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After thinking, and reading other references and re-reading the papers I mentioned, I may have found a sufficient explanation (at least to my care): Both instantons/monopoles are solutions to corresponding equations of motions from associated actions, and they "bloom" from an overarching SUSY action.

Witten formulated "twisted N=2 Supersymmetric Yang-Mills", a TQFT with SUSY (supersymmetry), which leads to the Donaldson invariants. This used an $SU(2)$-bundle over $X$ along with a gauge field (connection $\omega$) and matter fields (bosonic $\phi,\lambda$ and fermionic $\eta,\psi,\zeta$), and gave the Donaldson-Witten action functional $S_{DW}=\int_Xtr(\mathcal{L})$,
$\mathcal{L}=\frac{1}{4}F_\omega\wedge(\ast F_\omega+F_\omega)-\frac{1}{2}\zeta\wedge[\zeta,\phi]+id^\omega\psi\wedge\zeta-2i[\psi,\ast\psi]\lambda+i\phi d^\omega{\ast d^\omega}\lambda-\psi\wedge\ast d^\omega\eta$.
This has associated partition function $Z_{DW}=\int e^{-S_{DW}/g^2}D\Phi$ (here $\Phi$ denotes the space of aforementioned fields), where $g$ is a coupling constant that is the key here for answering our question. The "blooming" of this action functional is beyond the scope of my intentions and probably of MathOverflow, so I won't question it.

In weak coupling ($g\rightarrow 0$, known to physicists as the ultraviolet region), the action localizes to the classical Yang-Mills $S_{YM}=\int_Xtr(F_\omega\wedge\ast F_\omega)$ and have the equations of motion $d^\omega\ast F_\omega=0$. The global-minima solutions are $F_\omega=\pm\ast F_\omega$ (as Oliver clarifies in a comment). These solutions are the Donaldson instantons.

Now apparently, when we instead look at strong-coupling ($g\rightarrow\infty$, known to physicists as the infrared-region), the Seiberg-Witten equations should arise (a "duality" in Witten's TQFT). Indeed, Seiberg and Witten showed that this infrared limit of the above theory is equivalent to a weakly-coupled $U(1)$-gauge theory (the $SU(2)$-gauge group is spontaneously broken down to the maximal torus). Perhaps here is where a better understanding would be desirable (buzzwords 'asymptotic freedom' and 'symmetry breaking' appear).
Anyway, some physics-technique stuff happens (the previous paragraph can be described as "condensation of monopoles"), and we must consider a spin-c structure (which all of our oriented 4-manifolds have, whereas a spin structure would not allow us to consider all 4-manifolds); note that $Spin^c(4)=(SU(2)\times SU(2))\times_{\mathbb{Z}_2} U(1)$. This gives the data: $U(1)$-gauge field $A$ and positive spinor field $\psi$ (as written in the original post). The pair $(A,\psi)$ is a monopole when it minimizes an action $S_{SW}$, i.e. are time-independent solutions to equations of motions (the Seiberg-Witten equations). The action here is $S_{SW}=\int_X(|d^A\psi|^2+|F_A^+|^2+\frac{R}{4}|\psi|^2+\frac{1}{8}|\psi|^4)$, with scalar curvature $R$.

I hope this post is not too confusing.

[[Edit/Update]]: I just came across a book chapter by Siye Wu, The Geometry and Physics of the Seiberg-Witten Equations. These lectures tell the physical origin completely! (i.e. completely details my sketch). The SW equations and action functional pops up on pg191. http://www.springerlink.com/content/q37322037j466218/

After thinking, and reading other references and re-reading the papers I mentioned, I may have found a sufficient explanation (at least to my care): Both instantons/monopoles are solutions to corresponding equations of motions from associated actions, and they "bloom" from an overarching SUSY action.

