Welcome to the RADAM database portal.

RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This data base has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014. The collected data aim to improve our understanding of radiation damage mechanisms of biological targets on the molecular level. Some of the nodes of the RADAM portal are integrated into the Virtual Atomic and Molecular Data Center (VAMDC). The RADAM portal has been created and is maintained by the team of MBN Research Center.

Recent progress in the database was described in the following paper.

Using the portal

In order to query data through the RADAM database portal one should do the following:

  1. Select the database node

  2. Select type of the data to query

  3. Specify conditions of selection using query language or using Modify query dialog.

  4. Press the Search button.

Then the following dialog window should appear:

After loading the data, results will be shown with the following interface:

The interface contains set of tabs that store tables for each type of data (in figure above: Sources, Atoms, Molecules, Particles and Col. transitions) and additional tab for the same data in XML format. Each row in the table contains a short list of the main parameters of a single database record. The detailed information can be accessed by clicking on the row. An example of such output is given below:

In figure results of the measured cross section for the electron attachment to thymine are shown. The Properties dialog window contains set of parameters of the measurement, bibliographic reference, plot and a table of values (accessible by clicking on Data button). Underlined source reference and other data properties provide the links to the corresponding detailed information.

Database format description

RADAM database consists of multiple nodes with the same software interface(HTTP API) for querying data. This interface is based on VAMDC standards of data exchange with some extensions. Each node in a database implements two types of requests:
  • Request for meta-information
  • Data query.

Additional data types

In order to describe multiscale phenomena new type of Processes was added. Section Multiscale contains following types of objects:
  • EnergyLoss - Energy loss and Bragg peak process
  • BeamSpreading - Angular spreading of the beam process
  • ComplexDielectricFunction - Description of beam propagation using complex dielectric function
  • ThermomechanicalDamage - Thermomechanical damage process during radiation with ions
  • DiffusionProcess - Diffusion process
  • ChemicalReaction - Chemical reactions of radical and molecular species
  • PenetrationDistance - Ion penetration into medium process
These processes are described with following properties:

EnergyLoss

Energy loss and Bragg peak process description parameters:
ElementTypeDescription
SpeciesRefReference IDReference to specie
InitialEnergyValueInitial energy
BraggPeakPositionValuePosition of maximum of stopping power
DataSetsSet of tablesSet of tables for description of process
envRefReference IDReference to environment description

BeamSpreading

Angular spreading of the beam process description parameters:
ElementTypeDescription
SpeciesRefReference IDReference to specie
InitialEnergyValueInitial energy
DataSetsSet of tablesSet of tables for description of process
envRefReference IDReference to environment description

ComplexDielectricFunction

Description of beam propagation using complex dielectric function:
ElementTypeDescription
SpeciesRefReference IDReference to specie
DataSetsSet of tablesSet of tables for description of process
envRefReference IDReference to environment description

ThermomechanicalDamage

Thermomechanical damage process during radiation with ions:
ElementTypeDescription
SpeciesRefReference IDReference to specie
InitialEnergyValueInitial energy
DataSetsSet of tablesSet of tables for description of process
envRefReference IDReference to environment description

DiffusionProcess

Diffusion process description parameters:
ElementTypeDescription
SpeciesRefReference IDReference to specie
DiffusionCoefficientValueDiffusion coefficient
DataSetsSet of tablesSet of tables for description of process
envRefReference IDReference to environment description

ChemicalReaction

Chemical reactions of radical and molecular species:
ElementTypeDescription
MaximalReactionDistanceValueMaximal reaction distance
ReactionRateConstantValueReaction rate constant
ReactantReference IDsList of reacting species
IntermediateStateReference IDsList of intermediate states
ProductReference IDsList of final states
DataSetsSet of tablesSet of tables for description of process
envRefReference IDReference to environment description

PenetrationDistance

Ion penetration into medium process parameters:
ElementTypeDescription
SpeciesRefReference IDReference to specie
InitialEnergyValueInitial energy
PenetrationDistanceValuePenetration distance
DataSetsSet of tablesSet of tables for description of process
envRefReference IDReference to environment description

Database nodes

RADAM portal provides data from the following sources:

Conferences and meetings

Development of RADAM database was one of the topics at following conferences and meetings:

  • 3rd Nano-IBCT conference "Radiation Damage in Biomolecular Systems: Nanoscale Insights into Ion-Beam Cancer Therapy", 27th-31st October 2014, Boppard, Germany.

