Lab-in-Silico https://sciengpub.com/lab-in-silico <p><strong>Lab-in-Silico</strong> (<em>eISSN</em>: <strong>2717-1922</strong>) is a multidisciplinary international research journal established by <strong>SciEng Publishing Group</strong> (<a href="https://sciengpub.com">https://sciengpub.com</a>) covering all fields of scientific works <em>in silico</em>.</p> <p>Computational Chemistry, Computational Physics, Computational Biology, Computational Mathematics, Computational Material Science, Computational Drug Design, and all other fields of theory and computations are very much welcome to this journal.</p> <p>This double-blind peer-reviewed journal aims to provide a rapid-processing platform for researchers from all around the world to share their latest findings.</p> <p>The journal policy is pure Open Access without article processing charges and all published articles of this journal are freely available for readers through online system at the journal homepage; <a href="https://lab-in-silico.com">https://lab-in-silico.com</a> without any subscription fee.</p> <p><strong>Lab-in-Silico</strong> has been publishing twice a year (2 issues per year; June and December) accepting all Original Research and Review Articles in addition to Short Communications and Letters.</p> <p>Please submit your manuscripts to<strong> Lab-in-Silico</strong> through <a href="https://www.sciengpub.com/lab-in-silico/about/submissions">on-line submission system</a> at the journal website: <a href="https://lab-in-silico.com">https://lab-in-silico.com</a></p> <p><strong>In case of any questions, please contact us;</strong> <em>E-mail</em>: <a href="https://www.sciengpub.com/lab-in-silico/management/settings/context/mailto:lab-in-silico@sciengpub.com">lab-in-silico@sciengpub.com</a></p> en-US lab-in-silico@sciengpub.com (Lab-in-Silico) help@sciengpub.com (Help Desk) Wed, 30 Jun 2021 00:00:00 +0430 OJS 3.2.1.4 http://blogs.law.harvard.edu/tech/rss 60 Computer-Based Tools for Structural Characterizations and Activity Specifications of Natural Products: A Quick Review https://sciengpub.com/lab-in-silico/article/view/labinsilico21021050 <p>Natural products have been always known for their benefits for supplying food and drug for human kind survival for whole history. Using original forms of such compounds or their essential substances could provide several types of applications. Besides highlighted benefits, several limitations prevent such substances to work properly for people of all around the world. Therefore, carful examining their structural characterizations and activity specifications could help to provide specified functions or to propose new related derivatives. Computer-based tools are among useful tools for achieving such purposes, in which the model systems could be investigated at the lowest molecular and atomic scales. Such works provide <em>in silico</em> media for investigating various features of structures and their related functions. As a consequence, further developments of natural products for specified purposes could be led by the means of computer-based tools.</p> Hasan Zandi, Kun Harismah Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021050 Wed, 10 Mar 2021 00:00:00 +0330 Loading Tacrine Alzheimer's Drug at the Carbon Nanotube: DFT Approach https://sciengpub.com/lab-in-silico/article/view/labinsilico21021003 <p>Density functional theory (DFT) calculations were performed to investigate complex formation of loaded tacrine (TAC) Alzheimer’s drug at carbon nanotube (CNT) to make such TAC@CNT complex. To this aim, each of singular TAC and CNT molecular systems were first optimized to achieve the minimum energy structures. Next, the complex formation of TAC@CNT was investigated by performing further optimization of interacting counterparts. The results were obtained to analyze the systems regarding quantitative and qualitative aspects, in which the main goal was to investigate features of such TAC@CNT complex system. It was indicated that TAC could be loaded at CNT and it could remain safe from interactions with other substances as the frontier molecular orbital distributions were moved from TAC to CNT in the complex of TAC@CNT. Finally, such complex formation of TAC@CNT could be proposes for applications regarding the purposes of targeted drug delivery systems.