Witten formulated "twisted N=2 Supersymmetric Yang-Mills", a TQFT with SUSY (supersymmetry), which leads to the Donaldson invariants. This used an $SU(2)$-bundle over $X$ along with a gauge field (connection $\omega$) and matter fields (bosonic $\phi,\lambda$ and fermionic $\eta,\psi,\zeta$), and gave the Donaldson-Witten action functional $S_{DW}=\int_Xtr(\mathcal{L})$,
$\mathcal{L}=\frac{1}{4}F_\omega\wedge(\ast F_\omega+F_\omega)-\frac{1}{2}\zeta\wedge[\zeta,\phi]+id^\omega\psi\wedge\zeta-2i[\psi,\ast\psi]\lambda+i\phi d^\omega{\ast d^\omega}\lambda-\psi\wedge\ast d^\omega\eta$.
This has associated partition function $Z_{DW}=\int e^{-S_{DW}/g^2}D\Phi$ (here $\Phi$ denotes the space of aforementioned fields), where $g$ is a coupling constant that is the key here for answering our question. The "blooming" of this action functional is beyond the scope of my intentions and probably of MathOverflow, so I won't question it.

In weak coupling ($g\rightarrow 0$, known to physicists as the ultraviolet region), the action localizes to the classical Yang-Mills $S_{YM}=\int_Xtr(F_\omega\wedge\ast F_\omega)$ and have the equations of motion $d^\omega\ast F_\omega=0$. The global-minima solutions are $F_\omega=\pm\ast F_\omega$ (as Oliver clarifies in a comment). These solutions are the Donaldson instantons.

Now apparently, when we instead look at strong-coupling ($g\rightarrow\infty$, known to physicists as the infrared-region), the Seiberg-Witten equations should arise (a "duality" in Witten's TQFT). Indeed, Seiberg and Witten showed that this infrared limit of the above theory is equivalent to a weakly-coupled $U(1)$-gauge theory (the $SU(2)$-gauge group is spontaneously broken down to the maximal torus). Perhaps here is where a better understanding would be desirable (buzzwords 'asymptotic freedom' and 'symmetry breaking' appear).
Anyway, some physics-technique stuff happens (the previous paragraph can be described as "condensation of monopoles"), and we must consider a spin-c structure (which all of our oriented 4-manifolds have, whereas a spin structure would not allow us to consider all 4-manifolds); note that $Spin^c(4)=(SU(2)\times SU(2))\times_{\mathbb{Z}_2} U(1)$. This gives the data: $U(1)$-gauge field $A$ and positive spinor field $\psi$ (as written in the original post). The pair $(A,\psi)$ is a monopole when it minimizes an action $S_{SW}$, i.e. are time-independent solutions to equations of motions (the Seiberg-Witten equations). The action here is $S_{SW}=\int_X(|d^A\psi|^2+|F_A^+|^2+\frac{R}{4}|\psi|^2+\frac{1}{8}|\psi|^4)$, with scalar curvature $R$.

I hope this post is not too confusing.

[[Edit/Update]]: I just came across a book chapter by Siye Wu, The Geometry and Physics of the Seiberg-Witten Equations. These lectures tell the physical origin completely! (i.e. completely details my sketch). The SW equations and action functional pops up on pg191. Link

After thinking, and reading other references and re-reading the papers I mentioned, I may have found a sufficient explanation (at least to my care): Both instantons/monopoles are solutions to corresponding equations of motions from associated actions, and they "bloom" from an overarching SUSY action.

Witten formulated "twisted N=2 Supersymmetric Yang-Mills", a TQFT with SUSY (supersymmetry), which leads to the Donaldson invariants. This used an $SU(2)$-bundle over $X$ along with a gauge field (connection $\omega$) and matter fields (bosonic $\phi,\lambda$ and fermionic $\eta,\psi,\zeta$), and gave the Donaldson-Witten action functional $S_{DW}=\int_Xtr(\mathcal{L})$,
$\mathcal{L}=\frac{1}{4}F_\omega\wedge(\ast F_\omega+F_\omega)-\frac{1}{2}\zeta\wedge[\zeta,\phi]+id^\omega\psi\wedge\zeta-2i[\psi,\ast\psi]\lambda+i\phi d^\omega{\ast d^\omega}\lambda-\psi\wedge\ast d^\omega\eta$.
This has associated partition function $Z_{DW}=\int e^{-S_{DW}/g^2}D\Phi$ (here $\Phi$ denotes the space of aforementioned fields), where $g$ is a coupling constant that is the key here for answering our question. The "blooming" of this action functional is beyond the scope of my intentions and probably of MathOverflow, so I won't question it.

