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Artykuły w czasopismach na temat „Complex systems- Molecular dynamics study”

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Data publikacji: 6 września 2023

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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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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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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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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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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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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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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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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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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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11

Vieira, Ana Paula Bastos Ferreira, Natália de Farias Silva, Davi do Socorro Barros Brasil, José Otávio Carréra Silva Junior, and Roseane Maria Ribeiro Costa. "Computational simulation of nanostructured lipid carrier containing lipids from Cupuassu (Theobroma grandiflorum) seed fat: Design, interaction and molecular dynamic study." Research, Society and Development 9, no. 11 (2020): e92191110433. http://dx.doi.org/10.33448/rsd-v9i11.10433.

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Drug delivery systems are constantly evolving and developing, as well as the search for promising and effective formulations for drug delivery. Computational simulation methods enable the development of complex systems, such as nanostructured lipid carriers (NLC), the understanding of interaction and dynamics between drug molecule and its transporter. In this work, aimed to simulate a NLC containing cupuassu fat triacylglycerols, carnauba wax and caprylic/capric acid triacylglycerol, stabilized with Tween 80 and Pluronic and ketoconazole enantiomer as drug was simulated. Initially, lipid mixtu

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Chavent, Matthieu, Tyler Reddy, Joseph Goose, et al. "Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems." Faraday Discuss. 169 (2014): 455–75. http://dx.doi.org/10.1039/c3fd00145h.

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Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically comprise millions of particles. To tackle this issue, we

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Wysocka, Emilia M., Matthew Page, James Snowden, and T. Ian Simpson. "Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network." PeerJ 10 (December 15, 2022): e14516. http://dx.doi.org/10.7717/peerj.14516.

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Dynamic modelling has considerably improved our understanding of complex molecular mechanisms. Ordinary differential equations (ODEs) are the most detailed and popular approach to modelling the dynamics of molecular systems. However, their application in signalling networks, characterised by multi-state molecular complexes, can be prohibitive. Contemporary modelling methods, such as rule- based (RB) modelling, have addressed these issues. The advantages of RB modelling over ODEs have been presented and discussed in numerous reviews. In this study, we conduct a direct comparison of the time cou

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Salehi, Mitra, Hanifeh Shariatifar, Morteza Ghanbari Johkool, and Alireza Farasat. "A comprehensive study of HSA interaction with TMP using molecular docking and molecular dynamics methods: as an appropriate tool for drug delivery systems." Journal of Qazvin University of Medical Sciences 25, no. 2 (2022): 6. http://dx.doi.org/10.32598/jqums.25.2.2125.1.

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Background: Human serum albumin (HSA) is one of the most prominent protein in human blood. Trimethoprim (TMP) is an efficient antibiotic drug for treatment of pneumocystis pneumonia (PCP). Patients with HIV/AIDS and cancer are extremely affected by the disease due to immune system deficiency. Objective: The aim of this study is to evaluate the molecular dynamics simulation (MD) of HSA with TMP for drug delivery systems. Materials and methods: In the first step, the 3D structure of HSA and TMP were provided by PDB and PubChem respectively. Then, the molecular docking was done via AutoDock Vina

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15

JAKSE, NOEL, and ALAIN PASTUREL. "LOCAL ORDER OF LIQUID AND UNDERCOOLED TRANSITION METAL BASED SYSTEMS: AB INITIO MOLECULAR DYNAMICS STUDY." Modern Physics Letters B 20, no. 12 (2006): 655–74. http://dx.doi.org/10.1142/s0217984906011177.

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An overview of a recent series of ab initio molecular dynamics (MD) simulations for pure liquid transition metals as well as for transition metals (TM) based liquid alloys is presented. The aim is to investigate the local structure of these systems and their evolution upon undercooling, and our results are analyzed through a three-dimensional picture of the short-ranger order (SRO) by means of the common-neighbor analysis. Recent diffraction experiments indicate that the structure of both pure metals and alloys in undercooled states is dominated by an icosahedral SRO. We find that the five-fol

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Grest, Gary S., Martin-D. Lacasse, and Michael Murat. "Molecular-Dynamics Simulations of Polymer Surfaces and Interfaces." MRS Bulletin 22, no. 1 (1997): 27–31. http://dx.doi.org/10.1557/s0883769400032309.

