Athika Darumas Putri

Bio: Athika Darumas Putri is an academic researcher from Taipei Medical University. The author has contributed to research in topics: Gene & Cancer. The author has an hindex of 4, co-authored 10 publications receiving 31 citations. Previous affiliations of Athika Darumas Putri include Durban University of Technology & Universitas Ahmad Dahlan.

Nanohybrid-based immunosensor prepared for Helicobacter pylori BabA antigen detection through immobilized antibody assembly with @ Pdnano/rGO/PEDOT sensing platform.

Abstract: The gastric colonization of human hosts by Helicobacter pylori (H. pylori) increases the risk of developing gastritis, ulcers and gastric cancer. To detect H. pylori, a nanohybrid-based BabA immunosensor is developed herein. BabA is an outer membrane protein and one of the major virulence factors of H. pylori. To design the immunosensor, an Au electrode is loaded with palladium nanoparticles (Pdnano) by electrodeposition to generate reduced graphene oxide (rGO)/poly(3,4-ethylenedioxythiophene) (PEDOT). The immobilization of these nanostructured materials imparts a large surface area and electroconductivity to bio-immune-sensing molecules (here, the BabA antigen and antibodies). After optimization, the fabricated immunosensor has the ability to detect antigens (H. pylori) in a linear range from 0.2 to 20 ng/mL with a low LOD (0.2 ng/mL). The developed immunosensor is highly specific, sensitive and reproducible. Additionally, in silico methods were employed to better understand the hybrid nanomaterials of the fabricated Pdnano/rGO/PEDOT/Au electrode. Simulations performed by molecular docking, and Metropolis Monte Carlo adsorption studies were conducted. The results revealed that the hybrid nanomaterials exhibit a stable antigen-antibody complex of BabA, yielding the lowest binding energy in relation to the electrode materials, emphasizing the functionality of the constructed electrodes in the electrochemical immunosensor.

Computational studies on the molecular insights of aptamer induced poly( N -isopropylacrylamide)- graft -graphene oxide for on/off- switchable whole-cell cancer diagnostics

Abstract: This work deals with first-principles and in silico studies of graphene oxide-based whole-cell selective aptamers for cancer diagnostics utilising a tunable-surface strategy. Herein, graphene oxide (GO) was constructed as a surface-based model with poly(N-isopropylacrylamide) (PNIPAM) covalently grafted as an “on/off”-switch in triggering interactions with the cancer-cell protein around its lower critical solution temperature. The atomic building blocks of the aptamer and the PNIPAM adsorbed onto the GO was investigated at the density functional theory (DFT) level. The presence of the monomer of PNIPAM stabilised the system’s π-π interaction between GO and its nucleobases as confirmed by higher bandgap energy, satisfying the eigenvalues of the single-point energy observed rather than the nucleobase and the GO complex independently. The unaltered geometrical structures of the surface emphasise the physisorption type interaction between the nucleobase and the GO/NIPAM surface. The docking result for the aptamer and the protein, highlighted the behavior of the PNIPAM-graft-GO is exhibiting globular and extended conformations, further supported by molecular dynamics (MD) simulations. These studies enabled a better understanding of the thermal responsive behavior of the polymer-enhanced GO complex for whole-cell protein interactions through computational methods.

Light induced DNA-functionalized TiO2 nanocrystalline interface: Theoretical and experimental insights towards DNA damage detection

Abstract: Owing to the emerging applications of DNA-functionalized TiO2 nanocrystals towards DNA damage detection, it is inevitable to understand the better chemistry as well as in-depth molecular interaction phenomena. Fundamentally, energy difference underlies the layer-by-layer construction, resulted in the increase of the interaction energy and thus, altering the electrochemical behavior. Herein, Density functional theory (DFT) calculations were performed using DMol3 and DFTB+ codes successfully to elucidate the structural, electronics, and vibrational properties of the layer-by-layer components composing ss-DNA/dopamine/TiO2/FTO. The obtained results are in good agreement with the experimental findings. The band gaps of FTO and TiO2 were computationally obtained at 3.335 and 3.136 eV which are comparable with the experimental data (3.500 eV; FTO and 3.200 eV; TiO2). Frontier orbital analysis is also considered to elucidate their electron transfer phenomena. Further, a 100 ns MD simulations are carried out using canonical ensemble embedded with COMPASS-Universal Forcefields generating useful thermodynamics parameters. Binding energies indicate increasing interaction energies for the layer-by-layer nanosystem, in agreement with the increasing diameter of electrochemical impedance spectroscopy (EIS) semicircle. Our results reveal the fundamental understanding of the DNA-functionalized TiO2 nanocrystals down to molecular and electronic level and further, paving a way of its application towards nanoelectrochemical DNA biosensors.

