data sharing in molecular dynamics we distinguish between sharing for reads read writes and accumulations
Báo cáo "A new formulation for fast calculation of far field force in molecular dynamics simulations " ppt
... presented in section 3 A new formulation for fast calculation of far field force Eq (3) gives solution for outer expansion of P2 M2 Using a similar approach, we obtained solution for inner expansion ... (16 pipelines, 48GFlops) and a host computer Pentium 2.2GHz, Intel D850 motherboard In the tests, we distributed particles uniformly within a unit cube centered at origin, and evaluated force on ... potential field given by Anderson’s inner expansion Once the distribution of pseudoparticles is obtained, L2L stage can be performed using inner-P2M2 formula (Eq (5)), and then the force evaluation stage...
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data analysis in molecular biology and evolution - xuhua xia
... sequences for saving into any specified file format READSEQ does not read in long sequence names in several formats, resulting in truncation of sequence names READSEQ is slow when reading large ... contains a lot of information (e.g., beginning and ending sites of a coding sequence, an intron, an exon, a rRNA sequence, etc) about the sequences READSEQ simply ignores all this information and ... program for molecular xiii xiv Preface data analysis Chapters 2-5 cover routine techniques for retrieving, manipulating, converting, organizing, and aligning molecular sequence data Chapters 6-11 introduce...
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báo cáo khoa học: " Prostate cancer genomics: can we distinguish between indolent and fatal disease using genetic markers?" docx
... within the linkage-disequilibrium block defined by the associated variant: BIK, BCL2-interacting killer; CTBP2, C-terminal binding protein isoform 2; EEFSEC, elongation factor for selenoprotein ... discriminating between indolent and fatal forms of prostate cancer holds promise to improve detection and clinical management of this disease in several ways A genetic-based, targeted PSA screening ... trinucleotide repeat containing 6B isoform bRisk alleles as defined from published data cited in the column a for both of these variants, the alleles that are associated with increased risk for...
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Tài liệu Báo cáo khoa học: Analysis of the molecular dynamics of medaka nuage proteins by fluorescence correlation spectroscopy and fluorescence recovery after photobleaching doc
... microinjected into the medaka eggs and transfected into HeLa cells The olvas, nanos and tudor coding sequences were joined to the C-terminal region of the GFP or RFP coding sequence in an in- frame ... granule combining with another and one dividing into two or more parts (arrowhead in Fig 2B) OlvasGFP shuttles between the nuage and cytosol Next, we analyzed the diffusion of OlvasGFP in the PGCs ... dynamic properties of proteins in the PGC determined by FCS and FRAP A fusion protein consisting of Olvas and green uorescent protein (GFP) (OlvasGFP) expressed in the PGC forms granules that exhibit...
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Báo cáo khoa học: NMR and molecular dynamics studies of an autoimmune myelin basic protein peptide and its antagonist Structural implications for the MHC II (I-Au)–peptide complex from docking calculations ppt
... differences in their peptide-binding sites [67] Flexible docking calculations using HADDOCK [59] were performed for the docking of the MBP(74–85) epitope to the I-Aubinding pocket of the immunodominant ... H2O Lowest energy NMR structure in H2O Lowest energy NMR structure in H2O Lowest energy NMR structure in Me2SO Lowest energy NMR structure in Me2SO Lowest energy NMR structure in Me2SO in Me2SO ... rigidbody docking solutions were generated In addition, for each of the starting conformations, 10 rigid-body trials were performed, and only the best solution based on the intermolecular energy...
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Báo cáo khoa học: New roles of flavoproteins in molecular cell biology: An unexpected role for quinone reductases as regulators of proteasomal degradation pptx
... variety of ring-containing substrates Nevertheless, a number of naturally occurring quinones comprising vitamin K derivatives (menaquinone and phylloquinone), coenzyme Q (ubiquinone) and dopaquinone ... protein [21–23] The 19S caps are involved in recognition of the polyubiquitinated protein substrates, unfolding of the condemned protein [24], removing ubiquitin chains for recycling [25,26] and ... some amino acid side chains (Fig 2) [68] As mentioned in the introduction, QRs also adopt a flavodoxin-fold and the isoalloxazine ring engages in a similar interaction with a peptide chain In the...
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Báo cáo Y học: Identification of residues in the PXR ligand binding domain critical for species specific and constitutive activation docx
... observed for human and mouse PXR For that purpose we have built a homology model of human PXR in order to identify residues that were likely to be involved in ligand binding Since the initiation ... CRL-10741, loti1414101) in 6-well plates C3A cells were seeded at a concentration of · 105 cells in each well and incubated for 24 h at 37 °C in mL growth medium containing minimal essential medium ... change than the spatially and electrostatically moderate change of a histidine to a glutamine and thereby give additional information into its potential role in ligand binding We also made the three...
