Earlier Molecular Dynamics Research Articles

Atomistic modeling of electromechanical properties of piezoelectric zinc oxide nanowires

Currently, numerous articles are devoted to examining the influence of geometry and charge distribution on the mechanical properties and structural stability of piezoelectric nanowires (NWs). The varied modeling techniques adopted in earlier molecular dynamics (MD) works dictated the outcome of the different efforts. In this article, comprehensive MD studies are conducted to determine the influence of varied interatomic potentials (partially charged rigid ion model, [PCRIM] ReaxFF, charged optimized many-body [COMB], and Buckingham), geometrical parameters (cross-section geometry, wire diameter, and length), and charge distribution (uniform full charges versus partially charged surface atoms) on the resulting mechanical properties and structural stability of zinc oxide (ZnO) NWs. Our optimized parameters for the Buckingham interatomic potential are in good agreement with the existing experimental results. Furthermore, we found that the incorrect selection of interatomic potentials could lead to excessive overestimate (61%) of the elastic modulus of the NW. While NW length was found to dictate the strain distribution along the wire, impacting its predicted properties, the cross-section shape did not play a major role. Assigning uniform charges for both the core and surface atoms of ZnO NWs leads to a drastic decrease in fracture properties.

Sequence dependent influence of an A…A mismatch in a DNA duplex: An insight into the recognition by hZαADAR1 protein

Base pair mismatches can erroneously be incorporated in the DNA. An adenine pairing with another adenine is one of the eight possible mismatches. The atomistic insights about the structure and dynamics of an A…A mismatch in a DNA (unbound form) is not yet accessible to any experimental technique. Earlier molecular dynamics (MD) simulations have shown that A…A mismatch in the midst of 5′CAG/3′GAC, 5′GAC/3′CAG and 5′CAA/3′GAT (underline represents the mismatch) are highly dynamic in nature. By employing MD simulation, the influence of an A…A mismatch in the midst of 5′GAA/3′CAT, 5′GAG/3′CAC, 5′AAC/3′TAG, 5′AAG/3′TAC, 5′TAA/3′AAT, 5′TAT/3′AAA and 5′AAT/3′TAA sequences have been investigated here. The results indicate that irrespective of the flanking sequences, the mismatch samples a variety of transient conformations, including a B-Z junction. Further, circular dichroism studies have been carried out to explore the ability of these sequences to bind with hZαADAR1 which specifically recognizes B-Z junction/Z-DNA. The results indicate that hZαADAR1 could not lead to a complete B to Z transition in the above sequences. Notably, a complete transition to Z-form has been reported earlier for 5′GAC/3′CAG upon titrating with hZαADAR1. Intriguingly, 5′AAC/3′TAG, 5′AAG/3′TAC and 5′GAA/3′CAT exhibit a B-Z junction formation rather than a complete transition to Z-form, similar to the situation of 5′CAA/3′GAT. These indicate that although A…A mismatch could induce a local B-Z junction transiently, hZαADAR1 requires the presence of a G…C/C…G base pair adjacent to the A…A mismatch for the binding. Additionally, the extent of B-Z junction has enhanced upon binding with hZαADAR1 in the presence of the A…A mismatch (specifically when CG, CA, AC, GA and AG steps occur), but not in the presence of the canonical base pairs. These confirm the inclination of A…A mismatch towards the B-Z junction.

Direct observation of polar nanodomains in the incommensurate phase of (K0.96Rb0.04)2ZnCl4 crystals using piezo force microscopy

Piezo force microscopy has been used to visualize nanoscaled surface charge density waves in a modulated ferroelectric system for the first time. Those structures are found in incommensurate systems close to lock-in transition consisting of an ordered sequence of commensurate nanodomains separated by discommensurations. In ferroelectrics, these domains are antiparallel polarized. As a model system, K2ZnCl4 crystals doped with Rb2ZnCl4 is used where the nanodomain structure can be stabilized at room temperature. Lock-in amplifier techniques allow the mapping of domain morphology and also its coarsening in aged crystals. Our results directly confirm earlier molecular dynamics simulations found in the literature.

Anti-Correlation between the Dynamics of the Active Site Loop and C-Terminal Tail in Relation to the Homodimer Asymmetry of the Mouse Erythroid 5-Aminolevulinate Synthase.

