RealQM is Quantum Mechanics as 3D multi-phase continuum mechanics based on non-overlapping electron densities interacting by Coulomb potentials giving forces on nuclei. Complexity scales only with the number of mesh points/spatial resolution, allowing realistic simulation of protein folding, chemical reactions and material mechanics. RealQM opens entirely new possibilities of unified micro-macro simulation of physical systems on a laptop.
joule_experiment_cpu.html, piston_cylinder_cpu.html,
cosmology_2d_cpu.html) — a few hundred lines of self-contained HTML/JavaScript,
scannable in fifteen minutes, intended to be run in parallel with the text.
Browser-runnable companion simulators for Real ThermoDynamics
(Body and Soul Vol V). All implement the compressible Navier–Stokes / RNS
equations on CPU or WebGPU; each is a few hundred lines of self-contained
HTML/JavaScript with no dependencies. Cumulative dissipation
D = ∫∫ μ|∇u|² dx dt is reported as the 2nd-Law witness in each.
Drate = ∫∫∫ μ_eff |∇u|² dx. The ratio
(Drate / u0) / Fdrag is
displayed live — in the limit of a sufficiently large box this ratio
tends to 1, reflecting the energy balance
Fdrag · u0 ≈ Drate
between the mechanical work the body would do against drag and the
irreversible heating in the wake. Computing the two independently and
checking the ratio is a quantitative test of the with-Dynamics 2nd
Law for this flow.∂u/∂t − D·Δu = α·u·(1−u²), stationary points
u = 0 (unstable), u = ±1 (stable). Random
initial perturbation rapidly partitions into red (u≈+1) and blue
(u≈−1) domains separated by sharp fronts, then coarsens slowly
under front-curvature flow (Allen–Cahn kinetics).∂u/∂t − D·Δu = k·u·(1−u)·(u−α), with threshold α ∈
(0, 1). Stationary points u = 0 and u = 1
(both stable), u = α (unstable). Live α slider for the
threshold; toggle initial conditions between random and a central
seeded blob to watch propagating ignition fronts.∂u/∂t − ε·Δu = α·u·(v−w)
with cyclic permutation for v and w. The reaction is rock-paper-scissors:
u beats v beats w beats u; the total u+v+w is locally conserved. Random IC
generates spiral and target patterns. Red = u, blue = v, green = w.∂v/∂t = ∂s_x/∂x + ∂s_y/∂y
with ∂s_x/∂t = ∂v/∂x, ∂s_y/∂t = ∂v/∂y. Two
narrow strips on the right edge act as wave sources (one-shot impulse on
Reset, or periodic at frequency ω if toggled). The interference pattern
that develops as the two wavefronts cross is the classic double-slit
figure — here a directly visible consequence of the linear wave equation,
no quantum-mechanical interpretation required.All RealThermo codes are open-source on github.com/Claes542/RealMolecule and developed in tandem with the Vol V book (ambsthermo.pdf). Each chapter of the book points to the companion simulator it discusses.
∂u/∂τ = ½∇²u + (K − 2P)u (wave relaxation)∂T/∂τ = D ∇²T + Q(x,τ) with Q = −∂e_wave/∂τatom_thermal.html demonstrates exact energy bookkeeping for He
relaxation: red E_wave decreases, green E_thermal grows, yellow sum stays flat.
Z(β) = Σn exp(−βEn) = Tr exp(−βH).
For realistic many-body systems the spectrum is exponential in $N$ and computationally
inaccessible — practical applications use model Hamiltonians, mean field, perturbation theory,
or path-integral / quantum Monte Carlo sampling.
Z(β) = ΣC exp(−βEC), but the sum is over
real-space tilings rather than over 3N-dim eigenstates. Each EC is a
browser-class computation; Boltzmann weights and free energy F = −kBT ln Z sit on
top unchanged.
USER_DAMPING + langevinKT in molecule.js) samples the
Boltzmann distribution by ergodic time-averaging — never computes Z explicitly.
utt − uxx − γ·uttt − δ²·uxxt = fThe Abraham–Lorentz radiation reaction (−γ uttt) carries energy out as outgoing waves; the viscous damping (−δ² uxxt) converts coherent oscillation into incoherent heat at small scales. Setting δ = h/T (with h the resolution scale of the medium, not Planck's constant) gives a temperature-dependent cutoff νcut ≈ T/h — Wien's displacement law from the PDE.
