Skip to main content
Log in

Computational Modeling of Channelrhodopsin-2 Photocurrent Characteristics in Relation to Neural Signaling

  • Original Article
  • Published:
Bulletin of Mathematical Biology Aims and scope Submit manuscript

Abstract

Channelrhodopsins-2 (ChR2) are a class of light sensitive proteins that offer the ability to use light stimulation to regulate neural activity with millisecond precision. In order to address the limitations in the efficacy of the wild-type ChR2 (ChRwt) to achieve this objective, new variants of ChR2 that exhibit fast mon-exponential photocurrent decay characteristics have been recently developed and validated. In this paper, we investigate whether the framework of transition rate model with 4 states, primarily developed to mimic the biexponential photocurrent decay kinetics of ChRwt, as opposed to the low complexity 3 state model, is warranted to mimic the mono-exponential photocurrent decay kinetics of the newly developed fast ChR2 variants: ChETA (Gunaydin et al., Nature Neurosci. 13:387–392, 2010) and ChRET/TC (Berndt et al., Proc. Natl. Acad. Sci. 108:7595–7600, 2011). We begin by estimating the parameters of the 3-state and 4-state models from experimental data on the photocurrent kinetics of ChRwt, ChETA, and ChRET/TC. We then incorporate these models into a fast-spiking interneuron model (Wang and Buzsaki, J. Neurosci. 16:6402–6413, 1996) and a hippocampal pyramidal cell model (Golomb et al., J. Neurophysiol. 96:1912–1926, 2006) and investigate the extent to which the experimentally observed neural response to various optostimulation protocols can be captured by these models. We demonstrate that for all ChR2 variants investigated, the 4 state model implementation is better able to capture neural response consistent with experiments across wide range of optostimulation protocol. We conclude by analytically investigating the conditions under which the characteristic specific to the 3-state model, namely the monoexponential photocurrent decay of the newly developed variants of ChR2, can occur in the framework of the 4-state model.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6
Fig. 7
Fig. 8
Fig. 9

Similar content being viewed by others

References

  • Bass, C. E., Grinevich, V. P., Vance, Z. B., Sullivan, R. P., Bonin, K. D., & Budygin, E. A. (2010). Optogenetic control of striatal dopamine release in rats. J. Neurochem., 114(5), 1344–1352.

    Google Scholar 

  • Berndt, A., Schoenenberger, P., Mattis, J., Tye, K., Deisseroth, K., Hegemann, P., & Oertner, T. (2011). High-efficiency channelrhodopsins for fast neuronal stimulation at low light levels. Proc. Natl. Acad. Sci. USA, 108(18), 7595–7600.

    Article  Google Scholar 

  • Boyden, E. S., Zhang, F., Bamberg, E., Nagel, G., & Deisseroth, K. (2005). Millisecond-timescale, genetically targeted optical control of neural activity. Nat. Neurosci., 8(9), 1263.

    Article  Google Scholar 

  • Braun, F. J., & Hegemann, P. (1999). Two light-activated conductances in the eye of the green alga volvox carteri. Biophys. J., 76(3), 1668–1678.

    Article  Google Scholar 

  • Cardin, J., Carlén, M., Meletis, K., Knoblich, U., Zhang, F., Deisseroth, K., Tsai, L., & Moore, C. I. (2009). Driving fast-spiking cells induces gamma rhythm and controls sensory responses. Nature, 459(7247), 663–667.

    Article  Google Scholar 

  • Crick, F. H. (1979). Thinking about the brain. Sci. Am., 241(3), 219–232.

    Article  Google Scholar 

  • Deisseroth, K., Feng, G., Majewska, A. K., Miesenböck, G., Ting, A., & Schnitzer, M. J. (2006). Next-generation optical technologies for illuminating genetically targeted brain circuits. J. Neurosci., 26(41), 10380.

    Article  Google Scholar 

  • Golomb, D., Yue, C., & Yaari, Y. (2006). Contribution of persistent na+ current and m-type k+ current to somatic bursting in ca1 pyramidal cells: combined experimental and modeling study. J. Neurophysiol., 96(4), 1912–1926.

