups, which explains their pH sensitivity. In turn, conformational and environmental changes in the biomolecule affect the protonation state of these groups. With a few exceptions, conventional force field-based molecular dynamics (MD) simulations do not account for these effects, nor do they allow for coupling to a pH buffer. The $λ$-dynamics method implements this coupling and thus allows for MD simulations at constant pH. It uses separate Hamiltonians for the protonated and deprotonated states of each titratable group, with a $λ$ variable that continuously interpolates between them. However, rigorous implementations of Hamiltonian Interpolation (HI) $λ$-dynamics are prohibitively slow when used with Particle Mesh Ewald (PME). To circumvent this problem, it has been proposed to interpolate the charges instead of the Hamiltonians (QI). Here, we propose a rigorous yet efficient Multipole-Accelerated Hamiltonian Interpolation (MAHI) method to perform $λ$-dynamics in GROMACS. Starting from a charge-scaled Hamiltonian, precomputed with the Fast Multipole Method (FMM) or with PME, the correct HI forces are calculated with negligible computational overhead. We compare HI with QI and show that HI leads to more frequent transitions between protonation states, resulting in better sampling and accuracy. Our performance benchmarks show that introducing, e.g., 512 titratable sites to a one million atom MD system increases runtime by less than 20% compared to a regular FMM-based simulation. We have integrated the scheme into our GPU-FMM code for the simulation software GROMACS, allowing an easy and effortless transition from standard force field simulations to constant pH simulations.

The structural dynamics of biological macromolecules, such as proteins, DNA/RNA, or complexes thereof, are strongly influenced by protonation changes of their typically many titratable groups, which explains their sensitivity to pH changes. Conversely, conformational and environmental changes of the biomolecule affect the protonation state of these groups. With few exceptions, conventional force field-based molecular dynamics (MD) simulations do not account for these effects, nor do they allow for coupling to a pH buffer. Here we present a GROMACS implementation of a rigorous Hamiltonian interpolation $λ$-dynamics constant pH method, which rests on GPU-accelerated Fast Multipole Method (FMM) electrostatics. Our implementation supports both CHARMM36m and Amber99sb*-ILDN force fields and is largely automated to enable seamless switching from regular MD to constant pH MD, involving minimal changes to the input files. Here, the first of two companion papers describes the underlying constant pH protocol and sample applications to several prototypical benchmark systems such as cardiotoxin V, lysozyme, and staphylococcal nuclease. Enhanced convergence is achieved through a new dynamic barrier height optimization method, and high p$K_a$ accuracy is demonstrated. We use Functional Mode Analysis and Mutual Information to explore the complex intra- and intermolecular couplings between the protonation states of titratable groups as well as those between protonation states and conformational dynamics. We identify striking conformation-dependent p$K_a$ variations and unexpected inter-residue couplings. Conformation-protonation coupling is identified as a primary cause of the slow protonation convergence notorious to constant pH simulations involving multiple titratable groups, suggesting enhanced sampling methods to accelerate convergence.

Aqueous zinc-air batteries (ZABs) are a low-cost, safe, and sustainable technology for stationary energy storage. ZABs with pH-buffered near-neutral electrolytes have the potential for longer lifetime compared to traditional alkaline ZABs due to the slower absorption of carbonates at non-alkaline pH values. However, existing near-neutral electrolytes often contain halide salts, which are corrosive and threaten the precipitation of ZnO as the dominant discharge product. This paper presents a method for designing halide-free aqueous ZAB electrolytes using thermodynamic descriptors to computationally screen components. The dynamic performance of a ZAB with one possible halide-free aqueous electrolyte based on organic salts is simulated using an advanced method of continuum modeling, and the results are validated by experiments. XRD, SEM, and EDS measurements of Zn electrodes show that ZnO is the dominant discharge product, and operando pH measurements confirm the stability of the electrolyte pH during cell cycling. Long-term full cell cycling tests are performed, and RRDE measurements elucidate the mechanism of ORR and OER. Our analysis shows that aqueous electrolytes containing organic salts could be a promising field of research for zinc-based batteries, due to their Zn$^{2+}$ chelating and pH buffering properties. We discuss the remaining challenges including the electrochemical stability of the electrolyte components.