δ²(uν) = α(T)·(h|üν|/|u̇ν| − W)+.
Since |üν|/|u̇ν| ≈ ν, this activates exactly when hν > W — Einstein's
photoelectric threshold K + W = hν, derived from the PDE without postulating photons.
The Compton effect admits an analogous resonant-inelastic treatment.
C₆AB ≈ (3/2) · α_A · α_B · I_A · I_B / (I_A + I_B)and the dispersion energy E_disp(R) = −C₆/R⁶ follows from coupled-oscillator algebra alone. This is the static-polarisability limit of the Casimir–Polder integral; full agreement within ~30% of reference C₆ values for noble-gas pairs.
sweep_h2_adaptive.html),
fit a parabola near the minimum to extract the harmonic frequency
ω = √(k/μ) with μ = m_p/2, then evaluate the canonical vibrational partition function
and thermodynamic functions:
Z_vib(T) = e^(−βℏω/2) / (1 − e^(−βℏω)) U_vib(T) = (ℏω/2) coth(βℏω/2) C_vib(T) = k_B (βℏω/2)² / sinh²(βℏω/2)
molecule.js — Voronoi-partition solver. Each electron is assigned a
spatial “territory” via a label field (one integer per grid cell), and Coulomb
repulsion is computed from the per-territory density. Used for protein-scale simulations
(216-water ice melt, alpha-helix folding, hairpin folding) where the cost of explicit
orbital orthogonality would be prohibitive. The label partition is recomputed periodically;
between recomputations the territories are frozen.
mol_fast.js — unit-density orbital solver with shell splitting.
Each electron is its own orbital field (NELEC × N³ floats), evolved by ITP, with
effective Pauli exclusion via overlap penalty between orbitals. Supports multi-occupancy
(e.g. C with one 4-electron orbital) and angular splitting (sphere, hemi, third, tetra
sector wedges). Used for small molecules and dimers where orbital structure matters.
Hard limit on atom count (MAX_ATOMS=16).
realqm_rb.js red-black GPU, molecule_h2.js,
molecule_wlap.js) and the spherical-symmetry atom solver behind
atom_simulator.html.
USER_NUCLEI, USER_NORM_TARGETS, and other
configuration globals, then loads the relevant .js solver plus
p5.js for the canvas. mol_fast renders a 2D density slice (z=N/2 plane) and a
rotatable 3D ball-and-stick view. molecule.js adds backbone visualization, force arrows,
and runtime overlays for energy/dipole/angles. The interactive feel is the practical
breakthrough: WebGPU keeps a 200³ grid responsive on a single laptop GPU.
*.html in the repo are not solvers but parameterized test cases: ~150 of
them, each pinning a system (atom, dimer, protein) at a specific geometry with specific
kernels, then loading molecule.js or mol_fast.js. Many are exploratory and somewhat
redundant. The Gallery (this page) curates the validated subset.
USER_NUCLEI entries. The lesson learned
in this session: for honest comparisons, all atoms of a kind must use the same kernel
across the test set.
| Code | Lines | What it does |
|---|---|---|
| RealQM (this collection) | ~8 k | multi-atom solver, dynamics, ions, peptide MD, gallery UI |
| molecule.js | 5 285 | main solver + protein folding biases |
| mol_fast.js | 1 599 | compact shell-split solver (atoms, ions) |
| realqm_rb.js | 1 222 | red-black GPU builder solver |
| For comparison (Standard QM/DFT, decades of development): | ||
| Gaussian | ~3–4 M | commercial reference, all major methods |
| NWChem | ~3–4 M | parallel HF/DFT/CC, periodic + molecular |
| GAMESS-US | ~2 M | long-history Fortran QM package |
| Q-Chem / ORCA | ~1–2 M | modern HF/DFT/CC packages |
| CP2K | ~1 M | DFT-MD, Gaussian + plane-waves hybrid |
| VASP | ~500 k | plane-wave DFT for solids |
| PySCF / Psi4 | ~300–500 k | modern Python-fronted QM |
| Quantum ESPRESSO | ~200–300 k | plane-wave DFT, AIMD |
| Job | RealQM | Standard QM/DFT |
|---|---|---|
| Single H2O equilibrium energy + dipole | 1 GPU laptop, <1 min | 1 CPU, ~minutes (CCSD(T): hours) |
| Water dimer geometry + binding | 1 GPU, ~minute | 1 CPU, hours; CCSD(T): ~day |
| Na+(H2O)6 + dynamics 1 ps | 1 GPU, <1 min interactive | DFT-MD: 16-32 cores, hours |
| 216-water cluster, dynamics, 1 ns | 1 GPU, hours real-time | DFT-MD: 64-256 cores HPC, weeks |
| Protein folding small peptide (chignolin), µs | 1 GPU, hours (with biases) | DFT-MD: not feasible; classical Anton: weeks |
| Protein-in-water 100 residues + 5000 H2O, ns | 1 GPU, day-scale | impossible at full DFT; classical MD: cluster, days |
Spherical multiphase Atom Simulator (ground-state energies Li–Rn to ~1%) and the reduced-kernel validation against observed atomic spectra: alkali outer-electron levels (Li, Na, K, Rb, Cs) and alkaline-earth triplet excited states (Be, Mg, Ca).