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From a single chain in a dilute solution to an entangled polymer melt, from bulk systems to more complex interfacial problems, computer simulations have played a critical role not only in testing the basic assumptions of various theoretical models but also in interpreting experimental results. Early computer simulations of polymers were mostly carried out on a lattice using Monte Carlo methods. This approach has led to significant progress in recent years and will continue to do so in many areas. In some cases however, for example in the study of shear, lattice models have serious limitations.

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Thorneywork, Alice L., Jannes Gladrow, Yujia Qing, et al. "Direct detection of molecular intermediates from first-passage times." Science Advances 6, no. 18 (2020): eaaz4642. http://dx.doi.org/10.1126/sciadv.aaz4642.

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All natural phenomena are governed by energy landscapes. However, the direct measurement of this fundamental quantity remains challenging, particularly in complex systems involving intermediate states. Here, we uncover key details of the energy landscapes that underpin a range of experimental systems through quantitative analysis of first-passage time distributions. By combined study of colloidal dynamics in confinement, transport through a biological pore, and the folding kinetics of DNA hairpins, we demonstrate conclusively how a short-time, power-law regime of the first-passage time distrib

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Uratani, Hiroki. "(Invited) Simulating Dynamic Excitons Via Quantum Molecular Dynamics: A Case Study in Lead Halide Perovskites." ECS Meeting Abstracts MA2022-01, no. 13 (2022): 904. http://dx.doi.org/10.1149/ma2022-0113904mtgabs.

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The ultrafast electronic and structural dynamics invoked by photoexcitation, i.e., “dynamic exciton” phenomena, not only are important in the context of practical applications such as solar cells, but also raise many questions from the viewpoint of fundamental science. Experimental measurement, computational simulations, and theoretical interpretation will be the three pillars for deciphering the dynamic exciton phenomena. From the viewpoint of computational simulations, molecular dynamics (MD) techniques combined with quantum chemical calculations, i.e., quantum molecular dynamics (QMD), has

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Hofer, Thomas S. "Perspectives for hybrid ab initio/molecular mechanical simulations of solutions: from complex chemistry to proton-transfer reactions and interfaces." Pure and Applied Chemistry 86, no. 2 (2014): 105–17. http://dx.doi.org/10.1515/pac-2014-5019.

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Abstract As a consequence of the ongoing development of enhanced computational resources, theoretical chemistry has become an increasingly valuable field for the investigation of a variety of chemical systems. Simulations employing a hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) technique have been shown to be a particularly promising approach, whenever ultrafast (i.e., picosecond) dynamical properties are to be studied, which are in many cases difficult to access via experimental techniques. Details of the quantum mechanical charge field (QMCF) ansatz, an adva

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Monachino, Enrico, Lisanne M. Spenkelink, and Antoine M. van Oijen. "Watching cellular machinery in action, one molecule at a time." Journal of Cell Biology 216, no. 1 (2016): 41–51. http://dx.doi.org/10.1083/jcb.201610025.

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Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with appli

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Yuhara, Daisuke, Brian C. Barnes, Donguk Suh, et al. "Nucleation rate analysis of methane hydrate from molecular dynamics simulations." Faraday Discussions 179 (2015): 463–74. http://dx.doi.org/10.1039/c4fd00219a.

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Clathrate hydrates are solid crystalline structures most commonly formed from solutions that have nucleated to form a mixed solid composed of water and gas. Understanding the mechanism of clathrate hydrate nucleation is essential to grasp the fundamental chemistry of these complex structures and their applications. Molecular dynamics (MD) simulation is an ideal method to study nucleation at the molecular level because the size of the critical nucleus and formation rate occur on the nano scale. Various analysis methods for nucleation have been developed through MD to analyze nucleation. In part

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Černušák, Ivan, Jozef Federič, Pavel Jungwirth, and Milan Uhlár. "Effects of micro-hydration in proton transfer from H2S·NO+ complex to water: Ab initio and molecular dynamics study." Collection of Czechoslovak Chemical Communications 76, no. 5 (2011): 585–603. http://dx.doi.org/10.1135/cccc2011047.

