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molecular dynamics

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
Sara Conti, Luca Perico, Florian Grahammer, Tobias B Huber
PURPOSE OF REVIEW: The podocyte slit diaphragm is probably the least understood component of the kidney filtration barrier. In this review, we aim to integrate the most recent findings on the molecular make-up and structural architecture of this specialized cell-cell junction into a current concept of glomerular filtration. RECENT FINDINGS: Analysis of cryopreserved mammalian tissue revealed a bipartite composition of the slit diaphragm. Single NEPH1 molecules span the lower part of the slit close to the glomerular basement membrane whereas NEPHRIN molecules are positioned in the apical part toward Bowman's space...
February 16, 2017: Current Opinion in Nephrology and Hypertension
Ruoshi Yuan, Xiaomei Zhu, Gaowei Wang, Site Li, Ping Ao
Cancer is a complex disease: its pathology cannot be properly understood in terms of independent players-genes, proteins, molecular pathways, or their simple combinations. This is similar to many-body physics of a condensed phase that many important properties are not determined by a single atom or molecule. The rapidly accumulating large 'omics' data also require a new mechanistic and global underpinning to organize for rationalizing cancer complexity. A unifying and quantitative theory was proposed by some of the present authors that cancer is a robust state formed by the endogenous molecular-cellular network, which is evolutionarily built for the developmental processes and physiological functions...
February 17, 2017: Reports on Progress in Physics
Dennis Barton, Hong-Ying Gao, Philipp Alexander Held, Armido Studer, Harald Fuchs, Nikos L Doltsinis, Johannes Neugebauer
Possible origins of the formation of organometallic intermediates in on-surface Ullmann couplings have been investigated by surface tunneling microscopy (STM) and density functional theory (DFT) calculations. We consider the case of iodobenzenes on the coinage metals Au, Ag and Cu. We found experimental evidence for the formation of surface vacancies and the presence of metal adatoms in these coupling reactions, which are taken as a hint for the reactive extraction of surface atoms by adsorbates. In a second step, we demonstrate by ab initio molecular dynamics calculations for aryl-iodides on copper that metal atoms can be pulled out of the surface to form metalorganic species...
February 17, 2017: Chemistry: a European Journal
Xiaoyue Zhang, Jian Shao, Yun Chen, Weijin Chen, Jing Yu, Biao Wang, Yue Zheng
Azurin (Az) has been considered as the research hotspot in molecular electronics, as well as a promising material for building functional devices on the molecular scale because of its special electrical properties and force-dependent conductance effects. Here we carry out an in-depth investigation combined with molecular scale experiments, molecular dynamics simulations, first-principles calculations and theoretical models to reveal the dynamic conductance response of the Az monolayer under cyclic mechanical loading...
February 17, 2017: Physical Chemistry Chemical Physics: PCCP
M Radu, K Kremer
We study the crystal growth in binary Lennard-Jones mixtures by molecular dynamics simulations. Growth dynamics, the structure of the liquid-solid interfaces as well as droplet incorporation into the crystal vary with solution properties. For demixed systems we observe a strongly enhanced crystal growth at the cost of enclosed impurities. Furthermore, we find different interface morphologies depending on solubility. We relate our observations to growth mechanisms based on the Gibbs-Thomson effect as well as to predictions of the Kardar-Parisi-Zhang theory in 2+1 dimensions...
February 3, 2017: Physical Review Letters
Y Kasahara, Y Takeuchi, R H Zadik, Y Takabayashi, R H Colman, R D McDonald, M J Rosseinsky, K Prassides, Y Iwasa
Controlled access to the border of the Mott insulating state by variation of control parameters offers exotic electronic states such as anomalous and possibly high-transition-temperature (Tc) superconductivity. The alkali-doped fullerides show a transition from a Mott insulator to a superconductor for the first time in three-dimensional materials, but the impact of dimensionality and electron correlation on superconducting properties has remained unclear. Here we show that, near the Mott insulating phase, the upper critical field Hc2 of the fulleride superconductors reaches values as high as ∼90 T-the highest among cubic crystals...
