Browse Articles
Discover research articles across all indexed journals
RNA gradients can guide condensates toward promoters: Implications for enhancer–promoter contacts and condensate-promoter kissing
We study how protein condensates respond to a site of active RNA transcription (i.e., a gene promoter) due to electrostatic protein–RNA interactions. Our results indicate that condensates can show directed motion toward the promoter, driven by gradients in the RNA concentration. Analytical theory, consistent with simulations, predicts that the droplet velocity has a non-monotonic dependence on the distance to the promoter. We explore the consequences of this gradient-sensing mechanism for enhancer–promoter (E–P) communication using polymer simulations of the intervening chromatin chain. Directed motion of enhancer-bound condensates can, together with loop extrusion by cohesin, collaboratively increase the enhancer–promoter contact probability. Finally, we investigate under which conditions condensates can exhibit oscillations in their morphology and in the distance to the promoter. Oscillatory dynamics are caused by a delayed response of transcription to condensate-promoter contact and negative feedback from the accumulation of RNA at the promoter, which results in charge repulsion.
Complex-variable MP2 theory applied to core-vacant states for the computation of Auger spectra
We model Auger spectra using second-order Møller–Plesset perturbation (MP2) theory combined with complex-scaled basis functions. For this purpose, we decompose the complex MP2 energy of the core-hole state into contributions from specific decay channels and propose a corresponding equation-of-motion (EOM) method for computing the doubly ionized final states of Auger decay. These methods lead to significant savings in computational cost compared to our recently developed approaches based on coupled-cluster theory [F. Matz and T.-C. Jagau, J. Chem. Phys. 156, 114117 (2022)]. The test set for this study comprises water, ammonia, methane, hydrogen sulfide, phosphine, and silane. The energies of the final states of Auger decay are obtained with an accuracy comparable to EOM coupled-cluster singles and doubles (CCSD) theory. Partial decay widths and branching ratios between KLL, KLM, and KMM decay of K-shell holes in third-row hydrides are in good agreement with EOM-CCSD, while deviations are more significant for second-row hydrides. For L1-shell holes, which undergo Coster–Kronig decay, MP2 yields unphysical results. However, we show that a suitable shift of the MP2 energy denominators leads to more reliable branching ratios and spectra for these problematic cases.
Specific interactions and mechanism of association in highly viscous aldehyde 3-phenylpropanal
In this paper, we investigated the thermal, dynamical, and structural properties, as well as association patterns, in 3-phenyl-1-propanol (3P1Pol) and 3-phenyl-1-propanal (3P1Pal), with special attention paid to the latter compound. Both systems turned out to be good glass formers, differing by 17 K in the glass transition temperature, which indicated a strong change in the self-assembly pattern. This supposition was further confirmed by the analysis of dielectric spectra, where, apart from the α-relaxation, also a unique Debye (D)-mode, being a fingerprint of the self-association, characterized by different dynamical properties (dielectric strength, timescale separation from the α-process), was detected in both samples. Further diffraction and infrared investigations, supported by density functional theory computations and molecular dynamics (MD) simulations, revealed that hydrogen (H)-bonds play a key role in the association in 3P1Pol, while in 3P1Pal, there are at least five different intermolecular interactions involving dipole–dipole forces and π-stacking, as well as extraordinary H-bonds formed between methylene groups neighboring with the formyl unit and carbonyl moiety. Finally, optimized dimeric structures, along with MD simulations, allowed us to propose a molecular mechanism responsible for the D-process in 3P1Pal. The presented data systematize previous understanding of molecular association as well as open new ways of exploring this phenomenon in aldehydes.
Modeling the time evolution of the structure factor during polymeric spinodal decomposition using dynamic mode decomposition
The development of the microstructure during polymeric spinodal decomposition can be monitored in real time using small-angle scattering. Information about the microstructure can be deduced from measurements of the structure factor—a quantity directly proportional to the scattered intensity. While the time evolution of the structure factor can be measured relatively easily, modeling it has proved to be much more difficult. We believe the latter could be impeding our ability to control spinodal decomposition. Using synthetic data corresponding to two different polymer blends, we investigate the use of dynamic mode decomposition to model the time evolution of the structure factor during polymeric spinodal decomposition. Based on the accuracy and range of the predictions we obtained using dynamic mode decomposition, we believe our results are promising for the use of dynamic mode decomposition in an experimental setting, which could improve our ability to control spinodal decomposition in automated experiments.
