Multiscale simulation of condensed phase systems
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RESEARCH

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PROTEIN DYNAMICS AND ALLOSTERY

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CHARACTERIZATION OF STRUCTURAL AND FUNCTIONAL WATER

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POLYSACCHARIDES IN SOLUTION

Atomistic simulations, transport and catalysis, membrane proteins.

Molecular dynamics, DFT, tissue morphology, hybrid interfaces.

Conformational ensemble, environmental effects, polarizable force fields.

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POLYMER DESIGN FOR METAL CHELATION

Molecular dynamics, polarizable force fields, electrostatic interactions.

 

PUBLICATIONS

33. "Tuning the catalytic activity of synthetic enzyme KE15 with DNA." 

Y. Zheng and V. Vaissier Welborn

J. Phys. Chem. B, 2022, DOI:10.1021/acs.jpcb.2c00765

32. "Structural dynamics support electrostatic interactions in the active site of Adenylate Kinase." 

M. M. Lawal and V. Vaissier Welborn

ChemBioChem, 2022, DOI:10.1002/cbic.202200097

31. "Exploring the role of polymer hydrophobicity in polymer-metal binding thermodynamics." 

W. R. Archer, C. M. B. Gallagher, V. Vaissier Welborn and M. D. Schulz

Phys. Chem. Chem. Phys., 2022, 24, 3579-3585

30. "Beyond structural analysis of molecular enzyme-inhibitor interactions." 

V. Vaissier Welborn

Electron. Struct., 2022, 4, 014006

29. "The role of water dynamics in age-related bone weakening." 

V. Vaissier Welborn

Research Outreach, 2021, 127, DOI:10.32907/RO-127-1960557845

28. "Structural Dynamics and Computational Design of Synthetic Enzymes." 

V. Vaissier Welborn

Chem. Catalysis, 2021, 2, 19-28

27. "Organocatalytic trans Semireduction of Primary and Secondary Propiolamides: Substrate Scope and Mechanistic Studies." 

R. J. Grams, M. M. Lawal, C. Szwetkowski, D. Foster, C. A. Rosenblum, C. Slebodnick, V. Vaissier Welborn and W. L. Santos

Adv. Synth. Catal., 2021, 364, 172-178

26. "Critical Role of Thermal Fluctuations for CO Binding on Electrocatalytic Metal Surfaces." 

W-L. Li, C. Lininger, K. Chen, V. Vaissier Welborn, E. Rossomme, A. Bell, M. Head-Gordon and T. Head-Gordon

JACS Au, 2021, 1, 1708-1718

25. "Environment-controlled water adsorption at hydroxyapatite/collagen interfaces." 

V. Vaissier Welborn - Selected "Hot article 2021" - Front cover article

Phys. Chem. Chem. Phys., 2021, 23, 13789-13796

24. "Challenges for density functional theory: calculation of CO adsorption on electrocatalytically relevant metals." 

C. Lininger, J. Gauthier, W-L. Li, E. Rossomme, V. Vaissier Welborn, Z. Lin, T. Head-Gordon, M. head-Gordon and A. Bell

Phys. Chem. Chem. Phys., 2021, 23, 9394-9406

23. "ELECTRIC: Electric fields Leveraged from multipole Expansion Calculations in Tinker Rapid Interface Code." 

J. Nash, T. Barnes, V. Vaissier Welborn

J. Open Source Softw., 2020, 5, 2576

22. "The effect of inner-sphere reorganization on charge separated state lifetimes at sensitized TiO2 interfaces." 

M. C. Kessinger, C. Brillhart, V. Vaissier Welborn and A. J. Morris

J. Chem. Phys., 2020, 153, 124711

21. "Enamel synthesis explained." 

V. Vaissier Welborn

Proc. Natl. Acad. Sci. USA, 2020, 117, 21847-21848

20. "Investigation of external quantum efficiency roll-off in OLEDs using the mean field steady state kinetic model." 

