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Lili Cao, Ulf Ryde
The combined quantum mechanical (QM) and molecular mechanical (MM) approach (QM/MM) is a popular method to study reactions in biochemical macromolecules. Even if the general procedure of using QM for a small, but interesting part of the system and MM for the rest is common to all approaches, the details of the implementations vary extensively, especially the treatment of the interface between the two systems. For example, QM/MM can use either additive or subtractive schemes, of which the former is often said to be preferable, although the two schemes are often mixed up with mechanical and electrostatic embedding...
2018: Frontiers in Chemistry
Thorsten Deilmann, Kristian Sommer Thygesen
Vertically stacked two-dimensional materials form an ideal platform for controlling and exploiting light-matter interactions at the nanoscale. As a unique feature, these materials host electronic excitations of both intra- and interlayer type with distinctly different properties. In this Letter, using first-principles many-body calculations, we provide a detailed picture of the most prominent excitons in bilayer MoS2 , a prototypical van der Waals material. By applying an electric field perpendicular to the bilayer, we explore the evolution of the excitonic states as the band alignment is varied from perfect line-up to staggered (Type II) alignment...
April 19, 2018: Nano Letters
Fatemeh S Mohseni-Shahri, Farid Moeinpour, Masoumeh Nosrati
The interaction of pepsin with sunset yellow food additive (SY) was studied by fluorescence spectroscopy and molecular dynamics simulation. The experimental results indicated that SY can quench the fluorescence of pepsin with static quenching. The apparent binding constant Ka and binding site number n were evaluated at different temperatures. Thermodynamic analysis suggests that SY interact with pepsin spontaneously by van der Waal's forces and hydrogen bond formation. Three-dimensional fluorescence spectra showed that pepsin undergoes a slightly conformation change when it interacts with SY...
April 14, 2018: International Journal of Biological Macromolecules
Jiawei Lai, Xin Liu, Junchao Ma, Qinsheng Wang, Kenan Zhang, Xiao Ren, Yinan Liu, Qiangqiang Gu, Xiao Zhuo, Wei Lu, Yang Wu, Yuan Li, Ji Feng, Shuyun Zhou, Jian-Hao Chen, Dong Sun
Photodetectors based on Weyl semimetal promise extreme performance in terms of highly sensitive, broadband and self-powered operation owing to its extraordinary material properties. Layered Type-II Weyl semimetal that break Lorentz invariance can be further integrated with other two-dimensional materials to form van der Waals heterostructures and realize multiple functionalities inheriting the advantages of other two-dimensional materials. Herein, we report the realization of a broadband self-powered photodetector based on Type-II Weyl semimetal Td -MoTe2 ...
April 17, 2018: Advanced Materials
Jiadi Zhu, Yuchao Yang, Rundong Jia, Zhongxin Liang, Wen Zhu, Zia Ur Rehman, Lin Bao, Xiaoxian Zhang, Yimao Cai, Li Song, Ru Huang
Neuromorphic computing represents an innovative technology that can perform intelligent and energy-efficient computation, whereas construction of neuromorphic systems requires biorealistic synaptic elements with rich dynamics that can be tuned based on a robust mechanism. Here, an ionic-gating-modulated synaptic transistor based on layered crystals of transitional metal dichalcogenides and phosphorus trichalcogenides is demonstrated, which produce a diversity of short-term and long-term plasticity including excitatory postsynaptic current, paired pulse facilitation, spiking-rate-dependent plasticity, dynamic filtering, etc...
April 17, 2018: Advanced Materials
Jiahua Duan, Runkun Chen, Yuan Cheng, Tianzhong Yang, Feng Zhai, Qing Dai, Jianing Chen
The nontrivial topological origin and pseudospinorial character of electron wavefunctions make edge states possess unusual electronic properties. Twenty years ago, the tight-binding model calculation predicted that zigzag termination of 2D sheets of carbon atoms have peculiar edge states, which show potential application in spintronics and modern information technologies. Although scanning probe microscopy is employed to capture this phenomenon, the experimental demonstration of its optical response remains challenging...
April 17, 2018: Advanced Materials
Sourabh Palrecha, Dushant Lakade, Abhijeet Kulkarni, Jayanta K Pal, Manali Joshi
The heme-regulated inhibitor (HRI) kinase regulates globin synthesis in a heme-dependent manner in reticulocytes and erythroid cells in bone marrow. Inhibitors of HRI have been proposed to lead to an increased amount of hemoglobin, benefitting anemia patients. A series of indeno[1,2-c]pyrazoles were discovered to be the first known in vitro inhibitors of HRI. However, the structural mechanism of inhibition is yet to be understood. The aim of this study was to unravel the binding mechanism of these inhibitors using molecular dynamic simulations and docking...