Biosynthesis of heme represents a complex process that involves multiple stages controlled by different enzymes. The first of these proteins is a pyridoxal 5′-phosphate (PLP)-dependent homodimeric enzyme, 5-aminolevulinate synthase (ALAS), that catalyzes the rate-limiting step in heme biosynthesis, the condensation of glycine with succinyl-CoA. Genetic mutations in human erythroid-specific ALAS (ALAS2) are associated with two inherited blood disorders, X-linked sideroblastic anemia (XLSA) and X-linked protoporphyria (XLPP). XLSA is caused by diminished ALAS2 activity leading to decreased ALA and heme syntheses and ultimately ineffective erythropoiesis, whereas XLPP results from “gain-of-function” ALAS2 mutations and consequent overproduction of protoporphyrin IX and increase in Zn2+-protoporphyrin levels. All XLPP-linked mutations affect the intrinsically disordered C-terminal tail of ALAS2. Our earlier molecular dynamics (MD) simulation-based analysis showed that the activity of ALAS2 could be regulated by the conformational flexibility of the active site loop whose structural features and dynamics could be changed due to mutations. We also revealed that the dynamic behavior of the two protomers of the ALAS2 dimer differed. However, how the structural dynamics of ALAS2 active site loop and C-terminal tail dynamics are related to each other and contribute to the homodimer asymmetry remained unanswered questions. In this study, we used bioinformatics and computational biology tools to evaluate the role(s) of the C-terminal tail dynamics in the structure and conformational dynamics of the murine ALAS2 homodimer active site loop. To assess the structural correlation between these two regions, we analyzed their structural displacements and determined their degree of correlation. Here, we report that the dynamics of ALAS2 active site loop is anti-correlated with the dynamics of the C-terminal tail and that this anti-correlation can represent a molecular basis for the functional and dynamic asymmetry of the ALAS2 homodimer.

Free-standing graphene slit membrane for enhanced desalination

This study considers two novel ideas to further explore and enhance the graphene membrane for desalination. Firstly, while earlier molecular dynamics (MD) simulations studies have used frozen membranes, free-standing membrane is considered here. Since 2D membranes are usually embedded on porous support in the experimental reverse osmosis (RO) process, the free-standing membrane can more accurately model the behavior expected during operation. This study showed, using MD simulations, that a free-standing nanoporous graphene membrane can provide a higher salt rejection, but lower water permeability as compared to frozen membrane. Secondly, the performance of a slit membrane as compared to a membrane with circular pore is studied. At a pressure of 268 MPa, the critical diameter of circular pore that can maintain perfect salt rejection is found to be 5 Å and the critical size for a slit is determined to be 2.28 Å. It is shown that a slit membrane at its critical size can achieve water flux 3.5 times higher than a membrane with circular pore at its critical radius. This finding highlights the importance of slits over circular pores which can potentially widen the options for the design and fabrication of 2D graphene membranes for experimental verification of RO.

Microsecond Pore Dilation Kinetics and Hydrophobic Gating of Magnesium Transport in the Cora System

Although magnesium homeostasis is essential for life, the mechanism by which cells select Mg2+ among more prevalent biological ions like Na+ and K+ is unknown. In our earlier molecular dynamics (MD) simulation study [Chakrabarti et al., An Iris-like Mechanism of Pore Dilation in the CorA Magnesium Transport System, Biophys. J. (2010) 98: 784-792], we identified a 1.5-nm-long hydrophobic constriction in the CorA Mg2+ transport system which is dehydrated in the crystallographic state of the channel. In our simulations, an iris-like dilation of the pore led to a rapid wetting transition of the hydrophobic bottleneck, but only after regulatory magnesium ions were removed from their intracellular binding sites. Here we report large-scale atomistic simulations of CorA in a hydrated bilayer successively with and without regulatory ions. The results of hundreds of simulations confirm the allosteric mechanism linking the ionic occupancy of the regulatory sites to hydrophobic gating of the pore and provide quantitative insight into the early kinetics of pore dilation and hydration. Free energy simulations for magnesium permeation through a relatively dilated conformation of the channel are presented, and the interplay of hydration, ionic occupancy of the lumen, and structural fluctuations of the channel are analyzed. Together, these results provide insight into the molecular mechanisms governing the regulation, transport, and selectivity of magnesium permeation in the unusually long channel lumen of CorA.

