1\u00a0\u00a0\u00a0\u00a0 clear<\/p>\n
2\u00a0\u00a0\u00a0\u00a0 % This program computes the overall donor-to-acceptor<\/p>\n
3\u00a0\u00a0\u00a0\u00a0 % transfer time<\/p>\n
4\u00a0\u00a0\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
5\u00a0\u00a0\u00a0\u00a0 % Inputs related to building rate matrix<\/p>\n
6\u00a0\u00a0\u00a0\u00a0 hbar=0.6582*10^(-3); % in eV psec<\/p>\n
7\u00a0\u00a0\u00a0\u00a0 kb=0.02586\/300;\u00a0\u00a0\u00a0\u00a0\u00a0 % in eV\/Kelvin<\/p>\n
8\u00a0\u00a0\u00a0\u00a0 n=5;\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % number of states<\/p>\n
9\u00a0\u00a0\u00a0\u00a0 % temperature index to pick temp from temprange vector<\/p>\n
10\u00a0\u00a0\u00a0 tempindex=3;<\/p>\n
11\u00a0\u00a0\u00a0 ened=0;\u00a0\u00a0\u00a0\u00a0\u00a0 % donor (d) site energy (eV)<\/p>\n
12\u00a0\u00a0\u00a0 enea=ened;\u00a0\u00a0 % unbiased acceptor (a) site energy (eV)<\/p>\n
13\u00a0\u00a0\u00a0 enebr=0.2;\u00a0\u00a0 % unbiazed bridge site energy (eV)<\/p>\n
14\u00a0\u00a0\u00a0 vdb=0.1;\u00a0\u00a0\u00a0\u00a0 % donor-bridge electronic coupling (eV)<\/p>\n
15\u00a0\u00a0\u00a0 vba=vdb;\u00a0\u00a0\u00a0\u00a0 % acceptor-bridge electronic coupling (eV)<\/p>\n
16\u00a0\u00a0\u00a0 vbb=0.01;\u00a0\u00a0\u00a0 % bridge-bridge electronic coupling (eV)<\/p>\n
17\u00a0\u00a0\u00a0 dgda=0.0;\u00a0\u00a0\u00a0 % overal free energy bias between d and a (eV)<\/p>\n
18\u00a0\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
19\u00a0\u00a0\u00a0 % Inputs related to time evolution<\/p>\n
20\u00a0\u00a0\u00a0 nt=10^(6);\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % number of time steps<\/p>\n
21\u00a0\u00a0\u00a0 tin=0.0;\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % initial time<\/p>\n
22\u00a0\u00a0\u00a0 tfinalfact=1*10^(5); % determines tfinal<\/p>\n
23\u00a0\u00a0\u00a0 % initial probability distribution vector vec(P)(t=0)<\/p>\n
24\u00a0\u00a0\u00a0 p0=zeros(n,1);<\/p>\n
25\u00a0\u00a0\u00a0 % Set initial condition P_i(t=0)=delta_i,a<\/p>\n
26\u00a0\u00a0\u00a0 p0(1)=1.;<\/p>\n
27\u00a0\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
28\u00a0\u00a0\u00a0 % Initializing variables to build the rate matrix<\/p>\n
29\u00a0\u00a0\u00a0 ene=zeros(1,n);\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % unbiased site-energies vector<\/p>\n
30\u00a0\u00a0\u00a0 voltbias=zeros(1,n);\u00a0\u00a0 % voltage bias profile vector<\/p>\n
31\u00a0\u00a0\u00a0 % biased site-energies vector = unbiased + voltage bias<\/p>\n
32\u00a0\u00a0\u00a0 enebias=zeros(1,n);<\/p>\n
33\u00a0\u00a0\u00a0 % dgnn(i)=enebias(i+1)-enebias(i) nn’site enrgy gap vector<\/p>\n
34\u00a0\u00a0\u00a0 dgnn=zeros(1,n-1);<\/p>\n
35\u00a0\u00a0\u00a0 coupl=zeros(1,n-1);\u00a0\u00a0\u00a0 % nearest-neighbor couplings<\/p>\n
36\u00a0\u00a0\u00a0 kforw=zeros(1,n-1);\u00a0\u00a0\u00a0 % quantum forward rates vector<\/p>\n