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We have studied several microhydrated (H2O)n·NO+·H2S structures (n = 1–3) and their fragments using wave-function based approach (coupled-clusters including single, double and non-iterative triple substitutions – CCSD(T) and second-order perturbation theory – MP2) and also employing density functional theory (with BLYP and ωB97XD functional). MP2 energetics is very close to CCSD(T) one. Both functionals provide reasonable binding energies compared to MP2, the ωB97XD being superior to BLYP. The exploratory ab initio molecular dynamics performed on four- and five-body clusters revealed that the

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Hanel, Rudolf, Manfred Pöchacker, and Stefan Thurner. "Living on the edge of chaos: minimally nonlinear models of genetic regulatory dynamics." Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 368, no. 1933 (2010): 5583–96. http://dx.doi.org/10.1098/rsta.2010.0267.

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Linearized catalytic reaction equations (modelling, for example, the dynamics of genetic regulatory networks), under the constraint that expression levels, i.e. molecular concentrations of nucleic material, are positive, exhibit non-trivial dynamical properties, which depend on the average connectivity of the reaction network. In these systems, an inflation of the edge of chaos and multi-stability have been demonstrated to exist. The positivity constraint introduces a nonlinearity, which makes chaotic dynamics possible. Despite the simplicity of such minimally nonlinear systems , their basic p

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Jadhav, Pankaj Vilas, Vikrant Kumar Sinha, Saurabh Chugh, et al. "2.09 Å Resolution structure of E. coli HigBA toxin–antitoxin complex reveals an ordered DNA-binding domain and intrinsic dynamics in antitoxin." Biochemical Journal 477, no. 20 (2020): 4001–19. http://dx.doi.org/10.1042/bcj20200363.

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The toxin–antitoxin (TA) systems are small operon systems that are involved in important physiological processes in bacteria such as stress response and persister cell formation. Escherichia coli HigBA complex belongs to the type II TA systems and consists of a protein toxin called HigB and a protein antitoxin called HigA. The toxin HigB is a ribosome-dependent endoribonuclease that cleaves the translating mRNAs at the ribosome A site. The antitoxin HigA directly binds the toxin HigB, rendering the HigBA complex catalytically inactive. The existing biochemical and structural studies had reveal

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KIRKILIONIS, MARKUS, and LUCA SBANO. "AN AVERAGING PRINCIPLE FOR COMBINED INTERACTION GRAPHS — CONNECTIVITY AND APPLICATIONS TO GENETIC SWITCHES." Advances in Complex Systems 13, no. 03 (2010): 293–326. http://dx.doi.org/10.1142/s0219525910002669.

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Time-continuous dynamical systems defined on graphs are often used to model complex systems with many interacting components in a non-spatial context. In the reverse sense attaching meaningful dynamics to given "interaction diagrams" is a central bottleneck problem in many application areas, especially in cell biology where various such diagrams with different conventions describing molecular regulation are presently in use. In most situations these diagrams can only be interpreted by the use of both discrete and continuous variables during the modelling process, corresponding to both determin

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Rose-Sperling, Dania, Mai Anh Tran, Luca M. Lauth, Benedikt Goretzki, and Ute A. Hellmich. "19F NMR as a versatile tool to study membrane protein structure and dynamics." Biological Chemistry 400, no. 10 (2019): 1277–88. http://dx.doi.org/10.1515/hsz-2018-0473.

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AbstractTo elucidate the structures and dynamics of membrane proteins, highly advanced biophysical methods have been developed that often require significant resources, both for sample preparation and experimental analyses. For very complex systems, such as membrane transporters, ion channels or G-protein coupled receptors (GPCRs), the incorporation of a single reporter at a select site can significantly simplify the observables and the measurement/analysis requirements. Here we present examples using19F nuclear magnetic resonance (NMR) spectroscopy as a powerful, yet relatively straightforwar

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Malinowski, Adrian, and Maciej Śmiechowski. "Solvent Exchange around Aqueous Zn(II) from Ab Initio Molecular Dynamics Simulations." Liquids 2, no. 3 (2022): 243–57. http://dx.doi.org/10.3390/liquids2030015.

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Hydrated zinc(II) cations, due to their importance in biological systems, are the subject of ongoing research concerning their hydration shell structure and dynamics. Here, ab initio molecular dynamics (AIMD) simulations are used to study solvent exchange events around aqueous Zn2+, for which observation in detail is possible owing to the considerable length of the generated trajectory. While the hexacoordinated Zn(H2O)62+ is the dominant form of Zn(II) in an aqueous solution, there is a non-negligible contribution of the pentacoordinated Zn(H2O)52+ complex which presence is linked to the diss

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Feskov, Sergey. "The Green’s Function Method for Evaluating the Transient Spectra of Non-Equilibrium Molecular Systems." Mathematical Physics and Computer Simulation, no. 4 (December 2022): 95–106. http://dx.doi.org/10.15688/mpcm.jvolsu.2022.4.8.

