We introduce "library based Monte Carlo" (LBMC) simulation, which performs Boltzmann sampling of molecular systems based on pre-calculated statistical libraries of molecular-fragment configurations, energies, and interactions. The library for each fragment can be Boltzmann distributed and thus account for all correlations internal to the fragment. LBMC can be applied to both atomistic and coarse-grained models, as we demonstrate in this "proof of principle" report. We first verify the approach in a toy model and in implicitly solvated poly-alanine systems. We next study five proteins, up to 309 residues in size. Based on atomistic equilibrium libraries of peptide-plane configurations, the proteins are modeled with fully atomistic backbones and simplified Gō-like interactions among residues. We show that full equilibrium sampling can be obtained in days to weeks on a single processor, suggesting that more accurate models are well within reach. For the future, LBMC provides a convenient platform for constructing adjustable or mixed-resolution models: the configurations of all atoms can be stored at no run-time cost, while an arbitrary subset of interactions is "turned on."

Given the global warming caused by excess CO 2 accumulation in the atmosphere, it is essential to reduce CO 2 by capturing and converting it to chemical feedstock using solar energy. Herein, a novel Cs 3 Bi 2 Br 9 /bismuth-based metal−organic framework (Bi-MOF) composite was prepared via an in situ growth strategy of Cs 3 Bi 2 Br 9 quantum dots (QDs) on the surface of Bi-MOF nanosheets through coshared bismuth atoms. The prepared Cs 3 Bi 2 Br 9 /Bi-MOF exhibits bifunctional merits for both the high capture and effective conversion of CO 2 , among which the optimized 3Cs 3 Bi 2 Br 9 /Bi-MOF sample shows a CO 2 −CO conversion yield as high as 572.24 μmol g −1 h −1 under the irradiation of a 300 W Xe lamp. In addition, the composite shows good stability after five recycles in humid air, and the CO 2 photoreduction efficiency does not decrease significantly. The mechanistic investigation uncovers that the intimate atomic-level contact between Cs 3 Bi 2 Br 9 and Bi-MOF via the coshared atoms not only improves the dispersion of Cs 3 Bi 2 Br 9 QDs over Bi-MOF nanosheets but also accelerates interfacial charge transfer by forming a strong bonding linkage, which endows it with the best performance of CO 2 photoreduction. Our new finding of bismuth-based metal−organic framework/lead-free halide perovskite by cosharing atoms opens a new avenue for a novel preparation strategy of the heterojunction with atomic-level contact and potential applications in capture and photocatalytic conversion of CO 2 .

We applied our previously developed library-based Monte Carlo (LBMC) to equilibrium sampling of several implicitly solvated all-atom peptides. LBMC can perform equilibrium sampling of molecules using the pre-calculated statistical libraries of molecular-fragment configurations and energies. For this study, we employed residue-based fragments distributed according to the Boltzmann factor of the OPLS-AA forcefield describing the individual fragments. Two solvent models were employed: a simple uniform dielectric and the Generalized Born/Surface Area (GBSA) model. The efficiency of LBMC was compared to standard Langevin dynamics (LD) using three different statistical tools. The statistical analyses indicate that LBMC is more than 100 times faster than LD not only for the simple solvent model but also for GBSA.

Building on our recently introduced library-based Monte Carlo (LBMC) approach, we describe a flexible protocol for mixed coarse-grained (CG)/all-atom (AA) simulation of proteins and ligands. In the present implementation of LBMC, protein side chain configurations are pre-calculated and stored in libraries, while bonded interactions along the backbone are treated explicitly. Because the AA side chain coordinates are maintained at minimal run-time cost, arbitrary sites and interaction terms can be turned on to create mixed-resolution models. For example, an AA region of interest such as a binding site can be coupled to a CG model for the rest of the protein. We have additionally developed a hybrid implementation of the generalized Born/surface area (GBSA) implicit solvent model suitable for mixed-resolution models, which in turn was ported to a graphics processing unit (GPU) for faster calculation. The new software was applied to study two systems: (i) the behavior of spin labels on the B1 domain of protein G (GB1) and (ii) docking of randomly initialized estradiol configurations to the ligand binding domain of the estrogen receptor (ERα). The performance of the GPU version of the code was also benchmarked in a number of additional systems.

It has been recognized that the control of crystalline orientation and thickness of Pb(Zr0.52Ti0.48)O3 (PZT) thin-films is very critical in the fabrication of piezoelectric thin-film devices with desirable dielectric and electromechanical properties. Here, we present our recent studies on the fabrication of PZT films with (001), (111), and random crystalline orientations onto platinized silicon substrates and the crystalline orientation dependence of the nanomechanical properties. A 1.0-μm PZT film with a strong (100) orientation is deposited by a 2–methoxyethanol- (2–MOE)-based sol–gel precursor solution, while random orientation is obtained by acetic acid-based sol–gel precursor. Rapid thermal annealing of 2–MOE sol-gel-based PZT films leads to strong (111) orientation. All PZT films show similar hysteresis behavior and large remnant polarizations; however, the nanomechanical test using AFM and nanoindentation indicates distinct values of Young’s modulus for PZT films with different orientations.