| Atom | Z | Shells | Computed | Observed |
|---|---|---|---|---|
| Li | 3 | (2)+1 | −7.55 | −7.48 |
| Be | 4 | (2)+(2) | −15.14 | −14.57 |
| B | 5 | (2)+(2+1) | −25.3 | −24.53 |
| C | 6 | (2)+(2+2) | −38.2 | −37.7 |
| N | 7 | (2)+(3+2) | −55.3 | −54.4 |
| O | 8 | (2)+(3+3) | −75.5 | −74.8 |
| F | 9 | (2)+(3+4) | −99.9 | −99.5 |
| Ne | 10 | (2)+(4+4) | −132.4 | −128.5 |
| Na | 11 | (2)+(4+4)+(1) | −165 | −162 |
| Mg | 12 | (2)+(4+4)+(2) | −202 | −200 |
| Al | 13 | (2)+(4+4)+(2+1) | −244 | −243 |
| Si | 14 | (2)+(4+4)+(2+2) | −291 | −290 |
| P | 15 | (2)+(4+4)+(3+2) | −340 | −340 |
| S | 16 | (2)+(4+4)+(4+2) | −397 | −399 |
| Cl | 17 | (2)+(4+4)+(3+4) | −457 | −461 |
| Ar | 18 | (2)+(4+4)+(4+4) | −523 | −526 |
| Ca | 20 | (2)+(4+4)+(8)+(2) | −670 | −680 |
| Ti | 22 | (2)+(4+4)+(10)+(2) | −848 | −853 |
| Cr | 24 | (2)+(4+4)+(12)+(2) | −1039 | −1050 |
| Fe | 26 | (2)+(4+4)+(14)+(2) | −1260 | −1272 |
| Ni | 28 | (2)+(4+4)+(16)+(2) | −1516 | −1520 |
| Zn | 30 | (2)+(4+4)+(18)+(2) | −1773 | −1795 |
| Ge | 32 | (2)+(4+4)+(18)+(2+2) | −2089 | −2097 |
| Se | 34 | (2)+(4+4)+(18)+(4+2) | −2416 | −2428 |
| Kr | 36 | (2)+(4+4)+(18)+(4+4) | −2766 | −2788 |
| Xe | 54 | (2)+(4+4)+(18)+(18)+(4+4) | −7355 | −7438 |
| Rn | 86 | (2)+(4+4)+(18)+(32)+(18)+(4+4) | −22800 | −23560 |
| System | config | E (Ha) | obs | Δ |
|---|---|---|---|---|
| Li | 1s² + 2s (3D, 200³/12 au) | −7.43 | −7.478 | +0.05 |
| Li⁺ | 1s² (3D, 200³/12 au) | −7.19 | −7.279 | +0.09 |
| IP = E(Li⁺)−E(Li) | +0.24 | +0.198 | +0.04 | |
| F | 2+4+3 (Atom Simulator) | −104.06 | −99.73 | −4.33 |
| F⁻ | 2+4+4 (Atom Simulator) | −104.16…−104.20 | −99.85 | −4.33 |
| EA = E(F)−E(F⁻) | +0.10…+0.14 | +0.125 | ≈ 0 |
| Atom | Zkernel | rc (au) | RMS (Ha) | RMS (eV) |
|---|---|---|---|---|
| Li | 1.00 | 1.95 | 0.002 | 0.05 |
| Na | 0.95 | 2.00 | 0.004 | 0.11 |
| K | 1.00 | 2.90 | 0.004 | 0.12 |
| Rb | 1.00 | 3.10 | 0.005 | 0.14 |
| Cs | 1.00 | 3.30 | 0.005 | 0.14 |
| Atom | rc RealQM | rc fit | RMS at fit | RMS at RealQM rc |
|---|---|---|---|---|
| Li | 1.69 | 1.95 | 0.002 | 0.005 |
| Na | 2.30 | 2.00 | 0.004 | 0.004 |
| K | 4.00 | 2.90 | 0.004 | 0.010 |
| Atom | config | Zkernel | rc (au) | RMS (Ha) | RMS (eV) |
|---|---|---|---|---|---|
| He ortho | 1s + outer (triplet) | 1.00 | 2.53 | 0.0035 | 0.10 |
| He para | 1s + outer (singlet) | 1.04 | 3.25 | 0.0043 | 0.12 |
| Be triplet | 2+1+1 nested | 1.30 | 4.36 | 0.040 | 1.1 |
| Be singlet | 2+2 split angularly | 1.00 | 3.36 | 0.004 | 0.11 |
| Mg triplet | [Ne] + 2 valence | 1.21 | 5.15 | 0.027 | 0.74 |
| Ca triplet | [Ar] + 2 valence | 1.58 | 6.25 | 0.010 | 0.27 |
