Brian Novak's CV

• Phone: +1 620 214 1850
• Email: brian.novak.simulation@gmail.com
• Location: Peoria, AZ
• Website: brian-novak.vercel.app
• GitHub: bnovak1
• LinkedIn: briannovak

Summary

• I have more than 15 years of experience as a computational scientist. My work involved designing, parameterizing, and optimizing molecular simulation models to analyze and predict molecular behavior and properties. I have applied molecular simulations to various systems including biomolecular systems (proteins, DNA, lipid bilayers, and lignin), metals and alloys (rapid solidification, deposition of Cu on TiN, liquid properties), bubble nucleation, self-assembly, and coupling molecular dynamics and continuum models.

• My work on over 15 projects has resulted in the publication of 21 research papers. I have collaborated with multidisciplinary teams from various backgrounds including engineering, computer science, physics, and chemistry, including both computational scientists and experimentalists. I also served as a leader and mentor for multiple undergraduate and graduate students as they worked on their research projects.

• I possess strong skills in statistics, machine learning, data analysis, data visualization, and programming in Python, bash, MATLAB, SQL, and other languages.

Education

University of Notre Dame, Ph.D. in Chemical Engineering

Jan 2008

• Thesis | Molecular simulation studies of heterogeneous bubble nucleation: Effects of surface chemistry and topology

Kansas State University, B.S. in Chemical Engineering

May 2002

Additional Courses Certifications

• Schrödinger’s Introduction to Molecular Modeling in Drug Discovery (08/2021)

• Medicinal Chemistry: The Molecular Basis of Drug Discovery (11/2019)

• Associate Data Scientist in Python Track (01/2025)

• Data Scientist in Python Track (01/2025)

• Associate Python Developer Track (07/2025)

• Python Developer Track (07/2025)

• Associate Data Engineer in SQL Track (06/2025)

• Data Engineer with Python Track (06/2025)

• SQL Fundamentals Track (10/2021)

• Data Analyst with Python Track (07/2023)

• AI for Scientific Research Specialization (01/2023)

• Statistics Fundamentals with Python (07/2023)

• GNNs: An Introduction to Graph Neural Networks (12/2023)

• Intermediate Julia (04/2023)

• Introduction to R (10/2019)

• Introduction to Time Series Analysis in Python (10/2019)

• Introduction to Programming with MATLAB (12/2015)

Skills

Computer languages: Python, Tcl, bash, Snakemake, MATLAB, SQL, Mathematica, Julia, R, Fortran

MD related software: LAMMPS, GROMACS, VMD, packmol, mdtraj, mdanalysis, PLUMED, Ovito, NAMD

Other: Linux, high performance computing, data analysis, version control, machine learning, scikit-learn

Research Experience

Research Associate - Molecular Simulation, Louisiana State University Baton Rouge

Nov 2007 – Oct 2021

• Function and dynamics of the enzyme biotin carboxylase: Estimated free energy differences for opening ATP binding domains for dimers or monomers with or without bound ATP to support experimental observations of monomer inactivity and dimer half-sites reactivity.

• Sequencing DNA using times-of-flight of single nucleotides: Determined the length of a slit necessary to achieve a particular sequencing error rate using a statistical analysis of extrapolated simulation data allowing various surfaces to be compared. Simulated 3 nanometer wide slits with walls composed of different self-assembled monolayers which showed that surface chemistry can greatly affect sequencing efficiency.

• Self-assembly of cationic linear peptide analogs (LPAs) and their interaction with lipid bilayers: Constructed LPA molecule force field parameters for molecular dynamics simulations.Demonstrated that longer hydrocarbon connectors lead to deeper penetration into lipid bilayers. Observed a long-lived trans-bilayer configuration for LPAs with 11 carbon hydrocarbon connectors.Showed that LPAs with connectors longer than 7 carbons form small micelles at high concentrations.

• Behavior of alpha-tocopherol (vitamin E) in lipid bilayers: Designed simulations for computation of the most probable depth of the tocopherol chromanol groups in several types of lipid bilayers. Used DBSCAN clustering to show that higher rates of tocopherol flipping between bilayer leaflets at high concentrations in thinner bilayers are associated with bilayer-spanning tocopherol clusters.