    Article  Google Scholar 

  • Gradinaru, V., Mogri, M., Thompson, K. R., Henderson, J. M., & Deisseroth, K. (2009). Optical deconstruction of parkinsonian neural circuitry. Science, 324(5925), 354.

    Article  Google Scholar 

  • Grossman, N., Nikolic, K., Toumazou, C., & Degenaar, P. (2011). Modeling study of the light stimulation of the neuron cell with channelrhodopsin-2 mutants. In IEEE trans, biomedical eng (pp. 1742–1751).

    Google Scholar 

  • Gunaydin, L., Yizhar, O., Berndt, A., Sohal, V., Deisseroth, K., & Hegemann, P. (2010). Ultrafast optogenetic control. Nat. Neurosci., 13(3), 387–392.

    Article  Google Scholar 

  • Hegemann, P., Ehlenbeck, S., & Gradmann, D. (2005). Multiple photocycles of channelrhodopsin. Biophys. J., 89(6), 3911–3918.

    Article  Google Scholar 

  • Huber, D., Petreanu, L., Ghitani, N., Ranade Hromádka, T., Mainen, Z., & Svoboda, K. (2008). Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. Nature, 451(7174), 61–64.

    Article  Google Scholar 

  • Ishizuka, T., Kakuda, M., Araki, R., & Yawo, H. (2006). Kinetic evaluation of photosensitivity in genetically engineered neurons expressing green algae light-gated channels. Neurosci. Res., 54(2), 85–94.

    Article  Google Scholar 

  • Koch, C., & Segev, I. (1998). Methods in neuronal modeling. Cambridge: MIT Press.

    Google Scholar 

  • Kravitz, A. V., Freeze, B. S., Parker, P. R. L., Kay, K., Thwin, M. T., Deisseroth, K., & Kreitzer, A. C. (2010). Regulation of parkinsonian motor behaviours by optogenetic control of basal ganglia circuitry. Nature, 466(7306), 622–626.

    Article  Google Scholar 

  • Kuehn, B. (2010). Optogenetics illuminates brain function. JAMA, 303, 20.

    Article  Google Scholar 

  • Nagel, G., Szellas, T., Huhn, W., Kateriya, S., Adeishvili, N., Berthold, P., Ollig, D., Hegemann, P., & Bamberg, E. (2003). Channelrhodopsin-2, a directly light-gated cation-selective membrane channel. Proc. Natl. Acad. Sci. USA, 100(24), 13940–13945.

    Article  Google Scholar 

  • Nikolic, K., Degenaar, P., & Toumazou, C. (2006). Modeling and engineering aspects of channelrhodopsin2 system for neural photostimulation. Conf. Proc. IEEE Eng .Med. Biol. Soc., 1, 1626–1629.

    Article  Google Scholar 

  • Nikolic, K., Grossman, N., Grubb, M. S., Burrone, J., Toumazou, C., & Degenaar, P. (2009). Photocycles of channelrhodopsin-2. Photochem. Photobiol., 85(1), 400–411.

    Article  Google Scholar 

  • Schoenlein, R. W., Peteanu, L. A., Mathies, R. A., & Shank, C. V. (1991). The first step in vision: femtosecond isomerization of rhodopsin. Science, 254(5030), 412–415.

    Article  Google Scholar 

  • Talathi, S. S., Carney, P. R., & Khargonekar, P. P. (2011). Control of neural synchrony using channelrhodopsin-2: a computational study. J. Comput. Neurosci., 31(1), 87–103.

    Article  MathSciNet  Google Scholar 

  • Tønnesen, J., Sørensen, A. T., Deisseroth, K., Lundberg, C., & Kokaia, M. (2009). Optogenetic control of epileptiform activity. Proc. Natl. Acad. Sci. USA, 106(29), 12162.

    Article  Google Scholar 

  • Wang, Q., Schoenlein, R. W., Peteanu, L. A., Mathies, R. A., & Shank, C. V. (1994). Vibrationally coherent photochemistry in the femtosecond primary event of vision. Science, 266(5184), 422–424.

    Article  Google Scholar 

  • Wang, X., & Buzsaki, G. (1996). Gamma oscillation by synaptic inhibition in a hippocampal interneuronal network model. J. Neurosci., 16(20), 6402–6413.

