Read by QxMD icon Read

MD simulation

Md Shamsul Arefin, Jean-Michel Redoute, Mehmet Rasit Yuce, Md Shamsul Arefin, Jean-Michel Redoute, Mehmet Rasit Yuce, Jean-Michel Redoute
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
Chizuru Honda, Md Shoaib Bhuiyan, Haruki Kawanaka, Eiichi Watanabe, Koji Oguri, Chizuru Honda, Md Shoaib Bhuiyan, Haruki Kawanaka, Eiichi Watanabe, Koji Oguri, Eiichi Watanabe, Haruki Kawanaka, Chizuru Honda, Koji Oguri, Md Shoaib Bhuiyan
General uroflowmetry method involves the risk of nosocomial infections or time and effort of the recording. Medical institutions, therefore, need to measure voided volume simply and hygienically. Multiple cylindrical model that can estimate the fluid flow rate from the photographed image using camera has been proposed in an earlier study. This study implemented a flow rate estimation by using a general-purpose camera system (Raspberry Pi Camera Module) and the multiple cylindrical model. However, large amounts of noise in extracting liquid region are generated by the variation of the illumination when performing measurements in the bathroom...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
Fahimeh Mehralian, Yaghoub Tadi Beni, Yaser Kiani
Current study is concentrated on the extraordinary properties of defective carbon nanotubes (CNTs). The role of vacancy defects in thermal buckling response of precompressed CNTs is explored via molecular dynamics (MD) simulations. Defective CNTs are initially compressed at a certain ratio of their critical buckling strain and then undergo a uniform temperature rise. Comprehensive study is implemented on both armchair and zigzag CNTs with different vacancy defects including monovacancy, symmetric bivacancy and asymmetric bivacancy...
January 25, 2017: Journal of Molecular Graphics & Modelling
Samuel Hayes Schneider, Huong T Kratochvil, Martin T Zanni, Steven G Boxer
The physical origins of vibrational frequency shifts have been extensively studied in order to understand non-covalent intermolecular interactions in the condensed phase. In the case of carbonyls, vibrational solvatochromism, MD simulations, and vibrational Stark spectroscopy suggest that the frequency shifts observed in simple solvents arises predominately from the environment's electric field due to the vibrational Stark effect. This is contrary to many previously invoked descriptions of vibrational frequency shifts, such as bond polarization, whereby the bond's force constant and/or partial nuclear charges are altered due to the environment, often illustrated in terms of favored resonance structures...
February 22, 2017: Journal of Physical Chemistry. B
Yeqing Lv, Xinran Wang, Xiaobin Yu, Shili Zheng, Shaona Wang, Yi Zhang, Hao Du
The effect of H2O2 concentration on the change of H-bonds at a water/quartz interface was systematically examined by surface-specific sum-frequency generation (SFG) spectroscopy. Molecular dynamics (MD) simulation was further utilized to interpret the specific molecular dynamics as well as the configuration and evolution of water and H2O2 molecules at the interface. The results from this study demonstrated the important role of surface H-bonds on determination of the stability of adsorbed H2O2 at solvated, silica, xerogel surfaces...
February 22, 2017: Physical Chemistry Chemical Physics: PCCP
Lukas N Wirz, Jane R Allison
Residual dipolar couplings (RDCs), unlike most other types of NMR observables, provide orientational information, reporting on the alignment of inter-spin vectors (ISVs) relative to the magnetic field. A great challenge in using experimental RDCs to restrain molecular dynamics (MD) simulations is how to represent this alignment. An alignment tensor is often used to parameterise the contribution of molecular alignment to the angular dependence of RDCs. All ISVs that share the same tensor have fixed relative alignment, i...
February 18, 2017: Progress in Biophysics and Molecular Biology
Hideaki Takahashi, Satoru Umino, Yuji Miki, Ryosuke Ishizuka, Shu Maeda, Akihiro Morita, Makoto Suzuki, Nobuyuki Matubayasi
Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy ΔGhyd of reaction and the insensitivity of ΔGhyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical (QM/MM) simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔGhyd...
