A Comprehensive Exploration of the Conformational and Energetic Landscape of a Rotaxane System: A Molecular Dynamics Study

Rotaxanes are composed of a dumbbell shaped molecule threaded through a ring shaped macrocycle; see Figure1. Rotaxanes are used in molecular machines due to the thread’s ability to rotate (pirouette) within the macrocycle. This rotation is often coupled with a shuttling movement as well making them especially useful. Unfortunately, rotaxanes are extremely difficult to synthesize, making it a challenge to study them. By being able to study them using molecular dynamics, one can predict their conformational energies before having to create them. In a previous study, energy barrier values were found for three DAP based rotaxane pirouettes using NMR spectroscopy. Our study looked at two of the previous study’s DAP based rotaxanes (figures 2 and 3). We intend to show that molecular dynamics is a viable approach to calculating energy barriers of rotaxane pirouettes

Competition between hydrogen bonding and electric field in single-file transport of water in carbon nanotubes

Recent studies have shown the possibility of water transport across carbon nanotubes, even in the case of nanotubes with small diameter (0.822 nm). In this case, water shows subcontinuum transport following an ordered 1D structure stabilized by hydrogen bonds. In this work, we report MD simulations describing the effect of a perpendicular electric field in this single-file water transport in carbon nanotubes. We show that water permeation is substantially reduced for field intensities of 2-3 V/nm and it is no longer possible under perpendicular fields of 4 V/nm.Comment: Accepted in Molecular Simulatio

Valid and efficient formula for free energy difference from nonequilibrium work

Atomic force microscopes and optical tweezers afford direct probe into the inner working of single biomolecules by mechanically unfolding them.^1-15^ Critical to the success of this type of probe is to correctly extract the free energy differences between the various conformations of a protein/nucleic acid along its forced unfolding pathways. Current studies rely on the Jarzynski equality^16^ (JE) or its undergirding Crooks fluctuation theorem^17^ (CFT), even though questions remain on its validity^17-19^ and on its accuracy.^13,20-21^ The validity of JE relies on the assumption of microscopic reversibility.^17,18^ The dynamics of biomolecules, however, is Langevin stochastic in nature. The frictional force in the Langevin equation breaks the time reversal symmetry and renders the dynamics microscopically irreversible even though detailed balance holds true. The inaccuracy of JE has largely been attributed to the fact that one cannot sample a large enough number of unfolding paths in a given study, experimental or computational.^13,15^ Here I show that both of these questions can be answered with a new equation relating the nonequilibrium work to the equilibrium free energy difference. The validity of this new equation requires detailed balance but not microscopic reversibility. Taking into the new equation equal number of unfolding and refolding paths, the accuracy is enhanced ten folds in comparison to a JE study based on a similar but larger number of unfolding paths

Single-Base DNA Discrimination via Transverse Ionic Transport

We suggest to discriminate single DNA bases via transverse ionic transport, namely by detecting the ionic current that flows in a channel while a single-stranded DNA is driven through an intersecting nanochannel. Our all-atom molecular dynamics simulations indeed show that the ionic currents of the four bases are statistically distinct, thus offering another possible approach to sequence DNA.Comment: 5 pages, 3 figure

Oblique shock wave effects on biological membranes

This paper was presented at the 3rd Micro and Nano Flows Conference (MNF2011), which was held at the Makedonia Palace Hotel, Thessaloniki in Greece. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, Aristotle University of Thessaloniki, University of Thessaly, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute.In the present study the effects of oblique shock waves on the lateral diffusion coefficients of a 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) biological membranes through molecular dynamics simulations are being under examination. Computational simulations have been carried out by utilising the NPT ensemble with shock impulses varying from 0.33mPa s to 100mPa s. The applied incident angles vary between 0° and 80° corresponding to the perpendicular and almost tangential case respectively. It is shown that the membrane thickness gets thinner under the application of a shock. The area per lipid is also reduced, while the volume increases in the beginning of the application of the shock and afterwards it reduces until it gets to the same values that correspond to the equilibrium state