Improvement of energy dissipative particle dynamics method to increase accuracy

In this article, dissipative particle dynamics with energy conservation eDPD is used for simulating hydrodynamic behavior and heat transfer of DPD particles in a two-dimensional channel with parallel planes. To this end, a Fortran programming code is developed and the results are presented as dimensionless velocity and temperature profiles on the cross section perpendicular to the flow direction inside the channel. For the indented geometry, thermal and dynamic boundary conditions have been considered. The dynamic boundary condition of solution domain in the flow’s direction is periodic, and for modeling the walls, freezing layers of DPD particles with Bounce-Back reflection has been used. For the thermal boundary condition, it is assumed that the wall temperature is constant and the temperature of each DPD particle in contact with the wall is the same as the wall temperature. In this article, for the first time, for modeling the walls four frozen layers with Bounce-Back reflection are used and the effect of particle exit on two and three-layers configurations is investigated. Furthermore, for the first time, modified velocity Verlet integration algorithm is improved by adding heat transfer equations. And considering λ?=?0.65 in the algorithm; the indented geometry is well simulated. In order to validate the results, first, the effect of regular and random initial distribution is compared. Furthermore, the results of wall alignment are compared with those obtained from CFD approach. In this paper, in addition to studying the effect of wall alignment and initial particle arrangement, the influence of the size of cells for averaging and the time steps in the output results are investigated.

     

Measuring persistence in a stationary time series using the complex network theory

A growing interest exists currently in the analysis of time series by the complex network theory. Here we present a simple and quick way for mapping time series to complex networks. Using a simple rule allows us to transform time series into a textual sequence then we divide it into words with fixed size. Distinct words are nodes of the network, and we have complete control on the network scale by adjusting the word size. Two nodes are linked if their associated words co-occur in sequence. We show that the network topological measures quantify the persistence and the long range correlations in fractional Brownian processes. For a particular word size we assume some relations between the topological measures and the Hurst exponent which characterised the persistence in fractional Brownian processes.     

A Novel Strategy for Determination of Paracetamol in the Presence of Morphine Using a Carbon Paste Electrode Modified with CdO Nanoparticles and Ionic Liquids

A voltammetric sensor for determination of paracetamol in the presence of morphine is described for the first time. The synthesized CdO nanoparticles were characterized with different methods such as scanning electron microscopy (SEM) and X‐ray diffraction (XRD). The paracetamol and morphine peaks are separated ca. 0.37 and 0.65 V, respectively; hence paracetamol can be analysed in the presence of morphine and more than 21 times of the current excess of paracetamol. The detection limits for paracetamol and morphine were 0.07 and 0.1 μM, respectively. The sensor has been successfully applied for the assay of the above compounds in real samples.     

Develop dissipative particle dynamics method to study the fluid flow and heat transfer of Ar and O2 flows in the micro- and nanochannels with precise atomic arrangement versus molecular dynamics approach

Fluid atomic behavior is an important factor for industrial applications. Computer simulations based on simple models predict Poiseuille flow for these atomic structures with the presence of external force. In this work, we describe the dynamical properties of Ar and O₂ flows with precise atomic arrangement via dissipative particle dynamics (DPD) and molecular dynamics (MD) simulation approaches. In these methods, each model is represented by using Large-scale Atomic/Molecular Massively Parallel Simulator package. Simulation results show that maximum rate for velocity of Ar flow in platinum and copper microchannels is 0.100 (unit less)/0.091 Å ps^?1 and 0.121 (unit less)/0.105 Å ps^?1 by using DPD/MD approach. This atomic parameter changes to 0.111 (unit less)/0.102 Å ps^?1 and 0.125 (unit less)/0.108 Å ps^?1 for O₂ fluid with mentioned approaches. By decreasing the microchannel size, the maximum rate of velocity reaches to 0.101 (unit less)/0.099 Å ps^?1 and maximum temperature rate decreases to 485 (unit less)/440 K with DPD/MD approaches. These calculated parameters can be used in industrial application designing for some processes such as heat transfer in structures. It was seen that the developed DPD approach was able to simulate the fluid flow and heat transfer of various types of fluids at micro- and nanoscales with suitable accuracy versus MD.