    Google Scholar 

  • Zhang, F., Wang, L.-P., Brauner, M., Liewald, J. F., Kay, K., Watzke, N., Wood, P. G., Bamberg, E., Nagel, G., Gottschalk, A., & Deisseroth, K. (2007). Multimodal fast optical interrogation of neural circuitry. Nature, 446(7136), 633–639.

    Article  Google Scholar 

Download references

Acknowledgements

We would like to thank Lisa Gunaydin and Andre Berndt for sharing their data with us. This research was funded by startup funds to SST; the intramural grant on Computational Biology at the University of Florida; and the Wilder Center of Excellence for Epilepsy Research and the Children’s Miracle Network. P.P.K. was partially supported by the Eckis Professor Endowment at the University of Florida.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Sachin S. Talathi.

Electronic Supplementary Material

Below is the link to the electronic supplementary material.

(PDF 408 kB)

Appendix

Appendix

1.1 A.1 Analytical Solution of the 3-State Model

The equations describing the model are:

$$\begin{aligned} \begin{aligned}[c] \dot{o} &= P(1-o-d) - G_{d}o \\ \dot{d} &= G_{d}o - G_{r}d \end{aligned} \end{aligned}$$
(24)

The photocurrent is

$$ I = Vg_{1}o $$
(25)

The equivalent theoretical solution is

$$ I = C_{1}e^{-\lambda_{1}t} + C_{2}e^{-\lambda_{2}t} + I_{\mathrm{plat}} $$
(26)

where

$$\begin{aligned} & \lambda_{1} = \alpha- \beta; \qquad\lambda_{2} = \alpha+ \beta \end{aligned}$$
(27)
$$\begin{aligned} & \begin{aligned}[c] &\alpha= \frac{P+G_{d}+G_{r}}{2}; \qquad\beta= \sqrt{\frac {(P-G_{d}-G_{r})^{2}}{2} - G_{d}G_{r}}; \\ & I_{\mathrm{plat}} = \frac{P(\lambda_{1} + \lambda_{2} - P - G_{d})}{\lambda_{1}\lambda _{2}} \end{aligned} \end{aligned}$$
(28)

and

$$\begin{aligned} \begin{aligned}[c] C_{1} &= \frac{D_{0}P\lambda_{1} + (\lambda_{2} -P -G_{d})(P - O_{0}\lambda_{1})}{\lambda_{1}(\lambda_{1}-\lambda_{2})} \\ C_{2}&=O_{0} - C_{1} + \frac{P(P+G_{d}-\lambda_{1}-\lambda _{2})}{\lambda_{1}\lambda_{2}} \end{aligned} \end{aligned}$$
(29)

When ideal initial conditions are satisfied (D 0=0; O 0=0), the solution presented in Berndt et al. 2011 is recovered.

1.2 A.2 Derivation of Formula (8) from the Main Manuscript

We start with the expression of the first eigenvalue given by Eq. (27) above:

$$ \lambda_{1} = \frac{P+G_{d}+G_{r}}{2} - \frac{\sqrt {(P-G_{d}-G_{r})^{2} - 4G_{d}G_{r}}}{2} $$
(30)

We multiply the equation above with 2 and rearrange the terms to obtain:

$$ P+G{d}+G_{r} - 2\lambda_{1} = \sqrt{(P-G_{d}-G_{r})^{2} - 4G_{d}G_{r}} $$
(31)

we raise the equation above to the second power and rearrange the terms to obtain

$$ \lambda_{1}^{2} - \lambda_{1}(G_{d}+G_{r}) +P(G_{d}+G_{r} - \lambda _{1}) +G_{d}G_{r} = 0 $$
(32)

which finally gives

$$ P = \lambda_{1} + \frac{G_{r}G_{d}}{\lambda_{1} - G_{r} - G_{d}} $$
(33)

1.3 A.3 Evaluation of Necessary Initial Conditions for the 3-State Model

We can find the initial conditions necessary to obtain a photocurrent, which will exhibit the appropriate I peak/I plat ratio by use of the following conditions:

  1. 1.