April 17, 2018: Journal of Biomolecular Structure & Dynamics
Yi-Yan Zhan, Tatsuo Kojima, Takuya Koide, Masanori Tachikawa, Shuichi Hiraoka
A thermally most stable molecular self-assembly in water (nanocube), whose decomposition temperature is 142 °C, has been developed by the design of a gear-shaped amphiphile (GSA) with an indented hydrophobic surface, even though the nanocube is stabilized only by van der Waals (vdW) and cation-pinteractions and the hydrophobic effect. The introduction of an electron-donating substituent in one of the benzene rings in GSA increased the decomposition temperature by 12 K, which is due to the stronger cation-p interactions between the benzene ring and positively charged pyridinium rings and the tighter molecular meshing between the GSAs in the nanocube...
April 16, 2018: Chemistry: a European Journal
Shigeki Kawai, Soichiro Nakatsuka, Takuji Hatakeyama, Rémy Pawlak, Tobias Meier, John Tracey, Ernst Meyer, Adam S Foster
Substituting heteroatoms into nanostructured graphene elements, such as graphene nanoribbons, offers the possibility for atomic engineering of electronic properties. To characterize these substitutions, functionalized atomic force microscopy (AFM)-a tool to directly resolve chemical structures-is one of the most promising tools, yet the chemical analysis of heteroatoms has been rarely performed. We synthesized multiple heteroatom-substituted graphene nanoribbons and showed that AFM can directly resolve elemental differences and can be correlated to the van der Waals radii, as well as the modulated local electron density caused by the substitution...
April 2018: Science Advances
Giedrius Sasnauskas, Kotryna Kauneckaite, Virginijus Siksnys
Arabidopsis thaliana requires a prolonged period of cold exposure during winter to initiate flowering in a process termed vernalization. Exposure to cold induces epigenetic silencing of the FLOWERING LOCUS C (FLC) gene by Polycomb group (PcG) proteins. A key role in this epigenetic switch is played by transcriptional repressors VAL1 and VAL2, which specifically recognize Sph/RY DNA sequences within FLC via B3 DNA binding domains, and mediate recruitment of PcG silencing machinery. To understand the structural mechanism of site-specific DNA recognition by VAL1, we have solved the crystal structure of VAL1 B3 domain (VAL1-B3) bound to a 12 bp oligoduplex containing the canonical Sph/RY DNA sequence 5'-CATGCA-3'/5'-TGCATG-3'...
April 6, 2018: Nucleic Acids Research
Sina Najmaei, Mahesh R Neupane, Barbara M Nichols, Robert A Burke, Alexander L Mazzoni, Matthew L Chin, Daniel A Rhodes, Luis Balicas, Aaron D Franklin, Madan Dubey
The mechanisms of carrier transport in the cross-plane crystal orientation of transition metal dichalcogenides are examined. The study of in-plane electronic properties of these van der Waals compounds has been the main research focus in recent years. However, the distinctive physical anisotropies, short-channel physics, and tunability of cross layer interactions can make the study of their electronic properties along the out-of-plane crystal orientation valuable. Here, the out-of-plane carrier transport mechanisms in niobium diselenide and hafnium disulfide are explored as two broadly different representative materials...
April 16, 2018: Small
Loureen Dahli, Dana Atrahimovich, Jacob Vaya, Soliman Khatib
High-density lipoprotein (HDL) plays an important role in preventing atherosclerosis. The antioxidant effect of HDL is mostly associated with paraoxonase 1 (PON1) activity. Increasing PON1 activity using nutrients might improve HDL function and quality and thus, decrease atherosclerotic risk. We previously isolated and identified a novel active compound, lyso-DGTS (C20:5,0) from Nannochloropsis sp. ethanol extract. In the present study, its effect on PON1 activities was examined and the mechanism by which the compound affects PON1 activity was explored...
April 16, 2018: BioFactors
Kai-Li Zhou, Dong-Qi Pan, Yan-Yue Lou, Jie-Hua Shi
The intermolecular interaction of fosinopril, an angiotensin converting enzyme inhibitor with bovine serum albumin (BSA), has been investigated in physiological buffer (pH 7.4) by multi-spectroscopic methods and molecular docking technique. The results obtained from fluorescence and UV absorption spectroscopy revealed that the fluorescence quenching mechanism of BSA induced by fosinopril was mediated by the combined dynamic and static quenching, and the static quenching was dominant in this system. The binding constant, Kb , value was found to lie between 2...
