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Self Assembly Simulation of CH4 & Protein Formation[]

Chin Keong Lam

De shaw Research


It is known for a fact that protein structure consist of result 20+ types of amino acids Chained to form a wrapped version of Polymer chain that is being controlled by RNA derived from DNA of a particular Strain depending on its function. For a certain behavior unknown to Life science community is how exactly is protein able to be formed with precisely pattern with certain form of self alignment and self assembly ability to form a Alpha Helix and Beta Sheet wrapped in a formation that enable its functionality to be valid in its purpose of creation. The following is information extracted from, As the primary components of the molecular machinery that makes life possible, proteins have a vast array of resources available to them for biomolecular self-assembly. Take for instance the eukaryotic nucleus of a multicellular organism (such as a human). The organization of the information contained within this tiny compartment is so vast that scientists are only now beginning to attempt to understand it. Containing the compartment is the nuclear membrane, which is filled with proteins that pump nutrients in and messages out. Entwined within what is called the "nuclear matrix" is the entire human genome, containing about 3 meters worth of DNA, packed into an area of only a few cubic micrometers. Keeping it all under control are then histones and thousands of other (non-histone) proteins that carry out processes such as transcription and translation. Each of these proteins has the appropriate information encoded within its peptide sequence for getting it to the location where it can do its job. In order for each of our cells to produce those proteins required for its specific task, only certain genes can be transcribed in certain cells. Thus, a very important amount of information is contained not only in the sequence of the DNA, but in its spatial organization within the nucleus. For instance, when the nucleus divides, all the contents must be unraveled, copied, and then reassembled back into two daughters of the original organized state. All this is accomplished by means of biomolecular self-assembly.


It is nature that points us to the right direction where the origin of life created by GOD is based on self assembly process in the mist of chance and external influence. Influence like thermodynamic, surrounding atmosphere and inter-molecule interaction abased on basic quantum mechanic rule like van de waal force field theory. In order to simulate this behavior, one have to model the basic interaction of inter-molecule force field repulse and attract rule based on individual molecule characteristic such as mass, and electron density, orbital force field constant. The most recent basic modeling work done by Japanese physicist Kagamiyama, Higashi-Hiroshima metaball have triggered our imagination of recreating what is going on in the everyday life of Atom to Atom interaction take constantly seek to balance the energy level by reacting with one another. For example, Iron atom in its raw form under the right temperature and atmosphere in the presence of abundant oxygen, will seek to bond with it to form its most stable state of Iron Oxide. That is why Iron will never be discovered in its raw state as FE in nature. It is this self assembly process of nature which constantly trying to find its righteous partner and path at the right surrounding to its most stable state that we need to respect that behavior. The consequence of taking heavy Matter such as uranium and try to purify it’s have its non-righteous path which in nature forbid this and we, human, constantly trying to destroy nature including our own existence will like to deviate from that and create uranium in its most un stable form and constantly trying to radiate toxic radiations that will take decades to reach its stable form and in the process destroy life by destroying the recipe( DNA) of cells of life. Only by understanding what nature desire to sustain life can human prevail and live in harmony with nature. Thus create a better world. This is the motivation behind the creation of Software and Hardware to simulate self assembly process of particular complex Form of life creation i.e. protein folding process.


