D Thirumalai

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 87

Top Topics

Molecular Dynamics Simulations

Genome Wide Association

Single Molecule

Top Venues

The journal of physical chemistry. B

Proceedings of the National Academy of Sciences of the United States of America

Journal of chemical theory and computation

This page only lists publications with an associated author ORCID identifier.

Publications

Hiranmay Maity, Hung T Nguyen, Naoto Hori, D Thirumalai
Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences. The journal of physical chemistry letters (2024)
Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T Nguyen, D Thirumalai
Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences. Journal of chemical theory and computation (2024)
Hiranmay Maity, Hung T Nguyen, Naoto Hori, D Thirumalai
Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences. The journal of physical chemistry letters 15 (14) (2024)
Debayan Chakraborty, Balaka Mondal, D Thirumalai
Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. Journal of chemical theory and computation (2024)
Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T Nguyen, D Thirumalai
Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences. Journal of chemical theory and computation 20 (7) (2024)
Davin Jeong, Guang Shi, Xin Li, D Thirumalai
Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion. eLife 12 (2024)
Debayan Chakraborty, Balaka Mondal, D Thirumalai
Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. Journal of chemical theory and computation (2024)
Rajsekhar Das, Sumit Sinha, Xin Li, T R Kirkpatrick, D Thirumalai
Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis. eLife 12 (2024)
Davin Jeong, Guang Shi, Xin Li, D Thirumalai
Structural basis for the preservation of a subset of topologically associating domains in interphase chromosomes upon cohesin depletion. eLife 12 (2024)
Rajsekhar Das, Sumit Sinha, Xin Li, T R Kirkpatrick, D Thirumalai
Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis. eLife 12 (2024)
Greg Morrison, D Thirumalai
Scaling regimes for wormlike chains confined to cylindrical surfaces under tension. The European physical journal. E, Soft matter 47 (1) (2024)
Sucheol Shin, Guang Shi, Hyun Woo Cho, D Thirumalai
Transcription-induced active forces suppress chromatin motion. Proceedings of the National Academy of Sciences of the United States of America 121 (12) (2024)
Balaka Mondal, Debayan Chakraborty, Naoto Hori, Hung T Nguyen, D Thirumalai
Competition between Stacking and Divalent Cation-Mediated Electrostatic Interactions Determines the Conformations of Short DNA Sequences. Journal of chemical theory and computation 20 (7) (2024)
Rajsekhar Das, Sumit Sinha, Xin Li, T R Kirkpatrick, D Thirumalai
Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis. eLife 12 (2024)
Rajsekhar Das, Sumit Sinha, Xin Li, T R Kirkpatrick, D Thirumalai
Free volume theory explains the unusual behavior of viscosity in a non-confluent tissue during morphogenesis. eLife 12 (2024)
Sucheol Shin, Guang Shi, Hyun Woo Cho, D Thirumalai
Transcription-induced active forces suppress chromatin motion. Proceedings of the National Academy of Sciences of the United States of America 121 (12) (2024)
Debayan Chakraborty, Balaka Mondal, D Thirumalai
Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. Journal of chemical theory and computation 20 (3) (2024)
Sucheol Shin, Guang Shi, Hyun Woo Cho, D Thirumalai
Transcription-induced active forces suppress chromatin motion. Proceedings of the National Academy of Sciences of the United States of America 121 (12) (2024)
Sucheol Shin, Guang Shi, Hyun Woo Cho, D Thirumalai
Transcription-induced active forces suppress chromatin motion. Proceedings of the National Academy of Sciences of the United States of America 121 (12) (2024)
Debayan Chakraborty, Balaka Mondal, D Thirumalai