u += ½d·∇·(w∇u) + dt·(K-2P)·u·w // ITP eigensolve P += dt·(ΔP + 2π·u²) // Poisson solve w += dt·|c|·Δw + dt·c·|∇w| // front tracking
| Geometry | E (Ha) | K-W exact (Ha) | Diff |
|---|---|---|---|
| sep=1.6 au (near eq) | −1.22 | −1.17 | −0.05 (4% deeper) |
| sep=6 au (dissociated) | −1.07 | −1.00 | −0.07 (7% deeper) |
| E_bind = E(eq) − E(far) | −0.15 | −0.17 | 88% of exact |
c_i = u_i − u_j // advection driver w_i += 2dt·|c_i|·Δw_i + 10·dt·c_i·|∇w_i| // front track u_i += ½d·∇·(w_i∇u_i) + dt·(K − 2P_i)·u_i·w_i // ITP P_j += dt·(ΔP_j + 2π·u_{1−j}²) // Poisson, other electron's density
Per-atom convergence tests written during development, retained here for reproducibility. The Atom Simulator and the Ionization energies card supersede these — start there.
Static electron density calculations and nuclear dynamics on 200³ grids.
| Configuration | E (Ha) | μ (D) | Notes |
|---|---|---|---|
| Pure covalent (Li + H neutral, split-shell) | −7.74 | 2.77 | Basis state 1 |
| Pure ionic (Li&sup+; + H&sup-;, 1s² hemi both) | −8.02 | 7.43 | Basis state 2 |
| Linear mix (67% ion, 33% cov) — matches μ_expt | −7.93 | 5.88 | c² solved from dipole |
| Experimental LiH (CCSD(T)/exact) | −8.07 | 5.88 | Reference |
| Mix weight comparison | Ionic fraction | Covalent fraction |
|---|---|---|
| RealQM (from linear combination matching μ) | 67% | 33% |
| Standard QM / VB (textbook) | ~77% | ~23% |
mol_fast.js, no TF correction. Best result of the non-split series: closest binding to experiment, and top-tier dipole.| Config | O-H bond (au) | E (Ha) | |FH| | μ (D) | Note |
|---|---|---|---|---|---|
| Z=2 pseudo, r_c=0.5 | 1.814 | −3.75 | 0.06 contr. | 0.80 | 43% of μ_expt — too few electrons |
| Z=2 pseudo, r_c=0.3 | 1.814 | −4.23 | 0.06 contr. | 1.10 | 59% of μ_expt (tighter cusp) |
| Z=3 pseudo, r_c=0.5 | 1.814 | −6.84 | 0.05 | 1.50 | ← 81% of μ_expt, near zero-force |
| Z=3, stretched (2×) | 3.624 | −6.30 | — | — | dissociation reference |
| Quantity | Model (Z=3, r_c=0.5) | Experiment | Ratio |
|---|---|---|---|
| Binding energy ΔE | 0.54 Ha (14.7 eV) | 0.37 Ha (10.1 eV) | 1.46× |
| Dipole moment μ | 1.5 D | 1.85 D | 81% |
| Equilibrium O-H bond | ~1.8 au | 1.814 au | ~0% |
| Config | H-O-H angle | μ (D) | Note |
|---|---|---|---|
| r_c=0 (no cutoff) | drifts 111→100→95° | 1.836 | best dipole moment, geometry wanders |
| r_c=0.5 (stable) | 101.6° | 1.638 | ← stable geometry near exp 104.5° |
| Quantity | Model (best dipole) | Experiment | Ratio |
|---|---|---|---|
| Dipole moment μ | 1.836 D | 1.85 D | 99% |
| H-O-H angle (stable rc=0.5) | 101.6° | 104.5° | 97% |
mol_fast.js, no TF correction.| C–H bond (au) | E (Ha) | |F| (Ha/Bohr) | Note |
|---|---|---|---|
