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How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis.

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Fortran · 857 lines · 19 KB · CC-BY-4.0

  1. ! Author: Sarthak Gupta
  2. ! Contact : [email hidden]
  4. ! This code takes equillibrated system
  5. ! Chromatin+Shell+Linkages+Crosslinkers
  6. ! and compress the system with parallel plates
  7. ! at tunable compression rates and strains
  9. ! Algorithim for compression
  10. ! 1) Read the coordinates from the files
  11. ! 2) Set the boundaries at the top most and bottom most particle
  12. ! 3)
  18. module combination
  19. implicit none
  20. integer,parameter :: NC=5000 ! No. of monomers in the polymer
  21. integer,parameter :: N_S=5000*2 ! No. of monomers in the shell
  22. integer,parameter :: Total=NC+N_S
  23. !integer,parameter :: NL=250 ! No. of Linkages
  24. !integer,parameter :: Num_C=2500 ! No. of Linkages
  26. Real*8,allocatable,dimension(:) :: R_O_Chromatin
  27. integer,allocatable,dimension(:) :: E1_CH,E2_CH
  28. Real*8,dimension(Total) :: X,Y,Z
  29. Real*8,dimension(Total) :: FX,FY,FZ
  30. Integer,dimension(Total,Total) :: Flag_Ignore
  31. integer :: N,NSE
  32. integer,allocatable,dimension(:) :: E1,E2
  33. integer,allocatable,dimension(:) :: E1_new,E2_new
  35. real*8,allocatable,dimension(:) :: R_O
  36. integer :: iset,seed,Total_Step,interval,step
  37. Real*8 :: del,mu,Diff
  38. Real*8 :: Temp_Seed,rrr
  40. Real*8 :: K_connect,sigma,Eq_length,K_Soft,sigma_Shell
  43. integer, parameter :: L=60 ! Length of one side cube box
  44. Real*8 :: Cell_Length,XCELL,YCELL,ZCELL
  45. integer :: NXCELL,NYCELL,NZCELL
  46. integer :: NCELL
  47. integer,dimension(:,:),allocatable :: neigh
  48. integer,dimension(:),allocatable :: HOC,LLIST
  49. integer :: HBOX
  53. Real*8 :: Upper_Plate_Ini,Upper_Plate_Final
  54. Real*8 :: Lower_Plate_Ini,Lower_Plate_Final
  55. Real*8 :: Upper_Plate_Move,Lower_Plate_Move
  57. Real*8 :: V_compress
  59. Real*8,dimension(Total) :: Fz_Compress_UP,Fz_Compress_Lower
  60. Real*8 :: Strain_rate,time
  63. integer :: NL,Num_C,F_M,Ens
  64. Character*20 :: NL_Ch,Num_C_Ch,F_M_Ch, Ens_Ch
  65. Character*50 :: filename1,filename2,filename3,filename4
  66. Character*50 :: filename5,filename6,filename7,filename8
  68. character(len=20), dimension(:), allocatable :: args
  69. integer :: num_args
  72. integer :: TC,NF
  74. Real*8 :: Strain,PIE,Energy_Shell,Energy_Chromatin,Energy_Linkage,Energy_CrossLinker,Energy_System
  75. Real*8 :: Plate_Diff_Ini
  77. end module combination
  79. program join
  80. use combination
  81. implicit none
  82. integer :: I,J
  83. real*8, external :: gauss
  84. real*8 :: ran2
  89. num_args = command_argument_count()
  90. allocate(args(num_args))
  92. do i = 1, num_args
  93. call get_command_argument(i,args(i))
  94. end do
  96. READ(args(1),*)NL
  97. READ(args(2),*)Num_C
  98. READ(args(3),*)Ens !then, convert them to REALs
  99. allocate(R_O_Chromatin(NL+Num_C),E1_CH(NL+Num_C),E2_CH(NL+Num_C))
  103. Call naming
  104. Call read_coordinates
  109. !_________________ Dynamics _________________________!
  111. !Strain_rate=5.d0/(10**(5)) ! Strain rate
  112. Strain=-0.20 ! Strain
  114. Total_Step=10000000
  115. del=0.0001 ! dt for the system
  116. mu=1.d0 ! Mobility Constant
  117. Diff=1.d0 ! Diffusion Constant
  118. NF=1000 ! Number of frames recorded
  119. interval=int(Total_Step/NF)
  120. PIE=4.D0*DATAN(1.D0) !Just pie, you know.
  123. !time= (5.d0/(10**(6)))/(Strain_rate)
