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Relevant bibliographies by topics / Complex systems- Molecular dynamics study

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Journal articles

Academic literature on the topic 'Complex systems- Molecular dynamics study'

Author: Grafiati

Published: 6 September 2023

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Journal articles on the topic "Complex systems- Molecular dynamics study"

1

Borodin, Vladislav, Mikhail Bubenchikov, Alexey Bubenchikov, Dmitriy Mamontov, Sergey Azheev, and Alexandr Azheev. "Study of the Unstable Rotational Dynamics of a Tor-Fullerene Molecular System." Crystals 13, no. 2 (2023): 181. http://dx.doi.org/10.3390/cryst13020181.

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This work is devoted to modeling the dynamics of large molecules. The key issue in modeling the dynamics of real molecular systems is to correctly represent the temperature of the system using the available theoretical tools. In most works on molecular dynamics, vibrations of atoms inside a molecule are modeled with enviable persistence, which has nothing to do with physical temperature. These vibrations represent the energy internal to the molecule. Therefore, it should not be present in problems in the dynamics of inert molecular systems. In this work, by means of classical mechanics, it is

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2

Kahana, Amit, and Doron Lancet. "Protobiotic Systems Chemistry Analyzed by Molecular Dynamics." Life 9, no. 2 (2019): 38. http://dx.doi.org/10.3390/life9020038.

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Systems chemistry has been a key component of origin of life research, invoking models of life’s inception based on evolving molecular networks. One such model is the graded autocatalysis replication domain (GARD) formalism embodied in a lipid world scenario, which offers rigorous computer simulation based on defined chemical kinetics equations. GARD suggests that the first pre-RNA life-like entities could have been homeostatically-growing assemblies of amphiphiles, undergoing compositional replication and mutations, as well as rudimentary selection and evolution. Recent progress in molecular

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3

Rapaport, D. C. "GPU molecular dynamics: Algorithms and performance." Journal of Physics: Conference Series 2241, no. 1 (2022): 012007. http://dx.doi.org/10.1088/1742-6596/2241/1/012007.

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Abstract A previous study of MD algorithms designed for GPU use is extended to cover more recent developments in GPU architecture. Algorithm modifications are described, togther with extensions to more complex systems. New measurements include the effects of increased parallelism on GPU performance, as well as comparisons with multiple-core CPUs using multitasking based on CPU threads and message passing. The results show that the GPU retains a significant performance advantage.

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4

Wang, Xiunan, Yi Liu, Jingcheng Xu, et al. "Molecular Dynamics Study of Stability and Diffusion of Graphene-Based Drug Delivery Systems." Journal of Nanomaterials 2015 (2015): 1–14. http://dx.doi.org/10.1155/2015/872079.

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Graphene, a two-dimensional nanomaterial with unique biomedical properties, has attracted great attention due to its potential applications in graphene-based drug delivery systems (DDS). In this work graphene sheets with various sizes and graphene oxide functionalized with polyethylene glycol (GO-PEG) are utilized as nanocarriers to load anticancer drug molecules including CE6, DOX, MTX, and SN38. We carried out molecular dynamics calculations to explore the energetic stabilities and diffusion behaviors of the complex systems with focuses on the effects of the sizes and functionalization of gr

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5

Puzyrkov, Dmitry, Sergey Polyakov, Viktoriia Podryga, and Sergey Markizov. "Concept of a Cloud Service for Data Preparation and Computational Control on Custom HPC Systems in Application to Molecular Dynamics." EPJ Web of Conferences 173 (2018): 05014. http://dx.doi.org/10.1051/epjconf/201817305014.

