A charge-driven molecular water pump

Understanding and controlling the transport of water across nanochannels is of great importance for designing novel molecular devices, machines and sensors and has wide applications, including the desalination of seawater. Nanopumps driven by electric or magnetic fields can transport ions and magnetic quanta, but water is charge-neutral and has no magnetic moment. On the basis of molecular dynamics simulations, we propose a design for a molecular water pump. The design uses a combination of charges positioned adjacent to a nanopore and is inspired by the structure of channels in the cellular membrane that conduct water in and out of the cell (aquaporins). The remarkable pumping ability is attributed to the charge dipole-induced ordering of water confined in the nanochannels, where water can be easily driven by external fields in a concerted fashion. These findings may provide possibilities for developing water transport devices that function without osmotic pressure or a hydrostatic pressure gradient.     

Modelling transdermal delivery of high molecular weight drugs from microneedle systems

In the past few years, a number of microneedle designs have been proposed for transdermal drug delivery of high molecular weight drugs. However, most of them do not increase the drug permeability in skin significantly. In other cases, designs developed based on certain criteria (e.g. strength of the microneedles) have failed to meet other criteria (e.g. drug permeability in skin, throughputs of the drugs, etc.). It is obvious therefore that in order to determine the 'optimum' design of these microneedles, the effect of different factors (e.g. length of the microneedle, surface area of the patch, etc.) along with various transport properties of drug transport behaviour using microneedles should be determined accurately. Appropriate mathematical models for drug transport from these systems into skin have the potential to resolve some of these issues. To address this, a parametric analysis for transdermal delivery of a high molecular weight drug from a microneedle is presented in this paper. The simulations have allowed us to identify the significance of various factors that influence the drug delivery while designing microneedle arrays. A scaling analysis is also done which shows the functional dependence of drug concentration on other variables of skin and microneedle arrays.     

Pathways to state-selective control of vibrational wavepackets in the deuterium molecular ion

The capability of intense ultrashort laser pulses to initiate, control and image vibrational wavepacket dynamics in the deuterium molecular ion has been simulated with a view to inform and direct future femtosecond pump–control–probe experiments. The intense-field coherent control of the vibrational superposition has been studied as a function of pulse intensity and delay time, to provide an indication of key constraints for experimental studies. For selected cases of the control mechanism, probing of the subsequent vibrational wavepacket dynamics has been simulated via the photodissociation (PD) channel. Such PD probing is shown to elucidate the modified wavepacket dynamics where the position of the quantum revival is sensitive to the control process. Through Fourier transform analysis the PD yield is also shown to provide a characterisation of the vibrational distribution. It has been shown that a simple ‘critical R cut-off’ approximation can be used to reproduce the effect of a probe pulse interaction, providing a convenient and efficient alternative to intensive computer simulations of the PD mechanism in the deuterium molecular ion.     

Engineering molecular mechanics: an efficient static high temperature molecular simulation technique

Inspired by the need for an efficient molecular simulation technique, we have developed engineering molecular mechanics (EMM) as an alternative molecular simulation technique to model high temperature (T>0?K) phenomena. EMM simulations are significantly more computationally efficient than conventional techniques such as molecular dynamics simulations. The advantage of EMM is achieved by converting the dynamic atomistic system at high temperature (T>0?K) into an equivalent static system. Fundamentals of the EMM methodology are derived using thermal expansion to modify the interatomic potential. Temperature dependent interatomic potentials are developed to account for the temperature effect. The efficiency of EMM simulations is demonstrated by simulating the temperature dependence of elastic constants of copper and nickel and the thermal stress developed in a confined copper system.     

Binding and conformation of dendrimer-based drug delivery systems:a molecular dynamics study

All atomistic molecular dynamics simulations were performed on poly(amidoamine)(PAMAM) dendrimers that compound non-covalently with anticancer drug molecules including DOX,MTX,CE6,and SN38.The binding energies as well as their associated interaction energies and deformation energies were combined to evaluate the relative binding strength among drug,PAMAM,and PEG chains.We find that the deformation of dendrimers due to drug loading plays a crucial role in the drug binding.It is energetically favorable for the drug molecules to bind with PAMAM while the drugs bind with PEG metastable chains via kinetic confinement.Surface PEGylation helps dendrimers to accommodate more drug molecules with greater strength without inducing too much expansion.This work indicates that tuning the functionalized terminal groups of dendrimers is critical to design efficient dendrimer-based drug delivery systems.     

