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https://www.readbyqxmd.com/read/28441775/progress-in-the-correlative-atomic-force-microscopy-and-optical-microscopy
#1
REVIEW
Lulu Zhou, Mingjun Cai, Ti Tong, Hongda Wang
Atomic force microscopy (AFM) has evolved from the originally morphological imaging technique to a powerful and multifunctional technique for manipulating and detecting the interactions between molecules at nanometer resolution. However, AFM cannot provide the precise information of synchronized molecular groups and has many shortcomings in the aspects of determining the mechanism of the interactions and the elaborate structure due to the limitations of the technology, itself, such as non-specificity and low imaging speed...
April 24, 2017: Sensors
https://www.readbyqxmd.com/read/28441629/sex-matters-the-effects-of-biological-sex-on-adipose-tissue-biology-and-energy-metabolism
#2
REVIEW
Teresa G Valencak, Anne Osterrieder, Tim J Schulz
Adipose tissue is a complex and multi-faceted organ. It responds dynamically to internal and external stimuli, depending on the developmental stage and activity of the organism. The most common functional subunits of adipose tissue, white and brown adipocytes, regulate and respond to endocrine processes, which then determine metabolic rate as well as adipose tissue functions. While the molecular aspects of white and brown adipose biology have become clearer in the recent past, much less is known about sex-specific differences in regulation and deposition of adipose tissue, and the specific role of the so-called pink adipocytes during lactation in females...
April 13, 2017: Redox Biology
https://www.readbyqxmd.com/read/28441567/plant-development-from-dynamics-to-mechanics
#3
Jan Traas
A new study analyses the complex changes in shape occurring during petal development in snapdragon. Combining simulations with quantitative analysis leads to a new model, where molecular regulators control overall organ shape through mechanical conflicts operating at the level of entire tissues.
April 24, 2017: Current Biology: CB
https://www.readbyqxmd.com/read/28441541/molecular-interaction-of-2-4-diacetylphloroglucinol-dapg-with-human-serum-albumin-hsa-the-spectroscopic-calorimetric-and-computational-investigation
#4
Pragna Lakshmi T, Moumita Mondal, Krishna Ramadas, Sakthivel Natarajan
Drug molecule interaction with human serum albumin (HSA) affects the distribution and elimination of the drug. The compound, 2,4-diacetylphloroglucinol (DAPG) has been known for its antimicrobial, antiviral, antihelminthic and anticancer properties. However, its interaction with HSA is not yet reported. In this study, the interaction between HSA and DAPG was investigated through steady-state fluorescence, time-resolved fluorescence (TRF), circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetry (ITC), molecular docking and molecular dynamics simulation (MDS)...
April 18, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28441496/room-temperature-ferromagnetism-in-2d-fe2si-nanosheet-with-enhanced-spin-polarization-ratio
#5
Yingjie Sun, Zhiwen Zhuo, Xiaojun Wu, Jinlong Yang
Searching experimental feasible two-dimensional (2D) ferromagnetic crystals with large spin-polarization ratio, high Curie temperature and large magnetic anisotropic energy is one key to develop next-generation spintronic nano-devices. Here, 2D Fe2Si nanosheet, one counterpart of Hapkeite mineral discovered in meteorite, with novel magnetism is proposed on the basis of first-principles calculations. 2D Fe2Si crystal has a slightly buckled triangular lattice with planar hexacoordinated Si and Fe atoms. The spin-polarized calculations with hybrid HSE06 function method indicate that 2D Fe2Si is a ferromagnetic half metal at its ground state with 100% spin-polarization ratio at Fermi energy level...
April 25, 2017: Nano Letters
https://www.readbyqxmd.com/read/28441487/the-isomeric-preference-of-an-atypical-dopamine-transporter-inhibitor-contributes-to-its-selection-of-the-transporter-conformation
#6
Ara M Abramyan, Sebastian Stolzenberg, Zheng Li, Claus J Loland, Frank Noé, Lei Shi
Cocaine, a widely abused psychostimulant, inhibits the dopamine transporter (DAT) by trapping the protein in an outward-open conformation, whereas atypical DAT inhibitors such as benztropine have low abuse liability and prefer less outward-open conformations. Here, we use a spectrum of computational modeling and simulation approaches to obtain the underlying molecular mechanism in atomistic detail. Interestingly, our quantum mechanical calculations and molecular dynamics (MD) simulations suggest that a benztropine derivative JHW007 prefers a different stereoisomeric conformation of tropane in binding to DAT compared to that of a cocaine derivative, CFT...