  124. !TC=nint(time*10)
  126. ! print*,interval,TC
  128. !____________________________________________________!
  132. !________________ Seed ________________________!
  133. Call init_random_seed()
  134. Call Random_number(Temp_Seed)
  135. Seed=-987745878!Temp_Seed*(-10000)
  136. !____________________________________________________!
  138. !_________________ Spring ___________________________!
  140. K_connect=140.d0
  141. Eq_length=1.d0
  142. !____________________________________________________!
  144. !___________Soft_Repulsuion__________________________!
  145. K_Soft = K_connect*1.d0 ! No leak at this
  146. sigma =0.43089*2.d0
  147. sigma_Shell=0.43089*2.d0
  148. !____________________________________________________!
  152. !_______________Compression__________________________!
  154. Upper_Plate_Ini=maxval(Z)
  155. Lower_Plate_Ini=minval(Z)
  157. Plate_Diff_Ini=Upper_Plate_Ini-Lower_Plate_Ini
  159. Upper_Plate_Final=Upper_Plate_Ini + Strain*Plate_Diff_Ini
  160. Lower_Plate_Final=Lower_Plate_Ini - Strain*Plate_Diff_Ini
  164. V_compress=(Upper_Plate_Final-Upper_Plate_Ini)/Real(Total_Step)
  165. !print*,Upper_Plate_Ini,Upper_Plate_Final,Lower_Plate_Ini,Lower_Plate_Final
  166. !print*,(Upper_Plate_Ini-Upper_Plate_Final)/(Upper_Plate_Ini-Lower_Plate_Ini)
  167. !print*,(Lower_Plate_Final-Lower_Plate_Ini)/(Upper_Plate_Ini-Lower_Plate_Ini)
  169. Upper_Plate_Move=Upper_Plate_Ini
  170. Lower_Plate_Move=Lower_Plate_Ini
  171. !____________________________________________________!
  173. !_________________ Cell Linked Listing ___________________!
  174. Cell_Length=sigma
  175. XCELL=Cell_Length
  176. YCELL=Cell_Length
  177. ZCELL=Cell_Length
  180. NXCELL=nint(L/Cell_Length)
  181. NYCELL=NXCELL
  182. NZCELL=NYCELL
  183. NCELL=NXCELL*NYCELL*NZCELL
  185. HBOX=L/2.d0
  186. !_________________________________________________________!
  187. allocate(Neigh(0:NCELL-1,0:26))
  188. Do I=0,NCELL-1
  189. DO J=0,26
  190. Neigh(I,J)=0
  191. END Do
  192. END DO
  193. Call Neighbor
  194. allocate(HOC(0:NCELL-1),LLIST(Total))
  195. !print*,NCELL,Cell_Length,NXCELL
  196. !print*, NF,Upper_Plate_Ini,Lower_Plate_Ini,Upper_Plate_Ini-Lower_Plate_Ini
  198. iset=0 ! Initial flag setting for Gaussian random distribution function
  199. rrr=gauss(seed,iset) ! Calling function to set the flag
  202. Do step=1,Total_Step
  203. Call Sorting
  204. call Force_Calculation
  205. call update_position
  206. Upper_Plate_Move=Upper_Plate_Move + (V_compress)
  207. Lower_Plate_Move=Lower_Plate_Move - (V_compress)
  208. If(mod(step,interval)==0) then
  209. print*,step,Upper_Plate_Move,Lower_Plate_Move,1-((Upper_Plate_Move-Lower_Plate_Move)/(Upper_Plate_Ini-Lower_Plate_Ini))
  210. call Save_Pos
  211. end if
  213. End Do
  216. End Program join
  218. !********** finding out neighbours of cell ***********
  219. Subroutine Neighbor
  220. use combination
  221. implicit none
  222. integer :: icell
  223. integer :: ix,iy,iz
  224. integer :: ixx,iyy,izz
  225. integer :: j2,jcell
  228. !OPEN (102,file='neigh.dat')
  229. DO icell = 0,NCELL-1
  230. iz = int(dble(icell)/dble(NXCELL*NYCELL))
  231. iy = int(dble(icell-NXCELL*NYCELL*iz)/dble(NXCELL))
  232. ix = icell-NXCELL*NYCELL*iz-NXCELL*iy
  234. iz = iz-1 !- to find the neighbour
  235. iy = iy-1
  236. ix = ix-1
  238. DO izz = 0,2 ! neighbour cells form cube with (3*3*3)
  239. IF (iz .LT. 0) THEN ! 0,2 means 0,1,2
  240. iz = iz+NZCELL
  241. END IF
  242. IF ((iz+izz) .GT. (NZCELL-1)) THEN
  243. iz = iz-NZCELL
