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Quantum biology

Gael Sentís, Emilio Bagan, John Calsamiglia, Giulio Chiribella, Ramon Muñoz-Tapia
Sudden changes are ubiquitous in nature. Identifying them is crucial for a number of applications in biology, medicine, and social sciences. Here we take the problem of detecting sudden changes to the quantum domain. We consider a source that emits quantum particles in a default state, until a point where a mutation occurs that causes the source to switch to another state. The problem is then to find out where the change occurred. We determine the maximum probability of correctly identifying the change point, allowing for collective measurements on the whole sequence of particles emitted by the source...
October 7, 2016: Physical Review Letters
Jesús Ignacio Mendieta-Moreno, Daniel G Trabada, Jesus Mendieta, James P Lewis, Paulino Gómez-Puertas, Jose Ortega
The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics / molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between non-reactive and reactive conformations leading to the photolesion...
October 21, 2016: Journal of Physical Chemistry Letters
Hamid Reza Samadikhah, Maryam Nikkhah, Saman Hosseinkhani
Two quantum dots (QDs), a green emitter, CdSe and a red emitter, CdSe with ZnS shell are encapsulated into novel liposomes in two different formulations including cationic liposomes. Quantum dots have proven themselves as powerful inorganic fluorescent probes, especially for long-term, multiplexed imaging and detection. Upon delivery into a cell, in endocytic vesicles such as endosomes, their fluorescence is quenched. We have investigated the potential toxic effects, photophysical properties and cell internalization of QDs in new formulation of liposomes as an in vitro vesicle model...
October 21, 2016: Luminescence: the Journal of Biological and Chemical Luminescence
Hao Zhu, Jiangli Fan, Huiying Mu, Tao Zhu, Zhen Zhang, Jianjun Du, Xiaojun Peng
Polarity-sensitive fluorescent probes are powerful chemical tools for studying biomolecular structures and activities both in vitro and in vivo. However, the lack of "off-on" polarity-sensing probes has limited the accurate monitoring of biological processes that involve an increase in local hydrophilicity. Here, we design and synthesize a series of "off-on" polarity-sensitive fluorescent probes BP series consisting of the difluoroboron dippyomethene (BODIPY) fluorophore connected to a quaternary ammonium moiety via different carbon linkers...
October 21, 2016: Scientific Reports
Fan Zhang, Yue Sun, Demei Tian, Weon Sup Shin, Jong Seung Kim, Haibing Li
Host-guest recognition plays an important role in biological analysis and biosensing. Accordingly, great efforts have been devoted to the development of sensors using versatile 3D surface materials. These functionalized nanomaterials possess the advantages of high selectivity and visual signals, enabling the selective detection of ions, amino acids, proteins, and other biological molecules. Therefore, in this feature article, we present some significant and representative examples of molecular recognition on calixarene functionalized 3D surface nanomaterials...
October 20, 2016: Chemical Communications: Chem Comm
Justin A Lemkul, Alexander D MacKerell
Mg2+ ions are important in biological systems, particularly in stabilizing compact RNA folds. Mg2+ is strongly polarizing, and representing its interactions in heterogeneous environments is a challenge for empirical force field development. To date, the most commonly used force fields in molecular dynamics simulations utilize a pairwise-additive approximation for electrostatic interactions, which cannot account for the significant polarization response in systems containing Mg2+. In the present work, we refine the interactions of Mg2+ with water, Cl- ions, and nucleic acid moieties using a polarizable force field based on the classical Drude oscillator model...
October 19, 2016: Journal of Physical Chemistry. B
Tao Jiang, Menghua Wang, Li Li, Jinguang Si, Bo Song, Cao Zhou, Meng Yu, Xuewei Wang, Yonggang Zhang, Gang Ding, Zhongmei Zou
Overexpression of laeA in Chaetomium globosum CBS148.51 up-regulated expression of the chaetoglobosin gene cluster and resulted in the isolation of a new cytochalasan, chaetoglobosin Z (1), together with six known analogues, chaetoglobosins A (2), B (3), D (4), E (5), O (6), and V (7). RT-PCR analysis confirmed that the key genes in the chaetoglobosin gene cluster were significantly up-regulated. The structure of the new compound chaetoglobosin Z (1) was elucidated using NMR data. The relative and absolute configurations were determined by NOESY and electronic circular dichroism combined with quantum-chemical calculations adopting time-dependent density functional theory methods, respectively...
October 19, 2016: Journal of Natural Products
Yohei Okada, Masae Sugai, Kazuhiro Chiba
Fluorophores with emission wavelengths that shift depending on their hydrogen-bonding microenvironment in water would be fascinating tools for the study of biological events. Herein, we describe the design and synthesis of a series of water-soluble solvatochromic fluorophores, 2,5-bis(oligoethylene glycol)oxybenzaldehydes (8-11) and 2,5-bis(oligoethylene glycol)oxy-1,4-dibenzaldehydes (14-17), based on a push-pull strategy. Unlike typical examples in this class of fluorophores, the fluorescence properties of these compounds are independent of solvent polarity and become fluorescent upon intermolecular hydrogen-bonding, exhibiting high quantum yields (up to φ = 0...
