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MOLECULAR DYNAMICS SIMULATION ON THE EVOLUTION OF MICROSTRUCTURES OF LIQUID ZnxAl100?x ALLOYS DURING RAPID SOLIDIFICATION

Yunfei MO, Rangsu LIU, Yongchao LIANG, Naichao ZHENG, Lili ZHOU, Zean TIAN, Ping PENG
2012 ACTA METALLURGICA SINICA  
T g , the glass forming ability (GFA) and the chemical short-range order (P CSRO ) drop with the increase in content of Zn of Zn x Al 100−x (x=25, 50, 75) alloys.  ...  A molecular dynamics simulation of the rapid solidification process of liquid Zn x Al 100−x (x=25, 50, 75) alloys has been performed, and their microstructural evolutions have been analyzed by means of  ...  Al 100−x (x=25, 50, 75) Áª 1×10 12 K/s ( 3 ) 3 ¨ß¹ ¸, Zn x Al 100−x (x=25, 50, 75) ´, ¨Zn x Al 100−x (x=25, 50, 75) Áª¸, Ð Zn ÀAEÑ Ý  ... 
doi:10.3724/sp.j.1037.2012.00064 fatcat:jjbslpagcrdutog3di3odmrvoy

Application of new informatics tools for identifying allosteric lead ligands of the c-Src kinase [article]

Lili X Peng, Morgan Lawrenz, Diwakar Shukla, Grace W Tang, Vijay S Pande, Russ B Altman
2016 bioRxiv   pre-print
quality of structural information on the target protein. 3 A protein exists in a population of conformational states in dynamic equilibrium with one another, adopting conformations not always captured by X-ray  ... 
doi:10.1101/038323 fatcat:tx2ukrrgjncythvhupr6fmvr74

Characterization of a clinical polymer-drug conjugate using multiscale modeling

Lili X. Peng, Anthony Ivetac, Akshay S. Chaudhari, Sang Van, Gang Zhao, Lei Yu, Stephen B. Howell, J. Andrew McCammon, David A. Gough
2010 Biopolymers  
The molecular conformation of certain therapeutic agents has been shown to affect the ability to gain access to target cells, suggesting potential value in defining conformation of candidate molecules. This study explores how the shape and size of poly-γ-glutamyl-glutamate paclitaxel (PGG-PTX), an amphiphilic polymer-drug with potential chemotherapeutic applications, can be systematically controlled by varying hydrophobic and hydrophilic entities. Eighteen different formulations of PGG-PTX
more » ... ng in three PTX loading fractions of 0.18, 0.24, and 0.37 and six spatial arrangements of PTX ('clusters', 'ends,' even', 'middle', 'random', and 'side) were explored. Molecular dynamics (MD) simulations of all-atom (AA) models of PGG-PTX were run until a statistical equilibrium was reached at 100 ns and then continued as coarse-grained (CG) models until a statistical equilibrium was reached at an effective time of 800 ns. Circular dichroism spectroscopy was used to suggest initial modeling configurations. Results show that a PGG-PTX molecule has a strong tendency to form coil shapes, regardless of the PTX loading fraction and spatial PTX arrangement, although globular shapes exist at f PTX = 0.24. Also, less uniform PTX arrangements such as 'ends', 'middle', and 'side' produce coil geometries with more curvature. The prominence of coil shapes over globules demonstrates that PGG-PTX may confer a long circulation half-life and high propensity for accumulation to tumor endothelia. This multiscale modeling approach may be advantageous for the design of cancer therapeutic delivery systems. GG Backbone topology i j Bond length [nm] Force constant [kJ nm −2 mol −1 ] i j k Bond angle Force constant [kJ nm −2 mol −1 ]
doi:10.1002/bip.21474 pmid:20564048 pmcid:PMC3099131 fatcat:f5udstvaabfpblpnnqtzmjq35a

Engineering Polymeric Drug Delivery Systems For Cancer Therapeutics Using Multi-scale Modeling