• Interaction of lignin dimers with lipid bilayers or β-cyclodextrin: Captured lipid transition temperature by defining a normalized deuterium order parameter of the lipid tails. Utilized unsupervised machine learning to estimate proportions of different lignin-cyclodextrin bound states from simulation data.

• Interaction of lignin tetramers with microwaves: Showed that some bonds for lignin in deep eutectic solvents are more susceptible to microwaves including the most common monomer linkage.

• Effect of DMSO on lipid bilayers: Simulations of DMPC bilayers with and without added DMSO showed that DMSO increased the amount of water in the bilayer and the rate of permeation through the bilayer, changed the lipid head group orientations and dynamics, and modified the electrostatic potential profile across the bilayer.

• Self-assembly of VECAR (vitamin E-carnosine) bolaamphiphiles: Assisted collaborators at Southeastern Louisiana University with simulation setup and analysis. Assemblies were more elongated & branched and formed faster with decreasing acyl chain length between the vitamin E & carnosine ends.

• Bulk and interfacial properties of molten metals & alloys: Computed cohesive energies, densities, diffusivities, pair distribution functions, viscosities, surface tensions and their temperature dependences near the liquidus temperatures for molten Al, Cr, Ni, Ti, Al-Ni, Al-Ti, and Cr-Ni with assistance from REU students.

• Parameterization of phase field models for solidification using molecular dynamics simulations: Designed an algorithm to compute kinetic coefficients of alloys entirely from simulations for the first time. Developed software to analyze solid-liquid interfacial properties, including velocity, interfacial free energy, and concentration profiles.

• Growth of Cu on TiN: Simulations showed that during deposition of Cu on TiN(100), bcc phase grows initially followed by martensitic transformation of bcc to twinned fcc(110) consistent with experiments.

• Melting point estimation using unsupervised machine learning: Assisted collaborators in the Physics Department with the setup and analysis of simulations.

• Hybrid continuum/molecular dynamics simulations: Applied the method to two-phase liquid systems including a realistic system of hexane/water in contact with a PMMA surface.

Graduate Research Assistant, University of Notre Dame

Aug 2002 – Sept 2007

• Bubble nucleation simulation: Showed that 4.5 nm indentations cause a large increase in nucleation rate relative to a smooth surface, but 1.5 nm indentations have little effect. Applied a thermodynamic model using Mathematica that explained the location of critical bubble nuclei near flat surfaces and extended this model to geometric surface defects

Undergraduate Research Assistant, Kansas State University

Jan 1999 – Jan 2001

• Electrochemistry in silica gels: Showed the effects of solute-gel interactions by measuring electrochemiluminescence intensities of Ru(bpy)#sub[3]#super[2+] and diffusion coefficients of Co(bpy)#sub[3]#super[2+] in silica gels and organically modified silica gels

Publications

• Unraveling the Role of Charge Patterning in the Micellar Structure of Sequence-Defined Amphiphilic Peptoid Oligomers by Molecular Dynamics Simulations. Tsai, E.; Gallage Dona, H. K.; Tong, X.; Du, P.; Novak, B.; David, R.; Rick, S. W.; Zhang, D.; Kumar, R. Macromolecules 2022, 55, 5197–5212.

• Complexation of Lignin Dimers with β-cyclodextrin and Binding Stability Analysis by ESI-MS, Isothermal Titration Calorimetry and Molecular Dynamics Simulations. Dean, K.; Novak, B.; Moradipour, M.; Tong, X.; Moldovan, D.; Knutson, B. L.; Rankin, S. E.; Lynn, B. J. Phys. Chem. B 2021, 126, 1655–1667.

• A Combined Molecular Dynamics/Monte Carlo Simulation of Cu Thin Film Growth on TiN Substrates: Illustration of Growth Mechanisms and Comparison with Experiments. Namakian, R.; Novak, B. R.; Zhang, X.; Jin Meng, W.; Moldovan, D. Appl. Surf. Sci. 2021, 151013.