  244. END IF
  246. DO iyy = 0,2
  247. IF (iy .LT. 0) THEN
  248. iy = iy+NYCELL
  249. END IF
  250. IF ((iy+iyy) .GT. (NYCELL-1)) THEN
  251. iy = iy-NYCELL
  252. END IF
  254. DO ixx = 0,2
  255. IF (ix .LT. 0) THEN
  256. ix = ix+NXCELL
  257. END IF
  258. IF ((ix+ixx) .GT. (NXCELL-1)) THEN
  259. ix = ix-NXCELL
  260. END IF
  261. j2 = ixx+3*iyy+9*izz !bcz unit cell of 3 unit, so in z, pt should be multipd by 3**2 = 9
  262. jcell = (ix+ixx)+(iy+iyy)*NXCELL+(iz+izz)*NXCELL*NYCELL ! cell number, j2 is cell index
  263. neigh(icell,j2) = jcell
  264. ! WRITE(102,*)icell,j2,neigh(icell,j2)
  266. END DO !-ixx loop
  267. END DO !-iyy loop
  268. END DO !-izz loop
  269. End Do
  272. return
  273. end subroutine Neighbor
  276. !*******distribute the molecules to the cells***********!
  277. Subroutine Sorting
  278. use combination
  279. implicit none
  280. integer :: i
  281. integer :: ic
  282. integer :: icellx,icelly,icellz
  284. !IF(MOD(STEP,100).EQ.0)THEN
  285. DO I = 0,NCELL-1
  286. HOC(I) = 0
  287. END DO
  289. DO I = 1,Total
  292. !RXX(I) = RXX(I) - L*int((RXX(I)-HBOX)/HBOX)
  293. !RYY(I) = RYY(I) - L*int((RYY(I)-HBOX)/HBOX)
  294. !RZZ(I) = RZZ(I) - L*int((RZZ(I)-HBOX)/HBOX)
  296. icellx = int(X(I)/XCELL)!--x-index of cell
  297. icelly = int(Y(I)/YCELL)!--y-index of cell
  298. icellz = int(Z(I)/ZCELL)!--z-index of cell
  301. ic = icellx+icelly*NXCELL+icellz*NXCELL*NYCELL!--index of cell
  302. LLIST(I) = HOC(ic)
  303. HOC(ic) = I
  304. END DO
  305. !END IF
  308. return
  309. end subroutine Sorting
  311. subroutine Save_pos
  312. use combination
  313. implicit none
  314. integer :: I,J
  318. Do I=1,total
  319. Write(1000)X(I),Y(I),Z(I)
  320. IF(step==Total_Step) Write(2000)X(I),Y(I),Z(I)
  321. End Do
  323. return
  324. end subroutine Save_pos
  331. subroutine update_position
  332. use combination
  333. implicit none
  334. real*8, external :: gauss
  335. real*8 :: ran2
  336. integer :: I
  338. Do I=1,Total
  339. x(i)=x(i)+ mu*(FX(I))*del + ((sqrt(2.0*Diff*del))*gauss(seed,iset))
  340. y(i)=y(i)+ mu*(FY(I))*del + ((sqrt(2.0*Diff*del))*gauss(seed,iset))
  341. z(i)=z(i)+ mu*(FZ(I))*del + ((sqrt(2.0*Diff*del))*gauss(seed,iset))
  342. End Do
  344. return
  345. end subroutine update_position
  349. subroutine Force_Calculation
  350. use combination
  351. implicit none
  352. Real*8,dimension(Total) :: Fx_Har,Fy_Har,Fz_Har
  353. Real*8,dimension(Total) :: Fx_Rep,Fy_Rep,Fz_Rep
  355. integer :: i,j,Ed1,Ed2
  356. Real*8 :: xr,yr,zr,dis
  357. Real*8 :: r,const,ffx,ffy,ffz
  359. integer :: cellx,celly,cellz
  360. integer :: js,cell,jcell,M
  361. Real*8 :: X1,Y1,Z1,X2,Y2,Z2
  363. Energy_Shell=0.d0
  364. Energy_Chromatin=0.d0
  365. Energy_Linkage=0.d0
  366. Energy_CrossLinker=0.d0
  368. Do I=1,Total
  369. FX(I)=0.d0
  370. FY(I)=0.d0
  371. FZ(I)=0.d0
  374. Fx_Har(I)=0.d0
  375. Fy_Har(I)=0.d0
  376. Fz_Har(I)=0.d0
  378. Fz_Compress_UP(I)=0.d0
  379. Fz_Compress_Lower(I)=0.d0
  381. Fx_Rep(I)=0.d0
  382. Fy_Rep(I)=0.d0
  383. Fz_Rep(I)=0.d0
  384. End Do
  386. !___________ Chromatin Spring_______________!
  388. Do I=1,NC-1
  389. Ed1=E1_new(I)
  390. Ed2=E2_new(I)
  391. !print*,Ed1,Ed2,I
  392. Flag_Ignore(Ed1,Ed2)=1
  394. xr=x(Ed1)-x(Ed2)
  395. yr=y(Ed1)-y(Ed2)
  396. zr=z(Ed1)-z(Ed2)
  398. dis=sqrt(xr*xr + yr*yr + zr*zr)
  400. r=dis-Eq_length
  401. const=(-1.d0)*(K_Connect/(real(dis)))
  403. ffx=(const*r)*xr
  404. ffy=(const*r)*yr
  405. ffz=(const*r)*zr
  407. Fx_har(Ed1)=Fx_har(Ed1)+ffx
  408. Fx_har(Ed2)=Fx_har(Ed2)-ffx