Directed message passing neural networks enhanced graph convolutional learning for accurate polymer density prediction
Polymer density is a critical factor influencing material performance and industrial applications, and it can be tailored by modifying the chemical structure of repeating units. Traditional polymer density characterization methods rely heavily on domain expertise; however, the vast chemical space comprising over one million potential polymer structures makes conventional experimental screening inefficient and costly. In this study, we proposed a machine learning framework for polymer density prediction, rigorously evaluating four models: neural networks (NNs), random forest (RF), XGBoost, and graph convolutional neural networks (GCNNs). Using a curated dataset of 1432 homopolymers from the PoLyInfo database, our comparative analysis indicated that the GCNN model enhanced by a directed message passing neural network (D-MPNN) for feature extraction achieves superior predictive accuracy (mean absolute error, MAE = 0.0497 g/cm3; coefficient of determination, R2 = 0.8097) relative to the other models. Experimental validation on six polymers demonstrated strong agreement between measured densities and GCNN predictions with relative errors not exceeding 4.8%. In-depth error analysis combined with SHapley additive exPlanations (SHAP) and subgroup evaluations reveals fundamental relationships between specific functional groups and polymer density, improving the model’s interpretability. Furthermore, t-SNE visualization and kernel density estimation (KDE) analysis revealed that the D-MPNN framework effectively captures critical chemical space features governing density, explaining the GCNN’s superior performance. This work establishes a reliable and scalable computational framework for high-throughput polymer screening, providing scientific insights into structure–property relationships while positioning density prediction as a prerequisite for incorporating density-dependent properties into polymer informatics and accelerating the discovery of novel polymer materials.
Water catalytic effect on the carbinolamine reaction with amine-catalyzed mesoporous silica nanoparticles
The formation of carbinolamine represents the crucial initial step in the aldol reaction, specifically involving the interaction between p-nitrobenzaldehyde and acetone, facilitated by amine-catalyzed mesoporous silica nanoparticles (amine-MSN). In this process, a nitrogen atom from propylamine, which acts as the catalytic moiety, engages in the formation of a covalent bond with a carbon atom from acetone, leading to the generation of a carbinolamine intermediate. This reaction is significantly influenced by the presence of silanol groups located on the surface of the amine-MSN, which contribute to the catalytic activity. Moreover, the reaction solvent plays a vital role; water serves as an essential solvent that enhances the rate of the aldol reaction. In this work, a comprehensive investigation is conducted to understand the catalytic influence of water explicitly in carbinolamine formation via three distinct pathways: (1) without the assistance of silanol groups, (2) silanol assistance occurs indirectly through hydrogen bonding, and (3) a pathway that showcases direct silanol assistance in the hydrogen atom transfer processes. To analyze the reaction mechanism in the amine-MSN system, this study employs the fragment molecular orbital method, which can accurately treat the complexities associated with large molecular systems like the MSN pore model (Si392O958H348). The concerted mechanism study reveals that the presence of water molecules significantly lowers the energy barrier associated with carbinolamine formation, thereby enhancing the feasibility and efficiency of the reaction. This insight highlights the pivotal role of the solvent and the nature of catalytic sites in optimizing aldol reactions within mesoporous silica frameworks.
Atomistically resolved hot exciton relaxation dynamics in CdSe quantum dots: Experiment and theory
Semiconductor quantum dots (QDs) are well known to give rise to a quantum confined structure of excitons. Because of this quantum confinement, new physics of hot exciton relaxation dynamics arises. Decades of work using transient absorption (TA) spectroscopy have yielded initial simple observations, such as estimates of the cooling rate from single pump photon energy experiments. More detailed TA experiments employed variable pump photon energies to measure excitonic state-resolved transition rates. These TA measurements, usually the simplest form, have been employed to characterize QDs and their relaxation dynamics to this day. Yet, these TA measurements are fundamentally lacking in their ability to measure energy-resolved hot exciton cooling, which requires observation of the full cooling history through the real excitonic manifold. Here, we employ coherent multi-dimensional spectroscopy (CMDS) to perform an atomistically directed study of hot exciton cooling in CdSe QDs, revealing energy resolved relaxation dynamics. CMDS experiments are compared with simulations and prior TA measurements and simpler theories. Our findings reveal a hot exciton relaxation dynamics landscape. This relaxation dynamics landscape is a linear or sub-linear function of excess energy for different structures of QDs, with a strong size dependence. Our model simulations parameterized by the empirical pseudopotential model reproduces the experimental functional form and the dependence upon QD diameter and shell.
