Water self-diffusion within human aquaporin 4 has been studied using molecular dynamics (MD) simulations in the absence and presence of external ac and dc electric fields. The computed diffusive (p(d)) and osmotic (p(f)) permeabilities under zero-field conditions are (0.718 ± 0.24) × 10(-14) cm(3) s(-1) and (2.94 ± 0.47) × 10(-14) cm(3) s(-1), respectively; our p(f) agrees with the experimental value of (1.50 ± 0.6) × 10(-14) cm(3) s(-1). A gating mechanism has been proposed in which side-chain dynamics of residue H201, located in the selectivity filter, play an essential role. In addition, for nonequilibrium MD in external fields, it was found that water dipole orientation within the constriction region of the channel is affected by electric fields (e-fields) and that this governs the permeability. It was also found that the rate of side-chain flipping motion of residue H201 is increased in the presence of e-fields, which influences water conductivity further.

Spontaneous supercrystal organisation of semiconductor nanorods (CdS and CdSe) of different aspect ratios into ordered superstructures was obtained by controlled evaporation of a nanorod solution. The rods either align into two dimensional close packed perpendicular arrays or into one dimensional rail tracks depending on the total interaction energy between the rods in solution. A detailed study has 10 identified critical factors that affect this interaction energy such as nanorod concentration, surface charge, dipole moment and solvent nature (polarity and volatility), thereby allowing a general approach to control the nature of nanorod assembly (1D or 2D). Molecular dynamics (MD) of small charged nanorods showed that opposite dipolar alignment (antiferromagnetic) was the preferred rod orientation during selfassembly.15

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Connexins (Cxs) are a family of vertebrate proteins constituents of gap junction channels (GJCs) that connect the cytoplasm of adjacent cells by the end-to-end docking of two Cx hemichannels. The intercellular transfer through GJCs occurs by passive diffusion allowing the exchange of water, ions, and small molecules. Despite the broad interest to understand, at the molecular level, the functional state of Cx-based channels, there are still many unanswered questions regarding structure-function relationships, perm-selectivity, and gating mechanisms. In particular, the ordering, structure, and dynamics of water inside Cx GJCs and hemichannels remains largely unexplored. In this work, we describe the identification and characterization of a believed novel water pocket-termed the IC pocket-located in-between the four transmembrane helices of each human Cx26 (hCx26) monomer at the intracellular (IC) side. Using molecular dynamics (MD) simulations to characterize hCx26 internal water structure and dynamics, six IC pockets were identified per hemichannel. A detailed characterization of the dynamics and ordering of water including conformational variability of residues forming the IC pockets, together with multiple sequence alignments, allowed us to propose a functional role for this cavity. An in vitro assessment of tracer uptake suggests that the IC pocket residue Arg-143 plays an essential role on the modulation of the hCx26 hemichannel permeability.

Water-self-diffusion through single-walled carbon nanotubes (SWCNTs) inserted normal to a phospholipid membrane has been studied using equilibrium and nonequilibrium molecular dynamics simulations in the presence of static and alternating electrical fields. Four different SWCNTs were investigated: (5,5), (6,6), (8,8), and (11,11) and also three arrays of four (6,6) SWCNTs separated by 15, 20, and 25 A, respectively. The (5,5) system shows interesting behavior, where an increase in the applied field frequency in the z direction decreases the water permeation rates, reaching values at higher frequencies similar to zero-field conditions. The (6,6) arrays simulations demonstrated that there is a friction effect, when the nanotubes are closely packed, which retards the movement of the individual water files.

Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a visual molecular dynamics (VMD) plugin to facilitate the study of RINs using trajectories obtained from MD simulations of proteins. Our software generates RINs from MD trajectory files. The non-covalent interactions defined by RIP-MD include H-bonds, salt bridges, VdWs, cation-π, π–π, Arginine–Arginine, and Coulomb interactions. In addition, RIP-MD also computes interactions based on distances between Cαs and disulfide bridges. The results of the analysis are shown in an user friendly interface. Moreover, the user can take advantage of the VMD visualization capacities, whereby through some effortless steps, it is possible to select and visualize interactions described for a single, several or all residues in a MD trajectory. Network and descriptive table files are also generated, allowing their further study in other specialized platforms. Our method was written in python in a parallelized fashion. This characteristic allows the analysis of large systems impossible to handle otherwise. RIP-MD is available at .

Human aquaporin 4 has been studied using non-equilibrium molecular dynamics simulations in the absence and presence of pulses of external electric fields. The pulses were 100 ns in duration and 0.005–0.015 V/Å in intensity acting along the pores’ axes. Water diffusivity and the dipolar response of various residues of interest within the pores have been studied. Results show relatively little change in levels of water permeability per se within aquaporin channels during axially oriented field impulses, although care must be taken with regard to statistical certainty. However, the spatial variation of water permeability vis-à-vis electric-field intensity within the milieu of the channels, as revealed by heterogeneity in diffusivity-map gradients, indicates the possibility of somewhat enhanced diffusivity, owing to several residues being affected substantially by external fields, particularly for HIS 201 and 95 and ILE 93. This has the effect of increasing slightly intra-pore water diffusivity in the “pore-mouths” locale, albeit rendering it more spatially uniform overall vis-à-vis zero-field conditions (via manipulation of the selectivity filter).

Molecular mechanisms of electrophoretic deposition (EPD) of P3DT poly(3-decylthiophene) molecules onto vertically aligned cadmium selenide arrays have been studied using large-scale, nonequilibrium molecular dynamics (MD), in the absence and presence of static external electric fields. The field application and larger polymer charges accelerated EPD. Placement of multiple polymers at the same lateral displacement from the surface reduced average deposition times due to "crowding", giving monolayer coverage. These findings were used to develop and validate Brownian dynamics simulations of multi-layer polymer EPD in scaled-up systems with larger inter-rod spacings, presenting a generalised picture in qualitative agreement with random sequential adsorption.