  409. Fy_har(Ed1)=Fy_har(Ed1)+ffy
  410. Fy_har(Ed2)=Fy_har(Ed2)-ffy
  411. Fz_har(Ed1)=Fz_har(Ed1)+ffz
  412. Fz_har(Ed2)=Fz_har(Ed2)-ffz
  413. End Do
  414. !___________________________________________!
  418. !_________ Shell Spring ____________________!
  420. Do I=NC-1+1,NC-1+NSE
  421. Ed1=E1_new(I)
  422. Ed2=E2_new(I)
  423. !print*,Ed1,Ed2,I
  424. Flag_Ignore(Ed1,Ed2)=1
  426. xr=x(Ed1)-x(Ed2)
  427. yr=y(Ed1)-y(Ed2)
  428. zr=z(Ed1)-z(Ed2)
  430. dis=sqrt(xr*xr + yr*yr + zr*zr)
  432. r=dis-R_O(I)!r_knot
  433. const=(-1.d0)*(K_Connect/(real(dis)))
  435. ffx=(const*r)*xr
  436. ffy=(const*r)*yr
  437. ffz=(const*r)*zr
  439. Fx_har(Ed1)=Fx_har(Ed1)+ffx
  440. Fx_har(Ed2)=Fx_har(Ed2)-ffx
  441. Fy_har(Ed1)=Fy_har(Ed1)+ffy
  442. Fy_har(Ed2)=Fy_har(Ed2)-ffy
  443. Fz_har(Ed1)=Fz_har(Ed1)+ffz
  444. Fz_har(Ed2)=Fz_har(Ed2)-ffz
  446. End Do
  448. !___________________________________________!
  450. !_________ Linkage Spring ____________________!
  452. Do I=1,NL
  453. Ed1=E1_CH(I)
  454. Ed2=E2_CH(I)
  455. !print*,Ed1,Ed2,I
  456. Flag_Ignore(Ed1,Ed2)=1
  458. xr=x(Ed1)-x(Ed2)
  459. yr=y(Ed1)-y(Ed2)
  460. zr=z(Ed1)-z(Ed2)
  462. dis=sqrt(xr*xr + yr*yr + zr*zr)
  464. r=dis-R_O_Chromatin(I)!r_knot
  465. const=(-1.d0)*(K_Connect/(real(dis)))
  467. ffx=(const*r)*xr
  468. ffy=(const*r)*yr
  469. ffz=(const*r)*zr
  471. Fx_har(Ed1)=Fx_har(Ed1)+ffx
  472. Fx_har(Ed2)=Fx_har(Ed2)-ffx
  473. Fy_har(Ed1)=Fy_har(Ed1)+ffy
  474. Fy_har(Ed2)=Fy_har(Ed2)-ffy
  475. Fz_har(Ed1)=Fz_har(Ed1)+ffz
  476. Fz_har(Ed2)=Fz_har(Ed2)-ffz
  478. End Do
  480. !___________________________________________!
  483. !_________ Cross-Linker Spring ____________________!
  485. Do I=Nl+1,NL+Num_C
  486. Ed1=E1_CH(I)
  487. Ed2=E2_CH(I)
  488. !print*,Ed1,Ed2,I
  489. Flag_Ignore(Ed1,Ed2)=1
  491. xr=x(Ed1)-x(Ed2)
  492. yr=y(Ed1)-y(Ed2)
  493. zr=z(Ed1)-z(Ed2)
  495. dis=sqrt(xr*xr + yr*yr + zr*zr)
  497. r=dis-R_O_Chromatin(I)!r_knot
  498. const=(-1.d0)*(K_Connect/(real(dis)))
  500. ffx=(const*r)*xr
  501. ffy=(const*r)*yr
  502. ffz=(const*r)*zr
  504. Fx_har(Ed1)=Fx_har(Ed1)+ffx
  505. Fx_har(Ed2)=Fx_har(Ed2)-ffx
  506. Fy_har(Ed1)=Fy_har(Ed1)+ffy
  507. Fy_har(Ed2)=Fy_har(Ed2)-ffy
  508. Fz_har(Ed1)=Fz_har(Ed1)+ffz
  509. Fz_har(Ed2)=Fz_har(Ed2)-ffz
  511. Energy_CrossLinker=Energy_CrossLinker+(0.5*K_Connect*r*r)
  512. End Do
  514. !___________________________________________!
  516. !_________ Compression Force _______________!
  518. Do I=NC+1,Total
  520. IF(Z(I).GT.Upper_Plate_Move) Then
  521. zr=Z(I)-Upper_Plate_Move
  522. dis=sqrt(zr*zr)
  523. r=dis
  524. const=(-1.d0)*(K_Connect/(real(dis)))
  525. ffz=(const*r)*zr
  526. Fz_Compress_UP(I)=Fz_Compress_UP(I)+ffz
  527. End IF
  529. IF(Z(I).LT.Lower_Plate_Move) Then
  530. zr=Z(I)-Lower_Plate_Move
  531. dis=sqrt(zr*zr)
  532. r=dis
  533. const=(-1.d0)*(K_Connect/(real(dis)))
  534. ffz=(const*r)*zr
  535. Fz_Compress_Lower(I)=Fz_Compress_Lower(I)+ffz
  536. End IF
  538. End Do
  542. !___________________________________________!
  545. ! Purely repulsive soft potential for all the monomers which
  546. ! doesn't have any other interactions.
  548. DO I = 1,Total
  550. X1 = X(I)
  551. Y1 = Y(I)
  552. Z1 = Z(I)
  554. cellx = int(X(I)/XCELL) !--x-index of cell
  555. celly = int(Y(I)/YCELL) !--y-index of cell
  556. cellz = int(Z(I)/ZCELL) !--z-index of cell
  557. cell = cellx + celly*NXCELL + cellz*NXCELL*NYCELL!--index of cell having this catalytic particle
  558. !print*,step,I,CEll,X(I),Y(I),Z(I)
  560. DO M = 0,26