Lili X. Peng, Anthony Ivetac, Sang Van, Lei Yu, Stephen B. Howell, J. Andrew McCammon, David A. Gough
2009 Biophysical Journal  
Length-based fractionation of long DNA is a fundamental process in genomic analysis. Traditional methods, such as pulsed-field gel electrophoresis or capillary electrophoresis, are slow and not easily coupled to downstream analytical processes. Microfluidic devices containing arrays of micron-scale posts have previously been described for length-based fractionation of kilobase length DNA. [1] Here, we present experimental and computational studies defining and optimizing a broad array of
more » ... ers in order to maximize mass throughput and isolation of DNA > 150 kb. Parameters explored include post field geometry, electric field intensity, and field oscillation timing. Experimental studies were performed by analyzing of the mobility of single YOYO-1 intercalated DNA molecules in PDMS post arrays. Computational studies simulated kilobase length DNA as a worm-like chain model and investigated the interaction of such molecules with post arrays of various geometries. Optimization of our system results in the ability to isolate 165 kb DNA from 125 kb DNA and process 5 ng of DNA within 30 minutes of operation. Nanopores may provide the basis for a high-speed and inexpensive de novo DNA sequencing technique that could revolutionize medical and biological science. In this technique, single-stranded DNA is electrophoretically translocated through a pore with inner dimensions similar to that of DNA. The co-passing ion current is recorded to obtain sequence information. Since its inception, nanopore sequencing has had promising results with only one bacterial pore a-Hemolysin and various solid-state pores. The geometry of another bacterial pore, MspA, found in the outer membrane of Mycobacteria Smegmatis, appears to be ideally suited for nanopore sequencing. We used site-directed mutagenesis on MspA to produce mutants that allow DNA translocation. These mutants can resolve small chains of the nucleotides A, C, and T when a duplex region of hairpin DNA arrests translocation. Additionally, DNA interaction with the mutant MspA is significantly and predictably altered with further mutations to the MspA structure. Our results introduce MspA as a promising and engineerable framework for nanopore sequencing technology. Deletion or mutation of a variety of proteins localized at cell-matrix and cellcell junctions, such as vinculin and its splice-variant metavinculin, can lead to dilated cardiomyopathy in mice and humans, leading some to hypothesize that these molecules are involved in mechanotransmission or mechanotransduction in the heart. To investigate cardiac mechanotransduction mechanisms in single cells, we have combined laser tweezers with a fluorescence resonance energy transfer (FRET) biosensor to apply localized forces and probe localized signaling events in isolated mouse ventricular myocytes. Isolated murine ventricular cardiac myocytes were transfected with a focal adhesion kinase (FAK) FRET reporter to monitor integrin-mediated activation events. An integrin ligand-coated microsphere was adhered to the cell surface. Then laser tweezers were used to apply localized piconewton forces parallel or normal to the image plane either cyclically or statically. To ensure a constant force application on the microsphere, 10yM of blebbistatin was added to the imaging media. In conjunction with force application, a pulsed Ti:sapphire infrared laser was used for two-photon excitation of the FRET reporter. Phase contrast and fluorescent images were captured simultaneously, allowing quantification of applied forces and FRET ratio changes. Results indicate that piconewton level forces can be applied to the microsphere and FRET ratio changes validate that integrin-mediated events are being activated by the locally applied forces. This data suggests that the use of laser tweezers combined with FRET provides a means to study integrin-mediated events in cardiac mechanotransduction. Future studies include varying the type of integrin ligandcoated microsphere and FRET biosensors, as well as studying genetically manipulated murine lines in isolated adult cardiac myocytes. Polymers are of particular interest as drug delivery vehicles due to their ability of targeting drugs to tumors while simultaneously decreasing drug exposure to normal tissues. The classical method of designing polymer-drug conjugates invokes trial-and-error testing of chemical substances on animals and subsequently matching apparent effects to treatments. While effective, this procedure can be time-consuming and expensive. In our study, we use an ab initio approach to elucidate certain physicochemical properties of polymer-drug therapeutics that cannot as readily determined by traditional experimental methods: bottom-up atomistic-to-mesoscale computational modeling. Our polymeric DDS is poly-L-glutamyl-glutamine (PGG) covalently bound to Paclitaxel, a widely used anticancer therapeutic. Physicochemical properties of polymer-drug conjugates that have been shown to potentially affect the delivery and targeting of drugs to tumors are particle size and shape. The size and shape of polymer-drug conjugates have been shown to affect their abilities of adhering to tumor endothelium, being endocytosed by tumor cells, and diffusing through fenestrations of leaky tumor vasculature. We have developed coarse-grained models of PGG Paclitaxel in effort to achieve a variety of sizes and shapes by varying the Paclitaxel % weight loading (18%, 24%, 37% of total wt) and distribution (even, random, clusters, middle, side, ends) on PGG. Parameterization of PGG and PGG Paclitaxel was accomplished using the MARTINI force field, and simulations were run in GROMACS in explicit water solvent in 310 K for~1us. The aggregation of PGG Paclitaxel molecules into different sizes and shapes were then observed. We plan to demonstrate multi-scale modeling as a novel tool that allows us to successfully engineer a polymer-drug cancer therapeutic. With this model we expect to suggest optimal physicochemical properties of PGG Paclitaxel for future synthesis and testing. 1616-Pos Board B460 Impact Of Oxysterols On Endothelial Elastic Properties, Contractility Our previous studies, have shown that exposing bovine aortic endothelial cells (BAECs) to oxLDL resulted in an increase in cell stiffness, force generation, and endothelial network formation. The mechanisms responsible for these effects, however, were completely not clear. Since all three effects could be simulated by cholesterol depletion, we suggested that oxLDL may be mediated changes in the membrane cholesterol. However, the total amount of the cholesterol remains the same after exposing oxLDL to BAECs. To resolve this discrepancy, we tested whether oxLDL-induced effects can be reversed by supplying a surplus of cholesterol. To achieve this goal, we used the MBCD complexed with cholesterol, a known cholesterol donor. In all the experiments, cells were exposed first to oxLDL for one hour and then subsequently to MBCD-cholesterol for an additional 1 hour. Our observations show that after treating with MBCD -cholesterol, cell elastic modulus, force generation and network formation were back to the normal level as compared to control cells. It suggests that cholesterol plays an important role in oxLDL induced cell mechanics. Furthermore, we show that the impact of oxLDL on endothelial biomechanics and morphogenesis can be simulated by specific oxysterols, known components of oxLDL. Here, we show that specific oxysterols have distinct effects on endothelial biomechanical properties. Specifically, we tested four different oxysterol species that are present in oxLDL: 7B-hydroxycholesterol , 7-ketocholesterol , 25-hydroxycholesterol and 27-hydroxycholesterol to study their mechanic properties. The results show that 7k and 27HC are potent factors to increase cell elastic modulus. However, only 27HC raises the force 316a Monday,
doi:10.1016/j.bpj.2008.12.1583 fatcat:243wfxa44bcojox6chz3i2lg5u