The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp

Sliding clamps are toroidal proteins that encircle DNA and act as mobile platforms for DNA replication and repair machinery. To be loaded onto DNA, the eukaryotic sliding clamp Proliferating Cell Nuclear Antigen (PCNA) must be splayed open at one of the subunit-subunit interfaces by the ATP-dependent clamp loader, Replication Factor C, whose clamp-interacting sites form a right-handed spiral. Earlier molecular dynamics (MD) studies suggested that when PCNA opens, it preferentially adopts a right-handed spiral to match the spiral of the clamp loader. Here, analysis of considerably longer MD simulations shows that although the opened form of PCNA can achieve conformations matching the helical pitch of Replication Factor C, it is not biased toward a right-handed spiral structure. A coarse-grained elastic model was also built; its strong correspondence to the all-atom MD simulations of PCNA suggests that the behavior of the open clamp is primarily due to elastic deformation governed by the topology of the clamp domains. The elastic model was further used to construct the energy landscape of the opened PCNA clamp, including conformations that would allow binding to the clamp loader and loading onto double-stranded DNA. A picture of PCNA emerges of a rather flexible protein that, once opened, is mechanically compliant in the clamp opening process.

Sensitivity of ion-induced sputtering to the radial distribution of energy transfers: A molecular dynamics study

Using different models for the deposition of energy on the lattice and a classical molecular dynamics approach to the subsequent transport, we evaluate how the details of the energy deposition model influence sputtering yield from a Lennard-Jones target irradiated with a MeV/u ion beam. Two energy deposition models are considered: a uniform, instantaneous deposition into a cylinder of fixed radius around the projectile ion track, used in earlier molecular dynamics and fluid dynamics simulations of sputtering yields; and an energy deposition distributed in time and space based on the formalism developed in the thermal spike model. The dependence of the sputtering yield on the total energy deposited on the target atoms is very sensitive to the energy deposition model. To clarify the origin of this strong dependence, we explore the role of the radial expansion of the electronic system prior to the transfer of its energy to the lattice. The results imply that observables such as the sputtering yield may be used as signatures of the fast electron-lattice energy transfer in the electronic energy-loss regime, and indicate the need for more experimental and theoretical investigations of these processes.

Experimental study of filling carbon nanotubes with nucleic acids

AbstractEncapsulation of DNA molecules inside carbon nanotubes (CNT) in water were performed under the conditions of 400K and 3Bar. Double stranded DNAs of 2kb and 400bp in length, and single stranded oligonucleotides of 60bp in length were selected as target molecules. Au and Pt nanoparticles and fluorescent dye Cy3 were used as tags. Agarose gel electrophoresis was used to remove DNA molecules attached on the outside walls of CNTs. Laser confocal microscopy, scanning electron microscopy (SEM), high resolution transmission electron microscopy (HR-TEM), energy dispersive x-ray spectroscopy (EDX) were employed to confirm the encapsulation process. The results demonstrated that DNA molecules attached to the outside of CNTs can be removed by electrophoresis. Confocal microscopy and HR-TEM observations as well as EDX analysis confirmed that the Cy3-labelled DNA molecules, Au-labelled oligonucleotides and Pt-labelled DNA fragments can indeed be encapsulated inside CNTs. These experimental results support our earlier molecular dynamics simulations on encapsulating oligonucleotides inside CNTs. The DNA-CNT hybrids could be further explored for potential applications in bio-nanotechnology.

Simulating the amorphization of alpha -quartz under pressure.

Extensive molecular-dynamics simulations have been performed within a classical force-field model for the pressure-induced amorphization of quartz. In agreement with earlier molecular-dynamics studies, we find that a phase transition occurs within the experimental pressure range of the amorphization transformation. However, at variance with previous interpretations, we find that the resulting phase is not amorphous. The correlation functions of the equilibrated structure can be shown to be consistent with those of a crystalline phase. Two transformations to ordered structures occur sequentially during the simulations. The first transformation is likely to be related to the recently discovered transition of quartz to an intermediate crystalline phase before its amorphization. The second transformation, instead, yields a compact octahedrally coordinated Si sublattice. The latter structure may be an artifact of the classical force field.

Computer-simulation studies of the melting transition of Rb and K intercalated in graphite.

The energy histogram method, introduced by Ferrenberg and Swendsen [Phys. Rev. Lett. 61, 2635 (1988); 631, 1195 (1989)], was applied to the constant-temperature molecular-dynamics (MD) simulation of a two-dimensional system with incommensurate structures. We performed MD simulations for the stage-2 graphite intercalation compounds (GIC's) with Rb or K being the intercalants (Rb-GIC's and K-GIC's). The temperature dependence of the specific heat, C υ , is calculated for various sizes up to 864 atoms. The melting temperature was found to be 158 K for Rb-GIC's and 119 K for K-GIC's, which are in agreement with the experimental observations and an earlier MD result for Rb