Brewing COFFEE: A Sequence-Specific Coarse-Grained Energy Function for Simulations of DNA-Protein Complexes. Journal of chemical theory and computation 20 (3) (2024)
Greg Morrison, D Thirumalai
Scaling regimes for wormlike chains confined to cylindrical surfaces under tension. The European physical journal. E, Soft matter 47 (1) (2024)
Hiranmay Maity, Hung T Nguyen, Naoto Hori, D Thirumalai
Salt-Dependent Self-Association of Trinucleotide Repeat RNA Sequences. The journal of physical chemistry letters 15 (14) (2024)
Debayan Chakraborty, John E Straub, D Thirumalai
Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages. Science advances 9 (12) (2023)
D Thirumalai, Abhinaw Kumar, Debayan Chakraborty, John E Straub, Mauro Lorenzo Mugnai
Conformational fluctuations and phases in fused in sarcoma (FUS) low-complexity domain. Biopolymers (2023)
Mauro Lorenzo Mugnai, D Thirumalai
Allosteric communication between ACE2 active site and binding interface with SARS-CoV-2. The Journal of chemical physics 158 (21) (2023)
Guang Shi, D Thirumalai
A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants. Nature communications 14 (1) (2023)
Debayan Chakraborty, John E Straub, D Thirumalai
Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages. Science advances 9 (12) (2023)
Samuel S Cho, Adam T Green, Changbong Hyeon, D Thirumalai
TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond Interactions. The journal of physical chemistry. B 127 (2) (2023)
Samuel S Cho, Adam T Green, Changbong Hyeon, D Thirumalai
TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond Interactions. The journal of physical chemistry. B (2023)
Samuel S Cho, Adam T Green, Changbong Hyeon, D Thirumalai
TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond Interactions. The journal of physical chemistry. B 127 (2) (2023)
Hiranmay Maity, Hung T Nguyen, Naoto Hori, D Thirumalai
Odd-even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation. Proceedings of the National Academy of Sciences of the United States of America 120 (24) (2023)
Debayan Chakraborty, John E Straub, D Thirumalai
Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages. Science advances 9 (12) (2023)
Debayan Chakraborty, Balaka Mondal, D Thirumalai
Brewing COFFEE: a sequence-specific coarse-grained energy function for simulations of DNA-protein complexes. bioRxiv : the preprint server for biology (2023)
Guang Shi, D Thirumalai
A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants. Nature communications 14 (1) (2023)
Guang Shi, D Thirumalai
A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants. Nature communications 14 (1) (2023)
Samuel S Cho, Adam T Green, Changbong Hyeon, D Thirumalai
TMAO Destabilizes RNA Secondary Structure via Direct Hydrogen Bond Interactions. The journal of physical chemistry. B 127 (2) (2023)
Naoto Hori, D Thirumalai
Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time. Nucleic acids research (2023)
Guang Shi, D Thirumalai
A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural variants. Nature communications 14 (1) (2023)
Anja Henning-Knechtel, D Thirumalai, Serdal Kirmizialtin
Differences in ion-RNA binding modes due to charge density variations explain the stability of RNA in monovalent salts. Science advances 8 (29) (2022)
Zhenxing Liu, D Thirumalai
Cooperativity and Folding Kinetics in a Multidomain Protein with Interwoven Chain Topology. ACS central science 8 (6) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Zhenxing Liu, D Thirumalai
Residue-Dependent Transition Temperatures and Denaturant Midpoints in the Folding of a Multidomain Protein. The journal of physical chemistry. B 126 (50) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Ryota Takaki, Mauro Lorenzo Mugnai, D Thirumalai
Information flow, gating, and energetics in dimeric molecular motors. Proceedings of the National Academy of Sciences of the United States of America 119 (46) (2022)
Zhenxing Liu, D Thirumalai