Clinically oriented Alzheimer's biosensors: expanding the horizons towards point-of-care diagnostics and beyond

Abstract: The development of minimally invasive and easy-to-use sensor devices is of current interest for ultrasensitive detection and signal recognition of Alzheimer's disease (AD) biomarkers. Over the years, tremendous effort has been made on diagnostic platforms specifically targeting neurological markers for AD in order to replace the conventional, laborious, and invasive sampling-based approaches. However, the sophistication of analytical outcomes, marker inaccessibility, and material validity strongly limit the current strategies towards effectively predicting AD. Recently, with the promising progress in biosensor technology, the realization of a clinically applicable sensing platform has become a potential option to enable early diagnosis of AD and other neurodegenerative diseases. In this review, various types of biosensors, which include electrochemical, fluorescent, plasmonic, photoelectrochemical, and field-effect transistor (FET)-based sensor configurations, with better clinical applicability and analytical performance towards AD are highlighted. Moreover, the feasibility of these sensors to achieve point-of-care (POC) diagnosis is also discussed. Furthermore, by grafting nanoscale materials into biosensor architecture, the remarkable enhancement in durability, functionality, and analytical outcome of sensor devices is presented. Finally, future perspectives on further translational and commercialization pathways of clinically driven biosensor devices for AD are discussed and summarized.

Optimization and Development of Selective Histone Deacetylase Inhibitor (MPT0B291)-Loaded Albumin Nanoparticles for Anticancer Therapy.

Abstract: Histone deacetylase (HDAC) inhibitors have emerged as a new class of antitumor agent for various types of tumors. MPT0B291, a novel selective inhibitor of HDAC6, demonstrated significant antiproliferative activity in various human cancer cell types. However, MPT0B291 has very low water solubility, which limits its clinical use for cancer therapy. In the current study, MPT0B291 was encapsulated in human serum albumin (HSA), and its anticancer activities were investigated. Nanoparticles (NPs) were prepared using two-stage emulsification resulting in 100~200-nm NPs with a fine size distribution (polydispersity index of <0.3). The in vitro drug release profiles of MPT0B291-loaded HSA NPs presented sustained-release properties. The cytotoxic effect on MIA PaCa-2 human pancreatic carcinoma cells was found to be similar to MPT0B291-loaded HSA NPs and the free-drug group. The albumin-based formulation provided a higher maximum tolerated dose than that of a drug solution with reduced toxicity toward normal cells. Furthermore, in vivo pharmacokinetic studies demonstrated an effective increase (5~8-fold) in the bioavailability of NPs containing MPT0B291 loaded in HSA compared to the free-drug solution with an extended circulation time (t1/2) leading to significantly enhanced efficacy of anticancer treatment.

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

Abstract: : The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Essentials Of Computational Chemistry Theories And Models

