Interactions¶

Interactions are used to calculate forces on individual particles due to their neighbours. Pairwise short-range interactions are currently supported, and membrane forces.

Summary¶

 DPD() Pairwise interaction with conservative part and dissipative + random part acting as a thermostat, see [Groot1997] DPDWithStress() wrapper of DPD with, in addition, stress computation Density() TODO Interaction() Base interaction class JuelicherBendingParameters() Bending parameters for Juelicher model KantorBendingParameters() Bending parameters for Kantor model LJ() Pairwise interaction according to the classical Lennard-Jones potential The force however is truncated such that it is always repulsive. LJWithStress() wrapper of LJ with, in addition, stress computation MDPD() TODO must be used together with Density interaction MDPDWithStress() wrapper of MDPD with, in addition, stress computation MembraneForces() Abstract class for membrane interactions. MembraneForcesJuelicher() Mesh-based forces acting on a membrane according to the model in [Fedosov2010] with Juelicher bending model. MembraneForcesKantor() Mesh-based forces acting on a membrane according to the model in [Fedosov2010] MembraneParameters() Common membrane parameters

Details¶

class DPD

Pairwise interaction with conservative part and dissipative + random part acting as a thermostat, see [Groot1997]

$\begin{split}\mathbf{F}_{ij} &= \mathbf{F}^C(\mathbf{r}_{ij}) + \mathbf{F}^D(\mathbf{r}_{ij}, \mathbf{u}_{ij}) + \mathbf{F}^R(\mathbf{r}_{ij}) \\ \mathbf{F}^C(\mathbf{r}) &= \begin{cases} a(1-\frac{r}{r_c}) \mathbf{\hat r}, & r < r_c \\ 0, & r \geqslant r_c \end{cases} \\ \mathbf{F}^D(\mathbf{r}, \mathbf{u}) &= \gamma w^2(\frac{r}{r_c}) (\mathbf{r} \cdot \mathbf{u}) \mathbf{\hat r} \\ \mathbf{F}^R(\mathbf{r}) &= \sigma w(\frac{r}{r_c}) \, \theta \sqrt{\Delta t} \, \mathbf{\hat r}\end{split}$

where bold symbol means a vector, its regular counterpart means vector length: $$x = \left\lVert \mathbf{x} \right\rVert$$, hat-ed symbol is the normalized vector: $$\mathbf{\hat x} = \mathbf{x} / \left\lVert \mathbf{x} \right\rVert$$. Moreover, $$\theta$$ is the random variable with zero mean and unit variance, that is distributed independently of the interacting pair i-j, dissipation and random forces are related by the fluctuation-dissipation theorem: $$\sigma^2 = 2 \gamma \, k_B T$$; and $$w(r)$$ is the weight function that we define as follows:

$\begin{split}w(r) = \begin{cases} (1-r)^{p}, & r < 1 \\ 0, & r \geqslant 1 \end{cases}\end{split}$
 [Groot1997] (1, 2) Groot, R. D., & Warren, P. B. (1997). Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulations. J. Chem. Phys., 107(11), 4423–4435. doi
__init__(name: str, rc: float, a: float, gamma: float, kbt: float, power: float) → None

Args: name: name of the interaction

rc: interaction cut-off (no forces between particles further than rc apart) a: $$a$$ gamma: $$\gamma$$ kbt: $$k_B T$$ power: $$p$$ in the weight function
setSpecificPair(pv1: ParticleVectors.ParticleVector, pv2: ParticleVectors.ParticleVector, a: float = inf, gamma: float = inf, kbt: float = inf, power: float = inf) → None

Override some of the interaction parameters for a specific pair of Particle Vectors

class DPDWithStress

Bases: _ymero.Interactions.DPD

wrapper of DPD with, in addition, stress computation

__init__(name: str, rc: float, a: float, gamma: float, kbt: float, power: float, stressPeriod: float) → None
Parameters: name – name of the interaction rc – interaction cut-off (no forces between particles further than rc apart) a – $$a$$ gamma – $$\gamma$$ kbt – $$k_B T$$ power – $$p$$ in the weight function stressPeriod – compute the stresses every this period (in simulation time units)
setSpecificPair(pv1: ParticleVectors.ParticleVector, pv2: ParticleVectors.ParticleVector, a: float = inf, gamma: float = inf, kbt: float = inf, power: float = inf) → None