    We first find the coefficients of the homogeneous solution (C 1,C 2), which will satisfy the experimental data by solving the following system of equations:

    $$\begin{aligned} \begin{aligned}[c] \lambda_{1}C_{1}e^{-\lambda_{1}t_{p}} + \lambda_{2}C_{2}e^{-\lambda _{2}t_{p}} &= 0 \\ \frac{C_{1}e^{-\lambda_{1}t_{p}}}{I_{\mathrm{plat}}} + \frac {C_{2}e^{-\lambda_{2}t_{p}}}{I_{\mathrm{plat}}} + 1 &= \frac {1}{R} \end{aligned} \end{aligned}$$
    (34)

    where the first equation represents the condition that the derivative of the photocurrent function is zero for the I=I peak and the second equation instantiate the condition that the ration I peak/I plat must match the ratio \(\frac{1}{R}\) provided by the experimental data.

  2. 2.

    With C 1 and C 2 determined above, we can find the initial conditions (o 0,d 0) by solving Eqs. (34) given in the previous section; then C 0=1−o 0d 0.

The solutions for the all of the above equations have been evaluated symbolically in Matlab by using the function solve and then numerically by allowing the parameters to take the appropriate values in the symbolic solution.

1.4 A.4 Experimental Results—Additional Information

1.4.1 A.4.1 Evaluation of the Activation Time Constant τ rise

The evaluation of the time constant of the rising phase of the photocurrent from zero to peak has been performed by approximating the photocurrent curve with a mono-exponential function. Thus, we can write

$$ I(t) = I_{\max}\bigl(1-e^{-\frac{t}{\tau_{\mathrm{rise}}}}\bigr) $$
(35)

when the photocurrent reaches maximum (at t=t p ) we can approximate

$$ \frac{I}{I_{\max}}\simeq0.99999 $$
(36)

which leads to

$$ \tau_{\mathrm{rise}} = -\frac{t_{p}}{\ln(0.00001)} $$
(37)

1.4.2 A.4.2 Comparison Between the Photocurrent Induced by Continuous 1 s and Brief 2 ms Optostimulation in Cell Expressing ChRwt and the Fast ChRET/TC Variant

We present in Fig. 10a comparison between the ChR wt and ChRET/TC photocurrent elicited by 1 s and 2 ms continuous optostimulation.

Fig. 10
figure 10

Comparison example of the ChR2 photocurrent elicited by 1 s and 2 ms optostimulation. (A1) and (B1) Empirical data profile constructed for ChRwt and ChRET/TC variant using Eqs. (11) and (12) from the main paper as well as the experimental data provided in Table 1 is displayed for a continuous 1s optostimulation (A1) and for a brief 2 ms optostimulation (B1) The two normalized experimental photocurrent profiles are matching the experimental results reported in Berndt et al. (2011), Fig. 3c and Fig. 2d. (A2) and (B2) Photocurrent generated by the 3-state model starting from ideal initial conditions ((I): C(0)=1; O(0)=0; D(0)=0) for ChRwt and ChRET/TC variant for 1 s (A2), respectively, 2 ms (B2) optostimulation. (A3) and (B3) Photocurrent generated for ChRwt in comparison with ChR ET/TC, by the same 3-state model but starting from special initial conditions ((II): ChRwt: C(0)=0.0041; O(0)=0.0037; D(0)=0.9922; ChRET/TC: C(0)=0.00156; O(0)=0.0098; D(0)=0.9746) evaluated in Appendix A.3. (A4) and (B4) Photocurrent generated for the same ChR2 variants using the 4-state model with ideal initial conditions ((I): C 1(0)=1; O 1(0)=0; O 2=0; C 2(0)=0)

