Coupling a recombinant oxidase to catalase through specific noncovalent interaction to improve the oxidation of 5-hydroxymethylfurfural to 2,5-furandicarboxylic acid.

5-Hydroxymethylfurfural oxidase (HMFO) can catalyze both hydroxyl and aldehyde oxidations. It catalyzes 5-hydroxymethylfurfural into 2,5-furandicarboxylic acid. However, the application of HMFO encountered two problems: the expressed HMFO in Escherichia coli.

Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining.

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.

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model.

Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution.

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature.

A number of studies have constructed coarse-grained (CG) models of water to understand its anomalous properties. Most of these properties emerge at low temperatures, and an accurate CG model needs to be applicable to these low-temperature ranges. However, direct use of CG models parameterized from other temperatures, e.

Coarse-graining of many-body path integrals: Theory and numerical approximations.

Feynman's imaginary time path integral approach to quantum statistical mechanics provides a theoretical formalism for including nuclear quantum effects (NQEs) in simulation of condensed matter systems. Sinitskiy and Voth [J. Chem.

Coarse-graining involving virtual sites: Centers of symmetry coarse-graining.

Coarse-grained (CG) models allow efficient molecular simulation by reducing the degrees of freedom in the system. To recapitulate important physical properties, including many-body correlations at the CG resolution, an appropriate mapping from the atomistic to CG level is needed. Symmetry exhibited by molecules, especially when aspherical, can be lost upon coarse-graining due to the use of spherically symmetric CG effective potentials.

Ultra-Coarse-Grained Liquid State Models with Implicit Hydrogen Bonding.

Coarse-graining (CG) methodologies have been widely used to extend the time and length scales of computer simulations by averaging over the atomistic details beneath the resolution of the CG models. Despite the efficiency of CG models, important configurational information during a given process may be lost at the CG resolution. One example of this is the topology of the hydrogen bonding network in the liquid state.

Molecular transport through membranes: Accurate permeability coefficients from multidimensional potentials of mean force and local diffusion constants.

Estimating the permeability coefficient of small molecules through lipid bilayer membranes plays an important role in the development of effective drug candidates. simulations can produce acceptable relative permeability coefficients for a series of small molecules; however, the absolute permeability coefficients from simulations are usually off by orders of magnitude. In addition to differences between the lipid bilayers used and , the poor convergence of permeation free energy profiles and over-simplified diffusion models have contributed to these discrepancies.

Mesoscopic coarse-grained representations of fluids rigorously derived from atomistic models.

Mesoscopic models are widely used to study complex organization and transport phenomena in chemical and biological systems. Defining a rigorous procedure by which a mesoscopic coarse-grained (CG) representation for a fluid can be constructed from an atomistic fine-grained (FG) model is a long-standing question in the field. The connection of these CG models with the FG level of description, which might be built by CG mappings from the FG model, is often unclear.

Quantum theory of multiscale coarse-graining.

Coarse-grained (CG) models serve as a powerful tool to simulate molecular systems at much longer temporal and spatial scales. Previously, CG models and methods have been built upon classical statistical mechanics. The present paper develops a theory and numerical methodology for coarse-graining in quantum statistical mechanics, by generalizing the multiscale coarse-graining (MS-CG) method to quantum Boltzmann statistics.

Dynamics of ethyl cellulose nanoparticle self-assembly at the interface of a nematic liquid crystal droplet.

Design and fabrication of many next-generation liquid crystal (LC)-based devices rely on nematic LC domains in the form of drops or emulsions. In addition to surfactants, solid nanoparticles may be used to stabilize LC-in-water Pickering emulsions, possibly adding new dimensions to device functionality. In this work we quantitatively study the adsorption of ethyl cellulose (EC) nanoparticles, as a colloid model system, on the 4-cyano-4'-pentylbiphenyl (5CB)-water interface via a series of dynamic interfacial tension measurements.

Effects of repulsive interaction on the electric double layer of an imidazolium-based ionic liquid by molecular dynamics simulation.

The effects of repulsive interaction on the electric double layer (EDL) and differential capacitance (Cd) of an ionic liquid (IL) 1-butyl-3-methyl-imidazolium hexafluorophosphate (BMIM(+)/PF6(-)) on the graphite electrode were studied by molecular dynamics (MD) simulations. The strength of repulsive interaction was studied by manually tuning the parameter lambda (λ) with λ = 1.00 for normal Lennard-Jones interaction and smaller λ for stronger repulsion between IL and the electrode.

Temperature effects on the capacitance of an imidazolium-based ionic liquid on a graphite electrode: a molecular dynamics simulation.

Temperature-dependent electric double layer (EDL) and differential capacitance-potential (C(d)-U) curves of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate (BMIM(+)/PF6(-)) were studied on a graphite electrode by molecular dynamics simulations. It was found that all C(d)-U curves were asymmetric camel-shaped with higher C(d) at negative polarization, attributed to the specific adsorption of BMIM(+). In addition, the maxima of Cd at the negative polarization decrease monotonically with temperature due to the thicker EDL, whereas at the positive polarization they gradually increase from 450 to 550 K and decrease at 600 K.

A mean-field theory on the differential capacitance of asymmetric ionic liquid electrolytes.

The size of ions significantly influences the electric double layer structure of room temperature ionic liquid (IL) electrolytes and their differential capacitance (Cd). In this study, we extended the mean-field theory (MFT) developed independently by Kornyshev (2007J. Phys.