Linear scaling molecular orbital calculations of biological systems using the semiempirical divide and conquer method. - Arjan van der Vaart; Valentin Gogonea; Steven L. Dixon; Kenneth M. Merz Jr. (J. Comput. Chem., 2000)

Free energy simulation of helical transitions. - Ning Ma; Ying-Hua Chung; Arjan van der Vaart (J. Comput. Chem., 2013)

Enhanced sampling simulations of DNA step parameters. - Aleksandra Karolak; Arjan van der Vaart (J. Comput. Chem., 2014)

Biasing Simulations of DNA Base Pair Parameters with Application to Propellor Twisting in AT/AT, AA/TT, and AC/GT Steps and Their Uracil Analogs. - Alfredo Peguero-Tejada; Arjan van der Vaart (J. Chem. Inf. Model., 2017)

Free Energy Coupling between DNA Bending and Base Flipping. - Ning Ma; Arjan van der Vaart (J. Chem. Inf. Model., 2017)