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https://www.readbyqxmd.com/read/28532124/side-flow-effect-on-surface-generation-in-nano-cutting
#1
Feifei Xu, Fengzhou Fang, Xiaodong Zhang
The side flow of material in nano cutting is one of the most important factors that deteriorate the machined surface quality. The effects of the crystallographic orientation, feed, and the cutting tool geometry, including tool edge radius, rake angle and inclination angle, on the side flow are investigated employing molecular dynamics simulation. The results show that the stagnation region is formed in front of tool edge and it is characterized by the stagnation radius R s and stagnation height h s . The side flow is formed because the material at or under the stagnation region is extruded by the tool edge to flow to the side of the tool edge...
December 2017: Nanoscale Research Letters
https://www.readbyqxmd.com/read/28531815/chicken-interleukin-1%C3%AE-mutants-are-effective-single-dose-vaccine-adjuvants-that-enhance-mucosal-immune-response
#2
Wen-Ting Chen, Hao-Kai Chang, Cheng-Chung Lin, Shan-Min Yang, Hsien-Sheng Yin
The use of cytokines as adjuvants in poultry is promising because they may enhance immune responses to antigens. In this study, we created two mutants, chicken interleukin-1 beta (ChIL-1β) Q19A and R140A, which exhibited significantly increased in vivo biological activity compared with wild-type ChIL-1β. The potential mucosal adjuvant activity of the mutants Q19A and R140A was evaluated in chickens through the intranasal coadministration of a single dose of the Newcastle disease virus (NDV) vaccine with Q19A or R140A...
May 19, 2017: Molecular Immunology
https://www.readbyqxmd.com/read/28531371/wing-1-of-protein-hop2-is-as-important-as-helix-3-in-dna-binding-by-md-simulation
#3
Hem Moktan, Donghua H Zhou
The repair of programmed DNA double-strand breaks through recombination is required for proper association and disjunction of the meiotic homologous chromosomes. Meiosis specific protein HOP2 plays essential roles in recombination by promoting recombinase activities. The N-terminal domain of HOP2 interacts with DNA through helix 3 (H3) and wing 1 (W1). Mutations in wing 1 (Y65A/K67A/Q68A) slightly weakened the binding but mutations in helices 2 and 3 (Q30A/K44A/K49A) nearly abolished the binding. To better understand such differential effects at atomic level, molecular dynamics simulations were employed...
May 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28531354/monomeric-polyglutamine-structures-that-evolve-into-fibrils
#4
David Punihaole, Ryan S Jakubek, Riley James Workman, Lauren E Marbella, Patricia Campbell, Jeffry D Madura, Sanford A Asher
We investigate the solution and fibril conformations and structural transitions of the polyglutamine (polyQ) peptide, D2Q10K2 (Q10), by synergistically using UV Resonance Raman (UVRR) spectroscopy and Molecular Dynamics (MD) simulations. We show that Q10 adopts two distinct, monomeric solution conformational states, a collapsed β-strand and a PPII-like structure that do not readily interconvert. This clearly indicates a high activation barrier in solution that prevents equilibration between these structures...
May 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28531316/a-comprehensive-method-to-quantify-adaptations-by-male-and-female-mice-with-hot-flashes-induced-by-the-neurokinin-b-receptor-agonist-senktide
#5
Ashley A Krull, Sarah A Larsen, Donald K Clifton, Genevieve Neal-Perry, Robert A Steiner
Vasomotor symptoms (VMS, or hot flashes) plague millions of reproductive age men and women who have natural or iatrogenic loss of sex steroid production. Many affected individuals are left without treatment options because of contraindications to hormone replacement therapy and the lack of equally effective non-hormonal alternatives. Moreover, development of safer, more effective therapies has been stymied by the lack of an animal model that recapitulates the hot flash phenomenon and enables direct testing of hypotheses regarding the pathophysiology underlying hot flashes...