37\u00a0\u00a0\u00a0 kbackw=zeros(1,n-1);\u00a0\u00a0 % quantum\u00a0 backward rates vector<\/p>\n
38\u00a0\u00a0\u00a0 clkforw=zeros(1,n-1);\u00a0 % clasical forward rates\u00a0 vector<\/p>\n
39\u00a0\u00a0\u00a0 clkbackw=zeros(1,n-1); % classical\u00a0 backward rates vector<\/p>\n
40\u00a0\u00a0\u00a0 kforwda=zeros(1,n-1);<\/p>\n
41\u00a0\u00a0\u00a0 kbackwda=zeros(1,n-1);<\/p>\n
42\u00a0\u00a0\u00a0 clkforwda=zeros(1,n-1);<\/p>\n
43\u00a0\u00a0\u00a0 clkbackwda=zeros(1,n-1);<\/p>\n
44\u00a0\u00a0\u00a0 % index used to pick energy gap values hbarw=dgnn(i) and<\/p>\n
45\u00a0\u00a0\u00a0 % corresponding FC factors at dgnn(i) (quantum and<\/p>\n
46\u00a0\u00a0\u00a0 % clasical) from fcond & fcondcl files produced by<\/p>\n
47\u00a0\u00a0\u00a0 % FCprodOCT21.m program<\/p>\n
48\u00a0\u00a0\u00a0 indexe=zeros(1,n-1);<\/p>\n
49\u00a0\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
50\u00a0\u00a0\u00a0 % Initalizing variables\u00a0 related to time evolution of<\/p>\n
51\u00a0\u00a0\u00a0 % probabilities<\/p>\n
52\u00a0\u00a0\u00a0 tvec=zeros(1,nt);\u00a0\u00a0\u00a0\u00a0\u00a0 % time vector given nt<\/p>\n
53\u00a0\u00a0\u00a0 pvec=zeros(1,nt);\u00a0\u00a0\u00a0\u00a0\u00a0 % 1st (d) state time-dep prob P_d(t)<\/p>\n
54\u00a0\u00a0\u00a0 p2vec=zeros(1,nt);\u00a0\u00a0\u00a0\u00a0 % nth (a) state time-dep prob P_a(t)<\/p>\n
55\u00a0\u00a0\u00a0 pt=zeros(n,1);\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % time dep prob distr vect vec(P)(t)<\/p>\n
56\u00a0\u00a0\u00a0 w=zeros(n,n);\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % Initializing rate matrix<\/p>\n
57\u00a0\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
58\u00a0\u00a0\u00a0 % Hamiltonian parameters given inputs<\/p>\n
59\u00a0\u00a0\u00a0 ene(1)=ened;<\/p>\n
60\u00a0\u00a0\u00a0 ene(n)=enea;<\/p>\n
61\u00a0\u00a0\u00a0 ene(2:n-1)=enebr;<\/p>\n
62\u00a0\u00a0\u00a0 coupl(1)=vdb;<\/p>\n
63\u00a0\u00a0\u00a0 coupl(n-1)=vba;<\/p>\n
64\u00a0\u00a0\u00a0 coupl(2:n-2)=vbb;<\/p>\n
65\u00a0\u00a0\u00a0 for i=2:n<\/p>\n
66\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 bias(i)=(i-1)*dgda\/(n-1);<\/p>\n
67\u00a0\u00a0\u00a0 end<\/p>\n
68\u00a0\u00a0\u00a0 enebias=ene+bias;<\/p>\n
69\u00a0\u00a0\u00a0 for i=1:n-1<\/p>\n
70\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 dgnn(i)=enebias(i+1)-enebias(i);<\/p>\n
71\u00a0\u00a0\u00a0 end<\/p>\n
72\u00a0\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
73<\/p>\n
74\u00a0\u00a0\u00a0 % Loading temperatures, and precomputed 2*pi*hbar*FC<\/p>\n
75\u00a0\u00a0\u00a0 mydata=load(‘temperature.mat’,’temprange’);<\/p>\n
76\u00a0\u00a0\u00a0 temprange=mydata.temprange;<\/p>\n
77\u00a0\u00a0\u00a0 % precomputed quantum 2*pi*hbar*FC to be used for computing<\/p>\n