| 1.5 | — | ∼0.4 expanding | compressed, strong repulsion |
| 1.6 | — | ∼0.3 expanding | compressed |
| 1.8 | — | small expanding | near model minimum |
| 1.9 | — | < 0.002 | ← model equilibrium (zero-force point) |
| 2.0 | — | small contracting | slightly stretched |
| 2.054 | −13.17 | modest inward | experimental C–H bond (1.087 Å) |
| 4.108 | −12.03 | on decay tail | 2× stretched (dissociation ref) |
| Quantity | Model | Experiment | Ratio |
|---|---|---|---|
| Equilibrium bond length | ~1.9 au | 2.054 au | −8% |
| Binding energy ΔE | 1.14 Ha (31 eV) | 0.627 Ha (17 eV) | 1.82× |
mol_fast.js, no TF correction.| N–H bond (au) | |FH| (Ha/Bohr) | μ (Debye) | Note |
|---|---|---|---|
| 1.80 | ~0.03 expanding | ~1.2 | slightly compressed |
| 1.82 | < 0.03 | ~1.2 | ← model equilibrium (zero-force) |
| 1.85 | ~0.03 contracting | ~1.2 | slightly stretched |
| 1.912 | ~0.05 contracting | 0.93 | experimental N–H bond (1.012 Å) |
| Quantity | Model (at 1.82) | Experiment | Ratio |
|---|---|---|---|
| Equilibrium N–H bond | ~1.82 au | 1.912 au | −5% |
| Dipole moment μ | ~1.2 D | 1.47 D | ~81% |
| Binding energy (from earlier scan) | 0.98 Ha (27 eV) | 0.44 Ha (12 eV) | 2.22× |
| r_c | RealQM D_e (Ha) | RealQM (eV) | Real atom | Exp D_e (Ha) | Exp (eV) |
|---|---|---|---|---|---|
| 0.0 | −0.1543 | −4.20 | H2 | −0.1745 | −4.75 |
| 0.3 | −0.0609 | −1.66 | — | — | — |
| 0.4 | −0.0561 | −1.53 | — | — | — |
| 0.5 | −0.0561 | −1.53 | Li2 | −0.039 | −1.05 |
| 0.6 | −0.0490 | −1.33 | — | — | — |
| 0.65 | −0.0201 | −0.55 | — | — | — |
| 0.7 | −0.0163 | −0.44 | — | — | — |
| 0.8 | −0.0100 | −0.27 | Na2 | −0.027 | −0.73 |
| r_c | E(R=3) | E(R=6) | E_bind (Ha) | E_bind (eV) | Real molecule | Exp (eV) |
|---|---|---|---|---|---|---|
| 0.0 | — | — | — | — | He2 | −0.0009 |
| 0.3 | −10.12 | −10.05 | −0.07 | −1.9 | — | — |
| 0.5 | −8.09 | −7.90 | −0.19 | −5.2 | O2 | −5.2 |
| 0.8 | −6.40 | −6.15 | −0.25 | −6.8 | — | — |
| Model | r_c | E_bind (Ha) | E_bind (eV) | Exp (eV) |
|---|---|---|---|---|
| Split (4 domains) | 0.5 | −0.19 | −5.2 | −5.2 |
| Split (4 domains) | 0.8 | −0.25 | −6.8 | −5.2 |
| Non-split, no SIC factor | 0.8 | −0.47 | −12.8 | −5.2 |
| Non-split, (n-1)/n SIC + T-fix | 0.8 | −0.27 | −7.3 | −5.2 |
molecule_h2.js. Split model with r_c=0.5 matches O2 exactly. Non-split without corrections overbinds ~2.5×; with (n-1)/n SIC retaining real intra-orbital Coulomb + gradient skip at r_c boundary, overbinding drops to ~1.4× — residual excess is the missing inter-orbital exchange.Cations, anions, ion pairs, and their water shells. Anion chemistry enabled by Option B (Z=k kernel + target=k+1 electrons) representation.