May 22, 2017: Endocrinology
https://www.readbyqxmd.com/read/28531298/evolution-of-bacterial-virulence
#6
Médéric Diard, Wolf-Dietrich Hardt
Bacterial virulence is highly dynamic and context-dependent. For this reason, it is challenging to predict how molecular changes affect the growth of a pathogen in a host and its spread in host population. Two schools of thought have taken quite different directions to decipher the underlying principles of bacterial virulence. While molecular infection biology is focusing on the basic mechanisms of the pathogen-host interaction, evolution biology takes virulence as one of several parameters affecting pathogen spread in a host population...
May 22, 2017: FEMS Microbiology Reviews
https://www.readbyqxmd.com/read/28530836/nuclear-quantum-effects-in-water-reorientation-and-hydrogen-bond-dynamics
#7
David Mark Wilkins, David E Manolopoulos, Silvio Pipolo, Damien Laage, James T Hynes
We combine classical and ring polymer molecular dynamics simulations with the molecular jump model to provide a molecular description of the nuclear quantum effects (NQEs) on water reorientation and hydrogen-bond dynamics in liquid H2O and D2O. We show that while the net NQEs is negligible in D2O, it leads to a ∼13% acceleration in H2O dynamics compared to a classical description. Large angular jumps exchanging hydrogen-bond partners are the dominant reorientation pathway (just as in a classical description); the faster reorientation dynamics arise from the increased jump rate constant...
May 22, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28530823/nanomechanically-visualizing-drug-cell-interaction-at-the-early-stage-of-chemotherapy
#8
Yun-Long Wu, Wilfried Engl, Benhui Hu, Pingqiang Cai, Wan Ru Leow, Nguan Soon Tan, Chwee Teck Lim, Xiaodong Chen
A detailed understanding of chemotherapy is determined by the response of cell to the formation of the drug-target complex and its corresponding sudden or eventual cell death. However, visualization of this early but important process, encompassing the fast dynamics as well as complex network of molecular pathways, remains challenging. Herein, we report that the nanomechanical traction force is sensitive enough to reflect the early cellular response upon the addition of chemotherapeutical molecules in a real-time and non-invasive manner, due to interactions between chemotherapeutic drug and its cytoskeleton targets...
May 22, 2017: ACS Nano
https://www.readbyqxmd.com/read/28530814/reactive-molecular-dynamics-simulations-to-understand-mechanical-response-of-thaumasite-under-temperature-and-strain-rate-effects
#9
Shahin Hajilar, Behrouz Shafei, Tao Cheng, Andres Jaramillo-Botero
Understanding the structural, thermal, and mechanical properties of thaumasite is of great interest to the cement industry, mainly because it is the phase responsible for the aging and deterioration of civil infrastructures made of cementitious materials attacked by external sources of sulfate. Despite its importance, the effects of temperature and strain rate on the mechanical response of thaumasite have remained unexplored to date. In this study, the mechanical properties of thaumasite are fully characterized using the reactive molecular dynamics (RMD) method...
May 22, 2017: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/28530813/enhanced-sampling-of-phase-transitions-in-coarse-grained-lipid-bilayers
#10
David N Stelter, Tom Keyes
Freezing and melting of dipalmitoylphosphatidylcholine (DPPC) bilayers are simulated in both the explicit (Wet) and implicit solvent (Dry) coarse-grained MARTINI force fields with enhanced sampling, via the isobaric, molecular dynamics version of the generalized replica exchange method (gREM). Phase transitions are described with the entropic viewpoint, based upon the statistical temperature as a function of enthalpy, TS(H) = 1/(dS(H)/dH), where S is the configurational entropy. Bilayer thickness, area per lipid, and the second-rank order parameter (P2) are calculated vs temperature in the transition range...