1.4.3 A.4.3 Dependence Between the Excitation Rate (P) and Light Intensity (I)

$$ P = \epsilon F = \epsilon\frac{\sigma_{\mathrm{ret}}\phi}{w_{\mathrm{loss}}} = \frac {\epsilon\sigma_{\mathrm{ret}}\lambda}{w_{\mathrm{loss}}hc}I $$
(38)

where ϵ is the quantum efficiency of photon absorbtion (a typical value for rhodopsin is ϵ≃0.5 Berndt et al. (2011)), F=σ ret ϕ/w loss is the number of photons absorbed by ChR2 molecule per unit time, σ ret is the retinal cross-section (σ ret≃1.2×10−20 m2 Berndt et al. 2011), w loss is the measure of the loss of incidental photons due to scattering and absorbtion phenomena, ϕ=λI/hc is the photon flux per unit area, λ≃480 nm is the wave length of the light used in the stimulation protocol, I (mW/mm2) is the light intensity, \(h = 6.626\times10^{-34}\ \mathrm{J\,s}\) is the Planck’s constant and c=3×108 m/s is the speed of light in vacuum.

1.5 A.5 Derivation of the Semi-analytical Solution for the Light on Condition in the 4-State Model

The 4 state model can be written as follows:

$$\begin{aligned} \begin{aligned}[c] \dot{o_{1}} &= P_{1}(1-c_{2}-o_{1}-o_{2}) - (G_{d1}+e_{12})o_{1} + e_{21}o_{2} \\ \dot{o_{2}} &= P_{2}c_{2} + e_{12}o_{1} - (G_{d2}+e_{21})o_{2} \\ \dot{c_{2}} &= G_{d2}o_{2} - (P_{2}+G_{r})c_{2} \end{aligned} \end{aligned}$$
(39)

With the notation y=[o 1 o 2 c 2]T, Eq. (39) can be than expressed as follows:

$$\begin{aligned} \dot{y} =& \left [ \begin{matrix} -(P_{1}+G_{d1}+e_{12})& e_{21}-P_{1} & -P_{1} \\ e_{12} & -(G_{d2}+e_{21}) & P_{2} \\ 0 & G_{d2} & -(P_{2}+G_{r}) \end{matrix} \right ]y + \left [ \begin{matrix} P_{1}\\ 0\\ 0 \end{matrix} \right ] \\ =& Ay+P \end{aligned}$$
(40)

The general solution that needs to be evaluated can be written as

$$ y = y_{c}+y_{p} $$
(41)

where y c of the homogeneous (complementary) solution and y p is the particular solution of the system of Eqs. (39). In the following, we will evaluate both components.

1.5.1 A.5.4 Finding the Eigenvalues

The characteristic equation is

$$ \det(A - \lambda I) = 0 $$
(42)

or

$$ \left| \begin{matrix} -(P_{1}+G_{d1}+e_{12}) - \lambda& e_{21}-P_{1} & -P_{1} \\ e_{12} & -(G_{d2}+e_{21}) - \lambda& P_{2} \\ 0 & G_{d2} & -(P_{2}+G_{r}) - \lambda \end{matrix} \right| =0 $$
(43)

which leads to

$$\begin{aligned} & {-}\bigl[(P_{1}+G_{d1}+e_{12}+\lambda) (G_{d2}+e_{21}+\lambda)\bigr] - P_{1}e_{12}G_{d2} \\ &\quad {}+P_{2}G_{d2}(P_{1}+G_{d1}+e_{12}+ \lambda) + e_{12}(e_{21}-P_{1}) (P_{2}+G_{r}+\lambda) = 0 \end{aligned}$$
(44)

This equation is solved symbolically in Matlab using the commend solve, which gives the expressions for the solutions: λ 1,λ 2,λ 3. The actual expressions are very elaborated, therefore they will not be included here. The numerical evaluation of these eigenvalues has been performed in Matlab using the function eval and the parameter values provided for each variant in the main paper, Table 3.

1.5.2 A.5.5 Finding the Eigenvectors

The characteristic equation is

$$ Av = \lambda v $$
(45)

or

$$ \left [ \begin{matrix} -(P_{1}+G_{d1}+e_{12})& e_{21}-P_{1} & -P_{1} \\ e_{12} & -(G_{d2}+e_{21}) & P_{2} \\ 0 & G_{d2} & -(P_{2}+G_{r}) \end{matrix} \right ] \left [ \begin{matrix} v_{1}\\ v_{2}\\ v_{3} \end{matrix} \right ] = \lambda_{1}\left [ \begin{matrix} v_{1}\\ v_{2}\\ v_{3} \end{matrix} \right ] $$
(46)