Residue-Dependent Transition Temperatures and Denaturant Midpoints in the Folding of a Multidomain Protein. The journal of physical chemistry. B 126 (50) (2022)
Hung T Nguyen, Naoto Hori, D Thirumalai
Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics. Nature chemistry 14 (7) (2022)
Yonghyun Song, D Thirumalai, Changbong Hyeon
Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in vivo. Proceedings of the National Academy of Sciences of the United States of America 119 (49) (2022)
Zhenxing Liu, D Thirumalai
Residue-Dependent Transition Temperatures and Denaturant Midpoints in the Folding of a Multidomain Protein. The journal of physical chemistry. B (2022)
Sumit Sinha, Xin Li, Rajsekhar Das, D Thirumalai
Mechanical feedback controls the emergence of dynamical memory in growing tissue monolayers. The Journal of chemical physics 156 (24) (2022)
Huong T Vu, Zhechun Zhang, Riina Tehver, D Thirumalai
Plus and minus ends of microtubules respond asymmetrically to kinesin binding by a long-range directionally driven allosteric mechanism. Science advances 8 (15) (2022)
Xin Li, D Thirumalai
A mathematical model for phenotypic heterogeneity in breast cancer with implications for therapeutic strategies. Journal of the Royal Society, Interface 19 (186) (2022)
Zhenxing Liu, D Thirumalai
Residue-Dependent Transition Temperatures and Denaturant Midpoints in the Folding of a Multidomain Protein. The journal of physical chemistry. B 126 (50) (2022)
George A Pantelopulos, Daisuke Matsuoka, James M Hutchison, Charles R Sanders, Yuji Sugita, John E Straub, D Thirumalai
Formation of extramembrane β -strands controls dimerization of transmembrane helices in amyloid precursor protein C99. Proceedings of the National Academy of Sciences of the United States of America 119 (52) (2022)
Pavel I Zhuravlev, Michael Hinczewski, D Thirumalai
Low Force Unfolding of a Single-Domain Protein by Parallel Pathways. The journal of physical chemistry. B 125 (7) (2021)
Sabeeha Hasnain, Mauro Lorenzo Mugnai, D Thirumalai
Effects of Gold Nanoparticles on the Stepping Trajectories of Kinesin. The journal of physical chemistry. B 125 (37) (2021)
Robert J Huebner, Abdul Naseer Malmi-Kakkada, Sena Sarıkaya, Shinuo Weng, D Thirumalai, John B Wallingford
Mechanical heterogeneity along single cell-cell junctions is driven by lateral clustering of cadherins during vertebrate axis elongation. eLife 10 (2021)
Ryota Takaki, Atreya Dey, Guang Shi, D Thirumalai
Theory and simulations of condensin mediated loop extrusion in DNA. Nature communications 12 (1) (2021)
Yonathan Goldtzvik, D Thirumalai
Multiscale Coarse-Grained Model for the Stepping of Molecular Motors with Application to Kinesin. Journal of chemical theory and computation 17 (8) (2021)
Dylan Suvlu, D Thirumalai, Jayendran C Rasaiah
Water-Mediated Interactions Determine Helix Formation of Peptides in Open Nanotubes. The journal of physical chemistry. B 125 (3) (2021)
Balaka Mondal, D Thirumalai, Govardhan Reddy
Energy Landscape of Ubiquitin Is Weakly Multidimensional. The journal of physical chemistry. B 125 (31) (2021)
Meng Qin, Natalia Denesyuk, Zhenxing Liu, Wei Wang, D Thirumalai
Temperature and Guanidine Hydrochloride Effects on the Folding Thermodynamics of WW Domain and Variants. The journal of physical chemistry. B 125 (41) (2021)
Mauro Lorenzo Mugnai, D Thirumalai
Step-Wise Hydration of Magnesium by Four Water Molecules Precedes Phosphate Release in a Myosin Motor. The journal of physical chemistry. B 125 (4) (2021)
Abhinaw Kumar, Debayan Chakraborty, Mauro Lorenzo Mugnai, John E Straub, D Thirumalai
Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants. The journal of physical chemistry letters 12 (37) (2021)
Naoto Hori, Natalia A Denesyuk, D Thirumalai
Shape changes and cooperativity in the folding of the central domain of the 16S ribosomal RNA. Proceedings of the National Academy of Sciences of the United States of America 118 (10) (2021)
Eda Koculi, D Thirumalai
Retardation of Folding Rates of Substrate Proteins in the Nanocage of GroEL. Biochemistry 60 (6) (2021)
