WHAT’S NEW IN
BIOVIA MATERIALS STUDIO 2023
Datasheet

BIOVIA Materials Studio 2023 is the newest version of BIOVIA’s modeling and simulation science tools for chemistry
and materials science research. Materials Studio empowers researchers to understand the relationships between amaterial’s molecular or crystal structure and properties.
The latest release provides scientists with extensive suite of world class solvers and parameter sets operating fromquantum to microscales. This release contains enhancements across the full range of solvers, with added conveniencefor coarse-graining atomistic models and substantial performance increases for classical simulations.
BIOIVA Materials Studio 2023 lets you simulate more material properties, more accurately, and more conveniently
than ever before.

BIOVIA MATERIALS STUDIO 2023
FOR COARSE GRAINED SIMULATIONS
Automatic Coarse Graining and Bead Typing
Coarse-grained molecular dynamics (CGMD), where groups ofatoms are represented by a single bead, are an increasingly popular way to probe the structure and properties of soft mattersystems from tens to hundreds of nanometers- scales that areotherwise out of reach to regular atomistic simulation. A successful CGMD simulation requires a well validated set of forcefieldparameters to describe the interactions of the beads and to allocate each bead the appropriate forcefield types.
Over the past 20 years, the approach of the Martini forcefield[1-3] has proved popular and applicable to a wide range of materials, culminating in a recent Martini 3 version [4,5] that can claim
to provide the most accurate representations to date. The Martini
3 forcefield is available to use as part of the Mesocite module andwith Materials Studio 2023 a new set of capabilities that automate the coarse-graining of structures from atomistic models.
This greatly simplifies what can be a complicated step to assign
bead types provided by Martini 3. This has the double benefit ofefficiency in building models and in reducing bead typing errors.
These tools are accessible both from new scripting menus andalso in the form of Pipeline Pilot protocols in the Materials StudioCollection. The inclusion of protocols make configuring a customized coarse-graining procedure extremely efficient.

A customized MS Martini 3 forcefield including all the required
valence terms is provided along with the mesostructure models,
ready for simulation with Mesocite. Mesocite coarse-grained
molecular dynamics also benefit from significant acceleration
when used with NVIDIA GPUs.

Figure 2: Templates are used to provide molecule
specific interaction terms to the forcefield file
generated by the coarse-graining tools.

New Tutorial!
A new tutorial demonstrates the use of the Coarse Grain andGenerate Custom Martini 3 Forcefield Protocol. This works
through the steps required to build mesostructure starting froman all-atom model, creating custom bead mapping templates andgenerating the coarse-grained structure and the customized MS
Martini 3 forcefield.
Material Studio 2023 offers state-of-the-art tools for coarsegrained simulation, speeding up the process of setting up
mesoscale materials models.

Figure 1: Atomistic and bead representations forpolymers with hinged structures. The coarse graining
tools automatically identify these configurations.

New Tools!
Martini 3 tools have undergone improvement and now features
a new MS Martini 3 Coarse Grainer function. This generates amesostructure model directly from an atomistic model (see Fig 1)
including bead mapping and forcefield typing by using a single
template study table. A template file of customized interactions
can be specified through the Materials Studio Visualizer such as
those shown in Figure 2. These templates allow complex cases,
such as hinged structures involving rings to be represented (wherequite often the bead centers do not reside on atom centers).

Figure 3: Representation of equivalent atomistic andcoarse-grained polymer structures.

Mesocite Dissipative Particle Dynamics
Dissipative Particle Dynamics (DPD) is a popular and provenmethod to study soft condensed matter self-assembly processes
in polymer mixtures, surfactant systems and more. The soft potential approach embodied in DPD provides a very efficient way toreach thermodynamic equilibrium states of the systems. Important
subclasses of these materials include polyelectrolytes and charged
surfactant systems and with Materials Studio 2023 these are moreaccurately represented through the inclusion of electrostatic interactions between charge beads within Mesocite DPD.

With Materials Studio 2023 you can also benefit from faster
dynamics by running Mesocite DPD on NVIDIA GPUs and theaddition of two new analysis features:• Calculation of the structure factor from a density field.
• Pressure analysis that provides anisotropic components.
In Materials Studio 2023, the Mesocite DPD module provides newfunctionality and at a greater speed for simulating more systems.