February 21, 2017: Journal of Physical Chemistry. B
Pan Chen, Yoshiharu Nishiyama, Jakob Wohlert, Ang Lu, Karim Mazeau, Ahmed E Ismail
The adsorption of urea on cellulose at room temperature has been studied using adsorption isotherm experiments and molecular dynamics (MD) simulations. Immer5sion of cotton cellulose into bulk urea solutions with concentrations between 0.01 g/mL and 0.30 g/mL led to a decrease of urea concentration in all solutions, allowing the adsorption of urea on the cellulose surface to be measured quantitatively. MD sim8ulations suggest that urea molecules form sorption layers on both hydrophobic and hydrophilic surfaces...
February 21, 2017: Journal of Physical Chemistry. B
Jyo Lyn Hor, Yijie Jiang, David J Ring, Robert A Riggleman, Kevin T Turner, Daeyeon Lee
In this work, we present the fabrication of nanoporous polymer-infiltrated nanoparticle films (PINFs) with either uniform or graded porosity based on undersaturated capillary rise infiltration (UCaRI) and study the processing-structure-property relationship of these nanoporous PINFs. The UCaRI process involves first generating a bilayer film of randomly packed nanoparticle layer atop a polymer layer, such that the volume of polymer is less than the void volume in the nanoparticle packing. Subsequently, the bilayer film is annealed above the glass transition temperature of the polymer to induce polymer infiltration into the voids of the nanoparticle packing...
February 21, 2017: ACS Nano
Hanwen Du, Junhao Li, Yingchun Cai, Hongxiao Zhang, Guixia Liu, Yun Tang, Weihua Li
Human cytochrome P450 3A4 (CYP3A4) is a major drug-metabolizing enzyme responsible for the metabolism of ~50% of clinically used drugs and is often involved in drug-drug interactions. It exhibits atypical binding and kinetic behavior towards many ligands. Binding of ligands to CYP3A4 is a complex process. Recent studies from both crystallography and biochemistry suggested the existence of a peripheral ligand-binding site at the enzyme surface. However, the stability of ligand bound at this peripheral site and the possibility of discovering new CYP3A4 ligands based on this site remain unclear...
February 21, 2017: Journal of Chemical Information and Modeling
Penghui Shi, Pan Qiao, Yeli Zhang, Shuaihua Li, Xuan Feng, Liujiao Bian
The molecular recognition and interaction of beta-lactamase II from Bacillus cereus (Bc II) with penicillin V (PV) and sulbactam (Sul) especially conformational changes of Bc II in the binding process were studied through spectroscopy analysis in combination with molecular dynamics (MD) simulation. The results show that in the binding process, a new coordination bond is observed between the Zn2 of Bc II and the carboxyl-O of PV or Sul by replacing His204. Electrostatic interaction between Zn2 and the ligand provide main driving force for the binding affinity...
February 11, 2017: Journal of Pharmaceutical and Biomedical Analysis
Toshiaki Matsubara, Tomoyoshi Ito
The mechanism of the σ bond cleavage of H2O, NH3, Me2C═O, H2, CH4, BH3, and SiH4 on the Ge═O bond of germanone is examined by means of both quantum mechanical (QM) and molecular dynamics (MD) methods. The QM calculations show that the σ bonds of all the substrates are heterolytically broken on the very largely polarized Ge═O bond. Before the σ bond cleavage, the substrate at first approach the Ge═O germanium in the cases of H2O, Me2C═O, and NH3, and in contrast, the Ge═O oxygen in the cases of H2, CH4, BH3, and SiH4...
February 20, 2017: Journal of Physical Chemistry. A
Alexander Kyrychenko, Dmitry A Pasko, Oleg N Kalugin
Chemical modification of silver nanoparticles (AgNPs) with a stabilizing agent, such as poly(vinyl alcohol) (PVA), plays an important role in shape-controlled seeded-growth and colloidal stability. However, theoretical aspects of the stabilizing mechanism of PVA are still poorly understood. To gain a better understanding of the role of PVA in water protecting effects for silver nanoparticles, we developed an atomistic model of a AgNP grafted with single-chain PVA of various lengths. Our model, designed for classical molecular dynamics (MD) simulations, approximates the AgNP as a quasi-spherical silver nanocrystal with 3...
February 20, 2017: Physical Chemistry Chemical Physics: PCCP
Huiming Cao, Yuzhen Sun, Ling Wang, Chunyan Zhao, Jianjie Fu, Aiqian Zhang
Polybrominated diphenyl ethers (PBDEs), one typical type of persistent environmental contaminant, have toxicological effects such as disrupting thyroid homeostasis in the human body. The high binding affinities of hydroxylated metabolites of PBDEs (OH-PBDEs) with transthyretin (TTR) were considered to be one major reason for their extraordinary capacity of passing through the blood-brain barrier via competitive thyroid hormone (T4) transport protein binding. Recent findings showed that sulfated PBDEs can be formed in human liver cytosol as phase-II metabolites...