78\u00a0\u00a0\u00a0 % bridge-bridge quantum rate, donor=bridge molecule,<\/p>\n
79\u00a0\u00a0\u00a0 % acceptor=bridge molecule<\/p>\n
80\u00a0\u00a0\u00a0 mydata2=load(‘fc_bb_hbgamma0point001.mat’,’fcond’);<\/p>\n
81\u00a0\u00a0\u00a0 fcondbb=mydata2.fcond;<\/p>\n
82\u00a0\u00a0\u00a0 % precomputed classical 2*pi*hbar*FC(classical) to be used<\/p>\n
83\u00a0\u00a0\u00a0 % for computing bridge-bridge classical rate<\/p>\n
84\u00a0\u00a0\u00a0 mydata3=load(‘fccl_bb_hbgamma0point001.mat’,’fcondcl’);<\/p>\n
85\u00a0\u00a0\u00a0 fcondclbb=mydata3.fcondcl;<\/p>\n
86\u00a0\u00a0\u00a0 % precomputed quantum 2*pi*hbar*FC, to be used<\/p>\n
87\u00a0\u00a0\u00a0 % for donor-acceptor rates<\/p>\n
88\u00a0\u00a0\u00a0 mydata4=load(‘fc_da_hbgamma0point001.mat’,’fcond’);<\/p>\n
89\u00a0\u00a0\u00a0 fcondda=mydata4.fcond;<\/p>\n
90\u00a0\u00a0\u00a0 % precomputed classical 2*pi*hbar*FC, to be used<\/p>\n
91\u00a0\u00a0\u00a0 % for donor-acceptor rates<\/p>\n
92\u00a0\u00a0\u00a0 mydata5=load(‘fccl_da_hbgamma0point001.mat’,’fcondcl’);<\/p>\n
93\u00a0\u00a0\u00a0 fcondclda=mydata5.fcondcl;<\/p>\n
94\u00a0\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
95<\/p>\n
96\u00a0\u00a0\u00a0 % forward quantum and classical rates for all site to site<\/p>\n
97\u00a0\u00a0\u00a0 % energy gaps defined in dgnn<\/p>\n
98\u00a0\u00a0\u00a0 % BRIDGE – BRIDGE RATES<\/p>\n
99\u00a0\u00a0\u00a0 hbarw_bb = fcondbb(1,:);<\/p>\n
100\u00a0\u00a0 for i=2:n-2<\/p>\n
101\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % pick dgnn values for hbarw which corresponds to the<\/p>\n
102\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % energy gap between each bridge site and also extract<\/p>\n
103\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % 2*pi*hbar*FC factors for the dgnn(i) and compute<\/p>\n
104\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % corresponding rates<\/p>\n
105\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 [abs1,indexe(i-1)] = min(abs(hbarw_bb – dgnn(i)));<\/p>\n
106\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % quantum rates at temperature picked by tempindex<\/p>\n
107\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 kforw(i)=((coupl(i)\/hbar)^2)*…<\/p>\n
108\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (fcondbb(tempindex+1,indexe(i-1)));<\/p>\n
109\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 kbackw(i)=kforw(i)*(exp(dgnn(i)\/…<\/p>\n
110\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (kb*temprange(tempindex))));<\/p>\n
111\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % classical marcus rates at temp picked by tempindex<\/p>\n
112\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 clkforw(i)=((coupl(i)\/hbar)^2)*…<\/p>\n
113\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (fcondclbb(tempindex+1,indexe(i-1)));<\/p>\n
