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https://www.readbyqxmd.com/read/28335252/stress-waves-and-characteristics-of-zigzag-and-armchair-silicene-nanoribbons
#1
Yu-Cheng Fan, Te-Hua Fang, Tao-Hsing Chen
The mechanical properties of silicene nanostructures subject to tensile loading were studied via a molecular dynamics (MD) simulation. The effects of temperature on Young's modulus and the fracture strain of silicene with armchair and zigzag types were examined. The maximum in-plane stress and the corresponding critical strain of the armchair and the zigzag silicene sheets at 300 K were 8.85 and 10.62, and 0.187 and 0.244 N/m, respectively. The in-plane stresses of the silicene sheet in the armchair direction at the temperatures of 300, 400, 500, and 600 K were 8...
June 24, 2016: Nanomaterials
https://www.readbyqxmd.com/read/28334084/molecular-dynamics-recipes-for-genome-research
#2
Tommaso Biagini, Giovanni Chillemi, Gianluigi Mazzoccoli, Alessandro Grottesi, Caterina Fusilli, Daniele Capocefalo, Stefano Castellana, Angelo Luigi Vescovi, Tommaso Mazza
Molecular dynamics (MD) simulation allows one to predict the time evolution of a system of interacting particles. It is widely used in physics, chemistry and biology to address specific questions about the structural properties and dynamical mechanisms of model systems. MD earned a great success in genome research, as it proved to be beneficial in sorting pathogenic from neutral genomic mutations. Considering their computational requirements, simulations are commonly performed on HPC computing devices, which are generally expensive and hard to administer...
February 18, 2017: Briefings in Bioinformatics
https://www.readbyqxmd.com/read/28333437/a-tio2-femnp-core-shell-nanorod-array-photoanode-for-efficient-photoelectrochemical-oxygen-evolution
#3
Desmond E Schipper, Zhenhuan Zhao, Andrew P Leitner, Lixin Xie, Fan Qin, Md Kamrul Alam, Shuo Chen, Dezhi Wang, Zhifeng Ren, Zhiming Wang, Jiming Bao, Kenton H Whitmire
A variety of catalysts have been developed for electrocatalytic oxygen evolution, but very few of them can be readily integrated with semiconducting light absorbers for photoelectrochemical or photocatalytic water splitting. Here, we demonstrate an efficient core/shell photoanode with a highly active oxygen evolution electrocatalyst shell (FeMnP) and semiconductor core (rutile TiO2) for photoelectrochemical oxygen evolution reaction (PEC-OER). Metal-organic chemical vapor deposition (MOCVD) from a single-source precursor was used to ensure good contact between the FeMnP and the TiO2...
March 23, 2017: ACS Nano
https://www.readbyqxmd.com/read/28330367/multiscale-simulations-of-anisotropic-particles-combining-molecular-dynamics-and-green-s-function-reaction-dynamics
#4
Adithya Vijaykumar, Thomas E Ouldridge, Pieter Rein Ten Wolde, Peter G Bolhuis
The modeling of complex reaction-diffusion processes in, for instance, cellular biochemical networks or self-assembling soft matter can be tremendously sped up by employing a multiscale algorithm which combines the mesoscopic Green's Function Reaction Dynamics (GFRD) method with explicit stochastic Brownian, Langevin, or deterministic molecular dynamics to treat reactants at the microscopic scale [A. Vijaykumar, P. G. Bolhuis, and P. R. ten Wolde, J. Chem. Phys. 143, 214102 (2015)]. Here we extend this multiscale MD-GFRD approach to include the orientational dynamics that is crucial to describe the anisotropic interactions often prevalent in biomolecular systems...