Theoretical study of Lewis base passivation of <i>p-</i>type surface defects in I–Br mixed-halide tin perovskites
Perovskite–silicon tandem solar cells have attracted considerable attention owing to their high power conversion efficiency (PCE), which exceeds the limits of single-junction devices. This study focused on lead-free tin-based perovskites with iodine–bromine mixed anions. Bromide perovskites have a wide bandgap; therefore, they are promising light absorbers for perovskite–silicon tandem solar cells. However, surface defects generally affect the PCE of Sn-based perovskite solar cells because they serve as trapping and recombination sites for excitons (electron–hole pairs). In this study, density functional theory calculations were employed to investigate the molecular passivation of surface defects in Sn-based mixed-halide perovskites. The results showed that a Lewis base is effective for passivating p-type defects. In addition, we established a molecule–defect interaction model to explain the passivation mechanism.
Relativistic two-component double ionization potential equation-of-motion coupled cluster with the Dirac–Coulomb–Breit Hamiltonian
We present an implementation of relativistic double ionization potential (DIP) equation-of-motion coupled cluster (EOMCC) with up to 4-hole–2-particle (4h2p) excitations that makes use of the molecular mean-field exact two-component (mmfX2C) framework. We apply mmfX2C-DIP-EOMCC to several neutral atoms and diatomic molecules to obtain the ground and first few excited states of the corresponding dication species, and we observe excellent agreement (to within 0.001 eV) between DIPs obtained from mmfX2C- and four-component DIP-EOMCC calculations that include 3-hole–1-particle (3h1p) excitations, with either the Dirac–Coulomb or Dirac–Coulomb–Gaunt Hamiltonians. We also compare double IPs for mmfX2C-DIP-EOMCC calculations with the full Dirac–Coulomb–Breit Hamiltonian to those from experiment. The mmfX2C-DIP-EOMCC with 3h1p excitations leads to errors in absolute double IPs that generally overestimate experimental data for noble gases by 0.1–0.4 eV, whereas the inclusion of 4h2p excitations results in double IPs that are too low by 0.1–0.2 eV, at the large basis set limit.
Operator forces for coarse-grained molecular dynamics
Coarse-grained (CG) molecular dynamics simulations extend the length and time scales of atomistic simulations by replacing groups of correlated atoms with CG beads. Machine-learned coarse-graining (MLCG) has recently emerged as a promising approach to construct highly accurate force fields for CG molecular dynamics. However, the calibration of MLCG force fields typically hinges on force matching, which demands extensive reference atomistic trajectories with corresponding force labels. In practice, atomistic forces are often not recorded, making traditional force matching infeasible on pre-existing datasets. Recently, noise-based kernels have been introduced to adapt force matching to the low-data regime, including situations in which reference atomistic forces are not present. While this approach produces force fields that recapitulate slow collective motion, it introduces significant local distortions due to the corrupting effects of the noise-based kernel. In this work, we introduce more general kernels based on normalizing flows that substantially reduce these local distortions while preserving global conformational accuracy. We demonstrate our method on small proteins, showing that flow-based kernels can generate high-quality CG forces solely from configurational samples.
Double-hybrid density-functional theory with density-based basis-set correction
We develop the theory justifying the application of the density-based basis-set correction (DBBSC) method to double-hybrid approximations in order to accelerate their basis convergence. We show that, for the one-parameter double hybrids based on the adiabatic connection, the exact dependence of the basis-set correction functional on the coupling-constant parameter λ involves a uniform coordinate scaling by a factor 1/λ of the density and of the basis functions. Neglecting this uniform coordinate scaling corresponds essentially to the recent work of Mester and Kállay, J. Phys. Chem. Lett. 16, 2136 (2025) on the application of the DBBSC method to double-hybrid approximations. Test calculations on molecular atomization energies and reaction barrier heights confirm that the DBBSC method efficiently accelerates the basis convergence of double-hybrid approximations and also show that neglecting the uniform coordinate scaling is a reasonable approximation.
Devitrification and melting in vapor deposited ice
The equilibration dynamics of ultrastable glasses subjected to heating protocols has attracted recent experimental and theoretical interest. With simulations of the mW water model, we investigate the devitrification and “melting” dynamics of both conventional quenched (QG) and vapor deposited (DG) amorphous ices under controlled heating ramps. By developing an algorithm to reconstruct hydrogen-bond networks, we show that bond ring statistics correlate with the structural stability of the glasses and allow tracking crystalline and liquid clusters during devitrification and melting. We find that QG melts in the bulk, whereas melting in DG preferentially begins near the free surface. During devitrification, the DG shows an excess of 5-membered rings near the free surface, which is consistent with its tendency to nucleate the crystal phase in this region. In addition, the DG shows an Avrami exponent exceeding the standard 1 + d behavior, while both glasses display the same sub-3d growth of liquid clusters across heating rates, indicating that the DG enhanced exponent stems from its higher kinetic stability.
