From 624f819d40ca2204b0a128970dcd3d9ca7e17699 Mon Sep 17 00:00:00 2001
From: mihaf <miha.fosnaric@gmail.com>
Date: Fri, 14 Mar 2014 09:36:05 +0000
Subject: [PATCH] Added filaments inside the vesicle. TODO: tape etc.
---
src/poly.c | 85 ++++++++++++++++++++++++++++--------------
src/tape | 10 ++++
src/initial_distribution.c | 2
src/general.h | 8 +++
src/poly.h | 2
5 files changed, 75 insertions(+), 32 deletions(-)
diff --git a/src/general.h b/src/general.h
index 3308faa..26e8b55 100644
--- a/src/general.h
+++ b/src/general.h
@@ -256,11 +256,17 @@
ts_double cm[3];
ts_double volume;
ts_spharm *sphHarmonics;
-
+// Polymers outside the vesicle and attached to the vesicle membrane (polymer brush):
ts_poly_list *poly_list;
+// Filaments inside the vesicle (not attached to the vesicel membrane:
+ ts_poly_list *filament_list;
+
ts_double spring_constant;
ts_double pressure;
ts_int pswitch;
+
+ ts_double R_nucleus;
+
} ts_vesicle;
diff --git a/src/initial_distribution.c b/src/initial_distribution.c
index 7601f13..f450dbf 100644
--- a/src/initial_distribution.c
+++ b/src/initial_distribution.c
@@ -38,7 +38,7 @@
ts_vesicle *create_vesicle_from_tape(ts_tape *tape){
ts_vesicle *vesicle;
vesicle=initial_distribution_dipyramid(tape->nshell,tape->ncxmax,tape->ncymax,tape->nczmax,tape->stepsize);
- vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist);
+ vesicle->poly_list=init_poly_list(tape->npoly,tape->nmono, vesicle->vlist, vesicle);
vesicle->spring_constant=tape->kspring;
poly_assign_spring_const(vesicle);
diff --git a/src/poly.c b/src/poly.c
index 2057db1..aa41184 100644
--- a/src/poly.c
+++ b/src/poly.c
@@ -20,8 +20,10 @@
ts_poly *poly=(ts_poly *)calloc(1,sizeof(ts_poly));
poly->vlist = init_vertex_list(n);
poly->blist = init_bond_list();
- poly->grafted_vtx = grafted_vtx;
- grafted_vtx->grafted_poly = poly;
+ if (grafted_vtx!=NULL){
+ poly->grafted_vtx = grafted_vtx;
+ grafted_vtx->grafted_poly = poly;
+ }
ts_uint i;
for(i=0;i<n-1;i++){
@@ -38,45 +40,72 @@
}
-ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist){
+ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle){
ts_poly_list *poly_list=(ts_poly_list *)calloc(1,sizeof(ts_poly_list));
poly_list->poly = (ts_poly **)calloc(n_poly,sizeof(ts_poly *));
ts_uint i=0,j=0; //idx;
ts_uint gvtxi;
ts_double xnorm,ynorm,znorm,normlength;
+ ts_double dphi,dh;
+ ts_uint ji;
- if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
+ // Grafting polymers:
+ if (vlist!=NULL){
+ if (n_poly > vlist->n){fatal("Number of polymers larger then numbero f vertices on a vesicle.",310);}
- while(i<n_poly){
- gvtxi = rand() % vlist->n;
- if (vlist->vtx[gvtxi]->grafted_poly == NULL){
- poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
- i++;
+ while(i<n_poly){
+ gvtxi = rand() % vlist->n;
+ if (vlist->vtx[gvtxi]->grafted_poly == NULL){
+ poly_list->poly[i] = init_poly(n_mono, vlist->vtx[gvtxi]);
+ i++;
+ }
}
}
-
+ else
+ {
+ for(i=0;i<n_poly;i++){
+ poly_list->poly[i] = init_poly(n_mono, NULL);
+ }
+ }
+
poly_list->n = n_poly;
-/* Make straight poylmers normal to membrane. Dist. between poly vertices put to 1*/
- for (i=0;i<poly_list->n;i++){
+ if (vlist!=NULL){
+ /* Make straight grafted poylmers normal to membrane (polymer brush). Dist. between poly vertices put to 1*/
