Abstract: The study reports about the influence of binding of orthosteric ligands as well as point mutations on the conformational dynamics of β-2-adrenoreceptor. Using molecular dynamics simulation we found that there was a little fraction of active states of the receptor in its apo (ligand free) ensemble corresponded to its constitutive activity. Analysis of MD trajectories indicated that such spontaneous activation of the receptor is accompanied by the motion in intracellular part of its alpha-helices. Thus receptor’s constitutive activity directly results from its conformational dynamics. On the other hand the binding of a full agonist resulted in a significant shift of the initial equilibrium towards its active state. Finally, the binding of the inverse agonist stabilized the receptor in its inactive state. It is likely that the binding of inverse agonists might be a universal way of constitutive activity inhibition in vivo. Our results indicate that ligand binding redistribute pre-existing conformational degrees of freedom (in accordance to the Monod-Wyman-Changeux-Model) of the receptor rather than cause induced fit in it. Therefore, the ensemble of biologically relevant receptor conformations is encoded in its spatial structure, and individual conformations from that ensemble might be used by the cell in conformity with the physiological behavior.
Abstract: Cementitious materials are an excellent example of a composite material with complex hierarchical features and random features that range from nanometer (nm) to millimeter (mm) scale. Multi-scale modeling of complex material systems requires starting from fundamental building blocks to capture the scale relevant features through associated computational models. In this paper, molecular dynamics (MD) modeling is employed to predict the effect of plasticizer additive on the mechanical properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown molecular configuration of CSH, a representative configuration widely accepted in the field of mineral Jennite is employed. The effectiveness of the Molecular Dynamics modeling to understand the predictive influence of material chemistry changes based on molecular / nanoscale models is demonstrated.
Abstract: Radiation shielding is an obstacle in long duration space exploration. Boron Nitride Nanotubes (BNNTs) have attracted attention as an additive to radiation shielding material due to B10’s large neutron capture cross section. The B10 has an effective neutron capture cross section suitable for low energy neutrons ranging from 10-5 to 104 eV and hydrogen is effective at slowing down high energy neutrons. Hydrogenated BNNTs are potentially an ideal nanofiller for radiation shielding composites. We use Molecular Dynamics (MD) Simulation via Material Studios Accelrys 6.0 to model the Young’s Modulus of Hydrogenated BNNTs. An extrapolation technique was employed to determine the Young’s Modulus due to the deformation of the nanostructure at its theoretical density. A linear regression was used to extrapolate the data to the theoretical density of 2.62g/cm3. Simulation data shows that the hydrogenated BNNTs will experience a 11% decrease in the Young’s Modulus for (6,6) BNNTs and 8.5% decrease for (8,8) BNNTs compared to non-hydrogenated BNNT’s. Hydrogenated BNNTs are a viable option as a nanofiller for radiation shielding nanocomposite materials for long range and long duration space exploration.
Abstract: This work focused on the interactions which occur between ester solvents and alcohol solutes. The alcohols selected ranged from the simplest alcohol (methanol) to C10-alcohols, and solubility predictions in the form of infinite dilution activity coefficients were made using the Modified UNIFAC Dortmund group contribution model. The model computation was set up on a Microsoft Excel spreadsheet specifically designed for this purpose. It was found that alcohol/ ester interactions yielded an increase in activity coefficients (i.e. became less soluble) with an increase in the size of the ester solvent molecule. Furthermore, activity coefficients decreased with an increase in the size of the alcohol solute. The activity coefficients also decreased with an increase in the degree of unsaturation of the ester hydrocarbon tail. Tertiary alcohols yielded lower activity coefficients than primary alcohols. Finally, cyclic alcohols yielded higher activity coefficients than straight-chain alcohols until a point is reached where the trend is reversed, referred to as the ‘crossover’ point.