March 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28330175/exploration-of-the-binding-modes-of-l-asparaginase-complexed-with-its-amino-acid-substrates-by-molecular-docking-dynamics-and-simulation
#5
Erva Rajeswara Reddy, Rajulapati Satish Babu, Potla Durthi Chandrasai, Pola Madhuri
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-glutamine (L-Gln) deamination plays crucial role in ALL treatment. Role of Erwinaze(®) (L-asparaginase from Erwinia chrysanthemi) in regulation of L-Asn and L-Gln has been confirmed by the experimental studies. Therapeutic research against ALL remained elusive with the lack of structural information on Erwinaze(®) enzyme. In this present study, homology model of the Erwinaze(®) was developed using MODELLER and the same was validated by various quality indexing tools...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330072/molecular-dynamic-simulations-of-escherichia-coli-l-asparaginase-to-illuminate-its-role-in-deamination-of-asparagine-and-glutamine-residues
#6
Rajeswara Reddy Erva, Satish Babu Rajulapati, Chandrasai Potla Durthi, Mayuri Bhatia, Madhuri Pola
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-Glutamine (L-Gln) deamination play a crucial role in ALL treatment. Role of Elspar(®) (L-asparaginase from Escherichia coli) in regulation of L-Asn and L-Gln has been confirmed by the other researchers through experimental studies. Therapeutic research against ALL remained elusive with the lack of information on molecular interactions of Elspar(®) with amino acid substrates. In the present study, using different docking tools binding cavities, key residues in binding and ligand binding mechanisms were identified...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28328501/monte-carlo-simulations-of-diffusion-weighted-mri-in-myocardium-validation-and-sensitivity-analysis
#7
Joanne Bates, Darryl McClymont, Irvin Teh, Peter Kohl, Jurgen Schneider, Vicente Grau
A model of cardiac microstructure and diffusion MRI is presented, and compared with experimental data from ex vivo rat hearts. The model includes a simplified representation of individual cells, with physiologically correct cell size and orientation, as well as intra- to extracellular volume ratio. Diffusion MRI is simulated using a Monte Carlo model and realistic MRI sequences. The results show good correspondence between the simulated and experimental MRI signals. Similar patterns are observed in the eigenvalues of the diffusion tensor, the mean diffusivity (MD) and the fractional anisotropy (FA)...
March 10, 2017: IEEE Transactions on Medical Imaging
https://www.readbyqxmd.com/read/28327752/umbrella-sampling-molecular-dynamics-simulations-reveal-concerted-ion-movement-through-g-quadruplex-dna-channels
#8
Parisa Akhshi, Gang Wu
We have applied the umbrella sampling (US) method in all-atom molecular dynamics (MD) simulations to obtain potential of mean force (PMF) profiles for ion transport through three representative G-quadruplex DNA channels: [d(TG4T)]4, [d(G3T4G4)]2, and d[G4(T4G4)3]. The US MD results are in excellent agreement with those obtained previously with the adaptive biasing force (ABF) method. We then utilized the unique features in the US MD method to investigate multi-ion effects in [d(G3T4G4)]2 and discovered that the concerted ion movement is crucial for fully explaining the unusual experimental results on ion movement in this particular G-quadruplex system...
March 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28326985/book-review-driving-simulation-for-assessment-intervention-and-training-a-guide-for-occupational-therapy-and-health-care-professionals-by-classen-s-ed-classen-s-ed-2017-driving-simulation-for-assessment-intervention-and-training-a-guide-for-occupational-therapy
#9
https://www.readbyqxmd.com/read/28325049/antibody-subclass-detection-using-graphene-nanopore
#10
Amir Barati Farimani, Mohammad Heiranian, Kyoungmin Min, Narayana R Aluru
Solid-state nanopores are promising for label free protein detection. The large thickness, ranging from several tens of nanometers to micrometers and larger, of solid-state nanopores prohibits atomic scale scanning or interrogation of proteins. Here, a single-atom thick graphene nanopore is shown to be highly capable of sensing and discriminating between different subclasses of IgG antibodies despite their minor and subtle variation in atomic structure. Extensive molecular dynamics (MD) simulations, rigorous statistical analysis with a total aggregate simulation time of 2...