A High-throughput Quantitative Multiplex Kinase Assay for Monitoring Information Flow in Signaling Networks

Kevin A. Janes, John G. Albeck, Lili X. Peng, Peter K. Sorger, Douglas A. Lauffenburger, Michael B. Yaffe
2003 Molecular & Cellular Proteomics  
Cells were washed once with ice-cold PBS and lysed in 1% Triton X-100, 50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 50 mM ␤-glycerophosphate, 10 mM sodium pyrophosphate, 30 mM NaF, 1 mM benzamidine, 2 mM EGTA  ...  strips (Pierce) were coated overnight with 10 g/ml anti-kinase antibody and washed three times with blocking buffer (1% bovine serum albumin (Sigma) in 50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 0.05% Triton X-  ... 
doi:10.1074/mcp.m300045-mcp200 pmid:12832460 fatcat:zlygvnego5fmlmopi6fvfq2lnm

The Free Energy Profile of Tubulin Straight-Bent Conformational Changes, with Implications for Microtubule Assembly and Drug Discovery

Lili X. Peng, Monica T. Hsu, Massimiliano Bonomi, David A. Agard, Matthew P. Jacobson, Mark S. Alber
2014 PLoS Computational Biology  
Using small-angle X-ray scattering (SAXS), Rice et al.  ...  It is noteworthy that the various X-ray crystallographic structures represented in Figure 3c differ in their space group and resolution.  ... 
doi:10.1371/journal.pcbi.1003464 pmid:24516374 pmcid:PMC3916224 fatcat:febhs45qsrflbnuliesq2e76ve

Topological edge states in a high-temperature superconductor FeSe/SrTiO3(001) film