A. R. McIsaac, V. Vaissier Welborn, M. Einzinger, N. Geva, H. Weir, M. A. Baldo and T. Van Voorhis

J. Phys. Chem. C, 2020, 124, 14424-14431

19. "Interplay of water and a supramolecular capsule for catalysis of reductive elimination reaction from gold" 

V. Vaissier Welborn, W-L Li and T. Head-Gordon

Nat. Commun., 2020, 11, 1-6

18. "Fluctuations of electric fields in the active site of the enzyme ketosteroid isomerase" 

V. Vaissier Welborn and T. Head-Gordon

J. Am. Chem. Soc., 2019, 141, 12487-12492

 

17. "Computational design of synthetic enzymes" 

V. Vaissier Welborn and T. Head-Gordon

Chem. Rev., 2019, 119, 6613-6630

16. "Electrostatics Generated by a Supramolecular Capsule Stabilizes the Transition State for Carbon-Carbon Reductive   Elimination from Gold(III) Complex" 

V. Vaissier Welborn and T. Head-Gordon

J. Phys. Chem. Lett., 2018, 9, 3814-3818

15. "Computational optimization of electric fields for better catalysis design"

V. Vaissier Welborn, L. R. Pestana and T. Head-Gordon

Nat. Catal., 2018, 1, 649-655

14. "Computational optimization of electric fields for improving catalysis of a designed Kemp eliminase"

V. Vaissier*, S. Sharma*, A. Bowhmick, K. Schaettle, T. Zhang and T. Head-Gordon

ACS Catal., 2018, 8, 219-227

13. "Non-radiative deactivation of cytosine derivatives at elevated temperatures"

V. Vaissier Welborn and T. Van Voorhis

Mol. Phys. Michael Baer Festschrift, 2018, 116, 2591-2598

12. "Geometry of molecular motions in dye monolayers at various coverages"

V. Vaissier and T. Van Voorhis

J. Chem. Phys. C, 2017, 121, 12562-12568

11. "Mean field treatment of heterogeneous steady state kinetics"

V. Vaissier*, N. Geva*, J. Sheperd and T. Van Voorhis

Chem. Phys. Lett., 2017, 685, 185-190

10. "Quantum chemical approaches to [NiFe] hydrogenase"

V. Vaissier and T. Van Voorhis

Essays Biochem., 2017, 61, 293-303

9. "The adiabatic approximation in explicit solvent models of redox chemistry"

V. Vaissier and T. Van Voorhis

J. Chem. Theory Comput., 2016, 12, 5111-5116

8. "Inter-dye hole transport accelerates electron to oxidized dye recombination in dye sensitized nanocrystals"

D. Moia, A. Szumska, V. Vaissier, M. Plannels, N. Robertson, B. O'Regan et al. 

J. Am. Chem. Soc., 2016, 138, 13197-13206

7. "How mobile are dye adsorbates and acetonitrile molecules on the surface of TiO2 nanoparticles?

A quasi-elastic neutron scattering study"

V. Vaissier, V. Garcia-Sakai, X. Li, G. Sakai, J. Cabral, J. Nelson and P. Barnes

Sci. Rep., 2016, 6, 39253

6. "Evidence for photo-induced charge separation between dye molecules adsorbed to aluminum oxide surfaces"  

U. Cappel, D. Moia, A. Bruno, V. Vaissier, S. Haque and P. Barnes

Sci. Rep., 2016, 6, 21276

5. "Influence of intermolecular interactions on the reorganization energy of charge transfer between surface attached      dye molecules"

V. Vaissier, J. Frost, P. Barnes and J. Nelson

J. Phys. Chem. C, 2015, 119, 24337-24341

4. "The influence of a nearby substrate on the outer sphere polarization energy and reorganization energy of charged       molecules"

F. Manke, J. Frost, V. Vaissier and P. Barnes

Phys. Chem. Chem. Phys. 2015, 17, 7345-7354

3. "Effect of molecular fluctuations on hole diffusion within dye monolayers"

V. Vaissier, E. Mosconi, D. Moia, M. Pastore, J. Frost, F. De Angelis, P. Barnes and J. Nelson

Chem. Mater. 2014, 26, 4731-4740

2. "The reorganization energy of intermolecular hole hopping between dyes anchored to surfaces"

D. Moia, V. Vaissier, I. Lopez-Duarte, T. Torres, M. Nazeeruddin, B. O'Regan et al.

Chem Sci. 2013, 5, 281-290

1. "Influence of polar medium on the reorganization energy of charge transfer between dyes in dye sensitized film"

V. Vaissier, P. Barnes, J. Kirkpatrick and J. Nelson

Phys. Chem. Chem. Phys. 2013, 15, 4804-4814

 

PEOPLE

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Valerie Welborn

2017-2019     Postdoc UC Berkeley

                        (advisor: Teresa Head-Gordon)

2015-2017     Postdoc MIT

                        (advisor: Troy Van Voorhis)

2011-2014     PhD Imperial College London, CDT TSM

                        (advisors: Jenny Nelson, Piers Barnes)

Graduate students

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Yi Zheng

Yi Zheng graduated from University of Iowa in 2019 with a Bachelor of Science in Biochemistry and a Bachelor of Art in Chemistry.

