Abstract: The study of dielectric properties in a binary mixture of liquids is very useful to understand the liquid structure, molecular interaction, dynamics, and kinematics of the mixture. Time-domain reflectometry (TDR) is a powerful tool for studying the cooperation and molecular dynamics of the H-bonded system. Here we discuss the basic calibration and normalization procedure for TDR measurements. Our aim is to explain different types of error occur during TDR measurements and how to minimize it.
Abstract: Surface wettability is a crucial factor in oil recovery. In oil industry, the rock wettability involves the interplay between water, oil, and solid surface. Therefore, studying the interplay between adsorptions of water and hydrocarbon molecules on solid surface would be very informative for understanding rock wettability. Here we use the in-situ Nuclear Magnetic Resonance (NMR) gas isotherm technique to study competitive adsorptions of water and isopropanol, an intermediate step from hydrocarbons. This in-situ NMR technique obtains information on thermodynamic properties such as the isotherm, molecular dynamics via spin relaxation measurements, and adsorption kinetics such as how fast the system can reach thermal equilibrium after changes of vapor pressures. Using surfaces of silica glass beads, which can be modified from hydrophilic to hydrophobic, we obtained information on the influence of surface hydrophilicity on the state of surface water via obtained thermodynamic and dynamic properties.
Abstract: Peridynamics is a new modeling concept of non-local interactions for solid structures. The formulations of Peridynamic (PD) theory are based on integral equations rather than differential equations. Through, undefined equations of associated problems are avoided. PD theory might be defined as continuum version of molecular dynamics. The medium is usually modeled with mass particles bonded together. Particles interact with each other directly across finite distances through central forces named as bonds. The main assumption of this theory is that the body is composed of material points which interact with other material points within a finite distance. Although, PD theory developed for discontinuities, it gives good results for structures which have no discontinuities. In this paper, displacement control of the isotropic plate under the effect of tensile and bending loading has been investigated by means of PD theory. A MATLAB code is generated to create PD bonds and corresponding surface correction factors. Using generated MATLAB code the geometry of the specimen is generated, and the code is implemented in Finite Element Software. The results obtained from non-local continuum theory are compared with the Finite Element Analysis results and analytical solution. The results show good agreement.
Abstract: Graphene material has found tremendous applications
in water desalination, DNA sequencing and energy storage. Multiple
nanopores are etched to create opening for water desalination and
energy storage applications. The nanopores created are of the order
of 3-5 nm allowing multiple ions to transport through the pore. In
this paper, we present for the first time, molecular dynamics study of
single ion transport, where only one ion passes through the graphene
nanopore. The diameter of the graphene nanopore is of the same
order as the hydration layers formed around each ion. Analogous to
single electron transport resulting from ionic transport is observed
for the first time. The current-voltage characteristics of such a device
are similar to single electron transport in quantum dots. The current
is blocked until a critical voltage, as the ions are trapped inside a
hydration shell. The trapped ions have a high energy barrier compared
to the applied input electrical voltage, preventing the ion to break free
from the hydration shell. This region is called “Coulomb blockade
region”. In this region, we observe zero transport of ions inside the
nanopore. However, when the electrical voltage is beyond the critical
voltage, the ion has sufficient energy to break free from the energy
barrier created by the hydration shell to enter into the pore. Thus, the
input voltage can control the transport of the ion inside the nanopore.
The device therefore acts as a binary storage unit, storing 0 when
no ion passes through the pore and storing 1 when a single ion
passes through the pore. We therefore postulate that the device can
be used for fluidic computing applications in chemistry and biology,
mimicking a computer. Furthermore, the trapped ion stores a finite
charge in the Coulomb blockade region; hence the device also acts
a super capacitor.
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 refractometric method has been used to determine optical properties of concentration features of aqueous solutions of ethanol, tetrahydrofuran and dimethylformamide at the room temperature. Changes in dielectric permittivity of aqueous solutions of ethanol, tetrahydrofuran and dimethylformamide in a wide range of concentrations (0÷1.0 molar fraction) have been studied using molecular dynamics method. The curves depending on the concentration of experimental data on excess refractive indices and excess dielectric permittivity were compared. It has been shown that stable heteromolecular complexes in binary solutions are formed in the concentration range of 0.3÷0.4 mole fractions. The real and complex part of dielectric permittivity was obtained from dipole-dipole autocorrelation functions of molecules. At the concentrations of C = 0.3 / 0.4 m.f. the heteromolecular structures with hydrogen bonds are formed. This is confirmed by the extremum values of excessive dielectric permittivity and excessive refractive index of aqueous solutions.
