unifying molecular dynamics and electronic structure

... binding more favored than the WT (4 and 0.3 kcal/mol more nega-tive than the WT for PB and GB, respecnega-tively) This Fig 4 Structural and Molecular Dynamics of W67F and W67F-L105W mutants a Cartoon ... diversification related to substrate specificity and substrate binding Keywords: Structure-function prediction, Functional redundancy and diversification, Molecular dynamics, Acid protease, Eqolisin, Glutamic ... both sedolisins and eqolisins are typically active below pH 4, they are of fundamental and industrial interest Here we study the eqolisins by means of molecular evolution and dynamics, a study

Ngày tải lên: 25/11/2020, 14:24

... cluster II ranged from 0.13 (DCS79 and DCS 80) to 0.84 (DCS 60 and DPC 17) and cluster III ranged from 0.00 (DPC 14 and DPC 16) to 0.8 (JI 220 and DCS 38; DCS 16 and DCS 81) Cluster Ia consists ... collected from Andaman and Nicobar Islands, India However, large range of PIC values (0.07 - 0.73; 0.01- 0.62) but with a low mean value of 0.32 and 0.36 was observed by Qiu et al., (2010) and Senthilvel ... 14 and DPC 16) to 0.88 (DCS 25 and DCS 102; 48-1 and DPC 9) with an average of 0.48 The pairwise simple matching coefficients of Cluster I ranged from 0.2 (JI 336 and DCS 1)) to 0.75 (DCS 45 and

Ngày tải lên: 14/01/2020, 15:51

... of novel antifungal agents containing thiadiazole: synthesis and a combined similarity search, homology modelling, molecular dynamics and molecular docking study Mustafa Er1*, Abdulati Miftah Abounakhla1, ... investigate antifungal activities Similarity search, molecular dynamics and molecular docking were also studied to find out a potential target and enlighten the inhibition mechanism Results: As ... Homology modelling was used to construct the protein structure The stabilised protein structure obtained from molecular dynamics simulation was used in molecular docking organ-Conclusion: The overall

Ngày tải lên: 29/05/2020, 13:24

... International Publishing AG 2018 T Abdoun and S Elfass (eds.), Soil Dynamics and Soil-Structure Interaction for Resilient Infrastructure, Sustainable Civil Infrastructures, DOI 10.1007/978-3-319-63543-9_1 ... International Publishing AG 2018 T Abdoun and S Elfass (eds.), Soil Dynamics and Soil-Structure Interaction for Resilient Infrastructure, Sustainable Civil Infrastructures, DOI 10.1007/978-3-319-63543-9_2 ... homogeneous interspersed withlittle pebbles and sand Shale beds have completely altered to very plastic green yellowclay structure with sandwiched sand The structure is of variable depth of 13 to

Ngày tải lên: 28/08/2020, 13:40

... target for inflammation and cancer Methods: We used molecular docking and experimental approaches to investigate the docking potential and molecular effects of embelin to TACE and human cancer cell ... including MMPs, VEGF and hnRNP-K in breast cancer cells Conclusion: Based on the molecular dynamics and experimental data, embelin is proposed as a natural anti-inflammatory and anticancer drug ... growth and cancerous properties including colony forming efficacy, migration and invasion that were mediated by down regulation of MMP-2, MMP-9, VEGF and hnRNP-K proteins Methods Protein and ligand

Ngày tải lên: 14/10/2020, 17:02

... grain boundaries (GBs), dislocations, and point defects4 The importance of understanding the atomic structure and electronic behavior of such defects in elemental and compound semiconductors has long ... Hornstra30 and has been observed in classical simulations by Nandedkar and Narayan31 Type II dislocations contain eight-fold ring, as shown in Figure 2 Atomic structure of Type I and II dislocation ... crystal to identify the separate Cd and Te columns and obtained the atomic structure To build a periodic supercell, we juxtaposed the structure with its mirror image and created a dislocation dipole

Ngày tải lên: 19/11/2022, 11:42

... [BMIM]þ, with anions having structures allowing a systematic comparison of the changes in the electronic structure and size To examine the influence of changes in the electronic structure, we considered ... ZIF-8 and IL/ZIF-8 composites to dual-site Langmuir, Langmuir-Freundlich, and dual-site Langmuir-Freundlich models and calculated their ideal and mixture selectivities Ideal CO2/CH4, CO2/N2, and ... [CF3SO3] ; [MeSO4] ; and [OcSO4] ) were incorporated into ZIF-8 to demonstrate the impact of changes in the electronic structure and the size of the anion on the gas adsorption and separation performance