The result of simulation of one carbon atom with 4 hydrogen atoms to form methane gas in human digesting system is of vast interest to many comedians and other individual including myself. The formation of methane gas during the bio-degenerate of food with presence of enzymes(complex protein) to extract amino acids and other basic elements to kick off biosynthesis process of new cells in other part of body for repair and energy to move and stimulate muscle is performed. The other simulation is done based on understanding that new protein cells are formed and folded based on the new amino acids extracted from protein cells which being degenerate after digestion process in the gut, new protein cells building recipe based on RNA messages transported from DNA in the heart of nuclei by transporter protein. This is extremely complex process, no simple self assembly process will be able to simulate this event, there are several factor influencing and engineering this formation of new protein cells, but the underlying self assembly behavior of nature is nevertheless present in this entire event. The problem is how to properly model the Recipe and formation of Alpha helix and beta sheet and the carbon backbone of initial chain sequence of amino acids with the right peptide and cause a folding to occur in the coherent way that new product (cell) is produced. The introduction of Aton Supercomputer have solved most of the modeling problem by hardwiring surrounding influences and modeling of basic Quantum Mechanic Principles so as to accelerate the simulation process using mesh-processor type of computer have improved the speed and accuracy of model without using empirical model that sacrifice real world phenomena vs. speed. Each processing node handle several parts of the environments variable and thus mimic the parallel world we live in. One Simple smart node networked to create super smart networked entity to improve productivity. This again is a analogue of insight of principle of Brain Neuron networks. One Brain cell will not create much music but network all this cells together based on GOD Given Rules, a Smart Human musician Brain is formed. Back to the basic of simulating Methane Gas formation, Anaerobic decomposition is a complex process. It occurs in three basic stages as the result of the activity of a variety of microorganisms. Initially, a group of microorganisms converts organic material to a form that a second group of organisms utilizes to form organic acids. Methane-producing (methanogenic) anaerobic bacteria utilize these acids and complete the decomposition process.

A variety of factors affect the rate of digestion and biogas production. The most important is temperature.

maintained at temperatures as low as 72°F (22.2°C). The complicated task of creating a anaerobic bacteria recipe of generating methanogenic in computer


environment is avoided here, the main idea is to simulate accurate behavior of atom in the abundance presence of Carbon and Hydrogen atoms in the absence of Oxygen to form CH4. The by product of Anaerobic decomposition.

The initial condition and vector position of Hydrogen atoms are represented in 2D simulation using cartoon simplified ionic and covalent bond model are shown in figure 1

This illustrated the principle of self assembly using very simple model and able to achieve the equivalent purpose of matching the model which is later being deployed in Anton supercomputer based on van de waal bond model. The van de waal repulsive and attractive force field are simulated using charge ions. After several run of 2D simulation, the ch4 is formed as shown in Figure 2.

Figure 2

The accuracy of the model is very importance, since the formation of CH4 is a result of Van de waal force and a random motion of atoms in solvent with hydrophobic modeling parameter(stickiness) , sometimes because of this chance, different form of Carbon Atom Chain other than methane is formed. The following is another simulation run with difference initial position of Carbon atoms, notice a X type Hydrocarbon chain is formed instead of two CH4. Refer to figure3 and 4

Figure 3



Figure 4

The attraction and repulsive Force field around the atom are modeled based on following

Based on (Wyvill and Trotman 1) and that rj is the dictance between center of atom and the force field.

The following is the update from Metaball simulation model

Drawing 1


As the model of energy field or Force field surrounding the Atom is very similar to the one we see in the Water Droplet or cells merging together under close proximity rj. The following is a drawing 2 showing a single atom force field.

Drawing 2.


The interaction between two atoms are a result of rj <= R and therefore attraction force are able to bond to form, Hydrogen bond is part of the importance “Glue” that make the formation of Alpha Helix possible based on Self Assembly process shown in the Drawing 3.

Drawing 3.

Under the influence of thermodynamic

and inter-atom bonding interaction, difference form of regular structure of molecule i.e. peptide and formed using even the simplest form of model, this indicate the true behavior of large biosystem are formed based on this complicated interaction. The following is different peptide bond formed by different simulation initial position of atom, Each polymer chain exhibit that of a Alpha Helix and Beta Sheet geometry with only modeling each atom correctly using quantum Mechanic Principle. Refer to Drawing 4.




The experiment show the importance of Self Assembly mechanism of nature to assist creating the most basic element like the H20 under its stable condition that make life possible. Any attempt to shift away from its natural stable state will be unnatural and will cause a disturbance to nature and will ultimately lead to consequen


ce of damage to system created by GOD. The recipe involve in creating lifFigure 5Figure 6e can be successfully simulated only by using the correct model of smallest and simplest form of atom and particle interaction behavior. With new Hardware and software co-working to produce faster and accurate model, Mesh Based Network computer simulated Self Assembly of Protein will ultimately reveal nature secret in disease formation and illness that cause distraction to life as we know it. By knowing how protein formation process under normal condition by simulation, new Drug can then be engineered to attack the problematic cause of ill-formed protein that turn toxin in life form.


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