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brium chain structure reveals that all chains studied are non-Gaussian. However, longer chains better approximate ideal chain dimensions than more rod-like shorter chains and thus are most closely described by a single friction parameter. We also find that the separability of the conservative and dissipative potentials is preserved.Since their emergence in the 1990s, mesoscopic models of fluids have been widely used to study complex organization and transport phenomena beyond the molecular scale. Even though these models are designed based on results from physics at the meso- and macroscale, such as fluid mechanics and statistical field theory, the underlying microscopic foundation of these models is not as well defined. This paper aims to build such a systematic connection using bottom-up coarse-graining methods. From the recently developed dynamic coarse-graining scheme, we introduce a statistical inference framework of explicit many-body conservative interaction that quantitatively recapitulates the mesoscopic structure of the underlying fluid. To further consider the dissipative and fluctuation forces, we design a novel algorithm that parameterizes these forces. By utilizing this algorithm, we derive pairwise decomposable friction kernels under both non-Markovian and Markovian limits where both short- and long-time features of the coarse-grained dynamics are reproduced. Finally, through these new developments, the many-body dissipative particle dynamics type of equations of motion are successfully derived. The methodologies developed in this work thus open a new avenue for the construction of direct bottom-up mesoscopic models that naturally bridge the meso- and macroscopic physics.In this work, a new parameterization for the Statistical Association Fluid Theory for potentials of Variable Range (SAFT-VR) is coupled to the discrete potential theory to represent the thermodynamic properties of several fluids, ranging from molecular liquids to colloidal-like dispersions. In this way, this version of the SAFT-VR approach can be straightforwardly applied to any kind of either simple or complex fluid. In particular, two interaction potentials, namely, the Lennard-Jones and the hard-core attractive Yukawa potentials, are discretized to study the vapor-liquid equilibrium properties of both molecular and complex liquids, respectively. Our results are assessed with Monte Carlo computer simulations and available and accurate theoretical results based on the self-consistent Ornstein-Zernike approximation.Strain in two-dimensional transition metal dichalcogenide has led to localized states with exciting optical properties, in particular, in view of designing one photon sources. selleck compound The naturally formed nanobubbles when the MoS2 monolayer is deposited on an hBN substrate lead to a local reduction in the band gap due to strain developing in the nanobubble. The photogenerated particles are thus confined in the strain-induced potential. Using numerical diagonalization, we simulate the spectra of the confined exciton states, their oscillator strengths, and their radiative lifetimes. We show that a single state of the confined exciton is optically active, which suggests that the MoS2/hBN nanobubbles are a good candidate for the realization of single-photon sources. Furthermore, our calculations show that the localized exciton gains in activation energy and radiative lifetime inside the nanobubble, the latter decreasing toward the one of free excitons when the nanobubble size increases.The vibrational quenching cross sections and corresponding low-temperature rate constants for the ν = 1 and ν = 2 states of CN-(1Σ+) colliding with He and Ar atoms have been computed ab initio using new three-dimensional potential energy surfaces. Little work has been carried out so far on low-energy vibrationally inelastic collisions for anions with neutral atoms. The cross sections and rates calculated at energies and temperatures relevant for both ion traps and astrochemical modeling are found by the present calculations to be even smaller than those of the similar C2-/He and C2-/Ar systems, which are in turn of the order of those existing for the collisions involving neutral diatom-atom systems. The implications of our finding in the present case mainly focus on the possible role of small computed rate constants in the dynamics of molecular cooling and the evolution of astrochemical modeling networks.In this paper, new Newton and Gauss-Newton methods for iterative coarse-graining based on integral equation theory are evaluated and extended. In these methods, the potential update is calculated from the current and target radial distribution function, similar to iterative Boltzmann inversion, but gives a potential update of quality comparable with inverse Monte Carlo. This works well for the coarse-graining of molecules to single beads, which we demonstrate for water. We also extend the methods to systems that include coarse-grained bonded interactions and examine their convergence behavior. Finally, using the Gauss-Newton method with constraints, we derive a model for single bead methanol in implicit water, which matches the osmotic pressure of the atomistic reference. An implementation of all new methods is provided for the open-source VOTCA package.We compare and contrast folding behavior in several coarse-grained protein models, both on- and off-lattice, in an attempt to uncover the effect of lattice constraints in these kinds of models. Using modern, extended ensemble Monte Carlo methods-Wang-Landau sampling, multicanonical sampling, replica-exchange Wang-Landau sampling, and replica-exchange multicanonical sampling, we investigate the thermodynamic and structural behavior of the protein Crambin within the context of the hydrophobic-polar, hydrophobic-"neutral"-polar (H0P), and semi-flexible H0P model frameworks. We uncover the folding process in all cases; all models undergo, at least, the two major structural transitions observed in nature-the coil-globule collapse and the folding transition. As the complexity of the model increases, these two major transitions begin to split into multi-step processes, wherein the lattice coarse-graining has a significant impact on the details of these processes. The results show that the level of structural coarse-graining is coupled to the level of interaction coarse-graining.
Homepage: https://www.selleckchem.com/products/lxs-196.html
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