April 16, 2018: Journal of Molecular Recognition: JMR
Daifeng Zou, Chuanbin Yu, Yuhao Li, Yun Ou, Yongyi Gao
The electronic structures of monolayer and bilayer SnSe2 under pressure were investigated by using first-principles calculations including van der Waals interactions. For monolayer SnSe2 , the variation of electronic structure under pressure is controlled by pressure-dependent lattice parameters. For bilayer SnSe2 , the changes in electronic structure under pressure are dominated by intralayer and interlayer atomic interactions. The n -type thermoelectric properties of monolayer and bilayer SnSe2 under pressure were calculated on the basis of the semi-classical Boltzmann transport theory...
March 2018: Royal Society Open Science
Shuai Zhang, Qinfu Liu, Hongfei Cheng, Feng Gao, Cun Liu, Brian J Teppen
Intercalation and surface modification of clays with surfactants are the essential process to tailor the clays' surface chemistry for their extended applications. A full understanding of the interaction mechanism of surfactants with clay surfaces is crucial to engineer clay surfaces for meeting a particular requirement of industrial applications. In this study, the thermodynamic mechanism involved in the intercalation and surface modification of methanol preintercalated kaolinite by three representative alkane surfactants with different head groups, dodecylamine, cetyltrimethylammonium chloride (CTAC), and sodium stearate, were investigated using the adaptive biasing force accelerated molecular dynamics simulations...
April 27, 2017: Journal of Physical Chemistry. C, Nanomaterials and Interfaces
Akram Abbasi, Geoffrey D Bothun, Arijit Bose
Alcanivorax borkumensis (AB) is a marine bacterium that dominates bacterial communities around many oil spills because it enzymatically degrades the oil while using it as a nutrient source. Several dispersants have been used to produce oil-in-water emulsions following a spill. Compared to surface slicks, the additional oil-water surface area produced by emulsification provides greater access to the oil, and accelerates its degradation. We deliberately cultured AB cells using hexadecane as the only nutrient source...
April 16, 2018: Langmuir: the ACS Journal of Surfaces and Colloids
Gavin P Campbell, Andrew Jacob Mannix, Jonathan D Emery, Tien-Lin Lee, Nathan P Guisinger, Mark C Hersam, Michael J Bedzyk
Atomically thin two-dimensional (2D) materials exhibit superlative properties dictated by their intralayer atomic structure, which is typically derived from a limited number of thermodynamically stable bulk layered crystals (e.g., graphene from graphite). The growth of entirely synthetic 2D crystals - those with no corresponding bulk allotrope - would circumvent this dependence upon bulk thermodynamics and substantially expand the phase space available for structure-property engineering of 2D materials. However, it remains unclear if synthetic 2D materials can exist as structurally and chemically distinct layers anchored by van der Waals (vdW) forces, as opposed to strongly bound adlayers...
April 13, 2018: Nano Letters
Renate Gessmann, Hans Brückner, Albrecht Berg, Kyriacos Petratos
The crystal structure of the natural nonapeptide antibiotic helioferin has been determined and refined to 0.9 Å resolution. Helioferin consists of helioferin A and B, which contain 2-(2'-aminopropyl)aminoethanol (Apae) and 2-[(2'-aminopropyl)methylamino]ethanol (Amae) at their respective alkanolamine termini. In addition, helioferin contains the unusual amino-acid residues α-aminoisobutyric acid (Aib) and (2S,4S,6S)-2-amino-6-hydroxy-4-methyl-8-oxodecanoic acid (Ahmod). The amino-terminus is capped with 2-methyl-n-1-octanoic acid (M8a)...
April 1, 2018: Acta Crystallographica. Section D, Structural Biology
M D Siao, W C Shen, R S Chen, Z W Chang, M C Shih, Y P Chiu, C-M Cheng
Because the surface-to-volume ratio of quasi-two-dimensional materials is extremely high, understanding their surface characteristics is crucial for practically controlling their intrinsic properties and fabricating p-type and n-type layered semiconductors. Van der Waals crystals are expected to have an inert surface because of the absence of dangling bonds. However, here we show that the surface of high-quality synthesized molybdenum disulfide (MoS2 ) is a major n-doping source. The surface electron concentration of MoS2 is nearly four orders of magnitude higher than that of its inner bulk...
April 12, 2018: Nature Communications
Satoru Masubuchi, Masataka Morimoto, Sei Morikawa, Momoko Onodera, Yuta Asakawa, Kenji Watanabe, Takashi Taniguchi, Tomoki Machida
Van der Waals heterostructures are comprised of stacked atomically thin two-dimensional crystals and serve as novel materials providing unprecedented properties. However, the random natures in positions and shapes of exfoliated two-dimensional crystals have required the repetitive manual tasks of optical microscopy-based searching and mechanical transferring, thereby severely limiting the complexity of heterostructures. To solve the problem, here we develop a robotic system that searches exfoliated two-dimensional crystals and assembles them into superlattices inside the glovebox...
April 12, 2018: Nature Communications
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