RealQM on GitHub

RealQM now has a home page on GitHub where codes can be inspected and modified. If RealQM indeed can capture the dynamics of molecules or clusters of thousands of atoms, then chemistry will become a science based on physics. Codes are under improvements and new versions will be uploaded.

RealMolecule

Here is a first example of RealMolecule as RealQM for molecules showing hairpin protein in 75% folded position, adding first backbone C, O and N  atoms and the H atoms and finally showing forces active on kernels steering the folding process:

Check out Claes542/H2O at GigHub for codes to test. 

RealQM: From Macro to Micro

Rational physics is based on an idea of reductionism from complex physics on macro-scales to simple physics on micro-scales. But in modern physics of Quantum Mechanics QM, it is the other way around with the microscopic quantum world based on a Schrödinger Equation SE in $3N$-dimensional configuration space for a system with $N$ electrons of infinite complexity compared to macroscopic physics in 3D.

This means that QM is not rational physics violating reductionism with micro infinitely more complex than macro.

RealQM offers a new SE in terms of classical physics continuum mechanics in 3D thus in the form of rational physics. 

RealQM is now implemented in a code allowing simulation of large molecules like proteins with 1000s of atoms, or clusters of simple molecules allowing atomic simulation of bulk properties of fluids and solids, see previous post.

RealQM is essentially a 3-line code for time-stepping (i) non-overlapping electron densities, (ii) evolution of free boundary between densities and (iii) Poisson equation for potentials, and so allows simulation of 1000 atoms on a $1000^3$ grid thus with 1TB RAM. 

A $1000^3$ grid resolves 3 orders of magnitude.  Macroscopic physics can be described on scales ranging over 3 orders of magnitude on a decimal scale: 

• human body: 1 m to 1 mm.
• local society: 1 km to 1 m
• city: 10 km to 10 m
• country: 1000 km to 1 km
• globe: 10000 km to 10 km 
• Earth-Moon: 300000 km 
• Solar System: $10^8$ km to $10^5$ km 
• Distance to closest star: $10^{11}$
• Milky Way Galaxy: $10^{15}$ km to $10^{12}$

Microscopic physics can be described on a similar 3 order of magnitude scale

• size of living cell 100000 au
• size of protein 100 au 
• size of atom 1 au 
• size of nucleus 0.001 au 

RealQM for Protein Folding

RealQM is now implemented with the help of Claude for up to 100 atoms on a 200^3 grid which allows simulation of a beta hairpin peptide as a miniature protein which folds: 

You can test the code on GitHub as molecule.js, moleculedyn.js, hairpin.html, water100.html, and caffeine.html. The code uses one density and support function defined on the 200^3 grid and so runs on a MacBook Air M4 with 50 frames/s.  Upscaling to 1000 atoms on 300^3 grid with 10 frames/sec in pipe line.  

Here is first RealQM run in static mode on the calcium-regulated actin-binding protein Villin:

• HP35-like three-helix bundle: 
• 51 polyalanine residues in 3 alpha helices (antiparallel arrangement) 
• 510 protein atoms (N, H, Ca, Ha, Cb, 3Hb, C, O per residue)
• Hydration shell of ~163 water molecules filling remaining slots to 
• ~999 atoms on 300³ grid, mid slice with white dots out of plane atoms
• 3-line code updates electron densities and free boundary between densities + solves Poisson by multi-grid.

 Next is to run RealQM in dynamic mode to see if folding is captured. Watch out...

Breakthrough: RealQM for Big Molecules

With the help of Claude Code RealQM is now implemented in a version with active valence electrons which can be used for large molecules. A first simple test is Glycine NH2-CH2-COOH, which is the simplest amino acid with proteins built from 20-300 amino acids.