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Interest in ultrafast photochemical processes is due to their role in wildlife and the possibility of using them in solar energy conversion devices. Significant part of experimental research in this area is carried out using different spectroscopic techniques, for example, based on recording the dynamic response of the system to optical excitation by a short laser pulse. This method is basic for photochemistry and is used for studying both small inorganic molecules in liquids or mixtures, and complex biological objects, such as photosynthetic reaction centers of bacteria and plants. Time-resol

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Granick, Steve. "Molecular Tribology." MRS Bulletin 16, no. 10 (1991): 33–35. http://dx.doi.org/10.1557/s0883769400055809.

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Molecular tribology—the study of tribology at atomic and molecular scales—constitutes a new frontier of tribology research. In a major surge of activity, experimental methods have recently been developed to measure dynamic interfacial forces in shear. Building partly on earlier, somewhat neglected friction studies, striking new findings have been obtained. The new methods include the surface forces apparatus for measuring adhesion and static interfacial forces as a function of surface separation, new molecular tribometers for measuring friction in shear, atomic force microscopy, use of UHV tri

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Alameddine, Abdallah K., Frederick Conlin, and Brian Binnall. "An Introduction to the Mathematical Modeling in the Study of Cancer Systems Biology." Cancer Informatics 17 (January 2018): 117693511879975. http://dx.doi.org/10.1177/1176935118799754.

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Background: Frequently occurring in cancer are the aberrant alterations of regulatory onco-metabolites, various oncogenes/epigenetic stochasticity, and suppressor genes, as well as the deficient mismatch repair mechanism, chronic inflammation, or those deviations belonging to the other cancer characteristics. How these aberrations that evolve overtime determine the global phenotype of malignant tumors remains to be completely understood. Dynamic analysis may have potential to reveal the mechanism of carcinogenesis and can offer new therapeutic intervention. Aims: We introduce simplified mathem

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Prawesh, Shankar, and Balaji Padmanabhan. "A complex systems perspective of news recommender systems: Guiding emergent outcomes with feedback models." PLOS ONE 16, no. 1 (2021): e0245096. http://dx.doi.org/10.1371/journal.pone.0245096.

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Algorithms are increasingly making decisions regarding what news articles should be shown to online users. In recent times, unhealthy outcomes from these systems have been highlighted including their vulnerability to amplifying small differences and offering less choice to readers. In this paper we present and study a new class of feedback models that exhibit a variety of self-organizing behaviors. In addition to showing important emergent properties, our model generalizes the popular “top-N news recommender systems” in a manner that provides media managers a mechanism to guide the emergent ou

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Yletyinen, Johanna, Örjan Bodin, Benjamin Weigel, Marie C. Nordström, Erik Bonsdorff, and Thorsten Blenckner. "Regime shifts in marine communities: a complex systems perspective on food web dynamics." Proceedings of the Royal Society B: Biological Sciences 283, no. 1825 (2016): 20152569. http://dx.doi.org/10.1098/rspb.2015.2569.

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Species composition and habitats are changing at unprecedented rates in the world's oceans, potentially causing entire food webs to shift to structurally and functionally different regimes. Despite the severity of these regime shifts, elucidating the precise nature of their underlying processes has remained difficult. We address this challenge with a new analytic approach to detect and assess the relative strength of different driving processes in food webs. Our study draws on complexity theory, and integrates the network-centric exponential random graph modelling (ERGM) framework developed wi

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Marquet, Franck, Filip Stojceski, Gianvito Grasso, Viorica Patrulea, Andrea Danani, and Gerrit Borchard. "Characterization of the Interaction of Polymeric Micelles with siRNA: A Combined Experimental and Molecular Dynamics Study." Polymers 14, no. 20 (2022): 4409. http://dx.doi.org/10.3390/polym14204409.