Quantum state-resolved rotational scattering of C5H+ by H2 in the interstellar medium
The interstellar medium (ISM) is a complex and dynamic environment in which molecular collisions play a crucial role. Among these, protonated carbon chains are of great interest due to the presence of a permanent dipole moment and their relevance in describing astrochemical processes, making their detection possible in cold molecular clouds such as TMC-1. C5H+ (1Σg+) is an important molecule for understanding the formation and evolution of carbon-rich environments. However, to accurately model its abundance and spectroscopic properties, it is essential to account for its collisional interactions with H2, the most abundant molecule in the ISM. In this study, we present a quantum dynamical study for the C5H+–H2 collision, employing high-level CCSD(T)-F12a/aug-cc-pVTZ calculations to construct an accurate potential energy surface (PES). The PES is further augmented using a neural network fitting model, ensuring spectroscopic accuracy. The PES is expanded into radial components using bispherical harmonics. Then, close coupling methods were used to calculate cross sections and rate coefficients for different rotational transitions of C5H+, up to 100 K. Throughout the temperature range, a propensity is observed for even transitions over odd transitions. The rate coefficients for He and H2 collisions are compared for C5H+, C5, and C6H−. For both low and high temperatures, rate coefficients for C5H+ are found to be higher than C5 and C6H− for both the He and H2 collisions.
Toward electron self-localization in H2 gas: Multiple scattering effects on the electron drift mobility at low temperature and intermediate densities
We report here the first measurements of the electron drift mobility μ in gaseous H2 in the intermediate density range 0.5 × 1026 m−3 ≤ N ≤ 5 × 1026 m−3, at low temperature, T = 49.7 K and T = 29.7 K. In this range, the density is small enough to make the presence of electron states self-localized in bubbles negligible but, at the same time, is large enough for multiple scattering effects to alter the prediction of the classical kinetic theory for the mobility of quasi-free electrons. The analysis of the present data confirms the validity of the model we have developed to describe the quasi-free electron mobility in dense noble gases, which is based on the heuristic inclusion of multiple scattering effects in the classical kinetic theory.
Improved rotational characterization of the E3Σ1+(63S1) Rydberg state of CdAr van der Waals diatom: Excitation of single-isotopologue and <i>J</i>-level population distribution
An improved rotational characterization of the E3Σ1+(63S1) Rydberg state of the CdAr diatom produced in a supersonic beam and studied using laser induced fluorescence (LIF) excitation spectra is presented. As an example, the spectra of the E3Σ1+←A3Π0+(53P1) transition, originating from the excitation of a single 116Cd40Ar isotopologue, are recorded and analyzed. In the experiment, the optical–optical double resonance method is employed, utilizing the E3Σ1+(υ′)←A3Π0+(53P1)(υ″=6)←X1Σ0+(υ=0) scheme. The excitation of a single isotopologue and the influence of the first-step excitation wavenumber on rotational level population distribution are carefully investigated, facilitating the simulation of the recorded rotational profiles. Spectra of several υ′ ← υ″ = 6 vibrational components are measured. Their analysis resulted in the determination of Be′, αe′, and βe′ rotational constants. In addition, the Re′ bond length in the E3Σ1 in+ Rydberg-state inner well of 116Cd40Ar was determined. For comparison, LIF excitation spectra in multi-isotopologue excitation are discussed.
Same-group element replacement enhances superconductivity in clathrate-like YH4
H3S, LaH10, and hydrogen-based compounds have garnered significant interest due to their high-temperature superconducting properties. However, the requirement for extremely high pressures limits their practical applications. In this study, YH4 is adopted as a base material, with partial substitution of yttrium (Y) by scandium (Sc), lanthanum (La), and zirconium (Zr). Pure YH4, stable at 120 GPa, exhibits a critical temperature (Tc) of 84–95 K. Substituting half of the Y atoms increases Tc to 124.43 K for (Y,Sc)H4 at 100 GPa but reduces it to 101.24 K for (Y,La)H4 at 120 GPa. In contrast, (Y,Zr)H4 at 200 GPa shows a further suppressed Tc of 69.55 K. The remarkable superconductivity in (Y,Sc)H4 might be related to its unique phonon dispersion without an optical-acoustic gap, compressed Y–H bonds, and significant electron delocalization under pressure, collectively boosting electron–phonon interactions. Furthermore, the lowest optical phonons play a crucial role in the superconductivity of these materials. This work suggests that substituting Y with same-group metal elements is an effective strategy to enhance Tc in hydride superconductors.