Z. F. Wang, Huimin Zhang, Defa Liu, Chong Liu, Chenjia Tang, Canli Song, Yong Zhong, Junping Peng, Fangsen Li, Caina Nie, Lili Wang, X. J. Zhou (+3 others)
2016 Nature Materials  
Wang1,2,3†, Huimin Zhang2,4†, Defa Liu5, Chong Liu2, Chenjia Tang2, Canli Song2, Yong Zhong2, Junping Peng2,4, Fangsen Li2, Caina Nie2,4, Lili Wang2,6, X. J. Zhou5,6*, Xucun Ma2,4,6*, Q. K.  ...  ← Γ → X′ (π/a) X′ ← Γ → X′ (π/a) X′ ← Γ → X′ (π/a) X′ ← Γ → X′ (π/a) f Left edge  ... 
doi:10.1038/nmat4686 pmid:27376684 fatcat:ffhn6ybmdrczncotr725dx2g2u

Coarse-grained modeling study of nonpeptide RGD ligand density and PEG molecular weight on the conformation of poly(γ-glutamyl-glutamate) paclitaxel conjugates

Lili X. Peng, Sanjib K. Das, Lei Yu, Stephen B. Howell, David A. Gough
2011 Journal of Molecular Modeling  
CG mapping of the GG, GG COO-, GG NH3+ , and GG-PTX residues was previously done in Peng et al. [22] .  ...  This method of determining the initial structure was originally applied to PGG-PTX in Peng et al. [22] .  ... 
doi:10.1007/s00894-011-0989-4 pmid:21360176 pmcid:PMC3203221 fatcat:jsldqqyvjjbj7javtiedkel5bu

Prevalence and spectrum of AKT1, PIK3CA, PTEN and TP53 somatic mutations in Chinese breast cancer patients

Guoli Li, Xinwu Guo, Ming Chen, Lili Tang, Hui Jiang, Julia X. Day, Yueliang Xie, Limin Peng, Xunxun Xu, Jinliang Li, Shouman Wang, Zhi Xiao (+3 others)
2018 PLoS ONE  
Resources: Lili Tang, Shouman Wang, Zhi Xiao. Software: Xinwu Guo, Ming Chen, Limin Peng, Jinliang Li. Supervision: Lizhong Dai, Jun Wang. Validation: Guoli Li.  ...  (XLSX)Author ContributionsConceptualization: Lizhong Dai, Jun Wang.Data curation: Xinwu Guo, Ming Chen, Hui Jiang, Julia X. Day, Yueliang Xie, Xunxun Xu, Lizhong Dai.  ... 
doi:10.1371/journal.pone.0203495 pmid:30212483 pmcid:PMC6136723 fatcat:b6jbzwr4abfatbjodh3pwf76be

Theory-driven design of high-valence metal sites for water oxidation confirmed using in situ soft X-ray absorption

Xueli Zheng, Bo Zhang, Phil De Luna, Yufeng Liang, Riccardo Comin, Oleksandr Voznyy, Lili Han, F. Pelayo García de Arquer, Min Liu, Cao Thang Dinh, Tom Regier, James J. Dynes (+6 others)
2017 Nature Chemistry  
We therefore synthesized NiCoFeP oxyhydroxides and probed their oxidation kinetics with in situ soft X-ray absorption spectroscopy (sXAS).  ...  From a DOS comparison of NiO 2 and Ni 1-x-y Co x Fe y O 2 , we found that the NiCoFe oxide introduces more d states within the gap than pure NiO 2 ( Supplementary Fig. 1) .  ...  In situ X-ray absorption. X-ray absorption measurements at the Ni, Co and Fe L-edges were performed at the Spherical Grating Monochromator (SGM) beamline 11ID-1 at the Canadian Light Source.  ... 
doi:10.1038/nchem.2886 pmid:29359759 fatcat:caop2lqv3nh4rignnzmylcqbv4

Synchrotron based phase contrast X-ray imaging combined with FTIR spectroscopy reveals structural and biomolecular differences in spikelets play a significant role in resistance to Fusarium in wheat

Rachid Lahlali, Chithra Karunakaran, Lipu Wang, Ian Willick, Marina Schmidt, Xia Liu, Ferenc Borondics, Lily Forseille, Pierre R Fobert, Karen Tanino, Gary Peng, Emil Hallin
2015 BMC Plant Biology  
The purpose of this study is to evaluate the potential of combining synchrotron based phase contrast X-ray imaging (PCI) with Fourier Transform mid infrared (FTIR) spectroscopy to understand the mechanisms  ...  The X-rays from a synchrotron have unique properties such as high intensity and wavelength selectability compared to laboratory based X-ray machines.  ...  The use of X-rays for agricultural applications started in the 1920s and 3D visualization of structures using X-rays was demonstrated in 1973 [26] [27] [28] .  ... 
doi:10.1186/s12870-014-0357-5 pmid:25628148 pmcid:PMC4340487 fatcat:gkuugijluff4nh5ftu6yzdifgy

