Prebiotic Multi-letter Polymerization Networks with Chiral Symmetry Breaking

Damian R. Sowinski, Department of Physics and Astronomy, Dartmouth College

The Model
We begin with an alphabet of N monomers:

Motivation
Living organisms on Earth, without exception, utilize chiral molecules within their metabolic networks. All sugars are right handed, dextromers, while chiral amino acids are left handed, levomers. Laboratory synthesis of both sugars and amino acids result in racemic solutions. This poses a very interesting problem for those delving into the most profound question of the Origin of Life. How and when did the enantiomeric excess in these biomolecules emerge from the natural conditions that existed in the prebiotic soup of the early Earth? In this work we examine a simple mathematical model of a polymerization network consisting of a multi-letter chiral monomer alphabet. Chiral and achiral monomer coupling dependent rate constants are considered, as is the delity of substrate to monomer generation and an explicit bias. The strength of the general multi-letter alphabet rests in its ability to describe chiral symmetry breaking in a wide range of systems. 1-letter alphabets: polymerization networks of sugars, such as glucose. 2-letter alphabets: chiral information strings, sugar-amino acid interaction networks 4-letter alphabets: RNA and DNA synthesis 20+ letter alphabets: polymerization of amino acids into unfolded proteins An explicit bias and delity can be put in by hand, though spontaneous symmetry breaking does occur for large segments of the parameter space of monomer couplings. Surprisingly, the effective potential the asymmetry eld lives in is not very sensitive to many parameters. We begin our analysis by examining a simplied model at the dimer level, under the adiabatic approximation wherein the substrate is kept at a constant amount and higher level polymer growth in negligible.

Future Directions
The next part of this work will go into examining the parameter space of the 2-letter alphabet, to determine the range of coupling parameters that are conducive to symmetry breaking. Moving beyond the dimer model will allow a more thorough exploration of the sequence space population as well. Spatial dependence will be introduced via a diffusion term with a polymer length dependent diffusion constant. Hydrolysis cycles will also be easy to incorporate by allowing for backow between polymer spaces. Finally, Universal Template Replication will be incorporated to begin modeling RNA and DNA. The future is bright with possibilities!

A = {A1 , A2 , . . . AN }
The sequence space is constructed by taking the union of quotient spaces of the m-letter primitive word lattices with respect to the equivalence relation generated by the reversal operator: 0 =w : A m Am : w ~ 7 w ~ 0 | wn mn

w ~1 w ~2 w ~ 1 = ( w ~ 2)
Wm Am =

S=

m=1

Wm

Due to the cross-inhibition of polymer growth, chirality is incorporated into the model by introducing four polymer families: 1. The homochiral polymers

Source
AC n =
C {A~ v

|~ v Wn , Chirality (Avi ) = C i}
AC 1
AC 1

2. The left-inhibited polymers ( n > 2 )

C C Bn = {B~ | ~ v W , Chirality ( A ) = C, n v 1 v

The last bits needed to describe the dynamics are the source equations for the monomers. To simplify the analysis, we made the sources have the same form for all the monomers of the same chirality. The delity, f, controls the accuracy with which the polymers of one chirality induce the production of same-chirality monomers. 1 c o r r e s p o n d t o p e r f e c t d e l i t y, w h e r e dextropolymers make only dextromonomers, and levopolymers make only levomonomers. 0 corresponds to each polymer making 50/50 of each type of monomer. The bias, g, determines how effective dextro versus levo monomer production is. 0 corresponds to perfect symmetry between dextro and levo production. Positive bias is in the levo direction.

Adiabatic Approximation and the Reduced Bias Model, N=1

In the adiabatic approximation we set the growth of polymers longer than the dimer level equal to 0. We examine the case of a one letter alphabet, and nd generalized results for the model developed by Gleiser and Walker. The symmetry (asymmetry) elds are dened by taking the sum (difference) of chiral concentrations. We nd that the asymmetry eld lives in an effective potential with spontaneous symmetry breaking when the symmetry eld is in equilibrium. Increasing the heterochiral chiral coupling, we nd the effective potential wells are pushed upward, eventually destroying the possibility of chiral symmetry breaking when bias is nonexistent.

