Dependence of Protein Structure on Environment: FOD Model Applied to Membrane Proteins

The natural environment of proteins is the polar aquatic environment and the hydrophobic (amphipathic) environment of the membrane. The fuzzy oil drop model (FOD) used to characterize water-soluble proteins, as well as its modified version FOD-M, enables a mathematical description of the presence and influence of diverse environments on protein structure. The present work characterized the structures of membrane proteins, including those that act as channels, and a water-soluble protein for contrast. The purpose of the analysis was to verify the possibility that an external force field can be used in the simulation of the protein-folding process, taking into account the diverse nature of the environment that guarantees a structure showing biological activity.

On the Dependence of Prion and Amyloid Structure on the Folding Environment

Currently available analyses of amyloid proteins reveal the necessity of the existence of radical structural changes in amyloid transformation processes. The analysis carried out in this paper based on the model called fuzzy oil drop (FOD) and its modified form (FOD-M) allows quantifying the role of the environment, particularly including the aquatic environment. The starting point and basis for the present presentation is the statement about the presence of two fundamentally different methods of organizing polypeptides into ordered conformations—globular proteins and amyloids. The present study shows the source of the differences between these two paths resulting from the specificity of the external force field coming from the environment, including the aquatic and hydrophobic one. The water environment expressed in the fuzzy oil drop model using the 3D Gauss function directs the folding process towards the construction of a micelle-like system with a hydrophobic core in the central part and the exposure of polarity on the surface. The hydrophobicity distribution of membrane proteins has the opposite characteristic: Exposure of hydrophobicity at the surface of the membrane protein with an often polar center (as in the case of ion channels) is expected. The structure of most proteins is influenced by a more or less modified force field generated by water through the appropriate presence of a non-polar (membrane-like) environment. The determination of the proportion of a factor different from polar water enables the assessment of the protein status by indicating factors favoring the structure it represents.

Au aerogel for selective CO2 electroreduction to CO: ultrafast preparation with high performance

Noble metal aerogels (NMAs) have been used in a variety of (photo-)electrocatalytic reactions, but pure Au aerogels (AG) have not been used in CO2 electroreduction to date. To explore the potential application in this direction, AG was prepared to be used as the cathode in CO2 electroreduction to CO. However, the gelation time of NMAs is usually very long, up to several weeks. Here, an excess NaBH4 and turbulence mixing-promoted gelation approach was developed by introducing magnetic stirring as an external force field, which therefore greatly shortened the formation time of Au gels to several seconds. The AG-3 (AG with Au loading of 0.003 g) exhibited a high CO Faradaic efficiency (FE) of 95.6% at an extremely low overpotential of 0.39 V, and over 91% of CO FE was reached in a wide window of -0.4 ~ -0.7 V vs. the reversible hydrogen electrode (RHE). Partial current density in CO was measured to be -19.35 mA cm-2 at -0.8 V vs. RHE under 1 atm of CO2. The excellent performance should be ascribed to its porous structure, abundant active sites, and large electrochemical active surface area. It provides a new method for preparation of AG with ultrafast gelation time and large production at room temperature, and the resulting pure AG was for the first time used in the field of CO2 electroreduction.

Emergence of a periodically rotating one-point cluster in a thermodynamic Cucker-Smale ensemble

We study emergent behaviors of thermomechanical Cucker-Smale (TCS) ensemble confined in a harmonic potential field. In the absence of external force field, emergent dynamics of TCS particles has been extensively studied recently under various frameworks formulated in terms of initial configuration, system parameters and network topologies. Moreover, the TCS model does not exhibit rotating motions in the absence of an external force field. In this paper, we show the emergence of periodically rotating one-point cluster for the TCS model in a harmonic potential field using elementary energy estimates and continuity argument. We also provide several numerical simulations and compare them with analytical results.

Symmetry of the isotropic Ornstein-Uhlenbeck process in a force field

We classify simple symmetries for an Ornstein-Uhlenbeck process, describing a particle in an external force field $f(x)$. It turns out that for sufficiently regular (in a sense to be defined) forces there are nontrivial symmetries only if $f(x)$ is at most linear. We fully discuss the isotropic case, while for the non-isotropic we only deal with a generic situation (defined in detail in the text).

Polarized Thermal Conductivity of Two-Dimensional Dusty Plasmas

The computation of thermalt properties of dusty plasmas is substantial task in the area of science and technology. The thermal conductivity (λ) has been computed by applying polarization effect through molecular dynamics (MD) simulations of two dimensional (2D) strongly coupled complex dusty plasmas (SCCDPs). The effects of polarization on thermal conductivity have been measured for a wide range of Coulomb coupling (Γ) and Debye screening (κ) parameters using homogeneous non-equilibrium molecular dynamics (HNEMD) method for suitable system sizes. The HNEMD simulation method is employed at constant external force field strength (F*) and varying polarization effects. The algorithm provides precise results with rapid convergence and minute dimension effects. The outcomes have been compared with earlier available simulation results of molecular dynamics, theoretical predictions and experimental results of complex dusty plasma liquids. The calculations show that the kinetic energy of SCCDPS depends upon the system temperature (≡ 1/Г) and it is independent of higher screening parameter. Furthermore, it has shown that the presented HNEMD method has more reliable results than those obtained through earlier known numerical methods.

The local meshless collocation method for solving 2D fractional Klein-Kramers dynamics equation on irregular domains

Purpose This study aims to propose a new numerical method for solving non-linear partial differential equations on irregular domains. Design/methodology/approach The main aim of the current paper is to propose a local meshless collocation method to solve the two-dimensional Klein-Kramers equation with a fractional derivative in the Riemann-Liouville sense, in the time term. This equation describes the sub-diffusion in the presence of an external force field in phase space. Findings First, the authors use two finite difference schemes to discrete temporal variables and then the radial basis function-differential quadrature method has been used to estimate the spatial direction. To discrete the time-variable, the authors use two different strategies with convergence orders O(τ1+γ) and O(τ2−γ) for 0 < γ < 1. Finally, some numerical examples have been presented to show the high accuracy and acceptable results of the proposed technique. Originality/value The proposed numerical technique is flexible for different computational domains.

Crystallization of Polymers under the Influence of an External Force Field

We simulated the crystallization and melting behavior of entangled polymer melts using molecular dynamics where each chain is subject to a force dipole acting on its ends. This mimics the deformation of chains in a flow field but represents a well-defined equilibrium system in the melt state. Under weak extension within the linear response of the chains, the mechanical work done on the system is about two orders of magnitude smaller as compared with the heat of fusion. As a consequence, thermodynamic and simple arguments following the secondary nucleation model predict only small changes of the crystalline phase. By contrast, an increase of the stem length up to a factor of two is observed in our simulations. On the other hand, the lamellar thickening induced by the external force is proportional to the increase of the entanglement length in the melt prior to crystallization as measured by the primitive path method. While the mechanical work done on the system is only a small perturbation for thermodynamics of polymer crystallization, the change of the primitive path is large. This suggests that a strong increase in the lamellar thickness induced, by external deformation, a topological rather than a thermodynamic origin.

Method of variable separation for investigating exact solutions and dynamical properties of the time-fractional Fokker-Planck equation

Based on the idea of variable separation, the time-fractional Fokker-Planck equation with external force field is studied by using the property of Mittag-Leffler function and some special algorithm skills. In the cases of various external potential functions such as linear potential, harmonic potential, logarithmic potential, exponential potential, and quartic potential, exact solutions and dynamical properties of the above mentioned equation is investigated. The some interesting dynamical behaviors and phenomena are discovered. The profiles of some representative exact solutions are illustrated by 3D-graphs.