114\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 clkbackw(i)=clkforw(i)*(exp(dgnn(i)\/…<\/p>\n
115\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (kb*temprange(tempindex))));<\/p>\n
116\u00a0\u00a0 end<\/p>\n
117\u00a0\u00a0 % DONOR-BRIDGE quantum rates<\/p>\n
118\u00a0\u00a0 hbarw_db = fcondda(1,:);<\/p>\n
119\u00a0\u00a0 % pick dgnn values for hbarw which corresponds to the<\/p>\n
120\u00a0\u00a0 % energy gap between donor & bridge site<\/p>\n
121\u00a0\u00a0 [abs2,indexe2] = min(abs(hbarw_db-dgnn(1)));<\/p>\n
122\u00a0\u00a0 kforwdb=((coupl(1)\/hbar)^2)*(fcondda(tempindex+1,indexe2));<\/p>\n
123\u00a0\u00a0 kbackwdb=kforwdb*(exp(dgnn(1)\/(kb*temprange(tempindex))));<\/p>\n
124\u00a0\u00a0 % BRIDGE-ACCEPTOR quantum rates<\/p>\n
125\u00a0\u00a0 % pick dgnn values for hbarw which corresponds to the<\/p>\n
126\u00a0\u00a0 % energy gap between bridge & acceptor site<\/p>\n
127\u00a0\u00a0 [abs3,indexe3] = min(abs(hbarw_db-dgnn(n-1)));<\/p>\n
128\u00a0\u00a0 kforwba=((coupl(n-1)\/hbar)^2)*…<\/p>\n
129\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (fcondda(tempindex+1,indexe3));<\/p>\n
130\u00a0\u00a0 kbackwba=kforwba*(exp(dgnn(n-1)\/…<\/p>\n
131\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (kb*temprange(tempindex))));<\/p>\n
132\u00a0\u00a0 % DONOR-BRIDGE classical rates<\/p>\n
133\u00a0\u00a0 hbarw_db_cl = fcondclda(1,:);<\/p>\n
134\u00a0\u00a0 [abs4,indexe4] = min(abs(hbarw_db-dgnn(1)));<\/p>\n
135\u00a0\u00a0 clkforwdb=((coupl(1)\/hbar)^2)*…<\/p>\n
136\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (fcondclda(tempindex+1,indexe4));<\/p>\n
137\u00a0\u00a0 clkbackwdb=clkforwdb*(exp(dgnn(1)\/…<\/p>\n
138\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (kb*temprange(tempindex))));<\/p>\n
139\u00a0\u00a0 % BRIDGE-ACCEPTOR classical<\/p>\n
140\u00a0\u00a0 [abs5,indexe5] = min(abs(hbarw_db-dgnn(n-1)));<\/p>\n
141\u00a0\u00a0 clkforwba=((coupl(n-1)\/hbar)^2)*…<\/p>\n
142\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (fcondclda(tempindex+1,indexe5));<\/p>\n
143\u00a0\u00a0 clkbackwba=clkforwba*(exp(dgnn(n-1)\/…<\/p>\n
144\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (kb*temprange(tempindex))));<\/p>\n
145\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
146<\/p>\n
147\u00a0\u00a0 % Kinetic matrix (W)<\/p>\n
148\u00a0\u00a0 % Nonzero off-diagonal elements<\/p>\n
149\u00a0\u00a0 for j=1:n-1<\/p>\n
150\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 w(j+1,j) = kforw(j);<\/p>\n
151\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 w(j,j+1) = kbackw(j);<\/p>\n
152\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % w(j+1,j) = clkforw(j);<\/p>\n
153\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 % w(j,j+1) = clkbackw(j);<\/p>\n
154\u00a0\u00a0 end<\/p>\n
155\u00a0\u00a0 % overwriting with d-b\/b0a rates<\/p>\n