In weak coupling ($g\rightarrow 0$, known to physicists as the ultraviolet region), the action localizes to the classical Yang-Mills $S_{YM}=\int_Xtr(F_\omega\wedge\ast F_\omega)$ and have the equations of motion $d^\omega\ast F_\omega=0$. The global-minima solutions are $F_\omega=\pm\ast F_\omega$ (as Oliver clarifies in a comment). These solutions are the Donaldson instantons.

Now apparently, when we instead look at strong-coupling ($g\rightarrow\infty$, known to physicists as the infrared-region), the Seiberg-Witten equations should arise (a "duality" in Witten's TQFT). Indeed, Seiberg and Witten showed that this infrared limit of the above theory is equivalent to a weakly-coupled $U(1)$-gauge theory (the $SU(2)$-gauge group is spontaneously broken down to the maximal torus). Perhaps here is where a better understanding would be desirable (buzzwords 'asymptotic freedom' and 'symmetry breaking' appear).
Anyway, some physics-technique stuff happens (the previous paragraph can be described as "condensation of monopoles"), and we must consider a spin-c structure (which all of our oriented 4-manifolds have, whereas a spin structure would not allow us to consider all 4-manifolds); note that $Spin^c(4)=(SU(2)\times SU(2))\times_{\mathbb{Z}_2} U(1)$. This gives the data: $U(1)$-gauge field $A$ and positive spinor field $\psi$ (as written in the original post). The pair $(A,\psi)$ is a monopole when it minimizes an action $S_{SW}$, i.e. are time-independent solutions to equations of motions (the Seiberg-Witten equations). The action here is $S_{SW}=\int_X(|d^A\psi|^2+|F_A^+|^2+\frac{R}{4}|\psi|^2+\frac{1}{8}|\psi|^4)$, with scalar curvature $R$.

I hope this post is not too confusing.

After thinking, and reading other references and re-reading the papers I mentioned, I may have found a sufficient explanation (at least to my care): Both instantons/monopoles are solutions to corresponding equations of motions from associated actions, and they "bloom" from an overarching SUSY action.

Witten formulated "twisted N=2 Supersymmetric Yang-Mills", a TQFT with SUSY (supersymmetry), which leads to the Donaldson invariants. This used an $SU(2)$-bundle over $X$ along with a gauge field (connection $\omega$) and matter fields (bosonic $\phi,\lambda$ and fermionic $\eta,\psi,\zeta$), and gave the Donaldson-Witten action functional $S_{DW}=\int_Xtr(\mathcal{L})$,
$\mathcal{L}=\frac{1}{4}F_\omega\wedge(\ast F_\omega+F_\omega)-\frac{1}{2}\zeta\wedge[\zeta,\phi]+id^\omega\psi\wedge\zeta-2i[\psi,\ast\psi]\lambda+i\phi d^\omega{\ast d^\omega}\lambda-\psi\wedge\ast d^\omega\eta$.
This has associated partition function $Z_{DW}=\int e^{-S_{DW}/g^2}D\Phi$ (here $\Phi$ denotes the space of aforementioned fields), where $g$ is a coupling constant that is the key here for answering our question. The "blooming" of this action functional is beyond the scope of my intentions and probably of MathOverflow, so I won't question it.

In weak coupling ($g\rightarrow 0$, known to physicists as the ultraviolet region), the action localizes to the classical Yang-Mills $S_{YM}=\int_Xtr(F_\omega\wedge\ast F_\omega)$ and have the equations of motion $d^\omega\ast F_\omega=0$. The global-minima solutions are $F_\omega=\pm\ast F_\omega$ (as Oliver clarifies in a comment). These solutions are the Donaldson instantons.