April 25, 2017: ACS Chemical Neuroscience
https://www.readbyqxmd.com/read/28441484/fully-quantum-description-of-the-zundel-ion-combining-variational-quantum-monte-carlo-with-path-integral-langevin-dynamics
#7
Félix Mouhat, Sandro Sorella, Rodolphe Vuilleumier, Antonino Marco Saitta, Michele Casula
We introduce a novel approach for a fully quantum description of coupled electron-ion systems from first principles. It combines the variational quantum Monte Carlo solution of the electronic part with the path integral formalism for the quantum nuclear dynamics. On the one hand, the path integral molecular dynamics includes nuclear quantum effects by adding a set of fictitious classical particles (beads) aimed at reproducing nuclear quantum fluctuations via a harmonic kinetic term. On the other hand, variational quantum Monte Carlo can provide Born-Oppenheimer potential energy surfaces with a precision comparable to the most advanced post Hartree-Fock approaches, and with a favorable scaling with the system size...
April 25, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28441017/equilibration-of-micelle-polyelectrolyte-complexes-mechanistic-differences-between-static-and-annealed-charge-distributions
#8
Jennifer E Laaser, Michael McGovern, Yaming Jiang, Elise Lohmann, Theresa M Reineke, David C Morse, Kevin D Dorfman, Timothy P Lodge
The role of charge density and charge annealing in polyelectrolyte complexation was investigated through systematic comparison of two micelle-polyelectrolyte systems. First, poly(dimethylaminoethyl methacrylate)-block-poly(styrene) (PDMAEMA-b-PS) micelles were complexed with poly(styrenesulfonate) (PSS) at pH values above and below the pKa of PDMAEMA to investigate the role of charge annealing in the complexation process. Second, complexes of poly(DMAEMA-stat-oligo(ethylene glycol) methyl ether methacrylate)-block-poly(styrene) (P(DMAEMA-stat-OEGMA)-b-PS) micelles with the same PSS at low pH were used to investigate how the complexation process differs when the charged sites are in fixed positions along the polymer chains...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28441003/chemical-interaction-guided-metal-free-growth-of-large-area-hexagonal-boron-nitride-on-silicon-based-substrates
#9
Sanjay Behura, Phong Nguyen, Rousan Debbarma, Songwei Che, Michael R Seacrist, Vikas Berry
Hexagonal boron nitride (h-BN) is an ideal platform for interfacing with two-dimensional (2D) nanomaterials to reduce carrier scattering for high-quality 2D electronics. However, scalable, transfer-free growth of hexagonal boron nitride (h-BN) remains a challenge. Currently, h-BN based 2D heterostructures require exfoliation or chemical transfer of h-BN grown on metals resulting in small areas or significant interfacial impurities. Here, we demonstrate a surface-chemistry influenced transfer-free growth of large-area, uniform, and smooth h-BN directly on silicon (Si)-based substrates including Si, silicon nitride (Si3N4), and silicon dioxide (SiO2) via low-pressure chemical vapor deposition...
April 25, 2017: ACS Nano
https://www.readbyqxmd.com/read/28440827/molecular-dynamics-investigations-of-membrane-bound-cyp2c19-polymorphisms-reveal-distinct-mechanisms-for-peripheral-variants-by-long-range-effects-on-the-enzymatic-activity
#10
Ying-Lu Cui, Rong-Ling Wu
Increasing sophistication in methods used to account for human polymorphisms in susceptibility to drug metabolism has been one of the success stories in the prevention of adverse drug reactions. Genetic polymorphisms in drug-metabolizing enzymes can affect enzyme activity and cause differences in treatment response or drug toxicity. CYP2C19 is one of the most highly polymorphic CYP enzymes and acts on 10-15% of drugs in current clinical use. Despite the number of experimental analyses carried out for this system, the detailed structural basis for altered catalytic properties of polymorphic CYP2C19 variants remains unexplained at the atomic level...
