pseudocode for the molecular dynamics example

... localization and to measure the mobility of the components in the PGCs The medaka embryo was peeled off the chorion, and the segment containing the part of PGCs was excised for observation by microscopy ... defective in formation of the functional granules, indicating that their formation is 346 dependent on the complete set of the DEAD-box motifs in olvas These results indicate that the granules ... measurements were performed on the same setup of the laser scanning microscope as used for FCS analysis The detection gain was adjusted to the uorescence of the GFP fusion proteins almost at the saturation...

Ngày tải lên: 18/02/2014, 16:20

... were considered as missing If the spot was 1.5-fold higher than the local background for one channel (for example, red), but not the other (for example, green), the difference between raw intensity ... action on Top2, they may therefore act on DNA in other ways Because most of the DNA-binding Top2 inhibitors clustered together and were in the same cluster as etoposide and teniposide, the Top2 activity ... as they have been removed from their in vivo environment and selected for growth characteristics in culture They should therefore be considered as surrogates that may contain information on the...

Ngày tải lên: 30/03/2014, 13:20

... demonstrates the importance of the P1 anchor for MHC II (I-Au, I-Ad, I-Ak) We speculate therefore that an extension of the MBP(74–85) epitope in the N-terminus could increase the binding and affinity for ... sclerosis For a better understanding of the molecular basis of the MBP(74–85) antigen– MHC II recognition, a model for the 3D structure of the MBP(74–85) antigen–MHC II complex is required The only ... among the peptide antigens are indicated in red) The alignment of MBP(74–85) was performed based on the highest aligned score with the three antigens, on the basis of the amino-acid preference for...

Ngày tải lên: 07/03/2014, 16:20

... enhanced affinity for the E2 binding sites containing AA(A ⁄ T)N spacers [16,17] The structure of the spacer region, which is not contacted by the protein, is critical for the formation of the high-affinity ... distribution of molecular flexibility The mechanical properties that characterize the two proteins, together with the different structural and conformational features of the spacer regions in the DNA ... represent the geometric centers of the cavities that are located over the protein surface, and the blue spheres indicate the geometric centers of the cavities that are located inside the b-barrel The...

Ngày tải lên: 16/03/2014, 10:20

... Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Second Round Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, ... Anton The committee concluded that the proposals listed below best meet the selection criteria set forth in the RFP for Biomolecular Simulation Time on Anton Detailed comments for each of the 81 ... letter describes the work and transmits the final report of the Committee on Proposal Evaluation for Allocation of Supercomputing Time for the Study of Molecular Dynamics, Second Round The committee...

Ngày tải lên: 16/03/2014, 15:20

... Measurements were performed during the first h 508 of the light phase, representing the time period of photosynthetic activity until plants were harvested for analysis of metabolites (see below) The rate ... also depends on the concentration of the reaction product and the dissociation constant Ki,B for inhibitor binding The rate of hexose-based sucrose synthesis was described by the mass action ... hexose-based sucrose resynthesis showed significant differences with respect to both their absolute values and the time course From the simulations, it appears that the ability to sustain the cycling of...

Ngày tải lên: 14/02/2014, 22:20

... Val24 at the membrane–water interface, the other with Lys28 at the interface [4,5] The location of the peptide within the membrane may affect the types of interactions that it has with the surrounding ... difference in the results for the sn-1 and sn-2 chains; hence, for the purpose of clarity, the data presented here are in direct reference to the sn-1 chain We find that the lipids in the top leaflet ... Ab, and the lipids of the lower leaflet elongate to become more ordered, filling the void in the center of the bilayer (Fig 1) The results of simulations C1 and C2 reflect the fact that the peptides...

Ngày tải lên: 18/02/2014, 08:20

... parameters (Tables and 5) for the glycoconjugates to determine the dependence of the individual rate constants on the changes in the enzymes structural dynamics The parameters for both the lactose and ... [17] The rest of 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 ... questions of whether and how the enzymes structural dynamics inuence the kinetics of a-CT catalysis This was done by determining the changes in the global structural dynamics (DGHX) [38] for the various...

Ngày tải lên: 19/02/2014, 05:20

... throughout the dynamics in DDwt leading to an uninterrupted stacking at the steps flanking the mismatch The difference in the A C mismatch hydrogen bond may therefore be attributed to the significant ... added to the DDmut and the DDwt, respectively The resultant periodic box sizes corres˚ ˚ ˚ pond to  50 A ·  47 A ·  77 A for the DDmut and, ˚ ˚ ˚  51 A ·  50 A ·  74 A for the DDwt MD for PDwt, ... as the WC hydrogen bond 4062 (Fig 9) Other transitions lead to a totally unstacked situation (data not shown) Further, the (gauche+, trans) conformational state for (a,e) promotes an intramolecular...

Ngày tải lên: 07/03/2014, 21:20

... and in the present simulation the load is along the [11 0] orientation and the resolved shear stress on the (111) plane causes the sliding After the formation of the neck, the plastic deformations ... Fig Before the melting behaviour starts, the atoms of the SiNW oscillate at their equilibrium position As the melting behaviour starts, the unstable atoms on the edge move to the facet of the SiNW ... as compared with those in the bulk, and the increasing dominance of the surface would decrease the strength of the structure 3.2 The melting properties of the SiNWs The variation of potential...

