why ab initio molecular dynamics

Ngày tải lên: 14/11/2014, 13:35

... of the system’s electron density A molecular electronic device is an open molecular system and cannot be directly dealt with ab initio methods such as DFT The molecular electronic device can be ... Nomenclature List of Figures Chapter Introduction 1.1 The End of Roadmap 1.2 Molecular Electronics 1.3 Ab Initio Methods for Molecular Electronic Device Simulation 1.4 Overview Chapter Density Functional ... characteristics of two-terminal molecular electronic devices which are the fundamental structures to design multi-terminal molecular electronic systems, an ab initio method based on density functional...

Ngày tải lên: 05/10/2015, 19:03

... production of Ab [43,44] The p3 peptide and Ab differ by only the absence or presence of these 16 N-terminal residues, and p3 is nontoxic, whereas Ab is neurotoxic The toxicity of Ab has been proposed ... dynamic behavior of Ab Because Ab unfolds to a much greater extent than melittin, thus interacting with more lipids, it is able to cause greater disruption of canonical lipid dynamics and orientation ... the Ab- DPPC systems, giving starting configurations comparable to those presented in the original studies Details of these systems are presented in Table The initial asymmetric orientation of Ab...

Ngày tải lên: 18/02/2014, 08:20

... conuence of 1020% on LAB-TEK chambered coverslips with eight wells (Nalge Nunc International, Naperville, IL, USA) for 12 h before transfection DMEM (20 lL) and FuGENE (1.2 lL; Roche Molecular Biochemicals, ... BMC Dev Biol 7, 3, doi:10.1186/1471-213X-7-3 Schwille P, Haupts U, Maiti S & Webb WW (1999) Molecular dynamics in living cells observed by uorescence correlation spectroscopy with one- and twophoton ... spectroscopy (FCS) and uorescence recovery after photobleaching (FRAP) are often used to assess the dynamics and kinetic properties of proteins in living cells [1219] FCS detects the uctuations of...

Ngày tải lên: 18/02/2014, 16:20

... p-nitroanilide (pNA) substrate Glycoconjugate modelling and molecular dynamics simulations For all molecular modelling and molecular dynamics (MD) simulation experiments the yasara suite of programs ... on structure and dynamics of MHC class I glycoprotein: a molecular dynamics study Biopolymers 59, 1123 Mukhopadhyay C (1998) Molecular dynamics simulation of glycoprotein-glycans of immunoglobulin ... protein dynamics in enzyme stability The case of glucose oxidase FEBS Lett 506, 216220 67 Tsai AM, Udovic TJ & Neumann DA (2001) The inverse relationship between protein dynamics and thermal stability...

Ngày tải lên: 19/02/2014, 05:20

... sulfoxide calculated using molecular dynamics simulation J Am Chem Soc 117, 4363–4366 53 Berendsen, H.J.C., Postma, J.P.M., DiNola, A & Haak, J.R (1984) Molecular dynamics with coupling to an ... solvents because of the absence of the above interactions Sequence alignment of MBP(74–85) with several species of MBP indicates the important role of Arg78, firstly in the stabilization of local ... a message-passing parallel molecular dynamics implementation Comp Phys Commun 91, 43–56 49 Lindahl, E., Hess, B & van der Spoel, D (2001) GROMACS 3.0: a package for molecular simulation and trajectory...

Ngày tải lên: 07/03/2014, 16:20

... this context, molecular dynamics (MD) simulations have been carried out on PNAÆDNA and DNA duplexes, formed out of a sequence present in the Ki-ras proto-oncogene, in the presence and absence of ... the hydrogen bond (Fig 5) These clearly indicate the absence of a stable hydrogen bond for the A24 C7 mismatch in PDwt In sharp contrast, a stable N1(A24) N4(C7) hydrogen bond (Fig 6B) prevails ... points to the greater changeability and destabilization of the A C mismatch hydrogen bond in PNAÆDNA than in DNA duplex As expected, these bring forth significant variableness in the water interactions...