INTEnsive ambulance-delivered blood pressure Reduction in hyper-ACute stroke Trial (INTERACT4): study protocol for a randomized controlled trial

Lili Song, Chen Chen, Xiaoying Chen, Yijia Guo, Feifeng Liu, Yapeng Lin, Laurent Billot, Qiang Li, Hueiming Liu, Lei Si, Menglu Ouyang, Hisatomi Arima (+79 others)
2021 Trials  
DSMB members: Professor Jesse Dawson (Chair, University of Glasgow, UK), Professor Lawrence Wong (The Chinese University of Hong Kong, Hong Kong, China), and Professor Bin Peng (Peking Union Medical College  ...  /re-consent X X Vital signs X X X X BP X b X X X X c GCS X X X NIHSS X X X Medical history X CT scan X X X MRI scan for AIS X mRS X X X EQ-5D X Routine blood tests X X Standard stroke care X X Final diagnosis  ...  X Medications in use X X X SAEs X X X Concealment mechanism {16b} Concealment of treatment group assignment until the patient has been randomized will be accomplished by making treatment allocation  ... 
doi:10.1186/s13063-021-05860-y pmid:34872617 pmcid:PMC8646007 fatcat:7cjyntq7bnagfcczyxgo2hjfiy

Dichotomy of the electronic structure and superconductivity between single-layer and double-layer FeSe/SrTiO3 films

Xu Liu, Defa Liu, Wenhao Zhang, Junfeng He, Lin Zhao, Shaolong He, Daixiang Mou, Fangsen Li, Chenjia Tang, Zhi Li, Lili Wang, Yingying Peng (+12 others)
2014 Nature Communications  
the Fe 1 À x Se compounds 28 .  ...  In the MBE-grown FeSe/ SrTiO 3 films, the atomic control of the composition makes it possible to prepare FeSe 1 þ x or FeSe 1 À x films that are nearly perfect for the Fe ordering, although there may be  ...  Reprints and permission information is available online at http://npg.nature.com/ reprintsandpermissions How to cite this article: Liu, X. et al.  ... 
doi:10.1038/ncomms6047 pmid:25248072 fatcat:iebfzpwmfbe3lpqhuauvhz7xoy

Phase diagram and electronic indication of high-temperature superconductivity at 65 K in single-layer FeSe films

Shaolong He, Junfeng He, Wenhao Zhang, Lin Zhao, Defa Liu, Xu Liu, Daixiang Mou, Yun-Bo Ou, Qing-Yan Wang, Zhi Li, Lili Wang, Yingying Peng (+12 others)
2013 Nature Materials  
Lee and Z-X. Shen for discussions. X.J.Z. acknowledges financial support from the NSFC (10734120) and the MOST of China (973 programme No: 2011CB921703 and 2011CB605903).  ...  The first is the loss of Se because it evaporates easily; in this case, its loss would give rise to electron doping in the FeSe 1−x system.  ...  LETTERS 0.0 ¬0.1 ¬0.2 ¬0.3 0 0.3 0.0 ¬0.1 E ¬ E F (eV) E ¬ E F (eV) E ¬ E F (eV) E ¬ E F (meV) 2); its band structure (Fig. 2e ) shows a clear resemblance to that of A x Fe 2−y Se 2 superconductors [  ... 
doi:10.1038/nmat3648 pmid:23708329 fatcat:7mdckdn4wjcwdjzcafh4uln66e

Electronic evidence of an insulator–superconductor crossover in single-layer FeSe/SrTiO3films

Junfeng He, Xu Liu, Wenhao Zhang, Lin Zhao, Defa Liu, Shaolong He, Daixiang Mou, Fangsen Li, Chenjia Tang, Zhi Li, Lili Wang, Yingying Peng (+12 others)
2014 Proceedings of the National Academy of Sciences of the United States of America  
This d xy orbital forms an electron-like band near the M(π,π) point in the A x Fe 2−y Se 2 superconductor (51).  ...  For convenience, we will label the samples annealed at different sequences with the carrier concentration x hereafter.  ... 
doi:10.1073/pnas.1414094112 pmid:25502774 pmcid:PMC4284572 fatcat:b6gpl4jmqbeltanrwe2kke4rr4
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