Rapid and accurate ranking of binding affinities of epidermal growth factor receptor sequences with selected lung cancer drugs

The epidermal growth factor receptor (EGFR) is a major target for drugs in treating lung carcinoma. Mutations in the tyrosine kinase domain of EGFR commonly arise in human cancers, which can cause drug sensitivity or resistance by influencing the relative strengths of drug and ATP-binding. In this study, we investigate the binding affinities of two tyrosine kinase inhibitors—AEE788 and Gefitinib—to EGFR using molecular dynamics simulation. The interactions between these inhibitors and the EGFR kinase domain are analysed using multiple short (ensemble) simulations and the molecular mechanics/Poisson–Boltzmann solvent area (MM/PBSA) method. Here, we show that ensemble simulations correctly rank the binding affinities for these systems: we report the successful ranking of each drug binding to a variety of EGFR sequences and of the two drugs binding to a given sequence, using petascale computing resources, within a few days.     

Evaluation of a grid based molecular dynamics approach for polypeptide simulations

Molecular dynamics is very important for biomedical research because it makes possible simulation of the behavior of a biological macromolecule in silico. However, molecular dynamics is computationally rather expensive: the simulation of some nanoseconds of dynamics for a large macromolecule such as a protein takes very long time, due to the high number of operations that are needed for solving the Newton's equations in the case of a system of thousands of atoms. In order to obtain biologically significant data, it is desirable to use high-performance computation resources to perform these simulations. Recently, a distributed computing approach based on replacing a single long simulation with many independent short trajectories has been introduced, which in many cases provides valuable results. This study concerns the development of an infrastructure to run molecular dynamics simulations on a grid platform in a distributed way. The implemented software allows the parallel submission of different simulations that are singularly short but together bring important biological information. Moreover, each simulation is divided into a chain of jobs to avoid data loss in case of system failure and to contain the dimension of each data transfer from the grid. The results confirm that the distributed approach on grid computing is particularly suitable for molecular dynamics simulations thanks to the elevated scalability.     

Simulating scratch behavior of polymers with mesoscopic molecular dynamics

Part replacement and repair is needed in structures with moving parts because of scratchability and wear. In spite of some accumulation of experimental evidence, scratch resistance is still not well understood. We have applied molecular dynamics to study scratch resistance of amorphous polymeric materials through computer simulations. As a first approach, a coarse grain model was created for high density polyethylene at the mesoscale. We have also extended the traditional approach and used real units rather than reduced units (to our knowledge, for the first time), which enable an improved quantification of simulation results. The obtained results include analysis of penetration depth, residual depth and recovery percentage related to indenter force and size. Our results show there is a clear effect from these parameters on the tribological properties. We also discuss a "crooked smile" effect on the scratched surface and the reasons for its appearance.     

Tight-binding molecular dynamics for materials simulations

Summary Tight-binding molecular dynamics has recently emerged as a useful method for atomistic simulation of the structural, dynamical and electronic properties of realistic materials. The method incorporates quantum-mechanical calculations into molecular dynamics through an empirical tight-binding Hamiltonian and bridges the gap between ab initio molecular dynamics and simulations using empirical classical potentials. In this paper, we review the accuracy, efficiency, and predictive power of the method and discuss some opportunities and challenges for future development.     

Vibrational study of a molecular device using molecular dynamics simulations

A Potential scenario for the implementation of molecular electronic systems is introduced by applying digital signal processing techniques to results from classical molecular dynamics simulations of a molecular system interconnected by nanosize gold clusters. Under this new scenario, signals can be introduced, processed, and read through interactions with the internal vibrational modes of the small molecular unit. We use modulation operations intrinsically inherent to any molecular system as a concept proof. As an example of this type of analysis, we focus on the individual oscillations between C-H and C-C bonds and cluster-cluster displacements.     

Buckling of defective single-walled and double-walled carbon nanotubes under axial compression by molecular dynamics simulation

Buckling of defective single-walled and double-walled carbon nanotubes (SWCNTs and DWCNTs, respectively) due to axial compressive loads has been studied by molecular dynamics simulations, and results compared with those of the perfect structures. It is found that single vacancy defect greatly weakens the carrying capacity of SWCNTs and DWCNTs, though it does slight harm to the effective elastic modulus of the tubes. The influence of defects on the buckling properties of nanotubes is related to the density of the defects, and the relative position of defects also plays an important role in buckling of DWCNTs. The van der Waals force among atoms in the inner and the outer tubes of short defective DWCNTs makes the critical buckling strain of DWCNTs greater than that of the inner tube.     