Govardhan Reddy, D Thirumalai
Asymmetry in histone rotation in forced unwrapping and force quench rewrapping in a nucleosome. Nucleic acids research 49 (9) (2021)
Mauro Lorenzo Mugnai, D Thirumalai
Molecular Transfer Model for pH Effects on Intrinsically Disordered Proteins: Theory and Applications. Journal of chemical theory and computation 17 (3) (2021)
Hung T Nguyen, D Thirumalai
Charge Density of Cation Determines Inner versus Outer Shell Coordination to Phosphate in RNA. The journal of physical chemistry. B 124 (20) (2020)
Debayan Chakraborty, John E Straub, D Thirumalai
Differences in the free energies between the excited states of Aβ40 and Aβ42 monomers encode their aggregation propensities. Proceedings of the National Academy of Sciences of the United States of America 117 (33) (2020)
Serdal Kirmizialtin, Felicia Pitici, Alfredo E Cardenas, Ron Elber, D Thirumalai
Dramatic Shape Changes Occur as Cytochrome c Folds. The journal of physical chemistry. B 124 (38) (2020)
D Thirumalai, Changbong Hyeon, Pavel I Zhuravlev, George H Lorimer
Symmetry, Rigidity, and Allosteric Signaling: From Monomeric Proteins to Molecular Machines. Chemical reviews 119 (12) (2019)
Upayan Baul, Debayan Chakraborty, Mauro L Mugnai, John E Straub, D Thirumalai
Sequence Effects on Size, Shape, and Structural Heterogeneity in Intrinsically Disordered Proteins. The journal of physical chemistry. B 123 (16) (2019)
Ryota Takaki, Mauro Lorenzo Mugnai, Yonathan Goldtzvik, D Thirumalai
How kinesin waits for ATP affects the nucleotide and load dependence of the stepping kinetics. Proceedings of the National Academy of Sciences of the United States of America 116 (46) (2019)
D Thirumalai, Changbong Hyeon
Signalling networks and dynamics of allosteric transitions in bacterial chaperonin GroEL: implications for iterative annealing of misfolded proteins. Philosophical transactions of the Royal Society of London. Series B, Biological sciences 373 (1749) (2019)
Himadri S Samanta, Mauro L Mugnai, T R Kirkpatrick, D Thirumalai
Giant Casimir Nonequilibrium Forces Drive Coil to Globule Transition in Polymers. The journal of physical chemistry letters 10 (11) (2019)
D Thirumalai, George H Lorimer, Changbong Hyeon
Iterative annealing mechanism explains the functions of the GroEL and RNA chaperones. Protein science : a publication of the Protein Society 29 (2) (2019)
Natalia A Denesyuk, Naoto Hori, D Thirumalai
Molecular Simulations of Ion Effects on the Thermodynamics of RNA Folding. The journal of physical chemistry. B 122 (50) (2018)
Zhenxing Liu, D Thirumalai
Denaturants Alter the Flux through Multiple Pathways in the Folding of PDZ Domain. The journal of physical chemistry. B 122 (4) (2018)
Debayan Chakraborty, Naoto Hori, D Thirumalai
Sequence-Dependent Three Interaction Site Model for Single- and Double-Stranded DNA. Journal of chemical theory and computation 14 (7) (2018)
Naoto Hori, Natalia A Denesyuk, D Thirumalai
Frictional Effects on RNA Folding: Speed Limit and Kramers Turnover. The journal of physical chemistry. B 122 (49) (2018)
Jie Chen, D Thirumalai
Interface Residues That Drive Allosteric Transitions Also Control the Assembly of l-Lactate Dehydrogenase. The journal of physical chemistry. B 122 (49) (2018)
Yuno Lee, D Thirumalai, Changbong Hyeon
Ultrasensitivity of Water Exchange Kinetics to the Size of Metal Ion. Journal of the American Chemical Society 139 (36) (2017)
Govardhan Reddy, D Thirumalai
Collapse Precedes Folding in Denaturant-Dependent Assembly of Ubiquitin. The journal of physical chemistry. B 121 (5) (2017)
Dylan Suvlu, Seneviratne Samaratunga, D Thirumalai, Jayendran C Rasaiah
Thermodynamics of Helix-Coil Transitions of Polyalanine in Open Carbon Nanotubes. The journal of physical chemistry letters 8 (2) (2017)
Changbong Hyeon, D Thirumalai
Ripping RNA by Force Using Gaussian Network Models. The journal of physical chemistry. B 121 (15) (2016)