  561. jcell = neigh(cell,M)
  562. Js = HOC(jcell) !--Head particle of a cell
  564. DO WHILE (Js .NE. 0)
  565. IF(Flag_Ignore(i,js)==1) then ! Ignore this interaction, if there is another interaction
  566. Else
  567. X2 = X(js)
  568. Y2 = Y(js)
  569. Z2 = Z(js)
  571. xr=X1-X2
  572. yr=Y1-Y2
  573. zr=Z1-Z2
  575. xr=xr-(L*nint(xr/L))
  576. yr=yr-(L*nint(yr/L))
  577. zr=zr-(L*nint(yr/L))
  580. dis= sqrt(xr*xr + yr*yr + zr*zr)
  583. if((dis.lt.Sigma).and.(js.gt.i)) then
  584. r=dis-Sigma
  585. const=(-1.d0)*(K_Soft/(real(dis)))
  587. ffx=(const*r)*xr
  588. ffy=(const*r)*yr
  589. ffz=(const*r)*zr
  591. fx_Rep(i)=fx_Rep(i)+ffx
  592. fx_Rep(js)=fx_Rep(js)-ffx
  593. fy_Rep(i)=fy_Rep(i)+ffy
  594. fy_Rep(js)=fy_Rep(js)-ffy
  595. fz_Rep(i)=fz_Rep(i)+ffz
  596. fz_Rep(js)=fz_Rep(js)-ffz
  597. end if !--dd.lt.cutoffsq1
  600. End IF
  601. Js = LLIST(Js) !--goto next particle of the cells
  602. END DO !--do while j .ne.0 loop
  603. END DO !--m =0,26 loop
  604. End do
  606. !_______________________________________________________________________________________________!
  610. Do I=1,total
  611. FX(I)=FX(I)+Fx_Har(I)+Fx_Rep(I)
  612. FY(I)=FY(I)+Fy_Har(I)+Fy_Rep(I)
  613. FZ(I)=FZ(I)+Fz_Har(I)+Fz_Rep(I)+Fz_Compress_UP(I)+Fz_Compress_Lower(I)
  614. End Do
  615. return
  616. end subroutine Force_Calculation
  621. subroutine read_coordinates
  622. use combination
  623. implicit none
  624. integer :: I,J,K
  625. Real*8 :: xr,yr,zr,dis
  626. Integer :: Ed1,Ed2
  627. real*8 :: xcm_shell,ycm_shell,zcm_shell
  628. real*8 :: xcm_chromatin,ycm_chromatin,zcm_chromatin
  630. Do I=1,Total
  631. read(100) X(I),Y(I),Z(I)
  632. !print*,i,X(I),Y(I),Z(I)
  633. End Do
  635. xcm_shell=0.d0
  636. ycm_shell=0.d0
  637. zcm_shell=0.d0
  639. Do I=1,NC
  640. xcm_shell=xcm_shell+x(i)
  641. ycm_shell=ycm_shell+y(i)
  642. zcm_shell=zcm_shell+z(i)
  643. End Do
  645. xcm_shell=xcm_shell/real(NC)
  646. ycm_shell=ycm_shell/real(NC)
  647. zcm_shell=zcm_shell/real(NC)
  650. Do I=1,NC
  651. x(i)=x(i)-xcm_shell+(L/2.d0)
  652. y(i)=y(i)-ycm_shell+(L/2.d0)
  653. z(i)=z(i)-zcm_shell+(L/2.d0)
  654. End Do
  658. xcm_chromatin=0.d0
  659. ycm_chromatin=0.d0
  660. zcm_chromatin=0.d0
  662. Do I=NC+1,Total
  663. xcm_chromatin=xcm_chromatin+x(i)
  664. ycm_chromatin=ycm_chromatin+y(i)
  665. zcm_chromatin=zcm_chromatin+z(i)
  666. End Do
  669. xcm_chromatin=xcm_chromatin/real(N_S)
  670. ycm_chromatin=ycm_chromatin/real(N_S)
  671. zcm_chromatin=zcm_chromatin/real(N_S)
  674. Do I=NC+1,Total
  675. x(i)=x(i)-xcm_chromatin+(L/2.d0)
  676. y(i)=y(i)-ycm_chromatin+(L/2.d0)
  677. z(i)=z(i)-zcm_chromatin+(L/2.d0)
  678. End Do
  681. read(30) N,NSE
  683. allocate(E1(NSE),E2(NSE))
  684. allocate(E1_new(NSE+NC-1),E2_new(NSE+NC-1),R_O(NSE+NC-1))
  686. ! Chromatin Edges reading
  687. ! Since, its a chain of NC=5000 particles
  689. Do I=1,NC-1
  690. E1_new(I)=I
  691. E2_new(I)=I+1
  692. End do
  693. ! Shell Edges reading from the file
  694. ! Writting into the edge variables
  696. Do I=1,NSE
  697. Read(20) E1(I),E2(I)
  698. E1_new(I+NC-1)=E1(I)+NC
  699. E2_new(I+NC-1)=E2(I)+NC
  700. End do
  702. Do I=1,NSE+NC-1
  703. read(50) R_O(I)
  704. End do
  706. Do I=1,NL
  707. read(110) E1_CH(I),E2_CH(I),R_O_Chromatin(I)
  708. !if(i.le.nl) print*,i,E1_CH(I),E2_CH(I),R_O_Chromatin(I)
  709. End do
  711. Do I=1,Num_C
  712. read(120) E1_CH(NL+I),E2_CH(NL+I),R_O_Chromatin(NL+I)
  713. !if(i.le.nl) print*,i,E1_CH(I),E2_CH(I),R_O_Chromatin(I)
  714. End do
  717. Do I=1,total
