Read by QxMD icon Read

molecular dynamics

Taraknath Mandal, Ronald G Larson
Using fully atomistic and coarse-grained (CG) molecular dynamics (MD) simulations, we report, for the first time, the self-assembly of initially randomly dispersed dodecyl-β-d-maltoside (DDM) surfactants into a striped cylindrical micelle (SCM) with lamellae of surfactant heads and tails alternating along the cylindrical axis, with both heads and tails in contact with the water. By changing the interaction strength of the head group with water relative to itself, we find that such micelles are most likely for head groups with marginal solubility in the water solvent...
March 22, 2018: Soft Matter
Jianchang Xu, Shuangqing Sun, Zhikun Wang, Shiyuan Peng, Songqing Hu, Lijuan Zhang
Dissipative particle dynamics (DPD) simulation is used to study the effect of pH on the morphological transition in micelles assembled from dirhamnolipids (diRLs), and analyze the pH-driven mechanism and influence factors of micellar surface patterns. At pH < 4.0, various multilayer structures with homogeneous surface patterns are observed, whereas diRLs can self-assemble into novel anisotropic morphologies with phase-separated surface patterns at pH > 7.4, such as patchy spherical micelles, rod-like micelles with helical surface patterns and a lamellar phase with anisotropic surface patterns...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Tuan Anh Ho, Yifeng Wang, Louise J Criscenti
Kerogen plays a central role in hydrocarbon generation in an oil/gas reservoir. In a subsurface environment, kerogen is constantly subjected to stress confinement or relaxation. The interplay between mechanical deformation and gas adsorption of the materials could be an important process for shale gas production but unfortunately is poorly understood. Using a hybrid Monte Carlo/molecular dynamics simulation, we show here that a strong chemo-mechanical coupling may exist between gas adsorption and mechanical strain of a kerogen matrix...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Neeladri Sekhar Roy, Subrata Debnath, Abhijit Chakraborty, Prasenjit Chakraborty, Indrani Bera, Raka Ghosh, Nanda Ghoshal, Saikat Chakrabarti, Siddhartha Roy
Localized separation of strands of duplex DNA is a necessary step in many DNA-dependent processes, including transcription and replication. Little is known about how these strand separations occur. The strand-separated E.coli RNA polymerase-promoter open-complex structure showed four bases of the non-template strand, the master base -11A, -7, -6 and +2, in a flipped state and inserted into protein pockets. To explore whether any property of these bases in the duplex state pre-disposes them to flipping, NMR studies were performed on a wild-type promoter in the duplex state...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Qiujing Dong, Chunhua Luo, Na Li, Jiaxiang Chi, Qingqing Zhang
A series of copolymers with an adamantyl side group (poly(NIPAM-co-AdMA) and poly(DMAM-co-AdMA)) were prepared by radical copolymerization of N -isopropylacrylamide (NIPAM) and N , N -dimethylacrylamide (DMAM) with a 2-methyl-2-adamantylmethacrylate (AdMA) monomer. The structure and composition of the as-synthesized copolymers were characterized by Fourier transform infrared (FT-IR) spectroscopy, proton nuclear magnetic resonance (¹H NMR) spectroscopy, gel permeation chromatography (GPC), thermogravimetric analysis (TGA), and elemental analysis...
March 22, 2018: Materials
Xiaofeng Niu, Shidong Feng, Shaopeng Pan
Structural defects were investigated by a recently proposed structural parameter, quasi-nearest atom (QNA), in a modeled Zr50 Cu50 metallic glass through molecular dynamics simulations. More QNAs around an atom usually means that more defects are located near the atom. Structural analysis reveals that the spatial distribution of the numbers of QNAs displays to be clearly heterogeneous. Furthermore, QNA is closely correlated with cluster connections, especially four-atom cluster connections. Atoms with larger coordination numbers usually have less QNAs...
