A measure to quantify the degree of strong convexity at the coarse-grained level is proposed. It is shown that the convexity score scheme can identify the interaction distance fairly well even while the position of the global minimum of the derivative of average transfer entropy does not. We also derive an analytical model to explain the relationship between the interaction domain and the change in transfer entropy that supports our cutoff distance technique to elucidate the underlying interaction domain from trajectories.The accurate description of iron oxides/water interfaces requires reliable force field parameters that can be developed through comparison with sophisticated quantum mechanical calculations. Here, a set of CLASS2 force field parameters is optimized to describe the Fe-Owater cross-interaction through comparison with hybrid density functional theory (HSE06) calculations of the potential energy function for a single water molecule adsorbed on the Fe3O4 (001) surface and with density functional tight binding (DFTB+U) molecular dynamics simulations for a water trilayer on the same surface. Selleckchem ND646 The performance of the new parameters is assessed through the analysis of the number density profile of a water bulk (12 nm) sandwiched between two magnetite slabs of large surface area. Their transferability is tested for water adsorption on the curved surface of a spherical Fe3O4 nanoparticle of realistic size (2.5 nm).We consider chemical reaction networks modeled by a discrete state and continuous in time Markov process for the vector copy number of the species and provide a novel particle filter method for state and parameter estimation based on exact observation of some of the species in continuous time. The conditional probability distribution of the unobserved states is shown to satisfy a system of differential equations with jumps. We provide a method of simulating a process that is a proxy for the vector copy number of the unobserved species along with a weight. The resulting weighted Monte Carlo simulation is then used to compute the conditional probability distribution of the unobserved species. We also show how our algorithm can be adapted for a Bayesian estimation of parameters and for the estimation of a past state value based on observations up to a future time.Perturbative nonlinear optical spectroscopies are powerful methods to understand the dynamics of excitonic and other condensed phase systems. Feynman diagrams have long provided the essential tool to understand and interpret experimental spectra and to organize the calculation of spectra for model systems. When optical pulses are strictly time ordered, only a small number of diagrams contribute, but in many experiments, pulse-overlap effects are important for interpreting results. When pulses overlap, the number of contributing diagrams can increase rapidly, especially with higher order spectroscopies, and human error is especially likely when attempting to write down all the diagrams. We present an automated Diagram Generator (DG) that generates all the Feynman diagrams needed to calculate any nth-order spectroscopic signal. We characterize all perturbative nonlinear spectroscopies by their associated phase-discrimination condition as well as the time intervals where pulse amplitudes are nonzero. Although the DG can be used to automate impulsive calculations, its greatest strength lies in automating finite pulse calculations where pulse overlaps are important. We consider third-order transient absorption spectroscopy and fifth-order exciton-exciton interaction 2D (EEI2D) spectroscopy, which are described by six or seven diagrams in the impulsive limit, respectively, but 16 or 240 diagrams, respectively, when pulses overlap. The DG allows users to automatically include all relevant diagrams at a relatively low computational cost, since the extra diagrams are only generated for the inter-pulse delays where they are relevant. For EEI2D spectroscopy, we show the important effects of including the overlap diagrams.Plasmon-enhanced coherent Raman scattering microscopy has reached single-molecule detection sensitivity. Due to the different driven fields, there are significant differences between a coherent Raman scattering process and its plasmon-enhanced derivative. The commonly accepted line shapes for coherent anti-Stokes Raman scattering and stimulated Raman scattering do not hold for the plasmon-enhanced condition. Here, we present a theoretical model that describes the spectral line shapes in plasmon-enhanced coherent anti-Stokes Raman scattering (PECARS). Experimentally, we measured PECARS and plasmon-enhanced stimulated Raman scattering (PESRS) spectra of 4-mercaptopyridine adsorbed on the self-assembled Au nanoparticle (NP) substrate and aggregated Au NP colloids. The PECARS spectra show a nondispersive line shape, while the PESRS spectra exhibit a dispersive line shape. PECARS shows a higher signal to noise ratio and a larger enhancement factor than PESRS from the same specimen. It is verified that the nonresonant background in PECARS originates from the photoluminescence of nanostructures. The decoupling of background and the vibrational resonance component results in the nondispersive line shape in PECARS. More local electric field enhancements are involved in the PECARS process than in PESRS, which results in a higher enhancement factor in PECARS. The current work provides new insight into the mechanism of plasmon-enhanced coherent Raman scattering and helps to optimize the experimental design for ultrasensitive chemical imaging.In this work, we show that van der Waals molecules X-RG (where RG is the rare gas atom) may be created through direct three-body recombination collisions, i.e., X + RG + RG → X-RG + RG. In particular, the three-body recombination rate at temperatures relevant for buffer gas cell experiments is calculated via a classical trajectory method in hyperspherical coordinates [Pérez-Ríos et al., J. Chem. Phys. 140, 044307 (2014)]. As a result, it is found that the formation of van der Waals molecules in buffer gas cells (1 K ≲ T ≲ 10 K) is dominated by the long-range tail (distances larger than the LeRoy radius) of the X-RG interaction. For higher temperatures, the short-range region of the potential becomes more significant. Moreover, we notice that the rate of formation of van der Walls molecules is of the same order of the magnitude independent of the chemical properties of X. As a consequence, almost any X-RG molecule may be created and observed in a buffer gas cell under proper conditions.