Extended non-Markovian stochastic Schrödinger equation with complex frequency modes for general basis functions
We introduce an extended formulation of the non-Markovian stochastic Schrödinger equation with complex frequency modes (extended cNMSSE), designed for simulating open quantum system dynamics under arbitrary spectral densities. This extension employs non-exponential basis sets to expand the bath correlation functions, overcoming the reliance of the original cNMSSE on exponential decompositions of the spectral density. Consequently, the extended cNMSSE is applicable to environments beyond those characterized by Debye-type spectral densities. The flexibility to employ general basis functions is particularly advantageous for handling spectral densities with higher-order poles, for which exponential decompositions are often inaccurate or unavailable. The extended cNMSSE is implemented in a pseudo-Fock space using conventional ladder operators and solved efficiently via matrix product state techniques, preserving the favorable linear-scaling and wavefunction-based nature of the original method. Benchmark simulations across four representative cases, including discrete spectral density, Ohmic spectral density with exponential and algebraic cutoffs, and critically damped Brownian spectral density, demonstrate excellent agreement with results of hierarchy of forward–backward stochastic Schrödinger equations and extended hierarchical equation of motion.
Reproducibility of fixed-node diffusion Monte Carlo across diverse community codes: The case of water–methane dimer
Fixed-node diffusion quantum Monte Carlo (FN-DMC) is a widely trusted many-body method for solving the Schrödinger equation, known for its reliable predictions of material and molecular properties. Furthermore, its excellent scalability with system complexity and near-perfect utilization of computational power make FN-DMC ideally positioned to leverage new advances in computing to address increasingly complex scientific problems. Even though the method is widely used as a computational gold standard, reproducibility across the numerous FN-DMC code implementations has yet to be demonstrated. This difficulty stems from the diverse array of DMC algorithms and trial wave functions, compounded by the method’s inherent stochastic nature. This study represents a community-wide effort to assess the reproducibility of the method, affirming that yes, FN-DMC is reproducible (when handled with care). Using the water–methane dimer as the canonical test case, we compare results from eleven different FN-DMC codes and show that the approximations to treat the non-locality of pseudopotentials are the primary source of the discrepancies between them. In particular, we demonstrate that, for the same choice of determinantal component in the trial wave function, reliable and reproducible predictions can be achieved by employing the T-move, the determinant locality approximation, or the determinant T-move schemes, while the older locality approximation leads to considerable variability in results. These findings demonstrate that, with appropriate choices of algorithmic details, fixed-node DMC is reproducible across diverse community codes—highlighting the maturity and robustness of the method as a tool for open and reliable computational science.
Kinetic rate calculation via non-equilibrium dynamics
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein–ligand complexes. By integrating Kramers’s theory with Bell’s equation, our method systematically investigates the relationship between the effective biasing force applied during simulations and the ligand residence times. The proposed technique is demonstrated through extensive simulations of the benzamidine–trypsin complex, employing first an implicit solvent model (multi-eGO) to set up the approach parameters and then an explicit solvent model. Our results illustrate the method’s reliability, accuracy, and computational efficiency, with calculated kinetic rates closely matching experimental values. Overall, this study highlights rMD as a versatile and efficient non-equilibrium methodology, broadly applicable to kinetic analyses in chemical and biological systems.
Reassignment of the vibronic structure in the absorption spectrum of carbon cluster anion C6− exhibiting fast radiative cooling
Linear carbon cluster anions, such as C6−, have been considered to be promising candidate interstellar molecules. Recent experiments have demonstrated that in a collision-free vacuum environment, C6− exhibits fast radiative cooling from its highly vibrationally excited states through inverse internal conversion (IIC). Since IIC is driven by vibronic coupling, the understanding of vibronic structures of C6− is of theoretical significance. Here, we utilize time-dependent density functional theory to calculate the absorption spectrum of C6−, allowing us to reassign the peaks in the experimental spectrum to the vibronic progressions associated with the C2Πg ← X2Πu and D2Πg ← X2Πu electronic transitions. A vibronic coupling density analysis reasonably explains the strong vibronic peaks and validates the reassignment. We also discuss the potential softening caused by quadratic vibronic coupling in the excited states and the partially allowed vibronic transitions. In addition, we show that a pseudo-Jahn–Teller distortion occurs along the ν4(σu+) antisymmetric stretching mode due to the pseudo-degeneracy of the A and B states.