March 21, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28324976/meandered-conformai-antenna-for-ism-band-ingestible-capsule-communication-systems
#11
Md Shamsul Arefin, Jean-Michel Redoute, Mehmet Rasit Yuce
The wireless capsule has been used to measure physiological parameters in the gastrointestinal tract where communication from in-body to external receiver is necessary using a miniaturized antenna with high gain and onmidirectional radiation pattern. This paper presents a meandered conformal antenna with center frequency of 433 MHz for a wireless link between an in-body capsule system and an ex-body receiver system. The antenna is wrapped around the wireless capsule, which provides extra space for other circuits and sensors inside the capsule as well as allows it having larger dimensions compared to inner antennas...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28322965/inhibitory-effect-of-hesperetin-on-%C3%AE-glucosidase-molecular-dynamics-simulation-integrating-inhibition-kinetics
#12
Yan Gong, Xiu-Yuan Qin, Yuan-Yuan Zhai, Hao Hao, Jinhyuk Lee, Yong-Doo Park
The α-glucosidase inhibitor is of interest to researchers due to its association with type-2 diabetes treatment. Hesperetin is a flavonoid with natural antioxidant properties. This paper presents an evaluation on the effects of hesperetin on α-glucosidase via inhibitory kinetics using a Molecular Dynamics (MD) simulation integration method. Due to the antioxidant properties of hesperetin, it reversibly inhibits α-glucosidase in a slope-parabolic mixed-type manner (IC50=0.38±0.05mM; Kslope=0.23±0.01mM), accompanied by tertiary structural changes...
March 18, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28321930/uncovering-allostery-and-regulation-in-samhd1-through-molecular-dynamics-simulations
#13
Kajwal Kumar Patra, Akash Bhattacharya, Swati Bhattacharya
The human sterile alpha motif and HD domain-containing protein 1 (SAMHD1) is a retroviral restriction factor in myeloid cells and non-cycling CD4+ T cells, a feature imputed to its phosphohydrolase activity - the enzyme depletes the cellular dNTP levels inhibiting reverse transcription. The functionally active form of SAMHD1 is an allosterically triggered tetramer which utilizes GTP-Mg(+2) -dNTP cross bridges to link and stabilize adjacent monomers. However, very little is known about how it assembles into a tetramer and how long the tetramer stays intact...
March 21, 2017: Proteins
https://www.readbyqxmd.com/read/28321028/durability-of-alkaline-agents-bactericidal-efficacies-in-litter-under-field-conditions
#14
Hakimullah Hakim, Chiharu Toyofuku, Mari Ota, Mayuko Suzuki, Miyuki Komura, Masashi Yamada, Md Shahin Alam, Natthanan Sangsriratanakul, Dany Shoham, Kazuaki Takehara
Alkaline agents are well-known for their disinfection capacities against pathogens even at the presence of organic materials, but the durability of their bactericidal efficacies under field conditions is unknown. Therefore, within the present study, two alkaline agents, namely bioceramic (BCX) derived from chicken feces and food additive grade Ca(OH)2 (FdCa(OH)2) derived from natural lime stone, were evaluated for the persistence of their bactericidal efficacies in litter, under simulated field conditions. BCX powder mixed at 50% concentration in litter or FdCa(OH)2 powder at 20% concentration in litter lost their bactericidal efficacies at 3 days post exposure of chicks, and thereafter, both mentioned alkaline agents could not inactivate bacteria down to the acceptable level (≥3 log10 CFU/ml reduction)...
March 19, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28320908/reaction-and-relaxation-at-surface-hotspots-using-molecular-dynamics-and-the-energy-grained-master-equation-to-describe-diamond-etching
#15
David R Glowacki, W J Rodgers, Robin Shannon, Struan H Robertson, Jeremy N Harvey
The extent to which vibrational energy transfer dynamics can impact reaction outcomes beyond the gas phase remains an active research question. Molecular dynamics (MD) simulations are the method of choice for investigating such questions; however, they can be extremely expensive, and therefore it is worth developing cheaper models that are capable of furnishing reasonable results. This paper has two primary aims. First, we investigate the competition between energy relaxation and reaction at 'hotspots' that form on the surface of diamond during the chemical vapour deposition process...