BIOVIA MATERIALS STUDIO 2023
FOR METAL ALLOY DESIGNBIOVIA Materials Studio PhaseField, based on OpenPhase_Core
solver was introduced in Materials Studio 2021 for simulating
hard material microstructures. With PhaseField module, you
can conveniently define the component phases, grain set up,thermodynamic and kinetic input, and temperature and pressure conditions, through an easy-to-use interface in the Pipeline
Pilot Connector. This allows phase transitions in multicomponent
metal alloys to be studied in detail.
Being able to accurately predict phase transitions is a key toimproving the quality of metal components created using theadditive manufacturing process. The size and shape of metal
grain microstructures are highly sensitive to the rate at which
the liquid metal solidifies during the printing process. Different
proportions of crystal phases can emerge during solidification
which ultimately impact the material properties. New features
for studying these transformations are provided in Materials
Studio 2023 and include:

Figure 4: Representations of interaction energies
between unlike charges in DPD both without (top) andwith (bottom) Gaussian smearing of charges.

New Protocol!
A new protocol to calculate continuous cooling transformation (CCT) diagrams is provided that can be used to predict thecritical cooling rate for the alloy. This protocol can make use of
co-installed ThermoCalc or OpenCalphad package to provide theCALPHAD thermodynamic input.

New Feature!
The Time-Temperature-Transformation (TTT) Diagram protocol
now fits and returns Johnson-Mehl-Avrami (JMA) coefficientsfor each simulation temperature. The JMA model describes
how solids transform from one phase to another at a constanttemperature.

Figure 5: Models demonstrating the distribution ofcharged beads in a salt solution near a charged plate.

Mesocite DPD now supports electrostatics by allowing the smearing of bead charges using a Gaussian distribution of charge. Thisavoids the collapse of unlike charges to a singularity as DPD beads(represented by soft finite potentials) pass through each other.

Figure 5: Images showing stages of solidification in ametal alloy PhaseField simulation.

BIOVIA MATERIALS STUDIO 2023
FOR CHEMICAL REACTIONSMaterials Studio already provides a broad suite of tools andfeatures to understand chemical reactions through; applicationof quantum mechanical solvers, DMol3 CASTEP, DFTB+ andVAMP; application of chemical transition state searching using
FlexTS module; and reaction kinetics predictions (Cantera andKinetix modules). Materials Studio 2023 provides further capabilities for the scientist using Materials Studio to understandchemical reactions by way of access to TURBOMOLE, and thebeyond DFT methods it provides.

New Protocols!
A set of protocols that provide TURBOMOLE workflows
through the Pipeline Pilot Protocols dialog are now available
which provides DFT, xTB and Wavefunction methods• Single-point energy calculation for all methods• Geometry optimizations (using xTB, DFT or MP2)
• Transition state optimizations (using xTB or DFT)
• IR spectra / Vibrational frequencies (using DFT)• Polarizabilities (using DFT)
• Optical spectra (using DFT)

Figure 7: New tools are available from a Materials
Studio Scripts menu, including an analysis ofsimulation box contents.

BIOVIA MATERIALS STUDIO 2023
FOR XPS SPECTROSCOPY
XPS (X-ray photoelectron spectroscopy) measures an excitation(binding) energy of a core electron in a molecule or periodic structure. A new tool is available in Pipeline Pilot Materials StudioCollection 2023 to conveniently provide the spectra. The protocol
also provides for convenient assignment of an offset throughcalculated or experimental data.

Figure 8: The XPS protocol automates the productionof XPS spectra from CASTEP calculations.

MATERIALS STUDIO MODULE ENHANCEMENTS
Classical Simulations
Enhanced Performance! More Parameters!
Figure 6: TURBOMOLE protocols can now be run throughPipeline Pilot Materials Studio Collection protocols.

New Utilities!
Protocol enhancements now make it simpler to construct customized workflows for automating reactive simulation studies• A new “Edit Sets” component allowing you to create andmanage sets in Pipeline Pilot• Scripting now recognizes SMILES and chemical names formolecules and fragments• A script to analyze the content of a simulation cell or the development of different reagents over the course of a trajectory isavailable from a new scripting menu

• Solver Features- Mesocite DPD now supports electrostatics by allowing thesmearing of bead charges using a Gaussian distribution.
• Solver Performance- Forcite GPU calculations now support the Embedded AtomModel.
- A review of the Forcite dynamics GPU algorithms has resulted
in updates providing significant performance enhancements.
- You can now run Mesocite Dissipative Particle Dynamics (DPD)
calculations on NVIDIA GPUs.