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Protecting the Elderly in Times of Disaster: The Critical Need for Comprehensive Disaster Planning and Exercise Design doc
... of Pandemic Influenza The potential for pandemic is still disturbingly real It is unfortunate that by being inundated with information pertaining to how to prepare ourselves for Pandemic Influenza, ... that supply chain was abruptly terminated? Area Five - Need for Evacuation and Sheltering -in- place Plans, and for the Exercising of Both In general, evacuation plans are in place for all long term ... point, the challenges of a potential Pandemic Influenza were not being considered, this risk is now also being addressed by the training Avian Influenza has continued its march across Europe and...
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Báo cáo y học: " Tumour necrosis factor-α stimulates dehydroepiandrosterone metabolism in human fibroblast-like synoviocytes: a role for nuclear factor-κB and activator protein-1 in the regulation of expression of cytochrome p450 enzyme 7b" doc
... were incubated for 45 with biotinylated anti-mouse IgG After washing, cells were incubated for 30 with avidin-biotin-peroxidase (Brunschwig Chemie, Amsterdam, The Netherlands) Following washing, ... × 105/well) were incubated in the presence and absence of TNF-α and in the presence of SN50 for hours, as described in Materials and methods Results are representative for one of the two independent ... activity We further investigated a putative role for MAPKs in the TNFα-induced increase in Cyp7b activity by using the MEK1 inhibitor PD98059 and the p38 inhibitor SB203580 The p38 inhibitor...
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Báo cáo y học: "The first influenza pandemic in the new millennium: lessons learned hitherto for current control efforts and overall pandemic preparedness" potx
... lines will focus on avoiding their indiscriminate use and therefore preventing speeding the spread of neuraminidase inhibitor resistance which has been currently identified in many settings In ... 1957, and the 1968 pandemics However, in facing the current influenza A(H1N1)v pandemic, there are epidemiologic similarities between the 1918–1919 influenza pandemic and the onset of the 2009 influenza ... a pandemic In summary, we should continue to learn and effectively apply the lessons we learn from this unfortunate influenza A(H1N1)v pandemic Theultimate goal of continuously improving pandemic...
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Tài liệu Báo cáo khoa học: Influence of modulated structural dynamics on the kinetics of a-chymotrypsin catalysis Insights through chemical glycosylation, molecular dynamics and domain motion analysis pptx
... rigid domains [domain (residues 1119) and domain (residues 151245)] linked by an interdomain hinge (residues 120150) Interestingly, the connection between the two domains and the hinge appears ... 0.4 mm) in a nal volume of mL For determination of steady state kinetic parameters, initial velocities were determined for seven initial substrate concentrations in the range between 0.01 and 0.5 ... the kinetic method was the same as that used for the p-nitroanilide (pNA) substrate Glycoconjugate modelling and molecular dynamics simulations For all molecular modelling and molecular dynamics...
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Báo cáo khoa học: Molecular dynamics structures of peptide nucleic acidÆDNA hybrid in the wild-type and mutated alleles of Ki-ras proto-oncogene ppt
... preference for sugar puckers conforms to the C2¢ endo domain Discussion Base pair mismatch in duplex DNA contributes an element of instability resulting in lowering of the melting temperature and increase ... bond and weak stacking and also (b) entropic and enthalpic contribution resulting from the nature of interaction of water in the vicinity of mismatch [16] However, lack of structural information ... both, are involved in interaction with water This is true irrespective of 4059 Effect of A .C mismatch in PNAÆDNA and DNA duplexes T Rathinavelan and N Yathindra Fig Interaction between the A24...
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Báo cáo khoa học: Structural flexibility in Trypanosoma brucei enolase revealed by X-ray crystallography and molecular dynamics pdf
... sulfate-bound form, including one containing a novel metal binding site Furthermore, they show structural heterogeneity in their inhibitor-bound forms, highlighting the potential to extend future inhibitors ... chemistry involving a Lys-Glu dyad [8,9] Also essential is the binding of two divalent metal ions to distinct sites: the first ‘conformational’ site being required for substrate binding and the ... preceding the natural initiator Met within the tail downstream of the thrombin cleavage site in the N-terminal extension containing the His tag) was observed at a crystal lattice interface between...