  • 2nd annual SUP@VAMDC meeting on 17th September 2014 at the University of Cambridge, UK.

  • 4th workshop on the creation of the RADAM database was held on 1st and 2nd October 2013 at the GANIL facility in the university of Caen, France.

  • The 2nd Nano-IBCT Conference was organized in the framework of the COST Action MP1002 (Nano-scale Insights into Ion Beam Cancer Therapy). It took place in Sopot (Poland) from May 20th to May 24th, 2013.

    This conference brought together experts from different disciplines (physics, chemistry, biology, hadron-therapy centers, medical institutions), specialized in the radiation damage of biological matter, and is under auspice of Rector of GdaƄsk University of Technology, Prof. Henryk Krawczyk.

  • 3rd workshop on the creation of the RADAM database was held on 22th and 23nd February 2013 at the university of Innsbruck, Austria.

Contacts

RADAM portal was created and is maintained by MBN Research center and is supported by COST Action Nano-scale insights in ion beam cancer therapy (Nano-IBCT) .

Please use team@mbnexplorer.com email address in case of any technical problems.

The contacts of the database nodes administration can be found on the Database nodes pages.

Search the database

Search for with conditions

Sources/bibliographic references

ID - source identifier

Name - name of the journal, database or other source

Title - title of the paper

Authors - list of authors of the paper

Year - publication year

Category - type of the source (journal/database)

URL - link to the source

DOI - link to the source with specified DOI


Description: Sources table describes the list of external sources of the information in the database. Each entry in the database must reference published paper or external database as a source of information.

EnergyLoss: (LETCurves)

MethodRef - reference to a method description

Comments - arbitrary comments

SourceRef - bibliographic reference to a source of the data

SpeciesRef - reference to specie description

InitialEnergy - initial energy of the particles

BraggPeakPosition - position of the Bragg peak

BraggPeakWidth - width of the Bragg peak in x

BraggPeakEnergyWidth - width of the Bragg peak in T

DataSets - arbitrary set of tables and plots

envRef - reference to environment description


Description: Linear Energy Transfer (LET) [eV/nm] :: energy absorbed by the medium per unit length of ion's path. LET depend on the medium and on the projectile. The main defining factors are the charge of the projectile, its velocity, and electron density of the medium. More detailed information includes specific information on states of the target. LET dependence is characterized by the Bragg peak, proximal plateau, and distal tail. For a given ion and medium, the position of the Bragg peak is largely defined by the initial energy of the ion; its height by the ion's charge. Since the charge changes as ions slow down (charge transfer effect) the height is proportional to the square of the effective charge that depends on velocity. For a single ion the Bragg peak is only defined by the above data. For the whole ion beam, the position of the Bragg peak is averaged over all ions, which have different scattering histories. Therefore the Bragg peak is significantly lower and wider (energy straggling effect).

StragglingAndBeams

MethodRef - reference to a method description

Comments - arbitrary comments

SourceRef - bibliographic reference to a source of the data

SpeciesRef - reference to specie description

StragglingSigma - value of longitudinal straggling deviation

AngularSigma - value of lateral straggling deviation

DataSets - arbitrary set of tables and plots

envRef - reference to environment description


For the whole ion beam, the position of the Bragg peak is averaged over all ions, which have different scattering histories. Therefore the Bragg peak is significantly lower and wider (energy straggling effect). This effect is taken into account by the assumption that the widening of the Bragg peak is Gaussian. The width of this Gaussian is stored below as StragglingSigma for different media and projectiles. AngularSigma is a similar parameter for the lateral widening of the beam.

ThermomechanicalDamage

MethodRef - reference to a method description

Comments - arbitrary comments

SourceRef - bibliographic reference to a source of the data

SpeciesRef - reference to specie description

InitialEnergy - initial energy of the particles

DataSets - arbitrary set of tables and plots, e.g. Dependence of temperature in the thermal spike as a function of radius and time.

envRef - reference to environment description


Secondary electrons deposit their energy in a very small region (radius of 1-1.5 nm) around the ion's path. As a result the temperature rapidly increases in this region. This temperature dependence on the distance from ions path and time after traverse has been predicted for a number of scenarios in [ThermalSpikes]. As a result of thermal spikes, the pressure in the small region near the pass rapidly increases as well and this becomes the source of cylindrical shock waves predicted in [ShockWaves]. The direct effect of shock waves on biomolecules have been studied; and the probability of strand breaks due to rupture of covalent bonds by stresses has been evaluated using molecular dynamics simulations. This probability depends on LET and the proximity of biomolecules to the ion's path. Another effect of shock waves relevant to biodamage is the radial transport of reactive species formed in the vicinity to the path. This transport is more effective than diffusion.