April 25, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28440650/comprehensive-computational-and-experimental-analysis-of-biomaterial-towards-the-behavior-of-imidazolium-based-ionic-liquids-an-interplay-between-hydrophilic-and-hydrophobic-interactions
#11
Reddicherla Umapathi, Suresh B Vepuri, Pannuru Venkatesu, Mahmoud E S Soliman
To provide insights into the aggregation behavior, hydration tendency and variation in phase transition temperature produced by the addition of ionic liquids (ILs) to poly(N-isopropylacrylamide) (PNIPAM) aqueous solution, systematic physicochemical studies, and molecular dynamic simulations were carried out. The influence of ILs possessing same [Cl]- anion and a set of cation [Cnmim]+ with increasing alkyl chain length such as 1-ethyl-3-methylimidazolium ([Emim]+), 1-allyl-3-methylimidazolium ([Amim]+), 1-butyl-3-methylimidazolium ([Bmim]+), 1-hexyl-3-methylimidazolium ([Hmim]+), 1-benzyl-3-methylimidazolium ([Bzmim]+), and 1- decyl-3-methylimidazolium ([Dmim] +) on the phase transition of PNIPAM was monitored by the aid of UV-visible absorption spectra, fluorescence intensity spectra, viscosity (ɳ), dynamic light scattering (DLS) and Fourier transform infrared (FTIR) spectroscopy...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28440644/direct-observation-of-the-ultrafast-evolution-of-open-shell-biradical-in-photochromic-radical-dimer
#12
Yoichi Kobayashi, Hajime Okajima, Hikaru Sotome, Takeshi Yanai, Katsuya Mutoh, Yusuke Yoneda, Yasuteru Shigeta, Akira Sakamoto, Hiroshi Miyasaka, Jiro Abe
Delocalized biradicals have been extensively studied because of fundamental interests to singlet biradicals and several potential applications such as to two-photon absorption materials. However, many of the biradical studies only focus on the static properties of the rigid molecular structures. It is expected that the biradical properties of the delocalized biradicals are sensitive to the subtle changes of the molecular structures and their local environments. Therefore, the studies of the dynamic properties of the system will give further insight into stable radical chemistry...
April 25, 2017: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/28440638/dielectric-relaxation-of-the-ionic-liquid-1-ethyl-3-methylimidazolium-ethylsulfate-microwave-and-far-ir-properties
#13
Nilesh Ramchandra Dhumal, Johannes Kiefer, David Andrew Turton, Klaas Wynne, Hyung J Kim
Dielectric relaxation of the ionic liquid, 1-ethyl-3-methylimidazolium ethylsulfate (EMI(+)ETS(-)), is studied using molecular dynamics (MD) simulations. The collective dynamics of polarization arising from cations and anions are examined. Character- istics of the rovibrational and translational components of polarization dynamics are analyzed to understand their respective roles in the microwave and terahertz regions of dielectric relaxation. The MD results are compared with the experimental low- frequency spectrum of EMI(+)ETS(-), obtained via ultrafast optical Kerr effect (OKE) measurements...
April 25, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28440557/implementation-of-probabilistic-algorithms-by-multi-chromophoric-molecular-networks-with-application-to-multiple-travelling-pathways
#14
Barbara Fresch, Francoise Remacle, Raphael D Levine
The implementation of probabilistic algorithms by deterministic hardware is demanding and requires hundreds of instructions to generate pseudo-random sequence of numbers. On the contrary, the dynamics at the molecular scale is physically governed by probabilistic laws because of the stochastic nature of thermally activated and quantum processes. By simulating the exciton transfer dynamics in a multi chromophoric system we demonstrate the implementation of a random walk that samples the possible pathways of a traveler through a network and can be probed by time resolved fluorescence spectroscopy...
