Molecular dynamics

This study focuses on investigating the effect of negative pressure on the structure and diffusion processes of Silicon dioxide at liquid nitrogen temperature. The insights gained from this study will serve as a foundation for future experimental research aimed at the development and manufacturing of advanced materials.

11p viengfa 28-10-2024 2 2   Download

The structural and density heterogeneity of the liquid 3Al2O3.2SiO2 (l-3Al2O3.2SiO2) system was studied using Molecular Dynamics (MD) and Monte Carlo (MC) simulations. The results showed that the structural phase transition occurred at an oxygen packing factor of approximately 0.58.

8p vimitsuki 30-03-2025 6 0   Download

In this research, Molecular Dynamics (MD) simulations were conducted to explore the temperature effect on the microstructure and phase transition of the Ag0.25Au0.75 alloy. The findings reveal that as the temperature rises, the material's phase transition switches from crystalline to liquid and vice versa.

9p viengfa 28-10-2024 6 1   Download

This study aims to generate the system of histone deacetylase enzymes (HDAC) with its cofactor zinc ion using two different parameter models and application of molecular dynamic (MD) study for structure of HDAC2 and vorinostat ligand. Materials and methods: Two non-bonded models, including 12-6-4 Lennard-Jones and cationic dummy atom, were applied for building a solvation system of HDAC2 crystal structure with presence of suber-anilohydroxamic acid (SAHA) and zinc ion.

9p vihyuga 04-03-2025 4 1   Download

Is a branch of polymer science dealing with analysis and characterisation of polymers. üThe complication of macromolecular chains, the dispersion in molecular weight, tacticity, crystallinity, orientation, composition of polymers etc. and complex morphological systems ⇒ analysis of polymer ≠ the small organic materials ⇒ Focus on viscoelastic properties, dynamic mechanical testing.

114p buitiendung87 06-01-2011 347 154   Download

In this thesis atomistic level modelling is conducted to investigate the design of an environmentally adaptable self-cleaning polymer paint coating that incorporates biomimetics to remain clean in various environmental setting. This work will be used to aid in the development of stay-clean polymer paint coating.

116p runthenight07 01-03-2023 11 3   Download

In this Masters thesis computational modelling techniques were employed to investigate iron-free apo-Lactoferrin (apo-Lf) structural conformation changes in the presence of variant temperature and pH. These conditions represent the environment most milk protein goes through in food processing and the production of food products.

162p runthenight04 02-02-2023 9 3   Download

The thesis is structured as follows: In Chapter 1, the scientific literature is summarized within the scope of this study. Chapter 2 provides a comprehensive overview of the principles of the applied computational approaches in this study. Chapter 3 identifies the important residues of the LsIA/α7 nAChR complex that affect the interactions between the toxin and the membrane protein due to C-terminal carboxylation of LsIA. The effects of C-terminal modification of LsIA on interactions with α3β2 nAChR, involved in cardiovascular diseases, were also investigated in Chapter 4.

234p runthenight04 02-02-2023 14 3   Download

In this paper a molecular dynamics simulation of nano-metric cutting of copper with a diamond tool is presented. MD simulations require the determination of the interaction of the involved atoms through a function of potential for the materials involved in the analysis and the accurate topography of the studied area, leading to high demand of computational time.

12p tohitohi 19-05-2020 30 1   Download

In  Molecular simulation of nanoparticle diffusion at fluid interfaces molecular dynamics simulations are used to exam- ine the transport properties of a nanoparticle in both bulk solvent and at a liquid–liquid interface. Specifically it aims to address the effect of interfacial adsorption on the diffusion of nanoparticles (at low concentration).

5p hoquangbio 22-07-2015 31 3   Download

Gomesin is the first peptide isolated from spider exhibiting antimicrobial activities. This highly cationic peptide is composed of 18 amino-acid residues including four cysteines forming two disulfide linkages. The solution structure of gomesin has been determined using proton two-dimensional NMR (2D-NMR) and restrained molecular dynamics calculations. The global fold of gomesin consists in a wellresolved two-stranded antiparallel b sheet connected by a noncanonical b turn.