Her undergraduate research in Dr. Ned Bowden’s group focused on the synthesis of polydiaminosulfides for application in drug delivery.

Her undergraduate research with Dr. Stefan Strack involved structural and functional characterization of mitochondria fission factor (Mff).

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Taoyi Chen

Taoyi Chen obtained his Bachelor’s degree in Chemical Engineering from both New Mexico State University and East China University of Science and Technology, China in 2016.

He graduated from New Mexico State University in 2018 and 2020 with Masters and PhD degrees in Chemical Engineering under the supervision of Dr. Thomas A. Manz.
His PhD project focuses on developing and utilizing atomic population analysis methods to describe interactions of atoms in materials for quantum chemistry calculations.

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Sarasi Banerjee

Sarasi Banerjee has completed her B.TECH. in Chemical Engineering from Sathyabama University, India in 2015.

 

After completion of her degree she worked at Unilever, India as GTA (2015-2016). She then started working as a Quality Executive in a chemical industry RM. Chemicals, India (2016-2018). In 2018-2019, she worked as a research assistant in Dow Chemicals, India where her research focused on using different polymers in different formulations. She is currently a graduate student in the Welborn group and her work focuses on atomistic modeling of polymers.

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Ronnie Mondal

Ronnie Mondal graduated from the Indian Institute of Technology, Bombay in 2020 with a BS in Chemistry.


His undergraduate research in Dr. Pradeepkumar’s group focused on prediction algorithms and Machine Learning-assisted ligand design for stabilisation of G-Quadruplexes and I-Motifs. After completion of his degree he worked with Swiggy, a food delivery app, where he campaign benchmarking and customer engagement. He is currently a graduate student in the Welboorn group and his work focuses on facilitating molecular dynamics simulations of polymer-based materials.

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Junbao Liang

Junbao Liang got his bachelor’s degree from China Univ. of Mining & Tech. in 2019 and Master’s degree from Univ. of Oregon in 2020.

 

His undergrad research in Prof. Lang Xu’s lab focuses on the synthesis of carbon-based material, trying to make some environment-friendly material with high performance in energy storage. His research at Univ. of Oregon followed the instruction of Dr. Chris Hendon. He tried to figure out how the functional groups tune the property of MOFs...

Luke Newman

Luke graduated from Liberty University in 2022, with a major in Chemistry and a minor in Biology.

 

His undergraduate research, directed by Dr. Matthew Brynteson, studied the binding affinities of BPA derivatives to the human estrogen receptor. Protein-ligand docking software, AutoDock, was utilized to study the binding orientations and obtain simulated energies. This research introduced Luke to molecular modeling as a tool for chemical research.

Alumni

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Monsurat M. Lawal (postdoc)
now in McCullagh's group (Oklahoma State University).

Monsurat Lawal graduated from University of KwaZulu-Natal, South Africa in 2016 and 2019 with Masters and PhD degrees, respectively, in Pharmaceutical chemistry (computational and theoretical option) under the supervision of Prof. Hendrik G. Kruger and Dr. Bahareh Honarparvar.

She obtained her first degree in Biochemistry at Ekiti State University, Nigeria in 2012.

 Her PhD project involves a computational understanding of the mechanism of action of the HIV

protease, including two drug resistant mutants where she theoretically explored the concerted mechanistic models of this enzyme.

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Chengen Li

Chengen Li is working on his B.Sc at Virginia Tech, with a major in Chemistry and Nanosciences. 

 

Chengen has joined the group in the Summer of 2021 to model  Lithium batteries, in collaboration with the Lin group in the department of Chemistry at Virginia Tech. He uses Quantum Espresso to estimate Li+ vacancy formation energy in cathode materials and rationalize Li+ migration kinetics at the microscopic scale.

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Zachary Hoyer

Zachary Hoyer is working on his B.Sc at Virginia Tech, with a major in clinical neuroscience and a minor in Chemistry. 

 

Zachary has joined the group in the Summer of 2021 to model  Lithium batteries, in collaboration with the Lin group in the department of Chemistry at Virginia Tech. He uses plane-wave DFT to resolve the structure of disordered cathode materials at the atomistic scale and estimate the corresponding Li+ migration kinetics.

 

CONTACT

Luke Newman

Luke graduated from Liberty University in 2022, with a major in Chemistry and a minor in Biology.

 

His undergraduate research, directed by Dr. Matthew Brynteson, studied the binding affinities of BPA derivatives to the human estrogen receptor. Protein-ligand docking software, AutoDock, was utilized to study the binding orientations and obtain simulated energies. This research introduced Luke to molecular modeling as a tool for chemical research.