156\u00a0\u00a0 w(2,1)=kforwdb;<\/p>\n
157\u00a0\u00a0 w(1,2)=kbackwdb;<\/p>\n
158\u00a0\u00a0 w(n,n-1)=kforwba;<\/p>\n
159\u00a0\u00a0 w(n-1,n)=kbackwba;<\/p>\n
160\u00a0\u00a0 % w(2,1)=clkforwdb;<\/p>\n
161\u00a0\u00a0 % w(1,2)=clkbackwdb;<\/p>\n
162\u00a0\u00a0 % w(n,n-1)=clkforwba;<\/p>\n
163\u00a0\u00a0 % w(n-1,n)=clkbackwba;<\/p>\n
164\u00a0\u00a0 % diagonal elements<\/p>\n
165\u00a0\u00a0 for j=2:n-1<\/p>\n
166\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 w(j,j) = -w(j+1,j)-w(j-1,j);<\/p>\n
167\u00a0\u00a0 end<\/p>\n
168\u00a0\u00a0 w(1,1)= -w(2,1);<\/p>\n
169\u00a0\u00a0 w(n,n)= -w(n-1,n);<\/p>\n
170\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
171\u00a0\u00a0 % find the eigevectors & eigenvalues of rate matrix<\/p>\n
172\u00a0\u00a0 [V,D]=eig(w);<\/p>\n
173\u00a0\u00a0 s=diag(D);<\/p>\n
174\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
175\u00a0\u00a0 % final time in multiples of timescale kfdb^-1<\/p>\n
176\u00a0\u00a0 tfin=tfinalfact\/kforwdb;<\/p>\n
177\u00a0\u00a0 % 1st choice for timestep = Total time interval\/number<\/p>\n
178\u00a0\u00a0 % of time steps<\/p>\n
179\u00a0\u00a0 dt=(tfin-tin)\/nt;<\/p>\n
180\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%<\/p>\n
181\u00a0\u00a0 for i=1:nt<\/p>\n
182\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 t=tin+(i-1)*dt; tvec(i)=t;<\/p>\n
183\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 pt= V*diag(exp(t*s))*inv(V)*p0;<\/p>\n
184\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 pvec(i)=pt(1);\u00a0 % 1st state time-dep prob<\/p>\n
185\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 p2vec(i)=pt(n); % last state time-dep prob<\/p>\n
186\u00a0\u00a0 end<\/p>\n
187<\/p>\n
188\u00a0\u00a0 plot(10^(-3)*tvec,p2vec,10^(-3)*tvec,pvec)<\/p>\n
189\u00a0\u00a0 xlabel(‘$t(ns)$’,’interpreter’,’latex’)<\/p>\n
190\u00a0\u00a0 ylabel(‘$P_{i}(t)$’,’interpreter’,’latex’)<\/p>\n
191\u00a0\u00a0 legend(‘$P_{N+2}(t)$’,’$P_{1}(t)$’,’interpreter’,’latex’)<\/p>\n
192<\/p>\n
193\u00a0\u00a0 % finding equilibrium values of site probabilities<\/p>\n
194\u00a0\u00a0 peq=zeros(1,n);<\/p>\n
195\u00a0\u00a0 normpeq=zeros(1,n);<\/p>\n
196\u00a0\u00a0 for k=1:n<\/p>\n
197\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 peq(k)=exp(-enebias(k)\/(kb*temprange(tempindex)));<\/p>\n
198\u00a0\u00a0 end<\/p>\n
199<\/p>\n
200\u00a0\u00a0 % fprintf(‘zero bias energy gap (ev)\u00a0 %f\\n’, dgnn(1));<\/p>\n
201\u00a0\u00a0 % fprintf(‘temperature (Kelvin) %f\\n’,temprange(tempindex));<\/p>\n
202\u00a0\u00a0 % fprintf(‘kforwbb (psec)\u00a0 %f\\n’,1\/kforw(2));<\/p>\n
203\u00a0\u00a0 % fprintf(‘1\/kforwbb (nsec) %f\\n’,(1\/kforw(2))*(10^(-3)));<\/p>\n
204\u00a0\u00a0 % fprintf(‘1\/kforwba (nsec) %f\\n’,(1\/kforwba)*(10^(-3)));<\/p>\n
205\u00a0\u00a0 % fprintf(‘1\/kforwdb (psec) %f\\n’,1\/kforwdb);<\/p>\n