Then the eigenvectors satisfying this equation are

$$ \begin{aligned}[c] &v = \left [ \begin{matrix} 1\\ \frac{(P_{2}+G_{r}+\lambda_{1})(\lambda _{1}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{1})-P_{1}G_{d2}}\\ \frac{G_{d2}(\lambda _{1}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda_{1})-P_{1}G_{d2}} \end{matrix} \right ];\qquad u= \left [ \begin{matrix} 1\\ \frac{(P_{2}+G_{r}+\lambda_{2})(\lambda _{2}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{2})-P_{1}G_{d2}}\\ \frac{G_{d2}(\lambda _{2}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda_{2})-P_{1}G_{d2}} \end{matrix} \right ]; \\ & w= \left [ \begin{matrix} 1\\ \frac{(P_{2}+G_{r}+\lambda_{3})(\lambda _{3}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{3})-P_{1}G_{d2}}\\ \frac{G_{d2}(\lambda _{3}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda_{3})-P_{1}G_{d2}} \end{matrix} \right ]. \end{aligned} $$
(47)

1.5.3 A.5.6 The Complementary Solution

The complementary solution can then be written as

$$ y_{c} = C_{1}e^{\lambda_{1}t}v + C_{2}e^{\lambda_{2}t}u + C_{3}e^{\lambda_{3}t}w $$
(48)

or

$$\begin{aligned} y_{c} &= \left[ \begin{matrix} e^{\lambda_{1}t}&e^{\lambda_{2}t}\\ \frac{(P_{2}+G_{r}+\lambda_{1})(\lambda _{1}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{1})-P_{1}G_{d2}}e^{\lambda_{1}t}& \frac{(P_{2}+G_{r}+\lambda_{2})(\lambda _{2}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{2})-P_{1}G_{d2}}e^{\lambda_{2}t} \\ \frac{G_{d2}(\lambda _{1}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{1})-P_{1}G_{d2}}e^{\lambda_{1}t}& \frac{G_{d2}(\lambda _{2}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{2})-P_{1}G_{d2}}e^{\lambda_{2}t} \end{matrix} \right. \\ & \left.\begin{matrix} e^{\lambda_{3}t}\\ \frac{(P_{2}+G_{r}+\lambda_{3})(\lambda _{3}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{3})-P_{1}G_{d2}}e^{\lambda_{3}t}\\ \frac{G_{d2}(\lambda _{3}+P_{1}+G_{d1}+e_{12})}{(e_{21}-P_{1})(P_{2}-G_{r}+\lambda _{3})-P_{1}G_{d2}}e^{\lambda_{3}t} \end{matrix}\right] \left [ \begin{matrix} C_{1}\\ C_{2}\\ C_{3} \end{matrix} \right ] \end{aligned}$$
(49)

or, by notation

$$ y_{c} = A_{c}C $$
(50)

1.5.4 A.5.7 Finding the Particular Solution

The following analytical steps are performed in Matlab:

  1. (a)

    We evaluate the inverse of the complementary matrix \(A_{c}^{-1}\);

  2. (b)

    We evaluate the product:

    $$ Z = A_{c}^{-1}\cdot P = A_{c}^{-1} \left [ \begin{matrix} P_{1}\\ 0\\ 0 \end{matrix} \right ] $$
    (51)
  3. (c)

    We integrate symbolically Z using the commend: R=int(Z,t);

  4. (d)

    We evaluate the particular solution: y p =A c R.

1.5.5 A.5.8 Finding Coefficients C 1,C 2,C 3 by use of Initial Conditions

To coefficients of the homogeneous solution can be found by considering the following condition:

$$ A_{c}(0)C +y_{p}(0) = y_{0} $$
(52)