Now apparently, when we instead look at strong-coupling ($g\rightarrow\infty$, known to physicists as the infrared-region), the Seiberg-Witten equations should arise (a "duality" in Witten's TQFT). Indeed, Seiberg and Witten showed that this infrared limit of the above theory is equivalent to a weakly-coupled $U(1)$-gauge theory (the $SU(2)$-gauge group is spontaneously broken down to the maximal torus). Perhaps here is where a better understanding would be desirable (buzzwords 'asymptotic freedom' and 'symmetry breaking' appear).
Anyway, some physics-technique stuff happens (the previous paragraph can be described as "condensation of monopoles"), and we must consider a spin-c structure (which all of our oriented 4-manifolds have, whereas a spin structure would not allow us to consider all 4-manifolds); note that $Spin^c(4)=(SU(2)\times SU(2))\times_{\mathbb{Z}_2} U(1)$. This gives the data: $U(1)$-gauge field $A$ and positive spinor field $\psi$ (as written in the original post). The pair $(A,\psi)$ is a monopole when it minimizes an action $S_{SW}$, i.e. are time-independent solutions to equations of motions (the Seiberg-Witten equations). The action here is $S_{SW}=\int_X(|d^A\psi|^2+|F_A^+|^2+\frac{R}{4}|\psi|^2+\frac{1}{8}|\psi|^4)$, with scalar curvature $R$.

I hope this post is not too confusing.

[[Edit/Update]]: I just came across a book chapter by Siye Wu, The Geometry and Physics of the Seiberg-Witten Equations. These lectures tell the physical origin completely! (i.e. completely details my sketch). The SW equations and action functional pops up on pg191. http://www.springerlink.com/content/q37322037j466218/

After thinking, and reading other references and re-reading the papers I mentioned, I have found a sufficient explanation (at least to my care): Both instantons/monopoles are solutions to corresponding equations of motions from associated actions, and they "bloom" from an overarching SUSY action.

Witten formulated "twisted N=2 Supersymmetric Yang-Mills", a TQFT with SUSY (supersymmetry), which leads to the Donaldson invariants. This used an $SU(2)$-bundle over $X$ along with a gauge field (connection $\omega$) and matter fields (bosonic $\phi,\lambda$ and fermionic $\eta,\psi,\zeta$), and gave the Donaldson-Witten action functional $S_{DW}=\int_Xtr(\mathcal{L})$,
$\mathcal{L}=\frac{1}{4}F_\omega\wedge(\ast F_\omega+F_\omega)-\frac{1}{2}\zeta\wedge[\zeta,\phi]+id^\omega\psi\wedge\zeta-2i[\psi,\ast\psi]\lambda+i\phi d^\omega{\ast d^\omega}\lambda-\psi\wedge\ast d^\omega\eta$.
This has associated partition function $Z_{DW}=\int e^{-S_{DW}/g^2}D\Phi$ (here $\Phi$ denotes the space of aforementioned fields), where $g$ is a coupling constant that is the key here for answering our question. The "blooming" of this action functional is beyond the scope of my intentions and probably of MathOverflow, so I won't question it.

In weak coupling ($g\rightarrow 0$, known to physicists as the ultraviolet region), the action localizes to the classical Yang-Mills $S_{YM}=\int_Xtr(F_\omega\wedge\ast F_\omega)$ and have the equations of motion $F_\omega=\pm\ast F_\omega$. The solutions are the Donaldson instantons.