March 22, 2018: Materials
Daniel Bonhenry, François Dehez, Mounir Tarek
The low bioavailability of most therapeutic compounds is often counterbalanced by association with molecular vectors capable of crossing cell membranes. Previous studies demonstrated that for vectors bearing titratable chemical groups, the translocation process might be accompanied by a change in the protonation state. For simple compounds e.g. a lysine analog, free energy calculations, using a single collective variable, namely the insertion depth, suggest that such a transition could only take place if the amino acid diffuses deep enough into the hydrophobic core of the membrane, a situation thermodynamically unfavorable...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Konda Reddy Karnati, Yixuan Wang
Two widely used anticancer drugs, doxorubicin (DOX) and paclitaxel (PTX), possess distinct physical properties and chemotherapy specificity. In order to investigate their interaction mechanism with single-walled carbon nanotubes (SWCNTs), co-loading and releasing from the SWCNTs, all-atom molecular dynamics (MD) simulations were firstly carried out for different SWCNT systems, followed by binding free energy calculation with MM-PBSA. The results indicate that the co-loading of DOX and PTX onto the pristine SWCNT is exothermic and spontaneous...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Jeannine Steinmeyer, Heidi-Kristin Walter, Mathilde A Bichelberger, Violetta Schneider, Tomáš Kubař, Franziska Rönicke, Bettina Olshausen, Karin Nienhaus, Gerd Ulrich Nienhaus, Ute Schepers, Marcus Elstner, Hans-Achim Wagenknecht
Two fluorescent dyes covalently attached in diagonal interstrand orientation to siRNA undergo energy transfer and thereby enable a dual color fluorescence readout (red/green) for hybridization. Three different structural variations were carried out and compared by their optical properties, including (i) the base surrogate approach with an acyclic linker as a substitute of the 2-deoxyriboside between the phosphodiester bridges, (ii) the 2'-modification of conventional ribofuranosides and (iii) the arabino-configured 2'-modification...
March 22, 2018: Organic & Biomolecular Chemistry
Madhusudhanan Gogul Ramnath, Ramaraj Thirugnanasampandan, Nagarajan NagaSundaram, Gunasekaran Bhuvaneswari
BACKGROUND: Genus Isodon (Lamiaceae) is a prolific source for bioactive terpenoids. Nowadays, people move towards natural products because of undesirable effects of chemotherapeutic drugs. OBJECTIVE: In silico and in vitro approach were attempted to screen bioactive terpenoids isolated from Isodon wightii with acetylcholinesterase and histone deacetylase3 receptors, Methods: Terpenoids such as abietic acid, oleanolic acid, α-amyrin acetate, β-amyrin acetate were docked with AchE and HDAC3 receptors using AutoDock Vina (version 1...
March 20, 2018: Current Computer-aided Drug Design
Manoj Kumar, Jie Zhong, Xiao Cheng Zeng, Joseph S Francisco
. The role of aqueous surfaces in promoting atmospheric chemistry is increasingly being recognized. However, the bimolecular chemistries of Criegee intermediates, which influence the tropospheric budget of OH radicals, organic acids, hydroperoxides, nitrates, sulfates and particulate material, remain less explored on an aqueous surface. Herein we have employed Born Oppenheimer molecular dynamics simulations and two-layer ONIOM(QM:MM) in electronic embedding scheme to study the reaction and the spectroscopic signal of anti-CH3CHOO with nitric acid (HNO3) at the air-water interface, which is expected to be an important reaction in the polluted urban environments...
March 22, 2018: Journal of the American Chemical Society
Luan Carvalho Martins, Pedro Henrique Monteiro Torres, Renata Barbosa de Oliveira, Pedro Geraldo Pascutti, Elio A Cino, Rafaela Salgado Ferreira
Chagas disease remains a major health problem in South America, and throughout the world. The two drugs clinically available for its treatment have limited efficacy and cause serious adverse effects. Cruzain is an established therapeutic target of Trypanosoma cruzi, the protozoan that causes Chagas disease. Our group recently identified a competitive cruzain inhibitor (compound 1) with an IC50  = 15 µM that is also more synthetically accessible than the previously reported lead, compound 2. Prior studies, however, did not propose a binding mode for compound 1, hindering understanding of the structure-activity relationship and optimization...
March 21, 2018: Journal of Computer-aided Molecular Design
Suying Bao, Lilong Jia, Xueya Zhou, Zhi-Gang Zhang, Hazel Wai Lan Wu, Zhe Yu, Gordon Ng, Yanhui Fan, Dana S M Wong, Shishu Huang, Kelvin Kai Wang To, Kwok-Yung Yuen, Man Lung Yeung, You-Qiang Song
Host genetic factors play an important role in diverse host outcomes after influenza A (H7N9) infection. Studying differential responses of inbred mouse lines with distinct genetic backgrounds to influenza virus infection could substantially increase our understanding of the contributory roles of host genetic factors to disease severity. Here, we utilized an integrated approach of mRNA-seq and miRNA-seq to investigate the transcriptome expression and regulation of host genes in C57BL/6J and DBA/2J mouse strains during influenza virus infection...
