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Peptide classification from statistical analysis of nanopore sensing experiments
Peptide classification using nanopore-based devices promises to be a breakthrough method in basic research, diagnostics, and analytics. However, the measured blockage currents suffer from a low signal-to-noise ratio and a high information density that has hitherto not been fully deciphered. Some simple machine learning approaches using average current blockade depths and dwell-times have been investigated to improve this situation. In this work, a comprehensive statistical analysis of nanopore current signals is performed and demonstrated to be sufficient for classifying up to 42 peptides with over 70% accuracy. Two sets of features, the statistical moments and the catch22 set, are compared both in their representations and after training small classifier neural networks. We demonstrate that complex features of the events, captured in both the catch22 set and the central moments, are key to classifying peptides with otherwise similar mean currents. These results highlight the efficacy of purely statistical analysis of nanopore data and suggest a path forward for more sophisticated classification techniques.
Behavioral effects of academic pressure on the risk of adolescent idiopathic scoliosis: a case-control study
From predictors and SHAKE toward unified integration scheme for molecular dynamics
Molecular dynamics (MD) simulations applied to various special tasks such as thermostats, barostats, external volume control, or external magnetic fields often require tailored integration methods, complicating software development. Here, we propose a unified integration scheme for solving the common sets of equations of motion in MD. To achieve this, we adapted the traditional SHAKE method for treating rigid bonds to a predictor–corrector integration scheme and combined it with the existing time-reversible velocity predictor and box predictor. This new approach enables using both the time-honored Verlet method and the recently improved Gear methods. The resulting unified integration scheme was tested on two simple models and two MD systems: SPC/E water and ionic liquid (1-ethyl-3-methylimidazolium tetrafluoridoborate). Trajectories in microcanonical, Nosé–Hoover canonical, and MTK isobaric ensembles were generated. The results for Verlet-based methods were in excellent agreement with those obtained using conventional integration methods. For particular tasks, the use of higher-order methods can be beneficial. Overall, in comparison with standard approaches, our universal scheme provides a significantly simpler route to devising new integrators and maintaining existing simulation software. Furthermore, our family of new integrators can be efficiently deployed in massively parallel MD software.
Investigation of sol-gel derived organic inorganic hybrid coatings based on commercial epoxy resin for improved corrosion resistance of 304 stainless steel
Picosecond imaging of dynamics of solvated electrons during femtosecond laser-induced plasma generation in water
The dynamics of solvated electrons were visualized using absorption imaging with sub-picosecond time resolution based on a pump–probe measurement during the early stages of femtosecond laser-induced plasma generation in water. The solvated electrons were generated by the propagation of a femtosecond laser pump pulse. In the area with a pump laser intensity over 2 × 1013 W/cm2, where a high density of free electrons was produced, solvated electrons exhibited an additional rapid increase in optical density (OD) at 800 nm, 7–9 ps after the pump pulse excitation. In contrast, no two-step increase in OD was observed when probed at 400 nm, suggesting that the absorption coefficient of the solvated electrons rapidly changed around 800 nm after femtosecond laser excitation for a few picoseconds. This observation might indicate the structural and electronic modulation of solvated electrons owing to the high density of free electrons in water, accompanied by femtosecond-laser-induced plasma generation.