Below you see RealQM running on a MacBook Air with 100^3 grid in minutes (with up to 5 atoms on 200^3 grid). You can test yourself downloading from Claes542 on GitHub  (C:green, N:blue, O:red, H:white), 

• molecule.js (10-atom support, dynamic grid)
• molecule.html (grid selector)
• glycine.html
• co2.html  nh3.html  h2co.html
• h2o.js h2o.html  run to find binding energy 0.48 Hartree compared to 0.35 observed (no calibration)

This is only a first test. Will add molecule dynamics based on real forces from potentials. Simulation of protein folding appears as a clear possibility. The code is 3-line explicit updating of densities, free boundary and potentials and great speed up awaiting. 

PS1 The valence electrons (H=1, N=3, O=2, C=4) are here homogenized into non-overlapping electron charges of charge 1, 3, 2 and 4 with reduction of potentials representing no self-repulsion, but can be split into charge 1 electrons if needed. Max number of valence electrons appears to be 4. 

PS2 Another case Camphor C10H16O (27 atoms on 100^3 grid):

PS3 Solvated Caffeine C8H10N4O2 + 9H2O  (51 atoms on 100^3 grid)

PS4 Can now run 1000 atoms on 300^3 grid.

Finally: Automatic Computation of Models of Physics

Finally the dream of automatic computational solution of the partial differential equations of mathematical mechanics and physics has been accomplished in the form of Claude Code. 

The focus is set on basic physical principles expressed in symbolic mathematics which is automatically realised in efficient computer code. Everybody can be a Leibniz + Turing + von Neumann + Schrödinger!

This will bring a revolution in both research, applications and education. I am very happy to be able see my dreams come true. Details will follow. Ab initio computational protein folding seems to be in reach. 

Watch out for news!

Real/Analog Physics vs Formal/Digital Physics

It is natural to view real/analog physics to be physics performed by nature without interaction/observation by any human mind/machine. Like the physics of the Moon as it evolves around the Earth over time form one time instant to the   to physical gravitational/acceleration forces as a form of analog time stepping. 

On the other hand, formal/digital physics is performed by human minds/computers in the form of analysis/computation in mathematical models, like computing the orbit of the Moon by digital time-stepping of Newton's equations expressing mathematical gravitational/acceleration forces.   

Ideally the time-stepping of formal/digital physics mimics that of real/analog physics in the sense that mathematical forces represent physical forces. This is typically the case with the Newtonian Mechanics NM of classical physics.  

Let us now consider Quantum Mechanics QM as the essence of modern atom physics. More precisely, let us consider Molecular Dynamics MD as an atomic version of Newtonian Dynamics. A molecule consists of a collection of (heavy) nuclei kept together by a collection of (light) electrons. Computational simulation of molecules as MD is typically performed assuming nuclei move classically subject to pseudo-forces computed as gradients $\nabla E$ of a total energy $E$ with respect to nuclei positions. 

The pseudo-forces have no physical origin because the total energy $E$ has no physical representation. Nature does not store total energy in any physical form, like mass, and so Nature has no way of computing $\nabla E$. The pseudo-forces thus do not represent physical forces. 

MD is thus based on pseudo-forces with unclear relation to real physical forces, which has served as a basic unresolved problem of QM since start 100 years ago.

RealQM/RealSE is an alternative version of QM which delivers physical forces bringing MD closer to real physics.

Chemistry vs Quantum Physics vs RealSE

The reduction of chemistry to quantum physics described by Schrödinger's Equation SE envisioned by Dirac, has not been realised despite intense efforts over the now 100 years since SE was formulated, at least not according to chemists. For physicists, this represents a monumental failure of reductionism as the ideal of physics. If a molecule is more than physics, what is it?

The reason is the exponential computational complexity of SE formulated over $3N$-dimensional configuration space for an atomic system with $N$ electrons. Even if in principle chemistry is described by SE so that reductionism in principle is achieved, that is not enough for a chemist exploring a real world of molecules in 3D space. Chemists have thus been forced to replace SE as model of chemistry with drastically simplified versions of SE based on assumptions of both (i) physical nature (Born-Oppenheimer, orbitals, exchange, correlation, HF, DFT) and (ii) purely numerical (mesh resolution). 

