The A-R binding mode is adopted. (a) Proportion of four categories [single subsystem with single pathways (S,S), single subsystem with mixing pathways (S,M), mixing subsystems with single pathways (M,S), and mixing subsystems with mixing pathways (M,M)] in systems with CR. (b) The proportion of systems with two-state transition. (c) Distribution of PRR and state probability of three subsystems (PRR + PTT for the MWC pathway, PRR + PIR + PRI + PII for the EAM pathway, and PRR + PTI + PIT for the Other pathway) for systems with CR ≈ 0.16. ΔGmax = 3 or 13 kcal/mol. The theoretical CR ~ PRR curve (blue line) for the two-state model is also plotted using Eq (9). The horizontal dashed line represents CR = 0.16.</p
Each domain (blue and yellow) can be in R (Relaxed), T (Tensed) and I (Disordered) state. R and T ar...
<p>Left: Resulting outcome as a function of the relative benefit <i>B</i>/<i>A</i> of showing the pr...
<p>The model illustrated in this diagram includes eight states that are denoted by . The allowed tra...
The stability free-energy parameters (ΔGR1, ΔGR2, ΔGRT1, ΔGRT2, Δgint,R, Δgint,T) vary randomly with...
The arrows indicate the population shifts caused by ligand binding which are capable of affecting th...
(a) The possibilities for three pathways [calculated with Eq (12)] obtained at different [–ΔGmax, +Δ...
(a,b) CR as a function of Δgint,R and Δgint,T (in kcal/mol) when the other parameters are fixed (cho...
(a) The relations among PRR, ΔGi and CR for the MWC model with two states, plotted according to Eqs ...
We developed a multiple state transition path sampling (TPS) approach in which it is possible to sim...
<p>(A-B) fast (<i>k</i><sub>+</sub><i>c</i><sub>0</sub> = 20<i>s</i><sup>−1</sup>, <i>k</i><sub>−</s...
<p>The conceptual scheme (A) and heat map of RMSE scores (B) for probabilistic combination of replic...
<p>(A) Four states are allowed in this example, two where transcription is inactive (states 1 and 3)...
Scenario 3, states B (left) and C (right) of the simple reaction model: Normalised state classificat...
<p>The simulation setup is described in Section 3.3. F denotes the start of each algorithm where all...
(A) Within the MWC model, cAMP (purple circles) may bind to a CRP subunit in either the active (dark...
Each domain (blue and yellow) can be in R (Relaxed), T (Tensed) and I (Disordered) state. R and T ar...
<p>Left: Resulting outcome as a function of the relative benefit <i>B</i>/<i>A</i> of showing the pr...
<p>The model illustrated in this diagram includes eight states that are denoted by . The allowed tra...
The stability free-energy parameters (ΔGR1, ΔGR2, ΔGRT1, ΔGRT2, Δgint,R, Δgint,T) vary randomly with...
The arrows indicate the population shifts caused by ligand binding which are capable of affecting th...
(a) The possibilities for three pathways [calculated with Eq (12)] obtained at different [–ΔGmax, +Δ...
(a,b) CR as a function of Δgint,R and Δgint,T (in kcal/mol) when the other parameters are fixed (cho...
(a) The relations among PRR, ΔGi and CR for the MWC model with two states, plotted according to Eqs ...
We developed a multiple state transition path sampling (TPS) approach in which it is possible to sim...
<p>(A-B) fast (<i>k</i><sub>+</sub><i>c</i><sub>0</sub> = 20<i>s</i><sup>−1</sup>, <i>k</i><sub>−</s...
<p>The conceptual scheme (A) and heat map of RMSE scores (B) for probabilistic combination of replic...
<p>(A) Four states are allowed in this example, two where transcription is inactive (states 1 and 3)...
Scenario 3, states B (left) and C (right) of the simple reaction model: Normalised state classificat...
<p>The simulation setup is described in Section 3.3. F denotes the start of each algorithm where all...
(A) Within the MWC model, cAMP (purple circles) may bind to a CRP subunit in either the active (dark...
Each domain (blue and yellow) can be in R (Relaxed), T (Tensed) and I (Disordered) state. R and T ar...
<p>Left: Resulting outcome as a function of the relative benefit <i>B</i>/<i>A</i> of showing the pr...
<p>The model illustrated in this diagram includes eight states that are denoted by . The allowed tra...