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At the present stage of computer technology development it is possible to study the properties and processes in complex systems at molecular and even atomic levels, for example, by means of molecular dynamics methods. The most interesting are problems related with the study of complex processes under real physical conditions. Solving such problems requires the use of high performance computing systems of various types, for example, GRID systems and HPC clusters. Considering the time consuming computational tasks, the need arises of software for automatic and unified monitoring of such computat

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Benton, Tim G., Stewart J. Plaistow, and Tim N. Coulson. "Complex population dynamics and complex causation: devils, details and demography." Proceedings of the Royal Society B: Biological Sciences 273, no. 1591 (2006): 1173–81. http://dx.doi.org/10.1098/rspb.2006.3495.

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Population dynamics result from the interplay of density-independent and density-dependent processes. Understanding this interplay is important, especially for being able to predict near-term population trajectories for management. In recent years, the study of model systems—experimental, observational and theoretical—has shed considerable light on the way that the both density-dependent and -independent aspects of the environment affect population dynamics via impacting on the organism's life history and therefore demography. These model-based approaches suggest that (i) individuals in differ

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7

Pieroni, Michele, Francesco Madeddu, Jessica Di Martino, et al. "MD–Ligand–Receptor: A High-Performance Computing Tool for Characterizing Ligand–Receptor Binding Interactions in Molecular Dynamics Trajectories." International Journal of Molecular Sciences 24, no. 14 (2023): 11671. http://dx.doi.org/10.3390/ijms241411671.

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Molecular dynamics simulation is a widely employed computational technique for studying the dynamic behavior of molecular systems over time. By simulating macromolecular biological systems consisting of a drug, a receptor and a solvated environment with thousands of water molecules, MD allows for realistic ligand–receptor binding interactions (lrbi) to be studied. In this study, we present MD–ligand–receptor (MDLR), a state-of-the-art software designed to explore the intricate interactions between ligands and receptors over time using molecular dynamics trajectories. Unlike traditional static

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8

Domínguez, D., A. R. Bishop, and N. Grønbech-Jensen. "Coherence and Complexity in Condensed Matter: Josephson Junction Arrays." International Journal of Bifurcation and Chaos 07, no. 05 (1997): 979–88. http://dx.doi.org/10.1142/s0218127497000790.

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The importance of the mesoscopic bridge between microscopic and mesoscopic descriptions of complex, nonlinear-nonequilibrium extended dynamical systems is illustrated in a condensed matter context through three-dimensional Josephson junction arrays. Large-scale Langevin molecular dynamics is used to study novel transformer and melting effects, emphasizing the central roles of topological excitations (flux vortex lines) in determining mesoscopic patterns and dynamics — through flux line creation, annihilation, interaction and statistical mechanics.

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9

Hordijk, Wim, Mike Steel, and Stuart Kauffman. "Molecular Diversity Required for the Formation of Autocatalytic Sets." Life 9, no. 1 (2019): 23. http://dx.doi.org/10.3390/life9010023.

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Systems chemistry deals with the design and study of complex chemical systems. However, such systems are often difficult to investigate experimentally. We provide an example of how theoretical and simulation-based studies can provide useful insights into the properties and dynamics of complex chemical systems, in particular of autocatalytic sets. We investigate the issue of the required molecular diversity for autocatalytic sets to exist in random polymer libraries. Given a fixed probability that an arbitrary polymer catalyzes the formation of other polymers, we calculate this required molecul

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10

Cassone, Giuseppe, Adriano Sofia, Jiri Sponer, A. Marco Saitta, and Franz Saija. "Ab Initio Molecular Dynamics Study of Methanol-Water Mixtures under External Electric Fields." Molecules 25, no. 15 (2020): 3371. http://dx.doi.org/10.3390/molecules25153371.

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Intense electric fields applied on H-bonded systems are able to induce molecular dissociations, proton transfers, and complex chemical reactions. Nevertheless, the effects induced in heterogeneous molecular systems such as methanol-water mixtures are still elusive. Here we report on a series of state-of-the-art ab initio molecular dynamics simulations of liquid methanol-water mixtures at different molar ratios exposed to static electric fields. If, on the one hand, the presence of water increases the proton conductivity of methanol-water mixtures, on the other, it hinders the typical enhanceme

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