• Interaction of Lignin Dimers with Model Cell Membranes: A Quartz Crystal Microbalance and Molecular Dynamics Simulation Study. Moradipour, M.; Tong, X.; Novak, B.; Kamali, P.; Asare, S. O.; Lynn, B. C.; Moldovan, D.; Rankin, S. E.; Knutson, B. L. Biointerphases 2021, 16 (4), 041003.

• Molecular Dynamics Simulation Study of the Positioning and Dynamics of α-Tocopherol in Phospholipid Bilayers. Kavousi, S.; Novak, B.; Tong, X.; Moldovan, D. Eur. Biophys. J. 2021.

• Quantitative Prediction of Rapid Solidification by Integrated Atomistic and Phase-Field Modeling. Kavousi, S.; Novak, B. R.; Moldovan, D.; Asle Zaeem, M. Acta Mater. 2021, 211, 116885.

• Single Nucleotides Moving Through Nanoslits Composed of Self-Assembled Monolayers via Equilibrium and Nonequilibrium Molecular Dynamics. Tong, X.; Novak, B.; Kavousi, S.; Moldovan, D. J. Phys. Chem. B 2021, 125 (4), 1259–1270.

• Interface Kinetics of Rapid Solidification of Binary Alloys by Atomistic Simulations: Application to Ti-Ni Alloys. Kavousi, S.; Novak, B. R.; Hoyt, J.; Moldovan, D. Comput. Mater. Sci. 2020, 184, 109854.

• Experimental and Molecular Dynamics Simulation Study of the Effects of Lignin Dimers on the Gel-to-Fluid Phase Transition in DPPC Bilayers. Tong, X.; Moradipour, M.; Novak, B.; Kamali, P.; Asare, S. O.; Knutson, B. L.; Rankin, S. E.; Lynn, B. C.; Moldovan, D. J. Phys. Chem. B 2019, 123 (39), 8247–8260.

• Modified Embedded-Atom Method Potential for High-Temperature Crystal-Melt Properties of Ti–Ni Alloys and Its Application to Phase Field Simulation of Solidification. Kavousi, S.; Novak, B. R.; Baskes, M. I.; Zaeem, M. A.; Moldovan, D. Modelling Simul. Mater. Sci. Eng. 2019, 28 (1), 015006.

• Rapid Microwave-Assisted Biomass Delignification and Lignin Depolymerization in Deep Eutectic Solvents. Muley, P. D.; Mobley, J. K.; Tong, X.; Novak, B.; Stevens, J.; Moldovan, D.; Shi, J.; Boldor, D. Energy Convers. Manag. 2019, 196, 1080–1088.

• Combined Molecular Dynamics and Phase Field Simulation Investigations of Crystal-Melt Interfacial Properties and Dendritic Solidification of Highly Undercooled Titanium. Kavousi, S.; Novak, B. R.; Zaeem, M. A.; Moldovan, D. Comput. Mater. Sci. 2019, 163, 218–229.

• Identifying Structural Changes with Unsupervised Machine Learning Methods. Walker, N.; Tam, K.-M.; Novak, B.; Jarrell, M. Phys. Rev. E 2018, 98 (5), 053305.

• The Role of the Asymmetric Bolaamphiphilic Character of VECAR on the Kinetic and Structural Aspects of Its Self-Assembly: A Molecular Dynamics Simulation Study. Kim, H.-Y.; Novak, B. R.; Shrestha, B.; Lee, S. E.; Moldovan, D. Colloids Surf. Physicochem. Eng. Asp. 2017, 523, 9–18.

• Electrophoretic Transport of Single DNA Nucleotides Through Nanoslits: A Molecular Dynamics Simulation Study. Xia, K.; Novak, B. R.; Weerakoon-Ratnayake, K. M.; Soper, S. A.; Nikitopoulos, D. E.; Moldovan, D. J. Phys. Chem. B 2015, 119 (35), 11443–11458.

• Cellular Fate of Delivery Systems and Entrapped Bioactives. Sabliov, C. M.; Moldovan, D.; Novak, B.; Borel, T.; Whaley, M. In Nanotechnology and Functional Foods: Effective Delivery of Bioactive Ingredients; Sabliov, C. M., Chen, H., Yada, R., Eds.; Wiley-Blackwell, 2015; pp 35–51.