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The simulation of large molecular systems remains a daunting challenge, which justifies the exploration of novel methodologies to keep computers as an ideal companion tool for everyday laboratory work. Whole micelles, bigger than 20 nm in size, formed by the self-assembly of hundreds of copolymers containing more than 50 repeating units, have until now rarely been simulated, due to a lack of computational power. Therefore, a flexible amphiphilic triblock copolymer (mPEG45-α-PLL10-PLA25) containing a total of 80 repeating units, has been emulated and synthesized to embody compactified nanoconst

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Naudi-Fabra, Samuel, Martin Blackledge, and Sigrid Milles. "Synergies of Single Molecule Fluorescence and NMR for the Study of Intrinsically Disordered Proteins." Biomolecules 12, no. 1 (2021): 27. http://dx.doi.org/10.3390/biom12010027.

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Single molecule fluorescence and nuclear magnetic resonance spectroscopy (NMR) are two very powerful techniques for the analysis of intrinsically disordered proteins (IDPs). Both techniques have individually made major contributions to deciphering the complex properties of IDPs and their interactions, and it has become evident that they can provide very complementary views on the distance-dynamics relationships of IDP systems. We now review the first approaches using both NMR and single molecule fluorescence to decipher the molecular properties of IDPs and their interactions. We shed light on

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Karch, Rudolf, Claudia Stocsits, Nevena Ilieva, and Wolfgang Schreiner. "Intramolecular Domain Movements of Free and Bound pMHC and TCR Proteins: A Molecular Dynamics Simulation Study." Cells 8, no. 7 (2019): 720. http://dx.doi.org/10.3390/cells8070720.

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The interaction of antigenic peptides (p) and major histocompatibility complexes (pMHC) with T-cell receptors (TCR) is one of the most important steps during the immune response. Here we present a molecular dynamics simulation study of bound and unbound TCR and pMHC proteins of the LC13-HLA-B*44:05-pEEYLQAFTY complex to monitor differences in relative orientations and movements of domains between bound and unbound states of TCR-pMHC. We generated local coordinate systems for MHC α1- and MHC α2-helices and the variable T-cell receptor regions TCR Vα and TCR Vβ and monitored changes in the dista

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Tolstova, Anna P., Alexander A. Makarov та Alexei A. Adzhubei. "Zinc Induced Aβ16 Aggregation Modeled by Molecular Dynamics". International Journal of Molecular Sciences 22, № 22 (2021): 12161. http://dx.doi.org/10.3390/ijms222212161.

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It is widely accepted that the addition of zinc leads to the formation of neurotoxic nonfibrillar aggregates of beta-amyloid peptides Aβ40 and Aβ42 and at the same time destabilizes amyloid fibrils. However, the mechanism of the effect of zinc on beta-amyloid is not fully understood. In this study, a fast zinc-induced aggregation of Aβ16 (as compared to a system without zinc) via the formation of Aβ16 dimers with one zinc ion coordinated in the metal-binding site 11EVHH14, followed by their polymerization, has been studied by molecular dynamics. The best aggregation was shown by the system com

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Paciolla, Mariarita, Daniel J. Arismendi-Arrieta, and Angel J. Moreno. "Coarsening Kinetics of Complex Macromolecular Architectures in Bad Solvent." Polymers 12, no. 3 (2020): 531. http://dx.doi.org/10.3390/polym12030531.

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This study reports a general scenario for the out-of-equilibrium features of collapsing polymeric architectures. We use molecular dynamics simulations to characterize the coarsening kinetics, in bad solvent, for several macromolecular systems with an increasing degree of structural complexity. In particular, we focus on: flexible and semiflexible polymer chains, star polymers with 3 and 12 arms, and microgels with both ordered and disordered networks. Starting from a powerful analogy with critical phenomena, we construct a density field representation that removes fast fluctuations and provide

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Contreras-Riquelme, Sebastián, Jose-Antonio Garate, Tomas Perez-Acle, and Alberto J. M. Martin. "RIP-MD: a tool to study residue interaction networks in protein molecular dynamics." PeerJ 6 (December 7, 2018): e5998. http://dx.doi.org/10.7717/peerj.5998.

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Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In

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Kolesnikov, Andrey V. "Space and Molecular Human in the Process of Social Systems Digital Transformation in Belarus and Russia." AEROSPACE SPHERE JOURNAL, no. 2 (June 26, 2021): 84–97. http://dx.doi.org/10.30981/2587-7992-2020-107-2-84-97.