May 22, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28530761/drop-spreading-on-a-superhydrophobic-surface-pinned-contact-line-and-bending-liquid-surface
#11
Yanbin Wang, Joseph Eugene Andrews, Liangbing Hu, Siddhartha Das
In this study, we employ molecular dynamics (MD) simulations to probe the spreading of a drop on a superhydrophobic (SH) surface. The SH surface consists of nanopillars and the drop spreads while being in the Cassie-Baxter (CB) state on the nanopillared surface. Most remarkably, unlike the spreading on non-SH surfaces, we witness that the spreading on SH surfaces is not dominated by the motion of the three-phase contact line (TPCL). Rather, the TPCL remains pinned at the edge of a nanopillar and the spreading is ensured by the liquid surface or the liquid-vapor interface (of this pinned TPCL) bending down and wetting the solid adjacent to the TPCL...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28530736/magnetic-field-controlled-graphene-oxide-based-origami-with-enhanced-surface-area-and-mechanical-properties
#12
Ok-Kyung Park, Chandra Sekhar Tiwary, Yang Yang, Sanjit Bhowmick, Soumya Vinod, Qingbo Zhang, Vicki L Colvin, S A Syed Asif, Robert Vajtai, Evgeni S Penev, Boris I Yakobson, Pulickel M Ajayan
One can utilize the folding of paper to build fascinating 3D origami architectures with extraordinary mechanical properties and surface area. Inspired by the same, the morphology of 2D graphene can be tuned by addition of magnetite (Fe3O4) nanoparticles in the presence of a magnetic field. The innovative 3D architecture with enhanced mechanical properties also shows a high surface area (∼2500 m(2) g(-1)) which is utilized for oil absorption. Detailed microscopy and spectroscopy reveal rolling of graphene oxide (GO) sheets due to the magnetic field driven action of magnetite particles, which is further supported by molecular dynamics (MD) simulations...
May 22, 2017: Nanoscale
https://www.readbyqxmd.com/read/28530729/what-are-the-key-factors-governing-the-nucleation-of-co2-hydrate
#13
Zhongjin He, Praveen Linga, Jianwen Jiang
Microsecond molecular dynamics simulations were performed to provide molecular insights into the nucleation of CO2 hydrate. The adsorption of sufficient CO2 molecules around CO2 hydration shells is revealed to be crucial to effectively stabilize the hydrogen bonds formed therein, catalyzing the hydration shells into hydrate cages and inducing the nucleation. Moreover, a high aqueous CO2 concentration is found to be another key factor governing the nucleation of CO2 hydrate, and only above a critical concentration can the nucleation of CO2 hydrate occur...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28530706/akt-is-indispensable-for-coordinating-par-4-jnk-cross-talk-in-p21-downmodulation-during-er-stress
#14
R U Rasool, D Nayak, S Chakraborty, M M Faheem, B Rah, P Mahajan, V Gopinath, A Katoch, Z Iqra, S K Yousuf, D Mukherjee, L D Kumar, A Nargotra, A Goswami
The double-edged role of p21 to command survival and apoptosis is emerging. The current investigation highlights ER stress-mediated JNK activation that plausibly triggers cell death by attenuating endogenous p21 level. Here, we demonstrated that ER stress activator 3-AWA diminishes the p21 levels in cancer cells by averting the senescent phenotype to commence G2/M arrest. In essence, the deceleration in p21 level occurs through ER stress/JNK/Caspase-3 axis via activation/induction of proapoptotic Par-4 and inhibition of AKT...
May 22, 2017: Oncogenesis
https://www.readbyqxmd.com/read/28530396/the-hydrotropic-action-of-cationic-hydrotrope-p-toluidinium-chloride-on-the-solubility-of-sparingly-soluble-gliclazide-drug-molecule-a-computational-study
#15
Shubhadip Das, Sandip Paul
We perform classical molecular dynamics simulations of sparingly soluble drug gliclazide (GLC) and hydrotrope p-toluidinium chloride (PTOL) in water with a regime of PTOL concentrations. Our results demonstrate that PTOL starts to self aggregate above its minimum hydrotrope concentration (MHC). Further these PTOL aggregates create a mixed micellar like framework in which the hydrophobic small tail part of most of the PTOL molecules direct towards the inside whereas in order to make favorable contact with water molecules its hydrophilic ammonium group points outward...