Abstract: We constructed an atomic structure model for a PAN-based carbon fiber containing amorphous structures using molecular dynamics methods. It was found that basic physical properties such as crystallinity, Young’s modulus, and thermal conductivity of our model were nearly identical to those of real carbon fibers. We then obtained the tensile strength of a carbon fiber, which has no macro defects. We finally determined that the limitation of the tensile strength was 19 GPa.
Abstract: Absorption spectra of infra-red (IR) radiation of the
disperse water medium absorbing the most important greenhouse
gases: CO2 , N2O , CH4 , C2H2 , C2H6 have been calculated by
the molecular dynamics method. Loss of the absorbing ability at the
formation of clusters due to a reduction of the number of centers
interacting with IR radiation, results in an anti-greenhouse effect.
Absorption of O3 molecules by the (H2O)50 cluster is investigated
at its interaction with Cl- ions. The splitting of ozone molecule on
atoms near to cluster surface was observed. Interaction of water
cluster with Cl- ions causes the increase of integrated intensity of
emission spectra of IR radiation, and also essential reduction of the
similar characteristic of Raman spectrum. Relative integrated
intensity of absorption of IR radiation for small water clusters was
designed. Dependences of the quantity of weight on altitude for
vapor of monomers, clusters, droplets, crystals and mass of all
moisture were determined. The anti-greenhouse effect of clusters was
defined as the difference of increases of average global temperature
of the Earth, caused by absorption of IR radiation by free water
molecules forming clusters, and absorption of clusters themselves.
The greenhouse effect caused by clusters makes 0.53 K, and the antigreenhouse
one is equal to 1.14 K. The increase of concentration of
CO2 in the atmosphere does not always correlate with the
amplification of greenhouse effect.
Abstract: The aim of this research was to calculate the
mechanical properties of Pd3Rh and PdRh3 ordered alloys. The
molecular dynamics (MD) simulation technique was used to obtain
temperature dependence of the energy, the Yong modulus, the shear
modulus, the bulk modulus, Poisson-s ratio and the elastic stiffness
constants at the isobaric-isothermal (NPT) ensemble in the range of
100-325 K. The interatomic potential energy and force on atoms were
calculated by Quantum Sutton-Chen (Q-SC) many body potential.
Our MD simulation results show the effect of temperature on the
cohesive energy and mechanical properties of Pd3Rh as well as
PdRh3 alloys. Our computed results show good agreement with the
experimental results where they have been available.
Abstract: A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.
Abstract: In this work we report the recent progresses that have been achieved by our group in the last half decade on the field of computational proteomics. Specifically, we discuss the application of Molecular Dynamics Simulations and Electronic Structure Calculations in drug design, in the clarification of the structural and dynamic properties of proteins and enzymes and in the understanding of the catalytic and inhibition mechanism of cancer-related enzymes. A set of examples illustrate the concepts and help to introduce the reader into this important and fast moving field.
Abstract: Viral influenza A subtypes H5N1 and pandemic
H1N1 (pH1N1) have worldwide emerged and transmitted. The most
common anti-influenza drug for treatment of both seasonal and
pandemic influenza viruses is oseltamivir that nowadays becomes
resistance to influenza neuraminidase. The novel long-acting drug,
laninamivir, was discovered for treatment of the patients infected
with influenza B and influenza A viruses. In the present study,
laninamivir complexed with wild-type strain of both H5N1 and
pH1N1 viruses were comparatively determined the structures and
drug-target interactions by means of molecular dynamics (MD)
simulations. The results show that the hydrogen bonding interactions
formed between laninamivir and its binding residues are likely
similar for the two systems. Additionally, the presence of
intermolecular interactions from laninamivir to the residues in the
binding pocket is established through their side chains in accordance
with hydrogen bond interactions.
