Intermittent permeation of cylindrical nanopores by water

Molecular Dynamics simulations of water molecules in nanometre sized cylindrical channels connecting two reservoirs show that the permeation of water is very sensitive to the channel radius and to electric polarization of the embedding material. At threshold, the permeation is {\emph{intermittent}} on a nanosecond timescale, and strongly enhanced by the presence of an ion inside the channel, providing a possible mechanism for gating. Confined water remains surprisingly fluid and bulk-like. Its behaviour differs strikingly from that of a reference Lennard-Jones fluid, which tends to contract into a highly layered structure inside the channel.Comment: 4 pages, 4 figure

Response to letter regarding “Evidence of natural occurence of the banned antibiotic chloramphenicol in herbs and grass”

# The Author(s) 2011. This article is published with open access at Springerlink.com We were surprised to read that the natural occurrence of chloramphenicol (CAP) was reported as long ago as 2003 by Hanekamp et al. [1]. We missed that information, probably because their findings were not published in a peer-reviewed journal. In our paper [2], we did not claim to be the first to suggest the natural occurrence of CAP; on the contrary, we included several references from earlier studies. We stated that our paper was the first to describe the detection of CAP in plant materials, sample material which had not been addressed before. Furthermore, there is an important issue which is not raised by Hanekamp et al. and that is the issue of ‘criteria for confirmation of the identity of a compound’. InEU legislation, viz. Commission Decision 2002/657/EC, it i

Magnetic friction due to vortex fluctuation

We use Monte Carlo and molecular dynamics simulation to study a magnetic tip-sample interaction. Our interest is to understand the mechanism of heat dissipation when the forces involved in the system are magnetic in essence. We consider a magnetic crystalline substrate composed of several layers interacting magnetically with a tip. The set is put thermally in equilibrium at temperature T by using a numerical Monte Carlo technique. By using that configuration we study its dynamical evolution by integrating numerically the equations of motion. Our results suggests that the heat dissipation in this system is closed related to the appearing of vortices in the sample.Comment: 6 pages, 41 figure

On "the complete basis set limit" and plane-wave methods in first-principles simulations of water

Water structure, measured by the height of the first peak in oxygen-oxygen radial distributions, is converged with respect to plane-wave basis energy cutoffs for ab initio molecular dynamics simulations, confirming the reliability of plane-wave methods.Comment: 9 pages, 3 figure

Long range molecular dynamics study of regulation of eukaryotic glucosamine-6-phosphate synthase activity by UDP-GlcNAc

Glucosamine-6-phosphate (GlcN-6-P) synthase catalyses the first and practically irreversible step in hexosamine metabolism. The final product of this pathway, uridine 5’ diphospho N-acetyl-D-glucosamine (UDP-GlcNAc), is an essential substrate for assembly of bacterial and fungal cell walls. Moreover, the enzyme is involved in phenomenon of hexosamine induced insulin resistance in type II diabetes, which makes it a potential target for antifungal, antibacterial and antidiabetic therapy. The crystal structure of the isomerase domain of GlcN-6-P synthase from human pathogenic fungus Candida albicans, in complex with UDP-GlcNAc has been solved recently but it has not revealed the molecular mechanism of inhibition taking place under UDP-GlcNAc influence, the unique feature of the eukaryotic enzyme. UDP-GlcNAc is a physiological inhibitor of GlcN-6-P synthase, binding about 1 nm away from the active site of the enzyme. In the present work, comparative molecular dynamics simulations of the free and UDP-GlcNAc-bounded structures of GlcN-6-P synthase have been performed. The aim was to complete static X-ray structural data and detect possible changes in the dynamics of the two structures. Results of the simulation studies demonstrated higher mobility of the free structure when compared to the liganded one. Several amino acid residues were identified, flexibility of which is strongly affected upon UDP-GlcNAc binding. Importantly, the most fixed residues are those related to the inhibitor binding process and to the catalytic reaction. The obtained results constitute an important step toward understanding of mechanism of GlcN-6-P synthase inhibition by UDP-GlcNAc molecule

Follow-up of curatively treated cancer in primary care:a qualitative study of the views of Dutch GPs

BACKGROUND: Follow-up for cancer typically occurs in secondary care, and improved survival has increased demands on these services. Other care models may alleviate this burden, such as moving (parts of) follow-up care for curatively treated patients from secondary to primary care (care substitution). AIM: To explore the opinions of GPs regarding the potential benefits, barriers, and requirements of care substitution for breast and colorectal cancer. DESIGN AND SETTING: A qualitative study of the opinions of purposively sampled GPs in Dutch primary care. METHOD: Focus group sessions and individual semi-structured interviews were recorded and transcribed verbatim. Data were analysed by two independent researchers using thematic analysis. RESULTS: Two focus groups (n = 14) were conducted followed by nine individual interviews. Three main themes were identified: perceived benefits, perceived barriers, and perceived requirements. Perceived benefits included better accessibility and continuity of care, and care closer to patients' homes. Uncertainty about cancer-related competences and practical objections were perceived as barriers. Requirements included close specialist collaboration, support from patients for this change, and stepwise implementation to avoid loss of existing care quality. CONCLUSION: Most GPs reported that they were not in favour of complete care substitution, but that primary care could have greater formal involvement in oncological follow-up if there is close collaboration with secondary care (that is, shared care), support from patients, sufficient resource allocation, stepwise implementation with clear guidelines, and monitoring of quality. Clear and broadly supported protocols need to be developed and tested before implementing follow-up in primary care