• Distinguishing Single DNA Nucleotides Based on Their Times of Flight through Nanoslits: A Molecular Dynamics Simulation Study. Novak, B. R.; Moldovan, D.; Nikitopoulos, D. E.; Soper, S. A. J. Phys. Chem. B 2013, 117 (12), 3271–3279.

• Molecular Dynamics Simulation Study of the Effect of DMSO on Structural and Permeation Properties of DMPC Lipid Bilayers. Lin, J.; Novak, B.; Moldovan, D. J. Phys. Chem. B 2012, 116, 1299–1308.

• Behavior of the ATP Grasp Domain of Biotin Carboxylase Monomers and Dimers Studied Using Molecular Dynamics Simulations. Novak, B. R.; Moldovan, D.; Waldrop, G. L.; de Queiroz, M. S. Proteins: Struct. Funct. Bioinform. 2011, 79, 622–632.

• Umbrella Sampling Simulations of Biotin Carboxylase: Is a Structure with an Open ATP Grasp Domain Stable in Solution? Novak, B. R.; Moldovan, D.; Waldrop, G. L.; de Queiroz, M. S. J. Phys. Chem. B 2009, 113 (30), 10097–10103.

• An Atomistic Simulation Study of the Role of Asperities and Indentations on Heterogeneous Bubble Nucleation. Novak, B. R.; Maginn, E. J.; McCready, M. J. J. Heat Trans.-T. ASME 2008, 130.

• Comparison of Heterogeneous and Homogeneous Bubble Nucleation Using Molecular Simulations. Novak, B. R.; Maginn, E. J.; McCready, M. J. Phys. Rev. B 2007, 75.

• Diffusion and Reactivity of Ruthenium (II) Tris(Bipyridine) and Cobalt (II) Tris(Bipyridine) in Organically Modified Silicates. Collinson, M. M.; Novak, B. J. Sol-Gel Sci. Technol. 2002, 23, 215–220.

• Electrochemiluminescence of Ruthenium(II) Tris(Bipyridine) Encapsulated in Sol–Gel Glasses. Collinson, M. M.; Novak, B.; Martin, S. A.; Taussig, J. S. Anal. Chem. 2000, 72 (13), 2914–2918.

Presentations

Oral - Invited

• Molecular Dynamics Simulations of Biological Systems: Enzyme Conformational Change and Small Molecule (DNA) Sequencing, Southeastern LA Univ. Chemistry & Physics Seminar (2010). In Southeastern LA Univ. Chemistry & Physics Seminar; 2010.

Oral - Conference

• Molecular Simulation of Single Nucleotides Moving through Nanoslits Composed of Self-Assembled Monolayers Terminated with Various Chemical Groups. Tong, X.; Novak, B.; Moldovan, D. In ACS Spring National Meeting; 2018.

• Properties of Liquid Ti Alloys from Electrostatic Levitation Experiments and Simulation. Novak, B.; Raush, J.; Zhang, X.; Moldovan, D.; Meng, W.; Guo, S. In APS March Meeting; 2017.

• Self-Assembly of Linear Peptide Analogs and Their Interaction with Lipid Bilayers Using MD Simulations. In Novak, B.; Moldovan, D. 89th ACS Colloid & Surface Science Symposium; 2015.

• MD Simulations of Cationic Linear Peptide Analogs: Self-Assembly and Interaction with DPPC and DPPC/DPPS Lipid Bilayers. Novak, B. R.; Lin, J.; Moldovan, D. In ACS Fall National Meeting; 2014.

• Interaction of Cationic Linear Peptide Analogs with Negatively Charged Lipid Bilayers Studied with Molecular Dynamics Simulations. Novak, B. R.; Lin, J.; Moldovan, D. In ACS Spring National Meeting; 2013.

• Interaction of PLGA nanoparticles with a DMPC bilayer studied using molecular dynamics simulations. Novak, B.; Astete, C.; Sabliov, C.; Moldovan, D. In APS March Meeting; 2012.

• Simulations of Single DNA Nucleotide Transport Through Nanoslits. Novak, B.; Xia, K.; Moldovan, D.; Nikitopoulos, D.; Soper, S. In APS March Meeting; 2011.