October 18, 2016: Journal of Organic Chemistry
Atanu Acharya, Alexey M Bogdanov, Bella L Grigorenko, Ksenia B Bravaya, Alexander V Nemukhin, Konstantin A Lukyanov, Anna I Krylov
Photoinduced reactions play an important role in the photocycle of fluorescent proteins from the green fluorescent protein (GFP) family. Among such processes are photoisomerization, photooxidation/photoreduction, breaking and making of covalent bonds, and excited-state proton transfer (ESPT). Many of these transformations are initiated by electron transfer (ET). The quantum yields of these processes vary significantly, from nearly 1 for ESPT to 10(-4)-10(-6) for ET. Importantly, even when quantum yields are relatively small, at the conditions of repeated illumination the overall effect is significant...
October 18, 2016: Chemical Reviews
Ruta Grinyte, Javier Barroso, Marco Möller, Laura Saa, Valeri Pavlov
Electrochemical detection strategies employing semiconductor quantum dots (QDs) open up new opportunities for highly sensitive detection of biological targets. We designed new a assay based on microbead linked enzymatic generation of CdS QDs (Microbead QD-ELISA) and employed it in optical and electrochemical affinity assays for the cancer biomarker superoxide dismutase 2 (SOD2). Biotinylated antibodies against SOD2 were immobilized on the surface of polyvinyl chloride microbeads bearing streptavidin. In order to prevent any non specific adsorption the microbeads were further blocked with bovine serum albumin...
October 18, 2016: ACS Applied Materials & Interfaces
Wen-Shuo Kuo, Chia-Yuan Chang, Hua-Han Chen, Chih-Li Lilian Hsu, Jiu-Yao Wang, Hui-Fang Kao, Lawrence Chao-Shan Chou, Yi-Chun Chen, Shean-Jen Chen, Wen-Tsan Chang, Shih-Wen Tseng, Ping-Ching Wu, Ying-Chih Pu
A graphene quantum dot (GQD) used as the photosensitizer with high two-photon absorption in the near-infrared region, a large absolute cross section of two-photon excitation (TPE), strong two-photon luminescence and impressive two-photon stability could be used for dual modality two-photon photodynamic therapy (PDT) and two-photon bioimaging with an ultrashot pulse laser (or defined as TPE). In this study, a GQD efficiently generated reactive oxygen species coupled with TPE, which highly increased the effective PDT ability of both gram-positive and -negative bacteria, with ultra-low energy and an extremely short photoexcitation time generated by TPE...
October 18, 2016: ACS Applied Materials & Interfaces
Maximiliano L Agazzi, M Belén Ballatore, Eugenia Reynoso, Ezequiel D Quiroga, Edgardo N Durantini
Two cationic BODIPYs 3 and 4 were synthesized by acid-catalyzed condensation of the corresponding pyrrole and benzaldehyde, followed by complexation with boron and methylation. Compound 3 contains methyl at the 1,3,5 and 7 positions of the s-indacene ring and a N,N,N-trimethylamino group attached to the phenylene unit, while 4 is not substituted by methyl groups and the cationic group is bound by an aliphatic spacer. UV-visible absorption spectra of these BODIPYs show an intense band at ∼500 nm in solvents of different polarities and n-heptane/sodium bis(2-ethylhexyl)sulfosuccinate (AOT)/water reverse micelles...
October 3, 2016: European Journal of Medicinal Chemistry
Guohua Tao
Accurately describing nuclear motion is crucial in electronically nonadiabatic dynamics simulations. In this work, a coherence-controlled (CC) approach is proposed based on the mapping between the classical state space and the full electronic matrix and that between the decomposed state space and different nuclear dynamics that allows nuclear motion to properly follow either Ehrenfest dynamics in the coherence domain or Born-Oppenheimer-like dynamics in the single-state domain in a consistent manner. This new method is applied to several benchmark models involving nonadiabatic transitions in two-state or three-state systems, and the obtained results are in excellent agreement with exact quantum calculations...
October 17, 2016: Journal of Physical Chemistry Letters
F Gorrini, M Cazzanelli, N Bazzanella, R Edla, M Gemmi, V Cappello, J David, C Dorigoni, A Bifone, A Miotello
Nanodiamonds are the subject of active research for their potential applications in nano-magnetometry, quantum optics, bioimaging and water cleaning processes. Here, we present a novel thermodynamic model that describes a graphite-liquid-diamond route for the synthesis of nanodiamonds. Its robustness is proved via the production of nanodiamonds powders at room-temperature and standard atmospheric pressure by pulsed laser ablation of pyrolytic graphite in water. The aqueous environment provides a confinement mechanism that promotes diamond nucleation and growth, and a biologically compatible medium for suspension of nanodiamonds...
