energy flow analysis in proteins via ensemble molecular dynamics simulations time resolved vibrational analysis and surficial kirkwood buff theory
Báo cáo "A new formulation for fast calculation of far field force in molecular dynamics simulations " ppt
... performed in the same way as in the original FMM At the M2M transition stage, we compute positions and charges of pseudoparticles, instead of forming multipole expansion as in the original FMM ... board (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 ... measured the calculation time at high (p = 5) and low (p = 1) accuracy, with and without GRAPE The finest refinement level lmax is set to lmax = and 5, for runs with and without GRAPE, respectively...
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Báo cáo hóa học: " Mechanical characterization of nanoindented graphene via molecular dynamics simulations" ppt
... respectively, indicating that the load increased with indentation depth This is due to the number of atoms in contact with the tip increasing with indentation depth Figure shows the elastic energy and ... various indentation velocities The load increases with increasing indentation velocity This is due to the atoms having enough time to release and transfer internal residual stress at slower indentation ... versus time for various indentation depths increase with increasing velocity Relaxation forces of 159.05, 222.93, 280.94, and 314.56 nN were obtained for indentation velocities of 25, 50, 75, 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 ... are in light grey color and the cutting chips ahead the cutting tools are shown in colors ranging from red to light blue Simulation Models and Conditions 123 446 the cutting simulations include: ... regimes; Komanduri et al [5–7] carried out MD simulations of nanometric cutting of single-crystal copper and aluminum They investigated the effects of crystal orientation, cutting direction and tool...
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Molecular dynamics simulations of the tensile and melting behaviours of silicon nanowires
... increasing temperature and with decreasing strain rate, and increases with increasing diameter Additionally, it is observed that the melting temperature of the SiNWs increases with increasing diameter, ... with decreasing diameter of SiNWs at a given temperature, which indicates that surface energy increases with decreasing diameter The potential energies also increase linearly with increasing temperature ... is observed and spreads toward the center as the strain increases With the strain increasing further more, we find that sliding along the {111} plane happens, and many atoms rearrange in the neck...
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convex analysis and non linear optimization theory and examples - borwein,lewis
... C and D in R satisfy inf C + inf D = inf(C + D) We also adopt the conventions · (±∞) = (±∞) · = A (global) minimizer of a function f : D → R is a point x in D at which f attains its in mum ¯ inf ... E, I and J are finite index sets, and the objective function f and inequality and equality constraint functions gi (i ∈ I) and hj (j ∈ J) respectively are continuous from C to R A point x in C ... convexity A set C in E is convex if the line segment joining any two points x and y in C is contained in C: algebraically, λx + (1 − λ)y ∈ C whenever ≤ λ ≤ An easy exercise shows that intersections...
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Báo cáo hóa học: "Molecular Dynamics Simulations of the Roller Nanoimprint Process: Adhesion and Other Mechanical Characteristics" pot
... distribution in the process of nanoimprinting a and roller imprinting (b and d) a and b were simulated at room temperature and c and d were simulated at a temperature of 400 K and 500 K, respectively simulations ... underwent loading The forming discrepancy can be explained by the different interaction forces Intra- and inter-chain forces are present in the polymer, so the chain molecules have complicated and lenghthy ... This indicates that the imprint depth dominates the magnitude of the maximum imprint force and the time when it happens In the unloading process, the adhesion increased as the imprint depth increased...
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Comprehensive molecular dynamics simulations of carbon nanotubes under axial force or torsion vibration and new continuum models
... Nominal strain in axial direction tZ Nominal stress in axial direction Shear strain τ Shear stress xxvii cr Compressive buckling strain Pcr Compressive buckling load cr Critical buckling ... Mechanical Engineering for helping me to enrich my analytical and critical thinking capabilities I want to express special thanks to both of them for listening to all of my ideas, and for mentoring me ... may be grouped into two categories: (1) First principle approach and (2) molecular dynamics or molecular mechanics calculations First principle approaches rely on solving the Schrödinger equation...