ChatGPT performance in assessing musculoskeletal MRI scan appropriateness based on ACR appropriateness criteria
Zero-point energies from bond orders and populations relationships
We report two analytical quantum mechanics (QM) models for approximating appropriately scaled harmonic zero-point energies (ZPEs) without Hessian calculations. Following our earlier bond energies from bond orders and populations model that takes a similar form as an extended Hückel model but uses well-conditioned orbital populations, this work demonstrates a proof of concept for approximating ZPEs, an important component in thermochemistry calculations, while eschewing unfavorably scaling algorithms involving Hessian matrices. The ZPE-BOP1 model uses Mulliken orbital populations from hybrid Kohn–Sham density functional theory calculations within an extended Hückel-type model that defines vibrational bond energy terms using two atom-pairwise parameters that are fit to reproduce ZPEs from B3LYP calculations. The more accurate ZPE-BOP2 model uses Mulliken orbital populations from Hartree–Fock calculations within a different extended Hückel-type model that includes a short-range anharmonic energy term and a coupled three-body oscillator energy term with seven atom-pairwise parameters. Both models predict ZPEs in molecules involving first row elements, but ZPE-BOP2 outperforms ZPE-BOP1 in strained and long-chain molecules and provides ZPEs more competitive with those from semi-empirical QM methods (e.g., AM1, PM6, PM7, and XTB-2) that compute ZPEs with Hessian calculations. This work shows progress and an outlook toward computational models that use well-conditioned orbital populations to efficiently predict useful physicochemical properties. It also shows opportunities for approximate QM models that would shift traditional computational bottlenecks away from costly algorithms such as Hessian calculations to others that focus on reliable orbital populations.
Effects of amino-acid functionalization and pH value on temperature-dependent water dynamics in silica confinement
2H nuclear magnetic resonance (NMR) field-cycling relaxometry and broadband dielectric spectroscopy (BDS) studies show that water dynamics in silica pores with similar diameters (∼6 nm) strongly depend on the functionalization of the inner surfaces. In all studied confinements, we observe two prominent changes in the temperature dependence of water reorientation. Specifically, the activation energy of Ea ∼ 0.3 eV in the fully liquid state more than triples to Ea ∼ 1.0 eV upon partial crystallization at Tm ∼ 258 K. Furthermore, in the partially crystallized state, the liquid fraction shows a dynamical crossover at ∼185 K, where the common low-temperature behavior of confined water with Ea = 0.4–0.5 eV is established. However, the correlation times of water reorientation are up to two orders of magnitude longer in amino-acid functionalized silica pores than in pristine ones. Comparing the results for different functional groups, NMR and BDS consistently show that the slowdown is strongest for basic lysine followed by neutral alanine and, finally, acidic glutamic acid. Based on this order, one may speculate that the changed dynamics are a consequence of different pH values of water in confinements with different functional groups. Although pH measurements confirm that the pH value strongly depends on the amino-acid functionalization, this speculation must be rejected due to the observation that water with very different pH values does not show diverse reorientation dynamics when enclosed in identical pores.
Density fluctuations, solvation thermodynamics, and coexistence curves in grand canonical molecular dynamics simulations
Fluid transport across nanometric channels induced by electric, pressure, and concentration gradients is ubiquitous in biological systems and fosters various applications. In this context, computer simulation setups with well-defined open-boundary equilibrium starting states are essential in understanding and assisting experimental studies. However, open-boundary computational methods are scarce and do not typically satisfy all the equilibrium conditions imposed by reality. Namely, in the absence of external gradients, (1) the system of interest (SoI) must be at thermodynamic and chemical equilibrium with an infinite reservoir of particles; (2) the fluctuations of the SoI in equilibrium should sample the grand canonical ensemble; (3) the local solvation thermodynamics, which is extremely sensitive to finite-size effects due to solvent depletion, should be correctly described. This point is particularly relevant for out-of-equilibrium systems; and (4) finally, the method should be robust enough to deal with phase transitions and coexistence conditions in the SoI. In this study, we demonstrate with prototypical liquid systems embedded into a reservoir of ideal gas particles that the adaptive resolution simulation (AdResS) method, coupled with particle insertion/deletion steps (AdResS+PI), satisfies all these requirements. Therefore, the AdResS+PI setup is suitable for performing grand canonical and stationary non-equilibrium simulations of open systems.