October 12, 2016: Scientific Reports
Xiang-Yuan Deng, Jie Cheng, Xiao-Li Hu, Ling Wang, Da Li, Kun Gao
It is very important to have a good understanding of the biological effects of nanoparticles (NPs) on marine diatoms. In this study, the physiological and biochemical responses of a marine diatom Phaeodactylum tricornutum to titanium dioxide NPs (nano-TiO2) and cerium oxide NPs (nano-CeO2) were compared and evaluated using 96h growth tests in a batch-culture system. At 96h of exposure, the growth inhibition rate (IR, %) of P. tricornutum increased from 5.46 to 27.31% with increasing nano-TiO2 concentrations from 2...
October 8, 2016: Science of the Total Environment
Juan Liu, Viktoriia Y Postupalenko, Samuel Loercher, Dalin Wu, Mohamed Chami, Wolfgang Meier, Cornelia G Palivan
Self-organization of nano-components was mainly focused on solid nanoparticles, quantum dots or liposomes to generate complex architectures with specific properties, but intrinsically limited or not developed enough, to mimic sophisticated structures with biological functions in cells. Here, we present a biomimetic strategy to self-organize synthetic nano-compartments (polymersomes) into clusters with controlled properties and topology by exploiting DNA hybridization to interconnect polymersomes. Molecular- and external factors affecting the self-organization served to design clusters mimicking the connection of natural organelles: fine tune of the distance between tethered polymersomes, different topologies, no fusion of clustered polymersomes and no aggregation...
October 11, 2016: Nano Letters
Yixun Xing, Ashish K Jindal, Martín Regueiro-Figueroa, Mariane Le Fur, Nelly Kervarec, Piyu Zhao, Zoltan Kovacs, Laura Valencia, Paulo Pérez-Lourido, Raphaël Tripier, David Esteban-Gómez, Carlos Platas-Iglesias, A Dean Sherry
Recently developed dynamic nuclear polarization (DNP) technology offers the potential of increasing the NMR sensitivity of even rare nuclei for biological imaging applications. Hyperpolarized (89) Y is an ideal candidate because of its narrow NMR linewidth, favorable spin quantum number (I=1/2 ), and long longitudinal relaxation times (T1 ). Strong NMR signals were detected in hyperpolarized (89) Y samples of a variety of yttrium complexes. A dataset of (89) Y NMR data composed of 23 complexes with polyaminocarboxylate ligands was obtained using hyperpolarized (89) Y measurements or (1) H,(89) Y-HMQC spectroscopy...
October 10, 2016: Chemistry: a European Journal
Sadegh Askari, Atta Ul Haq, Manuel Macias-Montero, Igor Levchenko, Fengjiao Yu, Wuzong Zhou, Kostya Ken Ostrikov, Paul Maguire, Vladimir Svrcek, Davide Mariotti
Highly size-controllable synthesis of free-standing perfectly crystalline silicon carbide nanocrystals has been achieved for the first time through a plasma-based bottom-up process. This low-cost, scalable, ligand-free atmospheric pressure technique allows fabrication of ultra-small (down to 1.5 nm) nanocrystals with very low level of surface contamination, leading to fundamental insights into optical properties of the nanocrystals. This is also confirmed by their exceptional photoluminescence emission yield enhanced by more than 5 times by reducing the nanocrystals sizes in the range of 1-5 nm, which is attributed to quantum confinement in ultra-small nanocrystals...
October 6, 2016: Nanoscale
Xiaoqing Wang, Qingsong Liu, Fen Qi, Lin Li, Hai-Dong Yu, Zhipeng Liu, Wei Huang
A new family of BODIPY analogues (BDB1-8) derived from benzothiazole-pyrimidine-based bidentate ligands was synthesized and fully characterized. The photophysical properties of these boron complexes were measured both in solution and solid-state. These new luminophores exhibited intense fluorescence with high quantum yields ranging from 0.27 to 0.79, and moderate Stokes shifts ranging from 660 to 2120 cm(-1) in solution. Due to the existence of strong intermolecular interactions, BDB1-8 showed quenched fluorescence with low quantum yields ranging from 0...
October 7, 2016: Dalton Transactions: An International Journal of Inorganic Chemistry
N Shimomura, Y Egawa, R Miki, T Fujihara, Y Ishimaru, T Seki
A xanthene derivative containing a borinate moiety emitted red fluorescence with a high quantum yield. The interaction between the borinate and a sugar molecule induced a fluorescence change based on the change in the HOMO-LUMO gap. The response was pH-resistant in a wide range. In addition, catechol quenched through photoinduced electron transfer. The red fluorescence and polyol binding ability of dyes will pave the way for new biological applications of chemical sensors.
October 5, 2016: Organic & Biomolecular Chemistry
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