9p research12 01-06-2013 42 3   Download

Two-dimensional NMR and molecular dynamics simula-tions have been used to determine the three-dimensional structures of two hairpin DNA structures: d-CTAGAG GATCCUTTTGGATCCT (abbreviated as U1-hairpin) and d-CTAGAGGATCCTTUTGGATCCT (abbreviated as U3-hairpin). The 1 H resonances of both of these hairpin structures have been assigned almost completely.

9p research12 23-04-2013 23 3   Download

DNA ligases are the enzymes responsible for the repair of single-strandedanddouble-strandednicks indsDNA.DNA ligases are structurally similar, possibly sharing a common molecular mechanism of nick recognition and ligation catalysis. This mechanism remains unclear, in part because the structure of ligase in complex with dsDNAhas yet to be solved.DNA ligases share common structural elementswith DNA polymerases, which have been cocrystallized with dsDNA. Based on the observed DNA polymerase–dsDNA interactions, we propose a mechanism for recognition of a single-stranded nick by DNA ligase....

7p tumor12 22-04-2013 43 2   Download

Thyroid hormone has various effects on cell proliferation, growth and apoptosis. To gain more insight into the molecular dynamics caused by thyroid hormone, gene expression in HeLaTRcells that constitutively over-expressed the thyroid hormone receptor (TR) was analyzed. Gene expression profiling of the HeLaTRcells with an oligonucleotide microarray yielded 229 genes whose expression was significantly altered by T3.

10p fptmusic 16-04-2013 40 4   Download

Retinol-binding protein transports retinol, and circulates in the plasma as a macromolecular complex with the protein transthyretin. Under acidic con-ditions retinol-binding protein undergoes a transition to the molten globule state, and releases the bound retinol ligand. A biased molecular dynamics simulation method has been used to generate models for the ensemble of conformers populated within this molten globule state.

13p fptmusic 12-04-2013 44 3   Download

The low affinity of peptide nucleic acid (PNA) to hybridize with DNA in the presence of a mismatch endows PNA with a high degree of discriminat-ory capacity that has been exploited in therapeutics for the selective inhibi-tion of the expression of point-mutated genes. To obtain a structural basis for this intriguing property, molecular dynamics simulations are carried out on PNAÆDNA duplexes formed at the Ki-ras proto-oncogene, compri-sing the point-mutated (GAT), and the corresponding wild-type (GGT) codon 12. ...

16p fptmusic 11-04-2013 56 2   Download

Many organelle enzymes coded for by nuclear genes have N-terminal sequences, which directs them into the organelle (precursor) and are removed upon import (mature). The experiments described below charac-terize the differences between the precursor and mature forms of water-melon glyoxysomal malate dehydrogenase. Using recombinant protein methods, the precursor (p-gMDH) and mature (gMDH) forms were puri-fied to homogeneity using Ni 2+ –NTA affinity chromatography.

0p awards 05-04-2013 52 2   Download

The NMR solution structures of NTX-1 (PDB code 1W6B and BMRB 6288), a long neurotoxin isolated from the venom ofNaja naja oxiana, and the molecular dynamics simulation of these structures are reported. Calculations are based on 1114NOEs, 19 hydrogen bonds, 19 dihedral angle restraints and secondary chemical shifts derived from 1 Hto 13 C HSQC spectrum. Similar to other long neurotoxins, the three-finger like structure shows a double and a triple strandedb-sheet aswell as some flexible regions, particularly at the tip of loop II and the C-terminal tail....

0p awards 05-04-2013 50 2   Download

Experimental autoimmune encephalomyelitis can be induced in susceptible animals by immunodominant deter-minants of myelin basic protein (MBP). To characterize the molecular features of antigenic sites important for designing experimental autoimmune encephalomyelitis suppressing molecules, we report structural studies, based on NMR experimental data in conjunction with molecular dynamic simulations, of the potent linear dodecapeptide epitope of guinea pig MBP, Gln74-Lys75-Ser76-Gln77-Arg78-Ser79-Gln80-Asp81-Glu82-Asn83-Pro84-Val85 [MBP(74–85)], and its antagonist analogue Ala81MBP(74–85)....

15p awards 05-04-2013 56 3   Download

The catalytic competence of the natural thrombin mutant with deletion of the Lys9 residue in the A-chain (DK9) was found to be severely impaired, most likely due to modification of the 60-loop conformation and catalytic triad geometry, as supported by long molecular dynamics (MD) simula-tions in explicit water solvent.

11p dell39 27-03-2013 40 4   Download