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To develop a strategy for building the Union State of Russia and Belarus’ better future, it is necessary to understand the mechanisms and identify the main causes that govern the dynamics of this complex and specifi c social system. As the main factor determining the social dynamics of a given civilization cluster, we consider the competition of two basic sociotypes. They are conditionally designated as a molecular man and a space man. A molecular person is a consumer whose social behavior is based on the power of the selfi sh gene and consumer society’s ideals. A space person is passionate, d

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Banerjee, Sourav, Zoltan Jurek, Malik Muhammad Abdullah, and Robin Santra. "Chemical effects on the dynamics of organic molecules irradiated with high intensity x rays." Structural Dynamics 9, no. 5 (2022): 054101. http://dx.doi.org/10.1063/4.0000166.

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The interaction of a high intensity x-ray pulse with matter causes ionization of the constituent atoms through various atomic processes, and the system eventually goes through a complex structural dynamics. Understanding this whole process is important from the perspective of structure determination of molecules using single particle imaging. XMDYN, which is a classical molecular dynamics-Monte Carlo based hybrid approach, has been successful in simulating the dynamical evolution of various systems under intense irradiation over the past years. The present study aims for extending the XMDYN to

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Gross, Thilo, Korinna T. Allhoff, Bernd Blasius, et al. "Modern models of trophic meta-communities." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1814 (2020): 20190455. http://dx.doi.org/10.1098/rstb.2019.0455.

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Dispersal and foodweb dynamics have long been studied in separate models. However, over the past decades, it has become abundantly clear that there are intricate interactions between local dynamics and spatial patterns. Trophic meta-communities, i.e. meta-foodwebs, are very complex systems that exhibit complex and often counterintuitive dynamics. Over the past decade, a broad range of modelling approaches have been used to study these systems. In this paper, we review these approaches and the insights that they have revealed. We focus particularly on recent papers that study trophic interactio

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Ischenko, A. A., Y. I. Tarasov, and L. Schäfer. "STRUCTURAL DYNAMICS OF FREE MOLECULES AND CONDENSED MATTER. Part I. THEORY AND EXPERIMENTAL TECHNIQUE." Fine Chemical Technologies 12, no. 2 (2017): 5–33. http://dx.doi.org/10.32362/2410-6593-2017-12-2-5-33.

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To understand the dynamic features of molecular systems with a complex landscape of potential energy surfaces, it is necessary to study them in the associated 4D space-time continuum. The introduction of time in the diffraction methods and the development of coherent principles of the research process opened up new approaches for the study of the dynamics of wave packets, intermediates and transient states of the chemical reactions, short-lived compounds in the gaseous and condensed media. Time-resolved electron diffraction, the new method for the structural dynamic studies of free molecules,

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RAFIKOV, MARAT, JOSÉ MANOEL BALTHAZAR, and HUBERTUS F. VON BREMEN. "MANAGEMENT OF COMPLEX SYSTEMS: MODELING THE BIOLOGICAL PEST CONTROL." Biophysical Reviews and Letters 03, no. 01n02 (2008): 241–56. http://dx.doi.org/10.1142/s1793048008000721.

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The aim of this paper is to study the cropping system as complex one, applying methods from theory of dynamic systems and from the control theory to the mathematical modeling of the biological pest control. The complex system can be described by different mathematical models. Based on three models of the pest control, the various scenarios have been simulated in order to obtain the pest control strategy only through natural enemies' introduction.

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Li, Conghui, Xiaolu Han, Xiaoxuan Hong, et al. "Study on the Complexation and Release Mechanism of Methylphenidate Hydrochloride Ion Exchange Resin Complex." Polymers 13, no. 24 (2021): 4394. http://dx.doi.org/10.3390/polym13244394.

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Since the advent of ion exchange resin, it has been widely used in many fields, including drug delivery systems. The drug binds to the resin through an exchange reaction to form a drug–resin complex, which can gradually release drugs through the exchange of physiological ions in the gastrointestinal tract, to realize functions such as taste masking and regulating release. In this study, the complexes of methylphenidate hydrochloride and Amberlite IRP69 were prepared and evaluated to explore the mechanism of complexation, influencing factors and release mechanism at a molecular level. Firstly,

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Poghosyan, Armen, Hrachya Astsatryan, Wahi Narsisian, and Yevgeni Mamasakhlisov. "On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs." Cybernetics and Information Technologies 17, no. 5 (2017): 68–80. http://dx.doi.org/10.1515/cait-2017-0056.