April 25, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28440386/effect-of-chemical-structure-of-s-nitrosothiols-on-nitric-oxide-release-mediated-by-the-copper-sites-of-a-metal-organic-framework-based-environment
#15
Kiara Taylor-Edinbyrd, Tanping Li, Revati Kumar
The effect of chemical structure of different biologically compatible S-nitrosothiols on the solvation environment at catalytic copper sites in a metal organic framework (MOF) suspended in a solution of ethanol is probed using computational methods. The use of a copper based MOF as a storage vehicle and catalyst (copper sites of the MOF) in the controlled and sustained release of chemically stored nitric oxide (NO) from S-nitrosocysteine has been shown to occur both experimentally and computationally [J. Am...
April 25, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28440384/theoretical-and-numerical-analysis-of-nano-actuators-based-on-grafted-polyelectrolytes-in-an-electric-field
#16
N V Brilliantov, Yu A Budkov, C Seidel
We analyze, theoretically and by means of molecular dynamics (MD) simulations, the generation of mechanical force by a polyelectrolyte (PE) chain grafted to a plane and exposed to an external electric field; the free end of the chain is linked to a deformable target body. Varying the field, one can alter the length of the non-adsorbed (bulk) part of the chain and hence the deformation of the target body and the arising force. We focus on the impact of added salt on the magnitude of the generated force, which is especially important for applications...
April 25, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28440374/electrotunable-lubricity-with-ionic-liquids-the-influence-of-nanoscale-roughness
#17
Alessio David, Oscar Y Fajardo, Alexei A Kornyshev, Michael Urbakh, Fernando Bresme
The properties of ionic liquids can be modified by applying an external electrostatic potential, providing a route to control their performance in nanolubrication applications. Most computational studies to date have focused on the investigation of smooth surfaces. Real surfaces are generally inhomogeneous and feature roughness of different length scales. We report here a study of the possible effects that surface roughness may have on electrotunable lubricity with ionic liquids, performed here by means of non-equilibrium molecular dynamics simulations...
April 25, 2017: Faraday Discussions
https://www.readbyqxmd.com/read/28440370/structure-of-liquid-water-a-dynamical-mixture-of-tetrahedral-and-ring-and-chain-like-structures
#18
Jinfeng Liu, Xiao He, John Z H Zhang
The nature of the dynamical hydrogen-bond network of liquid water under ambient conditions has challenged both experimental and theoretical researchers for decades and remains a topic of intense debate. In this work, we addressed the structural issue of the hydrogen-bond network of liquid water based on an accurate ab initio molecular dynamics simulation. The present work showed clearly that liquid water is neither accurately described by a static picture of mostly tetrahedral water molecules nor dominated by "ring-and-chain" like structures...
April 25, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28440077/molecular-dynamics-simulations-of-the-standard-leonardite-humic-acid-microscopic-analysis-of-the-structure-and-dynamics
#19
Drazen Petrov, Daniel Tunega, Martin H Gerzabek, Chris Oostenbrink
Humic substances (HS) are abundant in the environment and play an important role in a number of biogeochemical processes including microbial activity, soil aggregation, plant growth, the retention and release of nutrients, the environmental fate of pollutants and carbon storage. They are flexible, relatively small molecules forming supramolecular structures through weak interactions. Despite the great importance of understanding their behavior at the atomic level, computational modeling, a premier high-resolution technique providing great level of detail, has been surprisingly little employed to study humic substances...
April 25, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28439315/36%C3%A2-h-fasting-of-young-men-influences-adipose-tissue-dna-methylation-of-lep-and-adipoq-in-a-birth-weight-dependent-manner
#20
Line Hjort, Sine W Jørgensen, Linn Gillberg, Elin Hall, Charlotte Brøns, Jan Frystyk, Allan A Vaag, Charlotte Ling
BACKGROUND: Subjects born with low birth weight (LBW) display a more energy-conserving response to fasting compared with normal birth weight (NBW) subjects. However, the molecular mechanisms explaining these metabolic differences remain unknown. Environmental influences may dynamically affect epigenetic marks, also in postnatal life. Here, we aimed to study the effects of short-term fasting on leptin (LEP) and adiponectin (ADIPOQ) DNA methylation and gene expression in subcutaneous adipose tissue (SAT) from subjects with LBW and NBW...
2017: Clinical Epigenetics
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