page offers some examples of AquaMem's molecular dynamics (MD)
simulations, publication links and more...
|RETURN to HOME PAGE... Movies
are in AVI or GIF format and will open in most media players, including WMP.
After clicking an image link, choose to open the movie immediately or
download it and view later.
|RO Membrane Modeling: Rotating model of an aromatic crosslinked polyamide reverse osmosis
membrane showing solvation (Connolly) surface using a 1.4 Angstrom
probe diameter. Water molecules (~25% by weight) can be seen scattered
throughout the structure. File Size = ~161 MB.
RO Membrane Modeling: Rotating model of an aromatic crosslinked polyamide reverse osmosis membrane. Space-filled model with about 25Wt% water (light blue). MPD crosslink points are shown as green tubes. Na+ counterions = magenta spheres. Carbon = brown. Hydrogen = black. Oxygen = red. Nitrogen = blue. File Size = ~11 MB.
RO Membrane Modeling: The disinfection byproduct nitrosodimethyl amine (NDMA) undergoing room-temperature (300K) diffusion inside a fully solvated and crosslinked FT30 polyamide membrane. Water molecules = blue tubes; Membrane atoms = brown; Sodium counterions = yellow. File Size = ~6 MB.
|Drug Discovery 1: This short movie shows various views of a putative beta-lactam inhibitor bound inside the pocket of a bacterial penicillin binding protein. This is a transmembrane protein. Dotted lines represent hydrogen bonds. H-bond thickness indicates the relative strength of each H-bond. File Size = ~38 MB.|
|Drug Design 2: Rotating surface mesh view of a single chain of a homodimeric bacterial SecA protein translocase, a potential antimicrobial target for small-molecule drug design. SecA is a motor ATPase involved in polypeptide transmembrane transport. Bound ADP can be seen in one of many druggable pockets for this protein. File Size = ~10 MB.|
|2019 Conference Poster: Biology of Pitvipers, 11-14 July 2019|
Download our recent drug-discovery conference poster (PDF file = 2.5MB):
"Prospects for Repurposing FDA-Approved Drugs as Snake Venom Antagonists"
|Zeolite Nanopore Water Transport: Non-equilibrium molecular dynamics (NEMD) simulation of water molecules being forced single file
through a zeolite nanopore embedded in an aromatic crosslinked
polyamide membrane matrix. Each of the 10 water molecules is assigned
(from left to right) a progressively increasing initial kinetic energy.
Simulaton allows calculation of minimum
kinetic energy required for nanopore transport. File Size = ~16 MB. Click HERE for close-up view of this simulation (File Size = ~30MB).
|Zeolite Nanopore Water Transport: Non-equilibrium
MD simulation of a groupd of water molecules being forced as a group
onto the surface of an LTA zeolite nanoparticle. All water molecules
were assigned the same initial kinetic energy. Note how some water
molecules become trapped inside the zeolite frmework (inside potential
energy wells) as they lose momentum during transit across the zeolite
nanopore. File Size = ~3.5MB.
|Zeolite Nanopore Water Transport: MD
simulation of water diffusion near the surface of an LTA zeolite
nanoparticle. Note that one water molecule is shown enlarged and
colored magenta. This particular water molecule eventually penetrates
the surface of the zeolite and enters the interior of the framework.
Sodium counterions are shown as small spheres inside the zeolite
framework. File Size = ~17MB.
Zeolite Nanopore Water Transport: Non-equilibrium MD simulation of a single water molecule being forced through the major nanopore of a hydroxylated zeolite nano-particle. The kinetic energy of the water molecule is refreshed at short intervals to maintain a semi-constant pressure on it as it passes across the nanopore. File Size = ~8 MB.
|Polymer Stetching: Non-equilibrium MD simulation showing a polypropylene oligomer undergoing forced stretching in a vacuum. The left-hand end of the oligomer is anchored in place while the right-hand end is "pulled" to the right at an assigned semi-constant kinetic energy value. Size = ~4 MB.|
Complex Fluid Dynamics Near a Membrane Surface: CFD simulation of a microfluidic chamber showing complexity of fluid motions near a convoluted surface.
|Water Transport Through an FT30 Nanopore: Non-equilibrium MD simulation of a single water molecule being forced
a nanopore inside an aromatic crosslinked polyamide
membrane matrix. By assigning different initial kinetic energies to the
probe water molecule, this type of simulaton allows calculation of
minimum kinetic energy
required for nanopore penetrtion and transport. File Size = ~16 MB.
|Dynamic Chemical Reaction Simulations: We use our proprietary code to predict the outcome of simulated chemical reactions carried out in an aqueous background. The approach, briefly described HERE, "manages" forced non-equilibrium collisions between reacting speces, such as a small organic and an oxidizing agent like HOCl, NH2Cl or ozone. Water present in the system may or may not be included in the reaction path. File Size = ~1 MB.|
|A Solid-State Chemical Reaction on an Inert Crystalline Surface: Non-equilibrium MD simulation of two ozone molecules reacting (via collision) with a single terpene molecule (sabinene) adsorbed on the surface of the mineral wurtzite (ZnS). Note that several products are formed as a result of this reaction. The collision process is controlled by a semi-empircal quantum mechanical method (RM1) to simulate bond breakage and formation through molecular orbital reaarangements. Water is not included in this simulation, but can be if so desired. This approach could permit the study of reaction at catalytic surfaces. File Size = ~36 MB.|
Static Model of a Hydroxylated TiO2 (Anatase) Surface: Various perspctive views of a crystalline titaniun dioxide surface. Atomic representations: Oxygen = red; Titanium = white; Surface hydroxyl groups = green. File Size = ~140 KB.
|Polymer-Polymer Slippage: Clicking on image to left will take you to a new webpage showing non-equilibrium MD simulation of a polypropylene oligomer undergoing forced slippage against a polyaniline oligomer.|