Now apparently, when we instead look at strong-coupling ($g\rightarrow\infty$, known to physicists as the infrared-region), the Seiberg-Witten equations should arise (a "duality" in Witten's TQFT). Indeed, Seiberg and Witten showed that this infrared limit of the above theory is equivalent to a weakly-coupled $U(1)$-gauge theory (the $SU(2)$-gauge group is spontaneously broken down to the maximal torus). Perhaps here is where a better understanding would be desirable (buzzwords 'asymptotic freedom' and 'symmetry breaking' appear).
Anyway, some physics-technique stuff happens (the previous paragraph can be described as "condensation of monopoles"), and we must consider a spin-c structure (which all of our oriented 4-manifolds have, whereas a spin structure would not allow us to consider all 4-manifolds); note that $Spin^c(4)=(SU(2)\times SU(2))\times_{\mathbb{Z}_2} U(1)$. This gives the data: $U(1)$-gauge field $A$ and positive spinor field $\psi$ (as written in the original post). The pair $(A,\psi)$ is a monopole when it minimizes an action $S_{SW}$, i.e. are time-independent solutions to equations of motions (the Seiberg-Witten equations). The action here is $S_{SW}=\int_X(|d^A\psi|^2+|F_A^+|^2+\frac{R}{4}|\psi|^2+\frac{1}{8}|\psi|^4)$, with scalar curvature $R$.

I hope this post is not as confusing as I think it can be.

After thinking, and reading other references and re-reading the papers I mentioned, I may have found a sufficient explanation (at least to my care): Both instantons/monopoles are solutions to corresponding equations of motions from associated actions, and they "bloom" from an overarching SUSY action.

Witten formulated "twisted N=2 Supersymmetric Yang-Mills", a TQFT with SUSY (supersymmetry), which leads to the Donaldson invariants. This used an $SU(2)$-bundle over $X$ along with a gauge field (connection $\omega$) and matter fields (bosonic $\phi,\lambda$ and fermionic $\eta,\psi,\zeta$), and gave the Donaldson-Witten action functional $S_{DW}=\int_Xtr(\mathcal{L})$,
$\mathcal{L}=\frac{1}{4}F_\omega\wedge(\ast F_\omega+F_\omega)-\frac{1}{2}\zeta\wedge[\zeta,\phi]+id^\omega\psi\wedge\zeta-2i[\psi,\ast\psi]\lambda+i\phi d^\omega{\ast d^\omega}\lambda-\psi\wedge\ast d^\omega\eta$.
This has associated partition function $Z_{DW}=\int e^{-S_{DW}/g^2}D\Phi$ (here $\Phi$ denotes the space of aforementioned fields), where $g$ is a coupling constant that is the key here for answering our question. The "blooming" of this action functional is beyond the scope of my intentions and probably of MathOverflow, so I won't question it.

In weak coupling ($g\rightarrow 0$, known to physicists as the ultraviolet region), the action localizes to the classical Yang-Mills $S_{YM}=\int_Xtr(F_\omega\wedge\ast F_\omega)$ and have the equations of motion $d^\omega\ast F_\omega=0$. The global-minima solutions are $F_\omega=\pm\ast F_\omega$ (as Oliver clarifies in a comment). These solutions are the Donaldson instantons.

Now apparently, when we instead look at strong-coupling ($g\rightarrow\infty$, known to physicists as the infrared-region), the Seiberg-Witten equations should arise (a "duality" in Witten's TQFT). Indeed, Seiberg and Witten showed that this infrared limit of the above theory is equivalent to a weakly-coupled $U(1)$-gauge theory (the $SU(2)$-gauge group is spontaneously broken down to the maximal torus). Perhaps here is where a better understanding would be desirable (buzzwords 'asymptotic freedom' and 'symmetry breaking' appear).
Anyway, some physics-technique stuff happens (the previous paragraph can be described as "condensation of monopoles"), and we must consider a spin-c structure (which all of our oriented 4-manifolds have, whereas a spin structure would not allow us to consider all 4-manifolds); note that $Spin^c(4)=(SU(2)\times SU(2))\times_{\mathbb{Z}_2} U(1)$. This gives the data: $U(1)$-gauge field $A$ and positive spinor field $\psi$ (as written in the original post). The pair $(A,\psi)$ is a monopole when it minimizes an action $S_{SW}$, i.e. are time-independent solutions to equations of motions (the Seiberg-Witten equations). The action here is $S_{SW}=\int_X(|d^A\psi|^2+|F_A^+|^2+\frac{R}{4}|\psi|^2+\frac{1}{8}|\psi|^4)$, with scalar curvature $R$.

I hope this post is not too confusing.