  718. Do J=1,total
  719. Flag_Ignore(I,J)=0
  720. End do
  721. End Do
  726. return
  727. end subroutine read_coordinates
  730. subroutine naming
  731. use combination
  732. implicit none
  733. integer :: No_of_crosslinkers,No_of_linkers
  734. write(NL_Ch,'(i0)') NL
  735. write(Num_C_Ch,'(i0)') Num_C
  736. write(Ens_Ch,'(i0)') Ens
  740. filename1='Shell_Polymer_Equb_'//trim(adjustl(Ens_Ch))//'.dat'
  741. filename2='Shell_Edges_'//trim(adjustl(Ens_Ch))//'.dat'
  742. filename3='Shell_Info_'//trim(adjustl(Ens_Ch))//'.dat'
  743. filename5='Result_'//trim(adjustl(NL_Ch))//'_'//trim(adjustl(Num_C_Ch))//'_' &
  744. //trim(adjustl(Ens_Ch))//'.dat'
  745. filename6='Last_Frame_'//trim(adjustl(NL_Ch))//'_'//trim(adjustl(Num_C_Ch))//'_' &
  746. //trim(adjustl(Ens_Ch))//'.dat'
  747. filename7='Rest_Length_'//trim(adjustl(Ens_Ch))//'.dat'
  751. Open(unit=100,file=filename1,form="unformatted")
  752. Open(unit=20,file=filename2,form="unformatted")
  753. Open(unit=30,file=filename3,form="unformatted")
  754. Open(unit=1000,file=filename5,form="unformatted")
  755. Open(unit=2000,file=filename6,form="unformatted")
  756. Open(unit=50,file=filename7,form="unformatted")
  759. No_of_linkers=400
  760. write(NL_Ch,'(i0)') No_of_linkers
  761. No_of_crosslinkers=2500
  762. write(Num_C_Ch,'(i0)') No_of_crosslinkers
  764. filename4='Linker_'//trim(adjustl(NL_Ch))//'_'//trim(adjustl(Ens_Ch))//'.dat'
  765. filename8='Crosslinker_'//trim(adjustl(Num_C_Ch))//'_'//trim(adjustl(Ens_Ch))//'.dat'
  767. Open(unit=110,file=filename4,form="unformatted")
  768. Open(unit=120,file=filename8,form="unformatted")
  770. Return
  771. end subroutine naming
  777. FUNCTION gauss(seed,iset)
  778. implicit none
  779. integer :: seed,iset
  780. real*8 :: gauss,w_gfx
  781. real*8 :: x1,x2,ran2,fac
  782. save fac,x2
  784. w_gfx=2.0
  786. if (iset==0) then
  787. do while(w_gfx>=1.0)
  788. x1=(2.0*ran2(seed))-1.0
  789. x2=(2.0*ran2(seed))-1.0
  790. w_gfx=(x1*x1)+(x2*x2)
  791. end do
  792. fac=sqrt(-2.0*log(w_gfx)/w_gfx)
  793. gauss=x1*fac
  794. iset=1
  795. else
  797. gauss=x2*fac
  798. iset=0
  799. end if
  802. return
  803. end function gauss
  807. SUBROUTINE init_random_seed()
  808. INTEGER :: i, n, clock
  809. INTEGER, DIMENSION(:), ALLOCATABLE :: seed
  811. CALL RANDOM_SEED(size = n)
  812. ALLOCATE(seed(n))
  814. CALL SYSTEM_CLOCK(COUNT=clock)
  816. seed = clock + 37 * (/ (i - 1, i = 1, n) /)
  817. CALL RANDOM_SEED(PUT = seed)
  819. DEALLOCATE(seed)
  820. END SUBROUTINE
  824. FUNCTION ran2(idum)
  825. INTEGER idum,IM1,IM2,IMM1,IA1,IA2,IQ1,IQ2,IR1,IR2,NTAB,NDIV
  826. real*8 ran2,AM,EPS,RNMX
  827. PARAMETER (IM1=2147483563,IM2=2147483399,AM=1./IM1,IMM1=IM1-1, &
  828. IA1=40014,IA2=40692,IQ1=53668,IQ2=52774,IR1=12211,IR2=3791, &
  829. NTAB=32,NDIV=1+IMM1/NTAB,EPS=1.2e-7,RNMX=1.-EPS)
  830. INTEGER idum2,j,k,iv(NTAB),iy
  831. SAVE iv,iy,idum2
  832. DATA idum2/123456789/, iv/NTAB*0/, iy/0/
  833. if (idum.le.0) then
  834. idum=max(-idum,1)
  835. idum2=idum
  836. do 11 j=NTAB+8,1,-1
  838. k=idum/IQ1
  839. idum=IA1*(idum-k*IQ1)-k*IR1
  840. if (idum.lt.0) idum=idum+IM1
  841. if (j.le.NTAB) iv(j)=idum
  842. 11 continue
  843. iy=iv(1)
  844. endif
  845. k=idum/IQ1
  846. idum=IA1*(idum-k*IQ1)-k*IR1
  847. if (idum.lt.0) idum=idum+IM1
  848. k=idum2/IQ2
  849. idum2=IA2*(idum2-k*IQ2)-k*IR2
  850. if (idum2.lt.0) idum2=idum2+IM2
  851. j=1+iy/NDIV
  852. iy=iv(j)-idum2
  853. iv(j)=idum
  854. if(iy.lt.1)iy=iy+IMM1
  855. ran2=min(AM*iy,RNMX)
  856. return
  857. END