March 21, 2018: Functional & Integrative Genomics
Tom Dyer, Ngamta Thamwattana, Barry Cox
The low bending rigidity of graphene facilitates the formation of folds into the structure. This curvature change affects the reactivity and electron transport of the sheet. One novel extension of this is the intercalation of small molecules into these folds. We construct a model incorporating a single-walled carbon nanotube into a sheet of folded graphene. Variational calculus techniques are employed to determine the minimum energy structure and the resulting curves are shown to agree well with molecular dynamics study...
March 22, 2018: Journal of Molecular Modeling
Emma Langella, Martina Buonanno, Daniela Vullo, Nina Dathan, Marilisa Leone, Claudiu T Supuran, Giuseppina De Simone, Simona Maria Monti
Human carbonic anhydrase IX (hCA IX) is a tumour-associated enzyme present in a limited number of normal tissues, but overexpressed in several malignant human tumours. It is a transmembrane protein, where the extracellular region consists of a greatly investigated catalytic CA domain and a much less investigated proteoglycan-like (PG) domain. Considering its important role in tumour biology, here, we report for the first time the full characterization of the PG domain, providing insights into its structural and functional features...
March 21, 2018: Cellular and Molecular Life Sciences: CMLS
Giuseppe Licari, Joseph S Beckwith, Saeideh Soleimanpour, Stefan Matile, Eric Vauthey
A planarizable push-pull molecular probe with mechanosensitive properties was investigated at several biomimetic interfaces, consisting of different phospholipid monolayers located between dodecane and an aqueous buffer solution, using the interface-specific surface-second-harmonic-generation (SSHG) technique. Whereas the SSHG spectra recorded at liquid-disordered interfaces were similar to the absorption spectra in bulk solutions, those measured at liquid-ordered phases exhibited a remarkable shift towards lower energies to an extent depending on the surface pressure of the phospholipid monolayer...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Lei Zhao, Jiangtao Cheng
Besides the Wenzel state, liquid droplets on micro/nanostructured surfaces can stay in the Cassie state and consequently exhibit intriguing characteristics such as a large contact angle, small contact angle hysteresis and exceptional mobility. Here we report molecular dynamics (MD) simulations of the wetting dynamics of Cassie-state water droplets on nanostructured ultrahydrophobic surfaces with an emphasis on the genesis of the contact line friction (CLF). From an ab initio perspective, CLF can be ascribed to the collective effect of solid-liquid retarding and viscous damping...
March 22, 2018: Nanoscale
Yunrui Duan, Jie Li, Tao Li, Xingfan Zhang, Zhichao Wang, Hui Li
Confinement presents the opportunity for novel structural transition scenarios not observed in three-dimensional systems. Here, we report a comprehensive molecular dynamic (MD) study of the structural phase transition induced by density for an ordinary metal copper (Cu) confined between two parallel panel walls. At 4.19 g cm-3 < ρ < 4.66 g cm-3, a notable structural phase transition occurs between the triangle unit cell structure and quasi-square unit cell structure upon densification. Both the bond order parameter (BOP) and angular distribution function (ADF) can provide evidence for the transition...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
Eduardo Duque-Redondo, Yamada Kazuo, Iñigo López-Arbeloa, Hegoi Manzano
Cementation is a widespread technique to immobilize nuclear waste due to the low leachability of cementitious materials. The capacity of calcium silicate hydrate (C-S-H), the main component of cement, to retain radionuclide Cs has been empirically studied at the macroscale, yet the specific molecular scale mechanisms that govern the retention have not been determined. In this work, we employed molecular dynamics simulations to investigate the adsorption and diffusivity of Cs into a C-S-H gel nanopore. From the simulations, it was possible to distinguish three types of Cs adsorption configurations on the C-S-H: an inner-sphere surface site where Cs is strongly bound, an outer-sphere surface site where Cs is loosely bound, and Cs free in the nanopore...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
João R Bezerra-Neto, Natalia G Sousa, Luis P M Dos Santos, Adriana N Correia, Pedro de Lima-Neto
The effect of water on the physicochemical properties of an ethylene glycol and choline chloride mixture containing Cu2+ ions was investigated by electrochemical techniques and molecular dynamics simulation. The experiments and computational calculations were carried out by increasing the water content from 0 up to 10% (v/v). The cyclic voltammetry and chronopotentiometry techniques showed that the diffusion coefficient of Cu2+ ions increased and that the peak potentials for both the Cu2+/Cu+ and Cu+/Cu redox couples shifted towards more positive potentials with the increase in the water content in the solution...
March 22, 2018: Physical Chemistry Chemical Physics: PCCP
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"