+ for (i=0;i<poly_list->n;i++){
+
+ xnorm=0.0;
+ ynorm=0.0;
+ znorm=0.0;
+ for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
+ xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
+ ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
+ znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
+ }
+ normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
+ xnorm=xnorm/normlength;
+ ynorm=ynorm/normlength;
+ znorm=znorm/normlength;
- xnorm=0.0;
- ynorm=0.0;
- znorm=0.0;
- for (j=0;j<poly_list->poly[i]->grafted_vtx->tristar_no;j++){
- xnorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->xnorm;
- ynorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->ynorm;
- znorm-=poly_list->poly[i]->grafted_vtx->tristar[j]->znorm;
+ for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
+ poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
+ poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
+ }
}
- normlength=sqrt(xnorm*xnorm+ynorm*ynorm+znorm*znorm);
- xnorm=xnorm/normlength;
- ynorm=ynorm/normlength;
- znorm=znorm/normlength;
-
- for (j=0;j<poly_list->poly[i]->vlist->n;j++){
- poly_list->poly[i]->vlist->vtx[j]->x = poly_list->poly[i]->grafted_vtx->x + xnorm*(ts_double)(j+1);
- poly_list->poly[i]->vlist->vtx[j]->y = poly_list->poly[i]->grafted_vtx->y + ynorm*(ts_double)(j+1);
- poly_list->poly[i]->vlist->vtx[j]->z = poly_list->poly[i]->grafted_vtx->z + znorm*(ts_double)(j+1);
+ }
+ else
+ {
+ /* Make filaments inside the vesicle. Helix with radius... Dist. between poly vertices put to 1*/
+ dphi = 2*asin(1/2/vesicle->R_nucleus)*1.001;
+ dh = dphi/2/M_PI*1.001;
+ for(i=0;i<poly_list->n;i++){
+ for (j=0;j<poly_list->poly[i]->vlist->n;j++){
+ ji = j + i*poly_list->poly[i]->vlist->n;
+ poly_list->poly[i]->vlist->vtx[j]->x = vesicle->R_nucleus*cos(ji*dphi);
+ poly_list->poly[i]->vlist->vtx[j]->y = vesicle->R_nucleus*sin(ji*dphi);
+ poly_list->poly[i]->vlist->vtx[j]->z = ji*dh;
+ }
}
}
diff --git a/src/poly.h b/src/poly.h
index 9bdec52..68c83c1 100644
--- a/src/poly.h
+++ b/src/poly.h
@@ -5,7 +5,7 @@
ts_poly *init_poly(ts_uint n, ts_vertex *grafted_vtx);
-ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist);
+ts_poly_list *init_poly_list(ts_uint n_poly, ts_uint n_mono, ts_vertex_list *vlist, ts_vesicle *vesicle);
ts_bool poly_free(ts_poly *poly);
diff --git a/src/tape b/src/tape
index bd02323..38871bd 100644
--- a/src/tape
+++ b/src/tape
@@ -14,7 +14,7 @@
# pressure difference: p_inside - p_outside (in units kT/l_min^3):
pressure=0.0
-####### Polymer definitions ###########
+####### Polymer (brush) definitions ###########
# npoly is a number of polymers attached to npoly distinct vertices on vesicle
npoly=0
# nmono is a number of monomers in each polymer
@@ -22,6 +22,14 @@
# Spring constant between monomers of the polymer
k_spring=800
+####### Filament (inside the vesicle) definitions ###########
+# npoly is a number of polymers attached to npoly distinct vertices on vesicle
+nfil=0
+# nmono is a number of monomers in each filament
+nfono=10
+# Spring constant between monomers of the filament
+k_sfring=800
+
####### Cell definitions ############
nxmax=60
nymax=60
--
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