Molecular dynamics

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 340 154   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 9 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 8 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 11 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 29 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 27 2   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 39 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 21 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 40 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 37 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 41 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 53 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 48 1   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 46 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 54 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 37 4   Download

The physiological phenomenon that the antisweet taste effect of gymnemic acid (GA) is diminished by application of c-cyclodextrin (c-CD) to the mouth was evaluated at the molecular level using isothermal titration calorimetry, NMR and dynamic light scattering. These analyses showed that GA specifically binds to c-CD.

7p dell39 27-03-2013 48 4   Download

Although the chemical nature of the catalytic mechanism of the serine pro-tease a-chymotrypsin (a-CT) is largely understood, the influence of the enzyme’s structural dynamics on its catalysis remains uncertain. Here we investigate whether a-CT’s structural dynamics directly influence the kinet-ics of enzyme catalysis.

17p inspiron33 23-03-2013 31 3   Download

A comprehensive study of the hydration mechanism of an enzyme in non-aqueous media was done using molecular dynamics simulations in five organic solvents with different polarities, namely, hexane, 3-pentanone, diisopropyl ether, ethanol, and acetonitrile.

13p galaxyss3 19-03-2013 58 4   Download

Papillomaviruses are small DNA tumor viruses that infect mammalian hosts, with consequences from benign to cancerous lesions. The Early pro-tein 2 is the master regulator for the virus life cycle, participating in gene transcription, DNA replication, and viral episome migration.

11p galaxyss3 19-03-2013 33 3   Download