Ngày tải lên: 20/12/2022, 22:02

... receptor, ligand, and ligand-receptor complex exist in a state of equilib- rium • The receptor has a single binding site for the ligand • The ligand and receptor swiftly interact to create the ligand-receptor ... compact and soluble. Figure 2.3: Structure of 20 amino acids [2] structure Fibrous and globular proteins may exhibit one of four kinds of protein structures, namely primary, secondary, tertiary, and ... prescription opioids and heroin drug poisoning This analysis aims to explore the differences in the structures of opioid receptors (àOR) and their ligands, both biased and unbiased, to understand how these

Ngày tải lên: 25/03/2025, 10:41

... Electrostatic and vdW energy components (kcal/mol) for intermolecular (intermolecular interaction energies between chains of tetrameric structures) and solute−solvent interactions (intermolecular ... helix structure is lower than in REMD, and in both cases, the propensities are low (Tables 1and2) For 2NAO, the beta content is about 40 and 35% in Amber and OPLS, respectively (Table 2), and these ... results from Barz et al.52 (4833 and 5027 Å2) and Brown and Bevan49(∼5400 Å2) In the case of consistent values with the compact structure (4833 Å2) and extended structure (5027 Å2) from Barz et

Ngày tải lên: 13/01/2020, 07:30

... article GPR17: Molecular modeling and dynamics studies of the 3-D structure and purinergic ligand binding features in comparison with P2Y receptors Address: 1 Laboratory of Cellular and Molecular ... Elucidation of the structure of GPR17 and of ligand binding mechanisms are the necessary steps to obtain selective and potent drugs for this new potential target On this basis, a 3-D molecular model ... responding to ADP and ATP This group includes human and rodent P2Y1, P2Y12, and P2Y13, and human P2Y11; (2) uracil nucleotide-preferring receptors This group includes human P2Y4 and P2Y6 responding

Ngày tải lên: 02/11/2022, 10:45

... Initial structures for cis and trans azobenzene were built and optimized using theGAMESS package27and a 6-31G∗ basis set The resulting structures were compared withestablished crystal structures and ... the molecular dynamics techniques used to calculate molecularvolumes are introduced Chapter 3 outlines the calculation of the molecular volumes of water, the β-sheet peptide, and methane and ... innovative experimental procedureswith computational and theoretical investigations yields a microscopic understanding ofthe structure and dynamics that are difficult to interpret based on experimental

Ngày tải lên: 14/11/2014, 07:41

... Mitra and Bharati Sengupta, and my mother Mina Roy Chowdhury for being so awesome, caring and supporting My special thanks also go to three of my very close childhood friends Sandip Saha, Sandip ... Hexagonal graphene lattice and CNT unit cell 40 Figure 2.2: Molecular dynamics simulation set-up for CNT under uniaxial deformation/torsion 41 Figure 2.3: Molecular dynamics simulation set-up ... on cr and M cr Filled symbols denote cr and M cr values under clockwise torsion and open symbols denote cr and M cr values under anticlockwise torsion 101 Figure 5.1: Displacement and rotation

Ngày tải lên: 09/09/2015, 11:19

... Trang 1 MOLECULAR TRANSPORT AND STRUCTURE OF DNA IN A CONGESTED STATE ZHU XIAOYING NATIONAL UNIVERSITY OF SINGAPORE 2010 Trang 2 MOLECULAR TRANSPORT AND STRUCTURE OF DNA IN A ... Conclusions and future work 107 5.1 Conclusions 107 5.2 Recommendation of future research 109 References 113 Trang 8vi In this thesis, the molecular transportation properties and the structure ... as replication, recombination, and transcription of the genome (4，5) DNA is often in crowded conditions and condensed into compact structures (6, 7, 8) Compaction and condensation are fundamental

Ngày tải lên: 11/09/2015, 10:06

... 48-atoms, and 96-atoms supercells 27 3.3 The PBE (a) and HSE06 (b) band structure of anatase 29 3.4 The PBE conduction band with Nb and Ta fraction of 30 3.5 The HSE06 conduction band with ... has recently shown the better lattice stants and band structure (reproducing the band gap, changing the width of the con-duction band and valence band) than Perdew-Burke-Ernzerhof (PBE) approach.[70]Because ... higher and a band gap above 3eV Since the degenerately dopedwide band gap oxides can achieve these requirements, such transparent conductingoxides (TCOs) can be used in the optoelectronic and photovoltaic