Compress.f90, under CC-BY-4.0 · at the source

Overview

Authors: Tao Zhang1, Sarthak Gupta2, Madeline A. Lancaster3, J. M. Schwarz2,4
ORCID iDs: Tao Zhang, Sarthak Gupta, J. M. Schwarz
  1. Department of Polymer Science and Engineering, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University Shanghai 200240 China
  2. Department of Physics, Syracuse University Syracuse NY 13244 USA
  3. MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus Francis Crick Avenue Cambridge CB2 0QH UK
  4. Indian Creek Farm Ithaca NY 14850 USA
Institutions: Shanghai Jiao Tong University (China); Syracuse University (United States); MRC Laboratory of Molecular Biology (United Kingdom); Indian Creek Farm (United States)
Journal: Soft matter, volume 22, issue 9, pages 1979-1993
Dates: received 7 November 2025; accepted 13 January 2026; published online 19 January 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1039/d5sm01116g · PMID 41586835 · PMCID PMC12834241 · OpenAlex W7124721152
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: human (organism)
Methods: Statistics, Spectral & time-frequency
MeSH: Brain*, Models, Biological*, Organoids*, Animals, Chromatin, Gorilla gorilla, Humans, Pan troglodytes (* major topic)
Journal subjects: Chemistry
Topic: Pluripotent Stem Cells Research (Molecular Biology, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: National Natural Science Foundation of China (National Science Foundation of China) (22303051); DOD (Isaac Newton Award for Transformative Ideas during the COVID19 Pandemic); UK Medical Research Council (MC UP 1201/9)
Citations: not cited yet (Europe PMC); 102 references in the paper