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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
... uorescence at time point t, T0 and Tt represent the uorescence in the whole cell at time points and t, respectively, and B0 and Bt represent the uorescence in the bleached region at time points and t ... report 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 ... 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...
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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
... 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 to be via ... 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 ... Change in protein exibility upon complex formation: analysis of Ras-Raf using molecular dynamics and a molecular framework approach Proteins 56, 322337 82 Adebodun F & Jordan F (1989) Multinuclear...
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Tài liệu Báo cáo khoa học: Constitutive oligomerization of human D2 dopamine receptors expressed in Spodoptera frugiperda 9 (Sf9 ) and in HEK293 cells Analysis using co-immunoprecipitation and time-resolved fluorescence resonance energy transfer pdf
... resuspended in buffer and stored at )80 °C in aliquots of 500 lL The protein concentration was determined by the method of Lowry et al [32], using BSA as the standard Radioligand-binding assay ... Jockers, R (2002) Monitoring of ligand-independent dimerization and ligand-induced conformational changes of melatonin receptors in living cells by bioluminescence resonance energy transfer J Biol ... limitations, for example changes in energy transfer observed could be caused by conformational changes in the proteins rather than changes in protein– protein interaction A combination of several methods...
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Báo cáo khoa học: Computer-assisted mass spectrometric analysis of naturally occurring and artificially introduced cross-links in proteins and protein complexes potx
... structures, chemical modifications and cross-linking in protein mixtures, complexes, and assemblies Proteins A single protein, a list of proteins from a mixture or from a protein complex or a complete ... the amino terminus and at lysine residues, and because modification at lysine residues prevents cleavage by trypsin Accordingly, analysis using virtualmslab including modifications with NEM in the ... spectrometric analysis of cross-links Table Candidate cross-links found in NK1 using BS3 as a crosslinking agent The cross-link candidates are nominated by the VIRTUALMSLAB program by assigning peaks in...
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field flow fractionation in biopolymer analysis
... loading: flowrate ¼ 0.1 ml/min, loop volume ¼ 10 ml, time ¼ Relaxation/focusing: focusing point (distance from inlet, z´) ¼ 5.0 cm, Fcross ¼ ml/min during and 9.9 ml/min during 15 s Elution: Fin ... Assessing Protein-Ultrafiltration Membrane Interactions Using Flow Field -Flow Fractionation Galina E Kassalainen and S Kim Ratanathanawongs Williams Abstract Flow FFF (FlFFF) is used to rapidly and ... Wahlund and Lars Nilsson Assessing Protein-Ultrafiltration Membrane Interactions Using Flow Field -Flow Fractionation 23 Galina E Kassalainen and S Kim...
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Báo cáo hóa học: " Review Article Multimodal Pressure-Flow Analysis: Application of Hilbert Huang Transform in Cerebral Blood Flow Regulation" docx
... method, because BP and BFV signals recorded in clinical settings are often nonstationary and are modulated by nonlinearly interacting processes at multiple time- scales corresponding to the beat-to-beat ... were measured during the Valsalva maneuver (VM) and during supine baseline conditions The straight line is the linear regression fit of the data The phase shifts during VM and baseline showed a strong ... IEEE Engineering in Medicine and Biology Magazine, vol 17, no 6, pp 32–39, 1998 [10] D Hoyer, R Bauer, B Walter, and U Zwiener, “Estimation of nonlinear couplings on the basis of complexity and predictability—a...
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MOLECULAR DYNAMICS – THEORETICAL DEVELOPMENTS AND APPLICATIONS IN NANOTECHNOLOGY AND ENERGY pot
... the kinetic and potential energy over time at the minimum temperature of 298 K and initial kinetic energy of 0.1 eV The kinetic energy oscillates during the collision with the slower cooling rate ... determine whether the MD simulation on a single PES is valid The three ingredients in a meta-MD simulation are electronic structure theory, molecular dynamics theory, and coupling method In principle, ... of energy was extracted at every single time step from any atom that had a kinetic energy greater than a defined minimum energy In this work two simulations were run with a minimum of 298 K and...
