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Multiscale simulation of condensed phase systems
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RESEARCH

RESEARCH

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PROTEIN DYNAMICS AND FUNCTION

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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

PUBLICATIONS

* denotes corresponding author

** denotes equal contribution

39. "Kinetics of calcite nucleation onto sulfated chitosan derivatives and implications for water-polysaccharide interactions during crystallization of sparingly soluble salts.

B. Knight, R. Mondal, N. Han, N. Pietra, B. Hall, K. Edgar, V. Vaissier Welborn, L. Madsen, J. De Yoreo, and P. Dove*

In revisions

38. "Preorganized electric fields facilitate ion binding and permeation in voltage-gated sodium channel Nav1. 7." 

Y. Zheng, T. Chen and V. Vaissier Welborn*

ChemRxiv, 2024, 10.26434/chemrxiv-2024-cm35v

37. "Dynamics accelerate the kinetics of ion diffusion through channels: Continuous-time random walk models beyond the mean field approximation." 

R. Mondal and V. Vaissier Welborn*

J. Chem. Phys. 2024, 160, 144109 (2024)

36. "Understanding cysteine reactivity in protein environments with electric fields." 

V. Vaissier Welborn*

J. Phys. Chem. B 2023, 127, 9936-9942

35. "Polymer tacticity effects in polymer-lanthanides chelation thermodynamics." 

W. R. Archer, T. Chen, V. Vaissier Welborn and M. D. Schulz*

Macromolecules, 2023, 56, 9062-9069

34. "Characterizing ion-polymer interactions in aqueous environment with electric fields." 

V. Vaissier Welborn*, W. R. Archer and M. D. Schulz

J. Chem. Inf. Model, 2022, 63, 2030-2036

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

Y. Zheng and V. Vaissier Welborn*

J. Phys. Chem. B, 2022, 126, 3407-3413

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

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)

Postdocs

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Stephen Koehler

Stephen obtained a BS in Chemistry from Duquesne University in 2017. He investigated gas phase reactions of group II metal-carbanion complexes using mass spectrometry under the supervision of Prof. Michael Van Stipdonk.

 

He completed his PhD in Chemistry at Penn State in 2023 working for Prof. Beth Elacqua. He used organic synthesis and density functional theory to investigate conjugated polymers toward high efficiency solar cells. Stephen is currently a postdoc in the Welborn and Figg labs where he is working to understand how α-synuclein fibrilizes using both molecular dynamics and experimental biochemistry.

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Mawuli Deegbey

Mawuli has a BSc in Chemistry from Kwame Nkrumah University of Science & Technology in Ghana, and then moved to Starkville to obtain a Masters in physical chemistry at Mississippi State University under the direction of Prof Steven R Gwaltney.

He completed his PhD in Chemistry at North Carolina State University in 2024 under the direction of Prof Elena Jakubikova. His PhD research focused on electronic structure and photochemistry of transition metal complexes, as well as the electrocatalytic reduction of CO/CO2. As a postdoc in the Welborn group, he will utilize ab initio modeling and molecular dynamic simulations to gain chemical insights into the reactivity of proteins and carbohydrates.

Graduate students

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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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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.

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Mark Rothermund

Mark earned his BSc in Chemistry from Western Carolina University in 2019, followed by a MSc in Chemistry in 2022.

 

During his master's program, his research focused on the application of chemometric analysis of infrared spectra to determine mosquito gonotrophic life stages. Now as a Ph.D. student, Mark is focused on modeling aggregates of the protein alpha-synuclein, which has been implicated as the main constituent of Lewy bodies involved in Parkinson's disease, Alzheimer's disease, and other Lewy body diseases.

Undergraduate students

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Ethan Sumner

Ethan is currently pursuing his undergraduate degree in Medicinal Chemistry and Biological Sciences from Virginia Tech.

 

During the summer, Ethan does undergraduate research at Fox Chase Cancer Center, working in an epigenetics lab focusing on DNA amplifications as a result of histone methylation. He is currently an Undergraduate student in the Welborn lab focusing on utilizing the Poltype2/AMOEBA+ force field to analyze carbohydrates.

Alumni

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Monsurat M. Lawal
(Postdoc)

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Chengen Li
(UG)

Zachary Hoyer
(UG)

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Sarasi Banerjee
(MS)

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Yi Zheng
(PhD)

CONTACT

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.

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