Relevant bibliographies by topics / Systems biology, density functional theory, computational modeling

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Systems biology, density functional theory, computational modeling'

Author: Grafiati
Published: 9 March 2023
Last updated: 31 July 2025

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Journal articles on the topic "Systems biology, density functional theory, computational modeling"

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Koch, Robert J., Guangfang Li, Shubham Pandey, Simon R. Phillpot, Hui Wang, and Scott T. Misture. "Complex modeling for the quantification of nanoscale disorder using genetic algorithms, density functional theory and line-profile analysis." Journal of Applied Crystallography 53, no. 4 (2020): 1087–100. http://dx.doi.org/10.1107/s1600576720008225.

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A new, computationally efficient, complex modeling approach is presented for the quantification of the local and average atomic structure, nanostructure and microstructure of an Au0.25Cu0.75 alloy. High-resolution X-ray powder diffraction and whole pattern fitting show that the sample is phase pure, with isotropic lattice strain and a distribution of equiaxed crystallites of mean size 144 (11) nm, where each crystallite has on average four twin boundaries and an average of three deformation faults per four crystallites. Both small- and large-box model optimizations were used to extract local a
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Czernek, Jiří, and Jiří Brus. "Reliable Dimerization Energies for Modeling of Supramolecular Junctions." International Journal of Molecular Sciences 25, no. 1 (2024): 602. http://dx.doi.org/10.3390/ijms25010602.

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Accurate estimates of intermolecular interaction energy, ΔE, are crucial for modeling the properties of organic electronic materials and many other systems. For a diverse set of 50 dimers comprising up to 50 atoms (Set50-50, with 7 of its members being models of single-stacking junctions), benchmark ΔE data were compiled. They were obtained by the focal-point strategy, which involves computations using the canonical variant of the coupled cluster theory with singles, doubles, and perturbative triples [CCSD(T)] performed while applying a large basis set, along with extrapolations of the respect
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Arora, Yashika, Pushpinder Walia, Mitsuhiro Hayashibe, et al. "Grey-box modeling and hypothesis testing of functional near-infrared spectroscopy-based cerebrovascular reactivity to anodal high-definition tDCS in healthy humans." PLOS Computational Biology 17, no. 10 (2021): e1009386. http://dx.doi.org/10.1371/journal.pcbi.1009386.

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Transcranial direct current stimulation (tDCS) has been shown to evoke hemodynamics response; however, the mechanisms have not been investigated systematically using systems biology approaches. Our study presents a grey-box linear model that was developed from a physiologically detailed multi-compartmental neurovascular unit model consisting of the vascular smooth muscle, perivascular space, synaptic space, and astrocyte glial cell. Then, model linearization was performed on the physiologically detailed nonlinear model to find appropriate complexity (Akaike information criterion) to fit functi
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Pandey, Anoop Kumar, Vijay Singh, and Apoorva Dwivedi. "Quantum chemical calculations of a novel Specie – Boron Nano Bucket (B16) and the interaction of its complex (B15-Li) with drug Resorcinol." Journal of Computational Methods in Sciences and Engineering 20, no. 3 (2020): 1017–28. http://dx.doi.org/10.3233/jcm-200032.

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At Nano-scale level, innovative biomedical techniques are developed in advanced drug delivery systems and targeted Nano-therapy. Ultrathin needles provide a low invasive and highly selective means for molecular delivery and cell manipulation. This article studies the geometry and the stability of Boron Nano-Bucket (B16 Cluster of Bucket Shape) and B15-Li complex by using computational modeling methods. The equilibrium geometry of Boron Nano-Bucket and BNB-Li complex in the ground state have been determined and analyzed by Density functional theory (DFT) employing 6-311 G (d, p) as the basis se
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Cruz-Cabeza, Aurora J., та Frank H. Allen. "Conformation and geometry of cyclopropane rings having π-acceptor substituents: a theoretical and database study". Acta Crystallographica Section B Structural Science 67, № 1 (2010): 94–102. http://dx.doi.org/10.1107/s0108768110049517.

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The 3e′ orbitals of cyclopropane have the correct symmetry to interact with low-lying unoccupied orbitals of π-acceptor substituents and maximum overlap occurs when the two orbital systems are parallel, i.e. when the π-acceptor bisects the ring in projection down the substituent bond. Since the cyclopropyl group is a common component of active pharmaceutical and agrochemical ingredients, it is important that these strong conjugative interactions are well modelled by computational techniques, and clearly represented in experimental crystal structures. Here we show that torsion angle distributio
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Czernek, Jiří, and Jiří Brus. "On the Intermolecular Interactions in Thiophene-Cored Single-Stacking Junctions." International Journal of Molecular Sciences 24, no. 17 (2023): 13349. http://dx.doi.org/10.3390/ijms241713349.

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There have been attempts, both experimental and based on density-functional theory (DFT) modeling, at understanding the factors that govern the electronic conductance behavior of single-stacking junctions formed by pi-conjugated materials in nanogaps. Here, a reliable description of relevant stacked configurations of some thiophene-cored systems is provided by means of high-level quantum chemical approaches. The minimal structures of these configurations, which are found using the dispersion-corrected DFT approach, are employed in calculations that apply the coupled cluster method with singles
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Kersen, David E. Chen, Gaia Tavoni, and Vijay Balasubramanian. "Connectivity and dynamics in the olfactory bulb." PLOS Computational Biology 18, no. 2 (2022): e1009856. http://dx.doi.org/10.1371/journal.pcbi.1009856.