There is more and more evidence that machine learning can be successfully applied in materials science and related fields. However, datasets in these fields are often quite small ($\ll1000$ samples). It makes the most advanced machine learning techniques remain neglected, as they are considered to be applicable to big data only. Moreover, materials informatics methods often rely on human-engineered descriptors, that should be carefully chosen, or even created, to fit the physicochemical property that one intends to predict. In this article, we propose a new method that tackles both the issue of small datasets and the difficulty of task-specific descriptors development. The SMILES-X is an autonomous pipeline for molecular compounds characterisation based on a \{Embed-Encode-Attend-Predict\} neural architecture with a data-specific Bayesian hyper-parameters optimisation. The only input to the architecture -- the SMILES strings -- are de-canonicalised in order to efficiently augment the data. One of the key features of the architecture is the attention mechanism, which enables the interpretation of output predictions without extra computational cost. The SMILES-X shows new state-of-the-art results in the inference of aqueous solubility ($\overline{RMSE}_{test} \simeq 0.57 \pm 0.07$ mols/L), hydration free energy ($\overline{RMSE}_{test} \simeq 0.81 \pm 0.22$ kcal/mol, which is $\sim 24.5\%$ better than molecular dynamics simulations), and octanol/water distribution coefficient ($\overline{RMSE}_{test} \simeq 0.59 \pm 0.02$ for LogD at pH 7.4) of molecular compounds. The SMILES-X is intended to become an important asset in the toolkit of materials scientists and chemists. The source code for the SMILES-X is available at \href{https://github.com/GLambard/SMILES-X}{github.com/GLambard/SMILES-X}.

Water autoionization plays a critical role in determining pH and properties of various chemical and biological processes occurring in the water mediated environment. The strikingly unsymmetrical potential energy surface of the dissociation process poses a great challenge to the mechanistic study. Here, we demonstrate that reliable sampling of the ionization path is accessible through nanosecond timescale metadynamics simulation enhanced by machine learning of the neural network potentials with ab initio precision, which is proved by quantitatively reproduced water equilibrium constant (p$K_\mathrm{w}$=14.14) and ionization rate constant (1.566$\times10^{-3}$ s$^{-1}$). Statistical analysis unveils the asynchronous character of the concerted triple proton transfer process. Based on conditional ensemble average calculations, we propose a dual-presolvation mechanism, which suggests that a pair of hypercoordinated and undercoordinated waters bridged by one \ce{H2O} cooperatively constitutes the initiation environment for autoionization, and contributes majorly to the local electric field fluctuation to promote water dissociation.

In a previous paper (math-ph/0202002) an Euler angle parameterization for SU(4) was given. Here we present the derivation of a generalized Euler angle parameterization for SU(N). The formula for the calculation of the Haar measure for SU(N) as well as its relation to Marinov's volume formula for SU(N) will also be derived. As an example of this parameterization's usefulness, the density matrix parameterization and invariant volume element for a qubit/qutrit, three qubit and two three-state systems, also known as two qutrit systems, will also be given.

Let H be a self-adjoint operator such that exp(-aH) is of trace class for some a<1. Let V be a symmetric operator, Kato bounded relative to H. We show that log Tr[exp(-H+xV)] is a real analytic function of x in a hood of x=0. We show that the Gibbs states of H+xV form a real analytic Banach manifold. This work has been extended in math-ph/9910031.

When a chromophore interacts with titrable molecular sites, the modeling of its photophysical properties requires to take into account all their possible protonation states. We have developed a multi-scale protocol, based on constant-pH molecular dynamics simulations coupled to QM/MM excitation energy calculations, aimed at sampling both the phase space and protonation state space of a short polypeptide featuring a tyrosine--tryptophan dyad interacting with two aspartic acid residues. We show that such a protocol is accurate enough to reproduce the tyrosine UV absorption spectrum at both acidic and basic pH. Moreover, it is confirmed that UV-induced radical tryptophan is reduced thanks to an electron transfer from tyrosine, ultimately explaining the complex pH-dependent behavior of the peptide spectrum.