</p> Mohsen Mirali, Zahra Jafariazar, Mahmoud Mirzaei Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021003 Thu, 18 Feb 2021 00:00:00 +0330 Cyclophosphamide@CNT: In Silico Exploration of Nano Drug Delivery System https://sciengpub.com/lab-in-silico/article/view/labinsilico21021009 <p>Within this work, cyclophosphamide (CP) anticancer drug was loaded at the surface of a representative carbon nanotube (CNT) to examine the formation and features of such CP@CNT hybrid model system. Density functional theory (DFT) calculations were performed to provide required information to reach the aim of this work <em>in silico</em>. The obtained results indicated that the formation of CP@CNT could be possible regarding the calculated adsorption energy and electrostatic potential (ESP) surface representation. Additionally, the reactivity of CP was significantly reduced in the hybrid showing the reduction of unfavorable side effects of CP consumption for cancerous patients. As a remark of this work, it could be mentioned that such CP@CNT hybrid model system could be proposed for further investigation of nano-based targeted drug delivery processes to reduce negative impacts of anticancer consumption for the cancerous patients.</p> Ardeshir Kakaei, Mahmoud Mirzaei Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021009 Thu, 18 Feb 2021 00:00:00 +0330 PNA-CNT Interacting System: In Silico Investigation of Nanocarbon Sensors for PNA Detection https://sciengpub.com/lab-in-silico/article/view/labinsilico21021015 <p>Formation of peptide nuclei acid (PNA) interacting system with carbon nanotube (CNT) was investigated in this work employing the <em>in silico</em> computer-based calculation and simulation. The major problem of this work was to examine the sensor role of CNT nanocarbon for detection of PNA. First, the model of CNT was prepared according to semi-empirical approach for geometrical optimization and electronic property evaluation. The results indicated proper length size of CNT for contributing to interactions with other substances. Next, the model of PNA was prepared for running molecular docking simulation process. To this aim, the best conformational localization of CNT versus the already fixed PNA was explored to reach the most suitable PNA-CNT hybrid system. As a result, such hybrid formation was confirmed based on the obtained thermodynamic parameters proposing such CNT sensor for detection of PNA to be investigated by further works.</p> Bahmsnshir Mousanasab, Mahmoud Mirzaei Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021015 Thu, 18 Feb 2021 00:00:00 +0330 Heat Treatment Calculations of CaTiO3 Material to Probe the Oxygen Non-Stoichiometry https://sciengpub.com/lab-in-silico/article/view/labinsilico21021020 <p>CaTiO<sub>3</sub> (CTO) is a popular material that has a wide application in electronics and its thermoelectric potential has led to its application in related fields. In this study, the electronic structure response of atoms in the CTO material to the temperature increase was probed by means of the x-ray absorption fine structure spectroscopy (XAFS) calculations. Very high stability was determined in the material against the temperature increase. However, decay at both calcium and oxygen atom data were determined as a response to the temperature increase which can give us clues about the oxygen non-stoichiometry in CaTiO<sub>3</sub> materials reported in the literature. Besides, with increasing temperature, a very slight increase at pre-edge features was observed. In this work, systematic calculations of XAFS features were performed to achieve the purpose of such CTO material characterization.</p> Osman Murat Ozkendir Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021020 Mon, 01 Mar 2021 00:00:00 +0330 Graphene Scaffold for Tioguanine Delivery: DFT Approach https://sciengpub.com/lab-in-silico/article/view/labinsilico21021025 <p>Density functional theory (DFT) approach was used to perform molecular scale calculations to examine the capability of graphene scaffold for delivery of tioguanine anticancer drug. To achieve the purpose, singular models were optimized to provide required components for bimolecular tioguanine@graphene complex formation in re-optimization processes. The calculation results indicated favorable perpendicular localization of tioguanine to the graphene surface, in which evaluated molecular descriptors approved such achievement of bimolecular complex formation. Each of frontiers molecular orbitals (HOMO and LUMO) distribution patterns and electrostatic potential (ESP) surfaces showed the existence of tioguanine@graphene complex. Finally, the obtained results of this work made sense the starting hypothetic idea of graphene scaffold application for delivery of tioguanine to be examined more by future practical works.