February 17, 2017: Nature Communications
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
Alexander Georgi, Peter Nemes-Incze, Ramon Carrillo-Bastos, Daiara Faria, Silvia Viola Kusminskiy, Dawei Zhai, Martin Schneider, Dinesh Subramaniam, Torge Mashoff, Nils Michael Freitag, Marcus Liebmann, Marco Pratzer, Ludger Wirtz, Colin R Woods, Roman Vladislavovich Gorbachev, Yang Cao, Kostya S Novoselov, Nancy Sandler, Markus Morgenstern
One of the intriguing characteristics of honeycomb lattices is the appearance of a pseudo-magnetic field as a result of mechanical deformation. In the case of graphene, the Landau quantization resulting from this pseudo-magnetic field has been measured using scanning tunneling microscopy. Here we show that a signature of the pseudo-magnetic field is a local sublattice symmetry breaking observable as a redistribution of the local density of states. This can be interpreted as a polarization of graphene's pseudospin due to a strain induced pseudo-magnetic field, in analogy to the alignment of a real spin in a magnetic field...
February 17, 2017: Nano Letters
Guido F von Rudorff, Tobias Watermann, Xiang-Yang Guo, Daniel Sebastiani
We investigate the conformational space of a polyphilic molecule with hydrophilic, lipophilic and fluorophilic parts inserted as a transmembrane agent into a dipalmitoylphosphatidylcholine bilayer by means of all-atom molecular dynamics simulations. Special focus is put on the competing structural driving forces arising from the hydrophilic, lipophilic and fluorophilic side chains and the aromatic backbone of the polyphile. We observe a significant difference between the lipophilic and the fluorophilic side chains regarding their intramembrane distribution...
April 5, 2017: Journal of Computational Chemistry
Greg Starek, J Alfredo Freites, Simon Bernèche, Douglas J Tobias
We used targeted molecular dynamics, informed by experimentally determined inter-atomic distances defining the pore region of open and closed states of the KvAP voltage-gated potassium channel, to generate a gating pathway of the pore domain in the absence of the voltage-sensing domains. We then performed umbrella sampling simulations along this pathway to calculate a potential of mean force that describes the free energy landscape connecting the closed and open conformations of the pore domain. The resulting energetic landscape displays three minima, corresponding to stable open, closed, and intermediate conformations with roughly similar stabilities...
February 16, 2017: Journal of Computational Chemistry
Anton Raskovalov
The molecular dynamics is one of the most widely used methods for the simulation of the properties corresponding to ionic motion. Unfortunately, classical molecular dynamics cannot be applied for electron transfer simulation. Suggested modification of the molecular dynamics allows performing the electron transfer from one particle to another during simulation runtime. All additional data structure and the corresponding algorithms are presented in this article. The method can be applied to the systems with pair Van der Waals and Coulomb interactions...
February 16, 2017: Journal of Computational Chemistry
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
Lu Peng, Dumitru Trucu, Ping Lin, Alastair Thompson, Mark A J Chaplain
Known as one of the hallmarks of cancer (Hanahan and Weinberg in Cell 100:57-70, 2000) cancer cell invasion of human body tissue is a complicated spatio-temporal multiscale process which enables a localised solid tumour to transform into a systemic, metastatic and fatal disease. This process explores and takes advantage of the reciprocal relation that solid tumours establish with the extracellular matrix (ECM) components and other multiple distinct cell types from the surrounding microenvironment. Through the secretion of various proteolytic enzymes such as matrix metalloproteinases or the urokinase plasminogen activator (uPA), the cancer cell population alters the configuration of the surrounding ECM composition and overcomes the physical barriers to ultimately achieve local cancer spread into the surrounding tissue...