ComplexDielectricFunction

MethodRef - reference to a method description

Comments - arbitrary comments

SourceRef - bibliographic reference to a source of the data

SpeciesRef - reference to specie description

DataSets - arbitrary set of tables and plots

envRef - reference to environment description


Complex dielectric function is used to calculate cross sections of ionization for a variety of organic molecules and biomolecules. The energy loss-function (ELF) is defined as the negative imaginary part of the inverse dielectric function (they can be stored in the database for a number of molecules as figures or parameterizations). Singly differential cross section obtained using the ELF for different species can be stored as well as the total cross sections depending on the energy of projectiles (protons).

TransportOfSecondaryParticles

MethodRef - reference to a method description

Comments - arbitrary comments

SourceRef - bibliographic reference to a source of the data

SpeciesRef - reference to specie

DiffusionCoefficient - value of the diffusion coefficient in a given medium

MeanFreePath - value of mean free path in a given medium (only for radicals and solvated electrons

DataSets - arbitrary set of tables and plots

envRef - reference to environment description


More than 80% of secondary electrons ejected by ions have energies less than 50 eV. At these energies, the cross sections are mostly isotropic. Therefore the random walk method can be used for the description of their transport. The random walk method is similar to the diffusion. Therefore, the diffusion coefficients for electrons are main parameters describing this transport. The diffusion coefficients are energy-dependent and given by D=lv/6, where l is the mean free path and v is the electron's velocity. Therefore, the dependence of the mean free paths (both elastic and inelastic) are stored here. For other species, such as free radicals, solvated electrons, and other secondary particles, the transport is also explained by diffusion and the diffusion coefficients are stored here. In addition the mean penetration lengths for all species including electrons (depending on their initial energies) can be stored here.

ChemReactionsSecondaries

MethodRef - reference to a method description

Comments - arbitrary comments

SourceRef - bibliographic reference to a source of the data

MaximalReactionDistance - maximal reaction distance value

ReactionRateConstant - value of the reaction rate constant

Reactant - references to species description

IntermediateState - list of intermediate states

Product - references to species description

DataSets - arbitrary set of tables and plots

envRef - reference to environment description


These are the main parameters of chemical reactions relevant for the secondary particle propagation.

Molecular state

Molecule Ref. - Reference to a molecule

State energy - Energy of the state

Energy origin - Reference to a ground state

ElecStateLabel - The label of the electronic state: X, a, A, b, etc...

V1 - The vibrational quantum number, v1

V2 - The vibrational quantum number, v2

L2 - The quantum number, l2, associated with the vibrational angular momentum of the nu2 bending mode

V3 - The vibrational quantum number, v3

J - The rotational quantum number, J, associated with the total angular momentum excluding nuclear spin

I - The quantum number associated with the total nuclear spin angular momentum resulting from the coupling of two individual nuclear spin angular momenta: I = I1 + I2

F1 - The quantum number, F1, associated with the intermediate angular momentum due to coupling the rotational angular momentum with one nuclear spin. F1 may not be a good quantum number.

F2 - The quantum number, F2, associated with the intermediate angular momentum due to coupling the rotational angular momentum with one nuclear spin. F2 may not be a good quantum number.

F - The quantum number, F, associated with the total angular momentum including nuclear spin

r - A ranking index for states of the same symmetry that can't be or haven't been differentiated any other way: r=1,2,...

Parity - Total parity with respect to inversion through the molecular centre of mass in the laboratory coordinate system

KronigParity - Kronig parity ('e' or 'f')

asSym - Symmetry of the rovibronic wavefunction for diatomic molecules with a centre of inversion: a or s such that the total wavefunction including nuclear spin is symmetric or antisymmetric under permutation of the identical nuclei, according to whether they are bosons or fermions respectively.