A neural network constitutive model for hyperelasticity based on molecular dynamics simulations

Numerical analysis of the hyperelastic behavior of polymer materials has drawn significant interest from within the field of mechanical engineering. Currently, hyperelastic models based on the energy density function, such as the Neo-Hookean, Mooney-Rivlin, and Ogden models, are used to investigate the hyperelastic responses of materials. Conventionally, constants relating to materials were determined from experimental data by using global least-squares fitting. However, formulating a constitutive equation to capture the complex behavior of hyperelastic materials was difficult owing to the limitations of the analytical model and experimental data. This study addresses these limitations by using a system of neural networks (NNs) to design a data-driven surrogate model without a specific function formula, and employs molecular dynamics (MD) simulations to calculate the massive amount of combined loading data of hyperelastic materials. Thus, MD simulations were used to propose an NN constitutive model for hyperelasticity to derive the constitutive equation to model the complex hyperelastic response. In addition, the probability distributions of the numerical solutions of hyperelasticity are used to characterize the uncertainty of the MD models. These statistical finite element results not only present numerical results with reliability ranges but also scattered distributions of the solution obtained from the MD-based probability distributions.     

Thermal resistance of nanoscopic liquid-liquid interfaces: dependence on chemistry and molecular architecture

Systems with nanoscopic features contain a high density of interfaces. Thermal transport in such systems can be governed by the resistance to heat transfer, the Kapitza resistance (RK), at the interface. Although soft interfaces, such as those between immiscible liquids or between a biomolecule and solvent, are ubiquitous, few studies of thermal transport at such interfaces have been reported. Here we characterize the interfacial conductance, 1/RK, of soft interfaces as a function of molecular architecture, chemistry, and the strength of cross-interfacial intermolecular interactions through detailed molecular dynamics simulations. The conductance of various interfaces studied here, for example, water-organic liquid, water-surfactant, surfactant-organic liquid, is relatively high (in the range of 65-370 MW/m2 K) compared to that for solid-liquid interfaces ( approximately 10 MW/m2 K). Interestingly, the dependence of interfacial conductance on the chemistry and molecular architecture cannot be explained solely in terms of either bulk property mismatch or the strength of intermolecular attraction between the two phases. The observed trends can be attributed to a combination of strong cross-interface intermolecular interactions and good thermal coupling via soft vibration modes present at liquid-liquid interfaces.     

Mechanics of molecular collagen is influenced by hydroxyapatite in natural bone

As often seen in biological structural materials, bone exhibits complex hierarchical structure. The primary constituents of bone are collagen and hydroxyapatite (HAP). HAP mineralizes at specific locations at collagen, in such a way that the c-axis of HAP aligns parallel to collagen molecule. The collagen molecule is helical overall with non-helical ends that are N- or C-telopeptides. The collagen molecule with telopeptides interacts with specific surfaces of mineralized HAP. When subjected to load, the interactions at the interface between HAP and collagen may significantly affect the overall mechanics of the collagen molecule. Here, we have performed molecular dynamics (MD) and steered MD (SMD) simulations in order to understand the load carrying behavior of collagen in the proximity of HAP. Our simulations indicate that the load-deformation response of collagen is different when it interacts with HAP as compared to its response in the absence of HAP. The interface between HAP and collagen affects the overall load-deformation response of collagen. Further, bone also has considerable amount of water and we have observed that water significantly influences the load-deformation response of collagen due to collagen-water-HAP interactions.     

Kv channel S6 helix as a molecular switch: simulation studies

Ion channels form pores of nanoscopic dimensions in biological membranes and play a key role in the physiology of cells. The majority of ion channels are gated, i.e. they contain a molecular switch that allows a transition between a closed (functionally 'off') and open (functionally 'on') state. Comparison of crystal structures of potassium channels suggest that the gating mechanism of voltage-gated potassium (Kv) channels involves a key role for the pore-lining S6 helix. There is a conserved PVP sequence motif in the S6 helix. Molecular dynamics simulations are used here to explore the conformational dynamics of the S6 helix hinge in models of fragments of a Kv channel, namely an S5-P-S6 monomer and an (S5-P-S6)4 tetramer. The latter is a model of the complete pore-forming domain of a Kv channel. All models were simulated embedded in an octane slab (a simple membrane mimetic). The results of these simulations indicate that the PVP motif may form a molecular hinge, even when the S6 helix forms part of a more complex model. The conformational dynamics of S6 are modulated by the remainder of protein, but it remains flexible. These simulation results are compatible with a channel gating model in which S6 bends in the vicinity of the PVP motif in addition to the region around the conserved glycine (G466) that is N-terminal to the PVP motif. This model is supported by comparison of the Kv S6 models with the S6 helix of the bacterial KvAP channel crystal structure. Thus, K channel gating may depend on a complex nanoswitch with three rigid helical sections linked by two molecular hinges.     