• Analysis- Mesocite and Forcite analysis now support calculation of thestructure factor from a density field.
- Mesocite and Forcite analysis now support pressure analysis
with anisotropic components.
• Parameters- The COMPASSIII water model now provides a much improved
prediction of diffusion coefficients and surface tension. Predicted values are now close to experimental accepted values.
- MS GULP is now equivalent to academic v6.1.
- A periodic version of the novel universal forcefield GFN-FF is
now implemented in GULP. This is a fully automated polarizable forcefield with nearly quantum-mechanical accuracy,
as described in [6].

Quantum Mechanics –More Parameters!
More Properties!
• CASTEP- A new protocol for calculating core-level XPS spectra andabsolute electron binding energies.
- Linear response calculations of vibrational properties for spinpolarized (magnetic) systems.
- CASTEP DFT+U no longer requires a spin-polarized setting
for systems that actually are not magnetic, making suchcalculations at least a factor of two faster.
- Force calculations in the presence of implicit solvent are now
available in CASTEP. This allows you to perform geometry
optimization, molecular dynamics, and other tasks taking into
account the effect of solvents.
• DFTB+• A utility protocol for selecting atoms and editing sets.
• Enhancements to the Coarse Graining protocols.
• Improvements to the PhaseField protocols.

Enhancements to MaterialsScript• Scripting now recognizes SMILES and chemical names formolecules and fragments. A script to analyze the content of asimulation cell or the development of different reagents overthe course of a trajectory is also available.
• You can now access wide range of prepared MaterialsScript
tools from Tools > Materials Studio Scripts in the menu bar.
These scripts were previously provided as examples to manually add to the User menu.

Materials Studio Infrastructure• On Linux, you can now configure and use SSH for communication between the Materials Studio client and server.

TUTORIALS
The following new tutorials have been added or updated• Polymer Coarse Graining with Martini 3 Tools and Mesocite:
Demonstrates how to generate templates for bead mapping,use templates with the Martini 3 Coarse Grainer, and customize the MS Martini 3 forcefield for a given polymer structure.
• Polymer Coarse Graining with Martini 3 Protocols: Demonstrates how to generate templates for bead mapping, use
templates with the Coarse Grain and Generate Custom Martini
3 Forcefield protocol, and customize the MS Martini 3 forcefield for a given polymer structure.
• Calculating the Minimum Energy Path of a molecular switch.
• Calculating the properties of diamond.

- Upgrade to version 22.1

REFERENCES- New libraries of DFTB+ parameters for Ti oxides and for Ce oxides

1.

S.J. Marrink, H.J. Risselada, S. Yefimov, D.P. Tieleman, A.H.
de Vries, The MARTINI forcefield: coarse grained model forbiomolecular simulations, J. Phys. Chem. B, 111, 78127824 (2007).

2.

S.J. Marrink, A.H. de Vries, A.E. Mark, Coarse Grainedmodel for semiquantitative lipid simulations, J. Phys.
Chem. B, 108, 750-760 (2004).

3.

Enhancements to Pipeline Pilot Materials StudioCollection

L. Monticelli, S.K. Kandasamy, X. Periole, R.G. Larson,
D.P. Tieleman, S.J. Marrink, The MARTINI coarse grained
forcefield: extension to proteins, J. Chem. Theo. Comp., 4,819-834 (2008).

4.

The Pipeline Pilot Protocols dialog provides access toenhancements available in the Materials Studio Collection for
Pipeline Pilot, including:Souza, P. C. T.; et al., “Martini 3: a general purpose forcefield for coarse-grained molecular dynamics”, Nature
Methods, 18, 382-388 (2021).

5.

Alessandri, R.; Barnoud, J.; Gertsen, A. S.; Patmanidis,I.; de Vries, A. H.; Souza, P. C. T.; Marrink, S. J. “Martini
3 Coarse-Grained Force Field: Small Molecules”, Adv.
Theory Simulations, 5, 2100391 (2021).

6.

J. Gale et al., J. Chem. Theory Comput., 17 (2021) 7827–7849.

- COSMO implicit solvation model is implemented.
• ONETEP- Upgrade to version 6.1.12- Hybrid exchange-correlation functional implementation for
3D periodic systems

MATERIALS STUDIO PRODUCTIVITY
ENHANCEMENTS• A new set of Quantum Chemistry protocols that provide
TURBOMOLE workflows.
• A Quantum Mechanics protocol that allows you to calculate
XPS spectra.

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