Ngày tải lên: 13/05/2016, 10:15

... Note that the Type-I and Type-II* structures correspond to i = 0 and 5, and structures corresponding to 0o i o 5 are the transition structures between the Type-I and Type-II* structures Fig 5 displays ... will the geometric structure, electronic structure, and magnetic pro-perties of Mn4 molecules be controlled by substituting peripheral-ligand couple (L1,L2) Three kinds of ligand couple (L1,L2) ... influence of ligand substitutions on the geometric structure, electronic structure, and magnetic properties of Mn4single-molecule magnets (SMMs), in order to investigate the role of ligands in controlling

Ngày tải lên: 16/12/2017, 17:21

... roots of both A0and A00symmetries for HCSSH–HCOOH, 6 and 3 roots of A0 and A00 symmetries for HCOSH–HCSOH, 8 and 6roots of A0and A00symmetries for HCSOH–HCSOH, and 5and 3 roots of A0and A00symmetries ... morning ses-sions, two afternoon sessions, and two poster sessions, andtheir speakers and titles are shown inFigs 2,3, and4(forWednesday 27, Thursday 28, and Friday 29) The scientificpart of ESPA-2012 ... (CI), and oscillator strengths (f), for the low-lying excited states of the HCOSH–HCOSH dimer -1023.962576 Eh (A) and (B) denote the two identical dimer moieties ( ?) and (-) stand for positive and

Ngày tải lên: 13/03/2018, 14:45

... H13, H16, and H17 and group_2 follows: H3, H4, H7, H10, H14, and H15 (15) Neuraminidase also forms two groups, group_1 follows N1, N4, N5, and N8 and group_2 follows: N2, N3, N6, N7, and N9 The ... nano-spacer and haemagglutinin- KDN dimer connected by CH-N1 nano-spacer were studied using molecular dynamics simulation each for 20ns Materials and Methods Molecular docking Molecular docking ... nano-spacer and KDN coupled by CH-N1 nano-spacer show docking score (XPG) of -11.31 and -10.80 respectively and glide docking energy of -56.24 and -50.11 kcal/mol respectively (Table 2) Molecular dynamics

Ngày tải lên: 14/01/2020, 15:06

... OSi2 and 49.36 % OSi3 (Figure 4) The structure liquid sodium silicate consists of the structural units SiOx and OSiy At ambient pressure, the structure consists of SiO4, OSi2 and meanwhile the structure ... June 2020 Abstract: Molecular dynamics simulation of sodium-silicate has been carried out to investigate the microstructural transformation and diffusion mechanism The microstructure of sodium ... Transformation and Dynamical Properties in Sodium-silicate: Molecular Dynamics Simulation Nguyen Thi Thanh Ha1,*, Tran Thuy Duong1, Nguyen Hoai Anh2 1 Hanoi University of Science and Technology,

Ngày tải lên: 27/09/2020, 17:46

... Selection Molecular Dynamics (PaCS-MD) [Harada and Kitao, J Chem Phys (2011)] and other methods not listed here are used for this purpose Recently, Yamashita and Fujitani showed that protein structures ... Computational Biology and Medical Sciences Tran Phuoc Duy Trang 2Doctoral Thesis 学位論文Association and dissociation simulations of bio-molecular complex using parallel cascade selection molecular dynamics 並列カスケード選択分子動力学法による生体分子の会合・解離シミュレーション ... Molecular dynamics NPT ensemble: isothermal-isobaric ensemble NVT ensemble: canonical ensemble
 PaCS-MD: Parallel Cascade Selection Molecular Dynamics PaCS-MDx,y: Parallel Cascade Selection Molecular

Ngày tải lên: 28/01/2021, 21:07

... the p-nitroanilide (pNA) substrate Glycoconjugate modelling and molecular dynamics simulations For all molecular modelling and molecular dynamics (MD) simulation experiments the yasara suite of ... (2001) Effect of glycosylation 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 ... and K Griebenow Structural dynamics and serine protease catalysis Table Kinetic and thermodynamic parameters derived from amide H D exchange rates for a-CT and for the various lactose-a-CT and...

Ngày tải lên: 19/02/2014, 05:20