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BIOPARTICLE

Specifies parameters for BIOPARTICLE reactions.

Required Cards:

BIOPARTICLE

Opens the reaction block.

PARTICLE_NAME_AQ <string>

Name of the species while suspended in the aqueous mobile phase.

PARTICLE_NAME_IM <string>

Name of the species while attached to the solid phase.

RATE_ATTACHMENT <string>

Defines how to calculate the attachment rate of particles. Available options are CONSTANT and FILTRATION_MODEL for colloid filtration theory.

RATE_DETACHMENT <string>

Defines how to calculate the detachment rate of particles. Currently, only a CONSTANT rate is supported.

DECAY_AQUEOUS <string>

Defines how to calculate the inactivation rate of particles while in the mobile phase. It can be a constant rate or derived from a temperature model.

DECAY_ADSORBED <string>

Defines how to calculate the inactivation rate of particles while immobilized. It can be a constant rate or derived from a temperature model.

Examples

Chemistry block - BIOPARTICLE with constant rates

CHEMISTRY
 PRIMARY_SPECIES
  Vaq
 /
 IMMOBILE_SPECIES
  Vim
 /
 REACTION_SANDBOX
  BIOPARTICLE
   PARTICLE_NAME_AQ Vaq
   PARTICLE_NAME_IM Vim
   RATE_ATTACHMENT CONSTANT
    VALUE 1.00E-04 1/h
   /
   RATE_DETACHMENT CONSTANT
    VALUE 1.00E-04 1/h
   /
   DECAY_AQUEOUS CONSTANT
    VALUE 1.00E-04 1/h
   /
   DECAY_ADSORBED CONSTANT
    VALUE 1.00E-04 1/h
   /
  /
 /
 LOG_FORMULATION
 TRUNCATE_CONCENTRATION 1.0E-35
 DATABASE rxn_database.dat
 OUTPUT
  TOTAL
  ALL
 /
END

Chemistry block - BIOPARTICLE with calculated rates

CHEMISTRY
 PRIMARY_SPECIES
  Vaq
 /
 IMMOBILE_SPECIES
  Vim
 /
 REACTION_SANDBOX
  BIOPARTICLE
   PARTICLE_NAME_AQ Vaq
   PARTICLE_NAME_IM Vim
   RATE_ATTACHMENT FILTRATION_MODEL
    DIAMETER_COLLECTOR 2.0E-03  !m
    DIAMETER_PARTICLE  1.0E-07  !m
    HAMAKER_CONSTANT   5.0E-21  !J
    DENSITY_PARTICLE   1.1E+03  !kg/m3
    ALPHA_EFFICIENCY   1.0E-03  !-adim-
   /
   RATE_DETACHMENT CONSTANT
    VALUE  1.00E-07 1/s
   /
   DECAY_AQUEOUS TEMPERATURE_MODEL
    TREF    4.0
    ZT      29.1
    N       2.0
    LOGDREF 2.3
   /
   DECAY_ADSORBED TEMPERATURE_MODEL
    TREF    4.0
    ZT      29.1
    N       2.0
    LOGDREF 2.3
   /
  /
 /
 LOG_FORMULATION
 TRUNCATE_CONCENTRATION 1.0E-35
 DATABASE rxn_database.dat
 OUTPUT
  TOTAL
  ALL
 /
END

Notes:

• FILTRATION_MODEL units are fixed to SI

• TEMPERATURE_MODEL uses the formulation given in Guillier et al. (2020) [DOI: 10.1128/AEM.01244-20].