The above system of equations cannot be solved in Matlab straightforward as the function solve is unable to find a solution when all three equations are presented simultaneously; the system can be solved, however, if the analytical expression of two of the coefficients is given and only one equation is solved symbolically. For this purpose, we derive the equations for the first and second coefficient and solve symbolically in Matlab only for the last coefficient. We expand the above equation as follows:

$$ \left [ \begin{matrix} A_{c_{11}}(0)&A_{c_{12}}(0)&A_{c_{13}}(0)\\ A_{c_{21}}(0)&A_{c_{22}}(0)&A_{c_{23}}(0)\\ A_{c_{31}}(0)&A_{c_{32}}(0)&A_{c_{33}}(0) \end{matrix} \right ]\left [ \begin{matrix} C_{1}\\ C_{2}\\ C_{3} \end{matrix} \right ] + \left [ \begin{matrix} y_{p_{1}}(0)\\ y_{p_{2}}(0)\\ y_{p_{3}}(0) \end{matrix} \right ] = \left [ \begin{matrix} 0\\ 0\\ 0 \end{matrix} \right ] $$
(53)

or

$$\begin{aligned} & A_{c_{11}}(0)C_{1} + A_{c_{12}}(0)C_{2} + A_{c_{13}}(0)C_{3} +y_{p_{1}}(0) = 0 \\ &A_{c_{21}}(0)C_{1} + A_{c_{22}}(0)C_{2} + A_{c_{23}}(0)C_{3} +y_{p_{2}}(0) = 0 \\ &A_{c_{31}}(0)C_{1} + A_{c_{32}}(0)C_{2} + A_{c_{33}}(0)C_{3} +y_{p_{3}}(0) = 0 \end{aligned}$$
(54)

We get

$$ C_{1} = \bigl(-y_{p_{1}}(0) - A_{c_{12}}(0)C_{2} - A_{c_{13}}(0)C_{3} \bigr)/A_{c_{11}}(0) $$
(55)

and

$$ C_{2} = \frac{A_{c_{21}}(0)y_{p_{1}}(0) - A_{c_{11}}(0)y_{p_{2}}(0) - C_{3}(A_{c_{23}}(0)A_{c_{11}}(0) - A_{c_{21}}(0)A_{c_{13}})(0)}{A_{c_{22}}(0)A_{c_{11}}(0) - A_{c_{21}}(0)A_{c_{12}}(0)} $$
(56)

We introduce Eqs. (55) and (56) in the last Eq. (54) and then solve symbolically this equation in Matlab for C 3; we then evaluate C 1 and C 2.

We are now able to evaluate the full theoretical solution:

$$\begin{aligned} \begin{aligned}[c] o_{1} &= C_{1}e^{\lambda_{1}t} +C_{2}e^{\lambda _{2}t}+C_{3}e^{\lambda_{3}t}+y_{p_{1}} \\ o_{2} &= A_{c_{21}}(0)C_{1}e^{\lambda_{1}t} + A_{c_{22}}(0)C_{2}e^{\lambda_{2}t}+A_{c_{23}}(0)C_{3}e^{\lambda_{3}t} + y_{p_{2}} \end{aligned} \end{aligned}$$
(57)

The photocurrent elicited in light on condition will be

$$ I = Vg_{1}(o_{1}+\gamma o_{2}) $$
(58)

or

$$\begin{aligned} I &= Vg_{1}\bigl[C_{1}\bigl(1+\gamma A_{c_{21}}(0)\bigr)e^{\lambda_{1}t} + C_{2}\bigl(1+\gamma A_{c_{22}}(0)\bigr)e^{\lambda_{2}t} + C_{3}\bigl(1+\gamma A_{c_{23}}(0)\bigr)e^{\lambda_{3}t}\bigr] \\ &\quad+ Vg_{1}(y_{p1}+ \gamma y_{p2}) \end{aligned}$$
(59)

The reader should note that all the eigenvalues above are negative. Therefore, we can write

$$ \lambda_{1} = -\varLambda_{1};\qquad \lambda_{2} = -\varLambda_{2}; \qquad\lambda_{3} = -\varLambda_{3} $$
(60)

where Λ 1,Λ 2,Λ 3>0.