Investigation of non-covalent association of single-walled carbon nanotube with amylose by molecular dynamics simulation

Functionalization of carbon nanotubes (CNTs) with the assistance of biological molecules remarkably improves the solubility of nanotubes in aqueous or organic environment and, thus, facilitates the development of novel biotechnology, biomedicine and bioengineering. In the present study, molecular dynamics (MD) simulations are performed on the complex amylose-nanotube system to study the mode of interaction between the initially separated amylose and SWNT fragments, which can be either wrapping or encapsulation. It has been found that the van der Waals force is dominant and it always plays an important role in promoting non-covalent association. The influence of the size of nanotube on MD simulation is also studied. Our study illustrates that amylose molecules can be used to bind with nanotubes and, thus, favor non-covalent functionalization of carbon nanotubes.     

Energy deposition control during cluster bombardment: a molecular dynamics view

Molecular dynamics simulations are performed to model C60 and Au3 bombardment of a molecular solid, benzene, in order to understand the energy deposition placement as a function of incident kinetic energy and incident angle. Full simulations are performed for 5 keV projectiles, and the yields are calculated. For higher energies, 20 and 40 keV, the mesoscale energy deposition footprint model is employed to predict trends in yield. The damage accumulation is discussed in relationship to the region where energy is deposited to the sample. The simulations show that the most favorable conditions for increasing the ejection yield and decreasing the damage accumulation are when most of the projectile energy is deposited in the near-surface region. For molecular organic solids, grazing angles are the best choice for achieving these conditions.     

C60 fullerene enhances cisplatin anticancer activity and overcomes tumor cell drug resistance

We formulated and analyzed a novel nanoformulation of the anticancer drug cisplatin (Cis) with C60 fullerene (C60+Cis complex) and showed its higher toxicity toward tumor cell lines in vitro when compared to Cis alone.The highest toxicity of the complex was observed in HL-60/adr and HL-60/vinc chemotherapyresistant human leukemia cell sublines (resistant to Adriamycin and Vinculin,respectively).We discovered that the action of the C60+Cis complex is associated with overcoming the drug resistance of the tumor cell lines through observing an increased number of apoptotic cells in the Annexin V/PI assay.Moreover,in vivo assays with Lewis lung carcinoma (LLC) C57BL/6J male mice showed that the C60+Cis complex increases tumor growth inhibition,when compared to Cis or C60 fullerenes alone.Simultaneous1y,we conducted a molecular docking study and performed an Ames test.Molecular docking specifies the capability of a C60 fullerene to form van der Waals interactions with potential binding sites on P-glycoprotein (P-gp),multidrug resistance protein 1 (MRP-1),and multidrug resistance protein 2 (MRP-2) molecules.The observed phenomenon revealed a possible mechanism to bypass tumor cell drug resistance by the C,o+Cis complex.Additionally,the results of the Ames test show that the formation of such a complex diminishes the Cis mutagenic activity and may reduce the probability of secondary neoplasm formation.In conclusion,the C60+Cis complex effectively induced tumor cell death in vitro and inhibited tumor growth in vivo,overcoming drug resistance likely by the potential of the C60 fullerene to interact with P-gp,MRP-1,and MRP-2 molecules.Thus,the C60+Cis complex might be a potential novel chemotherapy modification.     

Field effects on the statistical behavior of the molecular conductance in a single molecular junction in aqueous solution

We have combined molecular dynamics simulations with first-principles calculations to study electron transport in a single molecular junction of perylene tetracarboxylic diimide (PTCDI) in aqueous solution under external electric gate fields. It is found that the statistics of the molecular conductance are very sensitive to the strength of the electric field. The statistics of the molecular conductance are strongly associated with the thermal fluctuation of the water molecules around the PTCDI molecule. Our simulations reproduce the experimentally observed three orders of magnitude enhancement of the conductance, as well as the temperature dependent conductance, under the electrochemical gates. The effects of the molecular polarization and the dipole rearrangement of the aqueous solution are also discussed.      

Realizing Cancer Precision Medicine by Integrating Systems Biology and Nanomaterial Engineering

Many clinical trials for cancer precision medicine have yielded unsatisfactory results due to challenges such as drug resistance and low efficacy. Drug resistance is often caused by the complex compensatory regulation within the biomolecular network in a cancer cell. Recently, systems biological studies have modeled and simulated such complex networks to unravel the hidden mechanisms of drug resistance and identify promising new drug targets or combinatorial or sequential treatments for overcoming resistance to anticancer drugs. However, many of the identified targets or treatments present major difficulties for drug development and clinical application. Nanocarriers represent a path forward for developing therapies with these “undruggable” targets or those that require precise combinatorial or sequential application, for which conventional drug delivery mechanisms are unsuitable. Conversely, a challenge in nanomedicine has been low efficacy due to heterogeneity of cancers in patients. This problem can also be resolved through systems biological approaches by identifying personalized targets for individual patients or promoting the drug responses. Therefore, integration of systems biology and nanomaterial engineering will enable the clinical application of cancer precision medicine to overcome both drug resistance of conventional treatments and low efficacy of nanomedicine due to patient heterogeneity.