February 20, 2017: Molecular BioSystems
Joshua E Condon, Tyler B Martin, Arthi Jayaraman
Using atomistic and coarse-grained molecular dynamics (MD) simulations, we explain the shifts in lower critical solution temperature (LCST)-like phase transitions exhibited by elastin-like peptides (ELPs) upon conjugation to other macromolecules (e.g. collagen-like peptides or CLPs). First, using atomistic simulations, we study ELP oligomers with the sequence (VPGFG)6 in explicit water, and characterize the LCST-like transition temperature as one at which the ELP oligomers undergo a change in "hydration state"...
February 20, 2017: Soft Matter
Shubhangi Agarwal, Sanjay Dey, Biplab Ghosh, Maitree Biswas, Jhimli Dasgupta
Molecular mechanisms of xenosiderophore and heme acquisitions using periplasmic binding protein (PBP) dependent ATP-binding cassette transporters to scavenge the essential nutrient iron are elusive yet in Vibrio cholerae. Our current study delineates the structures, dynamics and ligand binding properties of two Type III PBPs of V. cholerae, VcFhuD and VcHutB. Through crystal structures and fluorescence quenching studies we demonstrate unique features of VcFhuD to bind both hydroxamate and catecholate type xenosiderophores...
February 20, 2017: Scientific Reports
Ming Chen, Song Li, Guang Feng
Room-temperature ionic liquids (RTILs) are an emerging class of electrolytes for supercapacitors. In this work, we investigate the effects of different supercapacitor models and anion shape on the electrical double layers (EDLs) of two different RTILs: 1-ethyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([Emim][Tf₂N]) and 1-ethyl-3-methylimidazolium 2-(cyano)pyrrolide ([Emim][CNPyr]) by molecular dynamics (MD) simulation. The EDL microstructure is represented by number densities of cations and anions, and the potential drop near neutral and charged electrodes reveal that the supercapacitor model with a single electrode has the same EDL structure as the model with two opposite electrodes...
February 16, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
Massimiliano Donato Verona, Vincenzo Verdolino, Ferruccio Palazzesi, Roberto Corradini
Peptide Nucleic Acids (PNAs) can efficiently target DNA or RNA acting as chemical tools for gene regulation. Their backbone modification and functionalization is often used to increase the affinity for a particular sequence improving selectivity. The understanding of the trading forces that lead the single strand PNA to bind the DNA or RNA sequence is preparatory for any further rational design, but a clear and unique description of this process is still not complete. In this paper we report further insights into this subject, by a computational investigation aiming at the characterization of the conformations of a single strand PNA and how these can be correlated to its capability in binding DNA/RNA...
February 17, 2017: Scientific Reports
Samaneh Ghassabi Kondalaji, Mahdiar Khakinejad, Amirmahdi Tafreshian, Stephen J Valentine
Collision cross-section (CCS) measurements with a linear drift tube have been utilized to study the gas-phase conformers of a model peptide (acetyl-PAAAAKAAAAKAAAAKAAAAK). Extensive molecular dynamics (MD) simulations have been conducted to derive an advanced protocol for the generation of a comprehensive pool of in-silico structures; both higher energy and more thermodynamically stable structures are included to provide an unbiased sampling of conformational space. MD simulations at 300 K are applied to the in-silico structures to more accurately describe the gas-phase transport properties of the ion conformers including their dynamics...
February 16, 2017: Journal of the American Society for Mass Spectrometry
Carla Schmidt, Jamie A Macpherson, Andy M Lau, Ken Wei Tan, Franca Fraternali, Argyris Politis
Mass spectrometry (MS) has become an indispensable tool for investigating the architectures and dynamics of macromolecular assemblies. Here we show that covalent labeling of solvent accessible residues followed by their MS-based identification yields modeling restraints that allow mapping the location and orientation of subunits within protein assemblies. Together with complementary restraints derived from cross-linking and native MS, we built native-like models of four heterocomplexes with known subunit structures and compared them with available X-ray crystal structures...
February 7, 2017: Analytical Chemistry
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"