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Dendrodendritic interactions between excitatory mitral cells and inhibitory granule cells in the olfactory bulb create a dense interaction network, reorganizing sensory representations of odors and, consequently, perception. Large-scale computational models are needed for revealing how the collective behavior of this network emerges from its global architecture. We propose an approach where we summarize anatomical information through dendritic geometry and density distributions which we use to calculate the connection probability between mitral and granule cells, while capturing activity patte
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Kostrobij, P. P., B. M. Markovych, and I. A. Ryzha. "Semi-infinite metallic system: QST versus DFT." Mathematical Modeling and Computing 9, no. 1 (2022): 178–85. http://dx.doi.org/10.23939/mmc2022.01.178.

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Modeling and investigation of thermodynamic characteristics of spatially-finite metallic systems is an essential task of modern nanophysics. We show that the widely used DFT (density functional theory) is less efficient than the QST (quantum-statistical theory) approach.
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Söderlind, Per, G. Kotliar, K. Haule, P. M. Oppeneer, and D. Guillaumont. "Computational modeling of actinide materials and complexes." MRS Bulletin 35, no. 11 (2010): 883–88. http://dx.doi.org/10.1557/mrs2010.715.

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In spite of being rare, actinide elements provide the building blocks for many fascinating condensed-matter systems, both from an experimental and theoretical perspective. Experimental observations of actinide materials are difficult because of rarity, toxicity, radioactivity, and even safety and security. Theory, on the other hand, has its own challenges. Complex crystal and electronic structures are often encountered in actinide materials, as well as pronounced electron correlation effects. Consequently, theoretical modeling of actinide materials and their 5f electronic states is very diffic
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KOLB, BRIAN, and T. THONHAUSER. "MOLECULAR BIOLOGY AT THE QUANTUM LEVEL: CAN MODERN DENSITY FUNCTIONAL THEORY FORGE THE PATH?" Nano LIFE 02, no. 02 (2012): 1230006. http://dx.doi.org/10.1142/s1793984412300063.

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Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory — a framework that can treat thousands of atoms on firm theoretical
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Dissertations / Theses on the topic "Systems biology, density functional theory, computational modeling"

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BARBIERI, VALENTINA. "Computational modeling of the enzymatic activities of biomolecules at different scales: from quantum mechanical reaction studies to systemic understanding of cell behavior." Doctoral thesis, Università degli Studi di Milano-Bicocca, 2012. http://hdl.handle.net/10281/29145.

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The aim of the thesis is the development of computational models of the enzymatic activity of biomolecules at different scales. Parallel investigations have been carried out at a quantum level to study the reactivity of an enzyme from an electronic point of view, and at a systemic level using simulation techniques to determine the role of enzymes in the network of cellular reactions. Starting from the lowest complexity level, the thesis begins with two computational studies with the aims of describing the molecular mechanism of the catalytic reaction between amavadin and methyl mercaptoacet
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Books on the topic "Systems biology, density functional theory, computational modeling"

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Sapse, Anne-Marie, ed. Molecular Orbital Calculations for Biological Systems. Oxford University Press, 1998. http://dx.doi.org/10.1093/oso/9780195098730.001.0001.

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Molecular Orbital Calculations for Biological Systems is a hands-on guide to computational quantum chemistry and its applications in organic chemistry, biochemistry, and molecular biology. With improvements in software, molecular modeling techniques are now becoming widely available; they are increasingly used to complement experimental results, saving significant amounts of lab time. Common applications include pharmaceutical research and development; for example, ab initio and semi-empirical methods are playing important roles in peptide investigations and in drug design. The opening chapter
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Book chapters on the topic "Systems biology, density functional theory, computational modeling"

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Abdul Moiz Hashmi, Syed, Waqar Hussain, Hina Moiz, and Muhammad Hammad Rasool. "Engineering Synthetic Zeolites for Enhanced CO₂ Capture: Strategies, Synthesis, and Applications." In Exploring the World of Zeolites [Working Title]. IntechOpen, 2025. https://doi.org/10.5772/intechopen.1010023.

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Synthetic zeolites offer a promising solution for CO2 capture due to their tunable pore structures, high stability, and selective adsorption properties. This chapter explores advanced synthesis techniques, including hydrothermal, solvothermal, and microwave-assisted methods, alongside post-synthetic modifications such as ion exchange and amine functionalization to enhance CO2 uptake and selectivity. Computational modeling using Density Functional Theory (DFT) and Grand Canonical Monte Carlo (GCMC) simulations provides molecular-level insights, guiding the optimization of adsorption performance
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Conference papers on the topic "Systems biology, density functional theory, computational modeling"

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Sisto, A., X. Ruan, T. S. Fisher, and J. B. Neaton. "Predicting the Properties of Nanostructured Metamaterials: Vertically Aligned Single-Walled Carbon Nanotube Arrays." In ASME 2011 International Mechanical Engineering Congress and Exposition. ASMEDC, 2011. http://dx.doi.org/10.1115/imece2011-64011.

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Recent advances in nanofabrication technology have facilitated the development of single-walled carbon nanotube (SWCNT) arrays with long-range order across macroscopic dimensions. However, an accurate generalized method of modeling these systems has yet to be realized. A multiscale computational approach combining first principles methods based on density functional theory (DFT) and extensions thereof to account for excited electron states, and classical electrodynamics simulations is described and applied to calculations of the optical properties of macroscopic SWCNT arrays. The first-princip
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