Abstract: Propellants based on Hydroxyl Terminated Polybutadiene/Ammonium Perchlorate (HTPB/AP) are the most commonly used in most of the rocket engines used by the Brazilian Armed Forces. This work aimed at the possibility of extending its useful life (currently in 10 years) by performing kinetic-chemical analyzes of its energetic material via Differential Scanning Calorimetry (DSC) and also performing computer simulation of aging process using the software Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). Thermal analysis via DSC was performed in triplicates and in three heating ratios (5 ºC, 10 ºC, and 15 ºC) of rocket motor with 11 years shelf-life, using the Arrhenius equation to obtain its activation energy, using Ozawa and Kissinger kinetic methods, allowing comparison with manufacturing period data (standard motor). In addition, the kinetic parameters of internal pressure of the combustion chamber in 08 rocket engines with 11 years of shelf-life were also acquired, for comparison purposes with the engine start-up data.
Abstract: In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.
Abstract: In this work, adsorption of chlorophylls a and b pigments in aqueous solution on the inner and outer surfaces of single-walled carbon nanotube (SWCNT) has been studied using molecular dynamics simulation. The linear interaction energy algorithm has been used to calculate the binding free energy. The results show that the adsorption of two pigments is fine on the both positions. Although there is the close similarity between these two pigments, their interaction with the nanotube is different. This result is useful to separate these pigments from one another. According to interaction energy between the pigments and carbon nanotube, interaction between these pigments-SWCNT on the inner surface is stronger than the outer surface. The interaction of SWCNT with chlorophylls phytol tail is stronger than the interaction of SWCNT with porphyrin ring of chlorophylls.
Abstract: The use of CO2 in oil recovery and in CO2 capture and storage is gaining traction in recent years. These applications involve heat transfer between CO2 and the base fluid, and hence, there arises a need to improve the thermal conductivity of CO2 to increase the process efficiency and reduce cost. One way to improve the thermal conductivity is through nanoparticle addition in the base fluid. The nanofluid model in this study consisted of copper (Cu) nanoparticles in varying concentrations with CO2 as a base fluid. No experimental data are available on thermal conductivity of CO2 based nanofluid. Molecular dynamics (MD) simulations are an increasingly adopted tool to perform preliminary assessments of nanoparticle (NP) fluid interactions. In this study, the effect of the formation of a nanolayer (or molecular layering) at the gas-solid interface on thermal conductivity is investigated using equilibrium MD simulations by varying NP diameter and keeping the volume fraction (1.413%) of nanofluid constant to check the diameter effect of NP on the nanolayer and thermal conductivity. A dense semi-solid fluid layer was seen to be formed at the NP-gas interface, and the thickness increases with increase in particle diameter, which also moves with the NP Brownian motion. Density distribution has been done to see the effect of nanolayer, and its thickness around the NP. These findings are extremely beneficial, especially to industries employed in oil recovery as increased thermal conductivity of CO2 will lead to enhanced oil recovery and thermal energy storage.
Abstract: The biaxial buckling behavior of single-layered graphene sheets (SLGSs) is studied in the present work. To consider the size-effects in the analysis, Eringen’s nonlocal elasticity equations are incorporated into classical plate theory (CLPT). A Generalized Differential Quadrature Method (GDQM) approach is utilized and numerical solutions for the critical buckling loads are obtained. Then, molecular dynamics (MD) simulations are performed for a series of zigzag SLGSs with different side-lengths and with various boundary conditions, the results of which are matched with those obtained by the nonlocal plate model to numerical the appropriate values of nonlocal parameter relevant to each type of boundary conditions.
Abstract: The laws of Newtonian mechanics allow ab-initio
molecular dynamics to model and simulate particle trajectories in
material science by defining a differentiable potential function. This
paper discusses some considerations for the coding of ab-initio
programs for simulation on a standalone computer and illustrates
the approach by C language codes in the context of embedded
metallic atoms in the face-centred cubic structure. The algorithms use
velocity-time integration to determine particle parameter evolution
for up to several thousands of particles in a thermodynamical
ensemble. Such functions are reusable and can be placed in a
redistributable header library file. While there are both commercial
and free packages available, their heuristic nature prevents dissection.
In addition, developing own codes has the obvious advantage of
teaching techniques applicable to new problems.
Abstract: The beginning of 21st century has witnessed new
advancements in the design and use of new materials for biosensing
applications, from nano to macro, protein to tissue. Traditional
analytical methods lack a complete toolset to describe the
complexities introduced by living systems, pathological relations,
discrete hierarchical materials, cross-phase interactions, and
structure-property dependencies. Materiomics – via systematic
molecular dynamics (MD) simulation – can provide structureprocess-
property relations by using a materials science approach
linking mechanisms across scales and enables oriented biosensor
design. With this approach, DNA biosensors can be utilized to detect
disease biomarkers present in individuals’ breath such as acetone for
diabetes. Our wireless sensor array based on single-stranded DNA
(ssDNA)-decorated single-walled carbon nanotubes (SWNT) has
successfully detected trace amount of various chemicals in vapor
differentiated by pattern recognition. Here, we present how MD
simulation can revolutionize the way of design and screening of DNA
aptamers for targeting biomarkers related to oral diseases and oral
health monitoring. It demonstrates great potential to be utilized to
build a library of DNDA sequences for reliable detection of several
biomarkers of one specific disease, and as well provides a new
methodology of creating, designing, and applying of biosensors.
Abstract: In the present study we have investigated axial
buckling characteristics of nanocomposite beams reinforced by
single-walled carbon nanotubes (SWCNTs). Various types of beam
theories including Euler-Bernoulli beam theory, Timoshenko beam
theory and Reddy beam theory were used to analyze the buckling
behavior of carbon nanotube-reinforced composite beams.
Generalized differential quadrature (GDQ) method was utilized to
discretize the governing differential equations along with four
commonly used boundary conditions. The material properties of the
nanocomposite beams were obtained using molecular dynamic (MD)
simulation corresponding to both short-(10,10) SWCNT and long-
(10,10) SWCNT composites which were embedded by amorphous
polyethylene matrix. Then the results obtained directly from MD
simulations were matched with those calculated by the mixture rule
to extract appropriate values of carbon nanotube efficiency
parameters accounting for the scale-dependent material properties.
The selected numerical results were presented to indicate the
influences of nanotube volume fractions and end supports on the
critical axial buckling loads of nanocomposite beams relevant to
long- and short-nanotube composites.
Abstract: The elastic properties and fracture of two-dimensional
graphene were calculated purely from the atomic bonding (stretching
and bending) based on molecular mechanics method. Considering the
representative unit cell of graphene under various loading conditions,
the deformations of carbon bonds and the variations of the interlayer
distance could be realized numerically under the geometry constraints
and minimum energy assumption. In elastic region, it was found that
graphene was in-plane isotropic. Meanwhile, the in-plane deformation
of the representative unit cell is not uniform along armchair direction
due to the discrete and non-uniform distributions of the atoms. The
fracture of graphene could be predicted using fracture criteria based on
the critical bond length, over which the bond would break. It was
noticed that the fracture behavior were directional dependent, which
was consistent with molecular dynamics simulation results.
Abstract: The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.
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: 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: 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: 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.