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molecular dynamics simulation of thermal and thermomechanical phenomena in picosecond laser material interaction
... of Engineering and Technology and the Department of Mechanical Engineering at the University of Nebraska at Lincoln References [1] H H€kkinen, U Landman, Superheating, melting, and a annealing ... distance between particles is larger than a certain distance rc , namely the cutoff distance, the interaction between them is negligible, and no interaction calculation is necessary The interaction ... Only the interaction between atoms in adjacent cells is considered The laser beam absorption in the target is simulated by exciting the kinetic energy of atoms, and is fulfilled by scaling the...
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molecular dynamics studies of ultrafast laser induced phase and structural change in crystalline silicon
... understand the interface kinetics, the relation between the melting/resolidification velocity and the interface superheating and undercooling, during which the RDF was tried to be applied in determining ... plotted in Fig 7(e) and (f) It is seen that for both 60 J/m2 and 90 J/m2, the interface velocity and interface temperature have similar trends, indicating that the interface kinetics – the interface ... velocity for forming crystalline silicon is estimated to be about 74 m/s and 67 m/s for 60 J/m2 and 90 J/m2, respectively, and the average velocity for forming amorphous silicon is 230 m/s and 120...
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Báo cáo hóa học: " Molecular Dynamics Simulation of Nanoindentation-induced Mechanical Deformation and Phase Transformation in Monocrystalline Silicon" potx
... 72 and nanoindentation-induced phase transformations during loading and unloading Both spherical and Berkovich indenters were considered Molecular Dynamics Simulation The interatomic ... monocrystalline Si(100) were investigated through MD simulations The Si-III and Si-XII were distinguished from Si-I by searching the presence of the fifth neighboring atom within a non-bonding length ... distributions induced by spherical and Berkovich indenters would result in different Si-III and Si-XII distributions within the nanoindentation-induced deformed region Boyer et al [20] have observed and...
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Báo cáo hóa học: " Study of Materials Deformation in Nanometric Cutting by Large-scale Molecular Dynamics Simulations" docx
... atomic interactions in the MD simulations of nanometric cutting processes: (1) the interaction in the workpiece; (2) the interaction between the workpiece and the tool; and (3) the interaction in ... the tool For the interaction between the copper atoms in the workpiece, we used the EAM potential for copper constructed by Johnson [14] For the interaction between the copper workpiece and the ... Cutting Depth on the Cutting Process For nanometric cutting, it is interesting to understand how the cutting depth in uences the cutting process Figure 7a–c show material deformation, chip formation,...
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MOLECULAR DYNAMICS – THEORETICAL DEVELOPMENTS AND APPLICATIONS IN NANOTECHNOLOGY AND ENERGY pot
... Molecular dynamics (MD) simulations have played increasing roles in our understanding of physical and chemical processes of complex systems and in advancing science and technology Over the past forty ... hope the readers can find connections between the liquid and solid ionic conductivities With strenuous and continuing efforts, a greater impact of MD simulations will be made on understanding various ... the ABINIT-MP input file containing the list of fragments and 3D atomic coordinates, executes an intermediate shell script to run ABINITMP, receives the resultant FMO energy and force, and updates...
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Báo cáo y học: " Early The glucocorticoid RU24858 does not distinguish between transrepression and transactivation in primary human eosinophils" pot
... ionomycin.[31] Cells were incubated for 18 h and supernatants were collected and stored at -20°C and cytokines were measured by ELISA The lower limits of detection were 3.9 pg/ml for MCP-1 and 4.1 ... dissociate between transactivation and transrepression in human eosinophils and thus is not suitable for evaluation of signalling in human eosinophils In the present study we report that RU24858 induces ... collaboration in laboratory and in apoptosis studies XZ and IA gave assistance in the design and drafting of the manuscript HK conceived the study, and participated in its design and coordination and helped...
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Báo cáo khoa học: " An Investigation of the Ability of the Glutaraldehyde Test to Distinguish between Acute and Chronic Inflammatory Disease in Horses" ppsx
... concentration of fibrinogen and/ or immunoglobulin Moderate increase in concentration of fibrinogen and/ or immunoglobulin Low increase in concentration of fibrinogen and/ or immunoglobulin No increase in concentration ... suspected in ammatory disease were evaluated using the GT (Glutarvaca), a complete clinical examination, CBC and routine serum biochemistries that included total protein, albumin, globulin and fibrinogen ... mildly increased globulin concentration and mildly decreased albumin/globulin ratio, and horses in Group had a globulin concentration and albumin/globulin ratio within normal range If the clinical...
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