Abstract

How genes influence tissue-scale organization remains a longstanding biological puzzle. While experimental efforts quantify gene expression, chromatin, cellular, and tissue structure, computational models lag behind. To help accelerate multiscale modeling, we demonstrate how a tissue-scale, cellular-based model can be merged with a cell nuclear model incorporating a deformable lamina shell and chromatin to test hypotheses linking chromatin and tissue scales. Specifically, we propose a hypothesis to explain structural differences between human, chimpanzee, and gorilla-derived brain organoids. Recent experiments reveal that a cell fate transition from neuroepithelial to radial glial cells includes a new intermediate state that is delayed in human-derived organoids, leading to significantly narrowed and lengthened apical cells. Additional experiments also demonstrated that ZEB2, a transcription factor, plays a major role in the onset of the novel intermediate state. We hypothesize that this delay stems from chromatin reorganization triggered by mechanical strain as the respective brain organoids develop, with a higher critical threshold in human-derived cells. Here, we computationally test the feasibility of such a hypothesis by exploring how slightly different initial configurations of chromatin, as modeled by different numbers of chromatin crosslinkers, organize in response to mechanical strain with increasingly different initial configurations representing less genetically-close relatives. We find that even small differences in the number of chromatin crosslinkers (>0.01%) yield distinguishable chromatin displacement on average beyond 35% mechanical strain. At higher strains, we observe a new type of nonlinear chromatin scaling law with an exponent of 3.24(5). Finally, we show how differences in chromatin strain maps and more conventional contact maps can reveal structural distinctions between genetically-close species.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Zenodo 17557600

License: CC-BY-4.0
State: the link answers, verified on 30 September 2026
Evidence: files inventoried
Languages: Fortran (1)
Size: 4 files, 1 script
Software Heritage: not checked
Found in: “Data availability”
Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 30 September 2026: the link answers (HTTP 200)
  • 30 September 2026: the link answers (HTTP 200)
1 file
At the source: doi.org/10.5281/zenodo.17557600

The paper's code and data availability statement is in the Data section.

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Data for this article, including codes and simulation raw data are available at Zenodo at https://doi.org/10.5281/zenodo.17557600.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Version 1, 30 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 4 authors, 8 MeSH terms, 3 funders, 95 references.

Cite

This paper

Zhang, T., Gupta, S., Lancaster, M. A., & Schwarz, J. M. (2026). How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis. Soft matter, 22(9), 1979-1993. https://doi.org/10.1039/d5sm01116g

BibTeX

@article{zhang2026how,
author = {Zhang, Tao and Gupta, Sarthak and Lancaster, Madeline A. and Schwarz, J. M.},
title = {{How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis}},
journal = {Soft matter},
year = {2026},
month = mar,
volume = {22},
number = {9},
pages = {1979--1993},
publisher = {Royal Society of Chemistry},
issn = {1744-683X},
doi = {10.1039/d5sm01116g},
url = {https://doi.org/10.1039/d5sm01116g},
pmid = {41586835},
pmcid = {PMC12834241}
}

RIS

TY - JOUR
AU - Zhang, Tao
AU - Gupta, Sarthak
AU - Lancaster, Madeline A.
AU - Schwarz, J. M.
TI - How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis
T2 - Soft matter
J2 - Soft Matter
PY - 2026
DA - 2026/03/04
VL - 22
IS - 9
SP - 1979
EP - 1993
SN - 1744-683X
PB - Royal Society of Chemistry
DO - 10.1039/d5sm01116g
UR - https://doi.org/10.1039/d5sm01116g
LA - en
ER -

CSL-JSON

{
"id": "10.1039/d5sm01116g",
"type": "article-journal",
"title": "How human-derived brain organoids are built differently from brain organoids derived from genetically-close relatives: a multi-scale hypothesis",
"container-title": "Soft matter",
"author": [
{
"family": "Zhang",
"given": "Tao"
},
{
"family": "Gupta",
"given": "Sarthak"
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{
"family": "Lancaster",
"given": "Madeline A."
},
{
"family": "Schwarz",
"given": "J. M."
}
],
"container-title-short": "Soft Matter",
"volume": "22",
"issue": "9",
"page": "1979-1993",
"DOI": "10.1039/d5sm01116g",
"PMID": "41586835",
"PMCID": "PMC12834241",
"ISSN": "1744-683X",
"publisher": "Royal Society of Chemistry",
"URL": "https://doi.org/10.1039/d5sm01116g",
"language": "en",
"issued": {
"date-parts": [
[
2026,
3,
4
]
]
}
}

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