Abstract: The fact that a new text book introducing the essentials of computational chemistry contains more than 500 pages shows impressively the grown and still growing size and importance of this field of chemistry. The author’s objectives of the book, using his own words, are “to provide a survey of computational chemistry its underpinnings, its jargon, its strengths and weaknesses that will be accessible to both the experimental and theoretical communities”. This design as a general introduction into computational chemistry makes it an alternative to Andrew R. Leach’s well-established “Molecular Modeling” (Prentice Hall) and Frank Jensen’s “Introduction to Computational Chemistry” (Wiley), although the latter focuses on the theory of electronic structure methods. Cramer’s “Essentials” covers force field and molecular orbital theory, Monte Carlo and Molecular Dynamics simulations, thermodynamic and electronic (spectroscopic) property calculation, condensed phase treatment and a few more topics. Moreover, the book contains thirteen selected case studies sexamples taken from the literature sto illustrate the application of the just presented theoretical and computational models. This especially makes the text book well suited for both classroom discussion and self-study. Each chapter of “Essentials” covers a main topic of computational chemistry and will be briefly described here; all chapters are ended by a bibliography and suggested additional readings as well as the literature references cited in the text. In chapter 1 the author defines basic terms such as “theory”, “model”, and “computation”, introduces the concept of the potential energy surface and provides some general considerations about hardware and software. Interestingly, the first equation occurring in the text is not Schro ̈dinger’s equation, as is the case for most computational chemistry introductions, but the famous Einstein relation. The second chapter deals with molecular mechanics. It explains the different potential energy contributions, introduces the field of structure optimization, and provides an overview of the variety of modern force fields. Chapter 3 covers the simulation of molecular ensembles. It defines phase space and trajectories and shows the formalism of, and problems and difference between, Monte Carlo and molecular dynamics. In chapter 4 the author introduces the foundations of molecular orbital theory. Basic concepts such as Hamilton operator, LCAO basis set approach, many-electron wave functions, etc. are explained. To illuminate the LCAO variational process, the Hu ̈ckel theory is presented with an example. Chapter 5 deals with semiempirical molecular orbital (MO) theory. Besides the classical approaches (extended Hu ̈ckel, CNDO, INDO, NDDO) and methods (e.g., MNDO, AM1, PM3) and their performance, examples are provided from the ongoing development in that still fascinating area. Ab initio MO theory is presented in chapter 6; the basis set concept is discussed in detail, and, after some considerations from an user’s point of view, the general performance of ab initio methods is explicated. The next chapter covers the problem of electron correlation and gives the most prominent solutions for its treatment: configuration interaction, theory of the multiconfiguration self-consistent field, perturbation, and coupled cluster. Practical issues are also discussed. Chapter 8’s topic is density functional theory (DFT). Its theoretical foundation, methodology, and some functionals as well as its pros and cons compared to MO theory are presented together with a general performance overview. The next two chapters deal with charge distribution, derived and spectroscopic properties (e.g., atomic charges, polarizability, rotational, vibrational, and NMR spectra), and thermodynamic properties (e.g., zero-point vibrational energy, free energy of formation, and reaction). The modeling of condensed phases is addressed in chapters 11 (implicit models) and 12 (explicit models), which closes with a comparison between the two approaches. Chapter 13 familiarizes the reader with hybrid quantum mechanical/molecular mechanical (QM/MM) models. Polarization as well as the problematic implications of unsaturated QM and MM components are discussed, and empirical valence bond methods are also presented. The treatment of excited states is the topic of chapter 14; besides CI and MCSCF as computational methods, transition probabilities and solvatochromism are discussed. The last chapter deals with reaction dynamics, mostly adiabaticskinetics, rate constants, reaction paths, and transition state theory are section topics here sbut also nonadiabatic, introducing curve crossing and Marcus theory in brief. The appendix is divided into four parts: an acronym glossary (which is very helpful), an overview of symmetry and group theory, an introduction to spin algebra, and finally a section about orbital localization. A rather detailed index ends the book. The “Essentials” writing style fits the fascinating topic: one reads on and on andssurprise! sanother chapter has been absorbed. The text is complemented by a large number of black and white figures and clear tables, mostly self-explanatory with descriptive captions. The use of equations and mathematical formulas in general is well-balanced, and the level of math should be understandable for every natural scientist with some basic knowledge of physics. There are only a few minor shortcomings: for example, a literature reference cited in the text (“Beck et al.”, p 142) is missing in the bibliography; “Kronecker” is mistyped with o ̈; and the author completely forgot to reference Leach’s text book when referring to other computational chemistry introductions. However, the author has established a specific errata web page (http://pollux.chem.umn.edu/ ∼cramer/Errors.html) with all known errors. These will be corrected in the next printing or next revised edition, respectively. With its emphasis, on one hand, on the basic concepts and applications rather than pure theory and mathematics, and on the other hand, coverage of quantum mechanical and classical mechanical models including examples from inorganic, organic, and biological chemistry, “Essentials” is a useful tool not only for teaching and learning but also as a quick reference, and thus will most probably become one of the standard text books for computational chemistry.

Critical Review of Advances in Engineering Nanomaterial Adsorbents for Metal Removal and Recovery from Water: Mechanism Identification and Engineering Design.

Abstract: Nanomaterial adsorbents (NAs) have shown promise to efficiently remove toxic metals from water, yet their practical use remains challenging. Limited understanding of adsorption mechanisms and scaling up evaluation are the two main obstacles. To fully realize the practical use of NAs for metal removal, we review the advanced tools and chemical principles to identify mechanisms, highlight the importance of adsorption capacity and kinetics on engineering design, and propose a systematic engineering scenario for full-scale NA implementation. Specifically, we provide in-depth insight for using density functional theory (DFT) and/or X-ray absorption fine structure (XAFS) to elucidate adsorption mechanisms in terms of active site verification and molecular interaction configuration. Furthermore, we discuss engineering issues for designing, scaling, and operating NA systems, including adsorption modeling, reactor selection, and NA regeneration, recovery, and disposal. This review also prioritizes research needs for (i) determining NA microstructure properties using DFT, XAFS, and machine learning and (ii) recovering NAs from treated water. Our critical review is expected to guide and advance the development of highly efficient NAs for engineering applications.

Spatiotemporal Intracellular Nitric Oxide Signaling Captured Using Internalized, Near-Infrared Fluorescent Carbon Nanotube Nanosensors

Abstract: Fluorescent nanosensor probes have suffered from limited molecular recognition and a dearth of strategies for spatial-temporal operation in cell culture. In this work, we spatially imaged the dynamics of nitric oxide (NO) signaling, important in numerous pathologies and physiological functions, using intracellular near-infrared fluorescent single-walled carbon nanotubes. The observed spatial-temporal NO signaling gradients clarify and refine the existing paradigm of NO signaling based on averaged local concentrations. This work enables the study of transient intracellular phenomena associated with signaling and therapeutics.