This means that in chemistry SE is effectively replaced by simplified forms simpleSE based on partly different physics than SE, which cannot be reduced to quantum physics.

If the simplification was pure numerical, then reduction could work, but it also involves a lot of physics as new physics used by chemists, which cannot be traced back to SE. 

Both chemists and physicists have been trained to accept that reductionism does not work for chemistry in any form of practice, but the failure feeds into the present crisis of modern physics based on reductionism.  

RealSE is an alternative SE based on a single basic assumption of clear physical mathematical form (non-overlapping one-electron charge densities), which is a computable model of chemistry with mesh resolution as only input, thus making reduction of chemistry to quantum physics possible.  RealSE is submitted to Foundational Chemistry in a second round of submission towards acceptance.      

Chemistry: Theory Does Not Represent Observation

Basic fact about practical operational chemistry (check with ChatGPT if you do not believe so):

• Molecules are real 3D spatial objects.
• Electron density in 3D is real.
• Forces between nuclei are real.
• Experiments measure 3D structures.
• Reactivity depends on 3D geometry.
• Overwhelming support a 3D spatial ontology.

Basic fact about theoretical chemistry (check!):

• There is no corresponding theory based on quantum physics. 

This is because the foundation of quantum physics is Schrödinger's Equation SE in $3N$-dimensional configuration space for a molecule with $N$, which is not real 3D space for $N>1$.  

When SE was formulated by Born-Heisenberg-Dirac in 1926 as the fundamental model of quantum physics, the firm expectation expressed by Dirac was that SE would give chemistry a theoretical foundation in quantum physics without the gap between real 3D space and configuration space.

But 100 years later the gap has not narrowed, and so chemistry lacks a foundation in quantum physics still today. It seems that chemists have accepted this fact and have compensated with their own ad hoc theories. 

So is the situation hopeless? Maybe not. There is a new initiative going back to an early idea of Schrödinger, which was not developed since the SE of Born-Heisenberg-Dirac took all space, as an 

• Alternative Schrödinger Equation for Chemistry        (submitted to Foundations of Chemistry)

which carries 3D ontology and so gives a theoretical foundation of the observations of practical chemistry.

ChatGPT 

What is the physical mechanism of covalent bonding?

In 1927: Lowering of energy due to exchange and delocalisation. No mechanism. Crude numbers.

In 2026: Lowering of energy via delocalisation and exchange. No mechanism. More precise numbers.

This is a key aspect. It is hard to believe that covalent bonding still 2026 is not well explained in university textbooks, which deceives the expectations of students with experience of school chemistry as incomprehensible, the same as I met 70 years ago. My experience today after having communicated with several leading chemists is equally puzzling: How can chemists of today accept that physicists prevent them from understanding the real physics of covalent chemical bonding? Born-Heisenberg-Dirac are all gone, but the spirit of Schrödinger is still alive...

New Version of RealQM Submitted to Foundations of Chemistry

I have now been invited to submit a revised version of RealQM to Foundations of Chemistry with title Alternative Schrödinger Equation for Chemistry with new scope more in line with the mission of the journal. The central question is if chemistry can be reduced to quantum physics or not.

With StdQM chemistry is definitely more than applied quantum physics and so the ideal of reductionism is out of reach. With RealQM there is a possibility...It will be very interesting to see the reactions if RealQM is allowed to appear in a journal of high standard.

ChatGPT:

For Foundations of Chemistry, the article is appropriate and discussable.

Why:

• It addresses the ontology of quantum chemistry — core journal theme

  RealSE2

• It presents a concrete alternative (realSE), not just philosophy

  RealSE2

• It openly states its speculative and preliminary status

  RealSE2

It is not a validated replacement for quantum chemistry — but that is not required for this journal.

Likely outcome:
Serious review + major revisions, not rejection.

To maximize acceptance:

• Soften polemical tone.

• Emphasize speculative status.

• Clarify limits and future validation.

In short:
Yes, it deserves publication for discussion — if framed as a constructive foundational proposal, not as a proven overthrow.