Ngày tải lên: 16/03/2014, 15:18

... across the 16 000 simulation conformers 4828 every 10 ps through the 160 unbiased MD simulations These data demonstrate the broadness of the conformational space explored in the study Analysis of the ... values seen for the MD conformers shows that there are three distinct peaks in the RMSD distribution (Fig 1B) These correspond to different levels of unfolding To aid the analysis, the conformers ... persistence in the group conformers, with a-helical populations in the range 0.59–0.99 for the residues involved In the group conformers the changes are more pronounced (Figs and 3, and Fig in the supplementary...

Ngày tải lên: 16/03/2014, 23:20

... expansions Therefore only a small fraction of the calculation procedure in the FMM can be performed on such hardware, and the speed up gain remains rather modest An outstanding problem is how to perform ... approximate the potential field of the original distribution of the particles The difference is that P2 M2 uses the distribution of point charges, while the Anderson’s method uses potential values In the ... and force evaluation Force-evaluation stage consists of near field and far field evaluation parts In the case of original FMM, only the near field part of the force-evaluation stage can be performed...

Ngày tải lên: 22/03/2014, 11:20

... adjusted to pH 8) The mixture was incubated on ice for 20 Cells were centrifuged at 6440 g at °C for 20 The supernatant containing the scFv protein was collected for further purification The pellet was ... protect the mice The affinity constants were determined in a biosensor of molecular interactions in real time (BIACORE) Table shows the values obtained for the binding kinetic constants The affinity ... corresponding germ lines For clone 3F, VH3-VK3 were the closest families for VH and VL domains, respectively In the case of C1, VH3Vk1 were the families with highest scores The specificity of these two scFvs...

Ngày tải lên: 23/03/2014, 13:20

... is the angle between the projection of the tilt of the z axis on the xÂ, y plane (dened direction of tilt of z and the x axis), and j % a + c denes the location of the rhombic (x, y) axes The ... to the iron and positioned to provide the H-bond to the bound cyanide, and by implication, to the bound O2 in the reduced form in each of the three globins The extensive sequence homology for ... [32] that will conrm whether the active site structure is closer to one or the other crystal forms, or distinct from both The hyperne shifts of the heme are sensitive to the presence of an H-bond...

Ngày tải lên: 23/03/2014, 17:22

... TKE  in  the horizontal  direction  is  more  important  than  that  in  the vertical  direction.  Therefore,  in  the present  study,  the TKE  is  assumed  uniformly  distributed in the whole water depth, and the ... wetted function is 1. For other cases, value of  the cell  side  wetted  function  equals  to  the ratio of the length of the wetted portion over  the total length of the cell side. After getting  all the wetted points on four sides of the cell,  ... To  verify  the accuracy  of  the numerical  model  on  the simulation  of  the wave  transformation  on  a  natural  beach,  existing  experimental data on the wave dynamics in  the nearshore ...

Ngày tải lên: 28/03/2014, 15:20

... were considered for the periodic boundary on the substrate’s Y-axis The periodic boundary on the substrate’s X-axis was movable in the direction toward the roller The ratio of the substrate’s ... are located on the left side of the roller, and the other is the ‘‘pulled behavior’’ that occurs on the right side of the roller The ‘‘push’’ and ‘‘pull’’ action contributes to the near-perpendicular ... when the rotation angle is beyond 90° This discrepancy can be explained by Fig 2d The adhesion occurred on the left side and at the bottom of the tooth during unloading Therefore, the imprint force...

Ngày tải lên: 21/06/2014, 20:20

... dynamical, uniform, and field-driven stretch can be performed From the above idea, one can search a coordinate transformation for the bending purpose For the simplest bending case, one may consider the ... that due to the surface effects, the smaller the cross-sectional area the higher the Young’s modulus in the NWs without undergoing the phase transformation Chen and Chen [23] studied the Au NWs ... real system For example, Nose–Hoover algorithm [5–7], the synthetic thermostat variable generates the NVT ensemble more stably and efficiently than the rescaled velocity method [8], the latter...

Ngày tải lên: 22/06/2014, 00:20

... regarding the case λ = ∆−2 ) Before stating our main theorem we formally define the Markov chain for the Glauber dynamics For the purposes of the proof, the chain is defined on the set of all subsets of ... bounds on the mixing time of this modified dynamics imply bounds on the mixing time of the original Glauber dynamics (See the remark at the end of Section for a discussion regarding the case λ ... chain (roughly speaking, they consider the Glauber dynamics with an extra slide-type move) They prove O(n log n) mixing time of their dynamics for the same range of λ for all graphs Dyer and Greenhill...

Ngày tải lên: 07/08/2014, 06:22

... situated on the side of the species in the majority represented in the neighbourhood, the sessile oak The comparison of the mean values of the groups on the first axis of DFAa by means of the F-test ... analysis In the second case of the figure, the heterozygote deficit (f) must be considered The frequency of the phenotype A+ is the sum of the frequency of the genotype P : +/+ All of the 41 ied ... zone) which fell in the space of the other species The distribution of the seedlings on the first axis of DFAs is shown in figure 2a The group ped/ses had a bimodal distribution, the second peak...

Ngày tải lên: 08/08/2014, 18:21

... representative mass for this bin and the procedure is repeated for the next mass bin We assume that the variation of peak masses is normally distributed within the bin and therefore the procedure should ... I(mi) is the intensity of the peak having mass m i , I max is the intensity of the most abundant peak within the bin B and mavg is the intensity weighted average mass The average mass is then stored ... interpreted the datasets with LipidXplorer Within the series of successive MS experiments, mass accuracy of the Orbitrap analyzer was dependent only on the target resolution R; therefore, for matching the...

Ngày tải lên: 09/08/2014, 22:23