• Opening/Closing Dynamics and Subunit Communication in Biotin Carboxylase. Novak, B.; Moldovan, D.; Waldrop, G. L.; de Queiroz, M. S. In Southwest & Southeastern Regional Meeting of the ACS; 2010.

• Molecular Dynamics Simulations of the Transport of Single DNA Nucleotides Through Nanochannels. Novak, B.; Moldovan, D.; Nikitopoulos, D.; Soper, S. In APS March Meeting; 2010.

• Applying a Thermodynamic Model to Predict the Size of Surface Indentations That Affect Bubble Nucleation. Novak, B.; Maginn, E. J.; McCready, M. J. In AIChE Annual Meeting; 2007.

• Molecular Dynamics Investigation of Bubble Nucleation at a Solid Surface. Novak, B.; Maginn, E. J.; McCready, M. J. In Midwest Thermodynamics and Statistical Mechanics Conference; 2006.

• Effects of Geometric Defects on Superheated Heterogeneous Bubble Nucleation: A Molecular Dynamics Study. Novak, B.; Maginn, E. J.; McCready, M. J. In AIChE Annual Meeting; 2006.

• Superheated Homogeneous and Heterogeneous Bubble Nucleation Rates Using NPT and NPzz T Molecular Dynamics: Effects of Surface Interactions. Novak, B.; Maginn, E. J.; McCready, M. J. In AIChE Annual Meeting; 2005.

Poster - Conference

• Insights into the Opening and Closing Dynamics of Biotin Carboxylase. Novak, B.; Moldovan, D.; Waldrop, G.; de Queiroz, M. In APS March Meeting; 2010.

• Opening and Closing of Biotin Carboxylase: Free Energies and Mean First Passage Times. Novak, B.; Moldovan, D.; Waldrop, G.; de Queiroz, M. In Mardi Gras Conference; 2010.

• Molecular Dynamics Simulations for Calculation of Times of Flight of Single DNA Nucleotides Driven through Nanochannels. Novak, B.; Moldovan, D.; Nikitopoulos, D.; Soper, S. In Mardi Gras Conference; 2010.

• MD Simulations of DNA Mononucleotide Transport through Nanochannels. Novak, B.; Lin, J.; Moldovan, D.; Jha, S.; Soper, S.; Nikitopoulos, D. In 21st EPSCoR National Conference; 2009.

• Umbrella Sampling Simulations of the Closure of Biotin Carboxylase. Novak, B.; Moldovan, D.; Waldrop, G.; de Queiroz, M. In International Conference on Multiscale Materials Modeling; 2008.

Author Only

• Molecular Dynamics Simulation Study of the Effect of Lignin Dimers on the Gel to Liquid-Crystalline Transition Temperature in DPPC Bilayers. Tong, X.; Maradipour, M.; Novak, B.; Knutson, B.; Rankin, S.; Lynn, B.; Moldovan, D. In ACS Spring National Meeting; 2019.

• Phase Field Modeling of Rapid Solidification of Ti-Ni Alloy Parameterized Using Interfacial Properties Calculated from Atomistic Simulations. Kavousi, S.; Novak, B.; Moldovan, D. In MRS Fall Meeting; 2019.

• Combined Molecular Dynamics and Phase Field Simulation Study of Directional Solidification of NiTi Alloy. Kavousi, S.; Novak, B.; Moldovan, D. In TMS Annual Meeting & Exhibition; 2019.

• Molecular Dynamics Simulation Study of Alpha-Tocopherol Interaction with Lipid Bilayers. Kavousi, S.; Novak, B.; Moldovan, D. In ACS Spring National Meeting; 2018.

• Ab Initio Calculations of Transport in Titanium and Aluminum Mixtures. Walker, N.; Novak, B.; Tam, K. M.; Moldovan, D.; Jarrell, M. In APS March Meeting; 2017.

• Finite Size Scaling of the First Order Transition of Molecular Systems. Tam, K. M.; Novak, B.; Walker, N.; Moldovan, D.; Jarrell, M. In APS March Meeting; 2017.