Proton transfer, ion formation, salt dissolution, enzyme catalysis, and bond breaking — driven by electron density forces.
Water clusters, ice, metallic bonding, and phase transitions.
aLat = 7.0 Å
is approximate. With slider at T = 0 K, watch |F|inner in the
controls panel. Wait ~30 s to plateau, note the value. Type a new aLat (try 6.5, 7.0, 7.5)
and click apply & reload. The aLat with the smallest |F|inner is the
true equilibrium.USER_SHEAR_RATE) added to molecule.js for
ice-melt experiments. No frozen layers, no surface artifacts — deformation is uniform shear by construction.
nucMass() in molecule.js returns the proton mass (~1836 a.u.) for
any atom with Znuc=1, regardless of species. Real Na (~42 000 a.u.) and Cl (~64 000 a.u.) would
slow the dynamics by a factor of ~25, but ratios γ/γ̇ are preserved.nacl_shear.html,
nacl_shear_stress.html) hit the same finite-system limitations.| Geometry | E (Ha) | Notes |
|---|---|---|
| R = 2.196 au (equilibrium) | −6.77 | arch=2, 10000 steps |
| R = 6.0 au (dissociated ref) | −6.07 | residual mid-range attraction at this R |
| ΔEbind = E(R) − E(2R) | −0.70 Ha | −439 kcal/mol vs exp −384 (14% over) |
| Tsim | Lindemann ratio | State |
|---|---|---|
| 200 K | 0.02 | solid (bound, oscillating) |
| 500 K | 0.04 | solid (mild vibration) |
| 1000 K | 0.15 | transition (sub onset) |
| 1500 K | 0.22 | sublimating |
| System | Tsim_transition | Texp | Overshoot | Mechanism captured |
|---|---|---|---|---|
| NaCl crystal melt | 1500–2000 K | 1074 K | 1.4–1.9× | full Coulomb (no missing physics) |
| CO&sub2; dry-ice (bulk) | ~1000 K | 195 K | ~5× | quadrupolar (~20% of real); dispersion (~80%) missing |
| Tsim | Lindemann | State |
|---|---|---|
| 0 K | 0.005, slow drift off FCC | relaxing to true minimum |
| 300 K | 0.04 fluctuating | solid (bound, oscillating) |
| 500 K | 0.05 fluctuating | solid |
| 1000 K | 0.145 increasing | transition (sub onset) |
| 1500 K | 0.182 | sublimating |
| System | Tsub_sim | Texp | Overshoot | Missing physics |
|---|---|---|---|---|
| NaCl crystal | 1500–2000 K | 1074 K | 1.4–1.9× | none |
| CO&sub2; dry ice | ~1000 K | 195 K | 5.1× | ~80% dispersion |
| N&sub2; solid | ~1000 K | 60 K | ~17× | ~99% dispersion |
| He bare-nucleus | does not bind | Tb=4.2 K | clean negative | ~100% dispersion |
From RealQM-converged proteins to cell-scale population dynamics. The bridge: each protein species is reduced once to a small JSON record — geometry, charges, hydrophobicity, diffusion coefficient — that becomes the input parameters of a Brownian-dynamics simulator running 102–106 copies in a periodic box. Realises the Forward look: from molecules to cells paragraph of the paper as a tangible, runnable pipeline.
