سیلواکو - 106902

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شرح پروژه

سلام، وقت تون بخیر؛

هزینه انجام پروژه های درسی زیر چقدر میشه؟

1.  Frequency-Dependent Molecular Docking and Poisson–Boltzmann Screening of Cyclic-di-GMP Receptor Protein under Low-Frequency Electromagnetic Field

2.   Multi-Scale Poisson–Boltzmann Modeling of Entire Bacterial Cellulose Synthase Terminal Complex under Rotating Magnetic Field – Induced Membrane Potential Oscillations

۱۰ روز

Project 1 – Title:

 Frequency-Dependent Molecular Docking and Poisson–Boltzmann Screening of Cyclic-di-GMP Receptor Protein under Low-Frequency Electromagnetic Field

Tool: Schrödinger Glide XP + Prime MM-GBSA + APBS via Bioluminate

Objective

The second messenger c-di-GMP directly controls cellulose synthase activity. Show that LF-EMF modifies the docking pose and electrostatics of c-di-GMP inside its receptor (e.g., BcsE or PilZ domain) through subtle magnetic torque on aromatic rings and induced dipoles.

Tasks

Prepare the crystal or AlphaFold structure of K. xylinus c-di-GMP-binding protein.

Perform high-precision Glide XP docking of c-di-GMP with and without induced magnetic dipole (implemented via restrained aromatic ring orientation at 0, 10, 25, 50 Hz).

Refine top 50 poses with Prime MM-GBSA and 20-ns MD in explicit solvent.

For every refined complex, run Poisson–Boltzmann electrostatics and calculate:

Local dielectric screening at the binding pocket

Change in electrostatic binding contribution ΔΔGₑₗₑc

Shift in surface potential at the allosteric cellulose-synthase interface

Reproduce the experimentally observed bell-shaped cellulose production curve (peak at ~25–30 Hz) purely from calculated ΔΔGₑₗₑc(frequency).

Project 2 – Title:

 Multi-Scale Poisson–Boltzmann Modeling of Entire Bacterial Cellulose Synthase Terminal Complex under Rotating Magnetic Field – Induced Membrane Potential Oscillations

Tool: Schrödinger Bioluminate + Maestro + PDB-wide APBS + custom Python scripting

Objective

Instead of single protein–ligand, model the whole ~15-nm cellulose synthase terminal complex embedded in a realistic outer-membrane patch and calculate how the rotating magnetic field generates oscillating transmembrane potential that directly gates the synthase.

Tasks

Assemble the full terminal complex (8–12 BcsA/BcsB units + periplasmic and cytoplasmic domains) in a POPC/POPG membrane patch (~40 × 40 nm).

Add physiological ion concentrations and magnetite nanoparticles on the periplasmic side.

Run a 1-μs Desmond simulation with imposed 25 Hz rotating 30 mT field.

Every 10 ns, extract the snapshot and solve the full 3D Poisson–Boltzmann equation (APBS) on a 400³ grid with multilevel focusing.

Calculate time-dependent membrane surface potential ψ(t) and transmembrane potential oscillation amplitude across the BcsA channel.

Perform Boltzmann-weighted statistical analysis to show that potential oscillations of ±30–50 mV at 25 Hz increase the open-state probability of the cellulose export gate by 3–5×, exactly matching the reported 300–500 % increase in bacterial cellulose yield.

Reference Articles:

Exposure to non-continuous rotating magnetic field induces metabolic strain-specific response of Komagataeibacter xylinus

Intensification of bacterial cellulose production process with sequential electromagnetic field exposure aided by dynamic modelling

Modification of bacterial cellulose through exposure to the rotating magnetic field

Chapter Two - The use of the electromagnetic field in microbial process bioengineering

Silvaco_Comsol

#M.G, 

مهارت ها و تخصص های مورد نیاز

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