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PROGRESS IN MOLECULAR AND ENVIRONMENTAL BIOENGINEERING – FROM ANALYSIS AND MODELING TO TECHNOLOGY APPLICATIONS_2 pps
... l-tryptophan l-glycine l-alanine l-cysteine l-histidine l-lysine l-arginine 1.0 nf, mol/m h l-glutamic acid l-aspartic acid l-tryptophan l-glycine l-alanine l-cysteine l-histidine l-lysine l-arginine 1.0 ... L-glycine, L-alanine, Ltryptophan and L-cysteine are pertracted, for pH of feed phase between and these amino acids and L-lysine and L-arginine, for pH of feed phase between and L-histidine can ... Progress in Molecular and Environmental Bioengineering – From Analysis and Modeling to Technology Applications differently in ion exchange chromatography As a main kind of bioactive protein, LF...
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PROGRESS IN MOLECULAR AND ENVIRONMENTAL BIOENGINEERING – FROM ANALYSIS AND MODELING TO TECHNOLOGY APPLICATIONS_1 ppsx
... the input can influence model selection, and how a single unit-impulse input might result in the most informative model Progress in Molecular and Environmental Bioengineering – From Analysis and ... only in the case of short chain acyls, and the yield was around 10% In the work of Kuruma et al (2009) 36 Progress in Molecular and Environmental Bioengineering – From Analysis and Modeling to ... world In fact, it consists of two parts: one dedicated to molecular and cellular engineering and the other to environmental bioengineering The content classification mainly reflects the increasing...
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Analysis and engineering of light in complex media via geometrical optics
... help of tensor analysis we generalize ray tracing machinery in a coordinate-free style and we show in detail how ray tracing in anisotropic media in arbitrary coordinate systems and curved spaces ... space-folding and its role in the perfect imaging and superscattering Interested readers are first referred to [21] in which the theory of space-folding and transformation media is explained comprehensively ... certain index of refraction distribution in space n x, y, z , it is exceedingly difficult to go in the opposite direction―to command light to certain things by engineering the refractive index...
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Molecular modeling of localized collective motions and dynamics in proteins
... the binding ligands and the host protein The structural changes in some proteins regulate the interaction between ligands and protein through induced fit and allosteric effects [2,3] The “induced ... effect is found in a special class of proteins, so-called allosteric proteins Substrate binding to one subunit of these multimeric proteins triggers conformational changes in proteins which alters ... understand the function of proteins requires a scientific investigation of protein motion and dynamics 1.2 Structure basis for protein motion and dynamics The motions of the atoms in a protein tend...
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material flow analysis of phosphorous and chemical oxygen demand in domestic wastewater and food waste in song cong town, vietnam
... An inflow (input) is entering a process and an outflow (output) is exiting FLOW a process Import and export are the flows in and out from the system The flow is defined as “mass per time and ... calculated since much of the substance is digested to energy and CO2 in the treatment processes Interesting in the context is solely the content of COD 24 in the waste flows (Ass Prof at Linköping University, ... current P and COD flows in wastewater and food waste using MFA Identify different solutions for wastewater treatment, focusing on their effectiveness in reducing P and COD Conduct and present...
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Implications of building energy standard for sustainable energy efficient design in buildings
... existing building designs and increasing demand for sustainable energy efficient design Buildings standards in developing countries While building energy efficiency standards exist in almost all ... building energy standards in developing countries, implications for sustainable energy efficient designs in building and how building energy standards can be used to fill the gap between existing ... frequently used instruments for energy efficient design in buildings [5] Energy standards provide minimum building requirements that are cost-effective in saving energy in building and provide a...
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