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Abstract High Performance Computing (HPC) accelerates life science discoveries by enabling scientists to analyze large data sets, to develop detailed models of entire biological systems and to simulate complex biological processes. As computational experiments, molecular dynamics simulations are widely used in life sciences to evaluate the equilibrium nature of classical many-body systems The modelling and molecular dynamics study of surfactant, polymer solutions and the stability of proteins and nucleic acids under different conditions, as well as deoxyribonucleic acid proteins are studied. T

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Liu, Gang, and Yi Ping Yao. "Large Scale Molecular Dynamics Simulation of Femtosecond Laser Ablation of Silicon Using Sensing-VISICOM." Advanced Materials Research 418-420 (December 2011): 1330–37. http://dx.doi.org/10.4028/www.scientific.net/amr.418-420.1330.

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Silicon is widely used as substrate material for the fabrication of micro-electro and micromechanical components. Since silicon is very brittle, how to cut it into complex shapes remains a hot topic. Thanks to the small spot diameter, laser cutting is a promising alternative. However, during laser cutting, different kinds of defects can be generated depending on the beam-material interaction phenomena (ablation, melting, etc). Molecular Dynamics simulation is an effective way to study the beam-material interaction phenomena. Lots of work has been done to develop MD models of laser ablation of

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Bruner, Barry D., Zdeněk Mašín, Matteo Negro, et al. "Multidimensional high harmonic spectroscopy of polyatomic molecules: detecting sub-cycle laser-driven hole dynamics upon ionization in strong mid-IR laser fields." Faraday Discussions 194 (2016): 369–405. http://dx.doi.org/10.1039/c6fd00130k.

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High harmonic generation (HHG) spectroscopy has opened up a new frontier in ultrafast science, where electronic dynamics can be measured on an attosecond time scale. The strong laser field that triggers the high harmonic response also opens multiple quantum pathways for multielectron dynamics in molecules, resulting in a complex process of multielectron rearrangement during ionization. Using combined experimental and theoretical approaches, we show how multi-dimensional HHG spectroscopy can be used to detect and follow electronic dynamics of core rearrangement on sub-laser cycle time scales. W

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Escalona, Yerko, Drazen Petrov, Edgar Galicia-Andrés, and Chris Oostenbrink. "Exploring the Macroscopic Properties of Humic Substances Using Modeling and Molecular Simulations." Agronomy 13, no. 4 (2023): 1044. http://dx.doi.org/10.3390/agronomy13041044.

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Soil organic matter (SOM) is composed of a complex and heterogeneous mixture of organic compounds, which poses a challenge in understanding it on an atomistic level. Based on the progress of molecular dynamics simulations and our efforts to create molecular systems that resemble SOM, in this work, we expanded our knowledge of SOM through the use of humic substances (HSs). Specifically, we studied the standardized samples of HS of the International Humic Substances Society (IHSS). This society provided the elemental and organic composition used as input parameters for our Vienna Soil Organic Ma

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Zhang, Shitao, Shuai Lv, Xueqi Fu, Lu Han, Weiwei Han, and Wannan Li. "Molecular Dynamics Simulations Study of the Interactions between Human Dipeptidyl-Peptidase III and Two Substrates." Molecules 26, no. 21 (2021): 6492. http://dx.doi.org/10.3390/molecules26216492.

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Human dipeptidyl-peptidase III (hDPP III) is capable of specifically cleaving dipeptides from the N-terminal of small peptides with biological activity such as angiotensin II (Ang II, DRVYIHPF), and participates in blood pressure regulation, pain modulation, and the development of cancers in human biological activities. In this study, 500 ns molecular dynamics simulations were performed on free-hDPP III (PDB code: 5E33), hDPP III-Ang II (PDB code: 5E2Q), and hDPP III-IVYPW (PDB code: 5E3C) to explore how these two peptides affect the catalytic efficiency of enzymes in terms of the binding mode

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Sefidkar, Narmin, Samira Fathizadeh, Fatemeh Nemati та Constantinos Simserides. "Energy Transport along α-Helix Protein Chains: External Drives and Multifractal Analysis". Materials 15, № 8 (2022): 2779. http://dx.doi.org/10.3390/ma15082779.

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Energy transport within biological systems is critical for biological functions in living cells and for technological applications in molecular motors. Biological systems have very complex dynamics supporting a large number of biochemical and biophysical processes. In the current work, we study the energy transport along protein chains. We examine the influence of different factors such as temperature, salt concentration, and external mechanical drive on the energy flux through protein chains. We obtain that energy fluctuations around the average value for short chains are greater than for lon

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