Abstract: We report here, the results of molecular dynamics
simulation of p-doped (Ga-face)GaN over n-doped (Siface)(
0001)4H-SiC hetero-epitaxial material system with one-layer
each of Ga-flux and (Al-face)AlN, as the interface materials, in the
form of, the total Density of States (DOS). It is found that the total
DOS at the Fermi-level for the heavily p-doped (Ga-face)GaN and ndoped
(Si-face)4H-SiC hetero-epitaxial system, with one layer of
(Al-face)AlN as the interface material, is comparatively higher than
that of the various cases studied, indicating that there could be good
vertical conduction across the (Ga-face)GaN over (Si-face)(0001)4HSiC
hetero-epitaxial material system.
Abstract: Hypertension is characterized with stress on the heart and blood vessels thus increasing the risk of heart attack and renal diseases. The Renin angiotensin system (RAS) plays a major role in blood pressure control. Renin is the enzyme that controls the RAS at the rate-limiting step. Our aim is to develop new drug-like leads which can inhibit renin and thereby emerge as therapeutics for hypertension. To achieve this, molecular dynamics (MD) simulation and receptor-based pharmacophore modeling were implemented, and three rennin-inhibitor complex structures were selected based on IC50 value and scaffolds of inhibitors. Three pharmacophore models were generated considering conformations induced by inhibitor. The compounds mapped to these models were selected and subjected to drug-like screening. The identified hits were docked into the active site of renin. Finally, hit1 satisfying the binding mode and interaction energy was selected as possible lead candidate to be used in novel renin inhibitors.
Abstract: The bonding configuration and the heat of adsorption
of a furfural molecule on the Pd(111) surface were determined by ab
initio density-functional-theory calculations. The dynamics of pure
liquid water, the liquid-solid interface formed by liquid water and the
Pd(111) surface, as well as furfural at the water-Pd interface, were
investigated by ab initio molecular dynamics simulations at finite
temperatures. Calculations and simulations suggest that the bonding
configurations at the water-Pd interface promote decarbonylation of
furfural.
Abstract: Molecular dynamics simulation of annular flow
boiling in a nanochannel with 70000 particles is numerically
investigated. In this research, an annular flow model is developed to
predict the superheated flow boiling heat transfer characteristics in a
nanochannel. To characterize the forced annular boiling flow in a
nanochannel, an external driving force F ext ranging from 1to12PN
(PN= Pico Newton) is applied along the flow direction to inlet fluid
particles during the simulation. Based on an annular flow model
analysis, it is found that saturation condition and superheat degree
have great influences on the liquid-vapor interface. Also, the results
show that due to the relatively strong influence of surface tension in
small channel, the interface between the liquid film and vapor core is
fairly smooth, and the mean velocity along the stream-wise direction
does not change anymore.
Abstract: Stress-strain curve of inter-tube connected carbon nanotube (CNT) reinforced polymer composite under axial loading generated from molecular dynamics simulation is presented. Comparison of the response to axial mechanical loading between this composite system with composite systems reinforced by long, continuous CNTs (replicated via periodic boundary conditions) and short, discontinuous CNTs has been made. Simulation results showed that the inter-tube connection improved the mechanical properties of short discontinuous CNTs dramatically. Though still weaker than long CNT/polymer composite, more remarkable increase in the stiffness relative to the polymer was observed in the inter-tube connected CNT/polymer composite than in the discontinuous CNT/polymer composite. The manually introduced bridge break process resulted in a stress-strain curve of ductile fracture mode, which is consistent with the experimental result.