May 22, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28530285/one-step-formulation-of-nonionic-surfactant-bicelles-nsbs-by-a-double-tailed-polyglycerol-type-nonionic-surfactant
#16
Kenji Aramaki, Chikahiro Iwata, Jitendra Mata, Tetsuya Maehara, Daisuke Aburano, Yuichi Sakanishi, Kyuhei Kitao
Bicelles are generally formed by phospholipid-based systems and are useful for various applications, such as nanocarriers or membrane protein crystallization. The same disc-like assemblies, nonionic surfactant bicelles (NSBs), can also be formed using nonionic amphiphiles, but this has not been reported extensively. We report a novel NSB system that employs the double-tailed nonionic amphiphile, polyglyceryl dialkyl ether (C12CmGn), which has two alkyl chains and a polyglyceryl group. A symmetric-tail molecule, C12C12G13...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28530269/a-critical-comparison-of-coarse-grained-structure-based-approaches-and-atomic-models-of-protein-folding
#17
Jie Hu, Tao Chen, Moye Wang, Hue Sun Chan, Zhuqing Zhang
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations...
May 22, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28529879/beyond-the-raccoon-roundworm-the-natural-history-of-non-raccoon-baylisascaris-species-in-the-new-world
#18
REVIEW
Sarah G H Sapp, Pooja Gupta, Melissa K Martin, Maureen H Murray, Kevin D Niedringhaus, Madeleine A Pfaff, Michael J Yabsley
A total of 10 species of Baylisascaris, a genus of ascaridoid nematodes, occur worldwide and 6 of them occur in the New World. Most of the Baylisascaris species have a similar life cycle with carnivorous mammals or marsupials serving as definitive hosts and a smaller prey host serving as paratenic (or intermediate) hosts. However, one species in rodents is unique in that it only has one host. Considerable research has been conducted on B. procyonis, the raccoon roundworm, as it is a well-known cause of severe to fatal neurologic disease in humans and many wildlife species...
August 2017: International Journal for Parasitology. Parasites and Wildlife
https://www.readbyqxmd.com/read/28529725/the-catalytic-function-of-cytochrome-p450-is-entwined-with-its-membrane-bound-nature
#19
REVIEW
Carlo Barnaba, Katherine Gentry, Nirupama Sumangala, Ayyalusamy Ramamoorthy
Cytochrome P450, a family of monooxygenase enzymes, is organized as a catalytic metabolon, which requires enzymatic partners as well as environmental factors that tune its complex dynamic. P450 and its reducing counterparts-cytochrome P450-reductase and cytochrome b 5 -are membrane-bound proteins located in the cytosolic side of the endoplasmic reticulum. They are believed to dynamically associate to form functional complexes. Increasing experimental evidence signifies the role(s) played by both protein-protein and protein-lipid interactions in P450 catalytic function and efficiency...
2017: F1000Research
https://www.readbyqxmd.com/read/28529634/novel-linear-peptides-with-high-affinity-to-%C3%AE-v%C3%AE-3-integrin-for-precise-tumor-identification
#20
Yi Ma, Guanhua Ai, Congying Zhang, Menglu Zhao, Xue Dong, Zhihao Han, Zhaohui Wang, Min Zhang, Yuxi Liu, Weidong Gao, Siwen Li, Yueqing Gu
Development of alternative linear peptides for targeting αvβ3 integrin has attracted much attention, as the traditional peptide ligand, cyclic RGD, is limited by inferior water-solubility and complex synthesis. Using pharmacophore-based virtual screening and high-throughput molecular docking, we identified two novel linear small peptides RWr and RWrNM with high affinity and specificity to αvβ3 integrin. The competitive binding with cyclic RGD (c(RGDyK)) and cellular uptake related to the integrin expression levels verified their affinity to αvβ3 integrin...
2017: Theranostics
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