</p> Esmaeil Moezi, Mahmoud Mirzaei Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021025 Wed, 03 Mar 2021 00:00:00 +0330 Molecular Docking of Some Novel Quinoline Derivatives as Potent Inhibitors of Human Breast Cancer Cell Line https://sciengpub.com/lab-in-silico/article/view/labinsilico21021030 <p>Breast Cancer is one of the major universal health problems affecting more than one million cases per year. Incidence of breast cancer would be seriously increased by inefficacy of the existing available drugs; therefore, designing novel drugs is almost a crucial issue for medication of breast cancer. In this work, some novel synthesized derivatives of quinoline were examined against human breast cancer cell line (MCF-7) through performing structural optimizations and molecular docking simulations to evaluate the binding affinity against topoisomerase (ii) (Topo2????) receptor target. Indeed, first-hand information for the design of novel and potent drugs for medication of breast cancer compounds were provided here. Molecular docking processes were carried out with the help of AutoDock-Vina of PyRx and Discovery Studio software programs. Evaluated binding scores indicated that ligand number 29 could work properly with the lowest binding energy value of -10.4 kcal/mol among 31 investigated ligands. Furthermore, this ligand showed higher binding affinity and bonding strength to the pocket of receptor target (Topo2????) in comparison with the hypothetical Doxorubicin reference drug with binding energy of -6.9 kcal/mol. The provided results of this work could be useful for those researchers working on designing novel medication protocols for breast cancer specially based on quinoline derivatives.</p> Momohjimoh Ovaku Idris, Shola Elijah Adeniji, Kekere Habib, Abubakar Abdulhafiz Adeiza Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021030 Thu, 04 Mar 2021 00:00:00 +0330 DFT Approach on SiC Nanotube for NO2 Gas Pollutant Removal https://sciengpub.com/lab-in-silico/article/view/labinsilico21021038 <p>This work was performed to investigate removal process of nitrogen dioxide (NO<sub>2</sub>) gas pollutant by its adsorption at the surface of a representative silicon carbide (SiC) nanotube through density functional theory (DFT) calculations. Singular models were optimized first and bimolecular models were optimized again to achieve complex formations. Two models of N@SiC and O@SiC were obtained regarding the initial starting position of NO2 from N site or O site towards the tubular surface. The results indicate that the strength of O@SiC complex could be more favorable than N@SiC complex in terms of energy and distance. Further analyses of frontier molecular orbitals showed the effects of such complex formations on the original energy levels in addition to values of their gap and average. The obtained values of atomic scale quadrupole coupling constants (Qcc) showed the effects of such complex formation on the atoms of NO2 gas providing information about the reason of Si-N and Si-O interacting configuration. As a consequence, the results of this work showed very well the benefit of using such bimolecular complex formation for removal of NO<sub>2</sub> gas pollutant by means of its adsorption at the SiC nanotube surface.</p> Alireza Iranimanesh, Mohammad Yousefi, Mahmoud Mirzaei Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021038 Thu, 04 Mar 2021 00:00:00 +0330 Algorithmic Approach to Design Single Strand DNA-Based OR Logic Gate https://sciengpub.com/lab-in-silico/article/view/labinsilico21021044 <p>In this paper a realistic algorithm for designing deoxyribozyme based logic gates was proposed. The algorithm was capable to provide desired output and maintain the law of logic gates that could be verified with their already proved truth table. The basic OR logic gate algorithm was designed. Significantly, oligonucleotide was utilized as input as well as in output so that they exposed the opportunity of connection between several computational components in the chemical solution to make bio-inspired circuit.</p> Pradipta Roy Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021044 Tue, 09 Mar 2021 00:00:00 +0330 An Introduction to Lab-in-Silico https://sciengpub.com/lab-in-silico/article/view/labinsilico21021001 <p>Lab-in-Silico (<em>e</em>ISSN: 2717-1922) is a multidisciplinary international research journal established by SciEng Publishing Group (<a href="https://sciengpub.com">https://sciengpub.com</a>) covering all fields of scientific works <em>in silico</em>. This double-blind peer-reviewed journal aims to provide a rapid-processing platform for researchers from all around the world to share their latest findings. The journal policy is pure Open Access without article processing charges for authors and all published articles of this journal are freely available for readers without any subscription fee through online system at the journal homepage: <a href="https://sciengpub.com/lab-in-silico">https://lab-in-silico.com</a>. In case of any questions or problems, please kindly contact us using <a href="https://sciengpub.com/lab-in-silico/workflow/index/22/4/mailto:lab-in-silico@sciengpub.com">lab-in-silico@sciengpub.com</a> e-mail.</p> Hamid Soleimanimehr, Mahmoud Mirzaei Copyright (c) 2021 Lab-in-Silico https://creativecommons.org/licenses/by/4.0 https://sciengpub.com/lab-in-silico/article/view/labinsilico21021001 Mon, 08 Mar 2021 00:00:00 +0330