Abstract: Aurein 1.2 is a 13-residue amphipathic peptide with antibacterial and anticancer activity. Aurein1.2 and its retro analog were synthesized to study the activity of the peptides in relation to their structure. The antibacterial test result showed the retro-analog is inactive. The secondary structural analysis by CD spectra indicated that both of the peptides at TFE/Water adopt alpha-helical conformation. MD simulation was performed on aurein 1.2 and retro-analog in water and TFE in order to analyse the factors that are involved in the activity difference between retro and the native peptide. The simulation results are discussed and validated in the light of experimental data from the CD experiment. Both of the peptides showed a relatively similar pattern for their hydrophobicity, hydrophilicity, solvent accessible surfaces, and solvent accessible hydrophobic surfaces. However, they showed different in directions of dipole moment of peptides. Also, Our results further indicate that the reversion of the amino acid sequence affects flexibility .The data also showed that factors causing structural rigidity may decrease the activity. Consequently, our finding suggests that in the case of sequence-reversed peptide strategy, one has to pay attention to the role of amino acid sequence order in making flexibility and role of dipole moment direction in peptide activity. KeywordsAntimicrobial peptides, retro, molecular dynamic, circular dichroism.
Abstract: 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGR) catalyzes the conversion of HMG-CoA to mevalonate using NADPH and the enzyme is involved in rate-controlling step of mevalonate. Inhibition of HMGR is considered as effective way to lower cholesterol levels so it is drug target to treat hypercholesterolemia, major risk factor of cardiovascular disease. To discover novel HMGR inhibitor, we performed structure-based pharmacophore modeling combined with molecular dynamics (MD) simulation. Four HMGR inhibitors were used for MD simulation and representative structure of each simulation were selected by clustering analysis. Four structure-based pharmacophore models were generated using the representative structure. The generated models were validated used in virtual screening to find novel scaffolds for inhibiting HMGR. The screened compounds were filtered by applying drug-like properties and used in molecular docking. Finally, four hit compounds were obtained and these complexes were refined using energy minimization. These compounds might be potential leads to design novel HMGR inhibitor.
Abstract: The aim of this research was to calculate the thermal
properties of Au3Ni Nanowire. The molecular dynamics (MD)
simulation technique was used to obtain the effect of radius size on
the energy, the melting temperature and the latent heat of fusion at
the isobaric-isothermal (NPT) ensemble. The Quantum Sutton-Chen
(Q-SC) many body interatomic potentials energy have been used for
Gold (Au) and Nickel (Ni) elements and a mixing rule has been
devised to obtain the parameters of these potentials for nanowire
stats. Our MD simulation results show the melting temperature and
latent heat of fusion increase upon increasing diameter of nanowire.
Moreover, the cohesive energy decreased with increasing diameter of
nanowire.
Abstract: Every 2-3 years the influenza B virus serves
epidemics. Neuraminidase (NA) is an important target for influenza
drug design. Although, oseltamivir, an oral neuraminidase drug, has
been shown good inhibitory efficiency against wild-type of influenza
B virus, the lower susceptibility to the R152K mutation has been
reported. Better understanding of oseltamivir efficiency and
resistance toward the influenza B NA wild-type and R152K mutant,
respectively, could be useful for rational drug design. Here, two
complex systems of wild-type and R152K NAs with oseltamivir
bound were studied using molecular dynamics (MD) simulations.
Based on 5-ns MD simulation, the loss of notable hydrogen bond and
decrease in per-residue decomposition energy from the mutated
residue K152 contributed to drug compared to those of R152 in wildtype
were found to be a primary source of high-level of oseltamivir
resistance due to the R152K mutation.
Abstract: In this paper, the Lennard -Jones potential is applied
to molecules of liquid argon as well as its vapor and platinum as solid
surface in order to perform a non-equilibrium molecular dynamics
simulation to study the microscopic aspects of liquid-vapor-solid
interactions. The channel is periodic in x and y directions and along z
direction it is bounded by atomic walls. It was found that density of
the liquids near the solid walls fluctuated greatly and that the
structure was more like a solid than a liquid. This indicates that the
interactions of solid and liquid molecules are very strong. The
resultant surface tension, liquid density and vapor density are found
to be well predicted when compared with the experimental data for
argon. Liquid and vapor densities were found to depend on the cutoff
radius which induces the use of P3M (particle-particle particle-mesh)
method which was implemented for evaluation of force and surface
tension.