# Computational Modeling of Chromatin Fiber to Characterize Its Organization Using Angle-Resolved Scattering of Circularly Polarized Light

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## Abstract

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## 1. Introduction

## 2. Materials and Method

#### 2.1. Computational Method

#### 2.2. Chromatin Fiber Model

## 3. Results and Discussions

## 4. Conclusions

## Author Contributions

## Funding

## Institutional Review Board Statement

## Informed Consent Statement

## Data Availability Statement

## Acknowledgments

## Conflicts of Interest

## Abbreviations

CIDS | Circular intensity differential scattering |

CD | Circular dichroism |

DDA | Discrete dipole approximation |

ADDA | DDA code |

LCP | Left circularly polarized |

RCP | Right circularly polarized |

## References

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**Figure 1.**(

**a**) Representation of CIDS, (

**b**) the discrete dipole model of chromatin fiber, (

**c**) projected view along the helical axis.

**Figure 2.**Pitch of chromatin solenoid is varied; the angular behaviour of CIDS and total scattered intensity is presented, respectively: (

**a**,

**b**) at a fixed orientation $(\alpha ,\beta ,\gamma )$ = $(0,0,0)$, (

**c**,

**d**) orientation averaging is performed.

**Figure 3.**(

**a**,

**b**) CIDS and total intensity angular dependence for different orientations of solenoid, $\lambda $ = 300 nm, (

**c**) extinction and absorption efficiency of chromatin fiber with pitch 11 nm, (

**d**) extinction efficiency of solenoid for different pitch values.

**Figure 4.**Radius of chromatin fiber is varied, the pitch is kept constant. CIDS and total scattered intensity calculations are presented, respectively; (

**a**,

**b**) at fixed orientation, (

**c**,

**d**) orientation averaging is perfromed. P = 11 nm, $\lambda $ = 300 nm.

**Figure 5.**The handedness of solenoid fiber is changed; CIDS and total scattered intensity for oppositely-handed chromatin helical fiber is given: (

**a**,

**b**) at a fixed orientation, (

**c**,

**d**) in the orientation average. $\lambda $ = 300 nm.

**Figure 6.**CIDS and total scattered intensity for the helical fiber as shown in the inset of (

**d**): 1-turn of left-handed fiber on a 1-turn right-handed helical fiber; (

**a**,

**b**) at a fixed orientation, (

**c**,

**d**) in the fixed orientation.

**Figure 7.**Solenoid helical turns are varied; (

**a**,

**b**) angular behavior of scattering quantities at fixed orientation $(\alpha ,\beta ,\gamma )$ = $(0,0,0)$; and (

**c**,

**d**) in the orientation average. P = 11 nm, R = 10 nm, $\lambda $ = 300 nm.

**Figure 8.**Varying pitch the scattering calculations are given: (

**a**,

**b**) at a fixed orientation $(\alpha ,\beta ,\gamma )$ = $(0,0,0)$, (

**c**) and in the orientation average, (

**d**,

**e**) chromatin fiber and its projected view looking along the helix axis.

**Figure 9.**(

**a**,

**b**) CIDS and extinction efficiency for two different shaped nucleosomes, respectively; (

**c**,

**d**) scattering calculations for the chromatin fiber with spherical shaped nucleosomes, $\lambda $ = 300 nm.

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**MDPI and ACS Style**

Ashraf, M.W.; Le Gratiet, A.; Diaspro, A.
Computational Modeling of Chromatin Fiber to Characterize Its Organization Using Angle-Resolved Scattering of Circularly Polarized Light. *Polymers* **2021**, *13*, 3422.
https://doi.org/10.3390/polym13193422

**AMA Style**

Ashraf MW, Le Gratiet A, Diaspro A.
Computational Modeling of Chromatin Fiber to Characterize Its Organization Using Angle-Resolved Scattering of Circularly Polarized Light. *Polymers*. 2021; 13(19):3422.
https://doi.org/10.3390/polym13193422

**Chicago/Turabian Style**

Ashraf, Muhammad Waseem, Aymeric Le Gratiet, and Alberto Diaspro.
2021. "Computational Modeling of Chromatin Fiber to Characterize Its Organization Using Angle-Resolved Scattering of Circularly Polarized Light" *Polymers* 13, no. 19: 3422.
https://doi.org/10.3390/polym13193422