     

N-Protection of amines using pyridinium 2, 2, 2-trifluoroacetate ionic liquid as an efficient and reusable catalyst

A simple, green, and efficient method for the N-tert-butoxycarbonylation of amines by pyridinium 2,2,2- trifluoroacetate （[Py][OTf]） as an efficient and reusable catalyst is reported. In general, electron donating groups on aryl group give rise to the higher yields than electron withdrawing groups. Clean reaction, short reaction times, high yields, reusability of catalyst, and easy preparation of it are some advantages of this work.     

The Effect of Arg on the Structure Perturbation and Chaperone Activity of α-Crystallin in the Presence of the Crowding Agent,Dextran

α-Crystallin is a protein that is expressed at high levels in all vertebrate eye lenses. It has a molecular weight of 20 kDa and is composed of two subunits: αA and αB. α-Crystallin is a member of the small heat shock protein (sHsps) family that has been shown to prevent protein aggregation. Small molecules are organic compounds that have low molecular weight (<800 Da). Arginin (Arg) is a small molecule and has been shown to prevent protein aggregation through interaction with partially folded intermediates. In this study, the effect of Arg on the chaperone activity of α-crystallin in the presence of dextran, as a crowding agent, against ordered and disordered aggregation of different target proteins (α-lactalbumin, ovotransferrin, and catalase) has been investigated. The experiments were done using visible absorption spectroscopy, ThT-binding assay, fluorescence spectroscopy, and CD spectroscopy. The results showed that in amorphous aggregation and amyloid fibril formation, both in the presence and absence of dextran, Arg had a positive effect on the chaperone action of α-crystallin. However, in the presence of dextran, the effect of Arg on the chaperone ability of α-crystallin was less than in its absence. Thus, our result suggests that crowding interior media decreases the positive effect of Arg on the chaperone ability of α-crystallin. This is a very important issue, since we are trying to find a mechanism to protect living cells against the toxic effect of protein aggregation.     

A new method for the synthesis of amides from imines

An efficient and straightforward method for the synthesis of amides by the reaction of imines and anhydrides in the presence of Et₃SiH/Zn is reported. Mild reaction conditions, good yields of products, short reaction times, and operational simplicity are advantages of this procedure.     

Synthesis of a new Pt(II) complex containing valganciclovir drug and calf-thymus DNA interaction study using multispectroscopic methods

A new complex, [Pt(valcyte)(DMSO)Cl]Cl, in which valcyte (trade name) served as valganciclovir hydrochloride drug ([2-[(2-amino-6-oxo-3H-purin-9-yl)methoxy]-3-hydroxypropyl](2S)-2-amino-3-methylbutanoate), was synthesized and characterized by different physicochemical methods. Binding interaction of this complex with calf-thymus DNA (ct-DNA) has been investigated by multispectroscopic techniques. The complex displays significant binding properties with ct-DNA. The results of fluorescence and UV–vis absorption spectroscopy indicated that this complex interacted with ct-DNA in a groove-binding mode, and the binding constant was 3.8 × 10⁴ M^?1. Furthermore, the complex induced detectable changes in the CD spectrum of ct-DNA and slightly changed its viscosity which verified the groove-binding mode. Finally, all results indicated that Pt(II) complex interact with DNA via groove-binding mode.     

All optical NOR and NAND gate based on nonlinear photonic crystal ring resonators

In this paper we proposed optical NOR and NAND gates. By combining nonlinear Kerr effect with photonic crystal ring resonators first we designed a structure, whose optical behavior can be controlled via input power intensity. The switching power threshold obtained for this structure equal to 2 kW/μm². For designing the proposed optical logic gates we employed two resonant rings with the same structures, both rings at the logic gates were designed such that their resonant wavelength be at λ = 1550 nm. Every proposed logic gate has one bias and two logic input ports. We used plane wave expansion and finite difference time domain methods for analyzing the proposed structures.