Override some of the interaction parameters for a specific pair of Particle Vectors

class Density

TODO

__init__(name: str, rc: float) → None
Parameters: name – name of the interaction rc – interaction cut-off
class Interaction

Bases: object

Base interaction class

__init__()

Initialize self. See help(type(self)) for accurate signature.

class JuelicherBendingParameters

Bases: object

Bending parameters for Juelicher model

__init__(self: Interactions.JuelicherBendingParameters) → None

Structure keeping parameters of the bending membrane interaction

class KantorBendingParameters

Bases: object

Bending parameters for Kantor model

__init__(self: Interactions.KantorBendingParameters) → None

Structure keeping parameters of the bending membrane interaction

class LJ

Pairwise interaction according to the classical Lennard-Jones potential The force however is truncated such that it is always repulsive.

$\mathbf{F}_{ij} = \max \left[ 0.0, 24 \epsilon \left( 2\left( \frac{\sigma}{r_{ij}} \right)^{14} - \left( \frac{\sigma}{r_{ij}} \right)^{8} \right) \right]$
__init__(name: str, rc: float, epsilon: float, sigma: float, max_force: float = 1000.0, object_aware: bool) → None
Parameters: name – name of the interaction rc – interaction cut-off (no forces between particles further than rc apart) epsilon – $$\varepsilon$$ sigma – $$\sigma$$ max_force – force magnitude will be capped not exceed max_force object_aware – if True, the particles belonging to the same object in an object vector do not interact with each other. That restriction only applies if both Particle Vectors in the interactions are the same and is actually an Object Vector.
setSpecificPair(pv1: ParticleVectors.ParticleVector, pv2: ParticleVectors.ParticleVector, epsilon: float, sigma: float, max_force: float) → None

Override some of the interaction parameters for a specific pair of Particle Vectors

class LJWithStress

Bases: _ymero.Interactions.LJ

wrapper of LJ with, in addition, stress computation

__init__(name: str, rc: float, epsilon: float, sigma: float, max_force: float = 1000.0, object_aware: bool, stressPeriod: float) → None
Parameters: name – name of the interaction rc – interaction cut-off (no forces between particles further than rc apart) epsilon – $$\varepsilon$$ sigma – $$\sigma$$ max_force – force magnitude will be capped not exceed max_force object_aware – if True, the particles belonging to the same object in an object vector do not interact with each other. That restriction only applies if both Particle Vectors in the interactions are the same and is actually an Object Vector. stressPeriod – compute the stresses every this period (in simulation time units)
setSpecificPair(pv1: ParticleVectors.ParticleVector, pv2: ParticleVectors.ParticleVector, epsilon: float, sigma: float, max_force: float) → None

Override some of the interaction parameters for a specific pair of Particle Vectors

class MDPD

TODO must be used together with Density interaction

__init__(name: str, rc: float, rd: float, a: float, b: float, gamma: float, kbt: float, power: float) → None

Args: name: name of the interaction

rc: interaction cut-off (no forces between particles further than rc apart) rd: density cutoff, assumed rd < rc a: $$a$$ b: $$b$$ gamma: $$\gamma$$ kbt: $$k_B T$$ power: $$p$$ in the weight function
class MDPDWithStress

Bases: _ymero.Interactions.MDPD

wrapper of MDPD with, in addition, stress computation

__init__(name: str, rc: float, rd: float, a: float, b: float, gamma: float, kbt: float, power: float, stressPeriod: float) → None
Parameters: name – name of the interaction rc – interaction cut-off (no forces between particles further than rc apart) rd – density cut-off, assumed rd < rc a – $$a$$ b – $$b$$ gamma – $$\gamma$$ kbt – $$k_B T$$ power – $$p$$ in the weight function stressPeriod – compute the stresses every this period (in simulation time units)
class MembraneForces

Abstract class for membrane interactions. Mesh-based forces acting on a membrane according to the model in [Fedosov2010]

The membrane interactions are composed of forces comming from:
• bending of the membrane, potential $$U_b$$
• shear elasticity of the membrane, potential $$U_s$$
• constrain: area conservation of the membrane (local and global), potential $$U_A$$
• constrain: volume of the cell (assuming incompressible fluid), potential $$U_V$$
• membrane viscosity, pairwise force $$\mathbf{F}^v$$
• membrane fluctuations, pairwise force $$\mathbf{F}^R$$