April 28, 2017: Philosophical Transactions. Series A, Mathematical, Physical, and Engineering Sciences
https://www.readbyqxmd.com/read/28319781/systematic-study-of-imidazoles-inhibiting-ido1-via-the-integration-of-molecular-mechanics-and-quantum-mechanics-calculations
#16
Yi Zou, Fang Wang, Yan Wang, Wenjie Guo, Yihua Zhang, Qiang Xu, Yisheng Lai
Indoleamine 2,3-dioxygenase 1 (IDO1) is regarded as an attractive target for cancer immunotherapy. To rationalize the detailed interactions between IDO1 and its inhibitors at the atomic level, an integrated computational approach by combining molecular mechanics and quantum mechanics methods was employed in this report. Specifically, the binding modes of 20 inhibitors was initially investigated using the induced fit docking (IFD) protocol, which outperformed other two docking protocols in terms of correctly predicting ligand conformations...
March 14, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28319659/improving-computational-predictions-of-single-stranded-rna-tetramers-with-revised-%C3%AE-%C3%AE-torsional-parameters-for-the-amber-force-field
#17
David J Wales, Ilyas Yildirim
With current advancements in RNA based therapeutics, it is becoming crucial to utilize theoretical and computational methods to describe properly the physical properties of RNA molecules. NMR and X-ray crystallography are two powerful techniques for investigating structural properties. However, if the RNA molecules are complex or dynamic, these methods might not be adequate. For computational approaches, the quality of the force field will determine accuracy of our predictions. In this contribution, we revise the α/γ torsional parameters of RNA for amber force field using a model system representing an RNA dimer backbone...
March 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28319394/a-network-of-conformational-transitions-in-the-apo-form-of-ndm-1-enzyme-revealed-by-md-simulation-and-a-markov-state-model
#18
Kaifu Gao, Yunjie Zhao
New Delhi metallo-β-lactamase-1 (NDM-1) is a novel β-Lactamase enzyme that confers enteric bacteria with nearly complete resistance to all β-lactam antibiotics, so raises a formidable and global threat to human health. However, the binding mechanism between apo-NDM-1 and antibiotics as well as related conformational changes remains poorly understood, which largely hinders the overcoming of its antibiotic resistance. In our study, long-time conventional molecular dynamics simulation and Markov state models were applied to reveal both dynamical and conformational landscape of apo-NDM-1: the MD simulation demonstrates that the loop L3, which is responsible for antibiotic binding, is the most flexible and undergoes dramatic conformational changes; moreover, the Markov state model built from the simulation maps four metastable states including open, semi-open and closed conformations of the loop L3 as well as frequent transitions between the states...
March 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28319376/anomalous-protein-protein-interactions-in-multivalent-salt-solution
#19
Coralie Pasquier, Mario Vazdar, Jan Forsman, Pavel Jungwirth, Mikael Lund
The stability of aqueous protein solutions is strongly affected by multivalent ions, which induce ion-ion correlations beyond the scope of classical mean-field theory. Using all-atom Molecular Dynamics (MD) and coarse grained Monte Carlo (MC) simulations, we investigate the interaction between a pair of protein molecules in 3:1 electrolyte solution. In agreement with available experimental findings of "reentrant protein condensation", we observe an anomalous trend in the protein-protein potential of mean force with increasing electrolyte concentration in the order: (i) double-layer repulsion, (ii) ion-ion correlation attraction, (iii) over-charge repulsion, and in excess of 1:1 salt, (iv) non Coulombic attraction...
March 20, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28319278/how-does-ceiii-nitrate-dissolve-in-a-protic-ionic-liquid-a-combined-molecular-dynamics-and-exafs-study
#20
Paola D'Angelo, Valentina Migliorati, Alessandra Serva, Riccardo Spezia
A diluted solution of Ce(NO₃)₃ in the protic ionic liquid (IL) ethylammonium nitrate (EAN) is investigated using molecular dynamics (MD) simulations and extended X-ray absorption fine structure (EXAFS) spectroscopy. For the first time polarizable effects are included in the MD force field to describe a heavy metal ion in a protic IL, but, unlike water, they are found to be unessential. The CeIII ion first solvation shell is formed by nitrate ions arranged in an icosahedral structure, and an equilibrium between monodentate and bidentate ligands is present in the solution...
March 20, 2017: Chemistry: a European Journal
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