Ngày tải lên: 07/03/2014, 21:20

... liệu Phương pháp ab initio dựa sở phương trình để xác định tính chất vật liệu công cụ hữu hiệu cho nhà nghiên cứu Sự đột phá khoa học vật liệu tính toán nói chung phương pháp ab initio nói riêng ... tính chất điện tử vật liệu nano diamondoids (C10H16C87H76) phương pháp ab initio" Để thực mục đích trên, phương pháp mô ab initio sở lý thuyết phiếm hàm mật độ (DFT), tiến hành nghiên cứu nội dung ... độ, 24 phương pháp ab initio phương pháp không sử dụng tham số bên [73], phương pháp bán thực nghiệm thực nghiệm [71] sở tương tác khớp với thực nghiệm hay với phương pháp ab initio THỜI GIAN Phương...

Ngày tải lên: 12/03/2014, 12:08

... Miller JL, Fox T, Darden TA & Kolman PA (1995) Molecular dynamics simulation on solvated biomolecular systems: the particle mesh Ewald method leads to stable trajectories of DNA, RNA and proteins ... with constraints: molecular dynamics of n-alkanes J Comput Phys 23, 327–341 39 Berendsen HJC, van der Spool D & van Drunen R (1995) GROMACS: a message-passing parallel molecular dynamics implementation ... (Table 2) in electrostatically favorable positions Optimization and relaxation of solvent and ions were initially performed by means of three energy minimizations and two MD simulations (Table...

Ngày tải lên: 16/03/2014, 10:20

... scale of molecular dynamics set by the atomic motion One consequence of the short time scale is that very high strain rates are required to get any reasonable deformation within the available time ... increase linearly with increasing temperature and change abruptly near the melting region The melting temperature Tm is defined as the point of an abrupt change in the potential energies for the heating ... nanowire finally collapses, which indicates the melting of the nanowire Conclusions In this paper, molecular dynamics simulations with Stillinger–Weber potentials are used to simulate the tensile and...

Ngày tải lên: 16/03/2014, 15:18

... dramatically increased molecular dynamics simulations compared to other currently available resources Over the past year (October 1, 2010 – September 30, 2011), DESRES has made available to the non-commercial ... specially designed for molecular dynamics simulations These special capabilities allow multi-microsecond to millisecond simulation timescales, which previously had been unobtainable The program seeks ... 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, Second Round Board on...

Ngày tải lên: 16/03/2014, 15:20

... interactions ther by ab initio quantum chemical methods It is clear that Nt can fit into the minor groove of the CAATTG tract, making contact with the bulky amino G9, but without destabilizing the binding ... guanidinium end fragments of Nt and proximal bases were investigated using ab initio quantum chemical calculations Intermolecular positions of the appropriate fragments were kept frozen based on ... interactions 44 Hobza P & Sponer J (1999) Structure, energetics, and dynamics of the nucleic acid base pairs: nonempirical ab initio calculations Chem Rev 99, 3247–3276 45 Sponer J, Leszczynski...

Ngày tải lên: 16/03/2014, 22:20

... alpha-lactalbumin by molecular dynamics simulation J Mol Biol 306, 329–347 Marchi M & Ballone P (1999) Adiabatic bias molecular dynamics: a method to navigate the conformational space of complex molecular ... i.e the native state is relatively stable with the implicit solvation method employed Following this, a ns simulation was performed using biased molecular dynamics, with a perturbation increasing ... Program Departments of Biochemistry and Molecular Biology, University College London, London Supplementary material available The following material is available for this article online: Fig S1...

Ngày tải lên: 16/03/2014, 23:20

... for molecular dynamics simulation of systems of arbitrary shape, Computer Physics Communications 144 (2002) 141 [4] J.A Lupo, Z.Q Wang, A.M McKenney, R Pachter, W Mattson, A large scale molecular ... that appropriate value of radius b is about 6.0, for particles inside a cell with side length 1.0 Anderson specified in his paper [12] that a should be about 0.4 Nguyen Hai Chau / VNU Journal ... (5)), and then the force evaluation stage is totally done on GRAPE (see table 2) Procedure of A2P conversion is as follows Table Mathematical expressions and operations used in the code B Bold parts...