February 16, 2017: Bulletin of Mathematical Biology
Chonghai Qi, Bo Zhou, Chunlei Wang, Yujun Zheng, Haiping Fang
Based on molecular dynamics simulations, we found a nonmonotonic relationship between the contact angle of water droplets and the surface polarity on a solid surface with specific hexagonal charge patterns at room temperature. The contact angle firstly decreases and then increases as polarity (denoted as charge q) increases from 0 e to 1.0 e with a vertex value of q = 0.5 e. We observed a different wetting behavior for a water droplet on a conventional nonwetted solid surface when q ≤ 0.5 e, and a water droplet on an ordered water monolayer adsorbed on a highly polar solid surface when q > 0...
February 17, 2017: Physical Chemistry Chemical Physics: PCCP
Chien-Yun Lee, Chu-Cheng Lin, Yi-Liang Liu, Guang-Yaw Liu, Jyung-Hurng Liu, Hui-Chih Hung
Our previous studies suggest that the fully active form of Peptidylarginine deiminase 4 (PAD4) should be a dimer and not a monomer. This paper provides a plausible mechanism for the control of PAD4 catalysis by molecular interplay between its dimer-interface loop (I-loop) and its substrate-binding loop (S-loop). Mutagenesis studies revealed that two hydrophobic residues, W347 and V469, are critical for substrate binding at the active site; mutating these two residues led to a severe reduction in the catalytic activity...
February 17, 2017: Scientific Reports
Xinxing Yang, Zhixin Lyu, Amanda Miguel, Ryan McQuillen, Kerwyn Casey Huang, Jie Xiao
The bacterial tubulin FtsZ is the central component of the cell division machinery, coordinating an ensemble of proteins involved in septal cell wall synthesis to ensure successful constriction. How cells achieve this coordination is unknown. We found that in Escherichia coli cells, FtsZ exhibits dynamic treadmilling predominantly determined by its guanosine triphosphatase activity. The treadmilling dynamics direct the processive movement of the septal cell wall synthesis machinery but do not limit the rate of septal synthesis...
February 17, 2017: Science
Jine Quan, Seng Meng, Erhui Guo, Sheng Zhang, Zhong Zhao, Xitian Yang
BACKGROUND: Indole-3-butyric acid (IBA) is applied to the cuttings of various plant species to induce formation of adventitious roots (ARs) in commercial settings. Tetraploid black locust is an attractive ornamental tree that is drought resistant, sand tolerant, can prevent sand erosion and has various commercial uses. To further elucidate the mechanisms of AR formation, we used Illumina sequencing to analyze transcriptome dynamics and differential gene expression at four developmental stages in control (CK) and IBA-treated groups...
February 16, 2017: BMC Genomics
Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García, Elena R Alvarez-Buylla
BACKGROUND: Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell-state transitions, in which normal epithelial cells acquire first a senescent state which is later surpassed to attain a mesenchymal stem-like phenotype with a potentially tumorigenic behavior. In this paper we aim to provide a system-level mechanistic explanation to the emergence of these cell types, and to the time-ordered transition patterns that are common to neoplasias of epithelial origin...
February 16, 2017: BMC Systems Biology
Edson Ishengoma, Morris Agaba
BACKGROUND: Toll-like receptors (TLRs) are the frontline actors in the innate immune response to various pathogens and are expected to be targets of natural selection in species adapted to habitats with contrasting pathogen burdens. The recent publication of genome sequences of giraffe and okapi together afforded the opportunity to examine the evolution of selected TLRs in broad range of terrestrial ungulates and cetaceans during their complex habitat diversification. Through direct sequence comparisons and standard evolutionary approaches, the extent of nucleotide and protein sequence diversity in seven Toll-like receptors (TLR2, TLR3, TLR4, TLR5, TLR7, TLR9 and TLR10) between giraffe and closely related species was determined...
February 16, 2017: BMC Evolutionary Biology
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