Chirality (Avi ) = C i 6= 1}

AC 2

D2

AC 2

3. The right-inhibited polymers ( n > 2 )

C Cn

C {C~ v

|~ v Wn , Chirality (Avn ) = C,

C B3

AC 3

C C3

C C3

AC 3

C B3

Chirality (Avi ) = C i 6= n}
C D4 C B4

AC 4

C C4

C C4

C A4

C B4

C D4

4. The frozen polymers ( n = 2, n > 3 )

C Dn

C {D~ v

|~ v Wn , Chirality (Av1 ) = C,
Chirality (Avn ) = C,

g=0.1

Asymmetry Field

The polymerization network can be visualized via a directed graph, with polymers in the above dened spaces getting mapped to higher sequence length spaces as they absorb monomers. Here the solid arrows represent homochiral polymerization, whereas dashed arrows represent heterochiral growth. The boxed regions show us that the rate reaction equations for the monomers, dimers, and trimers will be unique. All higher polymers will have similar evolution equations, all of which can be read off from the diagram.

o X X n d [ AC ] C C C i C C C C (i,s1 + i,s2 )[A~ (1 + i,s )i,s [As ] + i,s [As ] [Ai ] = Q i [ Ai ] s ] s ] + (i,s1 + i,s2 )[A~ dt ~ s W2 s W1 X X C C C C C C C (i,s1 + i,sn )[A~ s ] + i,sn [B~ s ] + i,sn [A~ s ] + i,s1 [C~ s ] + i,sn [B~ s ] + i,s1 [C~ s ] s ] + i,s1 [A~
n=3 ~ s Wn

Asymmetry Field

Chirality (Avi ) = C i 6= 1, n}

0.2 0.4 0.0 -0.2 -2 -1 0.0 0.2

-1

-1

C d[A~ C C C C C s ] = s1 ,s2 [AC ][ A ] | +( [ A ][ A ] + [ A ][ A ~ s W sWn ,n>2 s1 ,1 (~ s)1 s2 ,2 (~ s)2 s1 s2 s1 s2 2 1 (~ s) 2 (~ s) ]) |~ dt

-2 0.0 0.5 1.0 1.5 2.0

-2 0.0 0.5 1.0 1.5 2.0

-0.2 1 2 -0.4

Symmetry Field f=1, g=0, e=0

Symmetry Field f=1, g=.1, e =0

2

s0 W1

C C C 0 ,s + s0 ,s )[A 0 ][A ] ][ A ] + ( (s0 ,s1 + s0 ,s2 )[AC 0 s s s 2 1 ~ s ~ s

1
1

Asymmetry Field

Asymmetry Field

C X d[B~ ] C C C C C C C C s 0 ,s [B ][A 0 ] + s0 ,s [B ][A 0 ] ][ A ] | ] + [ B = s1 ,1 (~ s ~ s W ,n> 2 s)1 [As1 ][A1 (~ s , ( ~ s ) s s s 2 2 ~ s ~ s n s) 2 (~ s) 2 2 2 2 dt 0

s W1

g=0.2
0.2

AC i
C Ai

+
+

AC i +
AC i

C iv1 A~ v ivn C iv1 A~ v ivn C ivn B~ v

C ivn B~ v

C X d[C~ ] C C C C C C C s s0 ,s1 [AC = s2 ,2 (~ sWn ,n>2 s)2 [A2 (~ s)1 [As1 ][C1 (~ s0 ][C~ s ] + s0 ,s1 [As0 ][C~ s ] s) ][As2 ] + s1 ,1 (~ s) ] |~ dt 0

0.1

AC (i,~ v) ,
C B( i,~ v) , C B( ~ v ,i)
C D( ~ v ,i)

AC (~ v ,i)
C C( ~ v ,i)

QC i

g 1+f 1f C = Q = kC [S ](1 + C )( PC + PC ), PC = PC ([A~ s ]) 2 2 2

C

s W1

-1
-1

-2

-1

-2
-2

0.0

0.5

1.0

1.5

2.0
0.0 0.5 1.0 1.5 2.0

References
[1] ! Gleiser, Marcelo, and Sara I. Walker. "An Extended Model for the Evolution of Prebiotic Homochirality: A Bottom-Up Approach to the Origin ! of Life." ArXiv:0802.2884 (n.d.). [2] ! Gleiser, Marcelo, and Sara I. Walker. "The Chirality Of Life: From Phase Transitions To Astrobiology." ArXiv:0811.1291 (n.d.) [3] ! Gleiser, Marcelo, Bradley J. Nelson, and Sara I. Walker. "Chiral Polymerization in Open Systems From Chiral-Selective Reaction Rates." ArXiv: 1112.1393 (n.d.) [4] ! Gleiser, Marcelo. "Asymmetric Spatiotemporal Evolution of Prebiotic Homochirality." ArXiv:astro-ph/0606593 (n.d.) [5] ! Cronin, John R., and Sandra Pizzarello. "Enantiomeric Excesses in Meteoritic Amino Acids." Science. AAAS, n.d. Web. <http:// www.sciencemag.org/content/275/5302/951.short>.

Symmetry Field f=1, g=0, e=-1

Symmetry Field f=1, g=.1, e=.5

-0.1

AC i
C Ai

+
+

C iv1 C~ v C iv1 C~ v

C C( i,~ v)
C D( i,~ v)

The effects of indelity are to push the true vacua closer to one another, hence leading to an incomplete symmetry breaking event. It is surprising to see that all it takes is just a very small bias to pusht he system completely into a single chiral state.

-0.2