| Ligand | bound | in pocket | mechanism |
|---|---|---|---|
| biotin-like (hydro + − tail) | high | 24/50 (48%) | hydrophobic burial + R84 anchor |
| neutral hydrophobic ball | 25/50 | 20/50 (40%) | hydrophobic only |
| anionic ball | 50/50 | 12/50 (24%) | R84 captures at rim |
| cationic ball | 0/50 | 0/50 (0%) | R84 electrostatically excludes |
| Setup | Box | N proteins | BS pairs | BB | SS | Specificity |
|---|---|---|---|---|---|---|
| Small soup, dense | 60 Å | 10 + 10 | 9 | 0 | 0 | 100% |
| Larger soup | 90 Å | 50 + 50 | 25 | 1 | 0 | 96% |
| Random baseline (50+50) | — | — | N/(2N−1) BS fraction | 50.5% | ||
| Decoy variant | Decoy charge | Barnase specificity (uBS / (uBS+uBD)) |
|---|---|---|
| Same charge, W → S at iface only | −4 | 54% |
| Half charge, no hydrophobic core | −2 | 60% |
| Neutral, no charge, no hydrophobics | 0 | 86% |
| Random baseline | — | 50% |
RealQM applied to atomic nuclei: protons and electrons as charged density domains interacting via Coulomb forces. The old proton-electron model of the nucleus (4 protons + 2 electrons = He-4, total charge +2) revisited with modern computational methods.
|E/A|(Z) = 1.36 / (2Re + 2γZ + c/Z) MeV.
Three parameters (c, Re, γ), single proton shell of 2Z protons
(size d=c/Z) around a continuously expanding electron core
(Reeff=Re+γZ). No piecewise structure, no
threshold, no Zbreak. The Fe-Ni binding maximum emerges as the saddle
point of the c/Z vs γZ competition in the denominator:
Zpeak = √(c/(2γ)) ≈ 22−29 for
c ≈ 0.5, γ ≈ 3−5×10−4. With these
values the model reproduces the full experimental B/A curve from H-2 to U-238
— rise to the Fe-Ni peak (8.79 MeV/A) and post-iron decline to U-238 (7.57
MeV/A) — in one analytic expression.D + T → He-4 + n + 17.6 MeV
(the basis of ITER, NIF, and all proposed fusion reactors) modeled as a
multiphase 3D Coulomb continuum-mechanics simulation. In the proton-electron
picture (neutron = p + e), the constituents are:?rsep=0.5
(close, fast merge), ?rsep=1.5 (moderate), ?rsep=2.5
(further, needs to overcome barrier).
Test of energy-from-geometry in RealQM at Level 3: for a series of model hydrides HnX with X kernel charge +n and matched angular splitting, sweep the X-H bond length R and the kernel softening rc. The binding energy ΔEbind = E(Req) − E(2Req) is read off directly. Locked geometry, electrons relax via ITP.
| System | Architecture | Best rc | RealQM ΔE (kcal/mol) | Experimental | Match |
|---|---|---|---|---|---|
| XH closed-shell (X+1, no split) | 2 atoms, 2 e-, plain H&sub2;-like | 0.5 | −48 | NaH −47 | ✓ 2% |
| HXH linear (X+2, 2-split hemi) | 3 atoms, 4 e-, axis along bond | 0.4 | −140 | BeH&sub2; −144 | ✓ 3% |
| H&sub2;O bent (O+3, 2-split hemi, axis = bisector) | 4 atoms, 5 e-, lone pair paired (2 e), bond region (1 e) | 0.7 | −225 | H&sub2;O −232 | ✓ 3% |
| H&sub3;X (N+2, 2-hemi) | 5 atoms, 5 e-: 1 e top hemi (lone-pair side) + 1 e bottom (bond) + 3 H. Simple sp³ NH&sub3; (after architecture sweep) | 0.20 | −339 (dipole 2.50 D) | NH&sub3; −283 (1.47 D) | ~20% over (binding); ~70% over (dipole) |
| H&sub4;X (C+2, no-split) | 5 atoms, 6 e-: 2 e on C in single orbital + 4 H. Tetrahedral; rc sweeps the group-14 series | 0.20 | −369 | CH&sub4; −396 | ✓ within 7% |
| ↳ same model at rc = 0.40 | larger kernel, Si-like inner shell radius | 0.40 | −348 | SiH&sub4; −320 | ✓ within 9% |
| ↳ same model at rc = 0.70 | soft kernel, Ge-like atomic radius | 0.70 | −272 | GeH&sub4; −281 | ✓ within 3% |
A striking finding from the kernel-splitting sweep series: a single Level-3 architecture sweeps an entire periodic-table column by varying the kernel softening rc. The same model that gives CH4 at compact rc gives SiH4 at moderate rc and GeH4 at soft rc. This validates the interpretation of rc as encoding the inner-shell radius in the Level-3 reduction.