The form of these potentials is given by:

$\begin{split}U_b = \sum_{j \in {1 ... N_s}} k_b \left[ 1-\cos(\theta_j - \theta_0) \right], \\ U_s = \sum_{j \in {1 ... N_s}} \left[ \frac {k_s l_m \left( 3x_j^2 - 2x_j^3 \right)}{4(1-x_j)} + \frac{k_p}{l_0} \right], \\ U_A = \frac{k_a (A_{tot} - A^0_{tot})^2}{2 A^0_{tot}} + \sum_{j \in {1 ... N_t}} \frac{k_d (A_j-A_0)^2}{2A_0}, \\ U_V = \frac{k_v (V-V^0_{tot})^2}{2 V^0_{tot}}.\end{split}$

See [Fedosov2010] for more explanations. The viscous and dissipation forces are central forces and are the same as DPD interactions with $$w(r) = 1$$ (no cutoff radius, applied to each bond).

 [Fedosov2010] Fedosov, D. A.; Caswell, B. & Karniadakis, G. E. A multiscale red blood cell model with accurate mechanics, rheology, and dynamics Biophysical journal, Elsevier, 2010, 98, 2215-2225
__init__()

Initialize self. See help(type(self)) for accurate signature.

class MembraneForcesJuelicher

Mesh-based forces acting on a membrane according to the model in [Fedosov2010] with Juelicher bending model.

The bending potential $$U_b$$ is defined as:

$\begin{split}U_b = 2 k_b \sum_{\alpha = 1}^{N_v} \frac {\left( M_{\alpha} - C_0\right)^2}{A_\alpha}, \\ M_{\alpha} = \frac 1 4 \sum_{<i,j>}^{(\alpha)} l_{ij} \theta_{ij}.\end{split}$

See [Juelicher1996] for more explanations. Note that the current model is an extended version of the original form. The viscous and dissipation forces are central forces and are the same as DPD interactions with $$w(r) = 1$$ (no cutoff radius, applied to each bond).

 [Juelicher1996] Juelicher, Frank, and Reinhard Lipowsky. Shape transformations of vesicles with intramembrane domains. Physical Review E 53.3 (1996): 2670.
__init__(name: str, params: Interactions.MembraneParameters, params_bending: Interactions.JuelicherBendingParameters, stressFree: bool, grow_until: float = 0) → None
Parameters: name – name of the interaction params – instance of :any: MembraneParameters params_bending – instance of :any: JuelicherBendingParameters stressFree – equilibrium bond length and areas are taken from the initial mesh grow_until – time to grow the cell at initialization stage; the size increases linearly in time from half of the provided mesh to its full size after that time the parameters are scaled accordingly with time
class MembraneForcesKantor

Mesh-based forces acting on a membrane according to the model in [Fedosov2010]

The bending potential $$U_b$$ is defined as:
$U_b = \sum_{j \in {1 ... N_s}} k_b \left[ 1-\cos(\theta_j - \theta_0) \right]$

See [Fedosov2010] for more explanations. The viscous and dissipation forces are central forces and are the same as DPD interactions with $$w(r) = 1$$ (no cutoff radius, applied to each bond).

 [Fedosov2010] Fedosov, D. A.; Caswell, B. & Karniadakis, G. E. A multiscale red blood cell model with accurate mechanics, rheology, and dynamics Biophysical journal, Elsevier, 2010, 98, 2215-2225
__init__(name: str, params: Interactions.MembraneParameters, params_bending: Interactions.KantorBendingParameters, stressFree: bool, grow_until: float = 0) → None
Parameters: name – name of the interaction params – instance of :any: MembraneParameters params_bending – instance of :any: KantorBendingParameters stressFree – equilibrium bond length and areas are taken from the initial mesh grow_until – time to grow the cell at initialization stage; the size increases linearly in time from half of the provided mesh to its full size after that time the parameters are scaled accordingly with time
class MembraneParameters

Bases: object

Common membrane parameters

__init__(self: Interactions.MembraneParameters) → None

Structure keeping parameters of the membrane interaction