N-doped MoS2 nanoflowers for the ultrasonic-vibration-driven high piezoelectric catalytic degradation
In this study, N-doped few-layer MoS2 piezocatalysts were successfully prepared by a one-pot hydrothermal method with urea as a nitrogen source. Benefiting from the optimized proportion of minority layers at edge positions and higher conductivity by N doping, the optimal N-doped few-layer MoS2 (120 mg of added urea) sample showed the optimal piezocatalytic activity for Rhodamine B (RhB) and levofloxacin (LEV), reaching 84.6 and 73.1% with the reaction kinetic rate constant of 0.020 86 and 0.017 05 min−1, respectively. In addition, the generation of superoxide radicals (·O2−) from the 120-MoS2 sample was determined to be greater than that from the 0-MoS2 sample in the piezocatalyst process by free radical scavenging experiments and electron paramagnetic resonance tests. Based on experimental data, a potential mechanism has been proposed to explain the enhanced piezocatalyst performance of N-doped few-layer MoS2. This research sheds new light on the development of efficient, cost-effective MoS2 piezoelectric catalysts through the doping of non-metallic dopants.
Dynamics of quantum–classical systems in nonequilibrium environments
The dynamics of a quantum system coupled to a classical environment and subject to constraints that drive it out of equilibrium are described. The evolution of the system is governed by the quantum–classical Liouville equation. Rather than evaluating the evolution of the mixed quantum–classical density operator, we derive exact equations of motion for the nonequilibrium average values of a set of operators or variables, along with correlation function expressions for the dissipative coefficients that enter these equations. These equations are obtained by requiring that the exact nonequilibrium averages are equal to local nonequilibrium averages that depend on auxiliary fields whose values satisfy evolution equations obtained using projection operator methods. The results are illustrated by deriving reaction–diffusion equations coupled to fluid hydrodynamic equations for a solution of quantum particles that can exist in two metastable states. Nonequilibrium steady states are discussed along with the reaction rate and diffusion correlation functions that characterize such states.
Comment on “Microcanonical treatment of HCl dissociative chemisorption on Au(111): Reactive dampening through inefficient translational energy coupling and an active surface” [J. Chem. Phys. 160, 084702 (2024)]
Simulating nonadiabatic dynamics in benzophenone: Tracing internal conversion through photoelectron spectra
Benzophenone serves as a prototype chromophore for studying the photochemistry of aromatic ketones, with applications ranging from biochemistry to organic light-emitting diodes. In particular, its intersystem crossing from the first singlet excited state to triplet states has been extensively studied, but experimental or theoretical studies on the preceding internal conversion within the singlet manifold are very rare. This relaxation mechanism is particularly important because direct population transfer of the first singlet excited state from the ground state is inefficient due to its low oscillator strength. In this work, our aim is to fill this gap by employing mixed quantum-classical and full quantum dynamics simulations and time-resolved photoelectron spectroscopy for gas-phase benzophenone and meta-methyl benzophenone. Our results show that nonadiabatic relaxation via conical intersections leads to an increase in the population of the first singlet excited state, which appears linear within the simulation time of 500 fs. This population transfer due to conical intersections can be directly detected by a bifurcation of the photoelectron signal. In addition, we discuss to clarify the role of the third singlet excited state degenerate to the second excited state—a topic that remains largely unexplored in the existing literature on benzophenone.
Hidden asymmetry in one-dimensional alignment of chiral molecules
We studied the inversion symmetry of an ensemble of chiral molecules. We clarified that for rigid molecules aligned by dipole transitions, the positions of any two atoms depend on the molecular chirality, owing to the parity-odd second-rank tensors. This type of asymmetry, hidden in the so-called one-dimensional alignment, such as cos2θ, can be understood on the basis of the equivalence of inversion and rotation for any two points in space. Perfect chiral sensitivity is achieved when the transition dipole moment is 45° to an axis perpendicular to both position vectors of the two atoms. The positions of two specific atoms are calculated for a chiral isotopomer and methyloxirane using the spherical harmonic addition theorem. We discuss the absolute configuration and the orientation of chiral molecules.