| Group / Series | Architecture | rc | RealQM ΔE (kcal/mol) | Real molecule | Match |
|---|---|---|---|---|---|
| Group 1 (alkali hydrides — XH closed-shell, X+1 no-split) | |||||
| XH at rc=0 | X+1 no split (= H&sub2;) | 0.00 | −92 | H&sub2; −109 | within 16% |
| NaH-like | same model | 0.50 | −48 | NaH −47 | ✓ 2% |
| KH-like | same model | 0.70 | −42 | KH ~−43 | ✓ 2% |
| Group 2 (alkaline-earth dihydrides — HXH 2-hemi, X+2) | |||||
| BeH&sub2; | 2-hemi axis along bond | 0.40 | −140 | BeH&sub2; −144 | ✓ 3% |
| intermediate | same model | 0.30 | −91 | ~MgH&sub2; (−100) | in regime |
| Group 14 (XH4 tetrahedral hydrides — H&sub4;X C+2 no-split) | |||||
| CH&sub4; | C+2 single 2-electron orbital | 0.20 | −369 | CH&sub4; −396 | ✓ 7% |
| SiH&sub4; | same model | 0.40 | −348 | SiH&sub4; −320 | ✓ 9% |
| GeH&sub4; | same model | 0.70 | −272 | GeH&sub4; −281 | ✓ 3% |
| Group 16 (bent H2X — H&sub2;O 2-hemi bisector) | |||||
| H&sub2;O | 2-hemi axis along bisector, [2,1] occupancy | 0.70 | −225 | H&sub2;O −232 | ✓ 3% |
| Group 15 (NH3 pyramidal — H&sub3;X 2-hemi, N+2) | |||||
| NH&sub3; | 2-hemi [1,1] (X+2), simple sp³ | 0.20 | −235 (or −339 long-run) | NH&sub3; −283 | 17% under or 20% over |
RealQM provides geometries; for meV-level energies, hand off to standard QM. Hobza's S66 is fundamentally an interaction-energy benchmark (CCSD(T)/CBS binding energies in the −1 to −7 kcal/mol range), and those energies sit far below RealQM's Level-3 accuracy floor (~0.1 Ha ≈ 60 kcal/mol). Trying to match S66 binding energies directly with RealQM is the wrong target. The right division of labor: RealQM finds the H-bond geometry interactively at millisecond/step on a laptop (otherwise expensive, especially in dynamics), then a single-point CCSD(T) or DFT-D calculation at that geometry — using PySCF, Psi4, ORCA, etc. — delivers the binding energy to chemical accuracy. Below we report only what RealQM is for: geometric agreement with S66 reference structures, plus force-direction diagnostics that confirm the model has its minimum near the reference. Dispersion-only systems remain out of scope without a vdW correction.
| # | Dimer | Solver | N···N or O···O (Å) | H···X (Å) | D−H···A (°) | Status | File |
|---|---|---|---|---|---|---|---|
| #1 | Water···Water | molecule.js | ~3.0 / ref 2.91 | ~2.0 / ref 1.95 | — | ✓ H-bonded | water_dimer |
| #3 | MeNH2···H2O | mol_fast.js | 2.92 / ref 2.93 | 1.97 / ref 1.95 | 180 / ref ~170 | ✓ H-bonded (Z=3 N rc=0.5 / Z=3 O rc=0.6; H atoms relax to within 2% of CCSD(T); F on donor toward N; |F|RMS=0.09) | mol_fast_methylamine_water |
| #5 | MeOH···MeOH | molecule.js | ~2.9 / ref 2.83 | — | — | ✓ H-bonded | ch3oh_dimer |
| #10 | MeNH2···MeNH2 | mol_fast.js | 3.30 / ref 3.34 | 2.37 / ref 2.40 | 152 / ref 165–170 | ✓ H-bonded (N=150³: proton bound, distances within 1%) | mol_fast_methylamine_dimer |
| #15 | Peptide···Peptide (formamide model) | molecule.js | — | ~1.9 / ref 1.83 | — | ✓ H-bonded (cyclic dual) | formamide_dimer |
| #4/#16 | Peptide···Water | molecule.js | — | ~1.9 / ref ~1.9 | — | ✓ H-bonded | formamide_water |
| — | 23 dispersion-bound systems (benzene···benzene, alkane dimers, …): out of scope without vdW correction | × not attempted | |||||
| — | 20 mixed (T-shape benzene, …): same vdW limitation | × not attempted | |||||