Ngày tải lên: 22/03/2014, 11:20

... shown in Table The PDB [51] codes for the new structures are: sulfate_2 (2ptw), sulfate_3 (2ptx), PEP (2pty), PAH_1 (1ptz), PAH_2 (2pu0) and FPAH (2pu1) Molecular dynamics Molecular dynamics simulations ... allowed us to visualize to what extent the resulting modes of conformational variability were explored during molecular dynamics simulations (see later) The positions of the six new structures projected ... Fig (A) Projections of the six new crystal structures and molecular dynamics trajectories on to EVs and resulting from the essential dynamics analysis Blue circles are used for sulfate structures...

Ngày tải lên: 23/03/2014, 07:20

... • Obtain a rough overview about molecular structures and properties • Quickly pre-optimize structures for higher-level ab- initio calculations • Generate reasonable molecular structures for presentations ... http://www.scl.ameslab.gov/MacMolPlt J Mol Graphics Mod., 16, 1998, 133-138, [4] ArgusLab 4.0.1, Mark A Thompson, Planaria Software LLC, Seattle, WA, http://www.arguslab.com [5] The Role of Databases in ... all information about the VIBRATIONal modes and frequencies The vibrations can be visualized in the visualization program Molden (somewhat awkward in Windows) 7.3.3 High-level ab initio methods...

Ngày tải lên: 28/04/2014, 10:38

... some metal processing such as laser ablation, plasma processing, and ion deposition, the material could be heated to thermodynamic states close to or even above the critical point, and phase ... often very high and therefore are difficult to be measured accurately In this work, we use the molecular dynamics (MD) technique, a first principles method, to estimate the critical point and the phase ... the potential functions determining interatomic interactions are known NUMERICAL APPROACH In molecular dynamics (MD) simulations, interactions between molecules or atoms in a material are determined...

Ngày tải lên: 06/05/2014, 08:54

... Quantum molecular dynamics study on light-to-heat absorption mechanism: Two metallic atom system, Int J Heat Mass Transfer 40 (1997) 3209– 3222 [5] M Shibahara, S Kotake, Quantum molecular dynamics ... dynamics study of light-to-heat absorption mechanism in atomic systems, Int J Heat Mass Transfer 41 (1998) 839–849 [6] P.L Silvestrelli, M Parrinello, Ab initio molecular dynamics simulation of laser ... pulse laser ablation of silicon: An MD simulation study, Appl Phys A 66 (1998) 35–42 [10] E Ohmura, I Fukumoto, I Miyamoto, Modified molecular dynamics simulation on ultrafast laser ablation of...

Ngày tải lên: 06/05/2014, 08:54

... 300 K through a so-called “quenching” procedure [10] The structure of the Molecular dynamics simulation of ultrafast laser ablation of fused silica film obtained fused silica is analyzed and agrees ... of 5.4 J/cm2 (absorbed fluence 0.1 J/cm2 ) The temperature at 40 ps is about 16,000 K, as shown in Fig 4b (mass center velocity removed) Conclusion In conclusion, ultrafast laser ablation of fused ... ultrafast laser ablation of fused silica is simulated using the molecular dynamics technique Ionization and generation of free electrons, absorption of the laser energy by free electrons, and energy...

Ngày tải lên: 06/05/2014, 08:54

... II–Te II 0.066 2.876 4.312 5.0 Molecular dynamics studies of ultrafast laser-induced nonthermal melting Fig Snapshots of atomic distributions of (a) laser heating with absorbed laser fluence of 13.1 ... the laser energy is absorbed by electrons at time t = 0, and then the energy deposited into electrons is transferred to the lattice exponentially At time t, the laser energy absorbed between z ... phonon excitation, corresponding to absorbed fluence 13.1 J/m2 E = AF t τ exp(−t/τ ) exp(−z/δ) − exp −(z + z)/δ (2) where A is the illuminated area, F is the absorbed laser fluence, and t is the...

Ngày tải lên: 06/05/2014, 08:54