206\u00a0\u00a0 % fprintf(‘1\/kforwdb (nsec) %f\\n’,(1\/kforwdb)*(10^(-3)));<\/p>\n
207<\/p>\n
208\u00a0\u00a0 stath=sum(peq);<\/p>\n
209\u00a0\u00a0 normpeq=(1\/stath)*peq;<\/p>\n
210\u00a0\u00a0 tolerance=0.1;<\/p>\n
211\u00a0\u00a0 [avte,vadoum]=min(abs(p2vec-(normpeq(n)*(0.8))));<\/p>\n
212\u00a0\u00a0 if min(abs(p2vec-(normpeq(n)*(0.8)))) <=tolerance;<\/p>\n
213\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 fprintf(‘transfer time in psec %f\\n’, tvec(vadoum));<\/p>\n
214\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 fprintf(‘transfer time in nsec %f\\n’, tvec(vadoum)*…<\/p>\n
215\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 (10^(-3)));<\/p>\n
216\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 fprintf(‘Transfer time in units of 1\/kforwardb %f\\n’,…<\/p>\n
217\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 tvec(vadoum));<\/p>\n
218\u00a0\u00a0 else<\/p>\n
219\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 fprintf(‘Run for longer times’)<\/p>\n
220\u00a0\u00a0 end<\/p>\n","protected":false},"excerpt":{"rendered":"
1\u00a0\u00a0\u00a0\u00a0 clear 2\u00a0\u00a0\u00a0\u00a0 % This program computes the overall donor-to-acceptor 3\u00a0\u00a0\u00a0\u00a0 % transfer time 4\u00a0\u00a0\u00a0\u00a0 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% 5\u00a0\u00a0\u00a0\u00a0 % Inputs related to building rate matrix 6\u00a0\u00a0\u00a0\u00a0 hbar=0.6582*10^(-3); [\u2026]<\/span><\/p>\n","protected":false},"author":48,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_lmt_disableupdate":"","_lmt_disable":"","footnotes":""},"class_list":["post-1851","page","type-page","status-publish","hentry"],"publishpress_future_action":{"enabled":false,"date":"2026-06-22 13:55:47","action":"change-status","newStatus":"draft","terms":[],"taxonomy":"translation_priority","extraData":[]},"publishpress_future_workflow_manual_trigger":{"enabledWorkflows":[]},"_links":{"self":[{"href":"https:\/\/www.ucy.ac.cy\/biophysmolphys\/wp-json\/wp\/v2\/pages\/1851","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ucy.ac.cy\/biophysmolphys\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.ucy.ac.cy\/biophysmolphys\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.ucy.ac.cy\/biophysmolphys\/wp-json\/wp\/v2\/users\/48"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ucy.ac.cy\/biophysmolphys\/wp-json\/wp\/v2\/comments?post=1851"}],"version-history":[{"count":1,"href":"https:\/\/www.ucy.ac.cy\/biophysmolphys\/wp-json\/wp\/v2\/pages\/1851\/revisions"}],"predecessor-version":[{"id":1852,"href":"https:\/\/www.ucy.ac.cy\/biophysmolphys\/wp-json\/wp\/v2\/pages\/1851\/revisions\/1852"}],"wp:attachment":[{"href":"https:\/\/www.ucy.ac.cy\/biophysmolphys\/wp-json\/wp\/v2\/media?parent=1851"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}