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: Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).
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: Noninvasive diagnostics of diseases via breath
analysis has attracted considerable scientific and clinical interest for
many years and become more and more promising with the rapid
advancements in nanotechnology and biotechnology. The volatile
organic compounds (VOCs) in exhaled breath, which are mainly
blood borne, particularly provide highly valuable information about
individuals’ physiological and pathophysiological conditions.
Additionally, breath analysis is noninvasive, real-time, painless, and
agreeable to patients. We have developed a wireless sensor array
based on single-stranded DNA (ssDNA)-functionalized single-walled
carbon nanotubes (SWNT) for the detection of a number of
physiological indicators in breath. Seven DNA sequences were used
to functionalize SWNT sensors to detect trace amount of methanol,
benzene, dimethyl sulfide, hydrogen sulfide, acetone, and ethanol,
which are indicators of heavy smoking, excessive drinking, and
diseases such as lung cancer, breast cancer, and diabetes. Our test
results indicated that DNA functionalized SWNT sensors exhibit
great selectivity, sensitivity, and repeatability; and different
molecules can be distinguished through pattern recognition enabled
by this sensor array. Furthermore, the experimental sensing results
are consistent with the Molecular Dynamics simulated ssDNAmolecular
target interaction rankings. Thus, the DNA-SWNT sensor
array has great potential to be applied in chemical or biomolecular
detection for the noninvasive diagnostics of diseases and personal
health monitoring.
Abstract: Graphene, a single-atom sheet, has been considered as
the most promising material for making future nanoelectromechanical
systems as well as purely electrical switching with graphene
transistors. Graphene-based devices have advantages in scaled-up
device fabrication due to the recent progress in large area graphene
growth and lithographic patterning of graphene nanostructures. Here
we investigated its mechanical responses of circular graphene
nanoflake under the nanoindentation using classical molecular
dynamics simulations. A correlation between the load and the
indentation depth was constructed. The nanoindented force in this
work was applied to the center point of the circular graphene nanoflake
and then, the resonance frequency could be tuned by a nanoindented
depth. We found the hardening or the softening of the graphene
nanoflake during its nanoindented-deflections, and such properties
were recognized by the shift of the resonance frequency. The
calculated mechanical parameters in the force-vs-deflection plot were
in good agreement with previous experimental and theoretical works.
This proposed schematics can detect the pressure via the deflection
change or/and the resonance frequency shift, and also have great
potential for versatile applications in nanoelectromechanical systems.
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 thermal conductivity of a fluid can be
significantly enhanced by dispersing nano-sized particles in it, and
the resultant fluid is termed as "nanofluid". A theoretical model for
estimating the thermal conductivity of a nanofluid has been proposed
here. It is based on the mechanism that evenly dispersed
nanoparticles within a nanofluid undergo Brownian motion in course
of which the nanoparticles repeatedly collide with the heat source.
During each collision a rapid heat transfer occurs owing to the solidsolid
contact. Molecular dynamics (MD) simulation of the collision
of nanoparticles with the heat source has shown that there is a pulselike
pick up of heat by the nanoparticles within 20-100 ps, the extent
of which depends not only on thermal conductivity of the
nanoparticles, but also on the elastic and other physical properties of
the nanoparticle. After the collision the nanoparticles undergo
Brownian motion in the base fluid and release the excess heat to the
surrounding base fluid within 2-10 ms. The Brownian motion and
associated temperature variation of the nanoparticles have been
modeled by stochastic analysis. Repeated occurrence of these events
by the suspended nanoparticles significantly contributes to the
characteristic thermal conductivity of the nanofluids, which has been
estimated by the present model for a ethylene glycol based nanofluid
containing Cu-nanoparticles of size ranging from 8 to 20 nm, with
Gaussian size distribution. The prediction of the present model has
shown a reasonable agreement with the experimental data available
in literature.
Abstract: We propose a new alternative method for imposing
fluid-solid boundary conditions in simulations of Multiparticle
Collision Dynamics. Our method is based on the introduction of
an explicit potential force acting between the fluid particles and a
surface representing a solid boundary. We show that our method can
be used in simulations of plane Poiseuille flows. Important quantities
characterizing the flow and the fluid-solid interaction like the slip
coefficient at the solid boundary and the effective viscosity of the
fluid, are measured in terms of the set of independent parameters
defining the numerical implementation. We find that our method can
be used to simulate the correct hydrodynamic flow within a wide
range of values of these parameters.
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.