We evaluate the time constants associated with these eigenvalues to be

$$ \tau_{1} = \frac{1}{\varLambda_{1}}; \qquad\tau_{2} = \frac {1}{\varLambda_{2}}; \qquad\tau_{3} = \frac{1}{\varLambda_{3}} $$
(61)

The smallest time constant is associated with the rise phase (from zero to peak) of the photocurrent (the beginning of the optostimulation); the other two controls the fast and slow component of the photocurrent decay from peak to steady state. With the parameters found in the manuscript Table 3, we identify:

$$\begin{aligned} & \tau_{\mathrm{rise}(\mathrm{on})} = \tau_{2};\qquad\tau_{s(\mathrm{on})} = \tau_{1};\qquad \tau_{f(\mathrm{on})} = \tau_{3} \end{aligned}$$
(62)
$$\begin{aligned} & \begin{aligned}[c] &A_{\mathrm{rise}(\mathrm{on})} = C_{2}\bigl(1+\gamma A_{c_{22}}(0)\bigr); \qquad A_{s(\mathrm{on})} = C_{1}\bigl(1+ \gamma A_{c_{21}}(0)\bigr); \\ & A_{f(\mathrm{on})} = C_{3} \bigl(1+\gamma A_{c_{23}}(0)\bigr) \end{aligned} \end{aligned}$$
(63)
$$\begin{aligned} & \begin{aligned}[c] &I_{\mathrm{rise}(\mathrm{on})} = Vg_{1}A_{\mathrm{rise}(\mathrm{on})}; \qquad I_{s(\mathrm{on})} = Vg_{1}A_{s(\mathrm{on})};\\ & I_{f(\mathrm{on})} = Vg_{1}A_{f(\mathrm{on})}; \qquad I_{\mathrm {plat}} = Vg_{1}(y_{p1} + \gamma y_{p2}) \end{aligned} \end{aligned}$$
(64)
$$\begin{aligned} & I_{\mathrm{on}}(t) = I_{\mathrm{rise}(\mathrm{on})}e^{-\varLambda_{\mathrm{rise}(\mathrm{on})} t} + I_{s(\mathrm{on})}e^{-\varLambda_{s(\mathrm{on})} t} + I_{f(\mathrm{on})}e^{-\varLambda_{f(\mathrm{on})} t} +I_{\mathrm{plat}} \end{aligned}$$
(65)

For convenience, we reproduce here the analytical solution for light off condition provided in Gunaydin et al. 2010:

$$\begin{aligned} & \varLambda_{1} = b-c; \qquad\varLambda_{2} = b+c; \end{aligned}$$
(66)
$$\begin{aligned} & b = \frac{G_{d1}+G_{d2}+e_{12}+e_{21}}{2}; \qquad c = \sqrt {b^{2}-(G_{d1}G_{d2}+G_{d1}e_{21}+G_{d2}e_{12})} \end{aligned}$$
(67)
$$\begin{aligned} & I_{\mathrm{off}} = I_{s(\mathrm{off})}e^{-\varLambda_{s(\mathrm{off})} t} + I_{f(\mathrm{off})}e^{-\varLambda_{f(\mathrm{off})} t}; \end{aligned}$$
(68)

where

$$ I_{s(\mathrm{off})} = Vg_{1}A_{s(\mathrm{off})};\qquad I_{f(\mathrm{off})} = Vg_{1}A_{f(\mathrm{off})} $$
(69)

and

$$\begin{aligned} \begin{aligned}[c] &A_{s(\mathrm{off})} = \frac{[\varLambda_{2} - (G_{d1}+(1-\gamma)e_{12})]O_{10} + [(1-\gamma)e_{21} + \gamma(\varLambda_{2}-G_{d2})]O_{20}}{\varLambda _{2}-\varLambda_{1}} \\ &A_{f(\mathrm{off})} = \frac{[G_{d1} + (1-\gamma)e_{12} - \varLambda_{1}]O_{10} + [\gamma(G_{d2}-\varLambda_{1}) - (1-\gamma)e_{21}]O_{20}}{\varLambda _{2}-\varLambda_{1}} \end{aligned} \end{aligned}$$
(70)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Stefanescu, R.A., Shivakeshavan, R.G., Khargonekar, P.P. et al. Computational Modeling of Channelrhodopsin-2 Photocurrent Characteristics in Relation to Neural Signaling. Bull Math Biol 75, 2208–2240 (2013). https://doi.org/10.1007/s11538-013-9888-4

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11538-013-9888-4

Keywords

Navigation