• Measurement and Calculation of Liquid Ti Alloy Properties with Application to 3D Printing. Raush, J.; Novak, B.; Zhang, X.; Moldovan, D.; Meng, W.; Guo, S. In 4th World Congress on Integrated Computational Materials Engineering; 2017.

• Self-Assemblies of Novel Molecules, VECAR. Shrestha, B.; Kim, H.-Y.; Lee, S.; Novak, B.; Moldovan, D. In APS March Meeting; 2015.

• Investigation of Linear Peptide Analogs Self-Assembly and Interaction with DPPC and DPPC/DPPS Lipid Bilayers: A Molecular Dynamics Simulation Study. Novak, B.; Lin, J.; Moldovan, D. In The Central and Eastern European Conference on Health and the Environment; 2014.

• Molecular Dynamics Simulation of Electrically Driven Single DNA Nucleotides through Nanoslits. Xia, K.; Lin, J.; Nikitopoulos, D.; Moldovan, D. In ACS Spring National Meeting; 2013.

• Molecular Dynamics Simulation Study of Bile Salt Aggregation and Interaction with Vitamin E. Lin, J.; Novak, B.; Moldovan, D. In ACS Spring National Meeting; 2013.

• MD Simulation Study of the Effect of Electric Field on the Dynamics of DNA Nucleotides in Hydrophobic Nanoslits. Xia, K.; Novak, B.; Moldovan, D.; Nikitopoulos, D.; Soper, S. In ACS Spring National Meeting; 2012.

• Atomistic Simulation Study of Single DNA Nucleotide Transport through Nanoslits. Novak, B.; Xia, K.; Nikitopoulos, D.; Soper, S.; Moldovan, D. In ACS Spring National Meeting; 2012.

• Molecular Dynamics Simulation of Adsorption and Positioning of Vitamin E in DMPC Lipid Bilayers: Implication for Their Antioxidant Inhibition. Novak, B.; Lin, J.; Moldovan, D. In Colloids and Nanomedicine; 2012.

• Molecular Dynamics Simulation of Bile Salts Micelle Self-Assembly in Aqueous Solutions. Lin, J.; Novak, B.; Moldovan, D. In ACS Spring National Meeting; 2012.

• Molecular Dynamics Simulation Study of Structural Changes and Pore Formation in Phospholipid Bilayers in the Presence of Dimethylsulfoxide. Moldovan, D.; Alapati, R.; Novak, B.; Devireddy, R. In APS March Meeting; 2010.

• Molecular Dynamics Simulations of the Movement of Single DNA Nucleotides through Nanoslits. Novak, B.; Xia, K.; Moldovan, D.; Nikitopoulos, D.; Soper, S. In Southwest & Southeastern Regional Meeting of the ACS; 2010.

• Molecular Dynamics Simulation of Self-Assembly of Span80 into Micelles and Their Interaction with Vitamin E. Lao, J.; Lin, J.; Xia, K.; Sabliov, C.; Moldovan, D. In Mardi Gras Conference; 2010.

• Transport of Single Molecules through Nanochannels: A Novel Approach to DNA Sequencing. Chantiwas, R.; Hupert, M.; Lopez, J.; Datta, P.; Gottert, J.; Novak, B.; Moldovan, D.; Jha, S.; Park, S.; Murphy, M.; et al. In International Conference on Miniaturized Systems for Chemistry and Life Sciences; 2009.

Peer Reviewing

• Improved kinetic description of fast relaxation of cylindrical micelles, Physica A, 2018-10-11

• Shuffled lipidation pattern and degree of lipidation determines the membrane interaction behavior of a linear cationic membrane-active peptide, Mol. Pharm., 2018-04-29

• Rapid Transport of Deformation-Tuned Nanoparticles across Biological Hydrogels and Cellular Barriers, Nat. Commun., 2017-12-05

Leadership and Teaching

Mentor, Louisiana State University -- Baton Rouge, LA

Nov 2007 – Oct 2021

• 7 graduate students

• 10 undergraduate students

MATLAB Course Instructor, Louisiana State University

Aug 2015 – Dec 2015

Teaching Assistant, University of Notre Dame

Aug 2002 – May 2004