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Zhen Huang

Computational chemistry

Zhen Huang.

Postdoctoral researcher UC Irvine

Zhen Huang

Molecular simulation,
from model to code.

I study molecular interactions through physical models and high-performance simulation tools.

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Molecular polarization01 / Explore
Mutual induction · on
Molecular polarization in a water dimerGaussian charge-density contours surround two water molecules. Blue arrows show self-consistent induced dipoles on the atoms. Change the neighboring molecule's orientation or separation to explore their mutual response. An illustrative model, not a fitted water parameter set; arrow lengths are enlarged for visibility.H₂OH₂O · neighbor− density+ densitypᵢ
Molecules respond
to their surroundings.Gaussian densities
Coupled atomic dipoles

Conceptual water dimer · illustrative parameters · arrows enlarged

Research focus

01—03
01

Polarizable electrostatics

Gaussian multipoles and induced dipoles

Modelling the response of molecular charge distributions to their environment.

02

Force-field development

DEGAUSS and Gaussian van der Waals

Developing smooth interaction models for molecular simulation and free-energy calculations.

03

Biomolecular simulation

Enhanced sampling and molecular mechanisms

Studying membrane proteins and biomolecular interactions with molecular dynamics.

02 / Inside the pGM model

From atoms to a molecular dipole.

Explore Gaussian charges, CBV-based covalent dipoles, and self-consistent polarization. Select an atom to inspect its contribution.

Illustrative parameters

Drag to rotate · click an atom. Use arrow keys to rotate; Home resets the view. Double-click also resets the view.

− density+ density

Change the geometry; CBV coefficients uᵢ stay fixed.

Layer switches change the display only. Atomic arrows share a display scale; the molecular arrow shows direction.

Enter data for all atoms

Use the current atom order and the listed CBV neighbors: for example, O1 -0.8 H2:-0.04 H3:-0.04. Virtual directions are included. Enter CBV coefficients, not Cartesian dipole components. Edits last until reload; copy data to keep them.

How the layers fit together

qᵢ weights an atom-centered Gaussian. μᵢ is its covalent dipole, constructed as a sum of fixed uᵢ coefficients times the current CBV unit vectors; pᵢ is induced by the effective field of all other sites and any applied field. Both dipoles multiply derivatives of that Gaussian.

CBVs point from the selected atom to its listed neighbors. Using Wei’s convention, e²¹ points from atom 1 to atom 2. Dashed green arrows denote virtual covalent directions (such as H–H in water); no orthogonal frame is imposed. The model solves all atomic induced dipoles together. Their sum, the permanent atomic dipoles, and the charge-position terms give the molecular dipole. Contours show the signed charge density integrated along the viewing direction. βᵢ stays fixed as the molecule polarizes.

03 / Alchemical transformations

Changing interactions,
continuously.

Connect coupled and decoupled states through λ. Explore how DEGAUSS scales Gaussian electrostatics and double-exponential van der Waals interactions.

0 Decoupled1 Coupled

Finite pair potentials permit direct decoupling. Free energies come from sampling the ensembles along the path.

The DEGAUSS paper
Alchemically scaled DEGAUSS pair potentialPair potential versus separation. The blue curve follows the coupling parameter lambda; the dashed curve shows the fully coupled reference. The energy remains finite at complete overlap. These are reduced pair energies, not calculated free energies.
λ = 0.60 λ = 1 referenceFinite at r = 0
0 · decoupled1 · coupled

Stage 1 · scale solute charges; retain van der Waals interactions.

Opposite-charge pair · reduced units · linear charge scaling

Selected publications

All publications

Talks & presentations

All talks

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Home Research Molecular multipoles Alchemical transformations Publications About Writing Talks Games

Selected papers

A Density-Consistent, Finite van der Waals Potential from Gaussian Atomic DensitiesDEGAUSS: A Novel Softcore Force Field Using Double Exponential van der Waals and Gaussian Charge for Molecular Dynamics Simulations I: Theory and ValidationIsotropic Periodic Sum for Polarizable Gaussian Multipole ModelPerformance Tuning of Polarizable Gaussian Multipole Model in Molecular Dynamics SimulationsOptimal Scheme to Achieve Energy Conservation in Induced Dipole Models
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